Molecular and Biomolecular Physics Department, National Institute for Research and Development of Isotopic and Molecular Technologies Donath Street, No: 65 - 103, Ro-400293, Cluj-Napoca, Romania
Abstract: The interactions of the PO¯<sub>4</sub> groups of DNA and the positive parts of lysine/arginine were calculated in the nucleosomes using the ONIOM method. For the model system (3H2O; K<sup>+</sup> ion, PO¯<sub>4</sub> group, positive side chains of lysine, arginine, resp., Cl¯) a triple-ξ basis set with polarization functions was applied both at the HF and MP2 levels. For the real system two dezoxyriboses and two guanines were added, the calculations were performed with a double-ξ basis set at the HF level. The direct PO¯<sub>4</sub>4â¢â¢â¢Lys<sup>+</sup>/Arg<sup>+</sup> bonds are ~5 eV strong. These decrease by ~4 eV due to the Cl¯ ions. The water-mediated PO¯<sub>4</sub>â¢â¢â¢H2Oâ¢â¢â¢Lys<sup>+</sup>/Arg<sup>+</sup> bonds are ~1 eV strong and the Cl¯-s hardly change their strength.
Abstract: The present research paper is dedicated to the obtaining and physicochemical characterization of a highly potential anti-mycobacterial drug candidate with β-cyclodextrin (bCD). The active substance is a 1,3,4-oxadiazole derivative, 2-phenyl-5-{[(2-phenyl-1,3-dioxolan-2-yl) methyl]sulfanyl}-1,3,4-oxadiazole, further named DIOX. DIOXâbCD binary systems were obtained as a physical mixture and a lyophilized product with molar ratio between the main components equal to 1:1 and 1:2. The obtained systems were submitted to hysicochemical characterization applying the following instrumental methods: infrared spectrometry, differential scanning calorimetry, and X-ray crystallographic analysis. Besides, a molecular modeling analysis has been performed. The research data suggested certain intermolecular interaction between DIOX and βCD, suggesting formation of a three-molecular inclusion complex DIOX:bCD, including one DIOX molecule and two molecules of βCD. The main parts of the DIOX molecule included in the hydrophobic cavity of the cyclodextrin molecules most probably are dioxolane cycle and two benzene rings.
Abstract: Equilibrium geometries of methylene chloride dimers have been calculated using the local version of second orderMøllerâPlesset perturbation theory (LMP2), combinedwith the density fitting (DF) technique. Five distinct energy minimum bonded conformations have been resolved. The results have been compared to the intramolecular geometries and the intermolecular orientational correlations obtained previously from neutron and X-ray scattering experiments combined with molecular dynamics and reverse Monte Carlo modeling.
Abstract: Using the ab initio HartreeâFock crystal orbital method in its linear combination of atomic orbitals form we have calculated the band structures of poly(GâC) and poly(AâT). Here, besides the nucleotide bases, the sugar and phosphate parts of the nucleotide were also taken into account together with their first water shell and Na+ ions. We use the notation with a tilde above the abbreviation of a base for the whole nucleotide; for instance poly(G) means a guanine base with the deoxyribose and PO4â groups to which it is bound. The obtained band structures were compared with previous single chain calculations as well as with the earlier poly(GâC) and poly(AâT) calculation without water but in the presence of counterions. One finds that all the bands of poly(GâC) and poly(AâT) are shifted considerably upwards as compared to the previous single chain results (poly(G), poly(C), poly(A) and poly(T)). This effect is explained by the not, vert, similar0.2e charge transfer from the sugars of both chains to the nucleotide bases. The fundamental gaps between the nucleotide base-type highest filled and lowest unfilled bands are decreased in both cases by 1â3 eV, because the valence bands are purine-type and the conduction bands pyrimidine-type, respectively, while in the case of single homopolynucleotides they belong to the same base. We also pointed out that the LUMO is mainly Na+-like in both investigated cases and several unoccupied bands (belonging to the Na+ ions, the phosphate group and the water molecules) can be found between this and the first unoccupied pyrimidine-like empty band.
Abstract: The study aims to present a detailed theoretical investigation of noncovalent intermolecular interactions between different ÏâÏ stacking nitrogen substituted phenothiazine derivatives by applying second-order Møller-Plesset perturbation (MP2), density functional (DFT) and semiempirical theories. The conformational stability of these molecular systems is mainly given by the dispersion-type electron correlation effects. The density functional tight-binding (DFTB) method applied for dimer structures are compared with the results obtained by the higher level theoretical methods. Additionally, the optimal configuration of the investigated supramolecular systems and their self-assembling properties are discussed.
Abstract: We present an ab initio study of the vibrational properties of cytosine and guanine in the WatsonâCrick and Hoogsteen base pair configurations. The results are obtained by using two different implementations of the DFT method. We assign the vibrational frequencies to cytosine or to guanine using the vibrational density of states. Next, we investigate the importance of anharmonic corrections for the vibrational modes. In particular, the unusual anharmonic effect of the H<sup>+</sup> vibration in the case of the Hoogsteen base pair configuration is discussed.
Abstract: The use of chitosan as an excipient in oral formulations, as a drug delivery vehicle for ulcerogenic antiinflammatory drugs and as base in polyelectrolyte complex systems, to prepare solid release systems as sponges was investigated. The preparation by double emulsification of chitosan hydrogels carrying diclofenac, acetyl-salycilic acid and hydrocortisone acetate as anti-inflammatory drugs is reported. The concentration of anti-inflammatory drug in the chitosan hydrogel generating the sponges was 0.08 mmol. Chitosan-drug loaded sponges with anti-inflammatory drugs were prepared by freezeâdrying at 60 C and 0.009 atm. Structural investigations of the solid formulations were done by Fourier transformed
infrared and ultraviolet-visible spectroscopy, spectrofluorimetry, differential scanning calorimetry and X-ray diffractometry. The results indicated that the drug molecules are forming temporary chelates in chitosan hydrogels and sponges. Electron paramagnetic resonance demonstrates the presence of free radicals in a wide range and the antioxidant activity for chitosan-drug supramolecular crosslinked assemblies.
Abstract: Intermolecular interactions between a single water and two N,Nâ²-dimethylethyleneurea (DMEU) molecules have been investigated using ab initio quantum chemistry method. The local and density-fitting approximations of the standard MøllerâPlesset perturbation theory (DF-LMP2) have been employed together with the aug-cc-pVTZ basis set. Several trimeric systems were built where the water molecule, through the OâH...N hydrogen bond interactions, played the role of the bridge between the two DMEU molecules. The results show that the presence of the water molecule does not increase the stability of the trimeric systems. In the first three configurations the water molecule intercalates between two DMEU molecules, forming stable clusters. In the next three configurations, the water molecule is attached to a plane-parallel stacked DMEU dimer through the C=O...HâO hydrogen bond, and these structures are more stable than the first three. Small-angle neutron scattering data show clustering of DMEU molecules in their dilute aqueous solutions, and the ab initio results suggest that DMEU molecules could form contact pairs in dilute aqueous solutions.
Abstract: The work presented here is the last step of our research plan to compute the band structure, the mobilities and finally the conductivities of simple, single-stranded DNA models, infinite homopolynucleotides. We have calculated the d.c. specific conductivities of three crystalline, rigid homopolynucleotides: poly(guanilic acid), poly(adenilic acid) and polythymidine in the presence of water and ions using a combined quantum chemical and solid state physical method (HartreeâFock crystal orbital theory). The obtained specific conductivities are around 10^2 Omega^-1cm^-1. The results are compared to the available experimental values. The reliability of our method and the influence of static and dynamic disorder are also discussed. These results can pave the way to future computations, where the structural and dynamical disorder will gradually be introduced (of course in this case an appropriate form of hopping model has to be used).
Abstract: The equilibrium structures, binding energies, vibrational harmonic frequencies, and the anharmonic corrections for two different (cyclic and asymmetric) urea dimers and for the adenineâthymine DNA base pair system have been studied using the second-order MøllerâPlesset perturbation theory (MP2) method and different density functional theory (DFT) exchangeâcorrelation (XC) functionals (BLYP, B3LYP, PBE, HCTH407, KMLYP, and BH and HLYP) with the D95V, D95V**, and D95V++** basis sets. The widely used a posteriori BoysâBernardi or counterpoise correction scheme for basis set superposition error (BSSE) has been included in the calculations to take into account the BSSE effects during geometry optimization (on structure), on binding energies and on the different levels of approximation used for calculating the vibrational frequencies. The results obtained with the ab initio MP2 method are compared with those calculated with different DFT XC functionals; and finally the suitability of these DFT XC functionals to describe intermolecular hydrogen bonds as well as harmonic frequencies and the anharmonic corrections is assessed and discussed.
Abstract: Design of diamond-like lattices can be achieved by using some net operations. Hypothetical networks, thus obtained, can be characterized in their topology by various counting polynomials and topological indices from which they are derived. The repeat units of the proposed network are derived from adamantane, the constructive unit of diamond, and proved to be extremely stable, as shown by computed total energy. Their topology is described in terms of Omega polynomial.
Abstract: This study aims to present a detailed theoretical investigation of noncovalent intermolecular interactions between different ÏâÏ stacking phenothiazine derivatives and between different alkane chains varying from propane to decane. Second-order MøllerâPlesset perturbation (MP2), coupled cluster (CC), and density functional (DFT) theories were the quantum chemistry methods used in our calculation. For MP2 and CC methods, the density-fitting and local approximations were taken into account, while in the case of DFT, the M06 and M06-2x hybrid meta-GGA exchange-correlation functionals as well as the semiempirical correction to the DFT functional for dispersion (BLYP-D) was considered. The results obtained with the aforementioned methods were compared with the potential energy curve given by the DF-SCSN-LMP2 theory considered as benchmark. For all these calculations, the correlation-consistent basis sets of cc-pVNZ (where N = D, T, Q) were used. In addition, potential energy curves built using the semiempirical PM6-D2 and the MM3 molecular force field methods were also compared with the benchmark curve and their efficiency was discussed. As the next step, several geometry conformations were investigated for both phenothiazine derivatives and alkane chain dimers. It was found that the conformational stability of these molecular systems is exclusively given by the dispersion-type electron correlation effects. The density functional tight-binding (DFTB) method applied for dimer structures was compared with the results obtained by the higher level local perturbation theory method, and based on these conclusions larger phenothiazine derivative oligomers structures were investigated. Finally, the optimal configuration of the complex molecular systems built by phenothiazine derivative, alkane chain fragments, and thiol groups was determined, and their self-assembling properties were discussed.
Abstract: Recently X-ray diffraction provided the structure of nucleosomes. External disturbances can unwrap DNA from the histoneâprotein and their genetic information becomes readable. This is strongly connected with cancer initiation. Therefore, first we performed charge transfer (CT) calculations between polythymidine and a periodic model-protein chain with a lysine or arginine and three glycines. The CT calculations were repeated between the infinite chains using combined solid state physical and quantum chemical methods. We found that the CT between the unit cells of an infinite polythymidine and poly(lysine-triglycine) is 0.04 e and 0.03 e for poly(arginine-triglycine). We investigated the influence of the basis set quality on the calculated CT values using a molecular model built of a thymidine and lysine or arginine. We have calculated also the bands of polythymidine and the two protein model chains. We have found that the differences between the highest level of the valence band of single polythymidine chain and the lowest level of the conduction bands of the model protein chains (6-11 eV depending on the basis set) are too large to assume a direct CT between these two bands.
Abstract: Here we report an experimental and computational study of toluene clusters that were formed in a He supersonic jet. A tunable vacuum ultraviolet radiation source was used to measure the ionisation potentials of dimers, trimers and tetramers from the onset of their photoionisation efficiency curves. DFT calculations were performed for different structures of stacked and non-stacked dimers and trimers as well as for a fully-stacked tetramer. Through comparison of the measured and calculated ionisation potentials, we show that under our experimental conditions, toluene nucleation starts from stacked dimers and proceeds through non-stacked trimers and tetramers.
Abstract: The intermolecular Ï-Ï stacking interaction between some phenothiazine derivatives has been investigated using the Hartree-Fock (HF) and the local second order Møller-Plesset perturbation theory (LMP2) methods. Two different conformations (parallel and antiparallel stacking) of ethyl-phenothiazine and the parallel stacking of thio-methyl-phenothiazine were investigated. In all three cases the HF results show nearly unbounded dimers, while at LMP2 level they become stable structures, mainly due to the presence of large dispersion forces. The intermolecular optimal distances were also calculated by both methods the values obtained by HF being significantly larger as compared with those obtained by LMP2. Considering the LMP2 geometry, the HF contribution in the intermolecular interaction energy gives positive values acting as a repulsion forces and slacking the dimer interaction. This effect is compensated by the large contribution of the dispersion component which finally keeps together the binary stacking structures. These results show the major role of the dispersion effects in stabilizing stacking structures of the aromatic rings and the feasibility of self-assembling in molecular two-dimensional supra-structures.
Abstract: The Hartree-Fock crystal orbital (CO) method in its linear combination of atomic orbitals form was applied to determine the band structure of histone proteins taking 0.041e charge transfer per nucleotide base from the PO groups of poly(guanilic acid) to the arginine, and lysine side chains in histones (see text). Assuming that there are infinite COs, perpendicular to the main chain, formed by the amide groups of one segment of the protein chain bound together by H-bonds with the CO groups of another segment of the chain, we have calculated the band structure. From this, we have determined the mobility using the deformation potential approximation. Multiplying this with the mobile electron concentration due to the charge transfer between the PO groups of DNA and the positive side chains in histones, we have obtained for the direct current (D.C.) electron conductivity fib = 1.07 Ã 10-9 -1 cm for a single fiber and after division by the cross-section of 9.10 Ã 10-16 cm2, spec = 1.18 Ã 106 -1 cm-1 for the specific conductivity.
Abstract: The formation and high stability of the H-bond-driven supramolecular architectures of the syn and anti isomers of the dioxime of bicyclo[3.3.1]nonane-3,7-dione were investigated by single crystal X-ray diffraction, NMR, FTIR, and molecular modeling. Self-assembly of the achiral syn isomer into a cyclic trimer (supramolecular wheel) and of the chiral anti isomer into homochiral cyclic dimers was observed.
Abstract: Covering fullerenes by circulene bowl-shaped units can be performed by using operations on maps, geometricalâtopological transformations of a polyhedral tessellation. Quantum chemical calculations and the HOMA geometric index of aromaticity are used to evaluate the stability of the novel designed fullerenes. Electronic structure and IR spectra are obtained by DFT calculations. The HOMO orbitals localized on circulenic faces in conjunction with more delocalized LUMO orbitals suggest possible JahnâTeller distortions of the structures. Similarly tessellated classical or non-classical fullerenes show similar IR spectral properties. The variation in aromaticity of one and the same circulene/flower, function of the molecular context, is explained by considering the strain of cages as an important destabilizing factor.
Abstract: Using the ab initio Hartree-Fock crystal orbital method in its linear combination of atomic orbital form, the energy band structure of the four homo-DNA-base stacks and those of poly(adenilic acid), polythymidine, and polycytidine were calculated both in the absence and presence of their surrounding water molecules. For these computations Clementiâs double ζ basis set was applied. To facilitate the interpretation of the results, the calculations were supplemented by the calculations of the six narrow bands above the conduction band of poly(guanilic acid) with water. Further, the sugar-phosphate chain as well as the water structures around poly(adenilic acid) and polythymidine, respectively, were computed. Three important features have emerged from these calculations. (1) The nonbase-type or water-type bands in the fundamental gap are all close to the corresponding conduction bands. (2) The very broad conduction band (1.70âeV) of the guanine stack is split off to seven narrow bands in the case of poly(guanilic acid) (both without and with water) showing that in the energy range of the originally guanine-stack-type conduction band, states belonging to the sugar, to PO4â, to Na+, and to water mix with the guanine-type states. (3) It is apparent that at the homopolynucleotides with water in three cases the valence bands are very similar (polycytidine, because it has a very narrow valence band, does not fall into this category). We have supplemented these calculations by the computation of correlation effects on the band structures of the base stacks by solving the inverse Dyson equation in its diagonal approximation taken for the self-energy the MP2 many body perturbation theory expression. In all cases the too large fundamental gap decreased by 2â3âeV. In most cases the widths of the valence and conduction bands, respectively, decreased (but not in all cases). This unusual behavior is most probably due to the rather large complexity of the systems. From all this emerges the following picture for the charge transport in DNA: There is a possibility in short segments of the DNA helix of a Bloch-type conduction of holes through the nucleotide base stacks of DNA combined with hopping (and in a lesser degree with tunneling). The motivation of this large scale computation was that recently in Zürich (ETH) they have performed high resolution x-ray diffraction experiments on the structure of the nucleosomes. The 8 nucleohistones in them are wrapped around by a DNA superhelix of 147 base pairs in the DNA B form. The most recent investigations have shown that between the DNA superhelix (mostly from its PO4â groups) there is a charge transfer to the positively charged side chains (first of all arginines and lysines) of the histones at 120 sites of the superhelix. This would cause a hole conduction in DNA and an electronic one in the proteins.
Abstract: Using first principle quantum chemical methods based on HartreeâFock, density functional theory and second order MøllerâPlesset perturbational theory, equilibrium configurations of N,Nâ²-dimethylethyleneurea (DMEU) dimer and DMEUâwater systems were studied using the D95**+ full double-zeta, cc-pVXZ and aug-cc-pVXZ (X = D, T, Q) basis sets. Three different structures for DMEU dimer and two for DMEUâwater systems were found. Method of the symmetry-adapted perturbational theory was applied for intermolecular interaction energy decomposition in order to elucidate the role of the physically relevant energy components. For all studied equilibrium configurations, dispersion effects are significant, while the contributions of the other energy components are relatively smaller. Two out of the three studied configurations of the DMEU dimers are strong enough to be not destroyed by binding with further water molecules. Such configurations are suggested to play role in dilute aqueous solutions of DMEU, in which DMEU aggregation was recently observed.
Abstract: We have calculated the charge transfer (CT) between the PO4- source group of DNA and the lysine (Lys) and arginine (Arg) positive side chains of histones in presence of water and K+ ions. The calculations were performed at the HF + MP2 level, using the TZVP basis set. The calculations were corrected for basis set superposition error and besides Mullikenâs population analysis we have introduced the â for charged systems more reliable â natural population analysis. The results show that the bare PO4--Lys and the PO4--Arg interactions become weaker, mainly, due to the presence of the K+ ion. We have found 0.067e CT for Lys and 0.050e for Arg.
Abstract: Recent high resolution x-ray diffraction experiments have determined the structure of nucleosomes. In it 147 base pair long DNA B superhelix is wrapped around the eight nucleohistone proteins. They have found that there are many hydrogen-bonds (H-bonds) between the negative sites phosphate (PO4â) groups DNA, and first of all there is the positively charged lysine and arginine side chains of the histones. This means that there is a non-negligible charge transfer from DNA to the proteins causing a hole current in DNA and an electronic one in the proteins. If the relative positions of the two macromolecules change due to some external disturbances, the DNA moves away from the protein and can be read. If this happens simultaneously at several nucleosomes and at many places in chromatin (built up from the nucleosomes), undesired genetic information becomes readable. This final end can cause the occurrence of oncoproteins at an undesired time point which most probably disturbs the self-regulation of a differentiated cell. The connection of these chain of events with the initiation of cancer is obvious. To look into the details of these events we have used the detailed band structures of the four homopolynucleotides in the presence of water and natrium (Na+) ions calculated previously with the help of the ab initio Hartree-Fock crystal orbital method. We have found that in the case of three homopolynucleotides the width of their valence band is broad enough (â¼10 times broader than the thermal energy at 300 K) for the application of the simple deformation potential approximation for transport calculations. With the help of this we have determined the hole mobilities at 300 K and 180 K of poly(guanilic acid), poly(adenilic acid), and polythimidine (polycytidine has a too narrow valence band for the application of the deformation potential method). The obtained mobilities are large enough to allow Bloch-type conduction in these systems. At the end of the paper we discuss briefly the possible mechanism of charge transport in aperiodic DNA as a combination of Bloch-type conduction, hopping, and tunneling.
Abstract: Using the Hartree-Fock crystal orbital method with a combined symmetry (helix) operation, the band structure of polyguanilic acid was calculated in the presence of water and Na+ ions. The water structure was optimized with the help of molecular mechanics.The obtained band structure shows that both the valence and conduction bands are purely guanine type. The three impurity bands in the 10.66 eV large gap are close to the conduction band and therefore cannot play any role in the assumed hole conduction of the system. Namely, according to detailed x-ray diffraction investigations of the nucleosomes in chromatin, there are possibilities of charge transfer from the negative sites of DNA to the positive ones in histones. Therefore most probably there is a hole conduction in DNA and an electronic one in the histone proteins.
Abstract: Using the HF + MP2 methods with full geometry optimizations the charge transfer (CT) from the PO4¯ groups of DNA to the arginine or lysine side chains of the proteins forming the nuclohistone cores were calculated. (X-ray investigation shows that in the nucleohistone core there are eight histones which are wrapped around by a DNA superhelix). We have found 0.21e and 0.26e CT, respectively. Knowing the structure of nucleohistones one can estimate a charge transfer at every fourth base pair. Taking as average 0.10e CT (there are also other attractive interactions) one can compute the concentrations of holes in DNA. From these one can obtain the dc conductivity for polyguanilic acid (the mobilities are known).
Abstract: The basis set superposition error (BSSE) influence in the geometry structure, interaction energies, and intermolecular harmonic and anharmonic vibrational frequencies of cyclic formamide-formamide and formamide-water dimers have been studied using different basis sets (6-31G, 6-31G**, 6-31++G**, D95V, D95V**, and D95V++**). The a posteriori "counterpoise" (CP) correction scheme has been compared with the a priori "chemical Hamiltonian approach" (CHA) both at the Hartree-Fock (HF) and second-order Moller-Plesset many-body perturbation (MP2) levels of theory. The effect of BSSE on geometrical parameters, interaction energies, and intermolecular harmonic vibrational frequencies are discussed and compared with the existing experimental data. As expected, the BSSE-free CP and CHA interaction energies usually show less deep minima than those obtained from the uncorrected methods at both the ET and MP2 levels. Focusing on the correlated level, the amount of BSSE in the intermolecular interaction energies is much larger than that at the HT level, and this effect is also conserved in the values of the force constants and harmonic vibrational frequencies. All these results clearly indicate the importance of the proper BSSE-free correlation treatment with the well-defined basis functions. At the same time, the results show a good agreement between the a priori CRA and a posteriori CP correction scheme; this agreement is remarkable in the case of large and well-balanced basis sets. The anharmonic frequency correction values also show an important BSSE dependence, especially for hydrogen bond stretching and for low frequencies belonging to the intermolecular normal modes.
Abstract: The equilibrium structures, the binding energies, and the second-order energy components of a series of hydrogen-bonded complexes involving acetylene are studied. The strength of the binding energy of the selected systems (HF...HCCH, HCl...HCCH, HCN...HCCH, and HCCH...HCCH) was different, ranging from a very weak interaction to a strong interaction. Calculations have been carried out at both the Hartree-Fock and correlated (second-order Moller-Plesset perturbation theory) levels of theory, using several different basis sets [6-31G(d,p), 6-311G(d,p), 631G++(d,p), 6-311G++(d,p), 6-31++G(2d,2p) and 6-311++G(2d,2p)]. The widely used a posteriori Boys-Bernardi counterpoise (CP) correction scheme has been compared with the a priori CHA/CE, CHA-MP2, and CHA-PT2 methods, using the chemical Hamiltonian approach (CHA). The results show that at both levels the CP and the appropriate CHA results are very close to each other. Only the monomer-based CHAPT2 theory gives slightly overcorrected results, reflecting that the charge transfer and polarization effects are not taken into account in this method up to second order. We have also applied our earlier developed energy decomposition scheme in order to decompose the second-order energy contribution into different physically meaningful components. The results show that at large and intermediate intermolecular distances, the second-order intermolecular contribution is almost equal to the sum of different physically meaningful components (e.g., polarization, charge transfer, dispersion), while at shorter distances the slightly strong overlap effects fairly disturb this simple additivity.
Abstract: The influence of basis set superposition error (BSSE) in optimized geometries, force constants and intermolecular harmonic vibrational frequencies of the ammonia-ammonia dimer have been studied both at the Hartree-Fock and correlated (second-order Moller-Plesset perturbation theory) levels of theory using several different basis sets as (6-31G, 6-311G, 6-31 + +G, 6-311 + +G, 6-31G(d,p), 6-311G(d,p), 6-31 + +G(d,p) 6-311 + +G(d,p) and 6-311 + +G(2d,2p)). The widely used a posteriori Boys-Bernardi "counterpoise" (CP) correction scheme has been compared with the a priori method utilizing the chemical Hamiltonian approach (CHA). The results show that practically there is no difference between these two methods, so the a priori CHA scheme can be considered as an ultimate solution of the BSSE problem. It is also concluded that the BSSE influence is very significant, so removing this effect is very important.
Abstract: Theoretical studies have been performed to Calculate the force constants and harmonic vibrational frequencies in the hydrogen fluoride and water dimers. The calculations have been undertaken both at the Hartree-Fock and correlated (second-order Moller-Plesset perturbation theory) levels of theory using several different basis sets ranging from the weak to the intermediate. The basis set superposition error (BSSE) has been excluded by using the chemical Hamiltonian approach. The results show that the BSSE influence is significant in the force constants and harmonic vibrational frequencies even if electron correlation is accounted for, so removing the BSSE is important. The results are compared with those obtained by the basis independent density-functional tight-binding method.
Abstract: The different configurations (linear, zig-zag, and cyclic) of formamide dieters have been studied at the level of both Hartree-Fock (HF) and second order Moller-Plesset perturbation theory (MP2). The widely used a posteriori Boys-Bernardi "counterpoise" (CP) correction scheme has been compared with our a priori methods utilizing the "chemical Hamiltonian approach" (CHA). The appropriate interaction energies have been calculated in six different basis sets (6-31G, 6-31G**, DZV, DZP, TZV and cc-pVDZ).
Abstract: The intra- and intermolecular hydrogen-bond dynamics plays an important role in thermal stability and molecular functionality of biomolecules like DNA base pairs and proteins. The phenomena of thermal relaxation, conformational changes as well as the ultrafast non-radiative decays in molecules, especially in biomolecules are realized among other physical effects also with the help of molecular vibrations. Intermolecular hydrogen- or weak chemical bonds (covalent bond including H atoms) usually present large anharmonic normal mode vibrations. The anharmonic effects of normal mode vibrations for some small molecular model systems (formamide and urea) as well as for guanine-cytosine and adenine-thymine DNA base pairs are presented considering DFT and ab initio second order Møller-Plesset (MP2) theoretical methods. The role of basis set superposition errors in harmonic and anharmonic frequency calculations is briefly discussed. It was observed that anharmonic effects can significantly change the blue- or red-shifted harmonic frequency values. Large anharmonic effects were found in the case of protonated molecular structures, especial for Hoogsteen conformation of guanine â cytosine base pairs.
