PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “quantum computing”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 559 records · Page 31Linked to original sources

Rapid quantum mechanical models for the computational estimation of C-H bond dissociation energies as a measure of metabolic stability.

Several relatively inexpensive levels of theory are surveyed together with alternative algorithmic methods for the estimation of C-H bond dissociation energies (BDEs), such energies being useful for the prediction of metabolic stability in drug-like molecules. In particular, bond stretching potentials of several C-H bonds are computed using the AM1, PM3, HF/MIDI!, and B3LYP/MIDI! levels of electronic structure theory, and selected points are fit to Morse and parabolic potentials. BDEs computed by an AM1 fit to the Morse function show the smallest mean unsigned error in prediction (+/- 3-4 kcal/mol) over 32 diverse C-H bonds. An alternative method for correlating the AM1 parabolic force constant from a two-point unrelaxed potential provides only a slightly decreased accuracy and is computationally particularly inexpensive. Both methods should prove to be useful for the rapid in silico screening of drug-like molecules for metabolic stability to C-H bond oxidizing enzymes.

Carbon↗

Calculated volume and energy profiles for water exchange on t2g6 rhodium(III) and iridium(III) hexaaquaions: conclusive evidence for an Ia mechanism.

An I(a) mechanism was assigned for water exchange on the hexaaquaions Rh(OH(2))(6)(3+) and Ir(OH(2))(6)(3+) on the basis of negative Delta V(++) experimental values (-4.2 and -5.7 cm(3) mol(-1), respectively). The use of Delta V(++) as a mechanistic criterion was open to debate primarily because Delta V(++) could be affected by extension or compression of the nonparticipating ligand bond lengths on going to the transition state of an exchange process. In this paper, volume and energy profiles for two distinct water exchange mechanisms (D and I(a)) have been computed using quantum chemical calculations which include hydration effects. The activation energy for Ir(OH(2))(6)(3+) is 32.2 kJ mol(-1) in favor of the I(a) mechanism (127.9 kJ mol(-1)), as opposed to a D pathway; the value for the I(a) mechanism being close to Delta H(++) and Delta G(++) experimental values (130.5 kJ mol(-1) and 129.9 kJ mol(-1) at 298 K, respectively). Volumes of activation, computed using Connolly surfaces and for the I(a) pathway (DeltaV(++)(calc) = -3.9 and -3.5 cm(3) mol(-1), respectively, for Rh(3+) and Ir(3+)), are in agreement with the experimental values. Further, it is demonstrated for both mechanisms that the contribution to the volume of activation due to the changes in bond lengths between Ir(III) and the spectator water molecules is negligible: -1.8 for the D, and -0.9 cm(3) mol(-1) for I(a) mechanism. This finding clarifies the debate about the interpretation of Delta V(++) and unequivocally confirms the occurrence of an I(a) mechanism with retention of configuration and a small a character for both Rh(III) and Ir(III) hexaaquaions.

Journal Article↗

Ab initio and quantum-defect calculations for the Rydberg states of ArH.

Potential energy curves were evaluated for the ground and thirteen low-lying excited electronic states of the ArH molecule over a wide range of internuclear distances by the multi-reference averaged quadratic coupled cluster method. The ab initio energy differences and transition dipole moments were used to estimate Einstein emission coefficients, absorption oscillator strengths and radiative lifetimes. Diagonal and off-diagonal quantum defects, as functions of internuclear distance, were extracted from ab initio potentials of the lowest Rydberg states of the neutral ArH molecule by taking account of configuration interaction between Rydberg series converging to the ground and two electronic excited states of the ArH(+) cation. The derived quantum-defect functions were used to generate manifolds of higher excited Rydberg states. The agreement between experimental and calculated energies and radiative transition probabilities was found to be as good as or better than that obtained by earlier calculations.

Argon↗

Electron density of semi-bridging carbonyls. Metamorphosis of CO ligands observed via experimental and theoretical investigations on [FeCo(CO)(8)](-).

The electron density distribution in a transition-metal dimer containing a semibridging carbonyl is determined through experimental X-ray diffraction and quantum chemical computations. The changes occurring during the evolution from terminal to bridging coordinations are described by a "structure-correlation-like" approach and by a theoretical investigation along the conversion path. The smooth continuum of conformations observed in the solid state is explained in terms of the mutual interplay of direct M-M and M-CO and indirect M- - -M and M- - -C interactions, which can be characterized by interatomic delocalization indexes, within the framework of Quantum Theory of Atoms in Molecules.

Journal Article↗

Computation of large molecules with the hartree-fock model.

The usual way to compute Hartree-Fock type functions for molecules is by an expansion of the one-electron functions (molecular orbitals) in a linear combination of analytical functions (LCAO-MO-SCF, linear combination of atomic orbitals-Molecular Orbital-Self Consistent field). The expansion coefficients are obtained variationally. This technique requires the computation of several multicenter two-electron integrals (representing the electron-electron interaction) proportional to the fourth power of the basis set size. There are several types of basis sets; the Gaussian type introduced by S. F. Boys is used herein. Since it requires from a minimum of 10 (or 15) Gaussian-type functions to about 25 (or 30) Gaussian functions to describe a second-row atom in a molecule, the fourth power dependency of the basis set has been the de facto bottleneck of quantum chemical computations in the last decade.In this paper, the concept is introduced of a "dynamical" basis set, which allows for drastic computational simplifications while retaining full numerical accuracy. Examples are given that show that computational saving in computer time of more than a factor of one hundred is achieved and that large basis sets (up to the order of several hundred Gaussian functions per molecule) can be used routinely.It is noted that the limitation in the Hartree-Fock energy (correlation energy error) can be easily computed by use of a statistical model introduced by Wigner for solid-state systems in 1934.Thus, large molecules can now be simulated by computational techniques without reverting to semi-empirical parameterization and without requiring enormous computational time and storage.

Journal Article↗

Neural network methods for identification and optimization of quantum mechanical features needed for bioactivity.

This paper presents a new approach to the discovery and design of bioactive compounds. The focus of this application will be on the analysis of enzymatic inhibitors. At present the discovery of enzymatic inhibitors for therapeutic use is often accomplished through random searches. The first phase of discovery is a random search through a large pre-fabricated chemical library. Many molecules are tested with refined enzyme for signs of inhibition. Once a group of lead compounds have been discovered the chemical intuition of biochemists is used to find structurally related compounds that are more effective. This step requires new molecules to be conceived and synthesized, and it is the most time-consuming and expensive step. The development of computational and theoretical methods for prediction of the molecular structure that would bind most tightly prior to synthesis and testing, would facilitate the design of novel inhibitors. In the past, our work has focused on solving the problem of predicting the bioactivity of a molecule prior to synthesis. We used a neural network trained with the bioactivity of known compounds to predict the bioactivity of unknown compounds. In our current work, we use a separate neural network in conjunction with a trained neural network in an attempt to gain insight as to how to modify existing compounds and increase their bioactivity.

Enzyme Inhibitors↗

Triple-quantum MAS-NMR of quadrupolar nuclei.

From two-dimensional multiquantum NMR spectra of quadrupolar nuclei, it is now possible to obtain much greater resolution than in a classical single-quantum magic-angle spinning or variable-angle spinning spectrum. We describe here a very simple pulse scheme which efficiently excites the desired multiquantum NMR coherence and a new acquisition procedure which yields to pure-absorption mode 2D spectra. Experimental spectra for 87Rb in polycrystalline rubidium nitrate illustrate the method.

Magnetic Resonance Spectroscopy↗

Structures of tetrafluorocyclopropene, hexafluorocyclobutene, octafluorocyclopentene and related perfluoroalkene radical anions revealed by electron spin resonance spectroscopic and computational studies.

Isotropic and anisotropic ESR spectra were observed for the radical anions of hexafluorocyclobutene (c-C(4)F(6)(-)), octafluorocyclopentene (c-C(5)F(8)(-)) and perfluoro-2-butene (CF(3)CF=CFCF(3)(-)) in gamma-irradiated plastically crystalline neopentane, tetramethylsilane (TMS) and TMS-d(12) matrices, or the rigid 2-methyltetrahydrofuran (MTHF) matrix. The isotropic spectra of c-C(4)F(6)(-) and c-C(5)F(8)(-) are characterized by three different sets of pairs of (19)F nuclei with the isotropic hyperfine (hf) splittings of 15.2 (2F), 6.5 (2F), 1.1 (2F) mT for c-C(4)F(6)(-) and 14.7 (2F), 7.4 (2F), 1.0 (2F) mT for c-C(5)F(8)(-). By comparison with the results of ab initio quantum chemical computations, the large triplet (19)F hf splittings of ca. 15 mT are assigned to the two fluorines attached to the C=C bond. The UHF, B3LYP and MP2 computations predict that the geometrical structures of the perfluoroalkenes are strongly distorted by one-electron reduction to form their radical anions; c-C(3)F(4)(-): C(2) symmetry ((2)A state) <-- C(2)(v) ((1)A(1)), c-C(4)F(6)(-): C(1) ((2)A) <-- C(2)(v) ((1)A(1)) and c-C(5)F(8)(-): C(1) ((2)A) <-- C(s) ((1)A'). The structural distortion arises from a mixing of the pi* and higher-lying sigma* orbitals at the C=C carbons similar to that previously found for CF(2)=CF(2)(-) with a C(2)(h) distortion. The isotropic (19)F hf splittings computed with the B3LYP method with 6-311+G(2df,p) basis set for the geometry optimized by the UHF and/or MP2 methods are within 6% error of the experimental values. The experimental anisotropic spectra of c-C(4)F(6)(-), c-C(5)F(8)(-) and CF(2)=CF(2)(-) were satisfactorily reproduced by the ESR spectral simulation method using the computed hf principal values and orientation of (19)F nuclei. In addition, the electronic excitation energies and oscillator strengths for the CF(2)=CF(2)(-), c-C(3)F(4)(-), c-C(4)F(6)(-) and c-C(5)F(8)(-) radical anions were computed for the first time by TD-DFT methods.

Journal Article↗

Study of the hydrogen bond in different orientations of adenine-thymine base pairs: an ab initio study.

In order to gain deeper insight into structure, charge distribution, and energies of A-T base pairs, we have performed quantum chemical ab initio and density functional calculations at the HF (Hartree-Fock) and B3LYP levels with 3-21G*, 6-31G*, 6-31G**, and 6-31++G** basis sets. The calculated donor-acceptor atom distances in the Watson-Crick A-T base pair are in good agreement with the experimental mean values obtained from an analysis of 21 high resolution DNA structures. In addition, for further correction of interaction energies between adenine and thymine, the basis set superposition error (BSSE) associated with the hydrogen bond energy has been computed via the counterpoise method using the individual bases as fragments. In the Watson-Crick A-T base pair there is a good agreement between theory and experimental results. The distances for (N2...H23-N19), (N8-H13...O24), and (C1...O18) are 2.84, 2.94, and 3.63 A, respectively, at B3LYP/6-31G** level, which is in good agreement with experimental results (2.82, 2.98, and 3.52 A). Interaction energy of the Watson-Crick A-T base pair is -13.90 and -10.24 kcal/mol at B3LYP/6-31G** and HF/6-31G** levels, respectively. The interaction energy of model (9) A-T base pair is larger than others, -18.28 and -17.26 kcal/mol, and for model (2) is the smallest value, -13.53 and -13.03 kcal/mol, at B3LYP/6-31G** and B3LYP/6-31++G** levels, respectively. The computed B3LYP/6-31G** bond enthalpies for Watson-Crick A-T pairs of -14.4 kcal/mol agree well with the experimental results of -12.1 kcal/mol deviating by as little as -2.3 kcal/mol. The BSSE of some cases is large (9.85 kcal/mol) and some is quite small (0.6 kcal/mol).

Adenine↗

Control of exciton dynamics in nanodots for quantum operations.

We present a theory to further a new perspective of proactive control of exciton dynamics in the quantum limit. Circularly polarized optical pulses in a semiconductor nanodot are used to control the dynamics of two interacting excitons of opposite polarizations. Shaping of femtosecond laser pulses keeps the quantum operation within the decoherence time. Computation of the fidelity of the operations and application to the complete solution of a minimal quantum computing algorithm demonstrate in theory the feasibility of quantum control.

Journal Article↗

The blue brain project.

IBM's Blue Gene supercomputer allows a quantum leap in the level of detail at which the brain can be modelled. I argue that the time is right to begin assimilating the wealth of data that has been accumulated over the past century and start building biologically accurate models of the brain from first principles to aid our understanding of brain function and dysfunction.

Animals↗

Theoretical method for full ab initio calculation of DNA/RNA-ligand interaction energy.

In this paper, we further develop the molecular fractionation with conjugate caps (MFCC) scheme for quantum mechanical computation of DNA-ligand interaction energy. We study three oligonuclear acid interaction systems: dinucleotide dCG/water, trinucleotide dCGT/water, and a Watson-Crick paired DNA segment, dCGT/dGCA. Using the basic MFCC approach, the nucleotide chains are cut at each phosphate group and a pair of conjugate caps (concaps) are inserted. Five cap molecules have been tested among which the dimethyl phosphate anion is proposed to be the standard concap for application. For each system, one-dimensional interaction potential curves are computed using the MFCC method and the calculated interaction energies are found to be in excellent agreement with corresponding results obtained from the full system ab initio calculations. The current study extends the application of the MFCC method to ab initio calculations for DNA- or RNA-ligand interaction energies.

Algorithms↗

Computational and ESR studies of electron attachment to decafluorocyclopentane, octafluorocyclobutane, and hexafluorocyclopropane: electron affinities of the molecules and the structures of their stable negative ions as determined from 13C and 19F hyperfine coupling constants.

High-resolution ESR spectra of the ground-state negative ions of hexafluorocyclopropane (c-C3F6*-), octafluorocyclobutane (c-C4F8*-), and decafluorocyclopentane (c-C5F10*-) are reported and their isotropic 19F hyperfine coupling constants (hfcc) of 198.6 +/- 0.4 G, 147.6 +/- 0.4 G, and 117.9 +/- 0.4 G, respectively, are in inverse ratio to the total number of fluorine atoms per anion. Together with the small value of 5.2 +/- 0.4 G determined for the isotropic 13C hfcc of c-C4F8*-, these results indicate that in each case the singly occupied molecular orbital (SOMO) is delocalized over the equivalent fluorines and possesses a nodal plane through the carbon atoms of a time-averaged D(nh) structure. A series of quantum chemical computations were carried out to further characterize these anions and their neutral counterparts. Both the B3LYP density functional and second-order Møller-Plesset perturbation theory (MP2) indicate that c-C3F6*- adopts a D(3h) geometry and a (2)A2'' ground electronic state, that c-C4F8*- adopts a D(4h) geometry and a (2)A2u ground electronic state, and that c-C5F10*- adopts a C(s) structure and a (2)A' electronic state. Moreover, the 19F hyperfine coupling constants computed with the MP2 method and a high quality triple-zeta basis set are within 1% of the experimental values. Also, the values computed for the 13C hfcc of c-C4F8*- are consistent with the experimental value of 5.2 G. Therefore, in keeping with the ESR results, these negative ions derived from first-row elements can be characterized as pi* species. In addition, the hypervalency of these perfluorocycloalkane radical anions has been clarified.

Journal Article↗

Determination of the orientation and dynamics of ergosterol in model membranes using uniform 13C labeling and dynamically averaged 13C chemical shift anisotropies as experimental restraints.

A new strategy was established to determine the average orientation and dynamics of ergosterol in dimyristoylphosphatidylcholine model membranes. It is based on the analysis of chemical shift anisotropies (CSAs) averaged by the molecular dynamics. Static (13)C CSA tensors were computed by quantum chemistry, using the gauge-including atomic-orbital approach within Hartree-Fock theory. Uniformly (13)C-labeled ergosterol was purified from Pichia pastoris cells grown on labeled methanol. After reconstitution into dimyristoylphosphatidylcholine lipids, the complete (1)H and (13)C assignment of ergosterol's resonances was performed using a combination of magic-angle spinning two-dimensional experiments. Dynamically averaged CSAs were determined by standard side-band intensity analysis for isolated (13)C resonances (C(3) and ethylenic carbons) and by off-magic-angle spinning experiments for other carbons. A set of 18 constraints was thus obtained, from which the sterol's molecular order parameter and average orientation could be precisely defined. The validity of using computed CSAs in this strategy was verified on cholesterol model systems. This new method allowed us to quantify ergosterol's dynamics at three molar ratios: 16 mol % (Ld phase), 30 mol % (Lo phase), and 23 mol % (mixed phases). Contrary to cholesterol, ergosterol's molecular diffusion axis makes an important angle (14 degrees) with the inertial axis of the rigid four-ring system.

Anisotropy↗

The application of computational methods to the study of enzyme catalysis by triose-phosphate isomerase and stabilities of variants of bacteriophage T4 lysozyme.

We review our research on triose-phosphate isomerase and bacteriophage T4 lysozyme. In our studies over the last ten years we have used electrostatic potentials, computer graphics, quantum mechanics, molecular mechanics, molecular dynamics and free energy calculations to try to understand why triose-phosphate isomerase is such an efficient enzyme and why its efficiency is dramatically decreased by several site-specific mutations. For T4 lysozyme we have used free energy methods to analyse and try to understand why Thr-157----Val and Thr-157----Ala mutations decrease protein stability by about 1-2 kcal/mol.

Amino Acid Sequence↗

Enzymatic mechanism of Fe-only hydrogenase: density functional study on H-H making/breaking at the diiron cluster with concerted proton and electron transfers.

The mechanism of the enzymatic hydrogen bond forming/breaking (2H(+) + 2e<==>H(2)) and the plausible charge and spin states of the catalytic diiron subcluster [FeFe](H) of the H cluster in Fe-only hydrogenases are probed computationally by the density functional theory. It is found that the active center [FeFe](H) can be rationally simulated as [[H](CH(3)S)(CO)(CN(-))Fe(p)(CO(b))(mu-SRS)Fe(d)(CO)(CN(-))L], where the monovalence [H] stands for the [4Fe4S](H)(2+) subcluster bridged to the [FeFe](H) moiety, (CH(3)S) represents a Cys-S, and (CO(b)) represents a bridging CO. L could be a CO, H(2)O, H(-), H(2), or a vacant coordination site on Fe(d). Model structures of possible redox states are optimized and compared with the X-ray crystallographic structures and FTIR experimental data. On the basis of the optimal structures, we study the most favorable path of concerted proton transfer and electron transfer in H(2)-forming/breaking reactions at [FeFe](H). Previous mechanisms derived from quantum chemical computations of Fe-only hydrogenases (Cao, Z.; Hall, M. B. J. Am. Chem. Soc. 2001, 123, 3734; Fan, H.; Hall, M. B. J. Am. Chem. Soc. 2001, 123, 3828) involved an unidentified bridging residue (mu-SRS), which is either a propanedithiolate or dithiomethylamine. Our proposed mechanism, however, does not require such a ligand but makes use of a shuttle of oxidation states of the iron atoms and a reaction site between the two iron atoms. Therefore, the hydride H(b)(-) (bridged to Fe(p) and Fe(d)) and eta(2)-H(2) at Fe(p) or Fe(d) most possibly play key roles in the dihydrogen reversible oxidation at the [FeFe](H) active center. This suggested way of H(2) formation/splitting is reminiscent of the mechanism of [NiFe] hydrogenases and therefore would unify the mechanisms of the two related enzymes.

Catalysis↗

Raman spectrum, quantum mechanical calculations and vibrational assignments of (95% alpha-TeO2/5% Sm2O3) glass.

Chozen system of tellurite glasses doped with rare earth oxides (95% alpha-TeO(2)+5% Sm2O3) was prepared by melt quenching. Consequently, the Raman spectrum (150-1250 cm(-1)) of the modified tellurite have been recorded. As a continuation to our normal coordinate analysis, force constants and quantum mechanical (QM) calculations for tbp TeO4(4-) (triagonal bipyramid, C(2v)) and TeO(3+1); Te2O7(6-) (bridged tetrahedral), we have carried out ab initio frequency calculations for tpy TeO3(2-) (triagonal pyramidal, C(3v) and C(s)) and tp TeO3(2-) (triagonal planar, D(3h)) ions. The quantum mechanical calculations at the levels of RHF, B3LYP and MP2 allow confident vibrational assignments and structural identification in the binary oxide glass (95% alpha-TeO2 +5% Sm2O3). The dominant three-dimensional network structures in the modified glass are triagonal pyramidal TeO3 with minor features of short range distorted tbp TeO4 and bridged tetrahedral unit of TeO(3+1), leading to a structure of infinite chain. Therefore, alpha-TeO2/Sm2O3 (95/5%) glass experience structural changes from TeO4 (tbp); Te2O7 (TeO(3+1))-->TeO3 (tpy).

Ceramics↗

A theoretical study of the interaction of guanine and cytosine with specific amino acid side chains.

Quantum-mechanical computations are performed on the in vacuo and in water interactions between the purine bases guanine and cytosine and the side chains of the amino acids arginine, lysine, glutamic acid and glutamine. The results predict that while guanine should be the more strongly interacting base both in vacuo and in water, lysine should be the most strongly interacting amino acid in vacuo and arginine the most strongly interacting amino acid in water solvent. The theoretical results on the interactions in water agree satisfactorily with experimentation.

Amino Acids↗