Showing papers by "Pavel Hobza published in 2000"

The Effect of Metal Binding to the N7 Site of Purine Nucleotides on Their Structure, Energy, and Involvement in Base Pairing

Abstract: Direct binding of hydrated zinc and magnesium group divalent cations to the N7 position of purine nucleotides has been investigated by ab initio quantum chemical calculations. The sugar−phosphate b...

C−H···O Contacts in the Adenine···Uracil Watson−Crick and Uracil···Uracil Nucleic Acid Base Pairs: Nonempirical ab Initio Study with Inclusion of Electron Correlation Effects

Abstract: Structures and stabilities of H-bonded adenine···uracil Watson−Crick (AU WC) and two uracil···uracil nucleic acid base pairs possessing C−H···O contacts (UU7, UU−C) were determined using gradient optimization with inclusion of electron correlation via the second-order Moller−Plesset (MP2) perturbational method with a 6-31G** basis set of atomic orbitals. In the AU WC pair, closest contacts occur between the N6(A) and O4(U), N1(A) and N3(U), and C2(A) and O2(U) atoms: 2.969, 2.836, and 3.568 A, respectively. For the UU7 pair the closest contact corresponds to O4···N1 and C5···O2 pairs with distances of 2.860 and 3.257 A, respectively, while in UU−C pair the closest contact was found for O4···N3 and C5···O4 heteroatoms with distances of 2.913 and 3.236 A, respectively. The nature of all intermolecular contacts in the sense of a conventional H-bonding or improper, blue-shifting H-bonding was determined on the basis of harmonic vibrational analysis, atom-in-molecules (AIM) Bader analysis of electron density,...

Interaction Energies of Hydrogen-Bonded Formamide Dimer, Formamidine Dimer, and Selected DNA Base Pairs Obtained with Large Basis Sets of Atomic Orbitals

Abstract: Interaction energies of selected H-bonded nucleic acids base pairs, formamide dimer, and formamidine dimer have been evaluated using the second-order Moller−Plesset method (MP2) with extended basis...

Global Minimum of the Adenine···Thymine Base Pair Corresponds Neither to Watson−Crick Nor to Hoogsteen Structures. Molecular Dynamic/Quenching/AMBER and ab Initio beyond Hartree−Fock Studies

Abstract: Computational analysis of complete gas-phase potential energy and free energy surfaces of the adenine···thymine base pair has been carried out. The study utilizes a combination of molecular dynamics simulations performed with Cornell et al. empirical force field and quenching technique. Twenty seven energy minima have been located at the potential energy surface of the adenine···thymine base pair: nine of them are H-bonded structures, eight are T-shaped dimers, and the remaining nine correspond to various stacked arrangements. H-bonded structures are the most stable while stacked and T-shaped structures are by more than 4 kcal/mol less stable than the global minimum. The global minimum and the first two local minima utilize N9−H and N3 groups of adenine for the binding, i.e., the amino group N6, and ring N1 and N7 adenine positions are not involved in the base pairing. The most stable H-bonding patterns cannot occur in nucleic acids since the N9 position is blocked by the attached sugar ring. Hoogsteen a...

Anharmonic treatment of the lowest-energy conformers of glycine: A theoretical study

Abstract: The structure and energetics of the four lowest-energy conformers of glycine were determined at the MP2/aug-cc-pVDZ level of theory. The optimized structural parameters for these conformers agree with previous theoretical results obtained by highly correlated ab initio methods and with available experimental data. The only structure with planar heavy atom arrangement is conformer I (global minimum), the other conformers have nonplanar heavy atom arrangements. In accordance with temperature dependence studies of the vibrational spectra in various rare gas environments, conformers III and IV have small interconversion barriers to conformer I (940 and 740 cm−1). Our calculations have shown that full-dimensional anharmonic treatment is required for an accurate description of the vibrational modes in various glycine conformers. The most pronounced effect has been observed for conformer II with the intramolecular O–H⋅⋅⋅N bond. The theoretical results obtained at the MP2/aug-cc-pVDZ level reproduce quantitatively the argon matrix experiments. The calculation uses the quartic force field approximation in the framework of second-order perturbation theory. An estimate of the higher-order correction is also given.

Structural nonrigidity of nucleic acid bases. Post–Hartree–Fock ab initio study

Abstract: Pyrimidine ring deformation modes in uracil, thymine, cytosine, isocytosine, guanine, and adenine were analyzed using normal vibrations calculated at the MP2/6-31G(d,p) levels of theory. We have introduced the theoretical approach based on the combined analysis of the shape of the relaxed potential surface, normal out-of-plane frequencies, and the amplitudes of the corresponding vibrations. We have shown that the absolute value of the frequency is not the unique characteristic to determine the lowest modes of the molecular deformation. We have revealed the applications involved in the analysis of the amplitudes to locate the internal coordinates (torsional angels), which correspond to the set of lowest energy deformations. It was demonstrated that the pyrimidine ring possesses high structural nonrigidity. Two very soft modes of ring deformation were found for every molecule except adenine. An estimation of population of excited vibrational levels for the lowest out-of-plane ring vibrations reveals that in every moment of time about 50% of all considered molecules possess a nonplanar configuration in the pyrimidine ring with a relevant torsion angle up to 25° © 2000 John Wiley & Sons, Inc. Int J Quant Chem 80: 1116–1124, 2000

Already two water molecules change planar H-bonded structures of the adenine···thymine base pair to the stacked ones: a molecular dynamics simulations study

Abstract: The dynamical structure of the adenine···thymine nucleic acid base pair exposed to a small number of water molecules (from 1 to 216) was determined using molecular dynamics simulations with Cornell et al. force field (W. D. Cornell, P. Cieplak, C. I. Bayly, I. R.Gould, K. M. Merz, D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. E. Caldwell and P. Kollman, J. Am. Chem. Soc., 1995, 117, 5179). The gradual increase of hydration number results in a transition from planar base pair structures to nonplanar ones, and already for two water molecules the population of stacked structures is higher than that of planar structures.

Aromatic Base Stacking in DNA: From ab initio Calculations to Molecular Dynamics Simulations

Abstract: Aromatic stacking of nucleic acid bases is one of the key players in determining the structure and dynamics of nucleic acids. The arrangement of nucleic acid bases with extensive overlap of their aromatic rings gave rise to numerous often contradictory suggestions about the physical origins of stacking and the possible role of delocalized electrons in stacked aromatic π systems, leading to some confusion about the issue. The recent advance of computer hardware and software finally allowed the application of state of the art quantum-mechanical approaches with inclusion of electron correlation effects to study aromatic base stacking, now providing an ultimitate qualitative description of the phenomenon. Base stacking is determined by an interplay of the three most commonly encountered molecular interactions: dispersion attraction, electrostatic interaction, and short-range repulsion. Unusual (aromatic- stacking specific) energy contributions were in fact not evidenced and are not necessary to descr...

Methylated uracil dimers: potential energy and free energy surfaces

Abstract: Theoretical analysis of the formation of 1-methyluracil, 3-methyluracil and 1,3-dimethyluracil dimers was performed. Stabilization energies of these dimers were evaluated with the Cornell et al. force field (J. Am. Chem. Soc., 1995, 117, 5179). In total 16, 13 and 15 energy minima were studied for the three dimers. Thermodynamic data were obtained with the rigid rotor–harmonic oscillator–ideal gas approximation. Furthermore, populations of various structures were determined by molecular dynamic simulations in the NVE microcanonical ensemble and numerical evaluation of the configuration integrals in the NVT canonical ensemble. The potential energy surfaces (PESs) and the free energy surfaces (FESs) of these dimers differ. The largest difference was found for the 1-methyluracil dimer where the global and first local minima on the PES and FES do not coincide.

Structure, energetics, vibrational frequencies and charge transfer of base pairs, nucleoside pairs, nucleotide pairs and B-DNA pairs of trinucleotides: ab initio HF/MINI-1 and empirical force field study.

Abstract: Geometries, interaction energies and vibrational frequencies of base pairs, nucleoside pairs and nucleotide pairs were studied by ab initio Hartree-Fock (HF) method using MINI-1 basis set and empirical Cornell et al. force field (AMBER 4.1). A good agreement was found between HF/MINI-1 and AMBER results. In addition, both methods provide reasonable agreement with available high-level ab initio data. Finally, AMBER potential was used to determine the structure, energetics and vibrational frequencies of B-DNA pairs of trinucleotides. Stabilization energies of clusters are lowered when passing from base pairs to nucleoside pairs, nucleotide pairs and to pairs of trinucleotides. The lowest vibrations of base pairs and nucleoside pairs correspond to intermolecular motions of bases, specifically to buckle and propeller motions. In the case of pairs of larger subunits the lowest vibrations are of intramolecular nature (rotation around glycosidic bond, sugar and phosphate vibration). The spectra of these...