SVIBOR - Project code: 1-07-159

MINISTRY OF SCIENCE AND TECHNOLOGY

Strossmayerov trg 4, HR - 10000 ZAGREB
tel.: +385 1 459 44 44, fax: +385 1 459 44 69
E-mail: ured@znanost.hr

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Project code: 1-07-159


Development and applications of models in chemistry


Main researcher: TRINAJSTIĆ, NENAD (50450)


Assistants
Type of research: basic
Duration from: 01/01/91. to 12/31/95.
Papers on project (total): 286
Papers on project quoted in Current Contents: 162
Institution name: Institut "Ruđer Bošković", Zagreb (98)
Department/Institute: Department of Chemistry
Address: Bijenička cesta 54
City: 10000 - Zagreb, Croatia
Communication
Fax: 385 (0)1 272-648
Phone: 385 (0)1 424-689
Phone: 385 (0)1 4561-111/1635
Fax: 385 (0)1 425-497
E-mail: trina@olimp.irb.hr
Summary: 3-D molecular descriptors are developed and their applications in QSAR models are tested. QSAR models based on the connectivity index for calculation of the partition coefficients of commercial chemicals is also developed and tested. New molecular descriptors, based on topological, geometric and electronic properties, were generated and evaluated in order to be used in QSAR modelling. Physico-chemical processes on microscopic scale are studied by the methods of discrete and computational mathematics. The enumeration problems for acyclic walks and conjugated circuits in molecular graphs, as well as dimer covering of lattices and large graphs have also been studied. The range of the application of the conjugated-circuit model as well as of the bond orbital resonance theory is extended to large molecular systems. The structures and properties of carbon cages, named fullerenes, are studied. A particular attention is paid to the generation and counting of isomers, their interconversions, their symmetry properties, and their two- and three-dimensional geometric presentation. Inelastic collisions of atoms and molecules in the framework of the hard core model are investigated. The same model is used to study the process of molecular dissociation during the collision with an atom. The properties of resonance in the adiabatic collisions are studied in the presence of the external electrostatic field. An automated iterative method is being developed for predicting secondary structure of membrane proteins.

Keywords: Theoretical models, discrete mathematics in chemistry, molecular descriptors, QSAR models, secondary structure of membrane proteins, modelling of properties and stabilities of conjugated systems and surfaces, carbon clusters - fullerenes, low rank perturbation, conjugated-circuits model, inelastic scattering, hard-core model, collision induced dissociation, resonances, nonadiabatic collisions, environmental chemistry.

Research goals: The general aim of this project is to develop theoretical modelsas well as their application on a range of current problems in chemistry. More specifically, the main aims of this project are to develop mathematical, computational, quantum-chemical and dynamical models which will have application on important subjects of current chemistry and chemical physics. (a) Mathematical models. Quantitative models, based on topological indices and similar structural features, have been developed for the accurate calculation of 1-octanol/water partition coefficiens of polycyclic aromatic hyrocarbons (PAHs), their heteroanalogues with oxygen, nitrogen, and sulphur, their alkyl-, chloro-, amino-, and hydroxyl- derivatives, as well as for chlorinated benzenes and chlorinated biphenyls (PCBs). Our studies have also disclosed the limitations of earlier models as well as the need to experimentally recheck some reported 1-octanol/water partition coefficients. Various statistical methods (principal component analysis, cluster analysis, single and multiple linear regression) were applied to study a quantitative relationship between structural and quantum-chemical features with soil sorption characteristics of agricultural chemicals. A high quality QSAR model has been developed for estimating the soil sorption coefficients of organophosphate pesticides. In addition, the preliminary models were developed for 4 other important classes of agricultural chemicals: triazines, carbamates, acetanilides, and ureas. Our modelling procedure has shown that it is important to apply the combination of structural and electronic parameters to quantitatively model soil sorption characteristics of studied chemicals. Our study has also resulted in new information on mechanism of soil sorption process for organic chemicals. By the application of statistical methods described above, a high quality model was obtained for describing and estimating herbicidal selectivity of phenoxyacrilates in a rice/grass system. This is a very important result since there are only a few models reported in the literature which successfully describe selectivity of a wellknown commercial herbicides. Finally, the application of various mathematical models enabled us to rationalize a series of our own as well as literature results from homogeneous and heterogeneous equilibria in aqueous solutions of different ionic strength (low concentration aqueous solution of NaCl, natural waters and wastewaters, human serum). The majority of results described in this section are related to environmental pollution problems. (b) Computational models. Structural rules have been developed for a fast and slow biodegradation of organic pollutants in the environment by the application of an inductive machine learning method. Possibility of extending the transfer matrix method to multidimensional systems was examined. The first results indicate existence of a formalism for building up the transfer matrix for a monomer of any size in other dimensions. Besides to the dimer covering problem, transfer matrix has been applied to a construction of the conjugated circuits polynomial of benzenoid polymers. We have developed an algorithm for generation of fullerene isomers and analyzed the possibility of their interconversion by the Stone-Wales transformation. Symmetrical properties of fullerene isomers were investigated, and the methods for geometrical presentation of fullerene structures in 2 and 3 dimensions were studied separately. (c) Quantum-chemical models. The conjugated circuit model (the semi-empirical VB model) has been developed for prediction of structures, aromaticy and reactivity of heterocyclic systems (containing oxygen, nitrogen and sulphur) and big hydrocarbon clusters, which occur as centers of nucleation in formation of carbon soot and which can be of importance in astrochemistry. (d) Dynamical models. The goal is to find simple rules which will enable inversion of cross sections as well as the contribution towards kinetics of rarefied gases, e.g. the molecular clouds. Towards this aim a model was developed which treats molecules as having hard core, and it was used to analyze cross sections in atom and polyatomic molecule collisions. Classical theory of scattering with wave packets was developed, and applied to the analysis of dynamics of particles in strong electromagnetic fields.

COOPERATION - PROJECTS


  1. Name of project: F-918 EXPOSURE ASSESSMENT METHODS FOR GROUNDWATER QUALITY
    Name of institution: NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES
    City: NC 27709 - RESEARCH TRIANGLE PARK, U.S.A.

  2. Name of project: F-986 Collisions of Metal Clusters and Atoms
    Name of institution: University of Florida
    City: FL 32611 - Gainesville, Florida, U.S.A.

  3. Name of project: JF-001 Mathematical and computational studies in quantum chemistry
    Name of institution: Texas A&M University at Galveston, Galveston, Texas, USA
    City: Galveston, Texas, USA

COOPERATION - INSTITUTIONS


  1. Name of institution: Fakultet poljoprivrednih znanosti
    Type of institution: University/Faculty
    City: 10000 - Zagreb, Croatia

  2. Name of institution: National Institutes of Health
    Type of institution: State institute
    Type of cooperation: Occasional exchange of information
    City: MD 20892 - BETHESDA, U.S.A.

  3. Name of institution: Univeristy of Utrecht
    Type of institution: Economical/Production
    City: NL-3508 TD - UTRECHT, NIZOZEMSKA

  4. Name of institution: Kernforschungszentrum Karlsruhe
    Type of institution: University/Faculty
    City: D-76021 - KARLSRUHE, Njemačka

  5. Name of institution: LPC, d.o.o.
    Type of institution: Non-profit
    City: 10000 - Zagreb, Croatia

  6. Name of institution: National Institute of Environmental Health Sciences
    Type of institution: University/Faculty
    City: NC 27709 - RESEARCH TRIANGLE PARK, U.S.A.

  7. Name of institution: MacAda
    Type of institution: Non-profit
    City: 61000 - Ljubljana, Slovenija

  8. Name of institution: CEC-Joint Research Center
    Type of institution: State administration
    City: I-21020 - Ispra (VA), Italija

  9. Name of institution: Masaryk University
    Type of institution: Economical/Production
    City: 602 00 - Brno, Czech Republic

  10. Name of institution: National Institute of Public Health and Environmental Protection
    Type of institution: International organization
    City: NL-3720 BA - Bilthoven, Nizozemska

  11. Name of institution: University of Umea
    Type of institution: Economical/Production
    City: S-90187 - Umea, Švedska

  12. Name of institution: CTIS
    Type of institution: Non-profit
    City: F-69003 - Lyon, Francuska

  13. Name of institution: GSF-Forschungszentrum fur Umwelt und Gesundheit
    Type of institution: University/Faculty
    City: D-8042 - Neuherberg, Njemačka

  14. Name of institution: The Volcani Center, Agricultural Research Organization, Institute of Soils and Water
    Type of institution: University/Faculty
    City: 50250 - Bet-Dagan, Izrael

  15. Name of institution: Heinrich Heine University, Duesseldorf, Germany
    Type of institution: Economical/Production
    City: Duesseldorf, Germany

  16. Name of institution: Drake University, USA
    Type of institution: University/Faculty
    Type of cooperation: Systematic exchange of information
    City: Des Moines, Iowa, USA

  17. Name of institution: University of Bucharest
    Type of institution: University/Faculty
    Type of cooperation: Occasional exchange of information
    City: Bucharest, Romania

  18. Name of institution: University of Reading
    Type of institution: Economical/Production
    City: Reading, England, UK

  19. Name of institution: Institut Jožef Stefan
    Type of institution: State institute
    Type of cooperation: Systematic exchange of information
    City: 61000 - Ljubljana, Slovenija

  20. Name of institution: Texas A&M University at Galveston
    Type of institution: University/Faculty
    Type of cooperation: Systematic exchange of information
    City: Galveston, Texas, USA

  21. Name of institution: Farmaceutsko-biokemijski fakultet
    Type of institution: Economical/Production
    City: 10000 - Zagreb, Croatia

  22. Name of institution: Argonne National Laboratory
    Type of institution: University/Faculty
    City: IL 60439 - Argonne, U.S.A.

  23. Name of institution: University of Parma, Department of Informatics
    Type of institution: Economical/Production
    Type of cooperation: Occasional exchange of information
    City: Parma, Italija

  24. Name of institution: State University of New York at Stony Brook
    Type of institution: University/Faculty
    Type of cooperation: Occasional exchange of information
    City: Stony Brook, New York, U.S.A.

  25. Name of institution: University of Florida
    Type of institution: University/Faculty
    Type of cooperation: Occasional exchange of information
    City: FL 32611 - Gainesville, Florida, U.S.A.

  26. Name of institution: U.S. Geological Surwy
    Type of institution: University/Faculty
    City: Menlo Park, California, U.S.A.

  27. Name of institution: Kernforschungsanlage Juelich
    Type of institution: University/Faculty
    City: Juelich, Njemačka
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