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At least 1,225 records · Page 68Linked to original sources
PubMed2001

Order by disorder from nonmagnetic impurities in a two-dimensional quantum spin liquid.

We consider doping of nonmagnetic impurities in the spin-1/2, 1/5-depleted square lattice. This structure, whose undoped phase diagram offers both magnetically ordered and spin-liquid ground states, is realized physically in CaV4O9. Doping into the ordered phase results in a progressive loss of order, which becomes complete at the percolation threshold. By contrast, doping into the spin liquids creates a phase of weak but long-ranged antiferromagnetic order, a true order-by-disorder phenomenon. We study the phase diagram of the doped system by computing the static susceptibility and staggered magnetization using a stochastic series-expansion quantum Monte Carlo technique.

Journal Article↗
PubMed2004

Quantum dynamics study of the excited-state double-proton transfer in 2,2'-bipyridyl-3,3'-diol.

Density functional theory and quantum dynamics simulations have been used to study the double-proton transfer reaction in 2,2'-bipyridyl-3,3'-diol in the first singlet excited electronic state. This process is experimentally known to be branched: It consists of a fast, concerted reaction mechanism (tau approximately 100 fs) and a stepwise reaction mechanism [with a fast initial step (tau approximately 100 fs) and a slower final step (tau approximately 10 ps)]. Quantum dynamics simulations on a two-dimensional model reveal that the concerted reaction occurs despite the nonexistence of a concerted reaction path, but they fail to explain the relative slowness of the stepwise mechanism. A qualitative simulation using a three-dimensional model suggests that internal vibrational relaxation (IVR) might be the reason why the second stage of the stepwise mechanism is so slow.

2,2'-Dipyridyl↗
PubMed2006

Computational studies on thermodynamic properties, effective diameters, and free volume of argon using an ab initio potential.

A quantum mechanical derived ab initio interaction potential for the argon dimer was tested in molecular simulations to reproduce the thermophysical properties of the vapor-liquid phase equilibria using the Gibbs ensemble Monte Carlo simulations as well as the liquid and supercritical equation of state using the NVT Monte Carlo simulations. The ab initio interaction potential was taken from the literature. A recently developed theory [R. Laghaei et al., J. Chem. Phys. 124, 154502 (2006)] was used to compute the effective diameters of argon in fluid phases and the results were subsequently applied in the generic van der Waals theory to compute the free volume of argon. The calculated densities of the coexisting phases, the vapor pressure, and the equation of state show excellent agreement with experimental values. The effective diameters and free volumes of argon are given over a wide range of densities and temperatures. An empirical formula was used to fit the effective diameters as a function of density and temperature. The computed free volume will be used in future investigations to calculate the transport properties of argon.

Journal Article↗
PubMed2006

Photodissociation of HBr. 1. Electronic structure, photodissociation dynamics, and vector correlation coefficients.

Ab initio potential energy curves, transition dipole moments, and spin-orbit coupling matrix elements are computed for HBr. These are then used, within the framework of time-dependent quantum-mechanical wave-packet calculations, to study the photodissociation dynamics of the molecule. Total and partial integral cross sections, the branching fraction for the formation of excited-state bromine atoms Br(2P(1/2)), and the lowest order anisotropy parameters, beta, for both ground and excited-state bromine are calculated as a function of photolysis energy and compared to experimental and theoretical data determined previously. Higher order anisotropy parameters are computed for the first time for HBr and compared to recent experimental measurements. A new expression for the Re[a1(3) (parallel, perpendicular)] parameter describing coherent parallel and perpendicular production of ground-state bromine in terms of the dynamical functions is given. Although good agreement is obtained between the theoretical predictions and the experimental measurements, the discrepancies are analyzed to establish how improvements might be achieved. Insight is obtained into the nonadiabatic dynamics by comparing the results of diabatic and fully adiabatic calculations.

Anisotropy↗
PubMed2003

Molecular dynamics and quantum chemical studies on the catalytic mechanism of Delta5-3-ketosteroid isomerase: the catalytic diad versus the cooperative hydrogen bond mechanism.

To further understand Delta(5)-3-ketosteroid isomerase (KSI) catalysis, we carried out molecular dynamics (MD) simulations of the KSI dimer ligated with a substrate and reaction intermediate analogue and high level ab initio calculations on relevant enzymatic reaction models. Simulation of the enzyme-substrate complex dimer systems showed asymmetric dynamics between the two monomers, in which the hydrogen bond pattern between the substrate and active site residues in the first and the second subunits supported the cooperative hydrogen bond (CH) and the catalytic diad (CD) mechanisms, respectively. On the other hand, only the CH mechanism was supported in the MD simulation of the enzyme-intermediate complex dimer. From MP2/6-31+G**//RHF/6-31G** calculations, we found the kinetic barriers for the two reaction mechanisms were similar. The CH route afforded a greater stabilization to the enolate intermediate than did the CD counterpart. Thus, the present computational studies indicate that the CH mechanism would be favored over the CD one in the catalytic action of KSI. However, the latter could not be ruled out conclusively because of the explicit appearance of a CD configuration in the MD trajectories of the enzyme-substrate complex and because of the similar intrinsic activation barrier for the CH and CD mechanisms. The appearance of configurations that favor the CD pathway is rationalized in terms of a model in which the KSI-substrate complex does not have a strong preference for one hydrogen bonding pattern over another, while the KSI-intermediate complex favors a cooperative hydrogen bond pattern in order to stabilize the reaction intermediate. This hypothesis is supported by the ab initio calculations which indicate that the CH intermediate is more stable than the CD one by approximately 6.3 kcal/mol.

Catalysis↗
PubMedDate not supplied

Quantitative structure-activity relationships for the enantioselectivity of oxirane ring-opening catalyzed by epoxide hydrolases.

The enantioselective ring-opening catalyzed by epoxide hydrolases originating from seven different sources of a series of 2,2-disubstituted oxiranes containing alkyl chains of different lengths, unsaturated (alkenyl, alkinyl) and aromatic groups as well as electronegative heteroatoms at various positions within the side chain was analyzed by quantitative structure-activity relationships. Models for the enantioselectivity were derived with the aid of multiple linear regression analysis (MLR) using several steric and electronic (quantum chemical) descriptors. On the basis of the models derived by MLR nonlinear modeling with artificial neural networks (ANN) was also done. Good predictive performance was observed for both modeling approaches. The models also indicate that different steric and/or electronic features account for the enantioselectivities observed for the individual epoxide hydrolases.

Catalysis↗
PubMed2003

Identification of Glu166 as the general base in the acylation reaction of class A beta-lactamases through QM/MM modeling.

Bacterial class A beta-lactamases are responsible for the most known resistance against beta-lactam antibiotics. With the continuing rise in antibiotic resistance, improved knowledge of the mechanisms of action of these enzymes is needed in the development of effective therapeutic agents and strategies. The mechanism of the deacylation step in class A beta-lactamases is well accepted. In contrast, the mechanism of the acylation step has been uncertain, with several conflicting proposals put forward. We have modeled the acylation step in a class A beta-lactamase, using a combined quantum mechanics/molecular mechanics approach. The results provide an atomic level description of the reaction and show that Glu166 acts as the general base in the reaction, deprotonating Ser70 via an intervening water molecule. Ser70 acts as the nucleophile for attack on the lactam ring in a concerted reaction. The results do not rule out the importance of Lys73 in catalysis, in agreement with experimental data.

Acylation↗
PubMed2001

Determination of the detective quantum efficiency of a prototype, megavoltage indirect detection, active matrix flat-panel imager.

After years of aggressive development, active matrix flat-panel imagers (AMFPIs) have recently become commercially available for radiotherapy imaging. In this paper we report on a comprehensive evaluation of the signal and noise performance of a large-area prototype AMFPI specifically developed for this application. The imager is based on an array of 512 x 512 pixels incorporating amorphous silicon photodiodes and thin-film transistors offering a 26 x 26 cm2 active area at a pixel pitch of 508 microm. This indirect detection array was coupled to various x-ray converters consisting of a commercial phosphor screen (Lanex Fast B, Lanex Regular, or Lanex Fine) and a 1 mm thick copper plate. Performance of the imager in terms of measured sensitivity, modulation transfer function (MTF), noise power spectra (NPS), and detective quantum efficiency (DQE) is reported at beam energies of 6 and 15 MV and at doses of 1 and 2 monitor units (MU). In addition, calculations of system performance (NPS, DQE) based on cascaded-system formalism were reported and compared to empirical results. In these calculations, the Swank factor and spatial energy distributions of secondary electrons within the converter were modeled by means of EGS4 Monte Carlo simulations. Measured MTFs of the system show a weak dependence on screen type (i.e., thickness), which is partially due to the spreading of secondary radiation. Measured DQE was found to be independent of dose for the Fast B screen, implying that the imager is input-quantum-limited at 1 MU, even at an extended source-to-detector distance of 200 cm. The maximum DQE obtained is around 1%--a limit imposed by the low detection efficiency of the converter. For thinner phosphor screens, the DQE is lower due to their lower detection efficiencies. Finally, for the Fast B screen, good agreement between calculated and measured DQE was observed.

Biophysical Phenomena↗
PubMed2004

Evaluation of carbohydrate molecular mechanical force fields by quantum mechanical calculations.

A quantitative evaluation of 20 second-generation carbohydrate force fields was carried out using ab initio and density functional methods. Geometry-optimized structures (B3LYP/6-31G(d)) and relative energies using augmented correlation consistent basis sets were calculated in gas phase for monosaccharide carbohydrate benchmark systems. Selected results are: (i). The interaction energy of the alpha-d-glucopyranose.H(2)O heterodimer is estimated to be 4.9 kcal/mol, using a composite method including terms at highly correlated (CCSD(T)) level. Most molecular mechanics force fields are in error in this respect; (ii). The (3)E envelope (south) pseudorotational conformer of methyl 5-deoxy-beta-d-xylofuranoside is 0.66 kcal/mol more stable than the (3)E envelope (north) conformer and the alpha-anomer of methyl d-glucopyranoside is 0.82 kcal/mol more stable than the beta-anomer; (iii). The relative energies of the (gg, gt and tg) rotamers of methyl alpha-d-glucopyranoside and methyl alpha-d-galactopyranoside are (0.13, 0.00, 0.15) and (0.64, 0.00, 0.77) kcal/mol, respectively. The results of the quantum mechanical calculations are compared with the results of calculations using the 20 second-generation carbohydrate force fields. No single force field is consistently better than the others for all the test cases. A statistical assessment of the performance of the force fields indicates that CHEAT(95), CFF, certain versions of Amber and of MM3 have the best overall performance, for these gas phase monosaccharide systems.

Carbohydrate Metabolism↗
PubMed1996

Signal-to-noise ratio and detective quantum efficiency analysis of optically coupled CCD mammography imaging systems.

RATIONALE AND OBJECTIVES: Design considerations for x-ray systems with optically coupled charge-coupled devices require an understanding of the characteristics of cascaded multistage imaging chains. Performance evaluations rely on accurate analyses of signal-to-noise ratio, noise power spectrum, and detective quantum efficiency. METHODS: Theoretic models of signal-to-noise ratio, noise power spectrum, and detective quantum efficiency were extended to analyze the optically coupled charge-coupled device and other electronic x-ray imaging systems. The descriptions of how to measure or compute these parameters are provided. RESULTS: The results of our quantitative analysis illustrate that x-ray quantum-noise limitation can be obtained without an image intensifier by using a low additive noise charge-coupled device. CONCLUSION: This theoretic model and experimental method provide a useful tool for developing optoelectronic x-ray imaging systems for digital mammography and other radiologic procedures.

Female↗
PubMed1996

Selected new developments in computational chemistry.

Molecular dynamics is a general technique for simulating the time-dependent properties of molecules and their environments. Quantum mechanics, as applied to molecules or clusters of molecules, provides a prescription for predicting properties exactly (in principle). It is reasonable to expect that both will have a profound effect on our understanding of environmental chemistry in the future. In this review, we consider several recent advances and applications in computational chemistry.

Chemical Phenomena↗
PubMed2006

Influence of reagent rotation on (H-, D2) and (D-, H2) collisions: a quantum mechanical study.

Time-independent quantum mechanical (TIQM) approach (helicity basis truncated at k = 2) has been used for computing differential and integral cross sections for the exchange reaction H- + D2 (v = 0, j = 0-4) --> HD + D- and D- + H2 (v = 0, j = 0-3) --> HD + H- in three dimensions on an accurate ab initio potential energy surface. It is shown that the j-weighted differential reaction cross section values are in good agreement with the experimental results reported by Zimmer and Linder at four different relative translational energies (Etrans = 0.55, 0.93, 1.16 and 1.48 eV) for (H-, D2) and at one relative translational energy (Etrans = 0.6 eV) by Haufler et al. for both (H-, D2) and (D-, H2) collisions. The j-weighted integral reaction cross section values are in good agreement with the crossed beam measurements by Zimmer and Linder in the Etrans range 0.5-1.5 eV and close to the guided ion beam results by Haufler et al. for (H-, D2) in the range 0.8-1.2 eV. Time-dependent quantum mechanical (TDQM) results obtained using centrifugal sudden approximation are reported in the form of integral reaction cross section values as a function of Etrans in the range 0.3-3.0 eV for both reactions in three dimensions on the same potential energy surface. The TDQM reaction cross section values decline more sharply than the TIQM results with increase in the initial rotational quantum number (j) for the D2 molecules in their ground vibrational state (v = 0) for (H-, D2) collisions. The computed j-weighted reaction cross section values are in good agreement with the experimental results reported by Zimmer and Linder for (H-, D2) collisions and guided ion beam results by Haufler et al. for both (H-, D2) and (D-, H2) collisions for energies below the threshold for electron detachment channel.

Journal Article↗
PubMed1986

One- and two-dimensional NMR spectral analysis of the consequences of single amino acid replacements in proteins.

The traditional approach of using homologous sequences to elucidate the role of specific amino acid residues in protein structure and function becomes more meaningful as the number of differences is minimized, with the limit being alteration of a single residue. For small proteins in solution, NMR spectroscopy offers a means of obtaining detailed information about each residue and its response to a given change in the protein sequence. Extraction of this information has been aided by recent progress in spectrometer technology (higher magnetic fields, more sensitive signal detection, more sophisticated computers) and experimental strategies (new NMR pulse sequences including multiple-quantum and two-dimensional NMR methods). The set of avian ovomucoid third domains, which consists of the third domain proper plus a short leader (connecting peptide) and has a maximum of 56 amino acid residues, offers an attractive system for developing experimental methods for investigating sequence-structure and structure-function relationships in proteins. Our NMR results provide examples of sequence effects on pKa' values, average conformation, and internal motion of amino acid side chains.

Amino Acid Sequence↗
PubMed1977

Photochemical transformation of the DDT and methoxychlor degradation products, DDE and DMDE, by sunlight.

DDE and DMDE, degradation products of the pesticides DDT and methoxychlor, rapidly undergo an unusual photoisomerization in solution when exposed to sunlight. The isomerization involves the exchange of a vinyl chlorine and an ortho aromatic hydrogen. Other photoproducts identified were corresponding benzophenones and 1,1-diaryl-2-chloroethylenes. Quantum yields for the reactions were measured and then used to compute sunlight photolysis half-lives for DMDE and DDE. Although both compounds absorb only the short-wavelength ultraviolet component of sunlight, their photolysis was found to be surprisingly rapid. During summer at latitude 40 degrees N, the photolysis half-lives near the surface of a water body are one hour and one day for dissolved DMDE and DDE, respectively. Photolysis of the DDE photoisomers is about an order of magnitude slower than that of DDE, suggesting that they may accumulate under environmental conditions. The DDE photoisomers photocyclize to form chlorinated dibenzofulvene and dichlorofluorenone. Neither DDE nor its photoisomers photoreact in solution to form PCB's. The environmental significance of these results is discussed, and its is suggested that the persistence of DDE in inland surface waters may be related to its tendency to sorb onto sediments and biota where not light is present.

Dichlorodiphenyl Dichloroethylene↗
PubMed1995

Discriminating D1 and D2 agonists with a hydrophobic similarity index.

Currently, methods for calculating molecular similarity indices have been developed for comparing steric, charge density, and molecular electrostatic potential (MEP) properties. Much of the existing technology may, however, be applied to the quantitative comparison of molecular hydrophobicities. In this article we present an empirical hydrophobic similarity index. We utilize atomic hydrophobic parameters derived from a quantum mechanical semiempirical wavefunction. Hydrophobicity at points on a grid is computed with a recently introduced "molecular lipophilicity potential." The overlap of pairs of molecules is calculated with the metric introduced by Carbó. This approach is applied to a case in which steric and electrostatic criteria have already been shown to be inadequate in rationalizing selectivity, namely, requirements for recognition at the dopamine D1 and D2 receptors. We demonstrate that, for a set of dopamine agonists, D1 ligands show higher similarity in this property that D2 analogs. This indicator of similarity is more successful at accounting for D1 selectivity than previous methods.

8-Hydroxy-2-(di-n-propylamino)tetralin↗
PubMed2004

Molecular modeling insights into the catalytic mechanism of the retaining galactosyltransferase LgtC.

The bacterial enzyme lipopolysaccharyl alpha-galactosyltransferase C (EC 2.4.1.x, LgtC) is involved in the synthesis of lipooligosaccharides displayed on the cell surfaces of Neisseria meningitidis. LgtC catalyzes the transfer of a galactosyl residue from UDP-Gal to the terminal galactose residue of glycoconjugates with an overall retention of stereochemistry at the anomeric center. Several hypothetical catalytic mechanisms of the LgtC enzyme were examined herein using DFT quantum chemical methods up to the B3LYP/6-311++G**//B3LYP/6-31G* level. The computational model used to follow the reaction is based on the crystallographic structure of LgtC in complex with both the nucleotide-galactose donor and the oligosaccharide-acceptor analogues. The 136 atoms included in this model represent fragments of residues critical for the substrate binding and catalysis. From our calculations, the preferred pathway is predicted to be a one step mechanism with the nucleophilic attack of the acceptor oxygen onto the anomeric carbon and the proton transfer to a phosphate oxygen occurring simultaneously. This mechanism has an A(N)D(N)A(H)D(H) character, with the unique transition state structure in which the attacking galactose group is more closely bound to the anomeric carbon than to the UDP leaving group and where the hydrogen bond between the nucleophile and the leaving group oxygens facilitates the attack of the acceptor O4(') from the same side of the transferred galactose.

Bacterial Proteins↗
PubMed2004

Molecular determinants for ATP-binding in proteins: a data mining and quantum chemical analysis.

Adenosine 5'-triphosphate (ATP) plays an essential role in all forms of life. Molecular recognition of ATP in proteins is a subject of great importance for understanding enzymatic mechanism and for drug design. We have carried out a large-scale data mining of the Protein Data Bank (PDB) to analyze molecular determinants for recognition of the adenine moiety of ATP by proteins. Non-bonded intermolecular interactions (hydrogen bonding, pi-pi stacking interactions, and cation-pi interactions) between adenine base and surrounding residues in its binding pockets are systematically analyzed for 68 non-redundant, high-resolution crystal structures of adenylate-binding proteins. In addition to confirming the importance of the widely known hydrogen bonding, we found out that cation-pi interactions between adenine base and positively charged residues (Lys and Arg) and pi-pi stacking interactions between adenine base and surrounding aromatic residues (Phe, Tyr, Trp) are also crucial for adenine binding in proteins. On average, there exist 2.7 hydrogen bonding interactions, 1.0 pi-pi stacking interactions, and 0.8 cation-pi interactions in each adenylate-binding protein complex. Furthermore, a high-level quantum chemical analysis was performed to analyze contributions of each of the three forms of intermolecular interactions (i.e. hydrogen bonding, pi-pi stacking interactions, and cation-pi interactions) to the overall binding force of the adenine moiety of ATP in proteins. Intermolecular interaction energies for representative configurations of intermolecular complexes were analyzed using the supermolecular approach at the MP2/6-311 + G* level, which resulted in substantial interaction strengths for all the three forms of intermolecular interactions. This work represents a timely undertaking at a historical moment when a large number of X-ray crystallographic structures of proteins with bound ATP ligands have become available, and when high-level quantum chemical analysis of intermolecular interactions of large biomolecular systems becomes computationally feasible. The establishment of the molecular basis for recognition of the adenine moiety of ATP in proteins will directly impact molecular design of ATP-binding site targeted enzyme inhibitors such as kinase inhibitors.

Adenine↗
PubMed2006

Is emergency endovascular aneurysm repair associated with higher secondary intervention risk at mid-term follow-up?

OBJECTIVE: The study assessed mid-term outcome of emergency endovascular repair for acute infrarenal abdominal aortic aneurysms, with special attention to secondary interventions. METHODS: Between May 1998 and August 2005, 56 patients underwent emergent endovascular repair for a ruptured abdominal aortic aneurysm (n = 34) or an acute nonruptured abdominal aortic aneurysm (n = 22). During the same period, 322 consecutive patients underwent elective endovascular aneurysm repair and were used as control group. Five types of stent grafts were used: Vanguard, Talent, Excluder, Zenith, and Quantum. Follow-up included abdominal radiograph, duplex ultrasound scanning, and computed tomographic angiography. Outcome measures included all-cause and aneurysm-related mortality, complications, and secondary interventions. RESULTS: Mortality at 30 days was 18%, 5%, and 1% in the ruptured, acute nonruptured, and elective aneurysm groups, respectively. Overall mean follow-up was 38 +/- 26 months. In the ruptured aneurysm group, survival was 67.8% +/- 8.6% at 1 year and 62.1% +/- 9.5% at 2 and 3 years. Seven secondary interventions (4 early and 3 late) were required in five patients (15%), with a cumulative risk of 9.2% +/- 5.1% at 1 year and 16.2% +/- 8.2% at 2 and 3 years. In the acute nonruptured aneurysm group, survival was 90.9% +/- 6.1% at 1 year, 84.8% +/- 8.2% at 2 years, and 76.4% +/- 10.9% at 3 years. Four secondary interventions (1 early and 3 late) were required in four patients (18%), with a cumulative risk of 9.6% +/- 6.5% at 1 and 2 years and 20.9% +/- 12.0% at 3 years. In the elective aneurysm (control) group, survival was 95.2% +/- 1.2% at 1 year, 89.9% +/- 1.8% at 2 years, and 86.2% +/- 2.1% at 3 years. A total of 51 secondary interventions (4 early, 47 late) were required in 38 patients (12%), with a cumulative risk of 4.2% +/- 1.1% at 1 year, 7.6% +/- 1.6% at 2 years, and 12.9% +/- 2.2% at 3 years. CONCLUSIONS: To our surprise, emergency endovascular aneurysm repair did not present with higher secondary intervention rate at mid-term follow-up.

Angioplasty↗