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P Hobza

Publications and source records attributed to P Hobza.

31 records · Page 2Linked to original sources
PubMed1994

Interactions between amino groups in DNA. An Ab initio study and a comparison with empirical potentials.

An ab initio quantum chemical analysis of the close amino group contacts, existing in many DNA crystal structures, is presented. The calculations are made at the Hartree-Fock (HF) level with medium 6-31G* and 6-31G(NH2*) basis sets as well as with inclusion of correlation energy using the second order Møller-Plesset theory (MP2) with the 6-31G* basis set. We demonstrate that the model system (methylamine dimer, cytosine dimer) amino groups are forced to adopt significantly non-planar geometry to stabilize their mutual interaction. Comparison is made with a representative set of empirical potentials including AMBER, CHARMM and GROMOS. The empirical potentials are not reliable enough to analyze the amino group contacts occurring in the DNA double helices. We propose that the mutual amino group interactions contribute to the conformational variability of the CpG and ApT B-DNA steps.

Base Sequence↗
PubMed1994

G.C base pair in parallel-stranded DNA--a novel type of base pairing: an ab initio quantum chemical study.

It was shown recently that parallel stranded DNA also incorporates the Reverse Watson-Crick Guanine. Cytosine (RWC G.C) pair. It contains only one hydrogen bond surrounded by mutual carbonyl group and amino group contacts. Here we describe an ab initio quantum chemical analysis of this unusual base pair. The conclusions can be summarized as follows. (1) The RWC G.C base pair exhibits a previously unknown type of DNA base pairing. (2) Its stabilization energy is estimated to be above 20 kJ/mol. A significant part of the stabilization originates in attractive interactions between the amino group hydrogen atom on one base and lone electron pair of the amino group nitrogen atom of the other (opposite) base. (3) In contrast to any other base pairing patterns, observed in the DNA molecules, the two DNA base amino groups in the RWC G.C base pair are highly nonplanar. They can form additional bifurcated hydrogen bonds with neighboring base pairs. Coplanarity of the two DNA base rings is energetically acceptable. (4) The unique RWC G.C pair cannot be analyzed by the empirical potential calculations.

Base Composition↗
PubMed1985

Perturbation of hydrogen bonds in the adenine ... thymine base pair by Na+, Mg2+, Ca2+ and NH4+ cations.

Perturbation of the hydrogen bonds in the adenine ... thymine base pair by Na+, Mg2+, Ca2+ and NH4+ cations has been investigated by means of ab initio SCF calculations with the STO-3G basis set. The geometry of adenine...thymine, as well as those of the perturbed pairs were optimized. Approach of any cation to thymine at O6 leads to destabilization of the adenine...thymine pair; divalent cations (Mg2+, Ca2+) have a profound effect on the structure of the base pair. The approach of a cation to other available sites (thymine: O2, adenine N1 and N3) leads, on the other hand, to stabilization of the base pair. If a water molecule is placed between the cation and the base pair, the structure and stability of the base pair are changed only negligibly.

Adenine↗
PubMed1984

A quantum chemical study of the effect of Na+ on the hydrogen bonds in the adenine-thymine base-pair.

It is shown, by quantum chemical calculations, that an Na+ located in the neighborhood of the adenine thymine base-pair can dissociate the hydrogen bonds in it. However, a water molecule placed between Na+ and the base-pair would provide perfect protection for the hydrogen bonds. The suggestion is put forward that a hydrophobic carcinogen (for example) could perturb sufficiently the water structure around DNA to allow Na+ to penetrate to molecular distance from the base-pair. This could result in the 'breaking' of hydrogen bonds and, eventually, irregular cell division.

Adenine↗
PubMed1983

Perturbation of hydrogen bonds in the adenine . thymine base pair by Na+: A quantum chemical study.

Ab initio self-consistent field calculations with 4-31G and STO-3G basis sets show that Na+ are able to damage the H bonds in the formamidine . formamide complex, modeling the adenine . thymine base pair (both H bonds in the complex investigated are the same as in adenine . thymine). If a water molecule is placed between the complex and Na+, the H bonds of the model are fully protected. Covalent as well as noncovalent binding of polycyclic aromatic hydrocarbons to nucleic acids should decrease the local concentration of water as a result of the insertion of the hydrophobic hydrocarbon into the DNA and thereby increase the exposure of the DNA H bonds to Na+ attack. Thus, Na+ reaching the base pair could provoke or interfere with cell division.

Adenine↗
PubMed1971

Molecular-orbital study of hydroxylation of collagenous proline and lysine.

EHT and CNDO/2 types of calculations permit the interpretation of the course of hydroxylation of collagenous proline and lysine. Calculations were performed for the models of proline (I), zwitterion of proline (II), proline-containing peptide (III), and lysine (IV). The theoretical results are consistent with an electrophilic mechanism.

Collagen↗
PubMedDate not supplied

Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases.

This review summarizes results concerning molecular interactions of nucleic acid bases as revealed by advanced ab initio quantum chemical (QM) calculations published in last few years. We first explain advantages and limitations of modern QM calculations of nucleobases and provide a brief history of this still rather new field. Then we provide an overview of key electronic properties of standard and selected modified nucleobases, such as their charge distributions, dipole moments, polarizabilities, proton affinities, tautomeric equilibria, and amino group hybridization. Then we continue with hydrogen bonding of nucleobases, by analyzing energetics of standard base pairs, mismatched base pairs, thio-base pairs, and others. After this, the nature of aromatic stacking interactions is explained. Also, nonclassical interactions in nucleic acids such as interstrand bifurcated hydrogen bonds, interstrand close amino group contacts, C [bond] H...O interbase contacts, sugar-base stacking, intrinsically nonplanar base pairs, out-of-plane hydrogen bonds, and amino-acceptor interactions are commented on. Finally, we overview recent calculations on interactions between nucleic acid bases and metal cations. These studies deal with effects of cation binding on the strength of base pairs, analysis of specific differences among cations, such as the difference between zinc and magnesium, the influence of metalation on protonation and tautomeric equlibria of bases, and cation-pi interactions involving nucleobases. In this review, we do not provide methodological details, as these can be found in our preceding reviews. The interrelation between advanced QM approaches and classical molecular dynamics simulations is briefly discussed.

Cations↗
PubMedDate not supplied

Lipid hydration: headgroup CH moieties are involved in water binding.

To explore the interaction potential of phospholipids, we have studied the hydration of diacyl phosphatidylcholine (PC) and methylphosphocholine (MePC), a pertinent model compound, by ir spectroscopy. Related ab initio Hartree-Fock calculations were performed for MePC. Water is considered ideal as a relevant probe molecule. Spectroscopic data for MePC reveal a strong influence of bound hydration water not only on the phosphate groups but also onto the putatively apolar CH(n) groups. The same could be demonstrated for deuterated dimyristoyl PC taken as a "complete" lipid molecule: both headgroup methyl and methylene moieties are gradually, but remarkably affected by hydration, as evidenced by strong wavenumber upshifts of C-H stretching vibration bands. These findings may originate in directed interactions of the CH(n) groups with bound water molecules, but hydration-driven conformational changes of PC headgroups could also occur. The results of the ab initio calculations rationalize the first explanation by predicting a substantial contribution of specific C-H...OH(2) interactions, mainly characterized by a dramatic loss of electron density of the sigma* antibonding molecular orbitals of C-H bonds. Hence, the propensity of the lipid headgroup methyl and methylene groups to act as donor sites in hydrogen bonding must no longer be ignored when considering the interaction potential of PCs.

Biopolymers↗