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Doctoral Thesis
Full name
André Tsutomu Ota
Knowledge Area
Date of Defense
São Paulo, 1997
Ito, Amando Siuiti (President)
Canuto, Sylvio Roberto Accioly
Custódio, Rogério
Fornés, José Antonio
Title in Portuguese
Métodos Clássicos e Quânticos no Estudo de Geometrias de Moléculas Biológicas
Keywords in Portuguese
Estrutura eletrônica
Matéria condensada
Abstract in Portuguese
Duas são as principais características deste trabalho. A primeira é a introdução de um método para o cálculo da energia livre absoluta no programa de dinâmica molecular clássica Thor. Este método é geral e pode ser usado no vácuo ou em solução,sob quaisquer condições de pressão e/ou temperatura. Trata-se de um caso especial de integração termodinâmica para cálculos de energia livre, e compara um estado termodinâmico com um sistema modelo para o qual a energia livre é conhecidaanaliticamente. O estado modelo é conhecido no início, e após uma integração termodinâmica até o estado real final, a energia livre absoluta é calculada como uma soma desta integração mais a energia livre do estado modelo. A energia livredepende do modelo a partir do qual a função de partição é derivada analiticamente. O modelo definido é o sólido de Einstein. Os átomos deste sólido ideal não interagem entre si (como um gás ideal) e estão ligados harmonicamente às suas posiçõesideais. O acoplamento entre os dois estados é feito.
Title in English
Quantum Classical Methods Study Biological Molecules Geometries
Keywords in English
Condensed matter
Electronic structure
Abstract in English
This work has two main features. First it introduces a method for absolute free energy calculations in the classical molecular dynamics Thor program. This method is general and could be used in vacuum or in solution, under any conditions of pressure and/or temperature. It is a special case of thermodynamic integration for free energy calculations, and compares one thermodynamic state with a model system for which the free energy is analytically known. The initial model state is known and after an integration to a final real state, the absolute free energy is calculated as a sum of that integration plus the free energy of model state. The absolute free energy depends on the model from which the partition function is analytically derived. The model that we have defined is the Einstein solid. The atoms of this ideal system do not interact (like an ideal gas) and are linked harmonically to their ideal position. The coupling between the two states is done directly through the energy. We calibrated and tested this method of free energy calculations on the fentanyl molecule and our results were comparable to those presented by the Discover package for the same molecule. We applied this method to the aminoacid tryptophan, that is a fluorescent probe for the structure of peptides and proteins. The absolute free energy is proposed as the relevant parameter that determines the rotameric conformational states of tryptophan molecule. The second feature is the use of the semi empirical Geomop quantum program. The calculations made with this program gave us the electronic structure and the geometry's of Abz (anthranilic acid, an extrinsic probe for the study of peptides) and its compounds with alanine, phenilalanine and proline. The resulting spectra are comparable with those obtained experimentally. Another application of the program is the analysis of the paths of the inter-conversion of the thiocarbazone molecule in two isomeric forms, showing another possibility of use of semi empirical calculations.
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