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At least 343 records · Page 19Linked to original sources
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↗
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↗
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↗
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↗
PubMed2001

Quantitative structure-property relationships on photodegradation of PCDD/Fs in cuticular waxes of laurel cherry (Prunus laurocerasus).

By the use of the partial least squares (PLS) method and 13 fundamental quantum chemical descriptors computed by PM3 Hamiltonian, a OSPR model was developed for first order rate constants of photodegradation of 10 PCDD/Fs dissolved in cuticular wax from laurel cherry (Prunus laurocerasus) leaves and exposed to sunlight. The QSPR showed that photodegradation rates increase with the degree of chlorination of the homologues. PCDD/Fs with large values of Q(Cl) (the largest positive atomic charge on a chlorine atom in a molecule), Q(O)- (the most negative atomic charge on the oxygen atoms in a molecule), and mu (dipole moment) tend to photodegrade fastest. PCDD/Fs with large values of E(lumo) (the energy of the lowest unoccupied molecular orbital), E(homo) (the energy of the highest occupied molecular orbital), and E(lumo) - E(homo) tend to have the lowest photodegradation rates.

Benzofurans↗
PubMed2003

Quantitative structure-property relationships for octanol-air partition coefficients of polychlorinated naphthalenes, chlorobenzenes and p,p'-DDT.

The octanol-air partition coefficient (K(OA)) is a key descriptor of chemicals partitioning between the atmosphere and environmental organic phases. Quantitative structure-property relationships (QSPR) are necessary to model and predict K(OA) from molecular structures. Based on 12 quantum chemical descriptors computed by the PM3 Hamiltonian, using partial least squares (PLS) analysis, a QSPR model for logarithms of K(OA) to base 10 (logK(OA)) for polychlorinated naphthalenes (PCNs), chlorobenzenes and p,p'-DDT was obtained. The cross-validated Q(2)(cum) value of the model is 0.973, indicating a good predictive ability of the model. The main factors governing logK(OA) of the PCNs, chlorobenzenes, and p,p'-DDT are, in order of decreasing importance, molecular size and molecular ability of donating/accepting electrons to participate in intermolecular interactions. The intermolecular dispersive interactions play a leading role in governing logK(OA). The more chlorines in PCN and chlorobenzene molecules, the greater the logK(OA) values. Increasing E(LUMO) (the energy of the lowest unoccupied molecular orbital) of the molecules leads to decreasing logK(OA) values, implying possible intermolecular interactions between the molecules under study and octanol molecules.

Journal Article↗
PubMed2001

Is it possible to develop a QSPR model for direct photolysis half-lives of PAHs under irradiation of sunlight?

By the use of the partial least squares method and 11 fundamental quantum chemical descriptors computed from the PM3 Hamiltonian, a Quantitative Structure-Property Relationship model was obtained for direct photolysis half-lives of selected polycyclic aromatic hydrocarbons (PAHs) under irradiation of sunlight. Direct photolysis half-lives for some other PAHs without reported values were predicted. It was concluded from the model that the main factors affecting photolysis half-lives of PAHs under irradiation of sunlight are PAH absolute hardness and electronegativity, which are related to the energy difference between the lowest unoccupied molecular orbital and the highest occupied molecular orbital, (Elumo - Ehomo) and (Elumo + Ehomo), respectively. Increasing Ehomo and the average molecular polarizability (alpha) values of the PAHs leads to decrease of photolysis half-lives. Increasing (Elumo - Ehomo) and Elumo values of the PAHs leads to an increase of the PAH photolysis half-lives.

Environmental Pollutants↗
PubMed2002

Linear free energy relationships on rate constants for dechlorination by zero-valent iron.

By correlation analysis, molecular structural factors governing surface area-normalized rate constants (k) for dechlorination by zero-valent iron, were identified. Twenty-nine quantum chemical descriptors computed by MNDO, AM1 and PM3 Hamiltonians for gas-phase and the conductor-like screening model (COSMO) for incorporating solvent (H2O) effects were studied. Besides the energy of the lowest unoccupied molecular orbital (E(LUMO)), the character of carbon-chlorine bonds (C-Cl bonds) and especially the strength of C-Cl bonds was found significant in governing the magnitude of log k. By PLS analysis, six two-parameter linear free energy relationships (LFER) were obtained. The best two-parameter LFER model was the one using E(LUMO) and C (the Coulombic interaction energy of the two-center term for the C-Cl bonds) computed by PM3/H2O method as molecular structural descriptors. Chlorinated compounds with high E(LUMO) and C values tend to have low dechlorination rate constants.

Carbon↗
PubMed2001

Cajal and consciousness. Introduction.

One hundred years after Santiago Ramón Cajal established the bases of modern neuroscience in his masterpiece Textura del sistema nervioso del hombre y de los vertebrados, the question is stated again: What is the status of consciousness today? The responses in this book, by contemporary leading figures of neuroscience, evolution, molecular biology, computer science, and quantum physics, collectively compose a fascinating conceptual landscape. Both the evolutionary emergence of consciousness and its development towards the highest level may be analyzed by a wealth of new theories and hypotheses, including Cajal's prescient ones. Some noticeable gaps remain, however. Celebrating the centennial of Textura is a timely occasion to reassess how close--and how far--our system of the sciences is to explaining consciousness.

Animals↗
PubMed2001

Quantum energies of interfaces.

We present a method for computing the one-loop, renormalized quantum energies of symmetrical interfaces of arbitrary dimension and codimension using elementary scattering data. Internal consistency requires finite-energy sum rules relating phase shifts to bound state energies.

Journal Article↗
PubMed2003

Hydride transfer catalyzed by xylose isomerase: mechanism and quantum effects.

We have applied molecular dynamics umbrella-sampling simulation and ensemble-averaged variational transition state theory with multidimensional tunneling (EA-VTST/MT) to calculate the reaction rate of xylose-to- xylulose isomerization catalyzed by xylose isomerase in the presence of two Mg2+ ions. The calculations include determination of the free energy of activation profile and ensemble averaging in the transmission coefficient. The potential energy function is approximated by a combined QM/MM/SVB method involving PM3 for the quantum mechanical (QM) subsystem, CHARMM22 and TIP3P for the molecular mechanical (MM) environment, and a simple valence bond (SVB) local function of two bond distances for the hydride transfer reaction. The simulation confirms the essential features of a mechanism postulated on the basis of kinetics and X-ray data by Whitlow et al. (Whitlow, M.; Howard, A. J.; Finzel, B. C.; Poulos, T. L.; Winborne, E.; Gilliland, G. L. Proteins 1991, 9, 153) and Ringe, Petsko, and coworkers (Labie, A.; Allen, K.-N.; Petsko, G. A.; Ringe, D. Biochemistry 1994, 33, 5469). This mechanism involves a rate-determining 1,2-hydride shift with prior and post proton transfers. Inclusion of quantum mechanical vibrational energy is important for computing the free energy of activation, and quantum mechanical tunneling effects are essential for computing kinetic isotope effects (KIEs). It is found that 85% of the reaction proceeds by tunneling and 15% by overbarrier events. The computed KIE for the ratio of hydride to deuteride transfer is in good agreement with the experimental results. The molecular dynamics simulations reveal that proton and hydride transfer reactions are assisted by breathing motions of the mobile Mg2+ ion in the active site, providing evidence for concerted motion of Mg2+ during the hydride transfer step.

Aldose-Ketose Isomerases↗
PubMed1992

Computer simulations of enzymatic reactions: examination of linear free-energy relationships and quantum-mechanical corrections in the initial proton-transfer step of carbonic anhydrase.

Computer simulation approaches can provide a powerful tool for correlating the structure of enzymes with their catalytic activity. One of the most effective ways of simulating enzymatic reactions is provided by the empirical valence bond method. The general applicability of this method has been demonstrated in several enzymatic reactions and it is reexamined here in a study of the initial proton-transfer step in the catalytic reaction of carbonic anhydrase. The simulations produce a rate constant which is in agreement with the observed kinetic data and emphasizes the importance of the electrostatic effect associated with the catalytic zinc ion. The calculations are also used to examine the validity of linear free-energy relationships (LFERs) in enzyme catalysis and to evaluate quantum-mechanical corrections of the calculated rate constant. It is found that LFERs are valid in the present case and it is argued that this reflects the fact that the protein responds linearly to the development of electrostatic forces during the reaction. It is concluded that the present approach can be used to augment experimental studies in establishing the general validity of LFERs. It is noted, however, that such relationships are much more valid for transitions between different resonance structures than for transitions between reactants and product states.

Carbonic Anhydrases↗