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At least 703 records · Page 39Linked to original sources
PubMed2005

Quantum-instanton evaluation of the kinetic isotope effects.

A general quantum-mechanical method for computing kinetic isotope effects is presented. The method is based on the quantum-instanton approximation for the rate constant and on the path-integral Metropolis-Monte Carlo evaluation of the Boltzmann operator matrix elements. It computes the kinetic isotope effect directly, using a thermodynamic integration with respect to the mass of the isotope, thus avoiding the more computationally expensive process of computing the individual rate constants. The method should be more accurate than variational transition-state theories or the semiclassical instanton method since it does not assume a single tunneling path and does not use a semiclassical approximation of the Boltzmann operator. While the general Monte Carlo implementation makes the method accessible to systems with a large number of atoms, we present numerical results for the Eckart barrier and for the collinear and full three-dimensional isotope variants of the hydrogen exchange reaction H + H2 --> H2 + H. In all seven test cases, for temperatures between 250 and 600 K, the error of the quantum instanton approximation for the kinetic isotope effects is less than approximately 10%.

Journal Article↗
PubMed2006

Fractional charge revealed in computer simulations of resonant tunneling in the fractional quantum Hall regime.

The concept of fractional charge is central to the theory of the fractional quantum Hall effect. Here I use exact diagonalization as well as configuration space renormalization to study finite clusters which are large enough to contain two independent edges. I analyze the conditions of resonant tunneling between the two edges. The "computer experiment" reveals a periodic sequence of resonant tunneling events consistent with the experimentally observed fractional quantization of electric charge in units of e/3 and e/5.

Journal Article↗
PubMed2004

Structure and unexpected chiroptical properties of chiral 4-pyrrolidinyl substituted 2(5H)-furanones.

Planar 2(5H)-furanones substituted at C4 with a chiral pyrrolidinyl group show CD spectra which are apparently due to the distortion of the C4-N1 bond of sp2 character from the plane defined by the 2(5H)-furanone ring atoms and/or due to the presence of substituents in the pyrrolidine ring. This is a new, previously not encountered structural factor determining the chiroptical properties of 2(5H)-furanones and emerging from the analysis of X-ray diffraction data and quantum mechanical DFT computations. In the presence of a C5 pseudoaxial substituent in the furanone ring, the sign of the furanone n-pi* and pi-pi* transition Cotton effects is determined primarily by the previously postulated allylic helicity rule.

Journal Article↗
PubMed2005

Solvent and protein effects on the structure and dynamics of the rhodopsin chromophore.

The structure and dynamics of the retinal chromophore of rhodopsin are investigated systematically in different environments (vacuum, methanol solution, and protein binding pocket) and with different computational approaches (classical, quantum, and hybrid quantum mechanics/molecular mechanics (QM/MM) descriptions). Finite temperature effects are taken into account by molecular dynamics simulations. The different components that determine the structure and dynamics of the chromophore in the protein are dissected, both in the dark state and in the early photointermediates. In vacuum and in solution the chromophore displays a very high flexibility, which is significantly reduced by the protein environment. In the 11-cis chromophore, the bond-length alternation, which is correlated with the dipole moment, is found to be similar in solution and in the protein, while it differs greatly with respect to minimum-energy vacuum structures. In the model of the earliest protein photointermediate, the highly twisted chromophore shows a very reduced bond-length alternation.

Molecular Structure↗
PubMed2003

Catalysis on the coastline: theozyme, molecular dynamics, and free energy perturbation analysis of antibody 21D8 catalysis of the decarboxylation of 5-nitro-3-carboxybenzisoxazole.

Antibody 21D8 catalyzes the decarboxylation of 5-nitro-3-carboxybenzisoxazole. The hapten used was designed to induce an antibody binding site with anion binders for the carboxylate, plus a nonpolar environment to accelerate decarboxylation. A recent X-ray crystal structure of 21D8 has shown that the binding pocket contains an array of both polar and charged residues. Nevertheless, 21D8 is able to catalyze a reaction that involves a decrease in polarity from reactant to transition state. The origins of this phenomenon were explored using various computational strategies-quantum mechanics, theozyme models, docking, molecular dynamics, free energy perturbation, and linear interaction energy-the combination of which has produced a consistent picture of catalysis. By partially desolvating the charged carboxylate, 21D8 manages to effect "catalysis on the coastline," without burying the carboxylate in a nonpolar region of the binding pocket. The results have implications for that broad class of enzyme and antibody catalyzed reactions that involve the conversion of a substrate with a relatively localized charge into a transition state with a highly dispersed charge.

Algorithms↗
PubMed2003

Reassessment of methyl rotation barriers and conformations by correlated quantum chemistry methods.

Internal rotations of the methyl group in ortho-substituted and 2,6-disubstituted toluenes in their ground state have been investigated by means of various ab initio quantum chemistry methods. Computed barriers at the Hartree-Fock (HF) level using medium sized basis sets agreed reasonably with experimental results in the case of the studied ortho-substituted toluenes. However, this agreement worsens when using very large basis sets. Furthermore, the determination of the conformation and barriers of more weakly hindered methyl groups, that is, for 2,6-dihalogenotoluenes or toluene itself, necessitates high level correlated computations, because of a possible failure of HF calculations in this case. Density functional theory (DFT) techniques required, in several cases, much more extended basis sets than the post-HF Møller-Plesset perturbation (MP2, MP4) ones, to insure the convergence of the computed barriers. Non-negligible variations of the computed barriers when using different DFT functionals are observed for some systems.

Journal Article↗
PubMed1977

Luminescence quantum yields of sound and carious dental enamel.

The absorption and emission spectra of slabs of human and bovine dental enamel were determined. The absorption and scattering coefficients and emission quantum yields were computed according to theoretical models. The samples were gradually demineralized. The absorption, scattering, and emission parameters were determined as a function of the demineralization time. Using the theoretical models combined with the experimental values, ratio of the visible and UV luminescence, and the decrease of visible emission intensity upon demineralization are explained.

Absorption↗
PubMed2006

Quantitative structure-activity relationships for prediction of the toxicity of hydroxylated and quinoid PCB metabolites.

Quantitative structure-activity relationship (QSAR) models were developed for the in vitro potencies to downregulate gap junctional intercellular communication (GJIC) of hydroxylated polychlorinated biphenyls (OH-PCBs) and PCB quinines using partial least squares (PLS) regression. Quantum chemical descriptors computed by the semiempirical AM1, PM3 and MNDO methods were used as predictor variables. The cross-validated Q2cum values for the three optimal QSAR models are 0.784, 0.789 and 0.755, respectively, indicating good predictive capabilities for the acute inhibition of GJIC (IC(50)) of oxygenated PCB derivatives. The slightly higher Q2cum value of the model using computed molecular descriptors from the PM3 Hamiltonian suggested a slightly better predictive power than the models developed using AM1 or MNDO. However, given these dispersion parameters in these three optimal models, there would not be a significant difference between the Q2cum values. Results from this study showed that the logarithmic scale of IC(50) is affected by different molecular structural descriptors.

Chemistry, Pharmaceutical↗
PubMed1991

Spectrofluorimetric studies on C-terminal 34 kDa fragment of caldesmon.

Analysis of the tryptophan fluorescence emission spectra of caldesmon and its 34 kDa C-terminal fragment indicates that all tryptophan residues are located on the surface of the molecule, accessible to solvent. All three tryptophan residues of the 34 kDa fragment and four of the five tryptophan residues of intact protein are accessible to free water, whereas one located in the N-terminal region of molecule is accessible only to bound water molecules. The temperature dependence of the fluorescence parameters indicates higher thermal stability of the 34 kDa fragment than the whole caldesmon molecule. The interaction of the 34 kDa fragment of caldesmon (like that of the intact molecule) with calmodulin is accompanied by a blue shift of the fluorescence emission maximum and an increase in the relative quantum yield. Computer-calculated binding constants show that the binding of calmodulin to the 34 kDa fragment (K = 2.5 x 10(5) M-1) is of two orders of magnitude weaker than that to intact caldesmon (K = 1.4 x 10(7) M-1). The interaction with tropomyosin results in a blue shift of the spectrum of the 34 kDa fragment, yet there is no effect on the spectrum of intact caldesmon. Binding constants of tropomyosin to caldesmon (K = 3.8 x 10(5) M-1) and its 34 kDa fragment (K = 2.3 x 10(5) M-1) are similar. Binding of calmodulin to caldesmon and to the 34 kDa fragment affects their interaction with tropomyosin.

Animals↗
PubMed2005

Quantitative structure-property relationships on photolysis of PCDD/Fs adsorbed to spruce (Picea abies (L.) Karst.) needle surfaces under sunlight irradiation.

By partial least squares (PLS) regression, quantitative structure-property relationship (QSPR) models were developed for photolysis half-life (t1/2) of PCDD/Fs and PAHs sorbed to spruce (Picea abies (L.) Karst.) needle surfaces and irradiated by sunlight. Quantum chemical descriptors computed by PM3 Hamiltonian were used predictor variables. PLS analysis for the PCDDs and PAHs respectively resulted in no correlation by our statistical methods. The cross-validated Qcum2 value for the optimal QSPR model of PCDFs is 0.722, indicating a good predictive ability for logt1/2 of PCDFs adsorbed to spruce needle surfaces. The QSPR results show that the number of chlorine atoms bonded to the parent structure and (E(LUMO)-E(HOMO))2 has a dominant effect on t1/2 values of PCDFs. Increasing the number of chlorine atoms and (E(LUMO)-E(HOMO))2 values leads to increase of logt1/2 values of PCDFs.

Adsorption↗
PubMed2005

QSPR to aqueous solubility (lgSw) of alkyl(1-phenylsulfonyl) cycloalkane-carboxylates using MLSER model and ab initio.

Based on the modified linear solvation energy relationship (MLSER) model and quantum chemical descriptors computed at HF/STO-3G, HF/LANL2DZ, B3LYP/LANL2D and B3LYP/6-31G* levels, different quantitative structure-property relationships (QSPRs) to the aqueous solubility (lgSw) of 28 alkyl(1-phenylsulfonyl) cycloalkane-carboxylates were obtained. It is suggested that the eight models developed in the present study all have good correlation and relatively small error, in which the model with four variables, the most positive formal charge (qH+), molecular volume (Vi), melting point (mp) and free energy (G0) as descriptors obtained from B3LYP/6-31G* level, exhibited the best optimum correlation (r2=0.9743 and q2=0.9644, respectively) and smallest error, and thus are advantageous to other models. It was also found that molecular volume is the most significant factor influencing lgSw. The lgSw increased with increasing qH+ and G0, while decreased with increasing Vi and mp. The MLSER model achieved from ab initio calculation is better than that from the semiempirical AM1 method.

Carboxylic Acids↗
PubMed2005

Quantitative structure-property relationships on photodegradation of polybrominated diphenyl ethers.

By partial least squares (PLS) regression, quantitative structure-property relationship (QSPR) models were developed for photodegradation rates (k(p)) and quantum yields (Phi) of polybrominated diphenyl ethers (PBDEs) in methanol/water (8:2), and photodegradation rates in pure methanol by UV light in the sunlight region, respectively. Quantum chemical descriptors computed by PM3 Hamiltonian were used as predictor variables. The cross-validated Q(cum)(2) values for three optimal QSPR models of PBDEs are above 0.90 (remarkably higher 0.50), indicating good predictive abilities for logk(p) and logPhi values of PBDEs. The QSPR results show that logk(p) values of PBDEs in methanol/water (8:2) and in pure methanol are governed by different molecular structural descriptors, respectively, which implies that photodegradation rates of PBDEs are affected by the characteristics of solution in which it takes place.

Environmental Pollutants↗
PubMed2006

Modeling and prediction of photolysis half-lives of polycyclic aromatic hydrocarbons in aerosols by quantum chemical descriptors.

Quantitative structure-property relationship (QSPR) modeling is a powerful approach for predicting environmental fate parameters of organic pollutants with their structure descriptors. This study reports QSPR models for photolysis half-lives of polycyclic aromatic hydrocarbons (PAHs) in aerosols. Quantum chemical descriptors computed with density functional theory at B3LYP/6-31G(d) level and partial least squares (PLS) analysis with optimizing procedure were used for generating QSPR models. The correlation coefficient of the optimal model was 0.993, and the fitting results showed this optimal model had high fitting precision and good predictability. The predicted photolysis half-lives by the optimal model are very close to those observed. The PLS assistant analysis indicated that PAHs with large electronic spatial extent tend to be photolyzed faster, while PAHs with high molecular total energy and small Mulliken atomic charges on the most negative carbon atom tend to be photolyzed slower in aerosols.

Aerosols↗
PubMed2001

Quantitative structure-property relationship studies on direct photolysis of selected polycyclic aromatic hydrocarbons in atmospheric aerosol.

Based on some fundamental quantum chemical descriptors computed by PM3 Hamiltonian, by the use of partial least-squares analysis, a quantitative structure property relationship model for direct photolysis half-lives of 11 polycyclic aromatic hydrocarbons (PAHs) in atmospheric aerosol under UV irradiation was developed. PAHs with great molecular weight (bulkness) tend to photolyze fast, and PAHs with small absolute electronegativity values and large absolute hardness values, tend to photolyze fast.

Atmosphere↗
PubMed2001

Quantitative structure-property relationship studies on n-octanol/water partitioning coefficients of PCDD/Fs.

Based on some fundamental quantum chemical descriptors computed by PM3 Hamiltonian, by the use of partial least-squares (PLS) analysis, a significant quantitative structure-property relationship (QSPR) model for logKow of polychlorinated dibenzo-p-dioxins and dibenzo-p-furans (PCDD/Fs) was obtained. The QSPR can be used for prediction. The intermolecular dispersive interactions and thus the bulkness of the PCDD/Fs are the main factors affecting the logKow. The more chlorines in the PCDD/F molecule, the greater the logKow values.

Benzofurans↗
PubMed2001

Quantitative structure-property relationship study on reductive dehalogenation of selected halogenated aliphatic hydrocarbons in sediment slurries.

In this study, by the use of partial least squares (PLS) method and 26 quantum chemical descriptors computed by PM3 Hamiltonian, a quantitative structure-property relationship (QSPR) model was developed for reductive dehalogenation rate constants of 13 halogenated aliphatic compounds in sediment slurry under anaerobic conditions. The model can be used to explain the dehalogenation mechanism. Halogenated aliphatic compounds with great energy of the lowest unoccupied molecular orbital (Elumo), total energy (TE), electronic energy (EE), the smallest bond order of the carbon-halogen bonds (BO) and the most positive net atomic charges on an atom of the molecule (q+) values tend to be reductively dehalogenated slow, whereas halogenated aliphatic compounds with high values of molecular weight (Mw), average molecular polarizability (alpha) and core-core repulsion energy (CCR) values tend to be reductively dehalogenated fastest.

Electrons↗
PubMed2002

Quantitative structure-property relationships for octanol-air partition coefficients of polychlorinated biphenyls.

Based on nine quantum chemical descriptors computed by PM3 Hamiltonian, using partial least squares analysis, a significant quantitative structure-property relationship for the logarithm of octanol-air partition coefficients (logK(OA)) of polychlorinated biphenyls (PCBs) was obtained. The cross-validated Q2cum value of the model is 0.962, indicating a good predictive ability. The intermolecular dispersive interactions and thus the size of the PCB molecules play a key role in governing log K(OA). The greater the size of PCB molecules, the greater the logK(OA) values. Increasing ELUMO (the energy of the lowest unoccupied molecular orbital) values of the PCBs leads to decreasing logK(OA) values, indicating possible interactions between PCB and octanol molecules. Increasing Q(Cl)+, (the most positive net atomic charges on a chlorine atom) and Q(C)- (the largest negative net atomic charge on a carbon atom) values of PCBs results in decreasing lg K(OA) values, implying possible intermolecular electrostatic interactions between octanol and PCB molecules.

Environmental Pollutants↗
PubMed2003

Linear free energy relationships for dechlorination of aromatic chlorides by Pd/Fe.

Reductive dechlorination rate constants for five chlorobenzenes in the presence of Pd/Fe as catalyst were determined experimentally. Linear free energy relationships (LFER) for the dechlorination rate constants of five chlorobenzenes and three chlorophenols were developed by partial least squares (PLS) regression based on quantum chemical parameters computed by PM3 Hamiltonian. The optimal LFER model obtained is logk=-1.63+1.46 x 10(-3)DeltaH(f)-7.69 x 10(-1)E(LUMO)where k stands for the dechlorination rate constants, DeltaH(f) is the standard heat of formation, and E(LUMO) is the energy of the lowest unoccupied molecular orbital. The Q(2)(cum) value of the model is 0.879, indicating good robustness and predictive power of the model.

Chlorides↗