http://www.mdpi.com/journal/ijms/special_issues/proceedings-workshop-on-modeling-biomolecules/ http://www.mdpi.com/1422-0067/5/4/214/ 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. http://www.mdpi.com/1422-0067/5/4/214/ Mon, 31 May 2004 00:00:00 CEST International Journal of Molecular Sciences 2004-05-31 5 4 Article 214 223 1422-0067 Interactions between Physics and Biodisciplines within the Framework of Molecular Sciences 2004-05-31 doi: 10.3390/i5040214 Rudolf Zahradník http://www.mdpi.com/1422-0067/5/4/196/ 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. http://www.mdpi.com/1422-0067/5/4/196/ Mon, 31 May 2004 00:00:00 CEST International Journal of Molecular Sciences 2004-05-31 5 4 Article 196 213 1422-0067 Estimation of Electron Spectra Transitions of Free-Based Porphin and Mg-Porphin Using Various Quantum Chemical Approaches 2004-05-31 doi: 10.3390/i5040196 Josef Šeda Jaroslav V. Burda Veronika Brázdová Vojtěch Kapsa http://www.mdpi.com/1422-0067/5/4/186/ 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. http://www.mdpi.com/1422-0067/5/4/186/ Mon, 31 May 2004 00:00:00 CEST International Journal of Molecular Sciences 2004-05-31 5 4 Article 186 195 1422-0067 Visualization of the Differential Transition State Stabilization within the Active Site Environment 2004-05-31 doi: 10.3390/i5040186 Pawel Kedzierski Pawel Wielgus Adrian Sikora W. Andrzej Sokalski Jerzy Leszczynski http://www.mdpi.com/1422-0067/5/4/129/ n/a http://www.mdpi.com/1422-0067/5/4/129/ Fri, 28 May 2004 00:00:00 CEST International Journal of Molecular Sciences 2004-05-28 5 4 Editorial 129 129 1422-0067 Preface 2004-05-28 doi: 10.3390/i5040129 Jaroslav Burda Jerzy Leszczynski W. Andrzej Sokalski http://www.mdpi.com/1422-0067/5/4/174/ 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. http://www.mdpi.com/1422-0067/5/4/174/ Thu, 01 Apr 2004 00:00:00 CEST International Journal of Molecular Sciences 2004-04-01 5 4 Article 174 185 1422-0067 Intramolecular C−H···π Interactions in Metal-Porphyrin Complexes 2004-04-01 doi: 10.3390/i5040174 Goran A. Bogdanović Vesna Medaković Miloš K. Milčić Snežana D. Zarić http://www.mdpi.com/1422-0067/5/4/154/ 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. http://www.mdpi.com/1422-0067/5/4/154/ Thu, 01 Apr 2004 00:00:00 CEST International Journal of Molecular Sciences 2004-04-01 5 4 Article 154 173 1422-0067 Complexity and Convergence of Electrostatic and van der Waals Energies within PME and Cutoff Methods 2004-04-01 doi: 10.3390/i5040154 Radka Svobodová Vařeková Jaroslav Koča Chang-Guo Zhang http://www.mdpi.com/1422-0067/5/4/141/ 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. http://www.mdpi.com/1422-0067/5/4/141/ Thu, 01 Apr 2004 00:00:00 CEST International Journal of Molecular Sciences 2004-04-01 5 4 Article 141 153 1422-0067 The Mechanism of Phosphoryl Transfer Reaction and the Role of Active Site Residues on the Basis of Ribokinase-Like Kinases 2004-04-01 doi: 10.3390/i5040141 Edyta Dyguda Borys Szefczyk W. Andrzej Sokalski http://www.mdpi.com/1422-0067/5/4/130/ 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. http://www.mdpi.com/1422-0067/5/4/130/ Thu, 01 Apr 2004 00:00:00 CEST International Journal of Molecular Sciences 2004-04-01 5 4 Article 130 140 1422-0067 Electronic Density Approaches to the Energetics of Noncovalent Interactions 2004-04-01 doi: 10.3390/i5040130 Yuguang Ma Peter Politzer