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PubMed2001

Quantum mechanical quantitative structure activity relationships to avoid mutagenicity in dental monomers.

The objective of this study was to identify through quantum mechanical quantitative structure activity relationships (Q-QSARs) chemical structures in dental monomers that influence their mutagenicity. AMPAC, a semiempirical computer program that provides quantum mechanical information for chemical structures, was applied to three series of reference chemicals: a set of methacrylates, a set of aromatic and a set of aliphatic epoxy compounds. QSAR models were developed using this chemical information together with mutagenicity data (Salmonella TA 100, Ames Test). CODESSA, a QSAR program that calculates quantum chemical descriptors from information generated by AMPAC and statistically matches these descriptors with observed biological properties was used. QSARs were developed which had r2 values exceeding 0.90 for each study series. These QSARs were used to accurately predict the mutagenicity of BISGMA. a monomer commonly used in dentistry, and two epoxy monomers with developing use in dentistry, GY-281 and UVR-6105. The Q-QSAR quantum mechanical descriptors correctly predicted the level of mutagenicity for all three compounds. The descriptors in the correlation equation pointed to components of structure that may contribute to mutagenesis. The QSARs also provided 'dose windows' for testing mutagenicity, circumventing the need for extensive dose exploration in the laboratory. The Q-QSAR method promises an approach for biomaterials scientists to predict and avoid mutagenicity from the chemicals used in new biomaterial designs.

Dental Enamel↗
PubMed1993

Experimental detection of multiple-quantum coherence transfer in coupled spin solids by multi-dimensional NMR experiments.

Three-dimensional multiple-quantum coherence experiments in coupled 1/2 spin solids have been designed to directly detect coherence transfers among all the accessible coherence orders during irradiation. The experiments have been performed on the coupled four-spin polycrystalline sample 1,2,3,4-tetrachloronaphthalene-bis(hexachlorocyclopentadiene) adduct. The experimental results reveal how the coherences transfer in this spin system, which support the theoretically deduced selection rules and can be used to assist more precise description of multiple-quantum coherence dynamics.

Hydrocarbons, Chlorinated↗
PubMed2000

Experimental entanglement of four particles

Quantum mechanics allows for many-particle wavefunctions that cannot be factorized into a product of single-particle wavefunctions, even when the constituent particles are entirely distinct. Such 'entangled' states explicitly demonstrate the non-local character of quantum theory, having potential applications in high-precision spectroscopy, quantum communication, cryptography and computation. In general, the more particles that can be entangled, the more clearly nonclassical effects are exhibited--and the more useful the states are for quantum applications. Here we implement a recently proposed entanglement technique to generate entangled states of two and four trapped ions. Coupling between the ions is provided through their collective motional degrees of freedom, but actual motional excitation is minimized. Entanglement is achieved using a single laser pulse, and the method can in principle be applied to any number of ions.

Journal Article↗
PubMed2001

Effects of x-ray spectra on the DQE of a computed radiography system.

The effect of incident x-ray beam quality on the measured detective quantum efficiency (DQE) of a computed radiography system was investigated. The incident x-ray beams used had peak tube potentials of 70, 95, and 120 kVp, were filtered with various thicknesses of a "patient equivalent phantom" (PEP), aluminum, and copper, and provided a consistent exposure to the storage phosphor. For each peak tube potential and filter combination, the one-dimensional modulation transfer function and noise power spectrum were measured and the square of the incident signal-to-noise ratio was estimated. The spatial frequency dependent DQE was calculated from these data. The DQE was integrated to provide an overall estimate of the efficiency and frequency response of the computed radiography system for the various x-ray beams. There was found to be a wide range of integral DQE (IDQE) values for the peak tube potential and filter combinations used. For example, the IDQE ranged from 3.0 to 0.9 mm(-2) using the peak tube potential and filter combinations 70 kVp with 5.1 cm PEP and 120 kVp with 30.3 cm PEP, respectively. Finally, peak tube potential and filter combinations 70 kVp with 10.2 cm PEP and 120 kVp with 20.2 cm PEP were chosen as standard x-ray beams that will be used at our facility to measure the DQE of digital radiographic imaging systems for evaluation and acceptance testing.

Biophysical Phenomena↗
PubMed1998

Computational site-directed mutagenesis of haloalkane dehalogenase in position 172.

The application of molecular modelling and quantum-chemistry calculations for the 'computational site-directed mutagenesis' of haloalkane dehalogenase is described here. The exhaustive set of single point mutants of haloalkane dehalogenase in position 172 was constructed by homology modelling. The ability of substituting residues to stabilize the halide ion formed during the dehalogenation reaction in the enzyme active site was probed by quantum-chemical calculations. A simplified modelling procedure was adopted to obtain informative results on the potential activity of mutant proteins in a sufficiently short period of time, which, in the future, could be applicable for making bona fide predictions of mutants' activity prior to their preparation in the laboratory. The reaction pathways for the carbon-halide bond cleavage were calculated using microscopic models of wild type and mutant proteins. The theoretical parameters derived from the calculation, i.e. relative energies and selected atomic charges of educt, product and transition state structures, were statistically correlated with experimentally determined activities. The charge difference of educt and product on the halide-stabilizing hydrogen atom of residue 172 was the best parameter to distinguish protein variants with high activity from mutant proteins displaying a low activity. All mutants with significant activity in the experiment were found to have this parameter one order of magnitude higher than mutants with low activity. The results obtained are discussed in the light of the practical application of this methodology for the prediction of potentially active protein variants. Further automation of the modelling procedure is suggested for combinatorial screening of the large number of protein variants. Coupling of the dehalogenation reaction with hydrogenation of the halide ion formed during the reaction in the enzyme active site was proposed as a possible way to improve the catalytic activity of the haloalkane dehalogenase of Xanthobacter autotrophicus GJ10.

Amino Acid Substitution↗
PubMed1995

Fluorescent styryl dyes as probes for Na,K-ATPase reaction mechanism: significance of the charge of the hydrophilic moiety of RH dyes.

The fluorescence responses of a series of potential-sensitive styryl-based dyes (either zwitterionic RH160, RH421, di-4-ANEPPS, or positively charged RH795, RH414, RH461) to phosphorylation of Na,K-ATPase from ATP or inorganic phosphate, and ouabain binding to phospho- or dephosphoforms, have been characterized and compared in broken membrane preparations of the enzyme. Zwitterionic dyes were more sensitive to molecular events in the Na,K-ATPase reaction cycle than positively charged dyes, but the net charge did not affect the sensitivity of the dyes to a transmembrane electric field. The major part of the response of the zwitterionic dyes to formation of phosphoenzymes was due to a change in the quantum yield of fluorescence. Computer modeling of dyes with identical chromophore structure, and experimental characterization of their optical properties in bulk solvents, revealed two general trends: (1) the absorption maximum of the zwitterionic dye was blue-shifted with respect to the positively charged dye; (2) the quantum yield of the zwitterionic dye was higher and the fluorescence lifetime was longer than that for the positively charged dye. Spectral properties of the dyes in the membrane depended on the presence of Na,K-ATPase. We suggest, that (1) electrostatic interactions between the enzyme and the hydrophilic headgroup of the dye by changing the charge of hydrophilic moiety and thus modifying the net charge of the dye molecule cause both the spectral shifts and the changes in the quantum yield, and (2) interactions between the styryl dyes and the Na,K-ATPase depend on the conformational state of the enzyme.

Animals↗
PubMed1992

Computer-aided radiopharmaceutical design.

The ultimate goal of a QSAR analysis is prediction, which depends on the elaboration of the most appropriate set of molecular descriptors. As such, molecular description is the nucleus of QSAR and in the absence of exhaustive molecular description, rational drug design may be greatly impeded. As previously discussed, computational methods such as quantum mechanics and molecular mechanics provide molecular description at a fundamental level which then enhances the descriptive capability and predictive power of a QSAR analysis. In recognition of these capabilities, semi-empirical molecular orbital methods and molecular mechanics now have been incorporated into or interphased with QSAR programs. Such integrated packages are being successfully used in computer-aided molecular modeling. Computer-aided molecular modeling can provide the three-dimensional structure of a molecule, its chemical and physical characteristics, comparisons of structures of different molecules, and visualization of complexes formed between them. From the foregoing, predictions may be made about how related new molecules may function. Thus, the combination of quantum and/or molecular mechanics and QSAR provides a formidable weapon in the chemist's armamentarium. The molecular modeling approaches are certainly more practical to use than physicochemical methods. They also provide electronic and thermodynamic data that are not available from x-ray crystallographic data. Of course, these techniques are not confined to radiopharmaceutical development and they also could aid in the development of contrast agents for radiography or magnetic resonance imaging. We believe that as computational resources and capabilities increase over the next decade, computer-aided drug design will become a standard procedure in all drug development laboratories.

Binding Sites↗
PubMed2002

Experimental realization of the quantum universal NOT gate.

In classical computation, a 'bit' of information can be flipped (that is, changed in value from zero to one and vice versa) using a logical NOT gate; but the quantum analogue of this process is much more complicated. A quantum bit (qubit) can exist simultaneously in a superposition of two logical states with complex amplitudes, and it is impossible to find a universal transformation that would flip the original superposed state into a perpendicular state for all values of the amplitudes. But although perfect flipping of a qubit prepared in an arbitrary state (a universal NOT operation) is prohibited by the rules of quantum mechanics, there exists an optimal approximation to this procedure. Here we report the experimental realization of a universal quantum machine that performs the best possible approximation to the universal NOT transformation. The system adopted was an optical parametric amplifier of entangled photon states, which also enabled us to investigate universal quantum cloning.

Journal Article↗
PubMed1978

Three-dimensional molecular illustrations II: Isoelectrostatic energy contour spheres of influence applied to narcotic molecules.

A computer-generated method using quantum mechanics was applied to the calculation and subsequent plotting of nonperspective three-dimensional illustrations of molecules in vacuo. The purpose was to generate isoelectrostatic energy contour spheres for larger molecules and current drugs. The molecules chosen, morphine, meperidine, and alphaprodine, possess similar pharmacological properties. Minor configurational manipulation of meperidine and alphaprodine molecules was made to approximate the spatial configuration of the rigid morphine molecule so that direct comparisons were possible. Common areas of reactivity, potential energy minima, net atomic charges, spatial regions, and near neighbor influences are considered.

Computers↗
PubMed2001

Probabilistic quantum memories.

Typical address-oriented computer memories cannot recognize incomplete or noisy information. Associative (content-addressable) memories solve this problem but suffer from severe capacity shortages. I propose a model of a quantum memory that solves both problems. The storage capacity is exponential in the number of qbits and thus optimal. The retrieval mechanism for incomplete or noisy inputs is probabilistic, with postselection of the measurement result. The output is determined by a probability distribution on the memory which is peaked around the stored patterns closest in Hamming distance to the input.

Journal Article↗
PubMed1986

Modeling complex molecular interactions involving proteins and DNA.

We have presented a perspective of progress in three areas of simulations of complex molecules: the development of force fields for molecular simulation; the application of computer graphics, molecular mechanics and molecular dynamics in simulations of DNA and DNA-drug complexes and the application of computer graphics, molecular mechanics and quantum mechanics in studies of enzyme substrate interactions. It is our perspective that improvements are being made in force fields, and these will allow a more accurate simulation of structures and energies of complex molecules. In the area of DNA molecular mechanics and dynamics, it is clear that the use of computer graphics model building combined with NMR NOE data is a potentially very powerful tool in accurately determining structures of drug-DNA complexes using molecular mechanics and dynamics. Finally, we are in a position to reasonably simulate structures and (qualitatively) energies for complete reaction pathways of enzymes using a combination of computer graphics, molecular mechanics and quantum mechanics. More accurate energies and pathways are sure to follow, using the combined molecular mechanics/quantum mechanics optimization developed by Singh and the free energy perturbation methods pioneered in Groningen and Houston.

Base Sequence↗
PubMed1999

Prediction of inhibitor binding free energies by quantum neural networks. Nucleoside analogues binding to trypanosomal nucleoside hydrolase.

A computational method has been developed to predict inhibitor binding energy for untested inhibitor molecules. A neural network is trained from the electrostatic potential surfaces of known inhibitors and their binding energies. The algorithm is then able to predict, with high accuracy, the binding energy of unknown inhibitors. IU-nucleoside hydrolase from Crithidia fasciculata and the inhibitor molecules described previously [Miles, R. W. Tyler, P. C. Evans, G. Furneaux R. H., Parkin, D. W., and Schramm, V. L. (1999) Biochemistry 38, xxxx-xxxx] are used as the test system. Discrete points on the molecular electrostatic potential surface of inhibitor molecules are input to neural networks to identify the quantum mechanical features that contribute to binding. Feed-forward neural networks with back-propagation of error are trained to recognize the quantum mechanical electrostatic potential and geometry at the entire van der Waals surface of a group of training molecules and to predict the strength of interactions between the enzyme and novel inhibitors. The binding energies of unknown inhibitors were predicted, followed by experimental determination of K(i)() values. Predictions of K(i)() values using this theory are compared to other methods and are more robust in estimating inhibitory strength. The average deviation in estimating K(i)() values for 18 unknown inhibitor molecules, with 21 training molecules, is a factor of 5 x K(i)() over a range of 660 000 in K(i)() values for all molecules. The a posteriori accuracy of the predictions suggests the method will be effective as a guide for experimental inhibitor design.

Animals↗
PubMed1989

Molecular electrostatic potential studies on some nitroimidazolyl and nitroheterocyclic compounds.

The electronic wave functions of 11 nitroimidazolyl and nitroheterocyclic compounds were computed using the CNDO/2 quantum chemical method. The location of the greatest nucleophilic reactivity for each molecule was predicted to be mostly near or on the nitro group. As in our previous publication (Lin Liming et al. 1985) the maximum values of the superdelocalizability index for nucleophilic reactivity S(N)max and the sum of S(N)r for each of these compounds were discovered to be significantly correlated with the radiosensitivity as indicated by log(1/C1.6), where C1.6 is the concentration of the compound required to achieve an enhancement ratio of 1.6. The electrostatic potential distribution on a plane parallel to the plane of the imidazole or heterocyclic ring was computed for these compounds with the wave functions obtained from CNDO/2 calculations. In order to analyse the steric electrostatic potential maps, the overall electrostatic potential on an imaginary surface surrounding a molecule was calculated using the multicentre multipole expansion method. It was found that a wide and deep negative potential area exists in a compound which had significant radiosensitizing efficiency, while in metronidazole, which is not an efficient radiosensitizer, the corresponding area is narrow. This phenomenon may be related to the interaction between these compounds and certain biological macromolecules. These preliminary quantum chemical results support Adams' electron affinity theory, and might be helpful in searching for new radiosensitizers.

Heterocyclic Compounds↗
PubMed2002

An experimental comparison of detector performance for computed radiography systems.

The intrinsic resolution, noise, and signal-to-noise transfer characteristics of five commercial digital computed radiography (CR) systems were compared using identical experimental methods. The reader/screen combinations evaluated were Agfa ADC-Compact/MD-10, Agfa ADC-Compact/MD-30, Agfa ADC-Solo/MD-10, Agfa ADC-Solo/MD-30, Lumisys CR-2000/MD-10, Fuji FCR-9501 (HQ)/ST-Va, Kodak CR-400/GP-25, and Kodak CR-400/HR. Measurements were made at 70 and 115 kVp with 19 mm added aluminum filtration. The presampled modulation transfer functions (MTFs) of the systems were measured using an edge method. The noise power spectra (NPS) were determined by 2D Fourier analysis of uniformly exposed radiographs. The frequency-dependent detective quantum efficiencies (DQEs) were computed from the MTF, NPS, exposure measurements, and computational estimates of the ideal signal-to-noise ratios. Using 70 kVp and 0.1-0.12 mm pixel sizes, spatial frequencies of 2.1, 2.0, 2.2, 1.9, 2.0, 2.0, 2.3, 2.3, and 3.5 cycles/mm were measured at 0.2 MTF for the eight reader/screen combinations, respectively. Using 70 kVp, 7.74 x 10(-8) C/kg (0.3 mR), and 0.1-0.12 mm pixel sizes, DQE(0.15) values of 20.3%, 22.9%, 24.6%, 28.6%, 22.2%, 30.0%, 29.5%, and 17.3% were obtained for the eight combinations, respectively. The corresponding values at 115 kVp were 15.9%, 18.5%, 21.5%, 21.8%, 15.3%, 23.1%, 22.3%, and 13.8%, respectively. The findings of the study demonstrate the pixel size, orientation, beam quality, screen, and reader dependencies of image quality in CR systems. The physical performance of the systems having standard-resolution screens demonstrated similar resolution performance but more notable variations in DQE. The one high-resolution screen tested had reduced DQE and increased MTF at high frequencies.

Evaluation Studies as Topic↗
PubMed1996

NMR of residual protons in partly deuterated anisotropic materials with phase-alternated decoupling of deuterium spins.

A new method is presented for decoupling spins with S = 1 like deuterium in anisotropic media while observing other spins such as residual protons in partly deuterated samples. The carrier frequency of a weak radiofrequency (RF) field is applied near the center of the doublet arising from the quadrupolar interaction of the S = 1 spins. The phase of the RF field is periodically reversed with intervals matching the reciprocal of the magnitude of the quadrupolar splitting. It is shown by theory and experiment that, even when the irradiating field is quite weak, the efficiency of this phase-alternated decoupling scheme is much better than for simple continuous-wave irradiation at the center of the doublet, an established technique which is usually referred to as double quantum decoupling. The phase-alternated experiment makes it possible to decouple large quadrupolar interactions with a weak RF field. A theoretical analysis and numerical simulations are presented to demonstrate the decoupling performance. Proton spectra of partly deuterated dibromobutane in a liquid crystalline solvent have been recorded to illustrate the efficiency of phase-alternated deuterium decoupling.

Chemical Phenomena↗