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At least 775 records · Page 43Linked to original sources
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↗
PubMed2005

Magnetic trapping of ultracold Rydberg atoms.

We investigate the quantum dynamics of ultracold Rydberg atoms being exposed to a magnetic quadrupole field. A Hamiltonian describing the coupled dynamics of the electronic and center of mass motion is derived. Employing an adiabatic approach, the potential energy surfaces for intra-n-manifold mixing are computed. By determining the quantum states of the center of mass motion, we demonstrate that trapped states can be achieved if the total angular momentum of the atom is sufficiently large. This holds even if the extension of the electronic Rydberg state becomes equal to or even exceeds that of the ultracold center of mass motion.

Journal Article↗
PubMed2003

Controlled collisions for multi-particle entanglement of optically trapped atoms.

Entanglement lies at the heart of quantum mechanics, and in recent years has been identified as an essential resource for quantum information processing and computation. The experimentally challenging production of highly entangled multi-particle states is therefore important for investigating both fundamental physics and practical applications. Here we report the creation of highly entangled states of neutral atoms trapped in the periodic potential of an optical lattice. Controlled collisions between individual neighbouring atoms are used to realize an array of quantum gates, with massively parallel operation. We observe a coherent entangling-disentangling evolution in the many-body system, depending on the phase shift acquired during the collision between neighbouring atoms. Such dynamics are indicative of highly entangled many-body states; moreover, these are formed in a single operational step, independent of the size of the system.

Journal Article↗
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↗
PubMed2004

Linear scaling computation of the Fock matrix. VII. Parallel computation of the Coulomb matrix.

We present parallelization of a quantum-chemical tree-code for linear scaling computation of the Coulomb matrix. Equal time partition is used to load balance computation of the Coulomb matrix. Equal time partition is a measurement based algorithm for domain decomposition that exploits small variation of the density between self-consistent-field cycles to achieve load balance. Efficiency of the equal time partition is illustrated by several tests involving both finite and periodic systems. It is found that equal time partition is able to deliver 91%-98% efficiency with 128 processors in the most time consuming part of the Coulomb matrix calculation. The current parallel quantum chemical tree code is able to deliver 63%-81% overall efficiency on 128 processors with fine grained parallelism (less than two heavy atoms per processor).

Journal Article↗
PubMed2003

Superoperator representation of nonlinear response: unifying quantum field and mode coupling theories.

Computing response functions by following the time evolution of superoperators in Liouville space (whose vectors are ordinary Hilbert space operators) offers an attractive alternative to the diagrammatic perturbative expansion of many-body equilibrium and nonequilibrium Green's functions. The bookkeeping of time ordering is naturally maintained in real (physical) time, allowing the formulation of Wick's theorem for superoperators, giving a factorization of higher order response functions in terms of two fundamental Green's functions. Backward propagations and analytic continuations using artificial times (Keldysh loops and Matsubara contours) are avoided. A generating functional for nonlinear response functions unifies quantum field theory and the classical mode coupling formalism of nonlinear hydrodynamics and may be used for semiclassical expansions. Classical response functions are obtained without the explicit computation of stability matrices.

Journal Article↗
PubMed1996

Effects of the phi[NHCO] retromodification on dehydroalanine dipeptide.

The potential energy surface of the phi [NHCO] delta Ala dipeptide has been computed using ab initio quantum mechanical calculations at different theoretical levels. Three degenerate minima were found and characterized. The most favoured conformation is stabilized by an intramolecular hydrogen bonding interaction. The other two minima correspond to helical and malonamide-like conformations, being 4.6 kcal/mol and 6.9 kcal/mol less stable than the lowest energy conformation, respectively. Influence of solvent effects on the relative stabilities of the different conformations have been accounted using SCRF calculations. Two implicit solvent models have been considered: water and CCl4. The results indicate that in the both cases the conformation with an intramolecular hydrogen bonding interaction retains its lowest energy.

Alanine↗
PubMed2006

Nonequilibrium transport in quantum impurity models: the Bethe ansatz for open systems.

We develop an exact nonperturbative framework to compute steady-state properties of quantum impurities subject to a finite bias. We show that the steady-state physics of these systems is captured by nonequilibrium scattering eigenstates which satisfy an appropriate Lippman-Schwinger equation. Introducing a generalization of the equilibrium Bethe ansatz--the nonequilibrium Bethe ansatz--we explicitly construct the scattering eigenstates for the interacting resonance level model and derive exact, nonperturbative results for the steady-state properties of the system.

Journal Article↗
PubMed2006

The catalytic mechanism of peptidylglycine alpha-hydroxylating monooxygenase investigated by computer simulation.

The molecular basis of the hydroxylation reaction of the Calpha of a C-terminal glycine catalyzed by peptidylglycine alpha-hydroxylating monooxygenase (PHM) was investigated using hybrid quantum-classical (QM-MM) computational techniques. We have identified the most reactive oxygenated species and presented new insights into the hydrogen abstraction (H-abstraction) mechanism operative in PHM. Our results suggest that O(2) binds to Cu(B) to generate Cu(B)(II)-O(2)(.-) followed by electron transfer (ET) from Cu(A) to form Cu(B)(I)-O(2)(.-). The computed potential energy profiles for the H-abstraction reaction for Cu(B)(II)-O(2)(.-), Cu(B)(I)-O(2)(.-), and [Cu(B)(II)-OOH](+) species indicate that none of these species can be responsible for abstraction. However, the latter species can spontaneously form [Cu(B)O](+2) (which consists of a two-unpaired-electrons [Cu(B)O](+) moiety ferromagnetically coupled with a radical cation located over the three Cu(B) ligands, in the quartet spin ground state) by abstracting a proton from the surrounding solvent. Both this monooxygenated species and the one obtained by reduction with ascorbate, [Cu(B)O](+), were found to be capable of carrying out the H-abstraction; however, whereas the former abstracts the hydrogen atom concertedly with almost no activation energy, the later forms an intermediate that continues the reaction by a rebinding step. We propose that the active species in H-abstraction in PHM is probably [Cu(B)O](+2) because it is formed exothermically and can concertedly abstract the substrate HA atom with the lower overall activation energy. Interestingly, this species resembles the active oxidant in cytochrome P450 enzymes, Compound I, suggesting that both PHM and cytochrome P450 enzymes may carry out substrate hydroxylation by using a similar mechanism.

Catalysis↗
PubMed2003

Catalytic mechanism of the inverting N-acetylglucosaminyltransferase I: DFT quantum mechanical model of the reaction pathway and determination of the transition state structure.

The complex N-glycan structures on glycoproteins play important roles in cell adhesion and recognition events in metazoan organisms. A critical step in the biosynthetic pathway leading from high mannose to these complex structures includes the transfer of N-acetylglucosamine (GlcNAc) to a mannose residue by the inverting N-acetylglucosaminyltransferase I (GnT-I). The catalytic mechanism of this enzymatic reaction is explored herein using DFT quantum chemical methods. The computational model used to follow the reaction is based on the X-ray crystallographic structure of GnT-I and contains 127 atoms that represent fragments of residues critical for the substrate binding and catalysis. The mechanism of the catalytic reaction was monitored by means of a 2D potential energy map calculated as a function of predefined reaction coordinates at the B3LYP/6-31G** level. This potential energy surface revealed one transition state associated with a reaction pathway following a concerted mechanism. The reaction barrier was estimated, and the structure of the transition state was characterized at the B3LYP/6-311++G**// B3LYP/6-31G** level.

Binding Sites↗
PubMed2002

Carbon-13 NMR shielding in the twenty common amino acids: comparisons with experimental results in proteins.

We have used ab initio quantum chemical techniques to compute the (13)C(alpha) and (13)C(beta) shielding surfaces for the 14 amino acids not previously investigated (R. H. Havlin et al., J. Am. Chem. Soc. 1997, 119, 11951-11958) in their most popular conformations. The spans (Omega = sigma(33) - sigma(11)) of all the tensors reported here are large ( approximately 34 ppm) and there are only very minor differences between helical and sheet residues. This is in contrast to the previous report in which Val, Ile and Thr were reported to have large ( approximately 12 ppm) differences in Omega between helical and sheet geometries. Apparently, only the beta-branched (beta-disubstituted) amino acids have such large CSA span (Omega) differences; however, there are uniformly large differences in the solution-NMR-determined CSA (Deltasigma = sigma(orth) - sigma(par)) between helices and sheets in all amino acids considered. This effect is overwhelmingly due to a change in shielding tensor orientation. With the aid of such shielding tensor orientation information, we computed Deltasigma values for all of the amino acids in calmodulin/M13 and ubiquitin. For ubiquitin, we find only a 2.7 ppm rmsd between theory and experiment for Deltasigma over an approximately 45 ppm range, a 0.96 slope, and an R(2) = 0.94 value when using an average solution NMR structure. We also report C(beta) shielding tensor results for these same amino acids, which reflect the small isotropic chemical shift differences seen experimentally, together with similar C(beta) shielding tensor magnitudes and orientations. In addition, we describe the results of calculations of C(alpha), C(beta), C(gamma)1, C(gamma)2, and C(delta) shifts in the two isoleucine residues in bovine pancreatic trypsin inhibitor and the four isoleucines in a cytochrome c and demonstrate that the side chain chemical shifts are strongly influenced by chi(2) torsion angle effects. There is very good agreement between theory and experiment using either X-ray or average solution NMR structures. Overall, these results show that both C(alpha) backbone chemical shift anisotropy results as well as backbone and side chain (13)C isotropic shifts can now be predicted with good accuracy by using quantum chemical methods, which should facilitate solution structure determination/refinement using such shielding tensor surface information.

Amino Acids↗
PubMed2006

Calculation of solvation free energy from quantum mechanical charge density and continuum dielectric theory.

We have combined ultrasoft pseudopotential density functional theory utilizing plane wave basis with a Poisson-Boltzmann/solvent-accessible surface area (PB/SA) model to calculate the solvation free energy of small neutral organic compounds in water. The solute charge density obtained from density functional theory was directly used in solving the Poisson-Boltzmann equation to obtain the reaction field. The polarized electronic wave function of the solute in the solvent was solved by including the reaction field in the density functional Hamiltonian. The quantum mechanical and Poisson-Boltzmann equations were solved self-consistently until the charge density and reaction field converged. Using the solute charge density directly instead of a point-charge representation permitted asymmetric distortion and spreading out of the electron cloud. Because the electron density could leave the van der Waals surface to penetrate into the high-dielectric solvent, the reaction field generated by this density was generally smaller than that obtained by using the point-charge representation. In applying this model to calculate the solvation free energy of 31 small neutral organic molecules spanning a range of 25 kcal/mol, we obtained a root-mean-square error of only 1.3 kcal/mol if we allowed one adjustable parameter to shift the calculated solvation free energy.

Algorithms↗