Ab initio and DFT studies on tautomerism of indazole in gaseous and aqueous phases

Electronic structure of optimized Ge₅, Ge₁₇, Ge₅–O and Ge₅ embedded in SiO₂ nanoparticles have been studied by density functional theory to find out the effect of cluster size and Ge–O bond(s) on the optical energy gap between LUMO and HOMO. It was found that the optical energy gap depends on both cluster size and the number of Ge–O bonds nonlinearly. The optical energy gap was found to be in visible light range when the Ge₅ nanoparticle has been embedded in SiO₂ matrix.     

Theoretical study of CH…O hydrogen bond in proton transfer reaction of glycine

Density functional theory (DFT) calculations are used to study the strength of the CH…O H‐bond in the proton transfer reaction of glycine. Comparison has been made between four proton transfer reactions (ZW1, ZW2, ZW3, SCRFZW) in glycine. The structural parameters of the zwitterionic, transition, and neutral states of glycine are strongly perturbed when the proton transfer takes place. It has been found that the interaction of water molecule at the side chain of glycine is high in the transition state, whereas it is low in the zwitterionic and neutral states. This strongest multiple hydrogen bond interaction in the transition state reduces the barrier for the proton transfer reaction. The natural bond orbital analysis have also been carried out for the ZW2 reaction path, it has been concluded that the amount of charge transfer between the neighboring atoms will decide the strength of H‐bond. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

First and second coordination spheres in 8-azaxanthinato salts of divalent metal aquacomplexes – Ab initio and DFT study

The hydrogen bonding pattern in complexes of the type [M²⁺(H₂O)₆](dmax)₂ (M = Mn, Ni, Co, Zn, Cd, Hdmax = 1,3-dimethyl-8-azaxanthine), [M²⁺(H₂O)₄(py)₂](dmax)₂ (M = Mn, Co, Zn, Cd, py = pyridine) and [M²⁺(dmax)₂(H₂O)₂(py)₂]·2H₂O (M = Ni, Cu) were studied by ab initio (MP2/LANL2DZ//B3LYP/LANL2DZ) and density functional theory methods (B3LYP/LANL2DZ, B3LYP/6-31G^∗∗ and B3PW91/6-31G^∗∗). The investigation includes a variety of theoretical analyses, which include interaction energy, many body analyses, electron density analysis, topological analysis, Mulliken atomic charges, natural atomic charges and harmonic vibrational analysis. The geometrical parameters and vibrational frequencies of dmax (the mono anion of 1,3-dimethyl-8-azaxanthine), [M²⁺(H₂O)₆] (M = Mn, Ni, Co, Zn, Cd), [M²⁺(H₂O)₄·(py)₂] (M = Mn, Co, Zn, Cd) and the complexes, calculated by the theoretical methods, were compared with the recent X-ray crystallographic results and it was observed that the results are found to agree well with the crystallographic results. The present calculations provide an important physicochemical insight into metal cations with 1,3-dimethyl-8-azaxanthine. The results also reveal the active role of coordinated water molecules in modulating the binding of the cation through a specific network of hydrogen bonds. The topology of the motifs generated by these hydrogen bonds has been characterized, adapting to the second coordination sphere concepts usually applied to the first (monodentate, chelate, and bridge) coordination sphere. The optimized structures of the Cd²⁺, Zn²⁺ and Cu²⁺ complexes further interact among themselves in a less tight fashion to generate three dimensional structures (a tape-like hydrogen bond network). Finally these tape-like hydrogen bond network were optimized using the B3LYP/LANL2DZ basis set.     

FT-IR and Raman Spectra of Ammonium Hydrogen Tartrate and Potassium Hydrogen Tartrate Crystals

FT-IR and Raman spectra of ammonium hydrogen tartrate [NH₄HC₄H₄O₆] and potassium hydrogen tartrate [KHC₄H₄O₆] have been measured. Vibrational assignments have been made for both the internal and external vibrations. Because of the free rotation of the NH₄⁺ ion, it forms only weak hydrogen bonds with the oxygen atom.     

Structural and spectral properties of 4-bromo-1-naphthyl chalcones: a quantum chemical study

The structural and optical properties of 4-bromo-1-naphthyl chalcones (BNC) have been studied by using quantum chemical methods. The density functional theory (DFT) and the singly excited configuration interaction (CIS) methods were employed to optimize the ground and excited state geometries of unsubstituted and substituted BNC with different electron withdrawing and donating groups in both gas and solvent phases. Based on the ground and excited state geometries, the absorption and emission spectra of BNC molecules were calculated using the time-dependent density functional theory (TDDFT) method. The solvent phase calculations were performed using the polarizable continuum model (PCM). The geometrical parameters, vibrational frequencies, and relative stability of cis- and trans-isomers of unsubstituted and substituted BNC molecules have been studied. The results from the TDDFT calculations reveal that the substitution of electron withdrawing and electron donating groups affects the absorption and emission spectra of BNC.     

Structural properties and the effect of 2,6‐diaminoanthraquinone on G‐tetrad,non‐G‐tetrads,and mixed tetrads—A density functional theory study

Telomerase inhibitor causes the attrition of telomere length and consequently leading to senescence which require a lag period for cancer cells to stop proliferating. Telomeric sequences form quadruplex structures stabilized by tetrads. The structural and electronic properties related with interaction of 2,6‐diaminoanthraquinone and tetrads are the key step to elucidate the anticancer activity. The present study has been focused on the stability of the isolated tetrads and the effect of interaction of 2,6‐diaminoanthraquinone with G‐tetrad, non‐G‐tetrads, and mixed tetrads using density functional theory method in both gas and aqueous phases. The solvent interaction with the molecular systems has increased the stability of the isolated tetrads and complexes. The sharing of electron density between the interacting molecules is shown through electron density difference maps. The atoms in molecules theory and natural bond orbital analysis have been performed to study the nature of hydrogen bonds in the inhibitor interacting complexes. The linear correlation is shown between electron density [ρ(r)], and its Laplacian [(²ρ(r)] at the bond critical points. The strong binding nature of 2,6‐diaminoanthraquinone with studied tetrads reveals that this inhibitor is suitable to stabilize the above tetrads and inhibit the telomerase activity. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Study of chemical bonding in H2 and HF molecules: Wave function and density functional theory (DFT) parameters approach

Balint Kurti's Fourier grid Hamiltonian method is employed to obtain the molecular wave function and equilibrium bond length for H₂ and HF molecules. The density functional theory parameter, namely, the chemical hardness (η) value, was determined for some diatomic hydride molecules using this wave function and the results are found to be in good agreement with the values obtained from the ab initio HF–SCF method. A new formula for chemical hardness (η=1/2Dr, where D is the proportionality constant and r is the internuclear distance) is introduced in binding energy and change of hardness equations to determine the chemical hardness and chemical potential values for different bond lengths. The binding energy and change of hardness values are calculated for H₂, H, H, HF, HF⁺, and HF⁻ molecules and the bond stability is discussed. Finally, the concept of an atom in a molecule is examined in the context of DFT parameters and comparison is made between an atom in a molecule and the isolated atom. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 76: 662–669, 2000     

Charge transfer in polypeptides: effect of secondary structures on charge-transfer integral and site energies

We have theoretically studied the charge transfer in glycine polypeptide using quantum mechanical models based on a tight-binding Hamiltonian approach. The charge-transfer integrals and site energies involved in the transport of positive charge through the peptide bond in glycine polypeptide have been calculated. The charge-transfer integrals and site energies have been calculated directly from the matrix elements of the Kohn-Sham Hamiltonian defined in terms of the molecular orbitals of the individual fragments of the glycine polypeptide. In addition to this, we have calculated the rate of charge transfer between a neighboring amino acid subgroup through the Marcus rate equation. These calculations have been performed for the different secondary structures of the glycine model peptide such as linear, alpha-helix, 3(10)-helix, and antiparallel beta-sheet by varying the dihedral angles omega, varphi, and psi along the Calpha-carbon of amino acid subgroup. Present theoretical results confirm that the charge transfer through the peptide bond is strongly affected by the conformations of the oligopeptide.     

Theoretical investigation on intramolecular electron transfer in polypeptides

Theoretical investigations on the intramolecular electron transfer between the intermediate residues of different secondary structures of an oligopeptide have been carried out. Density functional theory calculations have been performed to calculate the charge transfer integral, spatial overlap integral and site-energies for the optimized secondary structures of the glycine oligopeptide by varying the dihedral angles ( and ψ) along the -carbon atom of amino acid subgroups. The reorganization energy has been calculated in the presence of an excess negative charge. The electron transfer rates for the model peptide have been estimated and the dependence of the rate on secondary structures is discussed.     

Structure,conformation and NMR studies on 1,2-dioxane and halogen substituted 1,2-dioxane molecules

Molecular structure and conformational stability of chair and twist conformers of 1,2-dioxane and halogen substituted compounds of the 1,2-dioxane have been studied using ab initio and density functional theory (DFT) methods. The molecular geometries of 1,2-dioxane, 3,6-difluoro, 3,6-dichloro, 3,3,6,6-tetrafluoro and 3,3,6,6-tetrachloro 1,2-dioxane compounds were optimized at HF, MP2, B3LYP and B3PW91 levels of theory by implementing 6-31G* basis set. To study the effect of polar medium, self-consistent reaction field theory is used to optimize the conformers at B3LYP/6-31G* level of theory. The geometrical parameters of chair and twist conformers have been discussed in the light of interaction between lone pair electrons present in the oxygen and substituted halogen atoms. The relative stability of the conformers have been studied using relative energy, maximum hardness principle and thermodynamical quantities. The 13C-NMR chemical shift study for carbon atoms in the title compounds are calculated and the results have been discussed.