Computational study of 4‐fluoro‐4‐chloro‐ and 4‐fluoro‐4‐bromo‐4‐silathiacyclohexane S‐oxides: Effect of halogen on the SO→Si intramolecular coordination in the boat and twist conformers

Chair, twist, and boat conformations of axial and equatorial 4‐fluoro‐4‐chloro‐ and 4‐fluoro‐4‐bromo‐4‐silathiacyclohexane S‐oxides have been calculated at the second‐order Møller–Plesset (MP2) and density functional theory (DFT) levels of theory. The 2,5‐twist and 1,4‐boat conformers of the axial sulfoxides are stabilized by transannular interaction between the sulfinyl oxygen and silicon to give trigonal bipyramidal geometry at silicon. The stability of conformers containing pentacoordinate silicon is governed by the balance of the transannular sulfinyl oxygen–silicon coordination, nonbonded H…H and O…Hlg_ax interactions, electronegativity of Hlg_ax and nucleofugality of Hlg_eq, and may approach the stability of the lowest‐energy chair conformers. The effect of pentacoordination on the energy and geometry of Si‐halogenated 4‐silathiane S‐oxides is analyzed as a function of the halogen nature and position. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Analysis of pair interaction in a bipolar mesogen 4‐(4‐hydroxylbutyloxy)‐4′‐cyano‐biphenyl: A comparative study based on semiempirical and DFT methods

Structure of 4‐(4‐hydroxylbutyloxy)‐4′‐cyano‐biphenyl (H4CBP) molecule has been optimized using density functional B3LYP with 6‐31G (d) basis set taking crystallographic geometry as input. Using the optimized geometry, electronic structure of the H4CBP molecule has been evaluated on the basis of semiempirical methods and DFT calculations. Intermolecular interaction energy between a pair of H4CBP molecules has been evaluated by using Rayleigh–Schrodinger perturbation theory modified with multicentered multipole expansion method for the electrostatic part while dispersion and repulsion terms have been calculated using Kitaigorodskii formula. The results obtained through semiempirical and DFT calculations have been compared for various interacting conditions, viz.: (a) stacking, (b) in‐plane, and (c) terminal interactions. A comparative analysis of the results has been carried out with a view to examine suitability of different methods to study molecular aggregations in moderately large organic systems. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Electron Attachment to Solvated dGpdG: Effects of Stacking on Base‐Centered and Phosphate‐Centered Valence‐Bound Radical Anions

To explore the nature of electron attachment to guanine‐centered DNA single strands in the presence of a polarizable medium, a theoretical investigation of the DNA oligomer dinucleoside phosphate deoxyguanylyl‐3′,5′‐deoxyguanosine (dGpdG) was performed by using density functional theory. Four different electron‐distribution patterns for the radical anions of dGpdG in aqueous solution have been located as local minima on the potential energy surface. The excess electron is found to reside on the proton of the phosphate group (dGp^H?dG), or on the phosphate group (dGp^.?dG), or on the nucleobase at the 5′ position (dG^.?pdG), or on the nucleobase at the 3′ position (dGpdG^.?), respectively. These four radical anions are all expected to be electronically viable species under the influence of the polarizable medium. The predicted energetics of the radical anions follows the order dGp^.?dG>dG^.?pdG>dGpdG^.?>dGp^H?dG. The base–base stacking pattern in DNA single strands seems unaffected by electron attachment. On the contrary, intrastrand H‐bonding is greatly influenced by electron attachment, especially in the formation of base‐centered radical anions. The intrastrand H‐bonding patterns revealed in this study also suggest that intrastrand proton transfer might be possible between successive guanines due to electron attachment to DNA single strands.     

Ab initio and semiempirical computational studies on 1‐{(2E)‐2‐[(aminocarbonothioyl)hydrazono]‐2‐(3‐mesityl‐3‐methylcyclobutyl)ethyl}‐pyrrolidine‐2,5‐dione

The molecular geometry, vibrational frequencies, and gauge including atomic orbital (GIAO) ¹H‐ and ¹³C NMR chemical shift values of the title compound in the ground state have been calculated using the Hartree‐Fock (HF) and density functional theory (DFT) methods with 6‐31G(d) basis sets, and compared with the experimental data. The calculated results show that the optimized geometries can well reproduce the crystal structural parameters and the theoretical vibrational frequencies, and ¹H‐ and ¹³C NMR chemical shift values show good agreement with experimental data. To determine conformational flexibility, the molecular energy profile of the title compound was obtained by semiempirical (AM1) calculations with respect to the selected torsion angle, which was varied from ?180° to +180° in steps of 10°. The energetic behavior of the title compound in solvent media was examined using the B3LYP method with the 6‐31G(d) basis set by applying the Onsager and the polarizable continuum model (PCM). The results obtained with these methods reveal that the PCM method provided more stable structure than Qnsager's method. By using TD‐DFT method, electronic absorption spectra of the title compound have been predicted and a good agreement with the TD‐DFT method and the experimental one is determined. The predicted nonlinear optical properties of the title compound are much greater than ones of urea. In addition, the molecular electrostatic potential (MEP), frontier molecular orbitals (FMO) analysis, NBO analysis and thermodynamic properties of the title compound were investigated using theoretical calculations. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

Theoretical study of excited states of DNA base dimers and tetramers using optimally tuned range‐separated density functional theory

Excited states of various DNA base dimers and tetramers including Watson‐Crick H‐bonding and stacking interactions have been investigated by time‐dependent density functional theory using nonempirically tuned range‐separated exchange (RSE) functionals. Significant improvements are found in the prediction of excitation energies and oscillator strengths, with results comparable to those of high‐level coupled‐cluster (CC) models (RI‐CC2 and EOM‐CCSD(T)). The optimally‐tuned RSE functional significantly outperforms its non‐tuned (default) version and widely‐used B3LYP functional. Compared to those high‐level CC benchmarks, the large mean absolute deviations of conventional functionals can be attributed to their inappropriate amount of exact exchange and large delocalization errors which can be greatly eliminated by tuning approach. Furthermore, the impacts of H‐bonding and π‐stacking interactions in various DNA dimers and tetramers are analyzed through peak shift of simulated absorption spectra as well as corresponding change of absorption intensity. The result indicates the stacking interaction in DNA tetramers mainly contributes to the hypochromicity effect. The present work provides an efficient theoretical tool for accurate prediction of optical properties and excited states of nucleobase and other biological systems. © 2015 Wiley Periodicals, Inc.     

Grid‐based density functional calculations of many‐electron systems

Exploratory variational pseudopotential density functional calculations are performed for the electronic properties of many‐electron systems in the 3D cartesian coordinate grid (CCG). The atom‐centered localized gaussian basis set, electronic density, and the two‐body potentials are set up in the 3D cubic box. The classical Hartree potential is calculated accurately and efficiently through a Fourier convolution technique. As a first step, simple local density functionals of homogeneous electron gas are used for the exchange‐correlation potential, while Hay‐Wadt‐type effective core potentials are employed to eliminate the core electrons. No auxiliary basis set is invoked. Preliminary illustrative calculations on total energies, individual energy components, eigenvalues, potential energy curves, ionization energies, and atomization energies of a set of 12 molecules show excellent agreement with the corresponding reference values of atom‐centered grid as well as the grid‐free calculation. Results for three atoms are also given. Combination of CCG and the convolution procedure used for classical Coulomb potential can provide reasonably accurate and reliable results for many‐electron systems. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Quantum chemistry aspects of the solvent effects on the ene reaction of 1‐Phenyl‐1,3,4‐triazolin‐2,5‐dione and 2‐methyl‐2‐butene

A density functional theory study was used to investigate the quantum aspects of the solvent effects on the kinetic and mechanism of the ene reaction of 1‐phenyl‐1,3,4‐triazolin‐2,5‐dione and 2‐methyl‐2‐butene. Using the B3LYP/6–311++ G(d,p) level of the theory, reaction rates have been calculated in the various solvents and good agreement with the experimental data has been obtained. Natural bond orbital analysis has been applied to calculate the stabilization energy of N18? H19 bond during the reaction. Topological analysis of quantum theory of atom in molecule (QTAIM) studies for the electron charge density in the bond critical point (BCP) of N18? H19 bond of the transition states (TSs) in different solvents shows a linear correlation with the interaction energy. It is also seen form the QTAIM analysis that increase in the electron density in the BCP of N18? H19, raises the corresponding vibrational frequency. Average calculated ratio of 0.37 for kinetic energy density to local potential energy density at the BCPs as functions of N18? H19 bond length in different media confirmed covalent nature of this bond. Using the concepts of the global electrophilicity index, chemical hardness and electronic chemical potentials, some correlations with the rate constants and interaction energy have been established. Mechanism and kinetic studies on 1‐phenyl‐1,3,4‐triazolin‐2,5‐dione and 2‐methyl‐2‐butene ene reaction suggests that the reaction rate will boost with interaction energy enhancement. Interaction energy of the TS depends on the solvent nature and is directly related to electron density of the bonds involved in the reaction proceeding, global electrophilicity index and electronic chemical potential. However, the chemical hardness relationship is reversed. Finally, an interesting and direct correlation between the imaginary vibrational frequency of the N18? H19 critical bond and its electron density at the TS has been obtained. © 2014 Wiley Periodicals, Inc.     

Modeling intercalation through the sandwich‐type interactions between benzene and 14 polyaromatic molecules: DFT and ab initio results

We use second order Moller Plesset perturbation theory and several density functional theory methods to calculate the counterpoise corrected electronic interaction energies between benzene and a series of polyaromatic molecules. These systems serve as a simple model for DNA intercalation. We show that addition of nitrogen atoms to the polyaromatic molecules always increases sandwich‐type interactions, and that, of the density functional theory methods studied, only SVWN can mimic the interaction energies and optimal separations obtained with perturbation theory. SVWN reproduces the optimal molecular distances obtained with perturbation theory very well, and often comes within less than 10% of the interaction energy. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

A comparison of the effect of nanotube chirality and electronic properties on the π–π interaction of single‐wall carbon nanotubes with pyrazinamide antitubercular drug

Theoretical investigation on local electronic structure and stability of the π–π stacking interaction of pyrazinamide (PZA) with armchair (5,5) and zigzag (9,0) single‐walled carbon nanotubes (SWCNTs) is performed using density functional theory (DFT). PZA is physisorbed onto nanotube sidewall through interaction of π orbitals of PZA and SWCNT and the enhanced structural stability of PZA/SWCNT systems is due to weak side‐on rather than the head‐on π‐interactions. The physisorption of PZA onto SWCNT sidewall is thermodynamically favored; as a consequence, it modulates the electronic properties of pristine nanotube in the vicinity of Fermi region and π–π stacked interactions is stronger in (9,0) SWCNT compared to (5,5) SWCNT. The density of states (DOS) analysis show that PZA contributes toward the enhancement of electronic states. Projected DOS and frontier orbital analysis in the vicinity of Fermi level region suggest the electronic states to be contributed from SWCNT rather than PZA. In addition, hybrid DFT calculation which includes the dispersion correction is employed to explain the non‐covalent π–π stacking interaction between PZA and SWCNT. The local density approximation and GGA results are compared with DFT‐D to explain near about accurately the weak nonbonded van der Waals interactions between PZA and SWCNTs. © 2012 Wiley Periodicals, Inc.     

A solvation‐free‐energy functional: A reference‐modified density functional formulation

The three‐dimensional reference interaction site model (3D‐RISM) theory, which is one of the most applicable integral equation theories for molecular liquids, overestimates the absolute values of solvation‐free‐energy (SFE) for large solute molecules in water. To improve the free‐energy density functional for the SFE of solute molecules, we propose a reference‐modified density functional theory (RMDFT) that is a general theoretical approach to construct the free‐energy density functional systematically. In the RMDFT formulation, hard‐sphere (HS) fluids are introduced as the reference system instead of an ideal polyatomic molecular gas, which has been regarded as the appropriate reference system of the interaction‐site‐model density functional theory for polyatomic molecular fluids. We show that using RMDFT with a reference HS system can significantly improve the absolute values of the SFE for a set of neutral amino acid side‐chain analogues as well as for 504 small organic molecules. © 2015 Wiley Periodicals, Inc.     

The Rearrangement of 2,2‐Diphenyl‐1‐[(E)‐2‐phenylethenyl]cyclopropane to 3,4,4‐Triphenylcyclopent‐1‐ene: a DFT Analysis

A computational study on the rearrangement of 2,2‐diphenyl‐1‐[(E)‐2‐phenylethenyl]cyclopropane ( 1 ) is presented, using density functional theory (DFT), (U)B3LYP with the 6‐31G* basis set (DFT1) and (U)M05‐2X with the 6‐311+G** basis set (DFT2). In agreement with a biradical character of the transition structure (TS) or intermediate, the potential‐energy hypersurface is lowered by the influence of three conjugated Ph groups. Surprisingly, two conformations of the geminal diphenyl group (different twist angles) induce two different minimum‐energy pathways for the rearrangement. Independent of the functional used, the first hypersurface harbors true biradical intermediates, whereas the second energy surface is a flat, slightly ascending slope from the starting material to the TS. The functional (U)M05‐2X with the basis set 6‐311+G** provides realistic energies which seem to be close to experiment. The activation energy for racemization of enantiomers of 1 is lower than that of rearrangement by 2.5 kcal mol^?1, in agreement with experiment.     

Evaluating Shielding‐Based Ring‐Current Models by Using the Gauge‐Including Magnetically Induced Current Method

Magnetically induced current densities and integrated ring‐current strength susceptibilities have been calculated at the density functional theory (DFT) level for a test set consisting of 17 ring‐shaped molecules using the gauge‐including magnetically induced current (GIMIC) method. Reliable values for the ring‐current strengths have been obtained by performing numerical integration of the current‐density susceptibility passing a cut plane perpendicularly to the molecular ring. The current densities and ring current strengths were calculated at the DFT level using the B3LYP functional and def2‐TZVP basis sets. Current densities and ring‐current strengths have also been calculated at the Hartree‐Fock self‐consistent field (HF‐SCF) level using Dunning’s aug‐cc‐pVTZ basis sets, which allow a direct comparison with ring‐current strengths that have previously been estimated using ring‐current models based on magnetic shielding calculations. Current density calculations at both levels of theory show that the magnetic shielding based ring‐current models are not a very accurate means to estimate the magnetically induced ring current strengths, whereas they provide qualitatively the correct aromaticity trends for the studied molecules.     

Theoretical study of the excited‐state double proton transfer in the (3‐methyl‐7‐azaindole)‐(7‐azaindole) heterodimer

Excited‐state double proton transfer (ESDPT) in the (3‐methyl‐7‐azaindole)‐(7‐azaindole) heterodimer is theoretically investigated by the long‐range corrected time‐dependent density functional theory method and the complete‐active‐space second‐order perturbation theory method. The calculated potential energy profiles exhibit a lower barrier for the concerted mechanism in the locally excited state than for the stepwise mechanism through the charge‐transfer state. This result suggests that the ESDPT in the isolated heterodimer is likely to follow the former mechanism, as has been exhibited for the ESDPT in the homodimer of 7‐azaindole. © 2012 Wiley Periodicals, Inc.     

First principles study on the structure and electronic properties of 2‐nitrimino‐1‐nitroimidazolidine

The properties of 2‐Nitrimino‐1‐nitroimidazolidine are calculated by using SIESTA code, which adopts the standard Kohn‐Sham self‐consistent density functional method in the local density approximation. The structures and electronic properties are analyzed, and the factors that affect the impact sensitivity are discussed based on the crystal structure, band energy, and projected density of state. The reason for the smaller impact sensitivity compared to RDX (hexahydro‐1,3,5‐trinitro‐1,3,5‐triazine) is also explored from several respects such as the weakest bond dissociation energy in single molecule, and hydrogen bond, band gap in the crystal. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Isatin‐Schiff base copper(II) complexes—A DFT study of the metal‐ligand bonding situation

Herein, we report results of calculations based on density functional theory (BP86/TZVP) of a set of isatin‐Schiff base copper(II) and related complexes, 1‐12, that have shown significant pro‐apoptotic activity toward diverse tumor cells. The interaction of the copper(II) cation with different ligands has been investigated at the same level of theory. The strength and character of the Cu(II)‐L bonding was characterized by metal‐ligand bond lengths, vibrational frequencies, binding energies, ligand deformation energies, and natural population analysis. The metal‐ligand bonding situation was also characterized by using two complementary topological approaches, the quantum theory of atoms‐in‐molecules (QTAIM) and the electron localization function (ELF). The calculated electronic g‐tensor and hyperfine coupling constants present significant agreement with the EPR experimental data. The calculated parameters pointed to complex 10 as the most stable among the isatin‐Schiff base copper(II) species, in good agreement with experimental data that indicate this complex as the most reactive in the series. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

Charge transport and optical properties of discotic liquid crystalline molecules THDDP and substituted THDP

The theoretical investigations have been carried out on the discotic liquid crystalline molecules, 2,3,6,7‐tetrakis‐hexyloxy‐9,16‐diaza‐dibenzo[a,c]phenazine (THDDP) and different substituted 2,3,6,7‐tetrakis‐hexyloxy‐dibenzo[a,c]phenazine (THDP) to study their charge transport and optical properties. The key parameters of charge transport such as charge transfer integrals and site energies have been calculated from the matrix elements of Kohn‐Sham Hamiltonian. The reorganization energy for the presence of excess charge and the rate of charge transfer calculated from Marcus theory have been used to find the mobility of the charge carrier in the studied molecules. The results show that the substitution and stacking angle change strongly affect the charge carrier mobility in π‐stacked THDDP and substituted THDP molecules. Molecular dynamics simulations have been performed to find the most favorable conformation. The time‐dependent density functional theory (TDDFT) calculations reveal that for these molecules the different substitutions does not alter the main features of optical properties and the molecules may be used as blue light emitters. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Conformational analysis of cycloheptane,oxacycloheptane, 1,2‐dioxacycloheptane, 1,3‐dioxacycloheptane,and 1,4‐dioxacycloheptane

The conformational analysis of cycloheptane (1), oxacycloheptane (2), 1,2‐dioxacycloheptane (3), 1,3‐dioxacycloheptane (4), and 1,4‐dioxacycloheptane (5) has been carried out using B3LYP, CCD, CCSD, and QCISD with the 6‐311+G(d,p) and cc‐pVDZ basis sets. The twist chair conformers are predicted to be lower in energy than their corresponding boat and chair conformations. All levels of theory predict (4) to be lower in energy than (3) and (5). CCSD predicts remarkably similar activation barriers for the conformational interconversion of the twist chair conformers to their corresponding boat conformers. Small barriers to pseudorotation are also predicted. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

On the relative stability of cobalt‐ and nickel‐based amidinate complexes against β‐migration

We present a first‐principles study on the relative stability of cobalt‐ and nickel‐based amidinate complexes against β‐migration using density functional theory. Factors that influence the reactivity of these compounds were carefully addressed and the calculated molecular structures are in excellent agreement with the available crystal structural data. Reaction energies as well as activation barriers of β‐migration were evaluated. The predicted relative stability of the selected compounds is consistent with experimental observations. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009