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PubMed2006

Water exchange dynamics of manganese(II), cobalt(II), and nickel(II) ions in aqueous solution.

The first row transition metal ions Mn(2+), Co(2+), and Ni(2+) have been studied by classical umbrella sampling molecular dynamics simulations. The water exchange mechanisms, estimates of reaction rates, as well as structural changes during the activation process are discussed. Mn(2+) was found to react via an I(A) mechanism, whereas Co(2+) and Ni(2+) both proceed via I(D). Reaction rate constants are generally higher than those obtained by experiment but the simply constructed metal(II) ion-water potential reproduces the relative order quite well.

Cobalt↗
PubMed2007

CHARMM force field parameters for simulation of reactive intermediates in native and thio-substituted ribozymes.

Force field parameters specifically optimized for residues important in the study of RNA catalysis are derived from density-functional calculations, in a fashion consistent with the CHARMM27 all-atom empirical force field. Parameters are presented for residues that model reactive RNA intermediates and transition state analogs, thio-substituted phosphates and phosphoranes, and bound Mg(2+) and di-metal bridge complexes. Target data was generated via density-functional calculations at the B3LYP/6-311++G(3df,2p)// B3LYP/6-31++G(d,p) level. Partial atomic charges were initially derived from CHelpG electrostatic potential fitting and subsequently adjusted to be consistent with the CHARMM27 charges. Lennard-Jones parameters were determined to reproduce interaction energies with water molecules. Bond, angle, and torsion parameters were derived from the density-functional calculations and renormalized to maintain compatibility with the existing CHARMM27 parameters for standard residues. The extension of the CHARMM27 force field parameters for the nonstandard biological residues presented here will have considerable use in simulations of ribozymes, including the study of freeze-trapped catalytic intermediates, metal ion binding and occupation, and thio effects.

Catalysis↗
PubMed2007

A valence bond study of the dioxygen molecule.

The dioxygen molecule has been the subject of valence bond (VB) studies since 1930s, as it was considered as the first "failure" of VB theory. The object of this article is to provide an unambiguous VB interpretation for the nature of chemical bonding of the molecule by means of modern VB computational methods, VBSCF, BOVB, and VBCI. It is shown that though the VBSCF method can not provide quantitative accuracy for the strongly electronegative and electron-delocalized molecule because of the lack of dynamic correlation, it still gives a correct qualitative analysis for wave function of the molecule and provides intuitive insights into chemical bonding. An accurate quantitative description for the molecule requires higher levels of VB methods that incorporate dynamic correlation. The potential energy curves of the molecule are computed at the various VB levels. It is shown that there exists a small hump in the PECs of VBSCF for the ground state, as found in previous studies. However, higher levels of VB methods dissolve the hump. The BOVB and VBCI methods reproduce the dissociation energies and other physical properties of the ground state and the two lowest excited states in very good agreement with experiment and with sophisticated MO based methods, such as the MRCI method.

Algorithms↗
PubMed2003

Electrostatic properties in the catalytic site of papain: A possible regulatory mechanism for the reactivity of the ion pair.

We present an analysis of the electrostatic properties in the catalytic site of papain (EC 3.4.22.2), an archetype enzyme of the C1 cysteine proteinase family, and we investigate their possible role in the formation, stabilization and regulation of the Cys25((-))...His159((+)) catalytic ion pair. The electrostatic properties were computed using a reassociation method based in multicentered multipolar expansions obtained from ab initio quantum calculations of overlapping protein fragments. Solvent effects were introduced by coupling the use of multicentered multipolar expansions to two continuum boundary element methods to solve the Poisson and the linearized Poisson-Boltzmann equations. The electrostatic profile found in the proton transfer region of papain showed that this enzyme has a well-defined electrostatic environment to favor the formation and stabilization of the catalytic ion pair. The papain catalytic site electrostatic profile can be considered as an electrostatic fingerprint of the papain family with the following characteristics: (i) the presence of a net electric field highly aligned in the (Cys25)-SG-->(His159)-ND1 direction; (ii) the electrostatic profile has a saddle-point character; (iii) it is basically a local environmental effect. Furthermore, our analysis describes a possible regulatory mechanism (the E(SG-->ND1) attenuation effect) controlling the ion pair reactivity and permits to infer the Asp57 acidic residue as the most probable candidate to act as the electrostatic modulator.

Amino Acids↗
PubMed1995

Breakthrough of single-quantum coherence and its elimination in double-quantum filtering.

Breakthrough of single-quantum coherence is shown to occur after application of a double-quantum filter with the conventional four-step phase-cycling scheme. This single-quantum breakthrough is due to the intersequence stimulated echo which has been generated by the radiofrequency pulses in the preceding pulse sequence and appears at the same time as the double-quantum coherence signal in the current pulse sequence. Moreover, the phase of the intersequence stimulated echo is the same as the phase of the double-quantum coherence signal; i.e., the phase of the intersequence stimulated echo is twice the phase change of the radiofrequency pulses in the creation period when their phase is rotated in accordance with the conventional four-step phase-cycling scheme. Consequently, the intersequence stimulated echo passes through the double-quantum filtration in the conventional four-step phase-cycling scheme and gradient pulses. A new phase-cycling scheme which can filter out the single-quantum breakthrough signal is proposed here and its effectiveness is verified experimentally and by computer simulations.

Computer Simulation↗
PubMed1989

Computer modelling: future directions.

Recent developments in computing and in the theory of simulation have extended greatly the successes of the modelling of ionic crystals pioneered by Mott and Littleton. This has changed the way in which computer experiments are brought to bear on an increasing range of solid-state phenomena. Yet applied science creates new demands, both in the form of new types of system and in terms of the complexity and subtlety of what is studied. The author's brief survey looks at some of the successes and gaps from interfaces and catalysts to neurotransmitters and from superconductors to slags.

Computer Simulation↗
PubMed1998

Role of temperature in quanta mechanisms of facilitation in the frog neuromuscular junction.

The results of computer simulations on the Double Barrier Synapse (DBS) model are presented which quantify the relationship between the synapse parameters and the quanta transfer process. The DBS model is applicable to a variety of states of synaptic activity, and by changing the synapse parameters it is possible to simulate various conditions of quanta transmission. The influence of the bathing solution temperature change on the synaptic parameters under different conditions of transmitter release in the frog neuromuscular junction is investigated. Simulations demonstrate that several synaptic parameters, including the parameters of the presynaptic membrane, are not affected by the temperature change. It is shown that a stimulation frequency exists at which the steady-state level of facilitation during a long train of stimuli is the same for a wide range of temperatures.

Animals↗
PubMed1992

Base compositional structure of genomes.

We model the base compositional structure of the human and Escherichia coli genomes. Three particular properties are first quantified: (1) There is a significant tendency for any region of either genome to have a strand-symmetric base composition. (2) The variation in base composition from region to region, within each genome, is very much larger than expected from common homogeneous stochastic models. (3) A given local base composition tends to persist over a scale of at least kilobases (E. coli) or tens of kilobases (human). Multidomain stochastic models from the literature are reviewed and sharpened. In particular, quantitative measurements of the third property lead us to suggest a significant shift in the style of domain models, in which the variation of A+T content with position is modeled by a random walk with frequent small steps rather than with large quantum jumps. As an application, we suggest a way to reduce the amount of computation in the assembly of large sequences from sequences of randomly chosen fragments.

Escherichia coli↗
PubMed1996

Theoretical study of anthracycline antibiotic analogues--III. Conformational analysis on different 2, 6-dideoxy-2-halo-alpha-l-hexopyranoses by molecular mechanics and semiempirical methods.

Conformational analysis of 2,6-dideoxy-2-halo-alpha-L-hexopyranoses (compounds 1-11) has been performed by molecular mechanics and molecular orbital calculations including solvation effects. The numerical results obtained and those obtained from the electrostatic potential calculation have been used together to interpret theoretically the influence of the introduction of the halogen atom at the C-2 position of the sugar moiety.

Antibiotics, Antineoplastic↗
PubMed2005

IR and quantum-chemical studies of carboxylic acid and glycine adsorption on rutile TiO2 nanoparticles.

Nanocrystalline TiO2 powders of the rutile polymorph, synthesized by a sol-gel method, were treated with water solutions containing, respectively, formic, acetic, and citric acid and glycine in order to study the adsorption properties of these organic species. The samples were characterized by FTIR, Raman, powder XRD, and TEM. It was found that HCOOH, CH3COOH and HOC(COOH)(CH2COOH)2--but not NH2CH2COOH--adsorbed onto TiO2. The adsorption of HCOOH, CH3COOH and NH2CH2COOH onto the (110) surface of rutile was also studied by quantum-chemical periodic density functional theory (DFT) calculations. The organic molecules were from the computations found to adsorb strongly to the surfaces in a bridge-coordinating mode, where the two oxygens of the deprotonated carboxylic acid bind to two surface titanium ions. Surface relaxation is found to influence adsorption geometries and energies significantly. The results from DFT calculations and ab initio molecular-dynamics simulations of formic acid adsorption onto TiO2 are compared and match well with the experimental IR measurements, supporting the bridge-binding geometry of carboxylic-acid adsorption on the TiO2 nanoparticles.

Journal Article↗
PubMed2005

Basic principles of magnetic resonance imaging.

We have come full circle from spinning quarks to 3D medical images. The bulk of MRI is now performed using slice-selective gradients, during which RF energy is applied to excite the hydrogen nuclei. By stepping a phase-encoding gradient during each TR and using a frequency-encoding gradient as the data are sampled, the 3D human object can be reduced to many individual points or voxels. By acquiring multiple slices at once, the time efficiency of imaging can be vastly improved. Many newer strategies use variations of this technique to acquire multiple lines of data during a single echo, enshrining spin warp imaging as the most important method of signal acquisition for MRI.

Electron Spin Resonance Spectroscopy↗
PubMed2007

A density functional theory study of the electronic properties of Os(II) and Os(III) complexes immobilized on Au(111).

We present a density functional theory (DFT) study of an osmium polypyridyl complex adsorbed on Au(111). The osmium polypyridyl complex [Os(bpy)2(P0P)Cl]n+ [bpy is 2,2'-bipyridine, P0P is 4,4'-bipyridine, n = 1 for osmium(II), and n = 2 for osmium(III)] is bound to the surface through the free nitrogen of the P0P ligand. The calculations illuminate electronic properties relevant to recent comprehensive characterization of this class of osmium complexes by electrochemistry and electrochemical scanning tunneling microscopy. The optimized structures for the compounds are in close agreement with crystallographic structures reported in the literature. Oxidation of the complex has little effect on these structural features, but there is a substantial reordering of the electronic energy levels with corresponding changes in the electron density. Significantly, the highest occupied molecular orbital shifts from the metal center to the P0P ligand. The surface is modeled by a cluster of 28 gold atoms and gives a good description of the effect of immobilization on the electronic properties of the complexes. The results show that the coupling between the immobilized complex and the gold surface involves electronic polarization at the adsorbate/substrate interface rather than the formation of a covalent bond. However, the cluster is too small to fully represent bulk gold with the result that, contrary to what is experimentally observed, the DFT calculation predicts that the gold surface is more easily oxidized than the osmium(II) complex.

Algorithms↗
PubMed2002

Enzymatic GTP hydrolysis: insights from an ab initio molecular dynamics study.

Ab initio methods were used to shed light on fundamental aspects of the enzymatic mechanism of guanosine triphosphate hydrolysis in the Cdc42/Cdc42GAP complex. The calculations focused on the nucleophilic addition of the catalytic water molecule to the gamma-phosphate phosphorus atom. A large model system was required to correctly reproduce the electrostatic properties on the active site. The model turned out to reproduce most of the electrostatic field of the biological complex at the reactants. Our calculations established the H-bond pattern of the catalytic water (WAT), which turned out to interact with Q61 and T35, in the most stable conformation. This ruled out the possibility that the catalytic water transferred its proton directly to the gamma-phosphate. Furthermore, the calculations suggested that the electronic structure of WAT was very different from that in the bulk. Finally, this study showed that during the reaction, WAT transferred a proton to Gln61, consistent with the available X-ray data on a transition-state analogue/enzyme complex(19) and with the decrease of activity in the Q61E mutant.

Binding Sites↗
PubMed2006

Theoretical studies of quantum amplified isomerizations for imaging systems involving hexamethyl Dewar benzene and related systems.

The ring-opening reactions of the radical cations of hexamethyl Dewar benzene (1) and Dewar benzene have been studied using density functional theory (DFT) and complete active-space self-consistent field (CASSCF) calculations. Compound 1 is known to undergo photoinitiated ring opening by a radical cation chain mechanism, termed "quantum amplified isomerization" (QAI), which is due to the high quantum yield. Why QAI is efficient for 1 but not other reactions is explained computationally. Two radical cation minima of 1 and transition states located near avoided crossings are identified. The state crossings are characterized by conical intersections corresponding to degeneracy between doublet surfaces. Ring opening occurs by formation of the radical cation followed by a decrease in the flap dihedral angle. A rate-limiting Cs transition state leads to a second stable radical cation with an elongated transannular C-C bond and an increased flap dihedral. This structure proceeds through a conrotatory-like pathway of Cs symmetry to give the benzene radical cation. The role of electron transfer was investigated by evaluating oxidation of various systems using adiabatic ionization energies and electron affinities calculated from neutral and cation geometries. Electron-transfer theory was applied to 1 to investigate the limiting effects of back-electron transfer as it is related to the unusual stability of the two radical cations. Expected changes in optical properties between reactants and products of Dewar benzene compounds and other systems known to undergo QAI were characterized by computing frequency-dependent indices of refraction from isotropic polarizabilities. In particular, the reaction of 1 shows greater contrast in index of refraction than that of the Dewar benzene parent system.

Journal Article↗
PubMed2005

On the mechanism of hydrogen transfer in the HSCH(O) <--> (S)CHOH and HSNO <--> SNOH reactions.

The 1,3-intramolecular hydrogen transfer in the HSCH(O) <--> (S)CHOH and HSNO <--> SNOH reactions is studied through density functional theory calculations. The reaction force together with structural and electronic properties is monitored along the reaction path to characterize the mechanism of hydrogen transfer. It is found that in both reactions the hydrogen transfer is activated by the structural rearrangement of the backbone atoms that allow the electrostatic interactions to promote the hydrogen transfer in a stepwise mechanism.

Carbon↗