International Journal of Molecular Sciences

Editorial

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Open AccessEditorial

Preface

by Jaroslav Burda, Jerzy Leszczynski and W. Andrzej Sokalski

Int. J. Mol. Sci. 2004, 5(4), 129; https://doi.org/10.3390/i5040129 - 28 May 2004

Cited by 8 | Viewed by 5471

Abstract

This special Issue of the International Journal of Molecular Sciences contains selected papers from the US-Czech-Polish workshop on Modeling Interaction in Biomolecules that took place between 15-th and 20-th September, 2003 in Nové Hrady, Czech Republic.[...] Full article

(This article belongs to the Special Issue Proceedings of the Workshop on Modeling Interaction in Biomolecules)

Research

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Open AccessArticle

Interactions between Physics and Biodisciplines within the Framework of Molecular Sciences

by Rudolf Zahradník

Int. J. Mol. Sci. 2004, 5(4), 214-223; https://doi.org/10.3390/i5040214 - 31 May 2004

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Abstract

In order to be able to study interactions within, between, and among biomolecules, it is highly desirable to use tools of experimental and theoretical physics, or preferably a combination thereof. Very brief comments are presented which concern biochemical reactivity, enzymatic catalysis, origin of [...] Read more.

In order to be able to study interactions within, between, and among biomolecules, it is highly desirable to use tools of experimental and theoretical physics, or preferably a combination thereof. Very brief comments are presented which concern biochemical reactivity, enzymatic catalysis, origin of life, experimental tools for structure elucidation and quantum chemistry methods. Additional remarks are related to ultrafast processes, experiments with individual molecules, and to symmetry considerations. Full article

(This article belongs to the Special Issue Proceedings of the Workshop on Modeling Interaction in Biomolecules)

751 KiB

Open AccessArticle

Estimation of Electron Spectra Transitions of Free-Based Porphin and Mg-Porphin Using Various Quantum Chemical Approaches

by Josef Šeda, Jaroslav V. Burda, Veronika Brázdová and Vojtěch Kapsa

Int. J. Mol. Sci. 2004, 5(4), 196-213; https://doi.org/10.3390/i5040196 - 31 May 2004

Cited by 12 | Viewed by 7743

Abstract

For optimized molecules of free-base porphin and magnesium-porphin (at Hartree-Fock level and 6-31G* basis set) excitation spectra were determined using several ab initio methods: CIS, RPA, CASSCF, and TDDFT. Obtained values were compared with semiempirical ZINDO method, other calculations found recently in literature [...] Read more.

For optimized molecules of free-base porphin and magnesium-porphin (at Hartree-Fock level and 6-31G* basis set) excitation spectra were determined using several ab initio methods: CIS, RPA, CASSCF, and TDDFT. Obtained values were compared with semiempirical ZINDO method, other calculations found recently in literature and experimental data. It was demonstrated that for qualitatively correct spectra description the AO basis must include both the polarization and diffuse functions. The later play an important role in formation of Rydberg MOs. Estimated energies of the spectra transitions using the CIS method remain relatively far from the measured values. RPA method can be already considered as a quantitatively accurate method when sufficiently large basis set is used. For CASSCF approach, it was shown that even the lowest energy transitions are insufficiently described in CAS formalism and much larger active space or inclusion of more inactive orbitals in correlation treatment would be necessary for obtaining sufficient accuracy. It can be stated that without sufficiently large correlation contributions, the determined spectra are not able to reach quantitative agreement with experimental data. From the methods treated in this study, only TDDFT can be considered as a useful tool for spectra prediction, at least for calculations of lower excited states. It is relatively fast and feasible for calculation of middle-size molecules. ZINDO approximation is also relatively successful for such large systems. Acceptable predictions of experimentally observed energy transitions in the range of Q and B bands were obtained. Until higher (UV) part of spectra is examined where the excitations to Rydberg orbital will happen, it can be considered as a good candidate for electron spectra calculations. Full article

(This article belongs to the Special Issue Proceedings of the Workshop on Modeling Interaction in Biomolecules)

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634 KiB

Open AccessArticle

Visualization of the Differential Transition State Stabilization within the Active Site Environment

by Pawel Kedzierski, Pawel Wielgus, Adrian Sikora, W. Andrzej Sokalski and Jerzy Leszczynski

Int. J. Mol. Sci. 2004, 5(4), 186-195; https://doi.org/10.3390/i5040186 - 31 May 2004

Cited by 5 | Viewed by 9911

Abstract

Increasing interest in the enzymatic reaction mechanisms and in the nature of catalytic effects in enzymes causes the need of appropriate visualization methods. A new interactive method to investigate catalytic effects using differential transition state stabilization approach (DTSS) [1, 2] is presented. The [...] Read more.

Increasing interest in the enzymatic reaction mechanisms and in the nature of catalytic effects in enzymes causes the need of appropriate visualization methods. A new interactive method to investigate catalytic effects using differential transition state stabilization approach (DTSS) [1, 2] is presented. The catalytic properties of the active site of cytidine deaminase (E.C. 3.5.4.5) is visualized in the form of differential electrostatic properties. The visualization was implemented using scripting interface of VMD [3]. Cumulative Atomic Multipole Moments (CAMM) [4,5,6] were utilized for efficient yet accurate evaluation of the electrostatic properties. The implementation is efficient enough for interactive presentation of catalytic effects in the active site of the enzyme due to transition state or substrate movement. This system of visualization of DTTS approach can be potentially used to validate hypotheses regarding the catalytic mechanism or to study binding properties of transition state analogues. Full article

(This article belongs to the Special Issue Proceedings of the Workshop on Modeling Interaction in Biomolecules)

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339 KiB

Open AccessArticle

Intramolecular C−H···π Interactions in Metal-Porphyrin Complexes

by Goran A. Bogdanović, Vesna Medaković, Miloš K. Milčić and Snežana D. Zarić

Int. J. Mol. Sci. 2004, 5(4), 174-185; https://doi.org/10.3390/i5040174 - 1 Apr 2004

Cited by 25 | Viewed by 8221

Abstract

Cambridge Structural Database (CSD) was screened in order to find intramolecular C−H···π interactions with a chelate ring of coordinated porphyrin. It was found 154 crystal structures with 244 intramolecular C−H···π interactions in transition metal complexes with derivatives of porphyrin. Comparison of interacting distances [...] Read more.

Cambridge Structural Database (CSD) was screened in order to find intramolecular C−H···π interactions with a chelate ring of coordinated porphyrin. It was found 154 crystal structures with 244 intramolecular C−H···π interactions in transition metal complexes with derivatives of porphyrin. Comparison of interacting distances indicates that interactions of hydrogen atoms in positions 2 and 6 of axially coordinated pyridine are more favorable with ruffled than with planar porphyrin. Full article

(This article belongs to the Special Issue Proceedings of the Workshop on Modeling Interaction in Biomolecules)

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357 KiB

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Complexity and Convergence of Electrostatic and van der Waals Energies within PME and Cutoff Methods

by Radka Svobodová Vařeková, Jaroslav Koča and Chang-Guo Zhang

Int. J. Mol. Sci. 2004, 5(4), 154-173; https://doi.org/10.3390/i5040154 - 1 Apr 2004

Cited by 7 | Viewed by 9784

Abstract

In this paper, we report a detailed comparison between the popularly used cutoff and Particle Mesh Ewald (PME) methods in terms of the time complexity and the energy convergence of the long-range electrostatic and van der Waals interaction calculations. For the comparison, we [...] Read more.

In this paper, we report a detailed comparison between the popularly used cutoff and Particle Mesh Ewald (PME) methods in terms of the time complexity and the energy convergence of the long-range electrostatic and van der Waals interaction calculations. For the comparison, we performed various calculations on various representative biological molecules, including seven peptides and proteins, eleven oligonucleotides, and three conformations of a nucleotide-sugar. The results provide useful insights into the appropriate choice of the methods (i.e. the cutoff or PME) and that of the cutoff values for the calculations on different kinds of molecules. It has also been demonstrated that for some cases using different cutoff values for calculating the electrostatic and van der Waals interaction energies will be computationally more efficient. Full article

(This article belongs to the Special Issue Proceedings of the Workshop on Modeling Interaction in Biomolecules)

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924 KiB

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The Mechanism of Phosphoryl Transfer Reaction and the Role of Active Site Residues on the Basis of Ribokinase-Like Kinases

by Edyta Dyguda, Borys Szefczyk and W. Andrzej Sokalski

Int. J. Mol. Sci. 2004, 5(4), 141-153; https://doi.org/10.3390/i5040141 - 1 Apr 2004

Cited by 13 | Viewed by 9463

Abstract

The role of ribokinase-like carbohydrate kinases consists in ATP dependent phosphorylation of small molecules containing hydroxymethyl group. Although they differ substantially in structural terms and exhibit a broad substrate specificity, some family-wide conserved features can be distinguished suggesting the common mode of action. [...] Read more.

The role of ribokinase-like carbohydrate kinases consists in ATP dependent phosphorylation of small molecules containing hydroxymethyl group. Although they differ substantially in structural terms and exhibit a broad substrate specificity, some family-wide conserved features can be distinguished suggesting the common mode of action. 4-methyl-5-β-hydroxyethylthiazole kinase (Thz kinase) was chosen as a representative model and the mechanism proposed in X-ray crystal structure paper provided the basis for calculations. In particular, the possible role of several active site residues (Arg121 and Cys198 among others) and of the two magnesium ions was examined. Static and dynamic catalytic fields for the reaction were generated revealing the most favourable environment for the preferential transition state stabilization. An attempt to model the phosphoryl transfer reaction as well as to investigate the influence of the cysteine residue on the reaction course at the semiempirical PM3 level of theory was undertaken. Full article

(This article belongs to the Special Issue Proceedings of the Workshop on Modeling Interaction in Biomolecules)

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213 KiB

Open AccessArticle

Electronic Density Approaches to the Energetics of Noncovalent Interactions

by Yuguang Ma and Peter Politzer

Int. J. Mol. Sci. 2004, 5(4), 130-140; https://doi.org/10.3390/i5040130 - 1 Apr 2004

Cited by 5 | Viewed by 8050

Abstract

We present an overview of procedures that have been developed to compute several energetic quantities associated with noncovalent interactions. These formulations involve numerical integration over appropriate electronic densities. Our focus is upon the electrostatic interaction between two unperturbed molecules, the effect of the [...] Read more.

We present an overview of procedures that have been developed to compute several energetic quantities associated with noncovalent interactions. These formulations involve numerical integration over appropriate electronic densities. Our focus is upon the electrostatic interaction between two unperturbed molecules, the effect of the polarization of each charge distribution by the other, and the total energy of interaction. The expression for the latter is based upon the Hellmann-Feynman theorem. Applications to a number of systems are discussed; among them are dimers of uracil and interacting pairs of molecules in the crystal lattice of the energetic compound RDX. Full article

(This article belongs to the Special Issue Proceedings of the Workshop on Modeling Interaction in Biomolecules)

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