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At least 1,747 records · Page 97Linked to original sources
PubMed2006

Conformation effects on the electronic structures of beta-alanine.

Ten low-lying conformers of beta-alanine have been studied by the hybrid density functional B3LYP/aug-cc-pVDZ method. Energetic extrapolation calculations at the MP3 and MP4(SDQ) levels of theory and the theoretical photoelectron spectra simulated with the electron propagation theory demonstrate that there are at least three gauche conformers (G1, G2, and G3) in gas-phase experiments. The calculated ionization potentials are in good agreement with the experimental data available in the literature. Natural bond orbital and atoms-in-molecules analyses exhibit a remarkable influence on the molecular electronic structures by the strong intramolecular hydrogen bonding O-H...N in the neutral conformer G2. Remarkable internal rotations of the COOH group are found in the cationic G1+ and G3+ with respect to the neutral conformers. A distonic [NH3+-(CH2)2-COO*] radical can be formed through the spontaneous intramolecular proton transfer in G2+. A novel intramolecular hydrogen bonding, C-H...O, is found in the anti A1+ cation.

Computer Simulation↗
PubMed2006

A self-consistent field quantum hydrodynamic approach for molecular clusters.

We present a novel self-consistent orbital-free method useful for quantum clusters. The method uses a hydrodynamical approach based on the de Broglie-Bohm description of quantum mechanics to satisfy an orbital-free density functional-like Euler-Lagrange equation for the ground state of the system. In addition, we use an information theoretical approach to obtain the optimal density function derived from a series of statistical sample points in terms of density approximates. These are then used to calculate an approximation to the quantum force in the hydrodynamic description. As a demonstration of the utility and flexibility of the approach, we compute the lowest-energy structures for small rare-glass clusters of argon and neon with 4, 5, 13, and 19 atoms. Extension to more complex systems is straightforward.

Journal Article↗
PubMed2006

Gas-phase DNA oligonucleotide structures. A QM/MM and atoms in molecules study.

QM/MM calculations have been employed to investigate the role of hydrogen bonding and pi-stacking in single- and double-stranded DNA oligonucleotides. DFT calculations and Atoms in Molecules analysis on QM/MM-optimized structures allow characterization and estimation of the energies of pi-stacking and hydrogen-bond interactions. This shows that pi-stacking interactions depend on the number and the nature of the DNA bases for single-stranded nucleotides; for instance, guanines are found to be involved in strong hydrogen bonds, whereas adenines interact mainly via stacking interactions. The role of interbase hydrogen bonding was explored: the -NH2 groups of guanine, adenine, and cytosine participate in N-H...O and N-H...N interactions. These are much stronger in single-strand oligonucleotides, where the -NH2 groups are highly nonplanar. In double-stranded DNA, the strong base-pairing hydrogen bonds of complementary bases lead to more planar -NH2 groups, which tend to be involved in pi-stacking interactions rather than H-bonds. The use of AIM also allows us to evaluate the interplay of pi-stacking and H-bonding, suggesting that cooperativity does occur, but is generally limited to about 1-2 kcal/mol.

Computer Simulation↗
PubMed2006

Second hyperpolarizabilities (gamma) of bisimidazole and bistriazole benzenes: diradical character, charged state, and spin state dependences.

The second hyperpolarizabilities of bisimidazole- and bistriazole-benzene compounds have been calculated at different levels of approximation to unravel the effects of diradical character as well as of charge and spin multiplicity. The largest second hyperpolarizabilities are associated with intermediate diradical character, provided positive charging does not compensate for this effect. For the neutral diradical bisimidazole compound, the singlet diradical species possesses a second hyperpolarizability two to three times larger than the corresponding triplet, demonstrating the possibility of spin state control of the third-order NLO responses for diradical species.

Benzene Derivatives↗
PubMed2006

An ab initio study of the absorption spectra of indirubin, isoindigo, and related derivatives.

The UV/visible spectra of a series of indirubin, isoindigo, and other indigo/thioindigo related dyes have been evaluated in various solvent environments by using the time-dependent density functional theory in conjunction with the polarizable continuum model. Even for molecules of the same family, significant differences in the excitation processes have been noted. Two hybrid functionals have been selected: B3LYP and PBE0. For a set of the 50 selected molecular cases, both functionals provide accurate lambda(max), with mean absolute deviations limited to 0.1 eV. Actually, isoindigo is the main challenging series, with systematically underestimated excitation energies, due to the different nature of the excitation process. In most cases, we found that PBE0 is more efficient in reproducing the experimental values than B3LYP for sulfur-containing dyes not featuring internal hydrogen bonds, the reverse assertion being also true. In addition, the spectra of a series of unknown dyes have been predicted.

Computer Simulation↗
PubMed2006

Isomer stability of N6C6H6 cages.

Recent theoretical studies have identified carbon-nitrogen cages that are potentially stable high energy density materials (HEDM). One such molecule is an N(6)C(6)H(6) cage in which a six-membered ring of nitrogen is bonded to C(3)H(3) triangles on both sides. This molecule is based on the structure of the most stable N(12) cage, with six carbon atoms substituted into the structure. In the current study, several N(6)C(6)H(6) isomers (including the previously studied cage) are examined by theoretical calculations to determine which is actually the most stable. Stability will be evaluated from two points of view: (1) thermodynamic stability of one isomer versus another and (2) kinetic stability of each isomer as determined by the energetics of bond breaking. Density functional theory (B3LYP), perturbation theory (MP2 and MP4), and coupled-cluster theory (CCSD(T)) are used in this study, along with the correlation-consistent basis sets of Dunning. Trends in thermodynamic and kinetic stability are discussed.

Carbon↗
PubMed2006

A molecular dynamics investigation of the influence of hydration and temperature on structural and dynamical properties of a dimyristoylphosphatidylcholine bilayer.

A series of molecular dynamics simulations of dimyristoylphosphatidylcholine bilayers, with different levels of hydration and temperature, were performed to examine the influence of hydration on properties of lipid membranes. Structural and dynamical properties such as area per lipid, electron densities, order parameters for all CH bonds and water, diffusion, and reorientation autocorrelation functions were determined and were all found to be affected by changes in the hydration level. The simulations give an overall picture of the bilayer going to a more ordered state when the hydration level is reduced. Lipid headgroups were found to adopt an orientation more parallel to the membrane plane when the water content was decreased. Dynamical properties such as lipid diffusion and relaxation of reorientation time correlation functions were found to become slower with the removal of water. Our simulation results generally agree with experimental data in cases where such data are available. One important conclusion drawn is that while structural properties are affected only moderately dynamical properties are affected very strongly by a decrease of water content.

Computer Simulation↗
PubMed2006

Parametrization of 1-butyl-3-methylimidazolium hexafluorophosphate/nitrate ionic liquid for the GROMOS force field.

A united-atom model of 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF(6)]) and 1-butyl-3-methylimidazolium nitrate ([BMIM][NO(3)]) is developed in the framework of the GROMOS96 43A1(1) force field. These two ionic liquids are parametrized, and their equilibrium properties in the 298-363 K temperature range are subjected to validation against known experimental properties, namely, density, self-diffusion, shear viscosity, and isothermal compressibility. The ionic radial/spatial distributions, pi interaction, gauche/trans populations of the butyl tail, and enthalpies of vaporization are also reported. The properties obtained from the molecular dynamics simulations agree with experimental data and have the same temperature dependence. The strengths and weakness of our model are discussed.

Computer Simulation↗
PubMed2006

Structure of the boronic acid dimer and the relative stabilities of its conformers.

Despite the widespread use of boronic acids in materials science and as pharmaceutical agents, many aspects of their structure and reactivity are not well understood. In this research the boronic acid dimer, [HB(OH)(2)](2), was studied by second-order Møller-Plesset (MP2) perturbation theory and coupled cluster methodology with single and double excitations (CCSD). Pople split-valence 6-31+G*, 6-311G**, and 6-311++G** and Dunning-Woon correlation-consistent cc-pVDZ, aug-cc-pVDZ, cc-pVTZ, and aug-cc-pVTZ basis sets were employed for the calculations. A doubly hydrogen-bonded conformer (1) of the dimer was consistently found to be lowest in energy; the structure of 1 was planar (C(2h)) at most computational levels employed but was significantly nonplanar (C(2)) at the MP2/6-311++G** and CCSD/6-311++G** levels, the result of an intrinsic problem with Pople-type sp-diffuse basis functions on heavy atoms. The dimerization energy, enthalpy, and free energy for the formation of (1) from the exo-endo conformer of the monomer were -10.8, -9.2, and +1.2 kcal/mol, respectively, at the MP2/aug-cc-pVTZ level. Several other hydrogen-bonded conformers of the dimer were local minima on the potential energy surface (PES) and ranged from 2 to 5 kcal/mol higher in energy than 1. Nine doubly OH-bridged conformers, in which the boron atoms were tetracoordinated, were also local minima on the PES, but they were all greater than 13 kcal/mol higher in energy than 1; doubly H-bridged structures proved to be transition states. MP2 and CCSD results were compared to those from the BLYP, B3LYP, OLYP, O3LYP, PBE1PBE, and TPSS functionals with the 6-311++G** and aug-cc-pVTZ basis sets; the PBE1PBE functional performed best relative to the MP2 and CCSD results. Self-consistent reaction field (SCRF) calculations predict that boronic acid dimerization is less favorable in solution than in vacuo.

Boronic Acids↗
PubMed2006

The reactivity of all-metal aromatic complexes: a theoretical investigation on the methane activation reaction.

The recent finding of all-metal aromaticity enlightens us to explore the reactivity of all-metal aromatic complexes. The methane activation reaction was chosen for this purpose. The whole catalysis process of all-metal aromatics was investigated by theoretical calculation. The results reveal that the reaction barriers with all-metal aromatic complexes are far lower than that without any catalysts. All-metal aromatic complexes are predicted to have potential to be used as catalysts for the first time.

Aluminum↗
PubMed2003

QM/MM calculations of kinetic isotope effects in the chorismate mutase active site.

Kinetic isotope effects have been computed for the Claisen rearrangement of chorismate to prephenate in aqueous solution and in the active site of chorismate mutase from B. subtilus. These included primary 13C and 18O and secondary 3H effects for substitutions at the bond-making and bond-breaking positions. The initial structures of the putative stationary points on the potential energy surface, required for the calculations of isotope effects using the CAMVIB/CAMISO programs, have been selected from hybrid QM/MM molecular dynamical simulations using the DYNAMO program. Refinement of the reactant complex and transition-state structures has been carried out by means of AM1/CHARMM24/TIP3P calculations using the GRACE program, with full gradient relaxation of the position of > 5200 atoms for the enzymic simulations, and with a box containing 711 water molecules for the corresponding reaction in aqueous solution. Comparison of these results, and of gas phase calculations, with experimental data has shown that the chemical rearrangement is largely rate-determining for the enzyme mechanism. Inclusion of the chorismate conformational pre-equilibrium step in the modelled kinetic scheme leads to better agreement between recent experimental data and theoretical predictions. These results provide new information on an important enzymatic transformation, and the key factors responsible for the kinetics of its molecular mechanism are clarified. Treatment of the enzyme and/or solvent environment by means of a large and flexible model is absolutely essential for prediction of kinetic isotope effects.

Bacillus subtilis↗
PubMed2005

Excited state tautomerization of azaindole.

Fluorescent tryptophan analogs, like azatryptophan, offer an advantage for exploring protein and peptide structure and dynamics. The chromophoric moieties, azaindole, of the azatryptophan analogs are investigated for their potential as fluorescent probes. The photophysical properties of 4-azaindole (4AI) and 5-azaindole (5AI) and their tautomers are characterized through computational and experimental methods. Both 4AI and 5AI undergo excited state tautomerization in the presence of 1 M NaOH. The protonated forms of 4AI and 5AI have a fluorescence emission of 415 and 410 nm, respectively, while the tautomers of 4AI and 5AI have a fluorescent emission of 480 and 450 nm, respectively. Gas phase computations (B3LYP/6-31+G**) show that the N1H azaindole tautomer is lower in energy in the ground state by as much as 12.5 kcal mol(-1), while the N(n)H azaindole tautomer is lower in energy in the excited state by as much as 18.1 kcal mol(-1). Solvent effects on the tautomer energy differences were computed using the isodensity polarized continuum model (IPCM). The polarity of the solvent helps to reduce the energy difference between the tautomers in the ground state by as much as 5.8 kcal mol(-1), but not enough to reverse the ground state tautomer preference.

Aza Compounds↗
PubMed2005

Accuracy and limitations of second-order many-body perturbation theory for predicting vertical detachment energies of solvated-electron clusters.

Vertical electron detachment energies (VDEs) are calculated for a variety of (H(2)O)(n)(-) and (HF)(n)(-) isomers, using different electronic structure methodologies but focusing in particular on a comparison between second-order Møller-Plesset perturbation theory (MP2) and coupled-cluster theory with noniterative triples, CCSD(T). For the surface-bound electrons that characterize small (H(2)O)(n)(-) clusters (n< or = 7), the correlation energy associated with the unpaired electron grows linearly as a function of the VDE but is unrelated to the number of monomers, n. In every example considered here, including strongly-bound "cavity" isomers of (H(2)O)(24)(-), the correlation energy associated with the unpaired electron is significantly smaller than that associated with typical valence electrons. As a result, the error in the MP2 detachment energy, as a fraction of the CCSD(T) value, approaches a limit of about -7% for (H(2)O)(n)(-) clusters with VDEs larger than about 0.4 eV. CCSD(T) detachment energies are bounded from below by MP2 values and from above by VDEs calculated using second-order many-body perturbation theory with molecular orbitals obtained from density functional theory. For a variety of both strongly- and weakly-bound isomers of (H(2)O)(20)(-) and (H(2)O)(24)(-), including both surface states and cavity states, these bounds afford typical error bars of +/-0.1 eV. We have found only one case where the Hartree-Fock and density functional orbitals differ qualitatively; in this case the aforementioned bounds lie 0.4 eV apart, and second-order perturbation theory may not be reliable.

Electrons↗
PubMed2004

Single molecule photon emission statistics in the slow modulation limit.

A framework for calculating photon emission statistics for single chromophores perturbed by slow environmental fluctuations is introduced. When internal chromophore dynamics are significantly faster than time scales for environmental modulation it becomes possible to invoke a type of adiabatic approximation, allowing for straightforward calculation of photon counting moments including explicitly quantum effects. Unlike previous exact treatments, the present methodology involves calculation of dynamics reflecting only the modulation characteristics of the environment and quantum dynamics of an isolated chromophore separately, i.e., the complicated intermingling of chromophore quantum dynamics and the environmental modulation are suppressed via the adiabatic approximation. This leads to significant conceptual and computational simplifications. Within its regime of applicability, the present approximation reproduces exact calculations quantitatively. We demonstrate this accuracy explicitly for the case of a two-level chromophore modulated by a number of different stochastic models.

Computer Simulation↗
PubMed2005

Correlated holes and their relationships with reduced density matrices and cumulants.

This paper describes a matrix formulation for the correlated hole theory within the framework of the domain-averaged model in many electron systems (atoms, molecules, condensed matter, etc.). General relationships between this quantity and one-particle reduced density matrices for any independent particle or correlated state functions are presented. This formulation turns out to be suitable for computational purposes due to the straightforward introduction of cumulants of two-particle reduced density matrices within the quantum field structure. Numerical calculations in selected simple molecular systems have been performed in order to determine preliminary correlated values for such a quantity.

Journal Article↗
PubMed2006

Structures and relative stability of neutral gold clusters: Aun (n=15-19).

We performed a global-minimum search for low-lying neutral clusters (Au(n)) in the size range of n=15-19 by means of basin-hopping method coupled with density functional theory calculation. Leading candidates for the lowest-energy clusters are identified, including four for Au(15), two for Au(16), three for Au(17), five for Au(18), and one for Au(19). For Au(15) and Au(16) we find that the shell-like flat-cage structures dominate the population of low-lying clusters, while for Au(17) and Au(18) spherical-like hollow-cage structures dominate the low-lying population. The transition from flat-cage to hollow-cage structure is at Au(17) for neutral gold clusters, in contrast to the anion counterparts for which the structural transition is at Au(16) (-) [S. Bulusu et al., Proc. Natl. Acad. Sci. U.S.A. 103, 8362 (2006)]. Moreover, the structural transition from hollow-cage to pyramidal structure occurs at Au(19). The lowest-energy hollow-cage structure of Au(17) (with C(2v) point-group symmetry) shows distinct stability, either in neutral or in anionic form. The distinct stability of the hollow-cage Au(17) calls for the possibility of synthesizing highly stable core/shell bimetallic clusters M@Au(17) (M=group I metal elements).

Computer Simulation↗
PubMed1994

The electronic factor in QSAR: MO-parameters, competing interactions, reactivity and toxicity.

Reactive chemicals pose unique problems in the development of SAR and QSAR in environmental chemistry and toxicology. Models of the stereoelectronic interactions of reactive toxicants with biological systems require formulation of parameters that quantify the electronic structure of the chemicals. A review of early approaches to modeling reactivity is presented in this work, with emphasis on the generalized polyelectronic perturbation theory. Applications of GPPT are demonstrated with QSARs for predicting toxicity of soft electrophiles and proelectrophiles using superdelocalizability and the charges on frontier orbitals. Prediction of toxicity for hard electrophiles such as organophosphates require atomic charges and bond orders in the QSAR. Special considerations for the orthogonality of factors and for the classification of reactive chemicals are reviewed.

Analysis of Variance↗
PubMed2001

Renormalization group in quantum mechanics at zero and finite temperature.

We apply the renormalization group formalism, to integrate quantum fluctuations of quantum mechanical systems at zero and finite temperature. At zero temperature a nonperturbative renormalization group equation allows to compute the ground state energy whereas at finite temperature a variational renormalization group equation is proposed to compute the free energy.

Journal Article↗