Showing papers by "Pavel Hobza published in 1997"
TL;DR: In this paper, the authors compared AMBER 4.1, AM1, MNDO/M, PM3, and the non-empirical ab initio self-consistent field (SCF) method utilizing a minimal basis set combined with the London dispersion energy (SCFD method) for calculation of stabilization energies of 26 H-bonded DNA base pairs.
Abstract: Empirical energy functions (AMBER 4.1, CFF95, CHARMM23, OPLS, Poltev), semiempirical quantum chemical methods (AM1, MNDO/M, PM3), and the nonempirical ab initio self-consistent field (SCF) method utilizing a minimal basis set combined with the London dispersion energy (SCFD method) were used for calculation of stabilization energies of 26 H-bonded DNA base pairs, 10 stacked DNA base pairs (thymine was replaced by uracil), and the B-DNA decamer (only DNA bases were considered). These energies were compared with nonempirical ab initio beyond Hartree–Fock values [second-order Moller–Plesset (MP2)/6–31G*(0.25)]. The best performance was exhibited by AMBER 4.1 with the force field of Cornell et al. The SCFD method, tested for H-bonded pairs only, exhibited stabilization energies that were too large. Semiempirical quantum chemical methods gave poor agreement with MP2 values in the H-bonded systems and failed completely for stacked pairs. A similar failure was recently reported for density functional theory calculations on base stacking. It may be concluded that currently available force fields provide much better descriptions of interactions of nucleic acid bases than the semiempirical methods and low-level ab initio treatment. © 1997 John Wiley & Sons, Inc. J Comput Chem18: 1136–1150
261 citations
TL;DR: In this paper, the interaction of adenine−thymine and guanine−cytosine base pairs with various metal cations (Mg2+,..., Hg2+) was studied by nonempirical ab initio methods with inclusion of correlation energy.
Abstract: Interaction of Watson−Crick adenine−thymine (AT) and guanine−cytosine (GC) base pairs with various metal (M) cations (Mg2+, ..., Hg2+) were studied by nonempirical ab initio methods with inclusion of correlation energy. Cations were allowed to interact with the N7 nitrogen of adenine and the N7 and O6 atoms of guanine. All of the cations were described by Christiansen's average relativistic effective potentials using the DZ+P basis set, while the 6-31G** basis set was used for the elements of base pairs. Disruption of the adenine−thymine as well as guanine−cytosine pairs in the presence of all studied cations is energetically more demanding than that for isolated base pairs; the addition stabilization of the base pair is about 100% for complexes with dication. The interaction is highly nonadditive. The three-body term is for the MGC complex considerably larger than that for MAT; the intercomplex charge transfer is also much larger for the former complex.
210 citations
TL;DR: Although the molecular orbital analysis does not rule out the charge-transfer n-pi* interaction of the sugar 04' with the aromatic base, the base-sugar contact is stabilized by dispersion energy similar to that of stacked bases, which could contribute to the propensity of short d(CG)n sequences to adopt the Z-conformation.
191 citations
TL;DR: In this article, three groups of molecular clusters were studied using the coupled cluster method with non-iterative triple excitations (CCSD(T)) and the second-order Moller-Plesset perturbational method (MP2): H-bonded DNA base pairs ((cytosine) 2, (isocytosa) 2 and (uracil) 2 ), aromatic stacked complexes ((pyrrol) 2), (pyrimidine) 2, (triazine) 2 ).
152 citations
TL;DR: In this article, the second-order Moller−Plesset perturbational method was used to study base stacking and H-bonding properties of thioguanine and thiouracils.
Abstract: Base stacking and H-bonding properties of thioguanine and thiouracils were studied using an ab initio quantum chemical method with inclusion of electron correlation (second-order Moller−Plesset perturbational method). Hydrogen-bonded base pairs containing thiobases are only slightly less stable (up to 2 kcal/mol) than the unmodified base pairs. The N···S distances are larger by 0.4−0.7 A compared to the N···O distances in the standard base pairs. The thio group enhances polarizability of the monomers and their dipole moments. Thus, in stacked complexes of thiobases, both dispersion attraction and electrostatic interactions are enhanced. Mutual contact of the sulfur atoms and their interaction with second-row elements lead to steric clashes destabilizing the stacking, though, in DNA, such clashes should be eliminated by rather small adjustments of the local DNA conformation. The thio group significantly destabilizes the hydration of the 6-position of thioguanine with respect to guanine. The first hydration...
109 citations
TL;DR: The calculations indicate an enhancement of the third-strand binding in the G.GC reverse-Hoogsteen trimer due to-metal cation coordination to the N7/O6 position of theThird-Strand guanine.
Abstract: Neutral (G.GC, A.AT, G.AT, T.AT, and C(imino).GC) and protonated (CH+.GC and AH+.GC) hydrogen-bonded trimers of nucleic acid bases were characterized by ab initio methods with the inclusion of electron correlation. In addition, the influence of metal cations on the third-strand binding in Purine-Purine-Pyrimidine (Pu.PuPy) reverse-Hoogsteen triplets has been studied. The ab initio calculations were compared with those from recently introduced force fields (AMBER4.1, CHARMM23, and CFF95). The three-body term in neutral trimers is mostly negligible, and the use of empirical potentials is justified. The only exception is the neutral G.GC Hoogsteen trimer with a three-body term of -4 kcal/mol. Protonated trimers are stabilized by molecular ion-molecular dipole attraction and the interaction within the complex is nonadditive, with the three-body term on the order of -3 kcal/mol. There is a significant induction interaction between the third-strand protonated base and guanine. The calculations indicate an enhancement of the third-strand binding in the G.GC reverse-Hoogsteen trimer due to-metal cation coordination to the N7/O6 position of the third-strand guanine. Interactions between metal cations and complexes of DNA bases are in general highly non-additive; the three-body term is above-10 kcal/mol in a complex of a divalent cation (Ca2+) with the GG reverse-Hoogsteen pair. The pairwise additive empirical potentials qualitatively underestimate the binding energy between cation and base.
69 citations
TL;DR: In this article, the H-bonded adenine/thymine WAT base pair was studied for the first time using multidimensional nonharmonic treatment, and a nonrigid reference was defined which covered all motions on the low-lying part of the intermolecular potential surface and which facilitates the derivation of a suitable model Hamiltonian.
Abstract: Intermolecular vibrational modes of the H-bonded adenine…thymine Watson–Crick (AT) base pair were studied for the first time using multidimensional nonharmonic treatment. Relying on a Born–Oppenheimer–like separation of the fast and slow vibrational motions, the complete multidimensional vibrational problem is reduced to a six-dimensional subproblem in which all rearrangements between the pair fragments (i.e., adenine and thymine) can be described. Following the Hougen–Bunker–Johns approach and using appropriate vibrational coordinates, a nonrigid reference is defined which covers all motions on the low-lying part of the intermolecular potential surface and which facilitates the derivation of a suitable model Hamiltonian. The potential energy surface is determined at the ab initio Hartree–Fock level with minimal basis set (HF/MINI-1) and an analytic potential energy function is obtained by fitting to the ab initio data. This function is used to calculate vibrational energy levels and effective geometries ...
61 citations
23 citations
TL;DR: In this article, the radical cations of hydrogen halogenide dimers (HX)2•+ (X = F−At) and products of their decomposition were investigated, using beyond-Hartree−Fock methods (MP2, QCISD, and CCSD(T)).
Abstract: The radical cations of hydrogen halogenide dimers (HX)2•+ (X = F−At) and products of their decomposition have been investigated, using beyond-Hartree−Fock methods (MP2, QCISD, and CCSD(T)). Both all-electron and pseudopotentials techniques were considered. The (HF)2•+ system differs significantly from the remaining (HX)2•+ systems. The energy barrier height for transfering the H-bonded system to the hemibond structure is very low, causing the spontaneous conversion of the H-bonded structures to the hemibond ones, with the exception of the (HF)2•+ dimer where the inverse situation exists. The characteristics for the overall process HX + HX•+ ⇌ H2X+ + X• were obtained from the experimental heats of formation and from calculated characteristics. The ΔH298 values based on the pseudopotentials are satisfactory for the F- and Cl-containing systems; however, the agreement is less satisfactory for heavier systems.
8 citations