Doctoral Studies

Organic Chemistry - Field

Brief description of field

The study field Organic Chemistry starting point is general knowledge of matter composition. It is based on knowledge of the organic molecules structure, methods of structural analysis, empirical relations of structure and chemical behaviour, methods of quantum organic chemistry and molecular modelling. The topic of the study field is study of chemical reactivity, study of mechanism of chemical reactions, investigation of chemical kinetics, searching new synthetic methods leading to chosen molecules, stereochemical behaviour, structure elucidation of new chemical entities based on the most modern spectral methods like NMR, IR, UV – VIS spectroscopies, on mass spectra and structure X-ray analysis. For the preparation of pure organic compounds as well as for investigation of reaction mixtures composition modern separation methods as GC, GC/MS, TLC and column chromatography and HPLC with UV - VIS, refractometric or CD detectors are used.

Targets of the study

The target of the study in the chosen field of the research according with the personal choice of the individual student is to reach deep specific knowledge and new scientific findings, which represent a basic contribution to the existing bank of knowledge of the scientific discipline and are competitive as papers in renown scientific journals. This activity is supposed to be based on perfect knowledge of the today’s state of art, which is based on literature search with application of modern computer assisted method and available databases. Lectures listening and passing examinations are a way for deepening of the theoretical knowledge of the studied field as well as are leading to broadening of a overview in the studied topic. The presentation of both scientific articles contents and results of their personal research at seminars are the way to develop students’ knowledge how to properly acquaint the public with his or hers new achievements in science. Engagement of students in education of bachelor and master students is directed to the same target, too. During the study the main stress is laid on personal research where new and proper customs of the laboratory practice and general knowledge of the research methods are obtained. The target is a preparation of a highly educated specialist with broad knowledge of the chemistry scientific discipline and deep understanding and governing the topic by student chosen. We expect flexible graduates who are dynamic in reaction to any practice requirements.

Profile of a typical graduate

Organic chemistry Ph.D. graduates have hot a broad knowledge of all chemistry disciplines that are able to apply for solution of ordered problems. Deep knowledge of organic chmistry is based upon physical and theoretical chemistry understanding. Graduate is able to carry out a literature search of known facts in the databases and apply them for a synthesis planning. He or she is capable to realize all the experimental techniques of laboratory practice, is mastering spectral methods of structure elucidation and from the submitted spectra to determine a structure. Graduate is able to apply various separation techniques, is well oriented in methods of molecular modelling and simple quantum chemical calculations with commercially available programs. Knowledge of stereochemistry as well as methods of stereoselective synthesis belongs to the list of managing experience. The holder of Ph.D. degree usually finds a job either in University facilities, Institutes of Academy of Sciences, various research institutes or in private research institutes and firms oriented towards organo-chemical and pharmaceutical research. Graduate is prepared to be flexible and adapt also to other requirements of other chemical working places, is able to fulfil demands of employers and be useful in management as well as in business and trade.

Requirements for applicants

Master degree in Chemistry is the basic condition. Afterwards successful passing entrance examination in the chosen branch of the chemistry as well as in the broader base, that is systematic organic chemistry, stereochemistry, physical chemical methods of structure elucidation, organic synthesis (comprising strategy of synthesis), foundations of physical chemistry (thermodynamic, chemical kinetic, electrochemistry and quantum chemistry).
Expected is knowledge of English (reading and translation of unknown chemical text, short conversation on existing research work and intentions for future.

Study requirements and completion of studies

The course of the program follows the individual study plan which is authorized by professional council (commission), according to the student´s proposal submitted through the supervisor mediation. The individual study plan takes precedence over the schedule of the academic year (Study and Examination Regulations of MU, par. 28, item 1). The individual study plan is assembled by the student on the basis of consultations and recommendations of the supervisor and in accordance with general rules of DSP. The supervisor is responsible for the content and extent of theoretical work and for the appropriate scientific level of the dissertation.

Suggested individual study plan – General description

The credit value of the following courses are determined by the regulations listed in the Masaryk University Study and Examination Regulations in force as of 1 September 2006 (http://www.muni.cz/general/legal_standards/study_examination_regulations?lang=en) as well as by the system of variable credit values ratified during the 2007 accreditation process for four year study of DSP in chemistry:

1. Compulsory

  1. Dissertation preparation XD 100: credit, 5 to 30 credits/semester.
  2. Teaching assistance XD 102: course-unit credit, (1 lesson teaching assistance weekly corresponds to 1 credit value).
  3. Lecture in foreign language XD 106: course-unit credit, 2 to 5 credits.
  4. DSP seminar in chemistry XD 107: course-unit credit, 1 credit/semester.
  5. Field seminar CD n01: course-unit credit, 2 credits/semester.
  6. Handling chemical substances C7777: course-unit credit, 0 credits/semester.

2. Compulsory optional

  1. Courses widening theoretical knowledge: implicit number of credits + number of credits upon course completion, for example 1+2, 2+2, 3+2.
  2. Knowledge deepening courses: implicit number of credits + number of credits upon course completion, for example 3+1, 2+1, 1+1.

3. Optional

  1. Literature study XD 101: course-unit credit, 1 to 5 credits.
  2. Internship XD 110: course-unit credit, to 30 credits.
  3. Search Project XD 104: course-unit credit, 1 to 5 credits.
  4. Publication preparation XD 105: course-unit credit, 2-10 credits
  5. Optional subject: implicit number of credits + number of credits upon course completion.

Overview of requirements for the four-year DSP in chemistry:

  1. Acquisition of a total of 240 credits during the whole study.
  2. Acquiring min. 120 credits for the course of Dissertation preparation (XD 100).
  3. Acquiring min. 150 credits in total for the following courses with variable credit value:
    • Dissertation preparation(XD 100).
    • Study of literature (XD 101) .
    • Publication preparation (XD 105).
  4. Acquiring min. 24 credits for the course Teaching assistance (XD 102).
  5. Acquiring min. 24 credits for the compulsory and compulsory optional courses, selected from the Study catalogue of Masaryk University, Faculty of Science, the Study catalogue of Masaryk University or other university:
    • Courses widening theoretical knowledge. Comprises courses defined in the Study and Examination Regulations of Masaryk University as „courses to enhance and amplify knowledge in the field beyond the scope of Master’s degree study“. Course is successfully completed with examination.
    • Knowledge deepening courses. Comprises courses defined in the Study and Examination Regulations of Masaryk University as „courses to amplify special knowledge“. Course is successfully completed with colloquium.
  6. Acquiring registered numbers of credits for the following seminars with compulsory attendance during the actual length of study:
    • Field seminar (CD n01, where n = 1 to k, while k is the number of actually completed semesters of DSP, maximum n = 8. Seminar is not compulsory for combined mode study.
    • DSP seminar in chemistry (XD 107), maximum total of 8 credits required during the actual length of study. This course takes place in the form of a student conference at the end of each semester. Students present two posters during the actual length of study. Moreover, in the semester prior to thesis defence, students deliver results of their dissertation work in the form of a lecture. The seminar XD 107 is compulsory for students in the combined mode of study during the actual length of study (the first 4 years), the lecture prior to thesis defence is compulsory for both modes of study.
  7. Acquiring registered number of credits for courses with variable credit value:
    • Internship (XD 110)
    • Search project (XD 104)
    • Lecture in foreign language (XD 106)
  8. Acquiring number of credits, which is completed with a number of credits acquired in section 1. to 7 in an overall value of 240 credits. The remaining number of credits can be acquired by completing one or more other optional courses:
    • Optional course 1 completed with examination.
    • Optional course 2 completed with colloquium.
    • Optional course 3 completed with course-unit credits.
  9. The successful completion of doctoral studies is conditioned by publishing of previously reviewed findings. The number of publications, which is a prerequisite for the final defence of dissertation, is determined by the following criterion, presuming at the same time that the student is the main author of at least one of the following publications:
    • 3 publications in a periodical with impact factor (IF); the value of the total IF is not specified.
    • 2 publications in a periodical with impact factor; the value of the total IF is minimum 4.

Comments on the study plan:

  1. The course CD n01 is a field seminar of respective doctoral fields of study (DFS) valid for DSP in chemistry. In case of a max. 8 semester study the credit value of uncompleted CD n01 seminars can be compensated by the credit value of a different compulsory, compulsory optional or optional course. Should the absence on seminars be caused due to prolonged illness, the seminar cannot be substituted, credits can be acquired by, say, performing XD 100 duties.
  2. DSP seminar in chemistry XD 107 is a common seminar for students of all DFS, falling under DSP in chemistry. In case of a max. 8 semester study the credit value of uncompleted XD 107 seminars can be compensated by the credit value of a different compulsory, compulsory optional or optional course. Should the absence on seminars be caused due to prolonged illness the seminar cannot be substituted, credits can be acquired by, say, performing XD 100 duties.
  3. For the following optional courses
    • XD 101 Literature study (1 to 5 credits)
    • XD 104 Search project (1 to 5 credits)
    • XD 105 Publication preparation (2-10 credits)
    the number of repeated enrolments is eligible and students can register the credit value after consulting their tutor, based on the scope and difficulty of the corresponding course.
  4. For the compulsory course Lecture in foreign language XD 106 (2 to 5 credits) the credit value is registered after tutor's consideration weighing the importance of the conference and difficulty of the paper.
  5. Internship XD 110 is registered as a course with a variable credit value up to 30 credits per semester. Depending on the duration of the internship the following credit values can be registered:
    • For every 2 weeks started of the Internship 5 credits are added to the total sum of length of 8 weeks.
    • For 9 to 12 weeks of foreign study 25 credits can be registered.
    • For more than 12 weeks of internship 30 credits per semester are registered.
    • The course can be registered repeatedly.
  6. The credit value of optional courses XD 110 Internship can compensate, under specified conditions, the credit value of selected study duties:
    • In case of a max. 12 week Internship (to 25 credits) the corresponding credit value compensates the credits for the course Preparation of dissertation XD 100.
    • If students undertaking an Internship register field seminar (CD n01) and seminar in DSP in chemistry XD 107 in the remaining part of semester, they are entitled to get credit value for the mentioned compulsory courses.
    • Should the internship last longer than 12 weeks (30 credits) the credit value is compensated by the credits acquired for compulsory courses of Preparation of dissertation XD 100, Field seminar (CD n01) and seminar DSP (XD 107).
  7. The credit value of optional courses XD 110 Internship does not recompense the credit value of compulsory courses:
    • Courses widening theoretical knowledge
    • Knowledge deepening courses
  8. The credit value of optional courses XD 110 Internship does not recompense the credit value of compulsory courses:
    • Teaching assistance XD 102
    • Lecture in foreign language XD 106
Example:
Courses ID Completion
of course
Semester TOTAL
credits
1. 2. 3. 4. 5. 6. 7. 8.
Compulsory course cr. cr. cr. cr. cr. cr. cr. cr.
Preparation of dissertation XD 100 credit 8 11 12 12 20 20 16 27 126
Teaching assistance XD 102 credit 6 6 6 6 0 0 0 0 24
Lecture in foreign language XD 106 credit 0 0 0 0 0 0 3 0 3
DSP seminar in chemistry XD 107 credit 1 1 1 1 1 1 1 1 8
Field seminar CD n01 credit 2 2 2 2 2 2 2 2 16
Handling chemical substances
C7777 credit 0 0 0 0 0 0 0 0 0
Compulsory optional courses cr. cr. cr. cr. cr. cr. cr. cr.
Courses widening theoretical knowledge yy nnn* examination 4 3 3 4 0 0 0 0 14
Knowledge deepening courses yy nnn* colloquium 3 2 2 3 0 0 0 0 10
Optional courses cr. cr. cr. cr. cr. cr. cr. cr.
Literature study XD 101 credit 0 2 2 2 2 2 3 0 13
Internship XD 110 credit 0 0 0 0 0 0 0 0 0
Search project XD 104 credit 2 0 0 0 0 0 0 0 2
Publication preparation XD 105 credit 0 0 0 0 5 5 5 0 15
Optional course 1 yy nnn* examination 4 0 0 0 0 0 0 0 4
Optional course 2 yy nnn* colloquium 0 3 0 0 0 0 0 0 3
Optional course 3 yy nnn* credit 0 0 2 0 0 0 0 0 2
Total credits 30 30 30 30 30 30 30 30 240
*course code in conformity with the Study catalogue of Masaryk University, Faculty of Science

Required knowledge for the final state examination

One part of regular finishing of doctoral study is the doctoral state examination, whose essentials are given by the Study and Examination Regulations of MU, par. 31, and when the responsibilities given by par. 28 are fulfilled. At the examination, a complete knowledge level of organic chemistry in broad context is examined, while knowledge of area of dissertation work is discussed in detail. Depending on the character of dissertation, special topics may be tested. The examination emphasizes thorough understanding of interrelations and knowledge gained during studies, requires broad view of the subject, tests ability of independent orientation in the studied area of chemistry, and investigates the student interest in current information in specialist literature. In this examination, candidate specialization and disseration topic is taken into account. If the examination takes place in a different term than the doctoral thesis defense, submitting the dissertation theses is required.

A part of the doctoral state examination is the doctoral thesis defense, where candidate proves his/her abilities to present obtained scientific results and orientation in the area of specialization and broader discipline at the current level of knowledge. The doctoral thesis defense is an oral prezentation in which the candidate explains to the commitee and audience the topics and aims of the work, examined problems, methods used in research and obtained results. The candidate gives answers to the questions and comments raised in reports of the supervisor and reviewers and reacts to questions in public discussion.

General topics for the doctoral state examination
  • Experimental and theoretical methods for study of structure and reactivity of organic compounds
  • Synthesis of organic compounds
  • Practical applications of organic compounds
  • Modern trends in organic chemistry
  • Prerequisites for submitting an application for the doctoral state examination, which must be completed by the end of the 4th year of study:

    1. submission of dissertation topics
    2. demonstration of proficiency in academic and technical English by means of either completing two designated courses, or by gaining credits for a publication submitted to a journal or proceedings and gaining credits for giving a lecture in English at a conference (XD 106)
    3. gaining 12 credits for compulsory optional knowledge broadening and enhancing courses
    4. gaining 24 credits for XD102 Teaching assistance
    5. acquiring 2 credits per semester for Field seminar (CD n01) and 1 credits per semester for XD107

    Requirements for Ph.D. thesis

    One of the first requirements for doctoral thesis (DT) is a paper containing the overview of up-to-date literary knowledge in given scientific field, important impulses for the work itself, experimental part describing experiments in detail and results which are described, documented and discussed in the context of contemporary science knowledge. There shall be also the final summary of results, English abstract, literature, and the list of abbreviations used in the thesis. The results must be published, or at least sent and accepted for publication, in a renowned scientific journal. The number of publications implicating the admission of the doctoral thesis for the doctoral thesis defense follows these criteria:

    1. the student is the first author of at least one publication
    2. the student participated in 3 publications, published in a journal with impact factor (IF), whereas the value of IF sum is not set down, or 2 publications in a journal with IF where the value of IF sum is minimally 4.

    An alternative of DT can be a paper containing the introduction and annotation for the set of published papers, which form a part of submitted DT as an appendix. In any case, DT is supplemented with the annotation which summarizes the themes and results of the work, list of publications and a resume in Czech, English, eventually in another language. DT can be submitted in Czech (Slovak) or English language.

    Individual study plan

    See above.

    List of members of doctoral committee

    List of supervisors

    Commission for state doctoral exams and defenses

    List of current doctoral topics

    Department pages


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