The University of Silesia - Uniwersytet Śląski

UPGOW – Uniwersytet Partnerem Gospodarki Opartej na Wiedzy Uniwersytet Śląski w Katowicach, ul. Bankowa 12, 40-007 Katowice, http://www.us.edu.pl

Projekt współfinansowany przez Unię Europejską w ramach Europejskiego Funduszu Społecznego

The University of Silesia Faculty of Mathematics, Physics and Chemistry ECTS European Credit Transfer and Accumulation System Major: chemistry

Fields of study: � general chemistry

� environmental chemistry � drug chemistry � computer chemistry

Study status: 2nd degree Duration: two years Admission requirements: 1st degree diploma Degree awarded: MSc in chemistry Continuation: 3rd degree ECTS coordinator: dr hab. Rafał Sitko

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CONTENTS PROFILE OF GRADUATE …………………………………………………………………….................. 4 General chemistry …………………………………………………………………..………………….. 4 Environmental chemistry ……………………………………………………………...……………….. 5 Drug chemistry ………………………………………………………………………...……………….. 6 Computer chemistry ……………………………………………………………………...…………….. 7 ECTS – INTRODUCTION ………………………………………………………………….…................... 8 University of Silesia – brief information ………………………………………………….……………. 9 Admission procedure …………………………………………………………………….…................... 10 Entry requirements ………………………………………………………………………….................... 10 Tuition fees ……………………………………………………………………………….….................. 11 How to obtain a scholarship? ……………………………………………………………….................... 11 Introduction to students’ life …………………………………………………………….….................... 12 Preparation before traveling to Poland …………………………………………………………………. 12 Medical treatment ………………………………………………………………………………………. 12 Accommodation …………………………………………………………………………....…………… 12 Academic Year …………………………………………………………………………...…………... 13 Cost of Living …………………………………………………………………………………………... 13 What do you do in your spare time? …………………………………………………...………………. 13 Polish language requirement …………………………………………………………...………………. 14 Scientific activity of the Institute of Chemistry ……………………………………....………………… 14 Studying chemistry at the University of Silesia ……………………………………….……………….. 15 STUDY PROGRAM …………………………………………………………………...….……................... 16 General chemistry ……………………………………………………………………….……………… 16 Environmental chemistry ………………………………………………………………………….……. 18 Drug chemistry …………………………………………………………………………….…………… 20 Computer chemistry …………………………………………………………………………………….. 22 BASIC CONTENTS …………………………………………………………………..……..……………... 24 Instrumental analysis ……………………………………………..……………...…….…….................. 25 Chromatography ……………………………………………………………………….…….................. 26 Theoretical chemistry ……………………………………………………….........…….………………. 27 MAJOR CONTENTS ……………………………………………………………………….……………… 28 Spectroscopy ……………………………………………………………………………..……………... 29 Crystallography …………………………………………………………………………..…………….. 30 OTHERS ……………………………………………………………………………………….……………. 31 Scientific information……………………………………………………………………….…………... 32 Laboratory of molecular design ………………………………………………………............................ 33 OPTIONAL COURSES ………………………………………………………………………..................... 34 General chemistry …………………………………………………………………………................... 34 Termodynamics ………...…………………………….……………............…............................... 35 Chemometrics ………………………………...……………………….…….………..…………... 36 Environmental chemistry …………………….....…….…………………………………………... 37 Environmental chemistry ……………………………………………………………………………... 38 Environmental geochemistry ………...…………………………….….............….......…………... 39 Environmental toxycology ………………………………...…………….….……..……………… 40 Atmospheric chemistry …………………….....………….……………………………...….…….. 41 Drug chemistry ………………………………………………………………………………………… 42 Medicinal chemistry ………………………………………….……......................…..................... 43 Biochemistry with elements of genetics …………………………………….…….…..………….. 44 Chemoinformatics ………………………………………………………………………………… 45 Computer chemistry …………………………………………..……….……………………………… 46 Fortran programming ………………………………………………………….…………………. 47 Operating systems and computer networks…………………………………….………................ 48 Computational chemistry. Applications…………………………………….…………................. 49 SPECIALISATION ………………………………………………………………………………………… 50 Specialization I: Analytical chemistry ……………………………………………………………….. 50 Sampling and preparation of samples for analysis ………….……………….…........................... 51 Validation of analytical methods …………………………………………………………………. 52 Design of experiments ……………………………………………………………………………. 53 Chemometrics in analytical chemistry …………………………………………………………… 54

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Processing of instrumental signals ……………………………………………………………….. 55 Automatisation in analytical chemistry …………………………………………………………... 56 Laboratory related to specialization ………………………………………………………………. 57 Specialization II: Synthesis and physical chemistry of organic and inorganic compounds ……… 58 Organometallic and bioinorganic chemistry – selected problems ………………………………... 59 Mechanisms of organic reactions ………………………………………………………………… 60 Selected problems concerning elucidation of organic and inorganic molecules, Par1 1 …………. 61 Selected problems concerning elucidation of organic and inorganic molecules, Part 2 …………. 62 Catalysis in organic and inorgamic chemistry ……………………………………………………. 63 Transition metal complexes in bioinorganic chemistry ………………………………………….. 64 Laboratory related to specialization ………………………………………………………………. 65 SPECIALISATION III: Theoretical methods in chemistr y………………………………………… 66 Computational methods for electronic correlation ……………………………………………….. 67 HF and DFT methods …………………………………………………………………………….. 68 Computational chemistry of large molecules …………………………………………………….. 69 Ionized and Excited states of atoms and molecules ………………………………………………. 70 Electric and optical molecular properties ………………………………………………………… 71 Intermolecular interactions ………………………………………………………………………. 72 Laboratory related to specialization ………………………………………………………………. 73 SPECIALISATION IV: Physical chemistry of condensed phases …………………………………. 74 Intermolecular interactions in condensed phases ………………………………………………… 75 Reactions in solid phase ………………………………………………………………………….. 76 Elements of molecular acoustics …………………………………………………………………. 77 Magnetic and electrical properties of the compounds with the spinel structure ………………….. 78 Thermodynamic properties of liquid mixtures …………………………………………………… 79 Selected topics of coordination chemistry ……………………………………………………….. 80 Laboratory related to specialization ………………………………………………………………. 81 SPECIALISATION V: Physicochemical methods in analytical chemistry ……………………….. 82 Physicochemical fundamentals of liquid chromatography ………………………………………. 83 Physicochemical bases of gas chromatography ………………………………………………….. 84 Chiral separations by means of chromatography ………………………………………………… 85 Design of experiments in chromatography ………………………………………………………. 86 Special chromatographic techniques ……………………………………………………………... 87 Application of chromatographic techniques to investigation of natural products ………………... 88 Laboratory related to specialization ………………………………………………………………. 89 MONOGRAPHIC LECTURES …………………………….…………………………………................... 90 Polymers as materials XXI century ……………………………..……………………………………… 91 Bioinformatics ………………………………………………………………………………………….. 92 QSAR modeling ………………………………………………………………………………………… 93 Pharma industry ……………………………………………………..………………………………….. 94 Cosmetic chemistry ……………………………………………………................................................... 95 Bioinorganic chemistry ………………….……………………………………....………........................ 96 Diagrammatic methods in quantum chemistry …………………………………………………………. 97 Biological Quantum Chemistry ………………………………………………………………………… 98 Coupled cluster method ………………………………………………………………………………… 99 Computational methods in design of new materials .…………………………………............................ 100 IR spectroscopy of hydrogen- bonded molecular systems ……………………………….…….............. 101 Chiral compounds – preparation and using ………………………………………………….…………. 102 Relationship between structure and reactivity of molecules …………………………………………… 103 The separation and concentration methods in chemical analysis ……………………………………… 104

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PROFILE OF GRADUATE: GENERAL CHEMISTRY A graduate of the second-degree studies in chemistry has a broader knowledge of chemistry compared to a graduate of the first-degree studies; is competent in the field of selected specialization (general chemistry); can think critically and identify their lack of knowledge and complete it individually; can solve problems at work including problems requiring consultation with experts in other fields of science; has a fundamental knowledge in environmental chemistry and can predict consequences of presence of pollutants in the environment; knows basic chemometric techniques and can use them for analysis of multivariate chemical data; has a fundamental knowledge in molecular design and design of biological effectors taking into account information about receptor’s structure and ligands; can use scientific databases including library of literature in chemistry; during discussion can clearly postulate and understand arguments of other party; when taking a decision use efficiently available knowledge; is ready for individual and teamwork including head position (after additional training period). A graduate can continue their education as a PhD student (the 3rd degree-studies); after completing additional training period and necessary requirements can teach chemistry at junior high school and high school levels; can work within interdisciplinary projects.

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PROFILE OF GRADUATE: ENVIRONMENTAL CHEMISTRY A graduate of the second-degree studies in chemistry has a broader knowledge of chemistry compared to absolvent of the first-degree studies; is competent in the field of selected specialization (environmental chemistry); can think critically and identify their lack of knowledge and complete it individually; can solve problems at work including problems requiring consultation with experts in other fields of science; has a fundamental knowledge of geochemistry and a broader knowledge of environmental processes; is aware of the role of major chemical elements and trace elements in ecosystems, understands their pathways and origins as well as their influence on the environment and organisms; has a fundamental knowledge of basic toxic substances and their influence on the cells and tissues of an organism; can estimate the potential risks caused by pollutants for fauna, flora, water, the atmosphere and soil; can use adequate methods for environmental monitoring, and markers to control the current status of the environment; can interpret chemical processes that occur in the atmosphere, can foresee the consequences of the presence of pollutants in the atmosphere; knows the analytical techniques applied for environmental monitoring; can use scientific databases including the library of literature in chemistry. A graduate can continue their education as a PhD student (the 3rd degree-studies); is ready for individual and teamwork including head position (after additional training period); after completing additional training period and necessary requirements can teach chemistry at gymnasium and high school level; can be employed as a chemist in a laboratory dealing with environmental monitoring; in other institutes (e.g. departments of environmental protection, institutions bearing in mind different aspects of environmental protection and conditions of the workplace, institutions producing and controlling quality of food products).

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PROFILE OF GRADUATE: DRUG CHEMISTRY A graduate of the second-degree studies in chemistry has a broader knowledge of chemistry compared to absolvent of the first-degree studies; is competent in the field of selected specialization (Drug chemistry); can think critically and identify her/his lack of knowledge and complete it individually; can solve problems at work including problems requiring consultation with experts in other fields of science; has a fundamental knowledge in Drug chemistry; knows modern methods used for organization, research and popularization of results in the field of Drug chemistry; is aware of the synthesis and testing of pharmaceutical and cosmetic substances; has knowledge about the fundamental metabolic processes in cells and their relation to certain diseases which enables a better understanding of the functioning and design of the drug; has a basic education in chemoinformatics, and thus can interpret the results of simulations in silico and understands the principles of coding molecular structures; has a general knowledge about planning organic synthesis using retro synthetic analysis; knows basic classes of drugs and is aware of their functioning; can use modern instrumental techniques in order to analyze the chemical components of pharmaceutical and drug substances; has a knowledge of molecular modeling in silico, design of biological effectors taking into account the receptor structure and active ligands characterizing the receptor. A graduate can continue their education as a PhD student (the 3rd degree-studies); is ready for individual and teamwork including head position (after additional training period); after completing additional training period and necessary requirements can teach chemistry at gymnasium and high school level; can be employed as a chemist in a laboratory dealing with quality control of drugs and supplements of diet; in other institutes (e.g. departments of public health, dealing with production of drugs and supplements of diet), can work as a sales representative in pharmaceutical companies.

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PROFILE OF GRADUATE: COMPUTER CHEMISTRY

A graduate of the second-degree studies in chemistry has a broader knowledge of chemistry compared to a graduate of the first-degree studies; is competent in the field of selected specialization (computer chemistry); can think critically and identify their lack of knowledge and complete it individually; can solve problems at work including problems requiring consultation with experts in other fields of science; has knowledge in computational chemistry and practical instrumental chemistry; can properly apply computation techniques to solve chemical problems using computers; has knowledge about the design and functioning of computer systems and networks; can program in one commonly used programming language, system and network programming; can code chemical structures, use simple molecular editors and analyze data obtained from chemoinformatic methods; can use scientific databases including the library of literature in chemistry. A graduate can continue their education as a PhD student (the 3rd degree-studies); is ready for individual and teamwork including the head position (after an additional training period); after completing the additional training period and necessary requirements can teach chemistry at junior high school and high school levels; can be employed as a chemist, analytical chemist, staff member in academia or other interdisciplinary institutes as a specialist in computational methods (e.g., institutions focused on chemo- and bioinformatic studies).

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ECTS – INTRODUCTION Cooperation among various institutions of higher education is considered to be an important factor for improving the level of student education by the European Commission. The most important element of the cooperation is the possibility of studying abroad. To make the study programmes easy to read and compare for all students (local and foreign), the European Credit Transfer and Accumulation System (ECTS) has been developed. The goal of the ECTS is to revise and improve the study programmes in order to make higher education more attractive to foreign students. The ECTS consists of three ‘core’ elements: information (on study programmes and students’ achievements), learning agreement (among the cooperating institutions), and the ECTS credits (characterising the student workload required to complete a given course unit successfully). The ECTS credits range from 1 to 60. They determine the amount of work required for a particular course unit in relation to the total amount of work required to complete a full academic year at the chosen academic institution. A total of 180 ECTS credits is required to obtain a BSc degree and 120 credits for an MSc degree at the University of Silesia. Person responsible for the ECTS Programme at the University of Silesia: Local coordinator in the Institute of Chemistry: dr hab. Rafał Sitko Institute of Chemistry, UŚ ul. Szkolna 9 40-006 Katowice tel.: +48 32 359 1556, e-mail: [email protected]

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University of Silesia – brief information The University of Silesia is an autonomous state university established in Katowice in 1968 as the ninth university in Poland. Located in the centre of the heavily industrialised region, the University has several regional campuses: Katowice, Sosnowiec, Chorzów, Rybnik, Jastrzębie Zdrój and Cieszyn. The main campus of the University and the majority of the facilities are situated in the centre of Katowice. There are ca. 40,000 students enrolled in the different disciplines offered by 12 main faculties such as: • Faculty of Art • Faculty of Biology and Environmental Protection • Faculty of Computer Science and Materials Science • Faculty of Earth Science • Faculty of Ethnology and Educational Studies • Faculty of Law and Administration • Faculty of Mathematics, Physics and Chemistry • Faculty of Pedagogy and Psychology • Faculty of Philology • Faculty of Radio and Television • Faculty of Social Sciences • Faculty of Theology

and interfaculty units such as the Silesian International Business School, International School of Political Sciences, the Business Language College, the School of Management, the Centre for Studies on the Human and Natural Environment, the School of the Polish Language, Literature and Culture, Interfaculty Program of Study in the Field of Humanities, Interfaculty Program of Study in the Field of Mathematics and Natural Sciences. The University of Silesia offers good research and learning facilities. Subjects can be studied at different levels and lead to undergraduate, postgraduate and research academic degrees or to certificates from various training courses of professional skills The Central Library of the University of Silesia provides access to a wide range of resources in all media: over 1,000,000 books, 1,200 journals, slides and computerized information. Computer databases are accessible through the local computer network.

The University is led by a Rector and four Vice-Rectors who are governed by the Faculty Senate. Each faculty is led by a Dean and Vice-Dean. All authorities are elected to four-year terms. The current appointments are listed in the table below.

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REKTOR prof. zw. dr hab. Wiesław Banyś

40-007 Katowice ul. Bankowa 12,

tel. (32) 258 71 19 fax (32) 259 96 05

Vice-Rector for Finance and Development

prof. zw. dr hab. Stanisław Kucharski

tel.: (32) 359 14 50 fax: (32) 359 20 40

Vice-Rector for Science and Economic Cooperation

prof. dr hab. Andrzej Kowalczyk

tel.: (32) 258 65 51 fax: (32) 259 73 98

Vice-Rector for Students Affairs, Promotion and

International Cooperation

prof. dr hab. Barbara KoŜusznik

tel.: (32) 258 97 39 fax: (32) 259 73 99

Vice-Rector for Education Affairs

prof. dr hab. Czesław Martysz

tel.: (32) 258 97 39 fax: (32) 259 73 99

Dean of the Faculty of Mathematics, Physics and

Chemistry

prof. UŚ, dr hab. Maciej Sablik

40-007 Katowice ul. Bankowa 14,

tel. (32) 258 44 12

Vice-Dean for Chemistry dr hab. Piotr Kuś Tel. (32) 258 15 50

Educational offers for international students and all necessary information can be found at: www.english.us.edu.pl

Admission procedure We warmly welcome International Students to all programmes offered by the University of Silesia. The Admission Office provide help and advice on any matters related to welfare, immigration and academic studies. For any queries candidates can contact the Department of Education , University of Silesia, ul. Bankowa 12, 40-007 Katowice, Poland, tel.: (+48 32) 359 2071; fax: (+48 32) 359 1178; e-mail: [email protected].

Entry requirements The policy of the University of Silesia is to consider all applications for each course equally on the basis of their academic merit without regard to sex, sexual orientation, age, disability, ethnicity, race, religious or political affiliation or national origin of the applicant. All applicants for full-time degree courses should submit the following documents to the International Students Office at the University of Silesia (at the address given before): • a completed admission questionnaire, • the BSc diploma, • a health certificate confirming a good health condition enabling the candidate to

study.

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A formal qualification in Polish language is required for entry to all of our degree courses.

University students who intend to continue their education at the University of Silesia should submit either copies or photocopies of the documents confirming the credits received in examinations.

Tuition fees Non-EU international students are responsible for payment of registration and tuition fees. The tuition fees in Euro per academic year are listed below:

BA/BSc studies 2 500 euro MA/MSc studies, 2 & 5 years (Humanities) MA/MSc studies, 2 & 5 years (experimental courses)

3 000 euro 3 500 euro

Studies in the fields of: – Film and Television Directing – Film and Television Production – Cinematography, Directing and Art Photography

4 000 euro 4 000 euro 3 000 euro

Postgraduate courses 3 000 euro Doctoral courses, artistic and academic scholarships, habilitation fellowships and specialization courses

4 000 euro

Additional courses and student internships 3 000 euro PhD procedure outside the PhD study 2 000 euro Habilitation procedure without the habilitation fellowship 3 000 euro Applicants must also pay a registration fee of 200 euro. Foreigners of Polish descent beginning their studies as fee-paying students are entitled to a 30% reduction in fees. See details: http://english.us.edu.pl/tuition-fees

How to obtain a scholarship?

The University of Silesia does not grant scholarships for foreign students. International students may complete their studies at the University of Silesia on scholarship conditions upon a decision granted by the Ministry of National Education. More information can be obtained from the Bureau for Academic Recognition and International Exchange, 00-375 Warszawa, Smolna 13, or from the nearest Polish diplomatic agencies abroad. For the annual enrolment procedure, the Polish agencies abroad

• inform the interested persons and institutions about the conditions of studying in

Poland; • complete the required documents concerning candidates for studies; • are responsible for the preliminary selection of candidates; the responsible officer

of the agency interviews every candidate; • submit the documents to proper institutions in Poland; • issue Polish visas.

The decision to qualify an international student to be enrolled at the University of Silesia is taken by the Qualification Commission.

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Introduction to students’ life There are many reasons for studying chemistry in Katowice. Katowice is the capital of the Upper Silesian region in southern Poland. It is located in a hilly area, close to the Beskidy Mountains, known for its beautiful resorts for winter sports. The natural environment of Silesia has suffered from heavy industry over the past 150 years. In recent decades, efforts have been undertaken to restore the natural beauty of the land.

The University of Silesia in Katowice is one of the leading universities in Poland. Traditionally, the scientific activity in the Institute of Chemistry has been focused on industry-related problems. At present, it is more closely related to environmental protection. Apart from applications, pure chemistry is also studied.

Katowice is an important cultural centre: the city hosts two symphony orchestras, several theatres and festivals. The well-known “Rawa Blues” festival (www.rawablues.com) grew out of local events in student clubs. It is organised annually in autumn and confirms Katowice as the blues capital of Poland.

Preparation before travelling to Poland International students are required to have a valid passport and visitors’ visa. To apply for the visa at the Polish embassy/consulate in your home country, you should have a valid passport and a letter of admission or original letter stating that you have been granted a scholarship.

Students can apply for a residence permit after arrival in Poland for a maximum of six months. To get the permit, a student should provide: a completed application form – 2 copies, two colour pictures, a birth certificate, a matriculation certificate, and a clear criminal record certificate. The student should also show a certificate of financial support or a document approving financial assistance during the entire period of study. All of these documents should be in Polish.

Although not obligatory, an ISIC Card may be useful during your travel and stay in Poland.

Medical treatment All students in Poland, including international students, are entitled to medical care and hospital treatment free of charge. Special medical IDs are provided to international students from the Dean’s Office. There are separate clinics for outpatients on each of the university campuses. Students can receive medical treatment through the following outpatient clinics: internal diseases, dental, ophthalmologic, throat diseases, neurological, audiometric, etc.

Accommodation The University of Silesia has about 3300 places for accommodation in 11 student halls of residence. They are mostly double study bedrooms equipped with self-catering facilities. The accommodation is charged on a monthly basis and the price depends on the standard. At present, the price varies from 270 to 450 zł per bed (1 € is approximately 4.0 zł). An application form for accommodation should be submitted to the University of Silesia, Dział Spraw Studenckich (Department of

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Students Affairs), ul. Bankowa 12, 40-007 Katowice. For more details, one may contact the following responsible persons: • Maria Gałuszka ([email protected]) • Dorota Pytka ([email protected]) • Marek Piestrzyński ([email protected]) Tel. +48 32 35913 40, 359 20 46; Fax. +48 32 359 12 95; e-mail: [email protected] Students may also look for accommodation through independent agencies, e.g.: Biuro Kwater Studenckich ZSP, ul. 3 Maja 7, 40-096 Katowice, e-mail: [email protected]

Academic Year The academic year is divided into two terms. The autumn (winter) term begins on 1st October and ends in mid-January when the examination session starts. The spring (summer) term starts in mid-February and ends in the beginning of June. There is usually short break of about two weeks from the end of December (Christmas and New Year) and another short break takes place during the Easter season. The non-teaching period is basically from mid-June to the end of August. During this period students are encouraged to take part in the summer courses organised by the University of Silesia.

Cost of Living Students have university canteens at their disposal where they can have lunch at reduced prices. The current average price for a two-course lunch is about 10 zł. Some practice in cooking before leaving home may be helpful. Prices of food, including meat, are reasonable and stable throughout the year. Prices of vegetables and fruits fluctuate and during the winter season they can be quite high. Most the shops and department stores are open from Monday to Friday from 8 am to 6 pm. They close in the early afternoon on Saturdays and are closed on Sundays, except for a very few of them in the city centre that remain open 24 hours a day.

What do you do in your spare time? There are many societies and clubs engaged in organizing lectures and different types of entertainment, e.g. music, dances, sport and other activities. Student Clubs: • “Straszny dwór” located in Student Hall no 7. The students in this Club prepare

an annual traditional rejoicing of university students and presentation of many musical groups.

• “Pod Rurą” at the Faculty of Pedagogy and Psychology. The club is engaged in the presentation of rock and roll music.

• “Remedium” in Student Hall no 1 – Disco-Club.

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Students can contribute to the activity of the student radio station “Rezonans” (99.1 FM) available in Katowice and Sosnowiec and at the wire broadcasting centre “Egida”.

Polish language requirement The School of Polish Language and Culture delivers courses for those whose level of Polish indicates that a further tuition is required.

All applicants whose native language is not Polish are required to submit evidence of their proficiency in the Polish language. If you are planning to attend courses at the University, language courses at the School of Polish Language and Culture should be taken in advance. More detailed information can be obtained from: the School of Polish Language, Pl. Sejmu Śląskiego 1, 40-032 Katowice, tel./fax: +48 32 2512 991 or + 48 32 2551260 ext: 424, e-mail: [email protected] Information for incoming students: www.socrates.us.edu.pl/information2007.php

Scientific activity at the Institute of Chemistry Institute of Chemistry, 40-006 Katowice, ul. Szkolna 9, tel.: +48 32 359 1545, fax.: +48 32 259 9978, www.chemia.us.edu.pl Scientific staff of the Institute of Chemistry Full professors: T. Kowalska, S. Krompiec (vice-Head), S. Kucharski, J. Polański (Head) i B. Walczak. Professors: M. Daszykowski (vice-Head), M. Dzida, H. Flakus, M. Jaworska, P. Kuś, B. Machura, J. Małecki, W. Marczak, M. Matlengiewicz, H. Mrowiec, M. Musioł, W. Pisarski, R. Sitko i W. Sułkowski. There are 48 scientists with PhD degrees, 23 technical staff (including 5 employees with PhD degree) and more than 400 undergraduate students. Several research groups are active at the Institute: • Department of Analytical Chemistry • Department of Chemical Physics • Department of Chemistry and Technology • Department of Crystallography • Department of Didactics • Department of General Chemistry and Chromatography • Department of Inorganic Chemistry • Department of Organic Chemistry • Department of Organic Synthesis • Department of Physical Chemistry • Department of Polymer Chemistry • Department of Theoretical Chemistry • Laboratory of Chemical Analysis • Technical Laboratory

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All research groups at the Institute are engaged in problems related to environmental chemistry and in the new educational project for graduate studies in this particular field.

Over the past 21 years the Institute has hosted the annual national chromatography symposium ‘Chromatographic Methods of Investigating of Organic Compounds’. Since 1992 the Institute of Chemistry has published the international journal Acta Chromatographica devoted to all branches of chromatography and related techniques.

Studying chemistry at the University of Silesia

The Institute of Chemistry grants the following diplomas:

*) The Polish equivalent for BSc is “Licencjat”. A person with a licencjat should obtain a

master`s degree to continue post-graduate education for a PhD degree. To obtain an MSc degree a student has to have a total of 300 ECTS credits (180 for Bachelor’s degree and 120 for Master’s degree). A short description of all courses offered at the Institute of Chemistry together with the corresponding ECTS credits is presented below. To complete one semester, a student has to earn 30 credits. Students of the first year are obliged to complete classes of physical education in both terms (winter and summer) obtaining 1 credit per term.

Main Study Diploma

Drug chemistry 3 years + + 2 years

BSc* in chemistry MSc in chemistry

Computer chemistry 3 years + 2 years


General chemistry 3 years + + 2 years


Environmental chemistry 3 years + 2 years


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STUDY PROGRAM: General Chemistry

Master's degree (II)Stationary studiesFrom academic year 2010/2011

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1 Instrumental analysis E 90 45 45 7 45 45 7

2 Chromatography E 60 15 30 15 6 15 45 6

3 Theoretical chemistry E 75 30 45 7 30 45 7

225 90 0 120 15 0 20 60 90 13 30 45 7 0 0 0 0 0 0

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4 Spectroscopy E 60 30 30 4 30 30 4

5 Crystallography E 45 15 30 5 15 30 5

105 45 0 60 0 0 9 30 30 4 15 30 5 0 0 0 0 0 0

No.

AII year

TOTAL A:

B MAJOR CONTENTS

semester 3 semester 4

No. Subject

Department of Mathematics, Physics and ChemistryMajor: ChemistrySpecialisation: General chemistry

BASIC CONTENTSI year


E/P

Tot

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15 weeks 15 weeksincludes

Tota

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15 weeks 15 weeks

I year II yearsemester 1 semester 2 semester 3 semester 4

15 weeks

TOTAL B:

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15 weeks 15 weeks 15 weeks

Subject E/PT

otal

includes

E – exam, P – pass/fail

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6 Scientif ic information P 15 15 1 15 1

7 Laboratory of molecular design P 30 15 15 2 15 15 2

8 Optional courses CHP:

8a Termodynamics P 45 30 15 5 30 15 5

8b Chemometrics P 45 30 15 5 30 15 5

8c Environmental chemistry P 45 15 30 5 15 30 5

9 Specialisation E 225 60 135 30 14 30 15 4 30 90 7 60 3

10 Monographic lecture P 75 75 5 15 1 30 2 30 2

11 MSc laboratory P 240 240 35 120 15 120 20

12 MSc seminar P 90 90 19 30 4 30 5 30 10

810 225 0 390 105 90 91 90 60 13 90 135 18 45 240 30 0 150 30

1 140 360 0 570 120 90 120 30 30 30 30

C OTHERSI year II year

semester 1 semester 2 semester 3 semester 4

No. Subject E/P

Tot

al


Tota

lE

CTS

15 weeks 15 weeks

TOTAL C:

TOTAL SEMESTERS (A+B+C) 360 345

TOTAL PER YEAR 705 435

TRAINING

285 150

TOTAL 1 140

Module ‘Master thesis’ consists of subjects nos. 11 and 12 (Master’s laboratory and Master’s seminar)

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STUDY PROGRAM: Environmental Chemistry


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225 90 0 120 15 0 20 60 90 13 30 45 7 0 0 0 0 0 0

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4 Spectroscopy E 60 30 30 4 30 30 4


105 45 0 60 0 0 9 30 30 4 15 30 5 0 0 0 0 0 0

No.

AII year

TOTAL A:

B MAJOR CONTENTS


No. Subject

Department of Mathematics, Physics and ChemistryMajor: ChemistrySpecialisation: Environmental chemistry



E/P

Tot

al


Tota

lE

CT

S

15 weeks 15 weeks


15 weeks

TOTAL B:

Tot

alEC

TS


Subject E/PT

otal

includes


19

lect

ures

clas

s

labo

rat.

clas

ses

sem

in.

lect

ure

clas

s

EC

TS

lect

ure

clas

s

EC

TS

lect

ure

clas

s

EC

TS

lect

ure

clas

s

EC

TS



8 Optional courses CHS:

8a Environmental geochemistry P 45 30 15 5 30 15 5

8b Environmental toxycology P 45 15 30 3 30 15 3

8c Atmospheric chemistry P 45 15 30 5 15 30 5



11 MSc laboratory P 240 240 35 120 15 120 20

12 MSc seminar P 90 90 19 30 4 30 5 30 10

810 210 0 420 90 90 89 90 60 13 90 135 16 45 240 30 0 150 30

1 140 345 0 600 105 90 118 30 28 30 30



No. Subject E/P

Tot

al


Tota

lE

CTS

15 weeks 15 weeks

TOTAL C:

TOTAL SEMESTERS (A+B+C) 360 345


TRAINING

285 150

TOTAL 1 140


20

STUDY PROGRAM: Drug chemistry


lect

ures

clas

s

labo

rat.

clas

ses

sem

in.

lect

ure

clas

s

EC

TS

lect

ure

clas

s

EC

TS

lect

ure

clas

s

EC

TS

lect

ure

clas

s

EC

TS




225 90 0 120 15 0 20 60 90 13 30 45 7 0 0 0 0 0 0

lect

ures

clas

s

labo

rat.

clas

ses

sem

in.

lect

ure

clas

s

EC

TS

lect

ure

clas

s

EC

TS

lect

ure

clas

s

EC

TS

lect

ure

clas

s

EC

TS

4 Spectroscopy E 60 30 30 4 30 30 4


105 45 0 60 0 0 9 30 30 4 15 30 5 0 0 0 0 0 0

No.

AII year

TOTAL A:

B MAJOR CONTENTS


No. Subject

Department of Mathematics, Physics and ChemistryMajor: ChemistrySpecialisation: Drug chemistry



E/P

Tot

al


Tota

lE

CT

S

15 weeks 15 weeks


15 weeks

TOTAL B:

Tot

alEC

TS


Subject E/PT

otal

includes


21

lect

ures

clas

s

labo

rat.

clas

ses

sem

in.

lect

ure

clas

s

EC

TS

lect

ure

clas

s

EC

TS

lect

ure

clas

s

EC

TS

lect

ure

clas

s

EC

TS



8 Optional courses CHL:

8a Medicinal chemistry P 45 15 15 15 5 15 30 5

8b Biochemistry w ith elements of genetics P 45 30 15 5 30 15 5

8c Spectroscopy in biological chemistry P 45 15 30 5 15 30 5



11 MSc laboratory P 240 240 35 120 15 120 20

12 MSc seminar P 90 90 19 30 4 30 5 30 10

810 210 0 435 75 90 91 75 75 13 90 135 18 45 240 30 0 150 30

1 140 345 0 615 90 90 120 30 30 30 30

1 140TOTAL



No. Subject E/P

Tot

al


Tot

alE

CT

S

15 weeks 15 weeks

TOTAL C:

TOTAL SEMESTERS (A+B+C) 360 345 285 150


TRAINING


22

STUDY PROGRAM: Computer Chemistry


lect

ures

clas

s

labo

rat.

clas

ses

sem

in.

lect

ure

clas

s

EC

TS

lect

ure

clas

s

EC

TS

lect

ure

clas

s

EC

TS

lect

ure

clas

s

EC

TS




225 90 0 120 15 0 20 60 90 13 30 45 7 0 0 0 0 0 0

lect

ures

clas

s

labo

rat.

clas

ses

sem

in.

lect

ure

clas

s

EC

TS

lect

ure

clas

s

EC

TS

lect

ure

clas

s

EC

TS

lect

ure

clas

s

EC

TS

4 Spectroscopy E 60 30 30 4 30 30 4


105 45 0 60 0 0 9 30 30 4 15 30 5 0 0 0 0 0 0

No.

AII year

TOTAL A:

B MAJOR CONTENTS


No. Subject

Department of Mathematics, Physics and ChemistryMajor: ChemistrySpecialisation: Computer chemistry



E/P

Tot

al


Tota

lE

CT

S

15 weeks 15 weeks


15 weeks

TOTAL B:

Tot

alEC

TS


Subject E/P

Tot

al

includes


23

lect

ures

clas

s

labo

rat.

clas

ses

sem

in.

lect

ure

clas

s

EC

TS

lect

ure

clas

s

EC

TS

lect

ure

clas

s

EC

TS

lect

ure

clas

s

EC

TS



8 Optional courses CHI:

8a Fortran programming P 45 15 30 5 15 30 5

8b Operating systems and computer netw orks P 45 30 15 5 30 15 5

8c Computational chemistry. Applications P 45 15 30 5 15 30 5



11 MSc laboratory P 240 240 35 120 15 120 20

12 MSc seminar P 90 90 19 30 4 30 5 30 10

810 210 0 465 45 90 91 75 75 13 90 135 18 45 240 30 0 150 30

1 140 345 0 645 60 90 120 30 30 30 30

1 140TOTAL



No. Subject E/P

Tot

al


Tot

alE

CT

S

15 weeks 15 weeks

TOTAL C:

TOTAL SEMETERS (A+B+C) 360 345 285 150


TRAINING


24

BASIC CONTENTS � general chemistry � environmental chemistry � drug chemistry � computer chemistry

25

Instrumental analysis

Lecturer: dr hab. Rafał Sitko Course code: 0310-2.03.1.001 Type of the course: Basic ECTS: 7 lecture + laboratory Number in study program: 1 Number of hours: 45 + 45 = 90 Semester: Winter (1) Course prerequisites: Analytical Chemistry (1st degree

study) Language: Polish or English

Teaching methods: Multimedia teaching techniques, laboratory exercises, teaching in small groups, solving tasks, calculus exercises

Assessment methods: Laboratory reports, problem-solving exercises, collaborative work, final examination (written)

Course contents: Characteristics of instrumental methods and their classification. Spectroscopic methods, theoretical foundations: absorption and emission spectra, absorption laws. Monochromatization, detection and recording of spectra. Molecular spectrophotometry: turbidimetry, nephelometry, polarimetry, refractometry – theoretical foundations, apparatus and determination examples. Atomic spectroscopy: emission and absorption AS – theoretical foundations, measuring techniques and analytical applications. X-ray fluorescence spectrometry and mass spectrometry. Electroanalytical methods – physico-chemical foundations and applications. Potentiometry, electrogravimetry, polarography, voltammetry and conductometry, elektrophoresis, and radiometric methods. Precision and accuracy of the measurement in instrumental techniques. Interfering effects, calibration. Sensitivity, selectivity and specificity of instrumental methods. Speciation and multicomponent analysis. Multiple techniques. Objectives of the course: Presenting the most important instrumental techniques, their theoretical foundations, apparatus and analytical applications. Learning outcomes: After graduation, students should acquire the skill of method and apparatus selection for a given analytical task, handling of the selected equipment, carrying out the analysis and interpreting the obtained results correctly. They should also be able to account for the method selection considering analytical and economic requirements. Textbooks and recommended reading: 1. W. Szczepaniak, Metody instrumentalne w analizie chemicznej, PWN, Warszawa, 2002, 2. A. Cygański, Metody spektroskopowe w chemii analitycznej, WNT, Warszawa, 2002, 3. A. Cygański, Podstawy metod elektroanalitycznych, WNT, Warszawa, 1999, 4. D.A. Skoog, D.M. West, F.J. Holler, S.R. Crouch, Fundamentals of analytical chemistry, Thomson Learning

Company, Brooks Cole, 2004.

26

Chromatography

Lecturer: prof. dr hab. Teresa Kowalska Course code: 0310-2.03.1.002 Type of the course: Basic ECTS: 6 Lecture + classes + laboratory Number in study program: 2 Number of hours: 15 + 15 + 30 = 60 Semester: Winter (1) Course prerequisites: None Language: Polish or English Teaching methods: Multimedia teaching techniques, using internet resources, laboratory exercises,

teaching in small groups, solving tasks Assessment methods: Laboratory reports, problem-solving exercises, oral presentation, collaborative work,

literature surveys, final examination (oral) Course contents: Theoretical fundamentals of chromatography. General characterisctics of chromatographic system and its individual elements. Definition of the retention process. Mechanism of chromatographic separation – adsorption chromatography, partition chromatography, ion chromatography etc. Classification of chromatographic techniques: planar chromatography, column chromatography. Classification with respect of mobile phase. Detection in different chromatographic techniques, with particular emphasis laid on hyphenated techniques, LC/MS and GC/MS. Choice of proper conditions for chromatographic separation. Methods of identifying chemical compounds – qualitative analysis. Application of chromatographic techniques to quantitative chemical analysis. Application of chromatographic techniques to environmental, pharmaceutical, biological, and food analysis. Objectives of the course: Explanation of elementary processes governing chromatographic separation. Presentation of the place and role of chromatographic techniques in modern chemical laboratories. Learning outcomes: Graduating from this course, students should obtain a sufficient theoretical knowledge of the fundamentals of chromatography. They should also be able to perform chromatographic separations of simple chemical compounds mixtures. Textbooks and recommended reading: 1. F. Geiss, Fundamentals of thin-layer chromatography (Planar Chromatography), Dr. Alfred Hőthig Verlag,

Heidelberg, 1987, 2. L.R. Snyder, J.J. Kirkland, Introduction to Modern Liquid Chromatography, Wiley, New York, 1979, 3. Z. Witkiewicz, Podstawy chromatografii, WNT, Warszawa, 2005.

27

Theoretical chemistry

Lecturer: prof. dr hab. Stanisław Kucharski Course code: 0310-2.03.1.012 Type of the course: Basic ECTS: 7 lecture + laboratory Number in study program: 3 Number of hours: 30 + 45 = 75 Semester: Summer (2) Course prerequisites: Mathematics and Physics (1st

degree study) Language: Polish or English

Teaching methods: Multimedia teaching techniques, using internet resources, laboratory exercises, teaching in small groups, solving tasks, calculus exercises

Assessment methods: Problem-solving exercises, collaborative work, literature surveys, final examination (oral)

Course contents: Approximate methods for solving Schroedinger equation. Theoretical basis of the ab initio methods (Self Consistent Field (SCF), Moeller Plesset (MPn), Configuration Interaction (CI), Coupled Cluster (CC)) and semi-empirical ones (NDDO, INDO, CNDO, AM1, PM3). Variational and perturbational methods – classification. Limitation of the independent particle model. Notion of the electron correlation. Reasons for going beyond the one-electron approximation. Electronic density functional theory (DFT). Definition of the density function. The Hohenberg-Kohn theorem. The Kohn-Sham equations. The exchange-correlation functional and potential. Important functionals (Local Density Approximation (LDA), Local Spin Density Approximation (LSDA), Non-Local Density Approximation, General Gradient Approximation (GGA), hybrid approximation (Becke-3-Lee-Young-Parr, B3LYP)). Intermolecular interactions based on quantum chemistry – non-specific and specific - electron-donor-acceptor and hydrogen bond. Quantum-mechanical description of the systems with translational symmetry. The Bloch function. Molecular dynamics – description of the structure and conformation changes for macromolecules. Newton’s equations of motion. Molecular modeling. Computer simulations. Molecular Mechanics (MM). Virtual experiment. Force Field method (FFM). Statistical thermodynamics in the description of the behavior of the gas and crystal systems. Thermodynamic and kinetic of the chemical reaction with help of quantum chemistry. The band theory and its practical application (e.g., in study and explanation of the molecular structure and chemical bonds). Potential energy curves for molecules in its ground and excited states. Prediction of the spectra characteristic with help of quantum chemistry. Application of the group theory in quantum chemistry and molecular spectroscopy. Symmetry operations, symmetry elements, point groups, representations and bases of representations. Role of the symmetry and consequences for atoms and molecules. Selection rules based on the group theory. Classification of the modes. Objectives of the course: Presentation of quantum chemical tools, methods based on molecular mechanics and dynamics. Learning outcomes: After the course students should have knowledge of the general aspects connected to the theoretical chemistry in a level that makes possible practical application in a structure description, spectral characteristic, properties and behavior of the chemical compounds in various states and also description of the chemical reaction (path) with help of theoretical chemistry tools. Textbooks and recommended reading: 1. L. Piela, Idee Chemii Kwantowej, PWN, Warszawa, 2003, 2. A. Gołębiewski, Elementy mechaniki i chemii kwantowej, PWN, Warszawa, 1982, 3. K. Gumiński, Elementy Chemii Teoretycznej, PWN, Warszawa, 1964, 4. I. N. Levine, Quantum Chemistry, Prentice Hall, 5 ed., 1999.

28

MAJOR CONTENTS � general chemistry � environmental chemistry � drug chemistry � computer chemistry

29

Spectroscopy

Lecturer: prof. UŚ., dr hab. Henryk Flakus Course code: 0310-2.03.2.003 Type of the course: Major ECTS: 4 lecture + laboratory Number in study program: 4 Number of hours: 30 + 30 = 60 Semester: Winter(1) Course prerequisites: Quantum chemistry and Physical

chemistry A (1st degree study) Language: Polish or English

Teaching methods: Multimedia teaching techniques, using internet resources, laboratory exercises, teaching in small groups, solving tasks

Assessment methods: Laboratory reports, problem-solving exercises, collaborative work, final examination (oral)

Course contents: Basic principles of spectroscopy. Vibrational spectra of molecules. Infrared spectroscopy. Raman spectroscopy. Infrared and Raman spectra of molecules. Applications of vibrational spectroscopy methods. Rotational spectroscopy in microwave region. Vibrational –rotational spectroscopy in infrared and Raman. Vibrational –rotational spectra of gaseous samples. Electronic spectroscopy. Absorption spectra in visible light and in ultraviolet. Emission electronic- vibrational spectroscopy. Fluorescence and phosphorescence. Spectroscopy of magnetic nuclear resonance. Magnetic resonance of protons. 1H-NMR spectroscopy. Magnetic resonance of 13C. 13C-NMR spectroscopy. Electron paramagnetic resonance (Electron spin resonance). EPR (ESR) spectroscopy. Construction of contemporary spectrometers. Methodology of spectral studies. Exemplary applications of modern spectroscopy methods in scientific studies in diverse research areas of chemistry, physics and biology. Objectives of the course: Presentation of the basic methods of molecular spectroscopy, theoretical principles of the most popular spectroscopy methods, spectra generation mechanisms, relations between molecular spectra and the molecular structure, the influence of various intra- and inter-molecular interactions onto molecular spectra, rules governing spectral transitions and selection rules for spectral transitions, interpretation of standard spectra of simple- structure molecular systems, understanding the role of spectral studies in solving of research problems, utilization of molecular spectroscopy methods in natural sciences. Learning outcomes: After the course students should have a knowledge and understanding of basic concepts of molecular spectroscopy in a level that makes possible to use this to solve the problems concerning molecular structure, reactivity and mutual interactions involving molecules as well as the interpretation of spectra of simple molecular systems. Textbooks and recommended reading: 1. Z. Kęcki, Spektroskopia Molekularna, Wyd. Naukowe PWN, Warszawa, 1992, 2. R.M. Silverstein, F.X. Webster, D.J. Kiemle, Spektroskopowe metody identyfikacji związków organicznych,

Wyd. Naukowe PWN, Warszawa, 2007, 3. W. Zieliński, A. Rajca, Metody spektroskopowe i ich zastosowanie do identyfikacji związków organicznych,

WNT, Warszawa, 1995.

30

Crystallography

Lecturer: prof. UŚ, dr hab. Barbara Machura Course code: 0310-2.03.2.013 Type of the course: Major ECTS: 5 lecture + laboratory Number in study program: 5 Number of hours: 15 + 30 = 45 Semester: Summer (2) Course prerequisites: None Language: Polish or English Teaching methods: Multimedia teaching techniques, using internet resources, laboratory exercises,

teaching in small groups, solving tasks, calculus exercises Assessment methods: Laboratory reports, problem-solving exercises, collaborative work, final examination

(oral) Course contents: Crystal as an ordered phase. Crystallization process. The single crystal growth from the vapour, liquid and solid phase. Crystallization of macromolecules and proteins. Generation and properties of X- rays. Geometry of X-ray diffraction: Laue theory and Bragg-Wulff theory. Reciprocal lattice and X-ray diffraction phenomenon. Intensity of X-ray diffraction reflections. Atomic scattering factor. Structure factor. Systematic extinctions of diffraction reflections. X-ray structure analysis methods for single crystals: Laue method, rotating crystal method, methods with photographic film shift and 4-circle single crystal diffractometer. X-ray crystal structure determination: basic studies on lattice and symmetry, Fourier transformation, searching for approximate structure, refinement of crystal structure model and interpretation of results. Powder diffraction methods: Debye-Scherer-Hull method, focusing methods, polycrystalline diffractometer. Diffraction reflections indexing of polycrystalline substances. Phase analysis. Electron and neutron diffraction. Crystal structure of chemical elements and compounds. Real structure of crystal substances. Structural databases. Objectives of the course: The presentation of basic methods of single crystal growth, explanation of X-ray diffraction geometry on crystal compounds and dependence of intensity of diffracted beam on atom kind and location in a unit cell. Discussion on basics of X-ray structure analysis methods for single crystals and powders, get acquitted with steps of crystal structure determination, introducing of basic concepts of electron and neutron diffraction. Learning outcomes: After the course students should know and understand basic concepts of X-ray crystallography, electron and neutron diffraction; should know and be able to use the known methods of the single crystals growth, should be able to choose a proper single crystal and prepare powder sample for X-ray examination, can use diffraction techniques to solve analytical, identification and structural problems, can use the structural data bases and describe structure using the standard CIF file (crystal information file). Textbooks and recommended reading: 1. P. Luger, Rentgenografia strukturalna monokryształów, PWN, Warszawa, 1989, 2. Z. Bojarski, E. Łągiewka, Rentgenowska analiza strukturalna, Wydawnictwo Uniwersytetu Śląskiego,

Katowice, 1995, 3. A. Oleś, Metody doświadczalne fizyki ciała stałego, WNT, Warszawa, 1998.

31

OTHERS � general chemistry � environmental chemistry � drug chemistry � computer chemistry

32

Scientific information

Lecturer: dr Tomasz Magdziarz Course code: 0310-2.03.3.004 Type of the course: Others ECTS: 1 Classes Number in study program: 6 Number of hours: 15 Semester: winter (1) Course prerequisites: None Language: Polish or English Teaching methods: Multimedia teaching techniques, using internet resources, teaching in small groups,

solving tasks Assessment methods: Problem-solving exercises, literature surveys, final examination (pass/fail) Course contents: Principles of documentation and reporting of scientific research. Technical and scientific documentation. Different types of chemical literature. Literature references. Patents. Authors' rights. Patent description, elements of patent description. Current state of scientific knowledge. Patent claims. Markush sctuctures. Scientific publications. Chemische Zentralblatt. Encyclopedia of organic compounds Beilsteins Handbuch der Organischen Chemie. Encyclopedia of inorganic and metaloorganic compounds Gmelins Handbuch der anorganischen chemie. Chemical Abstracts Service (CAS). CAS indexing concept. Specificity of chemical data. Databases and methods of building of queries. Contextual databases queries. Facts, compounds, reaction and methods of synthesis searches. Methods of coding of structures of chemical compounds. Molecular structures, molecular formulas. Molecular editors. Discoverygate database system. Crossfire Beilstein and Crossfire Gmelin databases. Patent databases. Patent Chemistry Database. PubMed database system (www.ncbi.nlm.nih.gov/pubmed/). Catalogs of chemical compounds as encyclopedias of chemical data (www.sigmaaldrich.com). Science Citation Index database. Journal Citation Report. ISI Web of Knowledge. Scopus. Other Internet sources of scientific data. Google Book Search usage for chemical literature searching. Internet bookstores (i.e. Amazon.com) usage for chemical book search. Polish library catalogs. Books and journals resources. Methods of requesting of chemical literature from domestic and international libraries. Law aspects of exploiting of foreign literature in research. Objectives of the course: The presentation of the most important topics in information technology, with emphasis on their further practical applications. The discussion of current issues related to the presented topics. Introduction to effective computer system and networking usage. Learning outcomes: Knowledge of the most important topics in information technology. Understanding of the issues related to the discussed topics. Basic skills in computer system and networking usage. Textbooks and recommended reading: 1. MDL, e-learning materials, http://www.mdl.com/solutions/videos, 2. J. March, Chemia organiczna, WNT, Warszawa, 1975, 3. Beilstein Crossfire, supporting materials.

33

Laboratory of molecular design

Lecturer: prof. dr hab. inŜ. Jarosław Polański prof. dr hab. Beata Walczak prof. dr hab. Stanisław Kucharski

Course code: 0310-2.03.3.005

Type of the course: Others ECTS: 2 Lecture + laboratory Number in study program: 7 Number of hours: 15 + 15 = 30 Semester: Winter (1) Course prerequisites: None Language: Polish or English Teaching methods: Multimedia teaching techniques, using internet resources, laboratory exercises,

teaching in small groups, solving tasks, calculus exercises Assessment methods: Laboratory reports, problem-solving exercises, oral presentation, collaborative work,

literature surveys, final examination (pass/fail) Course contents: Organic chemistry and chemoinformatics. Chemoinformatics vs. Chemometrics. Data. Information. Knowledge. Representation of chemical molecules. Matrix representation. Adjacency matrix. Distance matrix. Atom connectivity matrix. Incidence matrix. Incidence matrix. Bond matrix. Bond electron matrix. Connection table. Smiles. Handling chemical structure data in computers. Data formats. Structure databases. Database searching. Chemical structure elucidation. Modeling chemical molecules. Chemical reaction. Synthesis design. Synthon chemistry. Corey disconnection concept. Reaction prediction. Molecular design and quantitative structure-activity relationships paradigms. Molecular descriptors. Connectivity indices. Molecular editors. Analysis of multidimesional data sets: projection methods. Data compression and visualization (principal component analysis). Calibration methods (principal component regression and partial least squares). Discrimination methods (discriminant partial least squares, CART) and classification (SIMCA). Feature selection methods (univariate and multivariate). Significance analysis of selected features (randomization tests). Examples of linear and non-linear modeling of biological activity based on molecular descriptors and topological indices. Data reprezentativity and model validation approaches. Robust modeling techniques General description of computational chemical methods based on molecular mechanics and quantum chemistry. Hierarchy of approximations employed in applied computational methods. Characteristics of computational methods based on density functionals. Review of the computational packages: GAUSSIAN, GAMESS, HYPERCHEM, MOLCAS, ACES. Elements of molecular dynamics. Objectives of the course: Presentation of the basic concepts of chmeoinformatics, in particular, fundamental problems of representation, coding and in silico handling at molecular objects. Laboratory classes should provide practical introduction to this field. Learning outcomes: After the course students should have basic knowledge and practical skills in coding molecular structures, using common molecular editors Textbooks and recommended reading: 1. J. Gasteiger, Chemoinformatics. A textbook, Wiley, 2003, 2. B.G.M. Vandeginste, D.L. Massart, L.M.C. Buydens, S. de Jong, P.J. Lewi, J. Smeyers-Verbeke, Handbook

of chemometrics and qualimetrics: part B, Elsevier, Amsterdam, The Netherlands, 1998.

34

OPTIONAL COURSES: General chemistry

35

Thermodynamics

Lecturer: prof. UŚ, dr hab. Wojciech Marczak Course code: 0310-2.01.3.006 Type of the course: Optional ECTS: 5 lecture + classes Number in study program: 8a Number of hours: 30 + 15 = 45 Semester: Winter (1) Course prerequisites: Physical chemistry A (1st degree

study) Language: Polish

Teaching methods: Multimedia teaching techniques, using internet resources, solving tasks Assessment methods: Problem-solving exercises, oral presentation, collaborative work, literature surveys,

final examination (pass/fail) Course contents: Zeroth Law of thermodynamics, thermal equilibrium, adiabatic processes, empirical temperature, gas temperature scale. The First Law of thermodynamics, internal energy, heat and work in thermodynamics. Quasistatic and reversible processes. Enthalpy. The Second Law of thermodynamics, entropy, changes of entropy in reversible and irreversible (spontaneous) processes, changes of entropy in isolated systems. The Third Law of thermodynamics. Relations between thermodynamic quantities. Configurations and weights. The molecular partition function. The relation between internal energy and the molecular partition function. The statistical entropy. The canonical partition function and the thermodynamic information. Applications of statistical thermodynamics: mean energies for different modes of motions, heat capacities, equations of state, residual entropies, equilibrium constants. Objectives of the course: Presentation of the link between the classical thermodynamics and the molecular theory. Theoretical background for basic concepts of classical thermodynamics in terms of the statistical thermodynamics. Applications of thermodynamics in physical chemistry. Learning outcomes: Students should know basic concepts of classical and statistical thermodynamics. They understand physical meaning of thermodynamic functions and can discuss it in terms of statistical thermodynamics. They can apply methods of thermodynamics to problems in the field of physical chemistry. Textbooks and recommended reading: 1. P. Atkins, J. De Paula, Atkins’ physical chemistry, Oxford University Press, Oxford, 2006, 2. H. Buchowski, W. Ufnalski, Podstawy termodynamiki, WNT, Warszawa, 1994, 3. P. Atkins, C. Trapp, M. Cady, C. Giunta, Student's solutions manual to accompany Atkins' Physical Chemistry, Oxford University Press, Oxford, 2006, 4. K. Gumiński, Termodynamika, PWN, Warszawa, 1982.

36

Chemometrics

Lecturer: prof. dr hab. Beata Walczak Course code: 0310-2.01.3.014 Type of the course: Optional ECTS: 5 lecture + classes Number in study program: 8b Number of hours: 30 + 15 = 45 Semester: Summer (2) Course prerequisites: None Language: Polish Teaching methods: Multimedia teaching techniques, using internet resources, solving tasks, calculus

exercises Assessment methods: Problem-solving exercises, oral presentation, collaborative work, literature surveys,

final examination (pass/fail) Course contents: Introduction to unsupervised and supervised data modeling. Dealing with different types of data. Main steps of data modeling: Design of model and test sets. Data pre-processing. Data exploration (compression, visualization and detection of outliers in explanatory variables). Model selection. Model construction. Analysis of residuals. Model validation. Model fit and its predictive power. Techniques of multivariate calibration: Linear methods (Multiple Linear Regression. Principal Component Regression. Partial Least Squares Regression). Examples of applications in, e.g.. Quantitative Structure Activity Relationships. Techniques of classification and discrimination: Soft Independent Modeling of Class Analogies (SIMCA). K-Nearest Neighbour method. Classification and Regression Trees. Discriminant Partial Least Squares. Examples of applications in biomedical diagnostics. Objectives of the course: Discussion of basic stages in data analysis: Data compression and visualization, unsupervised and supervised modeling, models validation, and interpretation of the obtained results. Learning outcomes: After completing the course, students should possess basic knowledge of chemometric methods and practical skills to implement this knowledge to solving problems related to multidimensional data analysis. Textbooks and recommended reading: 1. B.G.M. Vandeginste, D.L. Massart, L.M.C. Buydens, S. de Jong, P.J. Lewi, J. Smeyers-Verbeke, Handbook of chemometrics and qualimetrics: part B, Elsevier, Amsterdam, The Netherlands, 1998.

37

Environmental chemistry

Lecturer: dr hab. Jan G. Małecki Course code: 0310-2.01.3.021 Type of the course: Optional ECTS: 5 lecture + classes Number in study program: 8c Number of hours: 15 + 30 = 45 Semester: winter (3) Course prerequisites: None Language: Polish Teaching methods: Multimedia teaching techniques, using internet resources, solving tasks Assessment methods: Problem-solving exercises, oral presentation, collaborative work, literature surveys,

final examination (pass/fail) Course contents: Environmental chemistry; composition of the environment; chemical processes in the environment; anthropogenic factors; agencies for gathering of data on the state of the environment; constituent elements of living organisms; natural cycles of selected elements. Objectives of the course: To familiarize students with environmental problems in the aspect of chemical basis of functioning of the environment both in the natural state and in the altered state in a global view; with composition of the environment, processes occurring in the environment, types of changes resulting from human activity. To discuss chemical composition, chemical processes occurring and disturbances observed as a result of natural and anthropogenic actions and introduce elements of „green chemistry” and environmental toxicology. To point out the links and dependencies between the individual elements of the environment. In such an aspect, the problems discussed during the lessons concern the atmosphere, hydrosphere and land environment. Learning outcomes: After graduation, students should acquire knowledge and recognition of dependencies between various element of the environment; they are able to forecast the effects of presence of harmful and toxic substances in the environment; they know basic concepts, methods of research, control and evaluation of the state of the environment; they know agencies monitoring the state of the environment and environmental standards; they can put their knowledge into practical use while evaluating the human influence on the environment. Graduating enables students to find a job in chemical industry, institutions connected with environmental protection, and in interdisciplinary teams examining or monitoring the environment. Textbooks and recommended reading: 1. G.W. VanLoon, S.J. Duffy, Chemia środowiska, Wydawnictwo Naukowe PWN, Warszawa, 2007, 2. S.E. Manahan, Toksykologia środowiska, aspekty chemiczne i biologiczne, Wyd. Nauk. PWM, Warszawa,

2006, 3. J.E. Andrew et al., Wprowadzenie do chemii środowiska, WNT, Warszawa, 1999, 4. B.J. Alloway, D.C. Ayres, Chemiczne podstawy zanieczyszczania środowiska, PWN, Warszawa, 1999, 5. J. Namieśnik, Z. Jamrógiewicz, M. Pisarczyk, L. Torres, Przygotowanie próbek środowiskowych do analizy,

WNT, Warszawa, 2000.

38

OPTIONAL COURSES: Environmental chemistry

39

Environmental geochemistry

Lecturer: prof. UŚ, dr hab. Ł. Karwowski dr Maria Racka

Course code: 0310-2.02.3.007

Type of the course: Optional ECTS: 5 Lecture + classes Number in study program: 8a Number of hours: 30 + 15 = 45 Semester: Winter (1) Course prerequisites: None Language: Polish Teaching methods: Multimedia teaching techniques, solving tasks Assessment methods: Problem-solving exercises, oral presentation, collaborative work, literature surveys,

final examination (pass/fail) Course contents: Geochemistry as a field of science. Structure of the Earth- actual knowledge. Geochemical environment and chemical elements migration. Geospheres - lithosphere, hydrosphere, atmosphere. Biosphere and anthroposphere. Physical and chemical geochemistry basis. Basic crystallochemical information. Crystallochemical evidences for presence of chemical elements in nature. Ecosystems, geochemical horizons. Biomass and productiveness of ecosystems. Photosynthesis and chemosynthesis. Breakdown of organic matter. Composition of life matter. Biochemical cycles. The water in biosphere. Migration of the elements in biosphere. Geochemical aspect of biosphere. Anthroposphere and chemical elements location in biosphere. Chemical equilibrium in natural environment. Environmental pollution caused by trace element. Objectives of the course: The subject made students aware of the relationships which are present between different Earth’s environments and theirs chemical aspects. Logical cognition of chemical differentiation of nature environments. The main aim of the subject is to understand what is the mechanism of chemical elements concentration in different the Earth’s phases with compilation to bio- and anthroposphere, respectively. Learning outcomes: Every student after finished course should have knowledge about the basic geochemistry. Students have to know what are the differences between various types of the Earth’s environments, what is the role of main and trace elements in selected ecosystems and understand the mechanisms of elements circulation in nature, especially called by human and its acting. Textbooks and recommended reading: 1. A. Polański, K. Smulikowski, Geochemia, Wydawnictwa Geologiczne, Warszawa, 1969, 2. A. Kabata-Pendias, H. Pendias, Pierwiastki Śladowe w Środowisku Biologicznym, Wydawnictwa

geologiczne, Warszawa, 1979, 3. A. Kabata-Pendias, H. Pendias, Biogeochemia Pierwiastków Śladowych, PWN, Warszawa,1999, 4. Z.M. Migaszewski, A. Gałuszka, Podstawy Geochemii Środowiska; Wyd. TWN, 2007, 5. G. vanLoon, S.J. Duffy, Geochemia Środowiska (tłum. Boczoń W., Wachowski L.), Wydawnictwo

Naukowe PWN, Warszawa, 2008, 6. P. O’Nelik, Chemia Środowiska; Wydawnictwo Naukowe PWN, Warszawa, 1997.

40

Environmental toxicology

Lecturer: prof. dr hab. Paweł Migula dr Alina Kafel

Course code: 0310-2.02.3.015

Type of the course: Optional ECTS: 5 Lecture + laboratory Number in study program: 8b Number of hours: 30 + 15 = 45 Semester: Summer (2) Course prerequisites: None Language: Polish Teaching methods: Multimedia teaching techniques, laboratory exercises, teaching in small groups,

solving tasks Assessment methods: Laboratory reports, problem-solving exercises, collaborative work, final examination

(pass/fail) Course contents: Elements of general toxicology: poison, biocide, xenobiotic, factors causing toxicity. Metabolism of poisons in the organism. Mechanisms of toxic activity, remote action of poisons. Toxicology of metals, non-metals and their compounds, solvents, herbicides, plastics. Potential toxicity of domestic items, cosmetics and food, selected products of chemical and pharmaceutical industry. Chemical contamination of the atmospheric air, public premises, water and soil. Toxic substances in the chemical laboratory: acids, solvents, organic compounds, metallorganic, inorganic and complex compounds. Legal regulations and standards of the environmental pollution, working environment and the handling of toxic substances. Objectives of the course: The graduate will gain knowledge of: chemical, physicochemical and physical characteristics of basis groups of poisons, routes of penetration of xenobiotics and their distribution in the organism, residence and accumulation of poisons, basic metabolisms and the effect of xenobiotics on components of the cell, tissue and organs of the living organism, problems of multigeneration interactions, epidemological aspects of the environmental toxicology, assessment of the present and potential dangers (threats) for the atmosphere, water, soil, risks at work place, in the learning (training) labs, application of adequate methods of analysis, monitoring, markers and biomarkers in the assessment of the present and potential dangers. Principles of safe work with toxic substances. Learning outcomes: Becoming aware of risks present at different places and situations (e.g. chemical warehouses, chemical labs, waste dumps). Skills necessary to work in groups monitoring the environmental toxicological levels, work and dwelling conditions, and in the protection units (groups) for the toxicological hazards (dangers). Skills needed for safe work in the presence of potential toxicological risks. The knowledge of legal norms and regulations dealing with the safety of work and environmental protection. Textbooks and recommended reading: 1. S.F. Zakrzewski, Podstawy toksykologii środowiska, PWN, Warszawa, 2000, 2. C.H. Walker, S.P. Hopkin et al., Podstawy ekotoksykologii, PWN, Warszawa, 2002, 3. E.S. Manahan, Toksykologia środowiska. Aspekty chemiczne i biochemiczne, PWN, Warszawa, 2006, 4. J.K. Piotrowski (Ed.), Podstawy toksykologii, WNT, Warszawa, 2006, 5. M. Siemiński, Środowiskowe zagroŜenia zdrowia. Inne Wyzwania, Wyd. Naukowe PWN, Warszawa, 2007.

41

Atmospheric chemistry

Lecturer: dr hab. Michał Daszykowski Course code: 0310-2.02.3.022 Type of the course: Optional ECTS: 5 lecture + classes Number in study program: 8c Number of hours: 15 + 30 = 45 Semester: Winter (3) Course prerequisites: None Language: Polish Teaching methods: Multimedia teaching techniques, using internet resources, solving tasks Assessment methods: Problem-solving exercises, oral presentation, collaborative work, literature surveys,

final examination (pass/fail) Course contents: The Earth’s atmosphere: chemical composition of the Earth atmosphere, regions of the atmosphere; types of chemical reactions taking place in the atmosphere; electromagnetic radiation; influence of electromagnetic radiation on chemical composition of the atmosphere and plants and animals, UV-B radiation, absorption of electromagnetic radiation by chemical molecules; stratospheric chemistry – ozone: the ozone layer, the ‘ozone hole’, catalytic decomposition process of ozone, chemical compounds and their influence of the ‘ozone hole’ formation, thickness of the ozone layer and its measurement, chemical processes in lower regions of the stratosphere, oxygen chemistry, reactions of chlorofluorocarbons; tropospheric chemistry – smog: smog and photochemical smog, smog chemistry, exhaust gases from combustion engines; tropospheric chemistry – precipitation: chemical composition of rain, atmospheric production of nitric acid and sulphuric acid, factors influencing pH of rain, chemistry of rain, snow and fog, aerosols, chemical properties of urban and indoor areas; global threads: greenhouse gases and aerosols, greenhouse effect and the ‘ozone hole’. Objectives of the course: To broaden students’ knowledge about current condition of the Earth environment, and in particular about current condition of Earth’s atmosphere and its chemical processes. During the course, students will be introduced to subject of atmospheric chemistry, fundamental chemical reactions and other physico-chemical processes that shape our environment. Learning outcomes: Ability to interpret basic chemical processes that take place in the Earth’s atmosphere; foreseeing potential threads and effects caused by a presence of hazard and toxic chemicals in the atmosphere. Textbooks and recommended reading: 1. G.W. vanLoon, S.J. Duffy, Chemia środowiska, Wydawnictwo Naukowe PWN, Warszawa, 2007, 2. C. Bard, Environmental chemistry, W.H. Freeman and Company, New York, 1995.

42

OPTIONAL COURSES: Drug chemistry

43

Medicinal chemistry

Lecturer: prof. dr hab. inŜ. Jarosław Polański dr Robert Musioł

Course code: 0310-2.05.3.009

Type of the course: Optional ECTS: 5 lecture + classes + laboratory Number in study program: 8a Number of hours: 15 + 15 + 15 = 45 Semester: Winter (1) Course prerequisites: Organic Chemistry A (1st degree



Assessment methods: Laboratory reports, problem-solving exercises, oral presentation, collaborative work, final examination (pass/fail)

Course contents: Objectives and basic concepts of medicinal chemistry. Medicinal vs. medical chemistry. Macromolecular drug targets. Enzymes. Receptors. Agonist. Antagonist. Nucleic acids as drug targets. The search for novel drugs. Drug design and development. Lead structure. Structure modifications. Variation of substitution pattern. Extension of the structure. Extension/contraction of the chain/ring. Isosteric groups. Structure simplification. Structure rigification. X-ray analysis. Molecular modeling. Fragment based design. Analogue based design. ADMET concept (Adsorption, Distribution, Metabolism, Excretion, Toxicity). Lipinski’s rule. Combinatorial chemistry vs. dynamic combinatorial chemistry. Serendipitous and rational approaches to drug design. Chemoinformatics in drug design. Biological testing. Basic drug classes. Antiviral. Antidepressants adrenergic nervous system. Cholinergic and anti cholinergic drugs. Inhibitory acetylcholinesterase inhibitors. Opium analgesics. Anticancer drugs and therapies. Photodynamic therapy (PDT). Clinical trials. Patents. Pharma and cosmetic industries. Cosmetic product. Chemical problems in skin structure and function. Kinetic determinants of transport through skin. Drug and cosmetic forms. Objectives of the course: Presentation of the objectives and basic concepts of medical, medicinal and cosmetic chemistry and providing the introduction to the problems of designing, testing and preparing drugs and cosmetics. Learning outcomes: After the course students should have basic knowledge on the current schemes for the investigations and commercialization of the results in medicinal and cosmetic chemistry as well as R&D organization. Textbooks and recommended reading: 1. G. Patrick, Chemia medyczna. Podstawowe zagadnienia, WNT, Warszawa, 2003, 2. G. Patrick, Chemia leków, PWN, Warszawa, 2004, 3. M.C. Martini, Kosmetologia i farmakologia skóry, PZWL, Warszawa, 2007.

44

Biochemistry with elements of genetics

Lecturer: prof. dr hab. Sylwia ŁabuŜek dr Izabela Greń

Course code: 0310-2.05.3.017

Type of the course: Optional ECTS: 5 lecture + classes Number in study program: 8b Number of hours: 30 + 15 = 45 Semester: Summer (2) Course prerequisites: Organic Chemistry A (1st degree


Teaching methods: Multimedia teaching techniques, using internet resources, solving tasks Assessment methods: Problem-solving exercises, oral presentation, literature surveys, final examination

(pass/fail) Course contents: Metabolism of proteins, saccharides and lipids – integration and regulation of metabolism. Mechanisms of enzyme activities. Enzyme blockers. Regulation of enzyme activities. Influence of drugs on enzyme activities. Therapeutic action of enzymes. Free radical processes in organisms. Biochemistry of vitamins. Metabolism of unsaturated fatty acids, eikozanoids and sterids. Biochemistry and pharmacology of the cell membrane. Mechanisms of molecules transport into/out of the cell. Structure and types of receptors. Kinds of ligands. Molecular mechanisms of signal transduction in cell. Drugs as ligands. Genetic processes in Procaryota and Eucaryota. Drugs acting on the nucleic acids. Drugs related to the nucleic acids. Biochemistry of antibiotics. Genetic bases and mechanisms of resistance to antibiotics. Biochemical and genetic fundamentals of disease (mutations, chromosomal aberrations, genetic therapy). Molecular bases of cancer development, oncogenes, growth factors, suppressor genes. Drugs applied in chemotherapy of tumor. Biochemical fundamentals of cell aging. Biochemical and genetic bases of apoptosis. Objectives of the course: Familiarization with biochemical and genetic fundamentals of drugs activities. Presentation of correlation between the basic metabolic pathways and disturbances in functioning of organism. Learning outcomes: At the end of the course student should get knowledge of metabolism of the cell and its connections with disease processes as an essential basis for the design of drugs. Knowledge of biochemistry and genetics provides opportunity for understanding the mechanisms of drugs activities. Textbooks and recommended reading: 1. R.K. Murray et al., Biochemia Harpera, PZWL, Warszawa, 2004, 2. A. Chmiel, S. Grudziński, Biotechnologia i chemia antybiotyków, PWN, Warszawa, 1998, 3. G.L. Patrick, Chemia medyczna, Wydawnictwa Naukowo-Techniczne, Warszawa, 2001.

45

Chemoinformatics

Lecturer: prof. dr hab. inŜ. Jarosław Polański dr Rafał Gieleciak

Course code: 0310-2.05.3.024

Type of the course: Optional ECTS: 5 lecture + laboratory Number in study program: 8c Number of hours: 15 + 30 = 45 Semester: Winter (3) Course prerequisites: Organic Chemistry A (1st degree



Assessment methods: Laboratory reports, problem-solving exercises, collaborative work, literature surveys, final examination (pass/fail)

Course contents: The scope and origins of chemoinformatics. Chemoinformatics vs. chemometrics. Data. Information. Model. Chemical space. Biological space. Computer sciences and chemistry. Coding chemical molecules. Structure representation and searching. Molecular connectivity. Linear notation. SMILES codes. Molecular editors. Coding chemical reactions. Dugundji-Ugi B+R=E notation. Computer generated chemical names. Structure to name and name to structure conversions. Molecular modeling. 2D and 3D structure generators. Model builders. Modeling 3D structures. Molecular mechanics. Semiempirical quantum chemistry methods. Molecular dynamics. Chemical databases. Structure and substructure searches. Molecular graphics. Chemical synthesis and retrosyntheses (disconnections). Synthon nomenclature. Operations on synthons: synthon modifications. Umpolung. Synthon vs. Reagent. Computer assisted synthesis design. Synthesis tree. Computer-assisted synthesis design (CASD): CHMTRN (chemistry translator). LHASA. WODCA. Chemical reaction predictions. EROS. Computer assisted chemical structure elucidation. Database mining for computer assisted knowledge discovery. Property oriented synthesis. Computer assisted molecular design. Drug design. Brut force combinatorial screening approaches to drug discovery. Target driven approaches. Ligand and structure based design. Modeling QSAR. Hansch model. Molecular descriptors. Multidimensionality in QSAR. 1D to 6D QSAR. Data analysis problems in QSAR. Comparative Molecular Field Analysis (COMFA). Comparative Binding Interaction Energy Analysis (COMBINE). Drug-likeness and druggability. Molecular diversity. Bioinformatics. Pharmacogenomics. Chemical genetics. Proteomics and other –omics concepts. Chemical internet resources. Objectives of the course: The presentation of the fundamental concepts of chemoinformatics, in particular, coding chemical molecules and reactions, modeling and molecular design in silico. Learning outcomes: After the course students should have an understanding of the basic problems of coding chemical data as well as performing and interpreting in silico chemical simulations. Textbooks and recommended reading: 1. J. Gasteiger, T. Engel (Eds.), Chemoinformatics. A textbook, Wiley-VCH, 2003, 2. J. Polański, Chemoinformatics, in: Comprehensive Chemometrics, S. Brown, R. Tauler, B. Walczak (Eds.),

Elsevier, 2008, 3. R. Kudowski (Ed.) Informatyka medyczna, PWN, Warszawa, 2003.

46

OPTIONAL COURSES: Computer chemistry

47

Fortran programming

Lecturer: dr Maciej Kołaski Course code: 0310-2.04.3.008 Type of the course: Optional ECTS: 5 lecture + laboratory Number in study program: 8a Number of hours: 15 + 30 = 45 Semester: Winter (1) Course prerequisites: Mathematics A (1st degree study) Language: Polish or English Teaching methods: Multimedia teaching techniques, laboratory exercises, teaching in small groups,

solving tasks, calculus exercises Assessment methods: Laboratory reports, problem-solving exercises, final examination (pass/fail) Course contents: Programming languages, algorithm, flow chart, algorithm design, flow chart building blocks, types of boxes in a flowchart, examples, What is Fortran?, syntax, program layout, header, specification part, execution part, data types, integer type, real type, character type, double precision types, complex type, logical type, variables, constants, arithmetic operations and functions, real arithmetic, integer arithmetic, mixed mode arithmetic, priority rules, Fortran functions, assignment statement, input and output (I/O) statement, file I/O, records, format specification, loops, DO loops, WHILE loops, UNTIL loops, array declaration, initial values for arrays, conditional statement, IF … THEN statement, arithmetic operators, logical operators, IF … THEN … ELSE statement, functions and subroutines, intrinsic functions, external functions, subroutines, BLOCK DATA statement, compilation, compiling a single source file, compiling multiple source files, making and using libraries, running a Fortran program, numerical software, BLAS, ATLAS, LAPACK, parallel programming. Objectives of the course: The presentation of the fundamental and advanced concepts used in Fortran programming: algorithm, flow chart, data types, integer type, real type, character type, complex type, arithmetic, conditional statement, loops, input and output procedures, format specification, compilation, numerical libraries. Learning outcomes: After the course students should have a basic knowledge of Fortran programming in a level that makes possible to write, debug, compile and run simple programs concerning matrix algebra, solving systems of linear equations, regression analysis, numerical differentiation and integration. Textbooks and recommended reading: 1. D. Chrobak, Fortran – praktyka programowania, Mikon, Warszawa, 2003, 2. W. Pachelski, Programowanie strukturalne w języku Fortran 77 dla IBM PC, WNT, Warszawa, 1993 3. J. Piechna, Programowanie w języku Fortran 90 i 95, Wydawnictwo Politechniki Warszawskiej, Warszawa,

2000, 4. S. J. Chapman, Fortran 90/95 for Scientists and Engineers, McGraw-Hill Science/Engineering/Math, 2ed,

2003.

48

Operating systems and computer networks

Lecturer: dr Joachim Włodarz Course code: 0310-2.04.3.016 Type of the course: Optional ECTS: 5 lecture + laboratory Number in study program: 8b Number of hours: 30 + 15 = 45 Semester: Summer (2) Course prerequisites: None Language: Polish or English Teaching methods: Multimedia teaching techniques, using internet resources, laboratory exercises,

teaching in small groups, solving tasks, calculus exercises Assessment methods: Laboratory reports, problem-solving exercises, collaborative work, final examination

(pass/fail)

Course contents: Operating system as hardware extension and resource manager, evolution and taxonomy, basic concepts and abstractions, system calls and internal structure, operating systems and networking, examples. Processes and threads: active system entities, interprocess communication, scheduling. Resources and deadlock: passive system entities, deadlocks: detection and recovery, avoidance and prevention, starvation. Memory management: basic methods, segmentation, swapping and paging, virtual memory, page replacement algorithms, implementation issues. Input/Output management: hardware and software issues, layered structure of input/output handling, disk storage, character- and block-oriented devices, user and network interfaces. File systems: files as data set abstractions, directory systems, implementation examples. Multimedia handling: introduction, process scheduling, storage and caching. Multiple processor systems: hardware support, synchronization and scheduling. Multiple computer systems: uses of computer networks, networking hardware and software, reference models and standarization, examples. Communication at the physical layer: theoretical background, guided and wireless transmission, satellite communication, telephone and television systems. Data link layer: communication channel abstraction, error detection and correction, medium access control, bridging and switching, representative technologies (Ethernet, WiFi, Bluetooth). Network layer: host-to-host communication abstraction, routing and traffic control algorithms, IP protocol. Transport layer: entity-to-entity communication abstraction, connection-based and connectionless transmission, TCP and UDP protocols. Application layer: naming and directory services, file-oriented services, electronic mail, distributed computer systems and middleware, computer clusters, grid/cloud computing. Security and data protection: the (in)secure environment, authentication and authorization, communication security, protection mechanisms and cryptography, trusted computer systems. Objectives of the course: The presentation of basic concepts and structures of modern computer operating systems and computer networks, with emphasis on their common layered organization. The discussion of various algorithms and protocols which are essential for proper functioning and performance. Introduction to system-level and network programming. Learning outcomes: Knowledge about the internals and functioning of a typical operating system and computer network. Understanding of the impact of various algorithms, protocols and tuning choices on the system/network performance and usability. Basic skills in system-level and network programming. Textbooks and recommended reading: 1. A. Silberschatz, P. Galvin, G. Gagne, Podstawy systemów operacyjnych, WNT, 2006, 2. A.S. Tanenbaum, Sieci komputerowe, Helion, 2004, 3. A.S. Tanenbaum, Modern operating systems, 2nd Ed., Prentice Hall, 2004.

49

Computational chemistry. Applications

Lecturer: prof. UŚ, dr hab. Maria Jaworska Course code: 0310-2.04.3.023 Type of the course: Optional ECTS: 5 Lecture + laboratory Number in study program: 8c Number of hours: 15 + 30 = 45 Semester: Winter (3) Course prerequisites: Quantum chemistry (1st degree



Assessment methods: Laboratory reports, problem-solving exercises, final examination (pass/fail) Course contents: Models in computational chemistry. Selection of model and computational method. Molecular structure. Potential energy surface (PES). Finding minima on PES. Local and global minima. Cartesian and internal coordinates. Geometry optimization of selected systems: application of DFT method for vitamin B12 and Molecular Mechanics (MM) for large organic molecules. Interaction with environment. Discrete model – aminoacid residues and solvent molecules in Quantum Mechanics metods (QM). QM/MM method. Dividing the system on QM and MM parts. Examples: solvated metal cations, molecules in the protein environment. Continuum solvation models: PCM and COSMO. Conformational analysis. Determination of the structure and energy of various isomers. Calculation of IR spectrum. Energy of chemical reactions. Transition state on PES. Characterization of transition state. Finding transition state on PES. Calculation of enzymatic reactions energy. Homogeneous catalysis reactions (olefin metathesis). Theoretical investigation of reaction mechanism – determination of activation energies for competitive mechanisms. Thermal corrections and zero point energy. Calculation of hydrogen bond energy with different methods (DFT, MP2). Electronic structure of molecules. Molecular orbital diagrams. Frontier orbitals and reactivity. Studying reactivity and molecular interactions with the use of electrostatic potentials. Example: interaction of antimalarial drugs with hematin. Application of Monte Carlo (MC) method for investigation of the molecular structure of large biomolecules. Molecular Dynamics (MD) method in studying biochemical processes (ion channels). Heterogeneous catalysis. Cluster model. Periodic methods in catalytic systems modeling. Examples of catalytic reactions on metal surfaces. Objectives of the course: The presentation of the fundamental concepts of computational chemistry. Studying the molecular structure and reactivity with theoretical methods. Electronic structure, electrostatic potentials. Presentation of applications of theoretical methods to biological systems and chemical materials. Learning outcomes: After the course students should have a knowledge and understanding of basic computational chemistry concepts in a level that makes possible to use this to solve the problems of modeling structure and reactivity of organic and inorganic systems. He also should be able to choose method appropriate to the problem and system size. Textbooks and recommended reading: 1. A.R. Leach, Molecular modelling principles and applications, Longman, Singapore, 1996, 2. D. Frenkiel, B. Smit, Understanding molecular simulations, Academic Press, 1996.

50

SPECIALISATION I: Analytical Chemistry

Number in study program: 9 Type of the course: Lecture + classes + laboratory Number of hours* 4×15 + 4×7.5 + 135 Semester: Winter (1) + summer (2) + winter (3) ECTS: 4×2 (lecture + classes) + 6 (laboratory)

* selected optionally in 4 × (15 + 7.5) hour modules (lecture + classes)

51

Sampling and preparation of samples for analysis

Lecturer: dr. Barbara Mikuła Course code: 0310-2.03.4.031 Type of the course: Specialization ECTS: 2 Lecture + classes Number in study program: 9 Number of hours: 15 + 7.5 = 22.5 Semester: 1 or 2 Course prerequisites: None Language: Polish or English Teaching methods: Multimedia teaching techniques, using internet resources, teaching in small groups,

solving tasks Assessment methods: Problem-solving exercises, oral presentation, collaborative work, literature surveys,

reporting thesis results, preparation and display of posters, final examination (oral) Course contents: The ranges of observed concentrations of ingredients in modern chemical analysis. Equipment and technician working in the laboratory chemical analysis. Sources of contamination. Sampling of bulk materials (soil, minerals, plant material, foodstuffs, etc.), liquid (water, waste water) and gas. Preparation of samples for analysis of modern spectroscopic techniques and electrochemical methods of distribution of the samples. reagents and materials used in procedures for the distribution of the samples. Reagents used in the analysis, methods for their purification. Standard solutions and reference materials. Systematic errors in chemical analysis Objectives of the course: Understanding the various stages of the analytical process, specific problem analysis and interpretation of the measuring result. Learning outcomes: Ability to use monographic studies, normative, and the original literature. Textbooks and recommended reading:

1. J. Minczewski, J. Chwastowska, R. Dybczyński, Analiza śladowa, WNT, Warszawa, 1973, 2. A. Mizuike, Enrichment techniques for inorganic trace analysis, Springer, Berlin, 1983, 3. R. Łoziński, Z. Marczenko, Spectrochemical trace analysis for metals and metalloids, vol. 30, Wilson &

Wilson, Comprehensive Analytical Chemistry, Elsevier, 1996, 4. J. Namieśnik, W. Chrzanowski, P. śmijewska, New horizons and challenges in environmental analysis and

monitoring, Centre of Excellence in Environmental Analysis and Monitoring, Gdańsk, 2003, 5. J. Namieśnik (Ed.), Przygotowanie próbek środowiskowych do analizy, WNT, 2000. 6. J. Namieśnik, J. Łukasiak, Z. Jamrózgiewicz, Pobieranie próbek środowiskowych do analizy, PWN,

Warszawa, 1995.

52

Validation of analytical methods

Lecturer: dr Beata Zawisza Course code: 0310-2.03.4.032 Type of the course: Specialization ECTS: 2 Lecture + classes Number in study program: 9 Number of hours: 15 + 7.5 = 22.5 Semester: 1 or 2 Course prerequisites: None Language: Polish or English Teaching methods: Multimedia teaching techniques, using internet resources, teaching in small groups,


reporting thesis results, preparation and display of posters, final examination (oral) Course contents: Terminology and definitions. Range of analytical method. Accuracy – selected methods of the determination of detection limit. Trueness, accuracy of the mean. Principles of calibration: selection and analysis of the calibration function (linearity), precision (homogeneity of the variance), gross errors, upper and lower warning limits. Estimation of mathematical models. Analysis of the sample composition and its influence on the calibration features (specificity and selectivity). The rugedness of the method in routine conditions. Objectives of the course: Presentation of the objectives and basic concepts of the validation of the analytical methods, in particular, validation parameters. Learning outcomes: After the course students should have basic knowledge on the validation parameters and the validation of the analytical methods. Textbooks and recommended reading: 1. B.M. Wenclawiak, M. Koch, E. Hadjicostas, Quality assurance in analytical chemistry, Springer, Berlin,

2004, 2. A. Hulanicki, Współczesna chemia analityczna, Wybrane zagadnienia, PWN, Warszawa, 2001, 3. Specjalistyczne artykuły z literatury naukowej, technicznej i materiały ISO, EURO.

53

Design of experiments

Lecturer: dr Ivana Stanimirova-Daszykowska Course code: 0310-2.03.4.033 Type of the course: Specialization ECTS: 2 Lecture + classes Number in study program: 9 Number of hours: 15 + 7.5 = 22.5 Semester: 1 or 2 Course prerequisites: None Language: Polish or English Teaching methods: Multimedia teaching techniques, using internet resources, teaching in small groups,


reporting thesis results, preparation and display of posters, final examination (oral) Course contents: Aims of experimental design. Definitions and terminology. Optimization strategies. Response function. Types of response functions. Coding of the experimental factors. Classification of experimental designs. Univariate linear regression model. Regression coefficients. Correlation coefficient. Multiple linear regression model. Advantages and limitations of the multiple linear regression model. Full factorial design. Direct estimation of the effects of individual factors and combinations of factors. Fractional factorial design and its practical use. An example of a half-fraction factorial design. Plackett-Burman designs and their applications in screening for the most important factors. Multi-level designs. Central composite designs. Types of central composite designs. Non-symmetrical designs and criteria for selection of an optimal number of experiments. D-optimality. Advantages of the Doehlert uniform design. Mixture designs. Introduction to optimization methods: looking for an optimum in the experimental domain, the Simplex method, steepest ascent methods, Pareto optimality methods. Objectives of the course: Students will be introduced to the basic concepts of experimental design and optimization methods. Learning outcomes: Ability to select a strategy to design her/his experiment using the principals of Experimental design and practical skills to perform the necessary calculations and to come to conclusions about the optimal experimental parameters. Textbooks and recommended reading: 1. M. Korzyński, Metodyka eksperymentu, WNT, Warszawa, 2006, 2. J. Kusiak, A. Danielewska-Tułecka, P. Oprocha, Optymalizacja, Wydawnictwo Naukowe PWN, Warszawa,

2009, 3. D.C. Montgomery, Design and analysis of experiments, John Wiley & Sons, Arizona, USA, 2005, 4. L. Eriksson, E. Johansson, N. Kettaneh-Wold, C. Wikström, S. Wold, Design of experiments, 3rd edition,

Umetrics Academy, Umeå, Sweden, 2008.

54

Chemometrics in analytical chemistry

Lecturer: dr hab. Michał Daszykowski Course code: 0310-2.03.4.034 Type of the course: Specialization lecture ECTS: 2 Lecture + classes Number in study program: 9 Number of hours: 15 + 7.5 = 22.5 Semester: 1 or 2 Course prerequisites: None Language: Polish or English Teaching methods: Multimedia teaching techniques, internet resources, problem-solving exercises Assessment methods: Oral presentation, final examination (oral) Course contents: Role of analytical chemistry. Major steps of analytical process. Introduction to chemometrics. Statistics versus chemometrics. Role of chemometrics in analytical process - from problem formulation to verification of hypothesis. Principles of experimental design. Supervised and unsupervised types of analytical problems. Modern instrumental techniques for studying complex samples/systems. Types of analytical signals. Components of analytical signals. One- and two-dimensional analytical signals, examples of single and multi-channel detectors and examples of signals they provide. Simple techniques for background removal and noise suppression. Different types of analytical data. Collecting analytical data. Types of measurement errors. Verification of data quality - the issue of outlying samples. Principles of fingerprinting and targeted approaches. Proteomics and metabolomics as fields providing complex analytical data. Exploration of multivariate chemical data. Construction of multivariate calibration and classification models. Applications of supervised and unsupervised techniques in solving analytical problems. Use and abuse of chemometrics in analytical chemistry. Objectives of the course: To present the role of chemometrics in modern analytical chemistry and fields where analytical instrumentation is used (e.g. proteomics and metabolomics). To draw attention of different issues related to collecting, processing and analysis of complex analytical data. To emphasize that each step of analytical process strongly influence the final interpretation of the problem being studied. Learning outcomes: Graduating from this course, students should: be aware about role of chemometrics in modern analytical chemistry, make a distinction between supervised and unsupervised problems, be familiar with the major steps of analytical process and their influence on data quality, be able to plan rationally experiment taking into account different factors and able to find literature dealing with applications of chemometrics to analytical chemistry problems. Textbooks and recommended reading: 1. Collection of articles in English presenting modern instrumentation and the use of chemometrics to solve

analytical problems and process analytical data, 2. S.D. Brown, R. Tauler, B. Walczak, Comprehensive chemometrics, Elsevier, 2009 (vol. 1-4), 3. D.L. Massart, B.G.M. Vandeginste, L.M.C. Buydens, S. de Jong, P.J. Lewi, J. Smeyers-Verbeke, Handbook

of Chemometrics and Qualimetrics; Part A, Elsevier, Amsterdam, 1998, 4. B.G.M. Vandeginste, D.L. Massart, L.M.C. Buydens, S. de Jong, P.J. Lewi, J. Smeyers-Verbeke, Handbook

of chemometrics and qualimetrics: Part B, Elsevier, Amsterdam, The Netherlands, 1998.

55

Processing of instrumental signals

Lecturer: prof. dr hab. Beata Walczak Course code: 0310-2.03.4.035 Type of the course: Specialization lecture ECTS: 2 Lecture + classes Number in study program: 9 Number of hours: 15 + 7.5 = 22.5 Semester: 1 or 2 Course prerequisites: None Language: Polish or English Teaching methods: Multimedia teaching techniques, internet resources, problem-solving exercises Assessment methods: Oral presentation, final examination (written) Course contents:: Definition of instrumental signals. Examples of the one- and two-dimensional instrumental signals. Signal components and their characteristics. Signal types (stationary and non-stationary signals) and noise types (white noise, heteroscedastic noise, and correlated noise). Methods of the background elimination (asymmetric penalized least squares approach). Methods of signals denoising: classical filters, Fourier Transform and Wavelet Transforms (Discrete Wavelet Transform and Wavelet Packet Transform). Methods of one-and two-dimensional signals alignment (Correlation Optimized Warping and Fuzzy Warping). Examples of application of the aforementioned methods in the proteomic and LC-MS data analysis. Objectives of the course: Introducing modern methods of the instrumental signal enhancement. Learning outcomes: Upon passing the course, students should be aware of the existing possibilities of improving the instrumental signals quality and the applicability of individual approaches. Textbooks and recommended reading: 1. Section 2 (Data preprocessing) in: Comprehensive Chemometrics, (Eds. S.D. Brown, R. Tauler, B.

Walczak), Elsevier, Amsterdam, 2009.

56

Automatisation in analytical chemistry

Lecturer: dr Andrzej Kita Course code: 0310-2.03.4.036 Type of the course: Specialization lecture ECTS: 2 Lecture + classes Number in study program: 9 Number of hours: 15 + 7.5 = 22.5 Semester: 1 or 2 Course prerequisites: None Language: Polish or English Teaching methods: Multimedia teaching techniques, internet resources, problem-solving exercises Assessment methods: Oral presentation, final examination (oral) Course contents: Modernization of the techniques used for the sample. Flow analysis methods. Theoretical principles of flow injection analysis. Components of the flow injection analysis set. Detectors used to flow injection analysis. Optimization of measurement. Examples of application flow injection analysis. Process analysis. The use of coupled techniques in analytical chemistry. Chemical sensors. Miniaturization of chemical analysis. Objectives of the course: Presentation of the objectives and basic concepts Presentation of the subject and the basic concepts of automation of analytical techniques. Presentation of the problem of preparing samples for analysis and optimization of process measurement. Presentation of the new trends in the automation of the analytical measurement. Learning outcomes: After the course students should have basic knowledge about the problems of automation in analytical chemistry Textbooks and recommended reading: 1. B. Karlberg , G. E. Pacey, Wstrzykowa analiza przepływowa dla praktyków, WNT, Warszawa, 1994, 2. A. Hulanicki, Współczesna chemia analityczna. Wybrane zagadnienia, PWN, Warszawa, 2001, 3. M. Trojanowicz, Automatyzacja w analizie chemicznej, WNT, Warszawa, 1992, 4. M. Trojanowicz, Flow injection analysis, World Scientific, Singapore, 2000.

57

Laboratory related to specialization

Course code: 0310-2.03.4.075 0310-2.03.4.076

Type of the course: Specialization ECTS: 6 Laboratory Number in study program: 9 Number of hours: 45 Semester: 2 and 3 Course prerequisites: None Language: Polish or

English Teaching methods: Laboratory exercises, teaching in small groups, solving tasks Assessment methods: Laboratory reports, problem-solving exercises, collaborative work, literature

surveys, final examination (pass/fail) Course contents: The scope of laboratory classes is related closely to the issues discussed during selected specialization lectures. Objectives of the course: Developing practical skills of laboratory work (for instance, acquiring principles of good laboratory, analytical and manufacturing practices, preparing samples for further measurement, planning synthesis and synthesis of complex materials, getting familiar with measurement equipment and its features). Teaching how to use professional software and programming languages (in the case of selecting specialization related to computational issues). Raising awareness of critical judgment of the results obtained and identification of potential errors in the procedure applied. Learning outcomes: Ability to use laboratory equipment and instrumental techniques Ability to pinpoint errors of the approach when results are different than the expected ones.

58

SPECIALISATION II: Synthesis and physical chemistry of organic and inorganic

compounds Number in study program: 9 Type of the course: Lecture + classes + laboratory Number of hours* 4×15 + 4×7.5 + 135 Semester: Winter (1) + summer (2) + winter (3) ECTS: 4×2 (lecture + classes) + 6 (laboratory)


59

Organometallic and bioinorganic chemistry – selected problems

Lecturer: prof. dr hab. inŜ. Stanisław Krompiec Course code: 0310-2.03.4.037 Type of the course: Specialization ECTS: 2 Lecture + classes Number in study program: 9 Number of hours: 15 + 7.5 = 22.5 Semester: 1 or 2 Course prerequisites: None Language: Polish or English Teaching methods: Multimedia teaching techniques, using internet resources, teaching in small groups,

solving tasks Assessment methods: Problem-solving exercises, oral presentation, literature surveys, reporting thesis results,

preparation and display of posters, final examination (written) Course contens: Presentation of the main classes of organometallic compounds: alkyl- and arylmetals, alkenyl, allyl, cyclopentadienyl and others complexes. Structure, nomenclature, preparation, properties, reactivity of selected orgsanometallics. Chemical bonds in organometallic compounds. Basic reaction of organometallics. Organometallic compounds as substrates and catalysts for various reactions. Mechanisms of selected reactions with the participation of organometallics as substrates or as catalysts. Bioelements, bioligands, metals in biological systems. The role of the meta ions and metal complexes in the biological processes. Mechanisms of selected biochemical processes with the participation of metals (in the form of complexing ions and neutral complexes). Objectives of the course: Presentation of selected classes of organometallic compounds and their reactivity. Showing the role of metal-biomolecule connections. for the functioning of organisms and various biological systems. Learning outcomes: After the course students should have knowledge concerning the role, preparation and application of organometallics. The student should be aware of the role of the metals for biological processes. Textbooks and recommended reading: 1. J. SkarŜewski, Wprowadzenie do syntezy organicznej, PWN, Warszawa, 1999, 2. C. Willis, M. Willis, Synteza organiczna, Wyd. UJ, Kraków, 2004, 3. M.B. Smith, J. March, Advanced organic chemistry, Wiley –Interscience, 2007, 4. P. Kafarski, B. Lejczak, Chemia bioorganiczna, PWN, Warszawa, 1994, 5. K. Burger (Editor), Biocoordination chemistry: coordination equilibria in biologically active systems, Ellis

Horwood, Chichester, 1990, 6. D. Astruc, Organometallic chemistry and catalysis, Springer, 2007.

60

Mechanisms of organic reactions

Lecturer: dr Halina Niedbała Course code: 0310-2.03.4.038 Type of the course: Specialization ECTS: 2 Lecture + classes Number in study program: 9 Number of hours: 15 + 7.5 = 22.5 Semester: 1 or 2 Course prerequisites: None Language: Polish or English Teaching methods: Multimedia teaching techniques, using internet resources, teaching in small groups,

solving tasks Assessment methods: Problem-solving exercises, oral presentation, literature surveys, final examination

(oral) Course contents: Organic reactions and their mechanisms. Classification of reactions in organic chemistry. Mechanisms and methods of determining them. Aliphatic substitution; SN1 and SN2 mechanisms. The neighboring-group mechanism. The SNi mechanism. The E2 mechanism. The E1 mechanism; regiochemistry of the double bond. Nucleophilic substitution at an aliphatic trigonal carbon; the tetrahydral mechanism. Addition to carbon-carbon the double bond; electrophilic, nucleophilic and a free-radical addition . Addition to conjugated systems. Nucleophilic addition to the carbon-oxygen double bonds. Electrophilic aromatic substitution; orientation and reactivity. Quantitative treatments of reactivity in the substrate - partial rate factor. Hammett equation and their application. Mechanisms for aromatic nucleophilic substitution; the SNAr mechanism, Meisenheimer salts; the benzyne mechanism; substitution in diazonium aromatic salts. Rearrangement reactions. Objectives of the course: At the final stage of the lecture it is necessary to sum up the knowledge of organic reactions gained by students during the course. The aim of the subject is to convince students that relatively low number of rules could be used to explain almost all organic reactions. Learning outcomes: After the course students should have basic knowledge on mechanisms of organic reactions and methods of determining them. Textbooks and recommended reading: 1. M.B. Smith, J. March, March’s advanced organic chemistry, Wiley-Interscience, New Jersey, 2007, 2. R.W. Alder, R. Baker, J.M. Brown, Mechanizmy reakcji w chemii organicznej, PWN, Warszawa, 1977, 3. N.S. Isaacs, Fizyczna chemia organiczna. Ćwiczenia, PWN, Warszawa, 1974, 4. J. McMurry, Chemia organiczna, PWN, Warszawa 2000.

61

Selected problems concerning elucidation of organic and inorganic molecules, Part 1

Lecturer: prof. UŚ, dr hab. Henryk Flakus prof. UŚ, dr hab. inŜ. Marek Matlengiewicz dr inŜ. Jacek Nycz

Course code: 0310-2.03.4.039

Type of the course: Specialization ECTS: 2 Lecture + classes Number in study program: 9 Number of hours: 15 + 7.5 = 22.5 Semester: 1 or 2 Course prerequisites: None Language: Polish or English Teaching methods: Multimedia teaching techniques, using internet resources, solving tasks Assessment methods: Problem-solving exercises, oral presentation, literature surveys, final examination

(oral) Course contents: The role of IR, NMR, EPR, MS in structure elucidation of organic, inorganic and biological compounds and processes related to their. IR ; the basic concept of IR spectroscopy. The physical background of IR. NMR the basic concept of NMR spectroscopy; nuclear spin, I, spin systems, relaxation time, line intensities, integration, chemical shifts, chemical coupling, J. The object of investigation; solid, liquid and gases, and diamagnetic and paramagnetic objects. Chemical shift analysis in the 1H NMR spectra interpretation of organic compounds. The spin- spin coupling analysis in the determination of organic compound molecular structures. Coupling constants versus the molecular structure. I-st order 1H NMR spectra. Prediction of spectra of simple molecular systems and the structure determination based on 1H NMR spectra. Practical interpretation of 1H NMR spectra. Multiple resonance. Spin- spin decoupling method in solving of complex spectra. Examples of spectra interpretation and solving of chemical problems with the help of the 1H NMR spectroscopy. 13C NMR spectroscopy. Specific properties of 13C NMR spectra. Proton- decoupled spectra and molecular structure. Information about structure of organic molecules provided by the multiplet structures of signals and by the spin- spin 13C - 1H coupling constants. Solving od structural probles in organic chemistry with the help of 13C NMR spectra analysis. Examples. Functionality. EPR overview, basic terms; the Zeeman effect, the Kramer’s doublet, zero-field splitting (ZFS), the most basic equations of EPR, the proton or electron relaxation. the synonyms names EPR, ESR, EMR, Comparison between NMR and ESR. Type of spectrometers. The history of EPR. Absorption signal, first derivative, the hyperfine structure, the hyperfine splitting (A) (or hyperfine coupling), the superhyperfine splitting, Isotropic g values variations for a series of paramagnetic species and organic free radicals, Nuclear spin, I, Line intensities, Pascal’s triangle, Spin traps, Gomberg’s radical, Drug Metabolism Studies, the purities control of medicines]; MS [overview, ionization source (electron ionization, chemical ionization), other ionization methods (electrospray ionization, desorption ionization] m/z analysis, natural isotopic abundances, atomic and molecular mass, intensities, ionization, fragmentation. Interpretation and solving of MS spectra. Objectives of the course: The aim of the course is to teach the students the substantial concepts in use of modern analytic methods used for the identification of chemicals. Their will receive basic knowledge and finally they will be able to elucidate the simple chemical structure from IR, NMR, EPR, MS spectra and additionally results from elementary analysis. Learning outcomes: After the course students should have a knowledge and understanding of basic modern analytic methods such as IR, NMR, EPR, MS, their scope and limitations in identification of simple products, which allows studying their physical and chemical behavior. Textbooks and recommended reading: 1. P. Atkins, W. Atkins, P. William, Chemia Fizyczna, chapter 18, 2. G. Gauglitz, T. Vo-Dinh, Solid-state NMR, in Handbook of Spectroscopy, volume: Methods 2: NMR

Spectroscopy, Wiley-VCH, Weinheim, 2003, 3. L.A. Kazicyna, N.B. Kuplerska, Metody spektroskopowe wyznaczania struktury związków organicznych,

Wyd. Naukowe PWN, Warszawa, 1976, 4. R.M. Silverstein, F.X. Webster, D.J. Kiemle, Spektroskopowe Metody identyfikacji związków organicznych,

Wydawnictwo Naukowe PWN, Warszawa, 2007, 5. R. Mazurkiewicz, A. Rajca, E. Salwińska, A. Skibiński, J. Suwiński, W. Zieliński, Metody spektroskopowe i

ich zastosowanie do identyfikacji związków organicznych, W. Zieliński and A. Rajca (Eds.), WNT, Warszawa, 1995.

62

Selected problems concerning elucidation of organic and inorganic molecules, Part 2

Lecturer: prof. UŚ, dr hab. Henryk Flakus prof. UŚ, dr hab. inŜ. Marek Matlengiewicz dr inŜ. Jacek Nycz

Course code: 0310-2.03.4.040

Type of the course: Specialization ECTS: 2 Lecture + classes Number in study program: 9 Number of hours: 15 + 7.5 = 22.5 Semester: 1 or 2 Course prerequisites: None Language: Polish or English Teaching methods: Multimedia teaching techniques, using internet resources, solving tasks Assessment methods: Problem-solving exercises, oral presentation, literature surveys, final examination

(oral) Course contents: The elucidation of organic, inorganic and biological compounds and processes related to their. IR ; interpretation of IR spectra. ATR (Attenuated Total Reflectance) technique. NMR; the 31P NMR, 19F NMR spectroscopy. The spin- spin decoupled spectra; 1H{ 19F} NMR, 31P{1H} NMR. The II-nd order spectra. Effects of molecular internal dynamics in the spectra (part 2). Practical interpretation of 31P NMR, 19F NMR spectra. Multiple resonance. Spin-spin decoupling method in solving of complex spectra. Examples of spectra interpretation and solving of chemical problems with the help of the multinuclear spectroscopy. 31P NMR spectroscopy. Specific properties of 31P NMR spectra. Proton- decoupled spectra and molecular structure. Information about structure of organic molecules provided by the multiplet structures of signals and by the spin- spin 31P-1H coupling constants. Solving of structural problems in organic chemistry with the help of 31P NMR spectra analysis. Examples. 19F NMR spectroscopy. Specific properties of 19F NMR spectra. Proton- decoupled spectra and molecular structure. Information about structure of organic molecules provided by the multipled structures of signals and by the spin-spin 19F-1H coupling constants. Solving of structural problems in organic chemistry with the help of 19F NMR spectra analysis. Examples. DEPT (distortionless enhancement by polarization transfer). Two- dimensional NMR spectroscopy. through bond: COSY (Correlated Spectroscopy), TOCSY (Total Correlated Spectroscopy also known as HOHAHA – Homonuclear Hartmann Hahn), heteronuclear correlation, (HSQC, HMBC, HMQC), 2D-INADEQUATE (incredible natural abundance double quantum transfer experiment), through-space: NOESY (Nuclear Overhause Effect Spectroscopy), ROESY (Rotating frame Overhause Effect Spectroscopy), HOESY, solid state NMR. EPR Comparison of NMR and ESR. Practical interpretation of EPR spectra. MS other ionization methods MS/MS, HRMS, elemental composition from peak intensities, natural isotopic abundance, atomic and molecular mass, calculated exact masses and mass defects, determining elemental composition from isotope peak intensities, chlorine and bromine, isotope peak intensity ratios for carbon-containing ions, ionization, fragmentation, and electron accounting, the nitrogen rule, fragmentation rates, metastable ions, Stevenson’s rule, neutral losses and ion series, -cleavage and related fragmentations, important mass spectral rearrangements, McLafferty-type rearrangement, retro Diels–Alder fragmentation, peptides]. Computer techniques: The use computer programs such as Mestrec, ChemDraw, ChemSketch and free databases such as SDBS to elucidate the chemical structure. Objectives of the course: The aim of the course is to teach the students the substantial concepts in use of modern analytic methods used for the identification of chemicals. They will receive necessary knowledge and finally they will be able to elucidate the chemical structure possessing IR, NMR, EPR, MS spectra and additionally results from elementary analysis. Learning outcomes: After completing the course students should have a basic knowledge and understanding of modern analytic methods such as IR, NMR, EPR, MS, their scope and limitations in identification of products. Textbooks and recommended reading: 1. P. Atkins, W. Atkins, P. William, Chemia fizyczna, chapter 18, 2. G. Gauglitz, T. Vo-Dinh, Solid-state NMR, in Handbook of Spectroscopy, volume: Methods 2: NMR

Spectroscopy, Wiley-VCH, Weinheim, 2003, 3. L.A. Kazicyna, N.B. Kuplerska, Metody spektroskopowe wyznaczania struktury związków organicznych,

Wyd. Naukowe PWN, Warszawa, 1976, 4. R.M. Silverstein, F.X. Webster, D.J. Kiemle, Spektroskopowe metody identyfikacji związków organicznych,

Wydawnictwo Naukowe PWN, Warszawa, 2007, 5. R. Mazurkiewicz, A. Rajca, E. Salwińska, A. Skibiński, J. Suwiński, W. Zieliński, Metody spektroskopowe i

ich zastosowanie do identyfikacji związków organicznych, W. Zieliński and A. Rajca (Eds.), WNT, Warszawa, 1995.

63

Catalysis in organic and inorganic chemistry

Lecturer: prof. dr hab. inŜ. Stanisław Krompiec Course code: 0310-2.03.4.041 Type of the course: Specialization ECTS: 2 Lecture + classes Number in study program: 9 Number of hours: 15 + 7.5 = 22.5 Semester: 1 or 2 Course prerequisites: None Language: Polish or English Teaching methods: Multimedia teaching techniques, using internet resources, teaching in small groups,


(written) Course contents: Basic definitions. Selected catalytic industrial processes: types of reactors, processes conditions, catalysts recycling. Catalysts in pharmaceutics synthesis: biocatalysts, chiral organometallics. Metal and metaloid compounds as catalysts. Catalysis in the environment protection. Designing the structure of homo- and heterogeneous catalysts. Immobilised catalysts. Mechanisms of selected catalytical reactions: oxidation, hydrogenation, coupling, metathesis, hydroformylation and others. Computational methods in catalysis. How to find the appropriate catalyst for selected reaction. Objectives of the course: The presentation of the state of knowledge concerning the application of catalysis to modern organic and inorganic synthesis and technology. Showing the role of catalysis for the civilization progress. Learning outcomes: After the course students should be able to select an appropriate catalyst for the selected reactions and suggest the way of the realization of the catalytical process. Textbooks and recommended reading: 1. J. SkarŜewski, Wprowadzenie do syntezy organicznej, PWN, Warszawa, 1999, 2. C. Willis, M. Willis, Synteza organiczna, Wyd. UJ, Kraków, 2004, 3. M.B. Smith, J. March, Advanced organic chemistry, Wiley – Interscience, 2007, 4. D. Astruc, Organometallic Chemistry and Catalysis, Springer, 2007, 5. STREM Catalog, No 23, Metal catalysts for organic synthesis, 2010, 6. M. Benaglia (Ed.), Recoverable and recyclable catalysts, John Wiley & Sons, 2009, 7. P. Kafarski, B. Lejczak, Chemia bioorganiczna, PWN, Warszawa, 1994, 8. F. Pruchnik, Kataliza homogeniczna, PWN, Warszawa, 1993, 9. E. Grzywa, J. Molenda, Technologia podstawowych syntez organicznych, WNT, Warszawa, 2000, 10. K. Schmidt-Szałowski, J. Setek, J. Raabe, E. Bobryk, Podstawy technologii chemicznej. Procesy w

przemyśle nieorganicznym, Oficyna Wydawnicza Pol. Warszawskiej, Warszawa, 2004.

64

Transition metal complexes in bioinorganic chemistry

Lecturer: dr hab. Barbara Machura Course code: 0310-2.03.4.042 Type of the course: Specialization ECTS: 2 Lecture + classes Number in study program: 9 Number of hours: 15 + 7.5 = 22.5 Semester: 1 or 2 Course prerequisites: None Language: Polish or English Teaching methods: Multimedia teaching techniques, using internet resources, teaching in small groups,


(oral) Course contents: Principles of coordination chemistry related to bioinorganic research – thermodynamic and kinetic aspects. Electronic and geometric structures of metal ions in biology. Binding of metal ions and complexes to active centres of biomolecules. Metalloproteins, metalloenzyme. Interactions of metal ions and nucleic acids. Metal functions in metalloproteins – dioxygen transport, electron transfer, structural roles for metal ions. Model complexes and the concept of spontaneous self-assembly. Communication roles for metals in biology. Some aspects of nitric oxide chemistry and biochemistry. Nitrosyl complexes as NO donors and scavengers. Cisplatin and its tissue distribution. Search for the new drugs based on cisplatin. Radiopharmaceuticals based on the rhenium and technetium complexes in cancer diagnosis and therapy. Objectives of the course: Presentation of the principles of bioinorganic chemistry, in particular, fundamental functions of bio-metal ions, role and structure of active centres, biological function of biomolecules incorporating metal ions and metal-based drugs and diagnostic agents. Learning outcomes: After the course students should have basic knowledge on the role of inorganic elements present in the living systems or introduced as drugs and diagnostic agents. Textbooks and recommended reading: 1. R.W. Hay, Chemia bionieorganiczna, PWN, Warszawa, 1990, 2. S.J. Lippard, J.M. Berg, Podstawy chemii bionieorganicznej, PWN, Warszawa, 1998, 3. G. Stochel, M. Pawalec, Z. Stasicka, Wybrane aspekty chemii i biochemii tlenku azotu, Wiadomości

Chemiczne, 51 (1997) 163, 4. M. Wysokiński, Poszukiwanie nowych leków na bazie cisplatyny, Wiadomości Chemiczne, 52 (1998) 529, 5. E. Mikiciuk-Olasik, K. Błaszczak-Świątkiewicz, Kierunki poszukiwania preparatów

przeciwnowotworowych, Wiadomości Chemiczne, 54 (2000) 707, 6. L. Królicki, Medycyna nuklearna, Fundacja im. Ludwika Rydygiera, Warszawa, 1996, 7. K. Samochocka, Radiochemia w medycynie nuklearnej. Radiofarmaceutyki, Wiadomości Chemiczne, 53

(1999) 661.

65


Course code: 0310-2.03.4.075 0310-2.03.4.076



surveys, final examination: pass/fail Course contents: The scope of laboratory classes is related closely to the issues discussed during selected specialization lectures. Objectives of the course: Developing practical skills of laboratory work (for instance, acquiring principles of good laboratory, analytical and manufacturing practices, preparing samples for further measurement, planning synthesis and synthesis of complex materials, getting familiar with measurement equipment and its features). Teaching how to use professional software and programming languages (in the case of selecting specialization related to computational issues). Raising awareness of critical judgment of the results obtained and identification of potential errors in the procedure applied. Learning outcomes: Ability to use laboratory equipment and instrumental techniques Ability to pinpoint errors of the approach when results are different than the expected ones.

66

SPECIALISATION III: Theoretical methods in chemistry



67

Computational methods for electronic correlation

Lecturer: prof. dr hab. Stanisław Kucharski Course code: 0310-2.03.4.043 Type of the course: Specialization ECTS: 2 Lecture + classes Number in study program: 9 Number of hours: 15 + 7.5 = 22.5 Semester: 1 or 2 Course prerequisites: None Language: Polish or English Teaching methods: Multimedia teaching techniques, using internet resources, solving tasks Assessment methods: Problem-solving exercises, oral presentation, literature surveys, final examination

(written) Course contents: Independent particle model. One-determinental wave function. Hartree-Fock equations. The notion of electronic correlation. Electronic correlation energy as a component of the total atomic and molecular energy. Correlational contributions to molecular properties, dissociation energy and transition states. Principal methods for the determination of electronic correlation effects in atoms and molecules. Going beyond a one-particle approximation. Second quantization operators, commutation rules for the creation annihilation operators, state vector in the occupation number formalism. Configuration interaction method (CI). The form of the wave function in the full configuration interaction (FCI) method. Limited CI approach: CID - CI with doubly excited configurations., CISD - CI with singly and doubly excited configurations. The CI models including higher electronic excitations. Derivation of the secular equations in the CI method. The Davidson procedure for diagonalization of large matrices. Energy of the ground and excited states. Direct CI method (DCI). Excitation operators expressed in terms of the creation-annihilation operators. Iteration scheme in the direct CI method. The perturbational methods in the electronic correlation theory. Brillouin-Wigner (BW) and Rayleigh-Schroedinger (RS) perturbation theory (PT). Perturbational corrections to the wave function and total energy. Renormalization terms in the RSPT theory and the methods of their generation (bracketing technique). Many body (MB) perturbation theory and Moeller-Plesset partition of the Hamiltonian. The operator for electronic correlation. Perturbational corrections to the Hartree-Fock reference state. First-order MP correction as a component of the Hartree-Fock enenergy. Second-order correction for Hartree-Fock and non-Hartree-Fock reference states. Hihger order Moeller-Plesset corrections (MP3 and MP4). 2n+1 rule. Coupled cluster (CC) method. Exponential parametrization of the wave function. Cluster expansion. Cluster excitation operators. CC models in use. General equations for the CC amplitudes. Iteration scheme for solving the CC equations. CCSD(T) model. Examples of the CC calculations in the studies of the electronic structure of atoms and molecules. Objectives of the course: Presentation of the most important methods to evaluate correlational effects, discussion of the advantages and disadvantages of particular computational scheme. Learning outcome: Ability to characterize the particular method, understanding of mutual interrelations among post-hartree-fock schemes, ability to interpret the results of the computations. Textbooks and recommended reading: 1. L. Piela, Idee chemii kwantowej, PWN, Warszawa, 2004, 2. F. Jensen, Introduction to computational chemistry, J. Wiley&Sons, 2004.

68

HF and DFT methods

Lecturer: prof. UŚ, dr hab. Maria Jaworska Course code: 0310-2.03.4.044 Type of the course: Specialization ECTS: 2 Lecture + classes Number in study program: 9 Number of hours: 15 + 7.5 = 22.5 Semester: 1 or 2 Course prerequisites: None Language: Polish or English Teaching methods: Multimedia teaching techniques, using internet resources, solving tasks Assessment methods: Problem-solving exercises, oral presentation, literature surveys, final examination

(written) Course contents: Schrödinger equation. The electronic Hamiltonian. Pauli exclusion principle. Wave function antisymmetrization. System of indistinguishable electrons. Variational principle. Model of independent particles. The one-determinantal wave function. Slater-Condon rules. Energy of one-determinantal wave function. Hartree-Fock equations. Coulomb and exchange operators. Fock operator. The coulomb and exchange integrals. Dirac notation. LCAO-MO method. Roothan-Hall method. Basis functions. Gaussian and Slater bases. Cartesian and spherical harmonic angular parts in Gaussian type bases. One and two-electron integrals. Calculation of Gaussian type integrals. HF matrix equations. Unrescticted HF method. The expectation value of spin operators for the one-determinantal wave function. Spin projection. The Mulliken and NBO population analysis. Density matrix. One and two-electron density functions. Spin densities. Koopmans theorem. Electron correlation. Density Functional Theory (DFT). Hohenberg-Kohn theorems. Energy as the functional of electron density. System of noninteracting electrons. Exchange-correlation functional. Adiabatic connection. Derivation of Kohn-Sham equations. The solution of the Kohn-Sham equations. Echange-correlation potential in the Kohn-Sham equations. DFT density function. Coulomb and exchange hole in Density Functional methods. Local functionals and gradient functionals. B3LYP functional. Asymptotic properties of the exchange-correlation potentials. Correlation energy in the DFT methods. TDDFT method. The time-dependent Kohn-Sham equations. Adiabatic approximation. Excitation energies in the TDDFT method. Examples of calculations with TDDFT method. Accuracy of the TDDFT method. Objectives of the course: Presentation of basic concepts in the HF, DFT and TDDFT methods. Derivation of the HF and KS equations. Application of the methods to calculation of electronic spectra and molecular properties. Learning outcomes: After the course students should have a knowledge and understanding of HF and DFT methods. They should understand the concepts of the methods, and know their applications in the calculations of molecular properties and electronic spectra. Textbooks and recommended reading: 1. A. Gołębiewski, Elementy mechaniki i chemii kwantowej, PWN, Warszawa, 1982 2. W. Kołos, Chemia kwantowa, PWN, Warszawa, 1978, 3. L. Piela, Idee chemii kwantowej, PWN, Warszawa, 2003.

69

Computational chemistry of large molecules

Lecturer: prof. UŚ, dr hab. Maria Jaworska Course code: 0310-2.03.4.045 Type of the course: Specialization ECTS: 2 Lecture + classes Number in study program: 9 Number of hours: 15 + 7.5 = 22.5 Semester: 1 or 2 Course prerequisites: None Language: Polish or English Teaching methods: Multimedia teaching techniques, using internet resources, solving tasks Assessment methods: Problem-solving exercises, oral presentation, final examination (written) Course contents: Objectives and basic concepts of computational chemistry. Chemical models. Types of computational methods. Quantum Mechanics methods (QM). Schrıdinger equation. Born-Oppenheimer approximation. Independent particle approximation. Hartree-Fock method. Density Functional Theory. Kohn-Sham equations. Spin polarized Kohn-Sham equations. UDFT method. Density functionals. Basis functions. Configuration Interaction method and Multiconfigurational methods. Molecular Mechanics (MM). Mixed methods (MM/QM). Modelling of solvent effects. PCM solvent model. Applications of computational methods. Molecular structure determination. Potential Energy Surface (PES). Geometry optimization. Binding energy calculation. Basis Set Superposition Error (BSSE). Calculation of reaction energy. Chemical reaction barrier. Reaction transition state . Spin states of transition metal complexes. Molecular magnetism. Heisenberg ladder. Heisenberg coupling constant. Calculation of redox potential. Determination of electronic spectra. TDDFT method. Electronic transition energy. Oscillator strength. Fluorescence and phosphorescence energy. Chemical reactions in electronic excited states. Mechanisms of enzymatic reactions. Selection of proper computational method for the given molecular system and chemical problem. Calculations with multiconfigurational methods for model systems. Objectives of the course: Presentation of the objectives and basic concepts of computational chemistry in application to large molecular systems and different chemical problems. Learning outcomes: After the course students should have basic knowledge on using proper computational method to given molecule and chemical problem. Textbooks and recommended reading: 1. A.R. Leach, Molecular modelling principles and applications, Addison Wesley Longman,1996 2. L. Piela, Idee chemii kwantowej, PWN, Warszawa, 2006, 3. D. Young, Computational Chemistry: A practical guide for applying techniques to real world problems, John Wiley & Sons, 2001.

70

Ionized and excited states of atoms and molecules

Lecturer: dr. hab. Monika Musiał Course code: 0310-2.03.4.046 Type of the course: Specialization ECTS: 2 Lecture + classes Number in study program: 9 Number of hours: 15 + 7.5 = 22.5 Semester: 1 or 2 Course prerequisites: None Language: Polish or English Teaching methods: Multimedia teaching techniques, using internet resources, solving tasks Assessment methods: Problem-solving exercises, literature surveys, final examination (oral) Course contents: Excited states. Characterization of the electronic excitation energies (EE), intensities, oscillator strengths, vertical and adiabatic excitation energies, Franck-Condon principle, Schroedinger equation for the excited states. Methods useful for the determination of the wave-functions for excitation energies: configuration interaction (CI) method, equation-of-motion coupled cluster (EOM-CC) method. Existing models for calculating EEs, diagrammatic form of the EOM-CC equations, method used to diagonalize large matrices – Davidson diagonalization. Example calculations for the vertical excitation energies for small molecules. Comparison of the accuracy of the results for various CC models. Ionized states. Schroedinger equation for the ionized and electron attached states. The equation-of-motion coupled cluster method for ionization potentials (IP) and electron affinity (EA). Construction of the EOM-CC equations for IP and EA case. Existing models. Test calculations for IPs (first IP, second IP, …). Discussion of the results (accuracy of the results). Application of the studied methods for determination of the electron affinity. Example of the molecules with positive EA values. Analysis of the accuracy of the EA results with respect to the applied model. Objectives of the course: Student should know how to define electronic excitation, ionization potential, electron affinity. Student should be able to derive general equations defining methods used to determine above quantities and how to choose method suitable for required accuracy of the results. Also student is expected to know how to do the test calculations. Learning outcomes: After the course student should have knowledge about quantum chemistry methods which can be applied to calculate excitation energies, ionization potentials and electron affinity. Textbooks and recommended reading: 1. L. Piela, Idee chemii kwantowej, PWN, Warszawa, 2003, 2. R.J. Bartlett, M. Musiał, Rev. Mod. Phys., 79 (2007) 291-352.

71

Electric and optical molecular properties

Lecturer: dr Tadeusz Pluta Course code: 0310-2.03.4.047 Type of the course: Specialization ECTS: 2 Lecture + classes Number in study program: 9 Number of hours: 15 + 7.5 = 22.5 Semester: 1 or 2 Course prerequisites: None Language: Polish or English Teaching methods: Multimedia teaching techniques, using internet resources, solving tasks Assessment methods: Problem-solving exercises, oral presentation, collaborative work, literature surveys,

reporting thesis results, preparation and display of posters, final examination (written) Course contents: Fundamentals of classical electrostatics: point charges, charge density, Coulomb interactions, electric field, electrostatic potential, multipole expansion. Definition of multipoles: dipole, quadrupole, octupole and higher moments, symmetry properties of multipoles, dependence of multipoles on the coordinate system, physical interpretation. Molecular Hamiltonian for the molecule in an external electric field, Taylor expansion of the potential energy, definition of the static dipole polarizability, multipole polarizabilities, hyperpolarizabilities. Molecular electric properties in spectroscopy, theory of intemolecular interactions, nonlinear optics. Perturbational description of the static electric properties: basics of the Rayleigh-Schrödinger perturbation theory (RSPT), the Hellmann-Feynman theorem, sum-over-state (SOS) approach, finite perturbation methods. Dynamic electric properties, the resonance phenomenon, electronic transitions, dispersion curves. Methods of perturbation theory in the Hartree-Fock method: Coupled Perturbed Hartree-Fock equations (CPHF). Derivatives of the perturbed energy of the molecule, Lagrangian techniques. Time Dependent Hartree-Fock (TDHF) equations, fundamentals of the response formalism. Objectives of the course: Review of the most important electric and optical properties and theoretical methods used to determine these properties. Learning outcomes: After the course completion student should know the definition and basis features of molecular electric properties, and be able to justify a choice of a computational method used for the property determination. Textbooks and recommended reading: 1. L. Piela, Idee chemii kwantowej, PWN, Warszawa, 2006, 2. P. Lazzeretti, Handbook of molecular physics and quantum chemistry, vol. 3, S. Wilson (Ed.), Wiley 2003.

72

Intermolecular interactions

Lecturer: dr Rafał Podeszwa Course code: 0310-2.03.4.048 Type of the course: Specialization ECTS: 2 Lecture + classes Number in study program: 9 Number of hours: 15 + 7.5 = 22.5 Semester: 1 or 2 Course prerequisites: None Language: Polish or English Teaching methods: Multimedia teaching techniques, using internet resources, teaching in small groups,


reporting thesis results, preparation and display of posters, final examination (oral) Course contents: Intermolecular interactions (van der Waals). Dimer, monomers, interaction energy of the dimer. Supermolecular methods, supermolecular Hartree-Fock, Møller-Plesset perturbation theory, coupled-cluster theory. Perturbational methods, polarization expansion, symmetry-adapted perturbation theory. Electrostatic, induction, dispersion, exchange-induction, exchange-dispersion interactions. Hydrogen bonds. Multipole expansion. Interactions of permanent multipole moments.. Static and dynamic polarizabilities. Asymptotic induction and dispersion interactions, Cn coefficients. Trimers and larger molecular clusters. Non-additive effects. Supermolecular and perturbative methods of calculating non-additive effects. Intermolecular interactions for condensed phases (liquids and solids). Examples of dispersion-bound systems (helium, argon and benzene dimers) electrostatic and induction-bound (water dimer). Objectives of the course: Presentation of the principles of the theory of intermolecular interactions, methods of calculating interaction energy, advantages and disadvantages of these methods, applications to dimers, molecular clusters and condensed phases. Learning outcomes: After the course, the student should know the principles of intermolecular interactions (van der Waals), know two general modeling techniques (supermolecular and perturbative), know the physical interpretation of the interaction energy components, know the principles of the asymptotic theory, understand the differences between interactions of polar and non-polar molecules, know the non-additive effects and their significance to molecular clusters and condensed phase. Textbooks and recommended reading: 1. C. Kittel, Wstęp do fizyki ciała stałego, PWN, Warszawa, 1999, 2. A. Groß, Theoretical surface science: A microscopic perspective, Springer, Berlin, 2003.

73


Course code: 0310-2.03.4.075 0310-2.03.4.076




74

SPECIALISATION IV: Physical chemistry of condensed phases



75

Intermolecular interactions in condensed phases

Lecturer: prof. UŚ., dr hab. Henryk Flakus Course code: 0310-2.03.4.049 Type of the course: Specialization ECTS: 2 Lecture + classes Number in study program: 9 Number of hours: 15 + 7.5 = 22.5 Semester: 1 or 2 Course prerequisites: None Language: Polish or English Teaching methods: Multimedia teaching techniques, using internet resources, solving tasks Assessment methods: Problem-solving exercises, oral presentation, literature surveys, final examination

(oral) Course contents: Basic principles of the quantum- chemical theory of molecular interactions. The super- molecule model. The Morokuma model of the energy partitioning of the energy of molecular complexes. Donor- acceptor complexes. Hydrogen bonding and donor- acceptor complexes. Identification of hydrogen bonds. Basic effects in the IR and 1H-NMR spectroscopy attributed to hydrogen bonds. Selected thermodynamic and structural properties if hydrogen –bonded systems. Diversity of hydrogen bonds and their classification. Hydrogen bonds in molecular complexes formed in the gaseous and the liquid phase. Hydrogen- bonded molecular crystals. The most popular types f the crystal lattices. Conventional and non- conventional hydrogen bonds in the nature. Static co-operative interactions involving hydrogen bonds. Classic hydrogen bonds in the nature H/D isotopic effects of the hydrogen bond. Conventional and non- conventional hydrogen bonds in crystals and in biological systems. Objectives of the course: The lecture is devoted to selected problems of intermolecular interactions occurring in diverse condensation states of the matter, mainly to the problem of the hydrogen bonding, Particular attention is paid to the relations between phenomenological physical properties of molecular systems and the molecular hydrogen- bonded aggregate structures. Learning outcomes: After the course students should have basic knowledge about intermolecular interactions, mainly about the hydrogen bond. Textbooks and recommended reading: 1. P. Schuster, G. Zundel, C. Sandorfy, The hydrogen bond, volumes I, II, III; North-Holland, Amsterdam,

1976, 2. D. HadŜi, Theoretical treatments of hydrogen bonding, John Wiley & Sons Ltd., Chichester, 1997, 3. Y. Marechal, The hydrogen bond and the water molecule, The Physics and Chemistry of Water, Aqueous and

Bio Media; Elsevier: Amsterdam, Oxford, 2006.

76

Reactions in solid phase

Lecturer: dr Izabela Jendrzejewska Course code: 0310-2.03.4.050 Type of the course: Specialization ECTS: 2 Lecture + classes Number in study program: 9 Number of hours: 15 + 7.5 = 22.5 Semester: 1 or 2 Course prerequisites: None Language: Polish or English Teaching methods: Multimedia teaching techniques, using internet resources, solving tasks Assessment methods: Problem-solving exercises, oral presentation, literature surveys, reporting thesis results,

preparation and display of posters, final examination (written) Course contents: General systematics of reactions in solid phase. Detailed systematics of reactions in solid phase. Diffusion in solids. Basic definitions and dependences. Ist and IInd Fick′s laws. Mechanism of diffusion. Vacancy, interstitial, surface, interfacial and dislocation diffusions. Dependence of diffusion coefficients on temperature. Correlation effect. Diffusion in the multiphase systems. Sintering and growth of grains. Mechanism of sintering. Elementary stages of reactions between solids. Kinetics of reactions between solids. Kinetics of reactions in systems consisting of pellets. Kinetics of reactions in a mixture of powders. Model of diffusion. Reaction of obtaining of spinels in policrystalline and monocrystalline form. Objectives of the course: Presentation of objectives and basic concepts of solid state chemistry. Gaining knowledge on mechanism and kinetics of reactions in solid state. Learning outcomes: After the course, students should have basic knowledge about chemical reactions in solid state and they should be able to design reactions in solid state. Textbooks and recommended reading: 1. H. Schmalzried, Reakcje w stanie stałym, PWN, Warszawa, 1978, 2. J. Dereń, J. Haber, R. Pampuch, Chemia ciała stałego, PWN, Warszawa, 1975, 3. J.A. Hedvall, Solid State Chemistry, Elsevier, Amsterdam, 1966.

77

Elements of molecular acoustics

Lecturer: dr Edward Zorebski Course code: 0310-2.03.4.051 Type of the course: Specialization ECTS: 2 Lecture + classes Number in study program: 9 Number of hours: 15 + 7.5 = 22.5 Semester: 1 or 2 Course prerequisites: None Language: Polish or English Teaching methods: Multimedia teaching techniques, using internet resources, solving tasks Assessment methods: Problem-solving exercises, oral presentation, collaborative work, literature surveys,

reporting thesis results, preparation and display of posters, final examination (oral) Course contents: Classical and quantum descriptions of the acoustic phenomena, subject and scope of molecular acoustics. Fundamentals of ultrasonics, methods of generating and receiving (piezoelectric and magnetostrictive transducers), applications. The propagation of ultrasound waves in non-dissipative and real materials. Acoustic relaxation processes (chemistry, biology, materials science). Investigation of thermodynamic properties of liquids on the basis of the speed of ultrasound measurements (adiabatic and isothermal compressibility, isochoric heat capacity, internal pressure). Basic principles of acoustic spectroscopy. Thermal and structural relaxation (longitudinal wave), application of the modern URT (Ultrasonic Resonator Technology) technique. Viscoelastic relaxation (shear wave). Volume and shear viscosity (Newtonian and Non-Newtonian liquids, fundamentals of rheology and ultrasonic rheology). Objectives of the course: Presentation of the objectives and basic concepts of molecular acoustics. Fundamentals of ultrasonic: methods and applications, in particular, in chemistry. Learning outcomes: After the course students should have basic knowledge on molecular and quantum acoustics as well as applications of ultrasound in chemistry. Textbooks and recommended reading: 1. Material related to specific topics handed during lectures, 2. S. Ernst, Zastosowanie spektroskopii ultradźwiękowej w badaniu reakcji chemicznych, Uniwersytet Śląski,

Skrypt 459, Katowice, 1991, 3. A.J. Matheson, Molecular acoustics, Willey-Interscience, 1971, 4. J. Ferguson, Z. Kembłowski, Reologia stosowana płynów, Marcus sc, Łódź 1995, 5. G. Sorge, Faszination Ultraschall, Teubner Verlag, 2002.

78

Magnetic and electrical properties of the compounds with the spinel structure

Lecturer: dr E. Malicka Course code: 0310-2.03.4.052 Type of the course: Specialization ECTS: 2 Lecture + classes Number in study program: 9 Number of hours: 15 + 7.5 = 22.5 Semester: 1 or 2 Course prerequisites: None Language: Polish or English Teaching methods: Multimedia teaching techniques, using internet resources, solving tasks Assessment methods: Problem-solving exercises, oral presentation, literature surveys, reporting thesis results,

preparation and display of posters, final examination (written) Course contents: Distribution of metal ions in the spinel structure. Ionic and atomic model of crystal lattice. Vacancy model. Magnetic properties of seleno-chromites. Magnetic exchange interactions. The theory of ferromagnetism. Ferrimagnetism. Antiferromagnetism. Metamagnetism. Spin glass. Methods of macroscopic and microscopic examination of magnetic materials. Band theory of solids. Electrical conductivity of spinels. Intrinsic semiconductors. Doped semiconductors. Methods of electrical resistance measurements. Magnetoresistance. Thermoelectric properties of spinels. Seebeck Effect. Objectives of the course: Acquainting students with factors influencing magnetic and electric properties of compounds with spinel structure. Learning of modern research methods of these properties and practical aspects of analysis of experimental results. Learning outcomes: The student should be able to analyse the experimental data and form conclusions on correlation of the crystal structure with physical properties of the spinels. Textbooks and recommended reading: 1. A. Oleś, Metody doświadczalne fizyki ciała stałego, WNT, Warszawa, 1998, 2. Z. Kleszczewski, Fizyka kwantowa, atomowa ciała stałego, Wydawnictwo Politechniki Śląskiej Gliwice,

1997, 3. C. Kittel, Wstęp do fizyki ciała stałego, PWN, Warszawa, 1976, 4. B. Staliński, Magnetochemia, PWN, Warszawa, 1966, 5. P. Haasen, E.I. Kramer, Material Science and Technology Eds. R.W. Cahn, P. Haasen, E.J. Kramer, Vol. 3A.

Part I. Weinheim-New York-Basel-Cambrid, 1991, 6. T. Groń, Wpływ luk sieciowych i mieszanej wartościowości na przewodnictwo elektryczne w roztworach

stałych o strukturze spinelowej, Wydawnictwo Uniwersytetu Śląskiego, Katowice, 1995, 7. J. Krok-Kowalski, Wpływ podstawników kationowych przy róŜnych anionach na uporządkowanie

magnetyczne związków zawierających chrom, Wydawnictwo Uniwersytetu Śląskiego, Katowice, 1998.

79

Thermodynamic properties of liquid mixtures

Lecturer: dr hab. Marzena Dzida Course code: 0310-2.03.4.053 Type of the course: Specialization ECTS: 2 Lecture + classes Number in study program: 9 Number of hours: 15 + 7.5 = 22.5 Semester: 1 or 2 Course prerequisites: None Language: Polish or English Teaching methods: Multimedia teaching techniques, using internet resources, solving tasks Assessment methods: Problem-solving exercises, oral presentation, literature surveys, reporting thesis results,

preparation and display of posters, final examination (oral) Course contents: Characteristic of the liquid state. Equations of state for liquids: examples and determination. Theories and models of pure liquids and liquid mixtures. Thermodynamics of solutions: mixing and excess functions, thermodynamically correct definition of an ideal mixture. Methods of approximation of excess and mixing functions. Statistical description of quality of fitting functions. Partial molar functions and methods of their calculations. Gibbsian and non-Gibbsian, Lewisian and non-Lewisian properties. Effect of temperature and pressure on thermodynamic properties of liquid mixtures. Thermodynamic models of liquid fuels and biofuels. Methods of calculation of material constants for liquid fuels. Objectives of the course: Give the relationships between intermolecular interactions and the physicochemical properties of liquids. Presentation of the concepts of thermodynamics of solutions. Show how thermodynamic properties can be applied for description of real systems. Learning outcomes: After the course, students know thermodynamically exact way of estimation the excess functions. They can calculate excess, mixing, partial molar functions, and approximate obtained results using appropriate fitting function. They can use experimental data and results of models calculations for discussion properties of investigated substances. Textbooks and recommended reading: 1. H. Buchowski, W. Ufnalski, Roztwory, WNT, Warszawa, 1995, 2. J.B. Czermiński, A. Iwasiewicz, Z. Paszek, A. Sikorski, Metody statystyczne dla chemików, PWN,

Warszawa, 1992, 3. J.C.R. Reis, M.J. Blandamer, M. I. Davis, G. Douhéret, The concepts of non-Gibbsian and non-Lewisian

properties in chemical thermodynamics, Phys. Chem. Chem. Phys., 2001, 3, 1465, 4. G. Douhéret, M.I. Davis, J.C.R. Reis, M.J. Blandamer, Isentropic compressibilities – experimental origin and

the quest for their rigorous estimation in thermodynamically ideal liquid mixtures, Chem. Phys. Chem., 2001, 2, 148.

80

Selected topics of coordination chemistry

Lecturer: dr hab. Jan Grzegorz Małecki Course code: 0310-2.03.4.054 Type of the course: Specialization ECTS: 2 Lecture + classes Number in study program: 9 Number of hours: 15 + 7.5 = 22.5 Semester: 1 or 2 Course prerequisites: None Language: Polish or English Teaching methods: Multimedia teaching techniques, using internet resources, solving tasks Assessment methods: Problem-solving exercises, oral presentation, final examination (oral) Course contents: The nomenclature, structure and geometric isomerism of coordination compounds; Durability of coordination compounds; statistical and chelate effects; molecular orbitals theory of transition metal complexes; model of electron pair repulsion of valence shell (VSEPR) octahedral complexes, tetrahedral and lower geometry complexes; The symmetry and crystal field theory, elements of group theory, the crystal field splitting; complexes of weak, strong and intermediate fields, plane-square complexes, ligand field theory, low symmetry ligand fields; electronic spectra of transition metal complexes, spin-forbidden transitions, spin-orbit coupling, Tanabe-Sugano diagrams; Determination of Racah parameters form electronic spectra; nepheloauxetic effect, Jahn-Teller effect; trans effect, contours and intensity of the electronic bands, charge transfer bands; luminescence properties of complexes, magnetic properties of transition metal complexes Objectives of the course: Presentation of the elements of coordination chemistry in the basic concepts and the relationships between the molecular structure of complexes and theirs electronic structures and physicochemical properties Learning outcomes: After completing the course students should have knowledge of coordination chemistry that allows the determination of the properties of complexes and the relationship between the structure and the spectroscopic properties Textbooks and recommended reading: 1. J.O. Dzięgielewski, Chemia nieorganiczna. Part 3., Uniwersytet Śląski, Katowice, 1989, 2. A.F. Williams, Chemia nieorganiczna - podstawy teoretyczne, PWN, Warszawa, 1986, 3. Y. Jean, Molecular Orbitals of Transition Metal Complexes, Oxford University Press, 2005.

81


Course code: 0310-2.03.4.075 0310-2.03.4.076




82

SPECIALISATION V: Physicochemical methods in analytical chemistry



83

Physicochemical fundamentals of liquid chromatography

Lecturer: prof. dr hab. Teresa Kowalska Course code: 0310-2.03.4.055 Type of the course: Specialization ECTS: 2 Lecture + classes Number in study program: 9 Number of hours: 15 + 7.5 = 22.5 Semester: 1 or 2 Course prerequisites: None Language: Polish or English Teaching methods: Multimedia teaching techniques, using internet resources, solving tasks Assessment methods: Problem-solving exercises, oral presentation, final examination (written) Course contents: General characteristics of the chromatographic system and its individual components in liquid chromatography. What does ‘retention’ really mean? Brief classification of chromatographic techniques. Adsorption and partition liquid chromatography in the planar and column chromatographic mode. Basic parameters of retention and separation efficiency in planar and column chromatography. Number of theoretical plates (N) and separation number (SN). Van Deemter equation. Isocratic and gradient liquid chromatography. Semiempirical models of solute retention in liquid chromatography. Characterization of chromatographic activity of sorbents and chromatographic polarity of solvents. Snyder’s concepts of solvents’ elution strength, their polarity index and selectivity parameters. Optimization of the chromatographic separation selectivity. Objectives of the course: This lecture course should introduce the students to the vocabulary and to basic physicochemical concepts used to explain the molecular-level mechanisms that govern separation of a mixture of compounds in the two universal modes of liquid chromatography, i.e., in the adsorption and partition chromatography. Learning outcomes: At the end of this lecture course, students should be able to explain the obtained chromatographic results in physicochemical terms and they should also gain an insight in basic strategies of practical improving the separation outcome. Textbooks and recommended reading: 1. Z. Witkiewicz, Podstawy chromatografii, WNT, Warszawa, 2005, 2. L.R. Snyder and J.J. Kirkland, Introduction to Modern Liquid Chromatography, Wiley, New York, 1979, 3. Handbook of Thin-Layer Chromatography, Eds J. Sherma and B. Fried, Dekker, New York, 1996, 4. F. Geiss, Fundamentals of Thin-Layer Chromatography (Planar Chromatography), Dr. Alfred Hőthig Verlag,

Heidelberg, 1987, 5. Planar Chromatography, Ed. R.E. Kaiser, Dr Alfred Hőthig Verlag, Heidelberg, 1986, 6. S.T. Balke, Quantitative Column Chromatography. A Survey of chemometric methods, Elsevier, Amsterdam,

1984.

84

Physicochemical bases of gas chromatography

Lecturer: dr Józef Rzepa Course code: 0310-2.03.4.056 Type of the course: Specialization ECTS: 2 Lecture + classes Number in study program: 9 Number of hours: 15 + 7.5 = 22.5 Semester: 1 or 2 Course prerequisites: None Language: Polish or English Teaching methods: Multimedia teaching techniques, using internet resources, solving tasks Assessment methods: Problem-solving exercises, oral presentation, final examination (written) Course contents: Principles of gas chromatography. Van Deemeter equation. Factors influencing chromatographic separation. Retention data and their usefulness for analysis and physicochemical research. Types of columns used in gas chromatography. Stationary Phases. Capillary columns. Detectors used in gas chromatography. Fast and ultrafast gas chromatography—columns and instrumentation. Coupling of gas chromatography with mass spectrometry. Using mass spectra to identify substances and quantitative analysis. Supercritical gas chromatography. Inverse gas chromatography. Sample preparation for chromatographic analysis. Sample derivatisation. Automatic injection systems. Objectives of the course: Introducing students to the theoretical background and instrumentation of gas chromatography and their usefulness in chemical analysis. Expected outcome: After completing the course the student should have basic knowledge of the theory of gas chromatography, the process of the chromatographic column selection and conditions of analysis. The student should be able to choose the detector and method of sample preparation best suited for a particular analytical problem. Textbooks and recommended reading: 1. Z. Witkiewicz, Podstawy Chromatografii, WNT, Warszawa, 2000, 2. Z. Witkiewicz, J. Hepter, Chromatografia gazowa, WNT, Warszawa, 2000, 3. K. Bielicka-Daszkiewicz, K. Milczewska, A. Voelkel, Zastosowanie metod chromatograficznych, WPP

Poznań, 2005, 4. R.L. Grob, E.F. Barry, Modern practice of gas chromatography (Fourth Edition), John Wiley & Sons, 2004, 5. M. McMaster, C. McMaster, GC/MS: A practical user’s guide, John Wiley & Sons, 1998, 6. H.J. Hubschmann, Handbook of GC/MS, Wiley – VCH, Weinheim, 2009, 7. W. Jennings, Analytical gas chromatography, Academic Press Inc., London, 1997, 8. E. deHoffmann, J. Charette, V. Stroobant, Spektrometria mas, WNT, Warszawa, 1998.

85

Chiral separations by means of chromatography

Lecturer: prof. dr hab. Teresa Kowalska Course code: 0310-2.03.4.057 Type of the course: Specialization ECTS: 2 Lecture + classes Number in study program: 9 Number of hours: 15 + 7.5 = 22.5 Semester: 1 or 2 Course prerequisites: None Language: Polish or English Teaching methods: Multimedia teaching techniques, using internet resources, solving tasks Assessment methods: Problem-solving exercises, oral presentation, final examination (written) Course contents: Direct and indirect separations of enantiomers in liquid chromatography– a general approach. The ”tailor-made” sorbents. Chiral stationary phases. Three generations of chiral stationary phases after Pirkle (CSP). Substituted polyacrylamides as chiral stationary phases for drug separations. Optically active poly(triphenylmethylmetacrylate) and its analogues as chiral stationary phases. Cellulose derivatives as chiral stationary phases. Chiral modifiers of mobile phases. Ion-pair chromatography with chiral heterons. Cyclodextrines as mobile phase modifiers – formation of inclusion complexes. Albumins as mobile phase modifiers. Tartaric acid esters as chiral selectors. Complexing agents (transition metal ions) as mobile phase modifiers. Analytical and preparative applications of chromatographic separations of enantiomers. Objectives of the course: Introduction to the students of chromatographic techniques that are applied to chiral separations. The main accent in this lecture course is laid on solving one of the most demanding practical separation tasks which is enantioseparation. Ability to successfully separate enantiomers both in the analytical and preparative mode is in great demand in pharmaceutical sciences, molecular biology and in most so-called life sciences. Learning outcomes: Students should acquire basic knowledge on chromatographic separation of chiral compounds and more specifically, on enantioseparations. They should also be able to distinguish among the different strategies applied to solving this practical problem and also be able to evaluate the advantages and disadvantages of each one of them in practical conditions. Textbooks and recommended reading: 1. Z. Witkiewicz, Podstawy chromatografii, WNT, Warszawa, 2005, 2. S.G. Allenmark, Chromatographic Enantioseparation, Ellis Horwood Ltd, Chichester, 1988, 3. Liquid Chromatography in Biomedical Analysis, Ed. T. Hanai, Journal of Chromatography Library, Vol. 50,

Elsevier, Amsterdam, 1991, 4. Thin Layer Chromatography in Chiral Separations and Analysis, T. Kowalska and J. Sherma (Eds.),

Chromatographic Science Series, Vol. 98, CRC Press, Boca Raton, 2007.

86

Design of experiments in chromatography

Lecturer: dr Ivana Stanimirova-Daszykowska Course code: 0310-2.03.4.058 Type of the course: Specialization ECTS: 2 Lecture + classes Number in study program: 9 Number of hours: 15 + 7.5 = 22.5 Semester: 1 or 2 Course prerequisites: None Language: Polish or English Teaching methods: Multimedia teaching techniques, using internet resources, solving tasks Assessment methods: Problem-solving exercises, oral presentation, final examination (written) Course contents: Experimental problems in chromatography. Basic experimental steps in any chromatographic procedure. Optimization strategies used in a chromatographic experiment. Parameters that can be used as response functions in chromatography (definition of resolution, separation factor, retention time). Selection of criterion for quantitative characterization of a chromatogram. Univariate and multivariate optimization. Correlation coefficient. Orthogonal least squares regression, OLSR and multiple linear regression, MLR. A full factorial design of type 2f. Applications of full factorial design to liquid chromatography, LC. Fractional factorial designs and their practical use in capillary electrophoresis. Plackett-Burman designs and their applications in HPLC of tetracycline. Three-level factorial designs. Central composite designs and their application in gas chromatography of pesticides. Application of Doehlert design in the development of fast HPLC procedure for optimization of the gradient elution regime. Criteria for optimization of non-symmetrical designs. D-optimality. Mixture designs and their application for an optimization of the modification agent quantity and a mobile phase content in the HPLC experiment. Introduction to optimization: looking for optimum with the use of Simplex and steepest ascent methods. Objectives of the course: Students will be introduced to the basic concepts of experimental design and optimization methods used particularly in chromatography. Learning outcomes: Ability to select a strategy to design her/his experiment using the principals of Experimental design and practical skills to perform the necessary calculations and to come to conclusions about the optimal experimental parameters in studied chromatographic system. Textbooks and recommended reading: 1. M. Korzyński, Metodyka eksperymentu, WNT, Warszawa, 2006, 2. D.L. Massart, B.G.M. Vandeginste, L.M.C. Buydens, S. De Jong, P.J. Lewi, J. Smeyers –Verbeke, Handook

of Cemometrics and Qualimetrics: Part A, Elsevier, Amsterdam, The Netherlands, 1997, 3. J. Kusiak, A. Danielewska-Tułecka i P. Oprocha, Optymalizacja, Wydawnictwo Naukowe PWN, Warszawa,

2009, 4. D.C. Montgomery, Design and analysis of experiments, John Wiley & Sons, Arizona, USA, 2005, 5. L. Eriksson, E. Johansson, N. Kettaneh-Wold, C. Wikström, S. Wold, Design of experiments, 3rd edition,

Umetrics Academy, Umeå, Sweden, 2008.

87

Special chromatographic techniques

Lecturer: prof. dr hab. Teresa Kowalska Course code: 0310-2.03.4.059 Type of the course: Specialization ECTS: 2 Lecture + classes Number in study program: 9 Number of hours: 15 + 7.5 = 22.5 Semester: 1 or 2 Course prerequisites: None Language: Polish or English Teaching methods: Multimedia teaching techniques, using internet resources, solving tasks Assessment methods: Problem-solving exercises, oral presentation, final examination (written) Course contents: Gel chromatography (analytical and physicochemical applications). Ion chromatography: ion exchange chromatography, ion exclusion chromatography and ion-pair chromatography. Extraction chromatography (stationary and mobile phases, basic applications). Affinity chromatography. Countercurrent chromatography and droplet countercurrent chromatography. Complexation chromatography. Supercritical fluid chromatography. Electrophoretical techniques (zone electrophoresis, moving boundary electrophoresis, isotachophoresis, isoelectrical focusing). Electrochromatography and the other hybrid techniques. Objectives of the course: This lecture course should introduce the students to the chromatographic techniques that serve the specific, i.e., the non-universal, separation problems. Particular attention of the students will be drawn to the problems of separating natural and synthetic macromolecules, compounds with the ionic structure, and also the radioactive isotopes. Learning outcomes: This lecture course should provide the students with basic understanding of the separation science and more specifically, with fundamentals on the special liquid chromatography techniques and the application areas thereof. Students should be aware of the chromatographic techniques of choice and of those the best suiting the demands of a given analytical problem. Textbooks and recommended reading 1. T. Kremmer, L. Boross, Gel Chromatography, Akademiai Kiado, Budapest, 1979, 2. Extraction Chromatography, Eds T. Braun and G. Ghersini, Journal of Chromatography Library, Vol. 2,

Elsevier, Amsterdam, 1975, 3. J. Turkova, Affinity Chromatography, Journal of Chromatography Library, Vol. 12, Elsevier, Amsterdam,

1978, 4. Electrophoresis, Ed. Z. Deyl, Journal of Chromatography Library, Vol. 18, Elsevier, Amsterdam, 1979, 5. Modern Supercritical Fluid Chromatography, Ed. C.M. White, Dr Alfred Hőthig Verlag, Heidelberg, 1988, 6. W.D. Conway, Countercurrent Chromatography, VCH Publishers Inc., New York, 1989, 7. Z. Witkiewicz, Podstawy chromatografii, WNT, Warszawa, 2005, 8. D. Berek, M. Dressler, M. Kubin, K. Marcinka, Chromatografia Ŝelowa, PWN, Warszawa, 1989.

88

Application of chromatographic techniques to investigation of natural products

Lecturer: dr Mieczysław Sajewicz Course code: 0310-2.03.4.060 Type of the course: Specialization ECTS: 2 Lecture + classes Number in study program: 9 Number of hours: 15 + 7.5 = 22.5 Semester: 1 or 2 Course prerequisites: None Language: Polish or English Teaching methods: Multimedia teaching techniques, using internet resources, solving tasks Assessment methods: Problem-solving exercises, oral presentation, final examination (written) Course contents: Preparation of the natural product samples for chromatographic analysis. Extraction methods: continuous extraction (Soxhlet), accelerated solvent extraction (ASE), solid phase extraction (SPE), supercritical fluid extraction (SFE), headspace extraction (HS). Applications of thin-layer chromatography (TLC), liquid chromatography (LC), and gas chromatography (GC). Applications of the hyphenated techniques: TLC/MS, LC/MS, and GC/MS. Application of chromatographic techniques to investigating plant material. Applications of chromatographic techniques in biochemical studies, food chemistry, pharmaceutical analysis, and in the analysis of petrochemical products. Qualitative and quantitative applications of chromatography. Objectives of the course: Introduction of students to the performance and potential of chromatographic techniques in the analysis of natural products. Learning outcomes: The course should cater to the students basic knowledge on sample preparation preceding proper chromatographic analysis and also instruct them as to the choice of a chromatographic method most adequate to the problem to be solved. Textbooks and recommended reading: 1. J. Namieśnik, Pobieranie próbek środowiskowych do analizy, Wydawnictwo Naukowe PWN, Warszawa,

1995, 2. Farmakopea Polska, 7th edition, Polskie Towarzystwo Farmaceutyczne, 2008, 3. Farmakopea polska VIII - suplement praca zbiorowa wydawca: Polskie Towarzystwo Farmaceutyczne, 2009, 4. Z. Witkiewicz, Podstawy chromatografii, WNT, Warszawa, 2005.

89


Course code: 0310-2.03.4.075 0310-2.03.4.076




90

MONOGRAPHIC LECTURES Number in study program: 10 Type of the course: Lecture Number of hours:* 5×15 Semester: Winter (1) + summer (2) + winter (3) ECTS: 5×1

* selected optionally in 5*15 hour modules

91

Polymers as materials XXI century

Lecturer: dr hab. inŜ. Ewa Schab-Balcerzak Course code: 0310-2.03.5.061 Type of the course: Monographic ECTS: 1 Lecture Number in study program: 10 Number of hours: 15 Semester: 1, 2 or 3 Course prerequisites: None Language: Polish or English Teaching methods: Multimedia teaching techniques, using internet resources Assessment methods: Final examination (pass/fail) Course contents: Concept of macromolecule. Significance of polymers in human life. Brief history of polymers. Basic concepts of macromolecules (molecular weight, glass transition temperature, morphology). Classification of polymers. Structure of polymers. Methods for synthesis of polymers (chain growth polymerization, step growth polymerization). Techniques for manufacturing of polymers (polyreaction in bulk, in solution, in dispersion). Polymer properties (thermal, mechanical, optical). Basic types of polymers. Design of macromolecules with desired properties. Liquid crystalline polymers. Biodegradable polymers. Semiconducting polymers. Directions of polymer investigations development. “Intelligent” polymers. Shape memory polymers (with thermal memory induced indirectly and directly, with chemomechanical memory and with memory induced by light). Electrostrictive polymers. Magnetostrictive materials. Piezoelectric polymers. Color changing polymers – “polymeric chameleons” (electrochromic, thermochromic). Light emitting polymers (electroluminescent and photoluminescent). Self repairing polymers. Amphiphilic polymers (LCST, UCST and schizophrenic) and its applications in medicine. Polymers in electronics (transistors, condensators, sensors). Polymeric solar cells. Polymers for photonics (holographic data storage, photonic structures). Objectives of the course: Presentation of the objectives, basic methods for synthesis of polymers, investigations of chosen physicochemical properties, strategy of design of macromolecules with desired properties and possibility of polymers applications in modern technologies. Learning outcomes: After the course students should have basic knowledge concerns polymers, their significance in life, polyreactions, physicochemical properties of polymers, relationship between polymer structure and properties and possibility of polymers applications in modern technologies: electronics, optolectronics, photonics and in medicine. Textbooks and recommended reading: 1. Praca zbiorowa, Chemia polimerów, red. Z. Florjańczyk, S. Penczek, Wydawnictwo Politechniki

Warszawskiej, tom 1-3, Warszawa, 2002, 2. J.F. Rabek, Współczesna wiedza o polimerach, PWN, Warszawa, 2008, 3. H. Galina, Fizyka materiałów polimerowych; makrocząsteczki i ich układy, WNT, Warszawa, 2008, 4. D. Braun, H. Cherdron, M. Ritter, B. Voit, Polymer Synthesis: Theory and Practice, 4th Ed. Springer-Verlag

Berlin Heidelberg, 2005.

92

Bioinformatics

Lecturer: prof. dr hab. inŜ. Jarosław Polański dr Andrzej Bąk

Course code: 0310-2.03.5.062

Type of the course: Monographic ECTS: 1 Lecture Number in study program: 10 Number of hours: 15 Semester: 1, 2 or 3 Course prerequisites: None Language: Polish or English Teaching methods: Multimedia teaching techniques, using internet resources Assessment methods: Final examination (pass/fail) Course contents: The objectives of bioinformatics. Chemical bases of bioinformatics. Information coded in biopolymeric structures of nucleic acids. Proteins. Polysaccharides. Genetic code. Analysis of biopolymer sequences. Gene expression. Genomics. Proteomics. Synthesis of biopolymers. Modeling biological systems. Modeling drug-receptor interactions. Chemogenomics. Cataloguing biological information. Bioinformatic databases. DNA and protein sequences. Computational methods inspired by natural strategies. Neural networks. Computational and biological neuron. Neural system. Synapsis. Input signals. Weights. Application of artificial neural networks. Activation function. Graphical neural representation. Hidden layer. Output layer. Fundamental methods for training neural systems. Supervised vs. unsupervised architectures. Self-organizing neural networks. Algorithms of self-organizing neural networks learning. Kohonen algorithm. application of Kohonen network in drug design. Multilayer unidirectional networks. Back propagation. Learning algorithms. Optimizing network architecture. Selected applications of multilayer neural networks. Potential application areas, in particular, supervised architectures in drug design. Software for neural network computations. Basics in MATLAB environment programming. Programming neural networks algorithms in MATLAB (Drug Design Toolbox (DDT) for MATLAB). Objectives of the course: Presentation of the objectives and basic concepts of bioinformatics, in particular, chemical bases of bioinformatics, investigations and cataloguing of biopolymer structures as well as computational methods inspired by natural strategies. Learning outcomes: After the course students should have knowledge on the fundamental problems of bioinformatics and bioinformatic database resources and be familiar with the use of these databases. Textbooks and recommended reading: 1. P.G. Higgs, T.K. Attwood, Bioinformatyka i ewolucja molekularna, PWN, Warszawa, 2008, 2. A.D. Baxevanis, B.F.F. Ouellette (Eds.) Bioinformatyka - Podręcznik do analizy genów i białek, PWN,

Warszawa, 2005, 3. J. Zupan, J. Gasteiger, Neural Networks in Chemistry and Drug Design, Wiley-VCH, Weinheim, 1999.

93

QSAR modeling

Lecturer: prof. dr hab. inŜ. Jarosław Polański Course code: 0310-2.03.5.063 Type of the course: Monographic ECTS: 1 Lecture Number in study program: 10 Number of hours: 15 Semester: 1, 2 or 3 Course prerequisites: None Language: Polish or English Teaching methods: Multimedia teaching techniques, using internet resources Assessment methods: Final examination (pass/fail) Course contents: Chemical molecules. Chemical space. Virtual chemical space. Factual chemical space. The architecture of chemistry. Molecular descriptors. Partial charges. Electronic effects. Steric effects. Hammett constant. Taft constant. Connectivity indices. Autocorrelation function and related descriptors. Hydrophobic constant. Hansch and Rekker approaches. Molecular interaction filed (MIF). Hammett approach to QSAR modeling. Hansch approach to QSAR modeling. QSAR modeling and real interaction processes. Drug transportation within organisms. Mathematical tools for QSAR modeling. QSAR domain. Kubinyi bilinear model. QSAR dimensionality. Formal QSAR classifications. 0D – 6D QSAR formalisms. Simple and complex 1D (0D) QSAR models. 2D QSAR modeling. Connectivity indices and QSAR modeling. 3D QSAR modeling. Comparative Molecular Field Analysis (COMFA). Corticosteroid binding globulin (CBG) and testosterone binding globulin (TBG) data in drug design. Principal component analysis (PCA) and partial least squares (PLS) methods. Model validation methods. Model visualization. Data reduction. Comparative Molecular Similarity Analysis (COMSIA). Comparative Molecular Surface Analysis (COMSA). Self organizing maps and sector COMSA formalisms. Molecular Shape Analysis (MSA). 4D QSAR modeling. Conformational space. Grid cell occupancy descriptors (GCOD). Molecular shape spectrum (MSS). 4D QSAR models. 5D and 6D QSAR modeling. Available software. QSAR and virtual screening. QSAR successes and failures. Objectives of the course: Presentation of the fundamental problems of QSAR modeling. Learning outcomes: After the course students should have basic knowledge on the current schemes for QSAR modeling and have basic skills allowing to apply related methods in drug design problems. Textbooks and recommended reading: 1. G. Patrick, Chemia medyczna, WNT, Warszawa, 2003, 2. R. Silverman, Chemia organiczna w projektowaniu leków, WNT, Warszawa, 2004, 3. A. Vedani, M. Dobler, M.A. Lill, The Challenge of Predicting Drug Toxicity in silico, Basic & Clinical

Pharmacology & Toxicology 2006, 99, 195–208.

94

Pharma industry

Lecturer: prof. dr hab. inŜ. Jarosław Polański Course code: 0310-2.03.5.064 Type of the course: Monographic ECTS: 1 Lecture Number in study program: 10 Number of hours: 15 Semester: 1, 2 or 3 Course prerequisites: None Language: Polish or English Teaching methods: Multimedia teaching techniques, using internet resources Assessment methods: Final examination (pass/fail) Course contents: History. Penicillin. medicinal drugs. R&D. Drug discovery and development. Discovery vs development. Industry and academia. Trends in worldwide R&D. Drug quality control. Contamination control. Design and discovery issues in pharma. Organic synthesis. Economical factors in pharma industry. Pharmacoeconomic. Organic synthesis issues in pharma indutry. Chromatography in pharma industry. Chirality control in drug industry. Biotechnology in pharma industry. Human insulin. Human growth hormon. Recombinant DNA and transgenic animals. Formulation. Dosing. Safety. In vitro. In vivo testing. Pre-clinical. Clinical trials. Drug market. Top-selling drugs. Vitamins. Amino acids. Food additives. Synthetic sweeteners. History of sweeteners. Historical development of sweetness consumption. Commercial alternative sweetener discoveries. Molecular design and alternative sweeteners. Screening and visualizing novel sweeteners. Molecular design in commercial sweeteners development. From discovery to commercial products. Pharmaceutical marketing. Dietetic and lifestyle issues in marketing. Priority rights and intellectual property rights. Innovation and cost of innovation. Industry revenues. Drug design business. Branded and generic drugs. Legal issues. Regulatory authorities. Food and Drug Agency. European Medicines Agency. Insurance and healthcare system. Drugs in developing countries. Drugs and lifestyle. Objectives of the course: Presentation of the fundamental problems of pharmaceutical and related industries, in particular, the industry of artificial sweeteners. Learning outcomes: After the course students should have basic knowledge on the current schemes relating the R&D and pharma industry, as well as economical background determining medicinal chemistry sector. Textbooks and recommended reading: 1. W.J. Spillane (Ed.), Optimizing sweet taste in foods, Woodhead Publishing Limited, Cambridge, 2006, 2. J. Emsley, Piękni, zdrowi, witalni, CIS, Warszawa, 2006, 3. E. Grzywa, J. Molenda, Technologia podstawowych syntez organicznych, WNT, Warszawa, 2008.

95

Cosmetic chemistry

Lecturer: dr Halina Niedbała Course code: 0310-2.03.5.065 Type of the course: Monographic ECTS: 1 Lecture Number in study program: 10 Number of hours: 15 Semester: 1, 2 or 3 Course prerequisites: None Language: Polish or English Teaching methods: Multimedia teaching techniques, using internet resources Assessment methods: Final examination (pass/fail) Course contents: Cosmetics – from ancient times till today, raw materials in cosmetics, emulsifiers, preservatives, thickeners, fragrances, surfactants, colorants and pigments, vitamins, stabilizers, waxes, active ingredients, emollients, liposomes, cosmetic types, moisturizers, shampoo, soap, sunscreens, tans, perfumes, toothpastes, antiperspirants, antiseptics in cosmetics: quaternary ammonium compounds, boric acid, hydrogen peroxide, phenol, iodine, antiseptic deodorants, nomenclature of cosmetic ingredients (ingredient labeling), skin – the main target of cosmetics, layers of skin, epidermis, dermis, skin components, function, aging, skin types, skin pigmentation, melanin, melanocytes, skin diseases, dermatology, skin anatomy and physiology - a consequence of chemical structures in skin, wound healing processes and enhancers, nail cosmetics, phytocosmetics, lecitins, saponins, tanins, anthocyanins, hormones, cosmetic forms, natural extracts as cosmetics, law regulations, cosmetic documentation, cosmetic labeling, cosmetic content abbreviations, drugs vs. cosmetics, domestic regulations, cosmetic R&D and industry, cosmetics and lifestyle, chemical operations in cosmetic technologies. Objectives of the course: Presentation of the chemical structures constituting skin being the main target of cosmetics, as well as providing the introduction to the cosmetic formulation and production from the chemical raw materials. Learning outcomes: After the course students should have basic knowledge on the cosmetic targets as well as the mechanisms of action of cosmetics, their formulations and law regulations in the field. Textbooks and recommended reading 1. M.C. Martini, Kosmetologia i farmakologia skóry, PZWL, W-wa, 2007, 2. R.W. Malinka, Zarys Chemii Kosmetycznej, Volumed, 1999, 3. R. Glinka, Receptura kosmetyczna, Oficyna Wydawnicza MA, Łódź, 2003.

96

Bioinorganic chemistry

Lecturer: prof. dr hab. inŜ. Stanisław Krompiec Course code: 0310-2.03.5.066 Type of the course: Monographic ECTS: 1 Lecture Number in study program: 10 Number of hours: 15 Semester: 1, 2 or 3 Course prerequisites: None Language: Polish or English Teaching methods: Multimedia teaching techniques, using internet resources Assessment methods: Final examination (pass/fail) Course contents: Principles of bioinorganic chemistry. Fundamentals of bioinorganic chemistry, bio-molecules as ligands, porphyrins, corrins, amino acids, nucleic acids, enzymes, coenzymes and other bio-ligands. Binding of metal ions and complexes to bio-molecule active centers, thermodynamic and kinetic aspects, coordination effects. Model complexes and the concept of spontaneous self-assembly. Metal-ion stabilization of nucleic acid and protein structure. Selection and insertion of metal ions for protein sites. Control and utilization of metal ion concentration in cell, beneficial and toxic effects of metal ions; beneficial metal: iron, toxic metal: mercury. Metal functions in metalloproteins, metalloenzymes functions, metalloenzymes as a selective biocatalysts. Dependence of the function of the metal centers on the biochemical environment (e.g. the protein environment). Communication role of metals in biology, transport and storage of metal ions. Atom and group transfer chemistry, dioxygen transport. Metals and their ions in medical science. Bioavailability of metal ions, metal-containing drugs – bioavailability, pharmacology, activity, toxicity. Physical methods in bioinorganic chemistry: X-ray methods, magnetic resonance methods, Mössbauer spectroscopy, electronic and vibrational spectroscopy, magnetic measurements, reduction potential measurements, electron microprobe analysis. Objectives of the course: Presentation of the role of metal ions and their complexes for biology, interactions metal ion – bioligand and of the coordination modes of bioligands. Discussion of the mechanisms of reactions involving metals coordinated by bioligands, physical methods for the study of the role of metal ions in biochemical processes. Learning outcomes: After this course, student should know the role of metals, their ions and compounds (especially complexes) in biology and biochemistry, in normal physiology of living organisms, in medicine. Student should be aware of biological impact of metals in the environment: in water, food, drugs. Textbooks and recommended reading: 1. S.J. Lippard, J.M. Berg, Podstawy chemii bionieorganicznej, PWN, Warszawa, 1998, 2. F.A. Cotton, G. Wilkinson, P.L. Gaus, Chemia nieorganiczna, PWN, Warszawa, 1995.

97

Diagrammatic methods in quantum chemistry

Lecturer: prof. dr hab. Stanisław Kucharski Course code: 0310-2.03.5.067 Type of the course: Monographic ECTS: 1 Lecture Number in study program: 10 Number of hours: 15 Semester: 1, 2 or 3 Course prerequisites: None Language: Polish or English Teaching methods: Multimedia teaching techniques, using internet resources Assessment methods: Final examination (pass/fail) Course contents: Creation-annihilation operators, state vector in the occupation number formalism. Quantum mechanical operators in second-quantized form: one-electron and two-electron operators. Expectation value for one- and two-electron operators. Normal order and contraction of the second-quantized operators.Commutation rules. Wick theorem. Diagrammatic picture of the one- and two-electron operators. Correspondence between algebraic and diagrammatic expressions. Diagrammatic methods in the many body perturbation theory. Diagrammatic form of the energy expression in the Hartree-Fock method. Moeller-Plesset (MP) pertubational operator. First order MP correction for non-Hartree-Fock states. Topologically equivalent and non-equivalent diagrams. Goldstone and antisymmetrized diagrams. Hugenholtz diagrams. Systematic generation of the Hugenholtz diagrams at the arbitrary order of the perturbation theory. Connected, disconnected and unlinked diagrams. Correspondence between Rayleigh-Schroedinger and many-body pertubational corrections. Linked diagram theorem. Second-,third- and fourth-order perturbational MP corrections in diagrammatic form. Direct configuration interaction (DCI) in diagrammatic form. Excitation operators. Iterative scheme in the DCI approach. Diagrammatic formulation of the coupled cluster (CC) method. Diagrammatic form of the energy expression within the CC formalism. Amplitude equations in terms of the antisymmetrized and Goldstone diagrams. Linked cluster theorem in the CC theory. Objectives of the course: Detailed presentation of one of most useful tools of the contemporary quantum chemistry: the Feynman diagram technique. Learning outcome: Understanding of the principles of diagrammatic technique and ability to derive equations and terms occurring in the post-Hartree-Fock methods via Feynman diagrams. Textbooks and recommended reading: 1. A. Szabo, N.S. Ostlund, Modern Quantum Chemistry, McGraw-Hill, New York, 1989, 2. R.J. Bartlett, M. Musiał, Coupled-Cluster theory in quantum chemistry, Rev. Mod. Phys., 79, 291 (2007).

98

Biological quantum chemistry

Lecturer: prof. UŚ, dr hab. Maria Jaworska Course code: 0310-2.03.5.068 Type of the course: Monographic ECTS: 1 Lecture Number in study program: 10 Number of hours: 15 Semester: 1, 2 or 3 Course prerequisites: None Language: Polish or English Teaching methods: Multimedia teaching techniques, using internet resources Assessment methods: Final examination (pass/fail) Course contents: Theoretical modeling of electronic spectra and photochemistry of biological molecules. Quantum chemical methods used for calculation of electronic spectra – TDDFT, CASPT2 and CIS. Electronic transitions description in TDDFT and CASPT2. Electronic transition types. Oscillator strength. Selection rules. Electronic spectrum of porphyrin molecule. Gouterman four-orbital model. Ground and excited state potential energy surfaces. Jablonski diagram. Franck-Condon principle. Modeling of fluorescence and phosphorescence. Avoiding crossings and conical intersections. Theoretical description of photodissociation – vitamin B12 and carboxyhemoglobin. Modeling of vision – retinal and rhodopsin. CASPT2 calculations for retinal isomerization. Retinal+rhodopsin – QM/MM calculations. Opsin shift interpretation. Continuum models of the effects of environment – PCM and COSMO. Bioluminescence – theoretical interpretation of luciferins activity. Quantum chemical calculations for the green fluorescent protein (GFP) chromophore fluorescence. Photochemical properties of nucleic bases – TDDFT and CASPT2 calculations. UV filters – electronic spectra and theoretical description of action. Theoretical calculation for cryptochromes, light sensing molecules in living organisms. Interaction of states with different multiplicity – spin-orbit coupling. Molecular magnetism. Van Vleck-Dirac-Heisenberg Hamiltonian. Calculation of Heisenberg exchange constant with the Unrestricted DFT and CASPT2 methods. Theoretical investigation of enzymatic reactions mechanisms and energetics, the heme enzymes example. Electron transfer in metaloenzymes. Marcus theory. Reorganization energy. Calculation of redox potential of biological molecules. Objectives of the course: Presentation of the basic methods and problems in the computational chemistry of biological molecules. Theoretical determination of the electronic spectra, photophysical and photochemical properties of the biochemical systems. Calculation of the magnetic properties of molecules and energy of enzymatic reactions. Learning outcomes: After the course students should have a knowledge and understanding of basic biological computational chemistry concepts in a level that makes possible to use this to solve the problems concerning structure, reactivity and photochemistry of biological compounds with theoretical methods. Textbooks and recommended reading: 1. M. Olivucci, Ed. , Computational Photochemistry, Elsevier, 2005, 2. L. Noodleman, T. Lovell, W.-G. Han, J. Li, F. Himo, Quantum Chemical Studies of Intermediates and

Reaction Pathways in Selected Enzymes and Catalytic Synthetic Systems Chem. Rev.; 104(2004)459-508, 3. P.E.M. Siegbahn, M.R.A. Blomberg, Transition-Metal Systems in Biochemistry Studied by High-Accuracy

Quantum Chemical Methods, Chem. Rev., 100 (2000) 421-438.

99

Coupled cluster method

Lecturer: dr Monika Musiał Course code: 0310-2.03.5.069 Type of the course: Monographic ECTS: 1 Lecture Number in study program: 10 Number of hours: 15 Semester: 1, 2 or 3 Course prerequisites: None Language: Polish or English Teaching methods: Multimedia teaching techniques, using internet resources Assessment methods: Final examination (pass/fail) Course contents: Definition of the coupled cluster (CC) wave function, exponential Ansatz, definition of the cluster operator, action of the cluster operator on the reference function, general form of the coupled cluster equations and expression for the CC energy, Campell-Baker-Hausdorff commutator theorem, size-extensivity in CC. Diagrammatic form of the one- and two-electron integrals and cluster operators, general rules for constructing of the CC diagrams, diagrammatic form of the T1 and T2 equations for the Hartree-Fock (HF) case in standard form. Non-equivalence of the external lines in the antisymmetrized diagrams of the CC equations. Systematic generation of the different type of the diagrams (connected, disconnected and unlinked) occurring in the CC equations, elimination of the disconnected and unlinked diagrams. Alternative way to derive CC equations. Iterative solution of the coupled cluster equations, generation of the MBPT (Many Body Perturbation Theory) diagrams by CC iterations. Coupled cluster with singles and doubles (CCSD model) for HF and non HF case, coupled cluster with full triples (CCSDT model) and full quadruples (CCSDTQ model). Notion of the intermediate in CC and computational cost (i.e. scaling of the CC models). Similarity transformation, definition of the transformed Hamiltonian. Quasilinear form of the CC equations. Determination of the molecular properties, optimized geometry, harmonic frequencies. Determination of the excitation energies in CC with help of Equation of Motion (EOM) method. Definition of the R operator, form of the Schroedinger equation for the excited state wave function, equations for R amplitudes and expression for the energy , form of the eigenvalue problem. Performance of the test calculations for the ground state energy, molecular properties and excitation energies. Objectives of the course: Skills to construct CC equations (algebraically and diagrammatically), to perform calculations, to choose appropriate CC model in order to do different molecular applications and determination of the molecular properties. Learning outcomes: After the course students should have a knowledge of the general aspects connected to the coupled cluster method in a level that makes possible practical application in theoretical study of the small molecules and also they should be able to recognize differences between various CC approaches. Textbooks and recommended reading: 1. L. Piela, Idee Chemii Kwantowej, PWN, Warszawa, 2003, 2. S.A. Kucharski, R.J. Bartlett, Advances in Quantum Chemistry, 18, 281-345 (1986), 3. R.J. Bartlett, M. Musiał, Rev. Mod. Phys., 79, 291-352 (2007).

100

Computational methods in design of new materials

Lecturer: dr Tadeusz Pluta Course code: 0310-2.03.5.070 Type of the course: Monographic ECTS: 1 Lecture Number in study program: 10 Number of hours: 15 Semester: 1, 2 or 3 Course prerequisites: None Language: Polish or English Teaching methods: Multimedia teaching techniques, using internet resources Assessment methods: Final examination (pass/fail) Course contents: Fundamentals: modeling and numerical simulation in materials science. Monte Carlo method: basic assumptions, historical notes, simple applications. The Metropolis algorithm for the canonical and microcanonical ensembles. Spin Monte Carlo methods: Ising and Heisenberg models. Molecular dynamics: models of interatomic potentials, tight-binding potentials, integration of equation of motion, boundary conditions. Density Functional Theory (DFT): Kohn-Sham equations, types of density functionals: local, gradient and hybrid, advantages of using DFT methods in materials science. Parallel computations, scaling of the algorithm, modern approaches to computations for large systems with many atoms. Numerical computations for carbon nanotubes: carbo materials, tight-binding-type calculations, geometry and electronic structure of nanotubes, enegy bands in nanotubes, Raman spectroscopy and elastic properties of nanotubes. Organic materials in nonlinear optics (NLO): nonlinear optical properties at micro- and macro scale, optimal parameters for NLO materials, (figures-of-merit), donor-bridge-acceptor type of molecular architecture, polyenes, polyynes, octupolar molecules for NLO applications. Determination of the hyperpolarizability tensor components for NLO materials, criteria of choice of the best algorithms. Objectives of the course: Introduction of basic notions and methods of materials science, review of numerical methods employed at various stages and scales of modeling in materials science. Learning outcomes: After the course completion student should know basis methods used in materials science and be able to select a numerical method most suitable at the given stage of the material design process. Textbooks and recommended reading: 1. D. Raabe, Computational Materials Science, Wiley-VCH, 1998.

101

IR spectroscopy of hydrogen- bonded molecular systems

Lecturer: prof. US. dr hab. Henryk Flakus Course code: 0310-2.03.5.071 Type of the course: Monographic ECTS: 1 Lecture Number in study program: 10 Number of hours: 15 Semester: 1, 2 or 3 Course prerequisites: None Language: Polish or English Teaching methods: Multimedia teaching techniques, using internet resources Assessment methods: Final examination (pass/fail) Course contents: Spectral effects in IR attributed to hydrogen bonds. The H/D isotopic effects in IR spectroscopy of hydrogen bonds. Qualitative theories of IR spectra of the hydrogen bond systems. Selected problems of the quantitative theory of IR spectra of the hydrogen bond. The “strong- coupling” theory. The problem of mutually interacting hydrogen bonds in centrosymmetric cyclic carboxylic acid dimers. Vibrational exciton interactions involving hydrogen bonds in their excited states. Basic elements of the theory of IR spectra of molecular crystals. The basic principles of the IR spectroscopy of molecular crystals in polarized light. Non-conventional properties of hydrogen bond systems: The H/D isotopic “self- organization” effects in IR spectra of isotopically diluted crystals. The vibrational- electronic mechanism of dynamical co-operative interactions in hydrogen bond systems in crystals of diverse symmetries. Biological consequences. Examples. Electronic effects in IR spectra of the hydrogen bond. The vibrational transition selection rule breaking in IR spectra of centrosymmetric hydrogen bond dimers. Objectives of the course: Presentation of the contemporary theories of IR spectra of hydrogen bond systems and the revealing of new facts in the area of experimental studies of the spectroscopy of the hydrogen bond. Some consequences of this discovery for the development of studies of the metabolism of biological systems in the heavy water environment will be discussed. Learning outcomes: After completing the course students should have an extended knowledge on the state –of –the art in the IR spectroscopy of hydrogen bonds and on the newly revealed phenomena in the physical chemistry of the hydrogen bond. Textbooks and recommended reading: 1. P. Schuster, G. Zundel, C. Sandorfy (Eds.), The Hydrogen Bond, Recent Developments in Theory and

Experiment, Parts I, II and III, North - Holland, Amsterdam, 1976, 2. H. Ratajczak and W.J. Orville - Thomas (Eds.), Molecular Interactions, Vol. I, Wiley, New York, 1980, 3. D. HadŜi (Ed.), Theoretical treatments of hydrogen bonding, Wiley, New York, 1997.

102

Chiral compounds – preparation and using

Lecturer: prof. dr hab. inŜ. Stanisław Krompiec Course code: 0310-2.03.5.072 Type of the course: Monographic ECTS: 1 Lecture Number in study program: 10 Number of hours: 15 Semester: 1, 2 or 3 Course prerequisites: None Language: Polish or English Teaching methods: Multimedia teaching techniques, using internet resources Assessment methods: Final examination (pass/fail) Course contents: The chirality of material objects, molecular chirality. The reasons of molecular chirality and the connection between chirality and the symmetry of molecules. Konfiguration of chiral molecules, determination, optical activity, methods of measurements, optical purity. Preparation of chiral compounds (organic, inorganic, organometallic): presentation of selected methods. Resolution of racemats: chemical and biochemical methods. Asymmetric synthesis; generation of new stereogenic centers - selected methods. Chiral catalysts in organic synthesis (asymmetric synthesis). Natural and chiral building blocks: application to synthesis of pharmaceutics. Selected applications of chiral compounds: chiral compounds as pharmaceutics, ligands in catalysis, bioligands. Objectives of the course: The presentation of the state of knowledge concerning the chirality of the material objects, particulary molecules. Showing the role of chiral molecules for the functioning of organisms and various biological systems. The presentation of modern methods of the synthesis and separation of chiral compounds. Learning outcomes: After the course students should have knowledge concerning the role, preparation and application of chiral compounds (particularly as pharmaceutics). Textbooks and recommended reading: 1. J. SkarŜewski, Wprowadzenie do syntezy organicznej, PWN, Warszawa, 1999, 2. J. McMurry, Chemia organiczna, PWN, Warszawa, 2000, 3. M.B. Smith, J. March, Advanced organic chemistry, Wiley –Interscience, 2007, 4. C. Willis, M. Willis, Synteza organiczna, Wyd. UJ, Kraków, 2004, 5. STREM Catalog, No 23, Metal catalysts for organic synthesis, 2010, 6. P. Kafarski, B. Lejczak, Chemia bioorganiczna, PWN, Warszawa, 1994.

103

Relationship between structure and reactivity of molecules

Lecturer: prof. dr hab. inŜ. Stanisław Krompiec Course code: 0310-2.03.5.073 Type of the course: Monographic ECTS: 1 Lecture Number in study program: 10 Number of hours: 15 Semester: 1, 2 or 3 Course prerequisites: None Language: Polish or English Teaching methods: Multimedia teaching techniques, using internet resources Assessment methods: Final examination (pass/fail) Course contents: Relation and connections between the structure of molecules, macromolecules and selected solid states and their properties. The relation between structure of molecules and their chemical reactivities. Application of HSAB (hard and soft acids and bases) theory to organic, inorganic, coordination and organometallic chemistry. Anticipation of the results of chemical reactions based on the HSAB theory. The Hammett equation and its varieties: the application to various chemical problems (particularly for anticipation of the stereochemistry of pericyclic reactions). The rules of symmetry of orbitals: application for the analysis of the mechanisms of various reactions (for instance cycloaddition’s reactions). The relationship between structure of metal complexes and their catalytic activity. Influence of donor-acceptor and steric properties of ligands on catalytic activity of transition metal complexes. Relationship between structure of homo- and heterogeneous catalyst and their catalytic properties (activity and selectivity). Presentation of the mechanisms of selected catalytic reactions. How to search the appropriate catalyst for selected reactions. Objectives of the course: The presentation of new chemistry paradigm: designing the structure of the molecules, taking into consideration expected properties. Showing the role of the correlation analysis in chemistry. Learning outcomes: After the course a student should know that the chemical reactivity is a function of structure. The student should be able to analyze chemical facts and plan the structure of compounds and materials, taking into the correlation analysis. Textbooks and recommended reading: 1. J. McMurry, Chemia organiczna, PWN, Warszawa, 2000, 2. M.B. Smith, J. March, Advanced organic chemistry, Wiley –Interscience, 2007, 3. J. Shorter, Analiza korelacyjna w chemii organicznej, PWN, Warszawa, 1980.

104

The separation and concentration methods in chemical analysis

Lecturer: dr Barbara Mikuła Course code: 0310-2.03.5.074 Type of the course: Monographic ECTS: 1 Lecture Number in study program: 10 Number of hours: 15 Semester: 1, 2 or 3 Course prerequisites: None Language: Polish or English Teaching methods: Multimedia teaching techniques, using internet resources Assessment methods: Final examination (pass/fail) Course contents: Enrichment is one of the stages of the procedures in chemical analysis. Basis method for enrichment of analytes. Application of precipitation and co-precipitation in chemical analysis. Co-precipitation of traces in the inorganic, organic and mixed carriers. Extraction as a method of enriching components in the sample. Physicochemical fundamentals of the process. Types of extraction. Methods of sorption (adsorption, absorption, ion exchange). Distillation (including expansion faction sublimation). Melting zone. Incineration. Electrochemical methods (electrodeposition, electrodialysis, cementation, iontophoresis, anode and cathode inversion voltammetry). Modern trends in the development of enrichment techniques, chemical analysis of sample components. Objectives of the course: Understanding the various stages of the analytical process, specific problem analysis and interpretation of the measuring result. Learning outcomes: After the course students should have basic knowledge on the components of the sample enrichment. Textbooks and recommended reading: 1. J. Minczewski, J Chwastowska, R. Dybczyński, Analiza Śladowa, WNT, Warszawa, 1973, 2. A. Mizuike, Enrichment Techniques for inorganic trace analysis, Springer, Berlin, 1983, 3. R. Łoziński, Z. Marczenko, Spectrochemical trace analysis for metals and metalloids, vol. 30, Wilson &

Wilson, Comprehensive Analytical Chemistry, Elsevier, 1996, 4. J. Namieśnik, W. Chrzanowski, P. śmijewska, New horizons and challenges in environmental analysis and

monitoring, Centre of Excellence in environmental analysis and monitoring, Gdańsk, 2003, 5. J. Namieśnik (Ed.), Przygotowanie próbek środowiskowych do analizy, WNT, 2000, 6. J. Namieśnik, J. Łukasiak, Z. Jamrózgiewicz, Pobieranie próbek środowiskowych do analizy, PWN,

Warszawa, 1995.

The University of Silesia - Uniwersytet Śląski

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