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At least 631 records · Page 35Linked to original sources
PubMed2005

Dynamical hydrogen atom tunneling in dichlorotropolone: a combined quantum, semiclassical, and classical study.

Based on the Cartesian Reaction Surface framework we construct a four-dimensional potential for the tropolone derivative 3,7-dichlorotropolone, a molecule with an intramolecular O-H...O hydrogen bond. The reduced configuration space involves the in-plane hydrogen atom coordinates, a symmetric O-O vibrational mode, and an antisymmetric mode related to deformations of the seven-membered ring. The system is characterized in terms of quantum mechanical computations of the low-lying eigenstates as well as a classical and semiclassical analysis of spectra obtained via Fourier transforming autocorrelation functions. For the semiclassical analysis we utilize the amplitude-free correlation function method [K. Hotta and K. Takatsuka, J. Phys. A 36, 4785 (2003)]. Our results demonstrate substantial anharmonic couplings leading to highly correlated wave functions even at moderate energies. Furthermore, the importance of dynamical tunneling in tropolone is suggested since many low-lying states--including the ground state--lie above the classical saddle point but nevertheless appear as split pairs.

Journal Article↗
PubMed2005

Vibrational energies for the X1A1, A1B1, and B1A1 states of SiH2/SiD2 and related transition probabilities based on global potential energy surfaces.

Transition probabilities were evaluated for the X(1)A(1)-A(1)B(1) and A(1)B(1)-B(1)A(1) systems of SiH(2) and SiD(2) to analyze the X-->A-->B photoexcitation. The Franck-Condon factors (FCFs) and Einstein's B coefficients were computed by quantum vibrational calculations using the three-dimensional potential energy surfaces (PESs) of the SiH(2)(X(1)A(1),A(1)B(1),B(1)A(1)) electronic states and the electronic transition moments for the X-A, X-B, and A-B system. The global PESs were determined by the multireference configuration interaction calculations with the Davidson correction and the interpolant moving least-squares method combined with the Shepard interpolation. The obtained FCFs for the X-A and A-B systems exhibit that the bending mode is strongly enhanced in the excitation since the equilibrium bond angle greatly varies with the three states; the barrier to linearity is evaluated to be 21,900 cm(-1) for the X state, 6400 cm(-1) for the A state, and 230-240 cm(-1) for the B state. The theoretical lifetimes for the pure bending levels of the A and B states were calculated from the fluorescence decay rates for the A-X, B-A, and B-X emissions.

Journal Article↗
PubMed2006

Theoretical transition probabilities for the A 1Pi-X 1Sigma+ system of AlNC and AlCN isomers based on global potential energy surfaces.

Transition probabilities were evaluated for the X (1)Sigma(+)-A (1)Pi system of AlNC and AlCN isomers to analyze photoabsorption and fluorescence spectra. The global potential energy surfaces (PESs) of the X (1)Sigma(+) and A (1)Pi (1 (1)A("),2 (1)A(')) electronic states were determined by the multireference configuration interaction calculations with the Davidson correction. Einstein's B coefficients were computed by quantum vibrational calculations using the three-dimensional PESs of these states and the electronic transition moments for the X-1 (1)A(") and X-2 (1)A(') systems. Einstein's B coefficients obtained for AlNC or AlCN exhibit that the Al-N or Al-C stretching mode is strongly enhanced in the transition. The absorption and fluorescence spectra calculated for the X-1 (1)A(") and X-2 (1)A(') systems are discussed comparing with the observed photoexcitation and fluorescence spectra. The lifetimes for the several vibrational levels of the A (1)Pi state were calculated to be ca. 7 ns for AlNC and 21-24 ns for AlCN from the fluorescence decay rates of the 1 (1)A(")-X and 2 (1)A(')-X emissions.

Journal Article↗
PubMed2006

Symmetry-, time-, and temperature-dependent strength of carbon nanotubes.

Although the strength of carbon nanotubes has been of great interest, their ideal value has remained elusive both experimentally and theoretically. Here, we present a comprehensive analysis of underlying atomic mechanisms and evaluate the yield strain for arbitrary nanotubes at realistic conditions. For this purpose, we combine detailed quantum mechanical computations of failure nucleation and transition-state barriers with the probabilistic approach of the rate theory. The numerical results are then summarized in a concise set of equations for the breaking strain. We reveal a competition between two alternative routes of brittle bond breaking and plastic relaxation, determine the domains of their dominance, and map the nanotube strength as a function of chiral symmetry, tensile test time, and temperature.

Journal Article↗
PubMed2004

3D structure model of the principal neutralizing epitope of Minnesota HIV-1 isolate.

A hierarchical procedure, using a "bottom-up" strategy and combining (i). a probabilistic approach for estimating all possible starting structures, (ii). restrained molecular mechanics algorithms for preliminary selection of all energetically preferred conformers, as well as (iii). quantum chemical computations for refining their geometry, was used to study the structural properties of the HIV-MN neutralizing epitope in terms of NMR spectroscopy data. As a result, only one of initial structures matching the experimental and theoretical data was found to be well-ground for implementing the function of immunoreactive conformation of the virus immunogenic crown. The geometric parameters of this structure in water solution were shown to correspond to a double beta-turn conformation similar to that revealed in crystal for synthetic molecules imitating the central region of the HIV-MN V3 loop. The following conclusion was drawn from the comparative analysis of simulated structure with the one computed previously: the HIV-MN immunogenic tip has some inherent conformational flexibility that manifests at the alterations of hexapeptide environment and leads to the structural transitions changing the local conformation of the stretch of interest but retaining its spatial main chain fold. As a matter of record, the high resolution 3D structure model for the HIV-MN principal neutralization site was constructed, and its geometric parameters were compared with the corresponding characteristics of conformers derived earlier for describing the conformational features of immunogenic tip of gp120 from Thailand HIV-1 isolate.

Epitopes↗
PubMed2004

Dual spatial folds and different local structures of the HIV-1 immunogenic crown in various virus isolates.

Local and global structural properties of the HIV-1 principal neutralizing epitope were studied in terms of NMR spectroscopy data reported in literature for the HIV-Haiti and HIV-RF isolates. To this effect, the NMR-based method comprising a probabilistic model of protein conformation in conjunction with the molecular mechanics and quantum chemical computations was used for determining the ensembles of conformers matching the NMR requirements and energy criteria. As a matter of record, the high resolution 3D structure models were constructed for the HIV-Haiti and HIV-RF immunogenic crowns, and their geometric parameters were collated with the ones of conformers derived previously for describing the conformational features of immunogenic tip of gp120 from Thailand and MN HIV-1 strains. The HIV-1 neutralization site was demonstrated to constitute in water solution highly flexible system sensitive to its environment. This inference is completely valid for the geometric space of dihedral angles where statistically significant differences in local structures of simulated conformers have been found for all virus isolates of interest. In spite of this fact, the stretch analyzed was shown to manifest a certain conservatism in the space of atomic coordinates, building up in four HIV-1 isolates two spatial folds similar to those observed in crystal for the V3 loop peptides bound to different neutralizing Fabs. The results are discussed in the light of literature data on HIV-1 neutralizing epitope structure.

Amino Acid Sequence↗
PubMed1994

Sequential method of estimating the LD50 using a modified up-and-down rule.

In this paper, the original up-and-down method, modified up-and-down method, the Robbins-Monro method, and a fixed-sample Spearman-Kärber method are compared for the point estimator as well as the confidence interval of LD50. In particular, three different designs of the modified up-and-down approach based on the combination of experiments on one test space and reduced test space are investigated. The standard normal distribution and chi-square distribution are used as tolerance distributions. Simulation results indicate that the modified up-and-down method tends to be somewhat better than the original up-and-down method in terms of the mean squared error under normal tolerance distribution. In case of chi-square distribution, the modified method is shown to be substantially better when the test space is wide and the initial dose is further away from the LD50.

Lethal Dose 50↗
PubMed2001

Parametric correlations of the energy levels of ray-splitting billiards.

Parameter-dependent statistical properties of the spectra of ray-splitting billiards are studied experimentally and theoretically. The autocorrelation functions c(x) and c(omega,x) of level velocities as well as the generalized conductance C(0) are calculated for two different classically chaotic ray-splitting billiards. Experimentally a modified Sinai ray-splitting billiard is studied consisting of a thin microwave rectangular cavity with two quarter-circle-shaped Teflon inserts. The length of the cavity serves as the experimentally adjustable parameter. For the theoretical estimates of the parametric correlations we compute the quantum spectrum of a scaling triangular ray-splitting billiard. Our experimental and numerical results are compared with each other and with the predictions of random matrix theory.

Journal Article↗
PubMed2001

High accuracy many-body calculational approaches for excitations in molecules.

Two state-of-the-art computational approaches: quantum Monte Carlo and GW with exciton effects [GW-BSE (Bethe-Salpeter equation)] are employed to calculate ionization potentials, electron affinities, and first excited singlet and triplet energies for the silane and methane molecules. Results are in excellent agreement between these dramatically different approaches and with available experiment. The optically forbidden triplet excitation in silane is predicted to lie roughly 1 eV higher than previously reported. In the GW-BSE method, we demonstrate that inclusion of off-diagonal matrix elements in the self-energy operator is crucial for an accurate picture.

Journal Article↗
PubMed2001

Surface temperature dependence of the inelastic scattering of hydrogen molecules from metal surfaces.

The surface temperature dependence of activated inelastic scattering and dissociation of D2 from the Cu(111) surface has been computed using quantum wave-packet methods. It is found, in agreement with experimental data, that the surface temperature dependence generally has an Arrhenius form with an activation energy dependent on molecular translational energy and on the initial and final internal molecular states. The translational energy dependence of the activation energy is linear up to the threshold energy, with an abrupt change thereafter. On the basis of the wave-packet calculations, a model has been developed to explain these findings and highlight their general nature.

Journal Article↗
PubMed2003

Predicting crystal structures with data mining of quantum calculations.

Predicting and characterizing the crystal structure of materials is a key problem in materials research and development. It is typically addressed with highly accurate quantum mechanical computations on a small set of candidate structures, or with empirical rules that have been extracted from a large amount of experimental information, but have limited predictive power. In this Letter, we transfer the concept of heuristic rule extraction to a large library of ab initio calculated information, and we demonstrate that this can be developed into a tool for crystal structure prediction.

Journal Article↗
PubMed1996

Conformational and electrostatic properties of V-G-G-V-G, a typical sequence of the glycine-rich regions of elastin. An ab initio quantum molecular study.

The conformational analysis and electrostatic properties of the monomeric sequence V-G-G-V-G of the glycine-rich regions of elastin is presented with the aim of explaining NMR and CD experimental results. On the basis of the molecular model NH+3-V-G-G-V-G-COO, Gaussian 92 quantum-molecular computations were performed by using principally an ab initio method at the 3-21G level and AM1. The occurrence of local secondary structures and of beta I, beta II, beta II' and VIa turns is discussed. Our results clearly demonstrate that the transconformations beta I-->half turn (which was invoked to explain experimental results) and beta I-->beta II' are theoretically allowed.

Computer Simulation↗
PubMed2000

Semiclassical calculation of chemical reaction dynamics via wavepacket correlation functions.

Calculation of chemical reaction dynamics is central to theoretical chemistry. The majority of calculations use either classical mechanics, which is computationally inexpensive but misses quantum effects, such as tunneling and interference, or quantum mechanics, which is computationally expensive and often conceptually opaque. An appealing middle ground is the use of semiclassical mechanics. Indeed, since the early 1970s there has been great interest in using semiclassical methods to calculate reaction probabilities. However, despite the elegance of classical S-matrix theory, numerical results on even the simplest reactive systems remained out of reach. Recently, with advances both in correlation function formulations of reactive scattering as well as in semiclassical methods, it has become possible for the first time to calculate reaction probabilities semiclassically. The correlation function methods are contrasted with recent flux-based methods, which, although providing somewhat more compact expressions for the cumulative reactive probability, are less compatible with semiclassical implementation.

Journal Article↗
PubMed2005

Analysis of molecular stereoelectronic similarity between N,N-diethyl-m-toluamide (DEET) analogs and insect juvenile hormone to develop a model pharmacophore for insect repellent activity.

Similarity analysis on molecular stereoelectronic properties of N,N-diethyl-m-toluamide (DEET), natural insect juvenile hormone (JH), a synthetic insect juvenile hormone mimic (JH-mimic, undecen-2-yl carbamate), and DEET compounds reveals remarkable similarities that lead to a reliable pharmacophore for the design of efficacious insect repellents and provide insights for understanding the mechanism of repellent action. The study involves an AM1 quantum chemical computational procedure enabling a conformational search for the lowest and most abundant energy conformers of JH, JH-mimic, and 15 DEET compounds and complete geometry optimization of the conformers. Similarity analyses of stereoelectronic properties such as structural parameters, atomic charges, dipole moments, molecular electrostatic potentials, and highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies were performed on JH, JH-mimic, and the DEET compounds. Similarity of stereoelectronic attributes of the amide/ester moiety, negative electrostatic potential regions beyond the molecular surface, and a large distribution of hydrophobic regions in the compounds appears to be the 3 important factors leading to a similar interaction with the JH receptor. The similarity of electrostatic profiles beyond the molecular surface is likely to play a crucial role toward molecular recognition interaction with the JH receptor from a distance which suggests a possible electrostatic bioisosterism of the amide group of the DEET compounds and JH-mimic and, thus, a model for molecular recognition at the JH receptor.

Aedes↗
PubMed1998

Quantum mechanical and experimental oxidation studies of pentadecylresorcinol, olivetol, orcinol and resorcinol.

Resorcinols (pentadecylresorcinol, olivetol, orcinol and resorcinol) exhibit antioxidant properties in liposomal systems. Antioxidant potency depends on the length of the alkyl chain. Pentadecylresorcinol has been demonstrated to be the most active antioxidant, indicating significance of its alkyl chain in a lipid bilayer. Quantum DFT computations demonstrated that hydroxyl group attached to the ring is the first target for the hydrogen abstraction after formation of the radical. However, the carbons of the side chain could also participate in the antioxidant properties of the alkylresorcinols. Formation of the radical at the hydroxyl oxygen initiates changes in the electron density which destabilise the whole system and subsequently leads to oxidation of the ring. The detailed study of lipophilicity and electrostatic properties of resorcinols is discussed.

Antioxidants↗