Sándor Suhai

Bond alternation in infinite polyene: Peierls distortion reduced by electron correlation

Abstract The formation of the bond-alternating structure in polyene is investigated both within the one-particle (Hartree-Fock) picture and including electron correlation effects by perturbation theory. An off-diagonal charge-density wave of the equi-distant structure is identified at the Hartree-Fock level as precursor of the bond-alternate state which is found by subsequent lattice optimization. The valence-shell correlation energy is calculated by using second-order Moller-Plesset perturbation theory. It is found to be finite also in the metallic one-dimensional chain and a comparison with results obtained for the acetylene unit shows that this method recovers ~-70–75% of the total valence-shell correlation. Correlation effects are shown to reduce the Peierls distortion and the corresponding energy barrier but the bond alternation persists also if the results are extrapolated to the case of full correlation.

Microhydration of the Guanine-Cytosine (GC) Base Pair in the Neutral and Anionic Radical States : A Density Functional Study

A density functional study of the effects of microhydration on the guanine-cytosine (GC) base pair and its anion radical is presented. Geometries of the GC base pair in the presence of 6 and 11 water molecules were fully optimized in the neutral (GC-nH2O) and anion radical [(GC-nH2O)*-] (n = 6 and 11) states using the B3LYP method and the 6-31+G** basis set. Further, vibrational frequency analysis at the same level of theory (B3LYP/6-31+G**) was also performed to ensure the existence of local minima in these hydrated structures. It was found that water molecules surrounding the GC base pair have significant effects on the geometry of the GC base pair and promote nonplanarity in the GC base pair. The calculated structures were found to be in good agreement with those observed experimentally and obtained in molecular dynamics (MD) simulation studies. The water molecules in neutral GC-nH2O complexes lie near the ring plane of the GC base pair where they undergo hydrogen bonding with both GC and each other. However, in the GC anion radical complexes (GC-nH2O, n = 6, 11), the water molecules are displaced substantially from the GC ring plane. For GC-11H2O*-, a water molecule is hydrogen-bonded with the C6 atom of the cytosine base. We found that the hydration shell initially destabilizes the GC base pair toward electron capture as a transient anion. Energetically unstable diffuse states in the hydration shell are suggested to provide an intermediate state for the excess electron before molecular reorganization of the water molecules and the base pair results in a stable anion formation. The singly occupied molecular orbital (SOMO) in the anion radical complexes clearly shows that an excess electron localizes into a pi orbital of cytosine. The zero-point-energy (ZPE-) corrected adiabatic electron affinities (AEAs) of the GC-6H2O and GC-11H2O complexes, at the B3LYP/6-31+G** level of theory, were found to be 0.74 and 0.95 eV, respectively. However, the incorporation of bulk water as a solvent using the polarized continuum model (PCM) increases the EAs of these complexes to 1.77 eV.

An efficient cluster elongation method in density functional theory and its application to poly‐hydrogen‐bonding molecules

The elongation method to synthesize the electronic states of polymers is developed at the level of the density functional theory using the linear combination of Gaussian‐type orbitals local spin density method. In this treatment, the interactions between the localized molecular orbitals of a cluster and the canonical molecular orbitals of an attacking monomer are successively included, where the Kohn–Sham equation is self‐consistently solved instead of the Hartree–Fock equation in the conventional ab initio method. In the process of the cluster extension, an efficient treatment is implemented to calculate the matrix elements of Coulomb integral and exchange‐correlation potential. The reliability and the efficiency of this method are examined via applications to hydrogen molecule cluster, linear water cluster (H2O)n and formamide cluster (CHONHH2)n. It was shown that the present method saves significantly the computational time and disk storage in the large cluster calculations, and provides good agreement...

Model calculation of the effect of hydration on the energy band structure of a nucleotide base stack

The energy band structure of the nucleotide base stacks poly C, poly T, poly A, and poly G have been calculated by the ab initio SCF LCAO crystal orbital method. For poly C, model calculations have been performed to investigate the effect of water molecules on its electronic structure. The presence of the water molecules, whose positions have been determined recently by a Monte Carlo simulation technique at T=300 K, causes significant band shifts and together with positive ions could substantially influence the conductive properties of native DNA.

A theoretical study of structures and electron affinities of radical anions of guanine-cytosine, adenine-thymine, and hypoxanthine-cytosine base pairs

Adiabatic electron affinities (AEA) and structural perturbations due to addition of an excess electron to each of the neutral guanine‐cytosine (G‐C), adenine‐thymine (A‐T), and hypoxanthine‐cytosine (HX‐C) base pairs were studied using the self‐consistent charge, density functional tight‐binding (SCC‐DFTB‐D) method, augmented by the empirical London dispersion energy term. Performance of the SCC‐DFTB‐D method was examined by comparing the calculated results using it with those obtained from experiment as well as ab initio and other different density functional theoretical studies. An excellent agreement between the SCC‐DFTB‐D results and those obtained by the other calculations regarding the structural modifications, hydrogen bonding, and dissociation energies of the neutral and radical anion base pairs was found. It is shown that adiabatic electron affinity can be better predicted by considering reaction enthalpies of formation of the respective neutral and anionic base pairs from their respective molecular components instead of taking the difference between their total energies. The calculated AEAs of the base pairs were compared with those obtained by the bracketing method from Schaefer and coworkers, where a satisfactory agreement was found. It shows applicability of the SCC‐DFTB‐D method to study charged DNA models at a highly economical computational cost.

Density functional investigations of carboxyl free radicals: Formyloxyl, acetyloxyl, and benzoyloxyl radicals

The structure of the lowest electronic states of HCOO· in C2v and Cs symmetries were optimized employing density functional theory (DFT) methods with extended basis sets including up to f- (on C and O) and d- (on H) polarization functions. Generalized gradient functionals (BLYP) and adiabatically connected functionals (B3LYP and B3PW91) were employed for studying HCOO·, as well as the isomer HOCO· (trans), the dissociation limit H·+CO2, and the transition state for the decomposition. At the best DFT levels employed, the ground state of HCOO· is 2A1 (in C2v) with equal CO bond lengths, while the low-lying 2B2 state is only about 4 kJ/mol above (without inclusion of zero-point energies). The broken-symmetry 2A′ state (with unequal CO bond lengths, i.e., Cs symmetry) is predicted to be about 13 kJ/mol above the 2A1 state and to be a transition state for the isomerization HCOO· (2A1)HOCO· (2A′), with the trans-HOCO· isomer about 55 kJ/mol more stable. These facts agree closely with the most recent CASPT2/ANO calculations on this system. Therefore, it is concluded that some DFT models can be used safely for the study of larger radicals of the same type (despite several drawbacks discussed at length in this study). B3PW91, using several basis sets, is subsequently applied to the study of the possible reaction mechanisms of acetyloxyl radical, which exhibits a much more complicated path than formyloxyl, due to the presence of the methyl group. The optimum structures of isomers with coplanar or perpendicular CH and CO bonds were obtained for CH3COO· and two saddle points identified on the path of decomposition into CH3· and CO2. On the other side, saddle points for isomerization into CH3OCO· and CH2COOH· were also located, and the decomposition of the former to CH3O·+CO investigated. Finally, the structure of the benzoyloxyl radical (C6H5COO·) and its possible decomposition products were investigated along the same lines.xa0© 1998 John Wiley & Sons, Inc. Int J Quant Chem 70: 253–267, 1998

Perturbational approach to the interaction between two nearly incommensurable polymers

The perturbational method developed in the present paper is applied to a few simple model systems, to two interacting hydrogen molecules–polymers and to polymeric systems of hydrogen molecules and hydrogen fluoride molecules. The validity of our method is studied by comparing the results obtained with the perturbation method and the tight‐binding SCF crystal orbital method. The obtained total electronic energies and the charge distributions are in good agreement with each other for both methods. This result leads to the conclusion that the present perturbational approach is promising for the application to the interactions between real, incommensurable polymers.

Density functional computational thermochemistry: determination of the enthalpy of formation of sulfine, CH2SO, at room temperature

Abstract Density functional and coupled-cluster calculations using Poples basis sets up to 6-311++G(3df,2pd) have been employed to determine the heat of formation of sulfine, CH 2 SO, 1 , using the isodesmic reaction CH 2 S + SO 2 ⇌ CH 2 SO + SO . Other reactions, employed previously to determine the enthalpy of formation of sulfine at the CAS-SDCI/ CASSCF ab initio level, were used as well. The analysis of the results shows that: (a) the errors in the calculation of the enthalpies for the individual molecules do cancel reasonably only for the isodesmic reaction, and not for those used previously; (b) density functional methods produce smaller errors than CCSDT in the calculation of the enthalpies of formation of the molecules involved in this reaction; (c) the actual heat of formation of sulfine is determined as Δ f H o 298.15 ( 1 )=−52±10 kJ/mol, more in agreement with the prediction of Benson than with the ab initio value derived by Ruttink et al.; (d) the proton affinity of sulfine, calculated at the density functional level (792.0 kJ/mol) agrees reasonably well with the experimental result, 787.6±2.6 kJ/mol, but the enthalpy of formation of 1 derived from this proton affinity using the assumptions of Ruttink or Bouchoux is in disagreement with the value determined previously.

Potential energy calculations for the double internal rotation in acetone and dimethylamine

In the present work, the problem of the determination of the potential energy surface of double rotor molecules is examined in the case of acetone and dimethylamine. From the symmetry adapted functional form for the potential of acetone that of dimethylamine is deduced and the minimum number of conformations to be calculated is derived in order to have a reliable surface (minimal expansion).The potential energy functions for acetone and dimethylamine are then determined using different standard procedures. Special emphasis is put on the electronic correlation effects in the calculation. It is found that these effects significantly improve the potential energy function.

Perturbational approach to the interaction between a polymer and a small molecule

The perturbational method developed in the present paper is applied to the interaction between a polymer and a small molecule using a few simple model systems. The validity of our method is studied by comparing the results obtained with the perturbation method and the tight binding SCF crystal orbital method. The total electronic energies and charge distributions obtained are in good agreement with each other for the two methods. This result leads to the conclusion that the present perturbational approach is promising for application to interactions between real polymers and impurities.