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At least 721 records · Page 40Linked to original sources
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↗
PubMed2004

5-substituted tetrazoles as bioisosteres of carboxylic acids. Bioisosterism and mechanistic studies on glutathione reductase inhibitors as antimalarials.

Plasmodium parasites are exposed to elevated fluxes of reactive oxygen species during intraerythrocytic life. The most important antioxidative systems are based on the glutathione reductases of the malarial parasite Plasmodium falciparum and the host erythrocyte. The development of menadione chemistry has led to the selection of the carboxylic acid 6-[2'-(3'-methyl)-1',4'-naphthoquinolyl] hexanoic acid M(5) as an inhibitor of the parasitic enzyme. As reported here, revisiting the mechanism of M(5) action revealed an uncompetitive inhibition type with respect to both NADPH and glutathione disulfide. Masking the polarity of the acidic function of M(5) by ester or amide bonds improved antiplasmodial activity. Bioisosteric replacement of the carboxylic function by tetrazole to increase bioavailability and to maintain comparable acidity led to improved antimalarial properties as well, but only with the cyanoethyl-protected tetrazoles. Using computed ab initio quantum methods, detailed analyses of the electronic profiles and the molecular properties evidenced the similarity of M(5) and the bioisoteric tetrazole T(4). The potential binding site of these molecules is discussed in light of the recently solved crystallographic structure of P. falciparum enzyme.

Animals↗
PubMed2005

Accurate quantum calculation of the bound and resonant rovibrational states of Li-(H2).

In a recent paper [B. Poirier, Chem. Phys. 308, 305 (2005)] a full-dimensional quantum method for computing the rovibrational dynamics of triatomic systems was presented, incorporating three key features: (1) exact analytical treatment of Coriolis coupling, (2) three-body "effective potential," and (3) a single bend angle basis for all rotational states. In this paper, these ideas are applied to the Li-(H2) electrostatic complex, to compute all of the rovibrational bound state energies, and a number of resonance energies and widths, to very high accuracy (thousandths of a wave number). This application is very challenging, owing to the long-range nature of the interaction and to narrow level spacings near dissociation. Nevertheless, by combining the present method with a G4 symmetry-adapted phase-space-optimized representation, only modest basis sizes are required for which the matrices are amenable to direct diagonalization. Several new bound levels are reported, as compared with a previous calculation [D. T. Chang, G. Surratt, G. Ristroff, and G. I. Gellene, J. Chem. Phys. 116, 9188 (2002)]. The resonances exhibit a clear-cut separation into shape and Feshbach varieties, with the latter characterized by extremely long lifetimes (microseconds or longer).

Journal Article↗
PubMed2005

Unimolecular rovibrational bound and resonance states for large angular momentum: J=20 calculations for HO2.

We explore the calculation of unimolecular bound states and resonances for deep-well species at large angular momentum using a Chebychev filter diagonalization scheme incorporating doubling of the autocorrelation function as presented recently by Neumaier and Mandelshtam [Phys. Rev. Lett. 86, 5031 (2001)]. The method has been employed to compute the challenging J=20 bound and resonance states for the HO2 system. The methodology has firstly been tested for J=2 in comparison with previous calculations, and then extended to J=20 using a parallel computing strategy. The quantum J-specific unimolecular dissociation rates for HO2-->H+O2 in the energy range from 2.114 to 2.596 eV have been reported for the first time, and comparisons with the results of Troe and co-workers [J. Chem. Phys. 113, 11019 (2000) Phys. Chem. Chem. Phys. 2, 631 (2000)] from statistical adiabatic channel method/classical trajectory calculations have been made. For most of the energies, the reported statistical adiabatic channel method/classical trajectory rate constants agree well with the average of the fluctuating quantum-mechanical rates. Near the dissociation threshold, quantum rates fluctuate more severely, but their average is still in agreement with the statistical adiabatic channel method/classical trajectory results.

Journal Article↗
PubMed2005

Nuclear-electronic orbital nonorthogonal configuration interaction approach.

The nuclear-electronic orbital nonorthogonal configuration interaction (NEO-NOCI) approach is presented. In this framework, the hydrogen nuclei are treated quantum mechanically on the same level as the electrons, and a mixed nuclear-electronic time-independent Schrodinger equation is solved with molecular orbital techniques. For hydrogen transfer systems, the transferring hydrogen is represented by two basis function centers to allow delocalization of the nuclear wave function. In the two-state NEO-NOCI approach, the ground and excited state delocalized nuclear-electronic wave functions are expressed as linear combinations of two nonorthogonal localized nuclear-electronic wave functions obtained at the NEO-Hartree-Fock level. The advantages of the NEO-NOCI approach are the removal of the adiabatic separation between the electrons and the quantum nuclei, the computational efficiency, the potential for systematic improvement by enhancing the basis sets and number of configurations, and the applicability to a broad range of chemical systems. The tunneling splitting is determined by the energy difference between the two delocalized vibronic states. The hydrogen tunneling splittings calculated with the NEO-NOCI approach for the [He-H-He]+ model system with a range of fixed He-He distances are in excellent agreement with NEO-full CI and Fourier grid calculations. These benchmarking calculations indicate that NEO-NOCI is a promising approach for the calculation of delocalized, bilobal hydrogen wave functions and the corresponding hydrogen tunneling splittings.

Chemical Phenomena↗
PubMed2006

Relaxation of the CH stretch in liquid CHBr3: solvent effects and decay rates using classical nonequilibrium simulations.

This article addresses two questions regarding the decay of the CH stretch in liquid CHBr3. The first is whether the initial steps of the relaxation primarily involve energy redistribution within the excited molecule alone. Gas phase quantum mechanical and classical calculations are performed to examine the role of the solvent in this process. At the fundamental excitation level, it is found that CH stretch decay is, in fact, strongly solvent driven. The second question is on the applicability of a fully classical approach to the calculation of CH stretch condensed phase decay rates. To this end, nonequilibrium molecular dynamics simulations are performed. The results are compared with quantum mechanical rates computed previously. The two methods are found to be in fair agreement with each other. However, care must be exercised in the interpretation of the classical results.

Journal Article↗
PubMed2006

The color of rhodopsins at the ab initio multiconfigurational perturbation theory resolution.

We demonstrate that "brute force" quantum-mechanics/molecular-mechanics computations based on ab initio (i.e., first principles) multiconfigurational perturbation theory can reproduce the absorption maxima of a set of modified bovine rhodopsins with an accuracy allowing for the analysis of the factors determining their colors. In particular, we show that the theory accounts for the changes in excitation energy even when the proteins display the same charge distribution. Three color-tuning mechanisms, leading to changes of close magnitude, are demonstrated to operate in these conditions. The first is based on the change of the conformation of the conjugated backbone of the retinal chromophore. The second operates through the control of the distance between the positive charge residing on the chromophore and the carboxylate counterion. Finally, the third mechanism operates through the changes in orientation of the chromophore relative to the protein. These results offer perspectives for the unbiased computational design of mutants or chemically modified proteins with wanted optical properties.

Animals↗
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↗
PubMed2004

Molecular structural characteristics governing biocatalytic chlorination of PAHs by chloroperoxidase from Caldariomyces fumago.

Based on some fundamental quantum chemical descriptors computed by PM3 Hamiltonian, a quantitative structure-property relationship (QSPR) for specific activity of 17 polycyclic aromatic hydrocarbons (PAHs) of biocatalytic chlorination by chloroperoxidase (CPO) from Caldariomyces fumago was developed using partial least squares (PLS) regression. The model can be used to estimate biocatalytic chlorination reaction rates of PAHs. The main factors affecting specific activity of PAHs of biocatalytic chlorination by CPO from Caldariomyces fumago are absolute hardness, dipole moment, absolute electronegativity, and molecular bulkness of the PAH molecules. The biocatalytic chlorination reaction rates of PAHs with large values of absolute hardness, absolute electronegativity, and molecular bulkness tend to be slow. Increasing dipole moment of PAHs leads to increase the specific activity.

Ascomycota↗
PubMed2004

Quantitative structure-property relationships on direct photolysis of PCDD/Fs on surfaces of fly ash.

Fly ash samples containing polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) were generated by combustion of polyvinyl chloride, wood, high-density polyethylene and styrene. By partial least-squares (PLS) regression, quantitative structure-property relationship (QSPR) models were developed for photolysis half-lives (t(1/2)) of PCDD/Fs adsorbed on fly ash surfaces and irradiated by UV-B of simulated sunlight. Quantum chemical descriptors computed by PM3 hamiltonian were used as predictor variables. The cross validated value for the optimal QSPR model was 0.678, indicating robustness and good predictive abilities of the model. The QSPR results showed that the stability of the PCDD/F molecules increased with the increase of chlorine atoms in the parent molecules. Increasing the energy of the highest occupied molecular orbital (E(HOMO)), the energy of the lowest unoccupied molecular orbital (E(LUMO)), E(LUMO)+E(HOMO) and E(LUMO)-E(HOMO) values of the PCDD/Fs led to decrease of log t(1/2) values. Increasing the most negative atomic charge on the oxygen atom of PCDD/Fs led to elevated log t(1/2) values. The log t(1/2) values of PCDD/Fs increased with the decrease of the largest negative atomic charge on a carbon atom.

Benzofurans↗
PubMedDate not supplied

Application of counterpropagation artificial neural network for modelling properties of fish antibiotics.

The present study focuses on fish antibiotics which are an important group of pharmaceuticals used in fish farming to treat infections and, until recently, most of them have been exposed to the environment with very little attention. Information about the environmental behaviour and the description of the environmental fate of medical substances are difficult or expensive to obtain. The experimental information in terms of properties is reported when available, in other cases, it is estimated by standard tools as those provided by the United States Environmental Protection Agency EPISuite software and by custom quantitative structure-activity relationship (QSAR) applications. In this study, a QSAR screening of 15 fish antibiotics and 132 xenobiotic molecules was performed with two aims: (i) to develop a model for the estimation of octanol--water partition coefficient (logP) and (ii) to estimate the relative binding affinity to oestrogen receptor (log RBA) using a model constructed on the activities of 132 xenobiotic compounds. The custom models are based on constitutional, topological, electrostatic and quantum chemical descriptors computed by the CODESSA software. Kohonen neural networks (self organising maps) were used to study similarity between the considered chemicals while counter-propagation artificial neural networks were used to estimate the properties.

Animals↗
PubMed2006

QSPRs for the prediction of photodegradation half-life of PCBs in n-hexane.

By partial least squares (PLS) regression analysis, a quantitative structure-property relationship (QSPR) model was developed for photodegradation half-life (t1/2) of polychlorinated biphenyls (PCBs) in n-hexane solution under UV irradiation. Quantum chemical descriptors computed by PM3 Hamiltonian were used as predictor variables. The cross-validated value for the optimal QSPR model was 0.589, indicating good predictive capability for log t1/2 values of PCBs in n-hexane. The QSPR results show that standard heat of formation (DeltaHf), total energy (TE), and molecular weight (Mw) have dominant effect on t1/2 values of PCBs in n-hexane. Increasing DeltaHf and TE values or decreasing Mw values of the PCBs leads to decrease of log t1/2 values. In addition, increasing the largest negative atomic charge on a carbon atom and dipole moment of the PCBs leads to decrease of log t1/2 values.

Environmental Pollutants↗
PubMed2005

High-performance guided-wave asynchronous heralded single-photon source.

We report on a guided-wave asynchronous heralded single-photon source based on the creation of nondegenerate photon pairs by spontaneous parametric downconversion in a periodically poled lithium niobate wave-guide. We show that, by use of the signal photon at 1310 nm as a trigger, a gated detection process permits announcement of the arrival of single photons at 1550 nm at the output of a single-mode optical fiber with a high probability of 0.37. At the same time the multiphoton emission probability is reduced by a factor of 10 compared with Poissonian light sources. Furthermore, the model we have developed to calculate those figures of merit is shown to be accurate. This study can therefore serve as a paradigm for the conception of new quantum communication and computation networks.

Journal Article↗
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↗
PubMed2005

Quantum mechanical determinations of reaction mechanisms, acid base, and redox properties of nitrogen oxides and their donors.

This chapter reviews computational methods based on quantum mechanics and commonly used commercial programs for the exploration of chemical phenomena, particularly in the field of nitrogen oxides. Examples from the literature are then used to demonstrate the application of these methods to the chemistry and biochemistry of various nitrogen oxides. These examples include determining reaction mechanisms using computed reaction energies, predicting rates of reactions using transition state theory, and determining chemical properties such as hydration equilibria, pKa's, and reduction potentials.

Acids↗
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↗