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At least 415 records · Page 23Linked to original sources
PubMed2000

Computer simulation of primary kinetic isotope effects in the proposed rate-limiting step of the glyoxalase I catalyzed reaction.

The proposed rate-limiting step of the glyoxalase I catalyzed reaction is the proton abstraction from the C1 carbon of the substrate by Glu(172). Here we examine primary kinetic isotope effects and the influence of quantum dynamics on this process by computer simulations. The calculations utilize the empirical valence bond method in combination with the molecular dynamics free energy perturbation technique and path integral simulations. For the enzyme-catalyzed reaction a H/D kinetic isotope effect of 5.0 +/- 1. 3 is predicted in reasonable agreement with the experimental result of about 3. Furthermore, the magnitude of quantum mechanical effects is found to be very similar for the enzyme reaction and the corresponding uncatalyzed process in solution, in agreement with other studies. The problems associated with attaining the required accuracy in order for the present approach to be useful as a diagnostic tool for the study of enzyme reactions are also discussed.

Catalysis↗
PubMed2003

Determining the strengths of hydrogen bonds in solid-state ammonia and urea: insight from periodic DFT calculations.

Plane-wave density functional theory has been applied to determine the strengths of hydrogen bonds in the phase I crystal structures of ammonia and urea. For ammonia, each component of the trifurcated hydrogen bond has been found to be almost as strong as a standard N-H.N interaction, and for urea the strengths of the two different N-H.O interactions have been determined by a quantum mechanical technique for the first time.

Ammonia↗
PubMedDate not supplied

A comparative study of isodensity surfaces using ab initio and ASA density functions.

In this article, we report a visual comparison between several of the available methods for constructing electronic density functions. The density forms studied include ab initio, atomic shell approximation, and promolecular densities. A graphical comparison is made for six different molecules at different levels of density function values. The differences between the various density functions are analysed by considering a molecular quantum self-similarity measure and the required computational time for all molecules at all computation levels is considered.

Algorithms↗
PubMed1993

Strategies for indirect computer-aided drug design.

This review is intended to describe some of the methods and procedures used for computer-aided drug design when the structure of the macromolecular target is unknown, as is the case for CNS active drugs. Strategies and methods used in computer-aided design of drugs in such instances must be "indirect," i.e., focusing on the characterization of the ligands themselves. This situation is different from one in which the three-dimensional structure of the macromolecular target for a drug is known, for example, for drugs that are enzyme inhibitors, allowing "direct" characterization of ligand-receptor interactions. Two qualitatively different "indirect" approaches are described here. One, called 2D-QSAR, is briefly reviewed. It is based on delineating regression relationships between a specified biological end point and properties of the compounds eliciting it. The other, based on pharmacophore development, constitutes the main part of this review. Several levels of pharmacophore development are described, which differ in the extent to which they encompass fundamental molecular properties that are determinants of receptor recognition and activation. The strengths and limitations of each procedure are discussed and illustrated by examples. Two methods for obtaining model receptor structures are then briefly described. Both rely on the prior success of the indirect methods in obtaining ligand properties that modulate receptor recognition and activation. These emerging capabilities have the potential to bridge the gap between indirect and direct methods of drug design, since, if successful, the design process can continue in a direct mode using explicit characterization of drug-receptor interactions. Strategies for hypothesis validation and use of hypothesis for drug design and discovery are also briefly reviewed. The final sections of this review describe specific computational tools such as molecular mechanics and quantum mechanical methods used to characterize and identify relevant molecular properties and indicate some areas for future development of computational chemistry methods that could increase its effectiveness in the design of novel drugs.

Computer Simulation↗
PubMed2003

Atomic properties of amino acids: computed atom types as a guide for future force-field design.

The quantum chemical topology (QCT) is able to propose atom types by direct computation rather than by chemical intuition. In previous work, molecular electron densities of 20 amino acids and smaller derived molecules were partitioned into a set of 760 topological atoms. Each atom was characterised by seven atomic properties and subjected to cluster analysis element by element, that is, C, H, O, N, and S. From the respective dendrograms, 21 carbon atom types were distinguished, 7 hydrogen, 2 nitrogen, 6 oxygen, and 6 sulfur atom types. Herein, we contrast the QCT atom types with those of the assisted model building with energy refinement (AMBER) force field. We conclude that in spite of fair agreement between QCT and AMBER atom types, the latter are sometimes underdifferentiated and sometimes overdifferentiated. In summary, we suggest that QCT is a useful guide in designing new force fields or improving existing ones. The computational origin of QCT atom types makes their determination unbiased compared to atom type determination by chemical intuition and a priori assumptions. We provide a list of specific recommendations.

Algorithms↗
PubMed2002

Quantum dissipation in unbounded systems.

In recent years trajectory based methodologies have become increasingly popular for evaluating the time evolution of quantum systems. A revival of the de Broglie--Bohm interpretation of quantum mechanics has spawned several such techniques for examining quantum dynamics from a hydrodynamic perspective. Using techniques similar to those found in computational fluid dynamics one can construct the wave function of a quantum system at any time from the trajectories of a discrete ensemble of hydrodynamic fluid elements (Bohm particles) which evolve according to nonclassical equations of motion. Until very recently these schemes have been limited to conservative systems. In this paper, we present our methodology for including the effects of a thermal environment into the hydrodynamic formulation of quantum dynamics. We derive hydrodynamic equations of motion from the Caldeira-Leggett master equation for the reduced density matrix and give a brief overview of our computational scheme that incorporates an adaptive Lagrangian mesh. Our applications focus upon the dissipative dynamics of open unbounded quantum systems. Using both the Wigner phase space representation and the linear entropy, we probe the breakdown of the Markov approximation of the bath dynamics at low temperatures. We suggest a criteria for rationalizing the validity of the Markov approximation in open unbound systems and discuss decoherence, energy relaxation, and quantum/classical correspondence in the context of the Bohmian paths.

Journal Article↗
PubMed2001

Anderson transition in a multiply-twisted helix.

We investigated the Anderson transition in a multiply-twisted helix in which a helical chain of components, i.e., atoms or nanoclusters, is twisted to produce a doubly-twisted helix, which itself can be twisted to produce a triply-twisted helix, and so on, in which there are couplings between adjacent rounds of helices. As the strength of the on-site random potentials increases, an Anderson transition occurs, suggesting that the number of dimensions is 3 for electrons running along the multiply-twisted helix when the couplings between adjacent rounds are strong enough. If the couplings are weakened, the dimensionality becomes less, resulting in localization of electrons. The effect of random connections between adjacent rounds of helices and random magnetic fields that thread the structure is analyzed using the spectral statistics of a quantum particle.

Computer Simulation↗
PubMed2002

Quantum theory of dissociative chemisorption on metal surfaces.

Recent theoretical progress in gas-surface reaction dynamics, a field relevant to heterogeneous catalysis, is described. One of the most fundamental reactions, the dissociative chemisorption of H2 on metal surfaces, can now be treated accurately using quantum mechanics. Density functional theory is used to compute the molecule-surface interaction, and the motion of the hydrogen atoms is simulated using quantum dynamics, modeling all six molecular degrees of freedom. Theory is in good quantitative agreement with molecular beam experiments, offering useful interpretations, and allowing reliable predictions. The success of the approach calls for extensions to larger systems, such as dissociative chemisorption of polyatomic molecules.

Journal Article↗
PubMed2001

Interplay of intrinsic and environmental effects on the magnetic properties of free radicals issuing from H-atom addition to cytosine.

Possible radical reaction products issuing from H-atom addition to cytosine have been characterized and analyzed by means of a comprehensive quantum mechanical approach including density functional computations (B3LYP), together with simulation of the solvent by the polarizable continuum model (PCM), and averaging of spectroscopic properties over the most important vibrational motions. The hyperfine couplings of the semirigid 5,6-dihydrocytos-6yl radical computed at the optimized geometry are in good agreement with their experimental counterparts. On the other hand, vibrational averaging is mandatory for obtaining an effectively planar structure for the 5,6-dihydrocytos-5yl radical with the consequent equivalence of beta-hydrogens. Finally, only proper consideration of environmental effects restores the agreement between computed and experimental couplings for the base anion protonated at N3.

Cytosine↗
PubMed1999

Performance characteristics of a Kodak computed radiography system.

The performance characteristics of a photostimulable phosphor based computed radiographic (CR) system were studied. The modulation transfer function (MTF), noise power spectra (NPS), and detective quantum efficiency (DQE) of the Kodak Digital Science computed radiography (CR) system (Eastman Kodak Co.-model 400) were measured and compared to previously published results of a Fuji based CR system (Philips Medical Systems-PCR model 7000). To maximize comparability, the same measurement techniques and analysis methods were used. The DQE at four exposure levels (30, 3, 0.3, 0.03 mR) and two plate types (standard and high resolution) were calculated from the NPS and MTF measurements. The NPS was determined from two-dimensional Fourier analysis of uniformly exposed plates. The presampling MTF was determined from the Fourier transform (FT) of the system's finely sampled line spread function (LSF) as produced by a narrow slit. A comparison of the slit type ("beveled edge" versus "straight edge") and its effect on the resulting MTF measurements was also performed. The results show that both systems are comparable in resolution performance. The noise power studies indicated a higher level of noise for the Kodak images (approximately 20% at the low exposure levels and 40%-70% at higher exposure levels). Within the clinically relevant exposure range (0.3-3 mR), the resulting DQE for the Kodak plates ranged between 20%-50% lower than for the corresponding Fuji plates. Measurements of the presampling MTF with the two slit types have shown that a correction factor can be applied to compensate for transmission through the relief edges.

Evaluation Studies as Topic↗
PubMed1982

Effect of quantum noise on the detection of incipient proximal caries.

The effect of quantum noise on the radiographyic detectability of proximal carious lesions was studied. Bitewing radiographs obtained from patients considered to be free of caries were digitized and stored in a computer using a sampling interval comparable to screen-film systems. Lesions limited in depth to one half the thickness of the enamel were induced by means of computer simulation. Various amounts of randomly generated quantum noise were added to each radiographic image. The results from observer-performance studies show that the lesions can be detected reliably in the presence of substantial amounts of quantum noise, suggesting that comparable diagnostic performance could be obtained with significantly faster imagining systems than those currently used in dentistry.

Analog-Digital Conversion↗
PubMed2000

QSAR treatment of electronic substituent effects using frontier orbital theory and topological parameters

A methodology for the estimation of Hammett substituent constants from computational-based descriptors utilizing quantitative structure activity/property relationships (QSAR/QSPR) formalism is presented. Electronic descriptors derived from quantum chemical calculations and molecular topology were used to generate computational-based analogues of empirical Hammett substituent constants from statistical analysis. Global quantum chemical reaction indices were drawn from frontier orbital theory and density functional theory and formulated from AM1-based calculations. A localized index based on the electrotopological state index was used to encode information on individual group properties. From a training set consisting of 150 meta and para-substituted benzoic acids, statistical analysis of computational-based descriptors as a function of empirical substituent constants yielded a five-parameter QSAR/QSPR model which generates computational-based constants exhibiting a strong correlation with empirical values (r2 = 0.958). Both internal (PRESS) and external (independent testing set of benzoic acids) validation procedures suggest that the electronic effects QSAR/QSPR model derived in this work from computational-based parameters is a statistically viable paradigm. Both predicted and empirical constants were used in Hammett-type validation analyses as functions of chemical, biological, and spectroscopic data for thirty structurally diverse meta and parasubstituted aromatic testing sets. Statistical measures of ensuing correlations were examined and compared, and the empirical and predicted results were of similar quality. Validation results reveal that a large number of computational-based substituent constants can be accurately estimated from semiempirical AM1 frontier orbital energies and electronic structure information obtained directly from substituted benzoic acids without the aid of empirical parametrization.

Journal Article↗
PubMed1989

The role of hydrated divalent metal ions in the bridging of two anionic groups. An ab initio quantum chemical and molecular mechanics study of dimethyl phosphate and formate bridged by calcium and magnesium ions.

Ab initio quantum chemical (Gaussian82) and molecular mechanics (AMBER2.0) computational techniques are employed to investigate the interaction of two anions (formate an dimethylphosphate) and a central divalent metal cation (magnesium or calcium). These systems are models for the essential GDP binding unit of the G-proteins (e.g., EF-Tu or the ras oncogene proteins) and for protein/phospholipid interactions, both of which are mediated by divalent metal cations. Various levels of hydration are utilized to examine coordination of differences between magnesium and calcium ions. Two different orientations of formate and dimethyl phosphate in direct ion contact with a magnesium ion and two waters of hydration were energy minimized with both quantum and molecular mechanics techniques. The structures and energy differences between the two orientations determined by either of the computational techniques are similar. Magnesium ion has a strong propensity to assume six coordination whereas calcium ion preferentially assumes a coordination greater than six. Likewise, water molecules attached to magnesium ion are held more rigidly than those of calcium ion, thus calcium ion is more accommodating in the exchange of water for negative ligands.

Calcium↗
PubMed1980

Cannabidiol and phenytoin: a structural comparison.

Conformational energy maps have been computed for the antiepileptic agents phenytoin and cannabidiol by the quantum-mechanical method of perturbative configuration interaction with localized orbitals (PCILO). The computation indicates that the spatial relationship between the two rings in the two drugs is similar and close to the respective structures in the crystal. This is supported by 1H and 13C NMR measurements. Hence, both compounds fulfill the stereochemical requirements suggested for anticonvulsant drug action.

Cannabidiol↗
PubMed2002

1,5-Hydride shift in Wolff-Kishner reduction of (20R)-3beta,20, 26-trihydroxy-27-norcholest-5-en-22-one: synthetic, quantum chemical, and NMR studies.

Heating (20R)-3beta,20,26-trihydroxy-27-norcholest-5-en-22-one (1) with hydrazine and KOH at 160 degrees C completely converted the steroid to a diastereoisomeric mixture of the new (20R,22RS)-27-norcholest-5-ene-3beta,20,22-triols (2). Exclusive formation of 2 suggests that the expected Wolff-Kishner reduction to a methylene group at the C-22 ketone in 1 was diverted to the C-26 position by a 1,5-hydride shift. All attempts under acid conditions failed to produce a C-22 phenyl hydrazone from 1. However, reaction of 1 was reacted with phenylhydrazine in hot KOH, gave the C-26 phenylhydrazone 4 as the sole product. Evidently, under alkaline conditions, first a hydride ion undergoes an intramolecular transfer from the C-26 CH(2)OH group to the C-22 ketone in 1, and then the phenylhydrazine traps the newly formed aldehyde. To examine this hypothesis, we constructed computer-simulated transition state models from quantum chemical calculations and then compared data from these models with NMR measurements of the reaction mixtures containing 2. The NMR data showed that the C-22 diastereoisomers of 2 are formed in a nearly 1:1 ratio exactly as predicted from the energy-optimized transition states, which were calculated for intramolecular 1,5-hydride shifts that produced each of the two C-22 diastereoisomers. Accordingly, these results support the hypothesis that an intramolecular 1,5-hydride shift mechanism promotes complete conversion of 1 to 2 under classical Wolff-Kishner reduction conditions.

Aldehydes↗
PubMed1984

[Analysis of factors limiting the applications of binomial statistics in studies of mediator secretion at neuromuscular synapses].

Binomial parameters of transmitter secretion were calculated on the basis of synaptic potential analyses at frog sartorius muscle. In some synapses negative values of parameter of the p were found. These negative values often occurred at low concentrations of Ca2+ ions and small amplitude of miniature end plate potentials. The obtained data were interpreted in terms of a model which presupposes the heterogeneity of the quantum transmitter release at different sites. A computer imitation of transmitter secretion showed that the appearance of the negative p parameter values and erroneous n estimations in the experiment are related with the shape of the distribution of quantum transmitter release probability and the amplitude of miniature end plate potentials.

Animals↗
PubMedDate not supplied

Molecular quantum similarity measures tuned 3D QSAR: an antitumoral family validation study.

In this work, a new methodology to construct a tuned QSAR model is presented, which is based on a convex set formalism. The present procedure continues previous 3D QSAR studies, performed using molecular quantum similarity measures (MQSM). With this new computational tool, the efficiency of MQSM applied to QSAR analysis is significantly improved. A reliable QSAR model is obtained using convex linear combinations of different kinds of MQSM, corresponding to different quantum-mechanical operators related to the quantum similarity integral. The active compounds studied here, as a case study, are a set of antitumor agents, the camptothecin molecule and analogues, and the property evaluated is the topoisomerase-I inhibition activity. Before performing a tuned QSAR analysis with this particular molecular set, a simple QSAR study for all the different possible types of MQSM is carried out. In addition, another application of MQSM is presented, to determine which method can be used to optimize molecular structures in order to reproduce experimental molecular geometries as well as possible.

Animals↗
PubMed1988

Molecular modelling in design of crop protection chemicals.

Specific examples from pesticide research are given which illustrate the types of analysis employed to design optimal inhibitors for a given receptor, based on the assumption that a congeneric series of compounds behave in a related mode in the biosystem. The examples illustrate the complementary role played by computational chemistry, X-ray crystallography and computer graphics and also raise questions as to the current limitations of existing molecular mechanics and quantum mechanics techniques.

Agriculture↗