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At least 1,243 records · Page 69Linked to original sources
PubMed2001

A new potential toxaphene congener: synthesis, GC/EI-MS study, crystal structure, NMR analysis, and ab initio calculations of 3-endo,5-endo-dichloro-7,7-bis-chloromethyl-4-dichloromethyl-tricyclo[2.2.1.0(2,6)]heptane.

A new potential toxaphene congener 3-endo,5-endo-dichloro-7,7-bis-chloromethyl-4-dichloromethyl-tricyclo[2.2.1.0(2,6)]heptane 2 has been isolated from reaction mixture obtained by the chlorination of 2-exo, 10,10-trichlorobornane 1. The X-ray structural analysis of 2 revealed an unusual tricyclic structure, where the two chlorine atoms occupying endo-positions are in close spatial proximity with each other and near to the neighbouring CHCl2 group. Further, it revealed that the symmetry of the molecule is distorted. The 1H and 13C NMR spectra of 2 have been assigned by means of 1H, 1H double-quantum filtered correlation spectroscopy (DQF COSY), PFG 1H, 13C HMQC (pulsed field gradient heteronuclear multiple-quantum coherence), 1H, 13C heteronuclear multiple bond correlation (HMBC) experiments, and computer aided 1H NMR spectral analysis. The asymmetry of 2 is also discernible on the 1H NMR parameters. In addition, gas chromatographic (GC) properties and electron impact (EI) mass spectrum of 2 has been studied. Ab initio Hartree-Fock (HF) method with the basis set 6-31G(d) has been used for the optimization of the equilibrium geometry and calculation of total energy for 2. The optimized geometry is in good agreement with the crystal structure. According to the rotation energy profile calculated at the HF/6-31G(d) level, rotation of the chloromethyl and dichloromethyl groups are highly unlikely at the room temperature.

Environmental Pollutants↗
PubMed2025

Enzymatic Anti-Baldwin Ring-Closure Cascade for Fused Bicyclic Ether Formation.

Pyrenulic acids are cytotoxic polyketides isolated from the ascomycete Pyrenula sp. derived from Vietnamese lichen that are characterized by complex fused cyclic core structures. Genome sequencing, in silico sequence analysis, and RT-PCR studies identified the pyrenulic acid (pya) biosynthetic gene cluster. Based on a functional analysis of the enzymes by expression of each gene in a heterologous host using Aspergillus nidulans, we discovered two cytochrome P450s PyaJ and PyaG that effect epoxidation and hydroxylation of the alkyl chain terminal, respectively, and an α/β hydrolase PyaF that constructs a 6- and 7-membered fused bicyclic diether skeleton by catalyzing successive epoxide ring-opening 6-endo and 7-endo cyclization reactions. To elucidate the detailed mechanism of pyrenulic acid formation, we obtained PyaF as a recombinant enzyme and performed an in vitro experiment, which confirmed catalysis by PyaF of the cyclization reaction. In addition, we performed alignment analysis of PyaF with α/β hydrolases with known functions, as well as an in-depth computational study. In-depth computational analyses of the cyclization reaction pathways with density functional theory quantum mechanics and detailed characterization of PyaF by Chai-1-based protein structure modeling with molecular dynamics simulations and site-specific mutagenesis predicted the active amino acid residues of this serine α/β hydrolase to be an unusual catalytic serine tetrad involving Ser170, Asn342, Asp314, and His169, with Tyr255 and His284 acting as general bases to facilitate opening of the epoxides. Our study provides insight into how regioselectivity of enzymatic anti-Baldwin epoxide ring-opening cascades for the formation of a fused cyclic ether structure is controlled.

Cyclization↗
PubMed2006

Explicit solvent DRF INDOs/CIS computations of charge transfer state energetics in a pyrenyldeoxyuridine nucleoside model.

In this work we present calculated absorption and emission spectra in acetonitrile (MeCN) solution of N-acetyl-1-aminopyrene (PAAc, a spectroscopic model compound) and N-(1-pyrenyl)-1-methyluracil-5-carboxamide (PAU(Me), a computational model for 5-(N-carboxyl-1-aminopyrenyl)-2'-deoxyuridine (PAdU)). The computational method used--the discrete reaction field approach (DRF)--combines a quantum mechanical (QM) description of the solute (here DFT and INDOs/CIS, i.e., the INDO parametrization for spectroscopy) with a classical, molecular mechanics (MM) description of the solvent molecules. The latter are modeled with point charges representing the permanent charge distribution and polarizabilities to account for many-body interactions among the solute and other solvent molecules. Molecular dynamics is used to sample the degrees of freedom of the solution around several solute conformations each in two electronic excited states. This leads to a large number of solute/solvent configurations from which 800 are selected for each excited state and collected into a single ensemble by means of proper Boltzmann averaging. DRF INDOs/CIS applied to the selected solute/solvent configurations give simulated absorption and emission band spectra--each based on 15,200 calculated transitions--that compare well with experimental results. For example, the much broader absorption and emission bands in PAdU compared with PAAc are reproduced, and the simulated emission spectra of PAU(Me) agree well with broad (380-550 nm) charge transfer (CT) emission seen for PAdU in MeCN. The observed multiexponential fluorescence decay profiles for PAdU in different polar solvents are interpreted in terms of solute/solvent conformational heterogeneity here generated in the MD simulations for PAU(Me) in MeCN. Additionally, the simulations demonstrate the mixing of the forbidden Py*+/dU*- CT states with allowed pyrenyl 1(pi,pi*) states.

Journal Article↗
PubMed2005

Influence of vibrational energy flow on isomerization of flexible molecules: incorporating non-Rice-Ramsperger-Kassel-Marcus kinetics in the simulation of dipeptide isomerization.

The conformational isomerization of a dipeptide, N-acetyl-tryptophan methyl amide (NATMA), is studied computationally by including important dynamical corrections to Rice-Ramsperger-Kassel-Marcus (RRKM) theory for the transition rate between pairs of isomers. The dynamical corrections arise from incomplete or sluggish vibrational energy flow in the dipeptide, a property suggested by the mode-selective chemistry that has been observed by Dian et al. [J. Chem. Phys. 120, 133 (2004)]. We compute the extent and rate of vibrational energy flow in NATMA quantum mechanically using local random matrix theory, which we then use to correct the RRKM theory rates. The latter rates are then introduced into a master equation to study the population dynamics of the dipeptide. Incomplete or slow vibrational energy flow is found to enhance the conformational selectivity of NATMA over RRKM estimates.

Chemistry, Physical↗
PubMed2006

On a singularity-free pair-polarizability anisotropy model for atomic gases.

We present a collision-induced light scattering spectrum of Ne(2) and analyze it, together with an induced spectrum of Ar(2), in terms of a model for the pair-polarizability anisotropy beta of an atomic gas. This model, which is in essence a slight modification of one introduced by Ceccherini et al. [J. Chem. Phys. 111, 6316 (1999)], is shown to describe the measured spectra much farther into the wings than does the original model. The agreement of our measurements with quantum-mechanical spectra from the most reliable, now available, ab initio computation methods for beta produces evidence in support of the data and counters criticism of our experiment.

Journal Article↗
PubMed2000

Leading ruelle resonances of chaotic maps

The leading Ruelle resonances of typical chaotic maps, the perturbed cat map and the standard map, are calculated by variation. It is found that, excluding the resonance associated with the invariant density, the next subleading resonances are, approximately, the roots of the equation z(4)=gamma, where gamma is a positive number that characterizes the amount of stochasticity of the map. The results are verified by numerical computations, and the implications to the form factor of the corresponding quantum maps are discussed.

Journal Article↗
PubMed2001

Semiclassical quantization by harmonic inversion: comparison of algorithms.

Harmonic inversion techniques have been shown to be a powerful tool for the semiclassical quantization and analysis of quantum spectra of both classically integrable and chaotic dynamical systems. Various computational procedures have been proposed for this purpose. Our aim is to find out which method is numerically most efficient. To this end, we summarize and discuss the different techniques and compare their accuracies by way of two example systems.

Journal Article↗
PubMed2001

Partition noise and statistics in the fractional quantum hall effect.

A microscopic theory of current partition in fractional quantum Hall liquids, described by chiral Luttinger liquids, is developed to compute the noise correlations, using the Keldysh technique. In this Hanbury-Brown and Twiss geometry, at Laughlin filling factors nu = 1/3, the real time noise correlator exhibits oscillations which persist over larger time scales than that of an uncorrelated Hall fluid. The zero frequency noise correlations are negative at filling factor 1/3 as for bare electrons (antibunching), but are strongly reduced in amplitude. These correlations become positive (bunching) for nu < or = 1/5, suggesting a tendency towards bosonic behavior.

Journal Article↗
PubMed2003

Structure, rotational dynamics, and superfluidity of small OCS-doped He clusters.

The structural and dynamical properties of carbonyl sulfide (OCS) molecules solvated in helium clusters are studied using reptation quantum Monte Carlo, for cluster sizes n=3-20 He atoms. Computer simulations allow us to establish a relation between the rotational spectrum of the solvated molecule and the structure of the He solvent, and of both with the onset of superfluidity. Our results agree with a recent spectroscopic study of this system and provide a more complex and detailed microscopic picture of this system than inferred from experiments.

Journal Article↗
PubMed2002

A dual-energy subtraction technique for microcalcification imaging in digital mammography--a signal-to-noise analysis.

Breast cancer may manifest as microcalcifications (microCs) in x-ray mammography. However, the detection and visualization of microCs are often obscured by the overlapping tissue structures. The dual-energy subtraction imaging technique offers an alternative approach for imaging and visualizing microCs. With this technique, separate high- and low-energy images are acquired and their differences are used to "cancel" out the background tissue structures. However, the subtraction process could increase the statistical noise level relative to the calcification contrast. Therefore, a key issue with the dual-energy subtraction imaging technique is to weigh the benefit of removing the cluttered background tissue structure over the drawback of reduced signal-to-noise ratio in the subtracted microC images. In this report, a theoretical framework for calculating the (quantum) noise in the subtraction images is developed and the numerical computations are described. We estimate the noise levels in the dual-energy subtraction signals under various imaging conditions, including the x-ray spectra, microC size, tissue composition, and breast thickness. The selection of imaging parameters is optimized to evaluate the feasibility of using a dual-energy subtraction technique for the improved detection and visualization of microCs. We present the results and discuss its dependence on imaging parameters.

Breast↗
PubMed1996

Lipoprotein changes in relation to body mass index in Native American adolescents.

In view of their known high incidence of noninsulin dependent diabetes (NIDDM), we sought to determine whether Native American (Plains Indian) children and adolescents show evidence of risk factors for both NIDDM and cardiovascular disease. Children and adolescents between the ages of 4 and 19 y were recruited, and field days were organized for data collection, which included height, weight [to compute body mass index (BMI)], waist and hip circumference, family histories, quantum of Native American ancestry, and blood sampling for fasting lipids, apolipoproteins, insulin, and glucose. BMI increased with age in boys and girls and tended to be higher than in Caucasian children. The difference was significant in 5-9-y-old (p < 0.05) and 10-14-y-old (p < 0.05) boys and 10-14-y-old girls (p < 0.001). Ten- to 14-y-old girls in the highest quartile for BMI had higher triglyceride levels (p < 0.05) and lower HDL cholesterol (p < 0.001) when compared with those in the lower quartiles. In contrast, 15-19 y olds in the highest quartile for BMI had higher cholesterol, LDL cholesterol, and apolipoprotein B (p < 0.001). The mean fasting insulin levels were not related to BMI. The data suggest that, within this Plains Indian population, obesity associated with elevated lipid levels tends to begin at an early age in Native American children. Insulin levels do not appear to be related to BMI, a putative index of adiposity, in this population of children known to be prone to NIDDM in adult life.

Adolescent↗
PubMed2005

Comparison of the light-harvesting networks of plant and cyanobacterial photosystem I.

With the availability of structural models for photosystem I (PSI) in cyanobacteria and plants it is possible to compare the excitation transfer networks in this ubiquitous photosystem from two domains of life separated by over one billion years of divergent evolution, thus providing an insight into the physical constraints that shape the networks' evolution. Structure-based modeling methods are used to examine the excitation transfer kinetics of the plant PSI-LHCI supercomplex. For this purpose an effective Hamiltonian is constructed that combines an existing cyanobacterial model for structurally conserved chlorophylls with spectral information for chlorophylls in the Lhca subunits. The plant PSI excitation migration network thus characterized is compared to its cyanobacterial counterpart investigated earlier. In agreement with observations, an average excitation transfer lifetime of approximately 49 ps is computed for the plant PSI-LHCI supercomplex with a corresponding quantum yield of 95%. The sensitivity of the results to chlorophyll site energy assignments is discussed. Lhca subunits are efficiently coupled to the PSI core via gap chlorophylls. In contrast to the chlorophylls in the vicinity of the reaction center, previously shown to optimize the quantum yield of the excitation transfer process, the orientational ordering of peripheral chlorophylls does not show such optimality. The finding suggests that after close packing of chlorophylls was achieved, constraints other than efficiency of the overall excitation transfer process precluded further evolution of pigment ordering.

Algorithms↗
PubMedDate not supplied

Information partnerships--shared data, shared scale.

How can one company gain access to another's resources or customers without merging ownership, management, or plotting a takeover? The answer is found in new information partnerships, enabling diverse companies to develop strategic coalitions through the sharing of data. The key to cooperation is a quantum improvement in the hardware and software supporting relational databases: new computer speeds, cheaper mass-storage devices, the proliferation of fiber-optic networks, and networking architectures. Information partnerships mean that companies can distribute the technological and financial exposure that comes with huge investments. For the customer's part, partnerships inevitably lead to greater simplification on the desktop and more common standards around which vendors have to compete. The most common types of partnership are: joint marketing partnerships, such as American Airline's award of frequent flyer miles to customers who use Citibank's credit card; intraindustry partnerships, such as the insurance value-added network service (which links insurance and casualty companies to independent agents); customer-supplier partnerships, such as Baxter Healthcare's electronic channel to hospitals for medical and other equipment; and IT vendor-driven partnerships, exemplified by ESAB (a European welding supplies and equipment company), whose expansion strategy was premised on a technology platform offered by an IT vendor. Partnerships that succeed have shared vision at the top, reciprocal skills in information technology, concrete plans for an early success, persistence in the development of usable information for all partners, coordination on business policy, and a new and imaginative business architecture.

Economic Competition↗
PubMed2006

A near linear-scaling smooth local coupled cluster algorithm for electronic structure.

We demonstrate near linear scaling of a new algorithm for computing smooth local coupled-cluster singles-doubles (LCCSD) correlation energies of quantum mechanical systems. The theory behind our approach has been described previously, [J. Subotnik and M. Head-Gordon, J. Chem. Phys. 123, 064108 (2005)], and requires appropriately multiplying standard iterative amplitude equations by a bump function, creating local amplitude equations (which are smooth according to the implicit function theorem). Here, we provide an example that this theory works in practice: we show that our algorithm leads to smooth potential energy surfaces and yields large computational savings. As an example, we apply our LCCSD approach to measure the post-MP2 correction to the energetic gap between two different alanine tetrapeptide conformations.

Algorithms↗
PubMed1996

Glycine and GABA receptors: molecular mechanisms controlling chloride ion flux.

We have been able to show that the three clearly identified atoms common to the inhibitory neurotransmitters glycine and GABA, that we previously hypothesized to serve as attachment points at the glycinergic and gabanergic receptor, can indeed interact through both electrostatic and hydrogen bonding to several amino acids, which have been identified in molecular biological investigations as both present and critical in the physiological functioning of key polypeptides common to these inhibitory receptors. In addition, amino acids also involved in stabilizing the interaction between the antagonists strychnine and R5135 at the glycinergic and gabanergic receptors, respectively, have been shown to fit our complex model. We identify in detail molecular mechanisms to explain how glycine and GABA initiate chloride ion movement from extraneuronal fluid in the synaptic cleft to intraneuronal volume. In addition, we also identify the molecular mechanisms involved in the blocking of chloride ion movement by strychnine at the glycinergic receptor and by R5135 at the gabanergic receptor. We also present two computer-generated color prints, one for the glycine receptor and one for the GABA receptor, which show the quantum mechanically geometry optimized complex formed between receptor side chains, i.e., the part of the amino acids in the polypeptide that interacts with the zwitterionic inhibitory neurotransmitters. These computer-generated color figures also show a) the important electrostatic and hydrogen bonding in these interactions, b) a van der Waals model of this complex to illustrate that no steric repulsions exist, and c) the molecular electrostatic potential energy map showing the electrostatic potentials of neurotransmitter bound to the receptor model. Finally, we show with computer calculations that the pseudo-rings, formed between the positive quanidinium group in arginine and one of the oxygen atoms in the carboxyl group in both glycine or GABA, result in a positive planar region which appears to be involved in a charge-transfer complex with aromatic benzene groups in amino acids such as phenylalanine and tryosine.

Androstanes↗
PubMedDate not supplied

Evaluation of computational chemistry methods: crystallographic and cheminformatics analysis of aminothiazole methoximes.

Cheminformatics is used to validate the capabilities of widely used quantum chemistry and molecular mechanics methods. Among the quantum methods examined are the semiempirical MNDO, AM1, and PM3 methods, Hartree-Fock (ab initio) at a range of basis set levels, density functional theory (DFT) at a range of basis sets, and a post-Hartree-Fock method, local Moller-Plesset second-order perturbation theory (LMP2). Among the force fields compared are AMBER, MMFF94, MMFF94s, OPLS/A, OPLS-AA, Sybyl, and Tripos. Programs used are Spartan, MacroModel, SYBYL, and Jaguar. The test molecule is (2-amino-5-thiazolyl)-alpha-(methoxyimino)-N-methylacetamide, a model of the aminothiazole methoxime (ATMO) side chain of third-generation cephalosporin antibacterial agents. The Ward hierarchical clustering technique yields an insightful comparison of experimental (X-ray) and calculated (energy optimized) bond lengths and bond angles. The computational chemistry methods are also compared in terms of the potential energy curves they predict for internal rotation. Clustering analysis and regression analysis are compared. The MMFF94 force field such as implemented in MacroModel is the best overall computational chemistry method at reproducing crystallographic data and conformational properties of the ATMO moiety. This work demonstrates that going to a higher level of quantum theory does not necessarily give better results and that quantum mechanical results are not necessarily better than molecular mechanics results.

Journal Article↗
PubMed2004

Transmission coefficient calculation for proton transfer in triosephosphate isomerase based on the reaction path potential method.

A global potential energy surface has been constructed through interpolation of our recently developed reaction path potential for chemical reactions in enzymes which is derived from combined ab initio quantum mechanical and molecular mechanical calculations. It has been implemented for the activated molecular dynamics simulations of the initial proton transfer reaction catalyzed by triosephosphate isomerase. To examine the dynamical effects on the rate constants of the enzymatic reaction, the classical transmission coefficient kappa(t) is evaluated to be 0.47 with the reactive flux approach, demonstrating considerable deviations from transition state theory. In addition, the fluctuations of protein environments have small effects on the barrier recrossing, and the transmission coefficient kappa(t) strongly depends on the fluctuations of atoms near the active site of the enzyme.

Algorithms↗
PubMed2004

Computational study of hydrogen binding by metal-organic framework-5.

We report the results of quantum chemistry calculations on H(2) binding by the metal-organic framework-5 (MOF)-5. Density functional theory calculations were used to calculate the atomic positions, lattice constant, and effective atomic charges from the electrostatic potential for the MOF-5 crystal structure. Second-order Møller-Plesset perturbation theory was used to calculate the binding energy of H(2) to benzene and H(2)-1,4-benzenedicarboxylate-H(2). To achieve the necessary accuracy, the large Dunning basis sets aug-cc-pVTZ, and aug-cc-pVQZ were used, and the results were extrapolated to the basis set limit. The binding energy results were 4.77 kJ/mol for benzene, 5.27 kJ/mol for H(2)-1,4-benzenedicarboxylate-H(2). We also estimate binding of 5.38 kJ/mol for Li-1,4-benzenedicarboxylate-Li and 6.86 kJ/mol at the zinc oxide corners using second-order Møller-Plesset perturbation theory. In order to compare our theoretical calculations to the experimental hydrogen storage results, grand canonical Monte Carlo calculations were performed. The Monte Carlo simulations identify a high energy binding site at the corners that quickly saturated with 1.27 H(2) molecules at 78 K. At 300 K, a broad range of binding sites are observed.

Journal Article↗