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PubMed2006

Dispersion and repulsion contributions to the solvation free energy: comparison of quantum mechanical and classical approaches in the polarizable continuum model.

We report a systematic comparison of the dispersion and repulsion contributions to the free energy of solvation determined using quantum mechanical self-consistent reaction field (QM-SCRF) and classical methods. In particular, QM-SCRF computations have been performed using the dispersion and repulsion expressions developed in the framework of the integral equation formalism of the polarizable continuum model, whereas classical methods involve both empirical pairwise potential and surface-dependent approaches. Calculations have been performed for a series of aliphatic and aromatic compounds containing prototypical functional groups in four solvents: water, octanol, chloroform, and carbon tetrachloride. The analysis is focused on the dependence of the dispersion and repulsion components on the level of theory used in QM-SCRF computations, the contribution of those terms in different solvents, and the magnitude of the coupling between electrostatic and dispersion-repulsion components. Finally, comparison is made between the dispersion-repulsion contributions obtained from QM-SCRF calculations and the results determined from classical approaches.

Acetaldehyde↗
PubMed2000

Quantum-dynamical picture of a multistep enzymatic process: reaction catalyzed by phospholipase A(2).

A quantum-classical molecular dynamics model (QCMD), applying explicit integration of the time-dependent Schrödinger equation (QD) and Newtonian equations of motion (MD), is presented. The model is capable of describing quantum dynamical processes in complex biomolecular systems. It has been applied in simulations of a multistep catalytic process carried out by phospholipase A(2) in its active site. The process includes quantum-dynamical proton transfer from a water molecule to histidine localized in the active site, followed by a nucleophilic attack of the resulting OH(-) group on a carbonyl carbon atom of a phospholipid substrate, leading to cleavage of an adjacent ester bond. The process has been simulated using a parallel version of the QCMD code. The potential energy function for the active site is computed using an approximate valence bond (AVB) method. The dynamics of the key proton is described either by QD or classical MD. The coupling between the quantum proton and the classical atoms is accomplished via Hellmann-Feynman forces, as well as the time dependence of the potential energy function in the Schrödinger equation (QCMD/AVB model). Analysis of the simulation results with an Advanced Visualization System revealed a correlated rather than a stepwise picture of the enzymatic process. It is shown that an sp(2)--> sp(3) configurational change at the substrate carbonyl carbon is mostly responsible for triggering the activation process.

Binding Sites↗
PubMed2001

Human aldehyde dehydrogenase catalytic activity and structural interactions with coenzyme analogs.

K(m) and V(max) values for 10 coenzyme analogs never previously studied with any aldehyde dehydrogenase and NADP(+) were compared with those for NAD(+) for three human aldehyde dehydrogenases (EC 1.2.1.3); the cytoplasmic E1 (the product of the aldh1 gene), the mitochondrial E2 (the product of the aldh2 gene) and the cytoplasmic E3 (the product of the aldh9 gene) isozymes. Structural information on changes in coenzyme-protein interactions were obtained via molecular dynamics (MD) studies with the E2 isozyme and quantum mechanical (QM) calculations were used to study changes in charge distribution of the pyridine ring and relative free energies of solvation of the purine ring in the analogs. E1 showed the broadest substrate specificity and was the only isozyme subject to substrate inhibition, both of which are suggested to be due to the two coenzyme conformations observed previously in the sheep crystal structure. NADP(+) selectivity is indicated to be influenced by Glu195 in E1 and E2. Substitutions in the purine ring affected K(m) but not V(max), with the changes in K(m) being dominated by the hydrophobicity of the purine ring as indicted by the QM calculations. Substitutions in the pyridine ring sometimes rendered the coenzymes inactive, with no consistent pattern observed for the three coenzymes. Structural analysis of the coenzyme analog-E2 MD simulations revealed different structural perturbations of the surrounding active site, though interactions with Asn169 and Glu399 were preserved in all cases.

Adult↗
PubMed2003

Protonation states of methionine aminopeptidase and their relevance for inhibitor binding and catalytic activity.

We have performed a computational study of different protomeric states of the methionine aminopeptidase active site using a combined quantum-mechanical/molecular mechanical simulation approach. The aim of this study was to clarify the native protonation state of the enzyme, which is needed for the development of novel irreversible inhibitors that can possibly be used as antiangiogenic and antibiotic drugs by virtual screening and other drug design methods. The results of the simulations indicated that two protonation states are possible without disturbing the overall geometry of the active site. We then verified experimentally the presence of the two protonation states by studying the substrate hydrolysis and inhibitor binding reactions at different pH values and come to the conclusion that one of the protomeric states is relevant for inhibitor binding, whereas the other is relevant for substrate hydrolysis. This result has implications for the development of other inhibitors of this class of enzymes and adds a new perspective to the pharmacological properties of the antiangiogenic drug fumagillin, which is an irreversible inhibitor of the human methionine aminopeptidase type II.

Aminopeptidases↗
PubMed2005

Improved excitation schemes for multiple-quantum magic-angle spinning for quadrupolar nuclei designed using optimal control theory.

We have investigated the use of optimal control theory for the design of improved multiple-quantum excitation schemes for the popular multiple-quantum magic-angle spinning NMR experiment for quadrupolar nuclei with half-integer quadrupolar spin. The advantage of the new low-power experiments, termed OCFASTER, is demonstrated by sensitivity improvements approaching 50% for 87Rb in RbClO4 and RbNO3 as compared to FASTER and standard strong-pulse excitation schemes.

Computer Simulation↗
PubMed1989

A new algorithm for deriving pulsatile blood flow waveforms tested using stimulated dynamic angiographic data.

In vascular pathology the assessment of disease severity and monitoring of treatment requires quantitative and reproducible measurements of arterial blood flow. We have developed a new technique for processing sequences of dynamic digital X-ray angiographic images. We have tested it using computer simulated angiographic data which includes the effect of pulsatile blood flow and X-ray quantum noise. A parametric image was formed in which the image grey-level represents dye concentration as a function of time and distance along a vessel segment. Adjacent concentration--distance profiles in the parametric image were re-registered along the vessel axis until a match occurred. A match was defined as the point where the sum of squares of the differences in the two profiles was a minimum. The distance translated per frame interval is equal to the bolus velocity. We have tested several contrast medium injection methods including constant flow and a range of discrete pulses per second. The technique proved to be robust and independent of injection technique. Average blood flow was measured for simulated pulsatile waveforms with mean flows of up to 650 ml/min (peak velocities up to 186 cm/s) in a range of diameters from 2 mm to 6 mm. The standard deviation of the error in the mean flow estimates over the whole range of velocities and vessel sizes was +/- 1.4 cm/s.

Algorithms↗
PubMed2005

Mechanism of hydroxyl radical generation from a silica surface: molecular orbital calculations.

The interaction of an H(2)O molecule with cluster models of fractured silica surfaces was studied by means of quantum mechanical calculations. Two clusters representing homolytic cleavage (triple bond Si(*) and triple bond SiO(*)) and two representing heterolytic cleavage (triple bond Si(+) and triple bond Si-O(-)) of silica surfaces were modeled. Vibrational frequencies of the reactants and products of these silica surfaces reacting with H(2)O have been calculated and compare favorably with experiment. Comparisons of the Gibbs free and potential energies for the model ionic and radical states were made, and the radical pair of sites was predicted to be more stable by approximately -70 to -85 kJ/mol, depending on the computational methodology. These calculations suggest that when silica is fractured in a vacuum homolytic cleavage is favored. Reaction pathways were investigated for these four model surface sites interacting with H(2)O. The reaction of H(2)O with triple bond SiO(*) was predicted to generate OH(*). Rate constants for these reactions were also calculated and predict a rapid equibrium for the reaction triple bond SiO(*) + H(2)O --> triple bond SiOH + OH(*). Stability of a finite number of triple bond SiO(*) sites at equilibrium in the above reaction with H(2)O was also predicted, which implies a long-term ability of silica surfaces to produce OH(*) radicals if the sites of the broken bonds do not repolymerize to form siloxane groups.

Adsorption↗
PubMed2006

Quantum chemical characterization of the vertical electron affinities of didehydroquinolinium and didehydroisoquinolinium cations.

Vertical electron affinities (EA) are predicted for the lowest energy singlet states of the 21 didehydroquinolinium cation isomers and the 21 didehydroisoquinolinium cation isomers, as well as the doublet states of the seven dehydroquinolinium cation isomers, the seven dehydroisoquinolinium cation isomers, the seven N-methyldehydroquinolinium cations, and the seven N-methyldehydroisoquinolinium cations, by using density functional theory. For the monoradicals, the calculated EA of the radical site depends only on the distance from the (formally charged) nitrogen atom, and is reduced by 0.14-0.24 eV when the NH+ group is replaced with an NCH3+ group. Nearly all of the calculated EAs for the ortho biradicals are lower (by 0.04-0.72 eV) than those for either of the corresponding monoradicals. For the meta biradicals, the calculated EAs lie either between the EAs of the corresponding monoradicals or higher (by 0.07-0.58 eV), and they are extremely sensitive to the separation (distance) between the two dehydrocarbon atoms. For the biradicals that do not have either an ortho or meta relationship the calculated EAs are all higher (by 0.02-1.93 eV) than those for either of the corresponding monoradicals. The EAs are examined to gain insight into the nature of inductive/field and resonance effects that influence the electrophilicity of the radical site(s), which is a major factor controlling the reactivity of these types of (bi)radicals.

Cations↗
PubMed2006

Backbone conformational preferences and pseudorotational ring puckering of 1-aminocyclopentane-1-carboxylic acid.

We have used quantum mechanical calculations at the B3LYP/6-311G(d,p) level to determine the conformational preferences of the N-acetyl-N'-methylamide derivative of 1-aminocyclopentane-1-carboxylic acid in the gas phase, chloroform solution, and water solution. The backbone conformation of this dipeptide has been described through the dihedral angles varphi and psi, while the pseudorotational phase angle was used to define the conformation of the cyclopentane ring. Results indicate that the backbone flexibility of this amino acid is restricted by the cyclic nature of the side chain, the relative stability of the different conformations depending on the polarity of the environment. The potential energy of the pseudorotation was also studied as a function of the backbone conformation. Interestingly, the conformation of the cyclic side chain depends on the backbone arrangement. Furthermore, the number of pseudorotational states accessible at room temperature is high in all the investigated environments, especially in aqueous solution. Finally, a set of force-field parameters for classical molecular mechanics calculations was developed for the investigated amino acid. Molecular dynamics simulations in both chloroform and aqueous solutions were performed to demonstrate the reliability of such parameters.

Computer Simulation↗
PubMed2006

Quantum solvation dynamics of HCN in a helium-4 droplet.

Ultracold nanodroplets of helium-4, containing several thousands of He atoms, offer considerable promise as microscopic cryogenic chambers. Potential applications include the creation of tailor-made chemical or biomolecular complexes and studies of superfluidity in nanoscale systems. Recent experiments have succeeded in interrogating droplets of quantum solvent which consist of as few as 1-20 helium-4 atoms and which contain a single solute molecule. This allows the transition from a floppy, but essentially molecular, complex to a dissolved molecule to be followed and, surprisingly, the transition is found to occur quite rapidly, in some cases for as few as N = 7-20 solvent atoms. For example, in experiments on helium-4 droplets seeded with CO molecules [Tang and McKellar, J. Chem. Phys. 119, 754 (2003)], two series of transitions are observed which correlate with the a-type (Delta K = 0) and b-type (Delta K = +/-1) lines of the binary complex, CO-He (K is the quantum number associated with the projection of the total angular momentum onto the vector connecting the atom and the molecular center of mass). The a-type series, which evolves from the end-over-end rotational motion of the CO-He binary complex, saturates to the nanodroplet limit for as few as 10-15 helium-4 atoms, i.e., the effective moment of inertia of the molecule converges to its asymptotic (solvated) value quite rapidly. In contrast, the b-type series, which evolves from the free-molecule rotational mode, disappears altogether for N approximately 7 atoms. Similar behavior is observed in recent computational studies of HCN(4He)N droplets [Paolini et al., J. Chem. Phys. 123, 114306 (2005)]. In this article the quantum solvation of HCN in small helium-4 droplets is studied using a new fixed-node diffusion Monte Carlo (DMC) procedure. In this approach a Born-Oppenheimer-type separation of radial and angular motions is introduced as a means of computing nodal surfaces of the many-body wave functions which are required in the fixed-node DMC method. Excited rotational energies are calculated for HCN(4He)N droplets with N = 1-20: the adiabatic node approach also allows concrete physical mechanisms to be proposed for the predicted disappearance of the b-type series as well as the rapid convergence of the a-type series to the nanodroplet limit with increasing N. The behavior of the a-type series is traced directly to the mechanics of angular momentum coupling-and decoupling-between identical bosons and the molecular rotor. For very small values of N there exists significant angular momentum coupling between the molecule and the helium atoms: at N approximately 10 solvation appears to be complete as evidenced by significant decoupling of the molecule and solvent angular momenta. The vanishing of the b-type series is predicted to be a result of increasing He-He repulsion as the number of solvent atoms increases.

Journal Article↗
PubMed2006

Modeling of ligation-induced helix/loop displacements in myoglobin: toward an understanding of hemoglobin allostery.

Combining quantum and molecular mechanics (QM/MM) methods and protein structure prediction algorithms, helix and loop movements are computed along the pathway of CO dissociation from myoglobin (Mb). The results are compared with high-resolution crystallographic data using sequence-displacement graphs. These graphs provide an unbiased method for evaluating main-chain segmental motions; they resolve an apparent disagreement between two sets of high-resolution crystal structures for MbCO and deoxyMb. The QM/MM modeling of the CO deligation reproduces the experimentally observed spin states and photodissociated crystal structure. The principal effect of CO dissociation is shown to be a concerted rotation of the E and F helices, which hold the heme like a clamshell. The rotation is a response to deligation forces, which impel the F helix away from the heme because of the Fe spin conversion, and which allow the E helix to collapse toward the heme as nonbonded contacts on the distal side are relieved. Additional helix and loop displacements stem from these primary events. In particular, the CD loop is found to be repositioned as a result of steric interactions with the water molecule that becomes H-bonded to the distal histidine in deoxyMb. A similar EF rotation and CD loop displacement are proposed to be the first steps along the allosteric pathway from the R to the T state in hemoglobin.

Allosteric Regulation↗
PubMed2005

Peroxy and alkoxy radicals from 2-methyl-3-buten-2-ol.

Quantum mechanical calculations were used to determine the structure and energetics of peroxy radicals (P1 and P2) and alkoxy radicals (A1-A3) formed in the atmospheric degradation of 2-methyl-3-buten-2-ol. At the level of theory employed (B3LYP/6-31G(d,p)) low energy conformers were identified with zero, one, or two hydrogen bonds. The beta C-C scission (decomposition) reactions are computed to occur with low barriers, and the 1,5 H-shift (isomerization) reaction of A2 is computed to be of negligible importance. Scission 2 of A2 is computed to be about 93% of the fate of A2, with the balance being scission 1. The new BB1K functional of Truhlar was employed to investigate activation barriers for single intramolecular H-atom transfers across the OH...O* hydrogen bonds, but the barriers to these reactions appear to be too high for these reactions to be important. Extensive searches for transition states for simultaneous double intramolecular H-atom transfer across OH...OH...O* hydrogen bond pairs were unsuccessful.

Alcohols↗
PubMed2006

Analysis of the kinestatic charge detection system as a high detective quantum efficiency electronic portal imaging device.

Megavoltage x-ray imaging suffers from reduced image quality due to low differential x-ray attenuation and large Compton scatter compared with kilovoltage imaging. Notwithstanding this, electronic portal imaging devices (EPIDs) are now widely used in portal verification in radiotherapy as they offer significant advantages over film, including immediate digital imaging and superior contrast range. However video-camera-based EPIDs (VEPIDs) are limited by problems of low light collection efficiency and significant light scatter, leading to reduced contrast and spatial resolution. Indirect and direct detection-based flat-panel EPIDs have been developed to overcome these limitations. While flat-panel image quality has been reported to exceed that achieved with portal film, these systems have detective quantum efficiency (DQE) limited by the thin detection medium and are sensitive to radiation damage to peripheral read-out electronics. An alternative technology for high-quality portal imaging is presented here: kinesatic charge detection (KCD). The KCD is a scanning tri-electrode ion-chamber containing high-pressure noble gas (xenon at 100 atm) used in conjunction with a strip-collimated photon beam. The chamber is scanned across the patient, and an external electric field is used to regulate the cation drift velocity. By matching the scanning velocity with that of the cation (i.e., ion) drift velocity, the cations remain static in the object frame of reference, allowing temporal integration of the signal. The KCD offers several advantages as a portal imaging system. It has a thick detector geometry with an active detection depth of 6.1 cm, compared to the sub-millimeter thickness of the phosphor layer in conventional phosphor screens, leading to an order of magnitude advantage in quantum efficiency (>0.3). The unique principle of and the use of the scanning strip-collimated x-ray beam provide further integration of charges in time, reduced scatter, and a significantly reduced imaging dose, enhancing the imaging signal-to-noise ratio (SNR) and leading to high DQE. While thick detectors usually suffer from reduced spatial resolution, the KCD provides good spatial resolution due to high gas pressure that limits the spread of scattered electrons, and a strip-collimated beam that significantly reduces the inclusion of scatter in the imaging signal. A 10 cm wide small-field-of-view (SFOV) prototype of the KCD is presented with a complete analysis of its imaging performance. Measurements of modulation transfer function (MTF), noise power spectrum (NPS), and DQE were in good agreement with Monte Carlo simulations. Imaging signal loss from recombination within the KCD chamber was measured at different gas pressures, ion drift velocities, and strip-collimation widths. Image quality for the prototype KCD was also observed with anthropomorphic phantom imaging in comparison with various commercial and research portal imaging systems, including VEPID, flat-panel imager, and conventional and high contrast film systems. KCD-based imaging provided very good contrast and good spatial resolution at very low imaging dose (0.1 cGy per image). For the prototype KCD, measurements yielded DQE(0)=0.19 and DQE(1 cy/mm)=0.004.

Computer-Aided Design↗
PubMed2006

Bond-forming reactions of dications with molecules: a computational and experimental study of the mechanisms for the formation of HCF2+ from CF3(2+) and H2.

The QCISD and QCISD(T) quantum chemical methods have been used to characterize the energetics of various possible mechanisms for the formation of HCF2+ from the bond-forming reaction of CF3(2+) with H2. The stationary points on four different pathways leading to the product combinations HCF2+ + H+ + F and HCF2+ + HF+ have been calculated. All four pathways begin with the formation of a collision complex [H2-CF3]2+, followed by an internal hydrogen atom migration to give HC(FH)F2(2+). In two of the mechanisms, immediate charge separation of HC(FH)F2(2+) via loss of either HF+ or a proton, followed by loss of an F atom, yields the experimentally observed bond-forming product HCF2+. For the other two mechanisms, internal hydrogen rearrangement of HC(FH)F2(2+) to give C(FH)2F(2+), followed by charge separation, yields the product CF2H+. This product can then overcome a 2.04 eV barrier to rearrange to the HCF2+ isomer, which is 1.80 eV more stable. All four calculated mechanisms are in agreement with the isotope effects and collision energy dependencies of the product ion cross sections that have been previously observed experimentally following collisions between CF3(2+) and H2/D2. We find that in this open-shell system, CCSD(T) and QCISD(T) T1-diagnostic values of up to 0.04 are acceptable. A series of angularly resolved crossed-beam scattering experiments on collisions of CF3(2+) with D2 have also been performed. These experiments show two distinct channels leading to the formation of DCF2+. One channel appears to correspond to the pathway leading to the ground state 1DCF2+ + D+ + F product asymptote and the other to the 3DCF2+ + D+ + F product asymptote, which is 5.76 eV higher in energy. The experimental kinetic energy releases for these channels, 7.55 and 1.55 eV respectively, have been determined from the velocities of the DCF2+ product ion and are in agreement with the reaction mechanisms calculated quantum chemically. We suggest that both of these observed experimental channels are governed by the reaction mechanism we calculate in which charge separation occurs first by loss of a proton, without further hydrogen atom rearrangement, followed by loss of an F atom to give the final products 1DCF2+ + D+ + F or 3DCF2+ + D+ + F.

Journal Article↗
PubMed2006

Quantum statistical study of O + O2 isotopic exchange reactions: cross sections and rate constants.

Using a wave packet based statistical model, we compute cross sections and thermal rate constants for various isotopic variants of the O + O2 exchange reaction on a recently modified ab initio potential energy surface. The calculation predicts a highly excited rotational distribution and relatively cold vibrational distribution for the diatomic product. A small but important threshold effect was identified for the (16)O + 18O2 reaction, which is suggested to contribute to the experimentally observed negative temperature dependence of the rate ratio, k(18O + 16O2)/k(16O + 18O2). Despite reasonable agreement with quasiclassical trajectory results, however, the calculated thermal rate constants are smaller than experimental measurements by a factor from 2 to 5. The experimentally observed negative temperature dependence of the rate constants is not reproduced. Possible reasons for the theory-experiment discrepancies are discussed.

Journal Article↗
PubMed2004

Quantum yields for product formation in the 120-133 nm photodissociation of O2.

The photodissociation of O(2) in the region from 120-133 nm has been investigated using product imaging. The spectrum in this region is dominated by transitions from the ground state to the first three vibrational levels of the E (3)Sigma(u) (-) state. The O((1)D)+O((3)P) channel is the only product channel observed by product imaging for dissociation at either 124.4 nm or 120.4 nm. The O((1)D(2)) product is aligned in the molecular frame in such a way that its J vector is perpendicular to the relative velocity vector between the O((1)D) and the O((3)P). The variation in the anisotropy of dissociation is approximately predicted by considering transitions on individual lines and then taking into account the coherent excitation of overlapping resonances. At 132.7 nm, both the O((1)D)+O((3)P) and the O((3)P)+O((3)P) channels are observed with branching ratios of 0.40+/-0.08 and 0.60+/-0.09, respectively. At 130.2 nm, the quantum yield for production of O((1)D) is 0.76+/-0.28.

Computer Simulation↗
PubMed2006

Orientation preferences of backbone secondary amide functional groups in peptide nucleic acid complexes: quantum chemical calculations reveal an intrinsic preference of cationic D-amino acid-based chiral PNA analogues for the P-form.

Geometric descriptions of nonideal interresidue hydrogen bonding and backbone-base water bridging in the minor groove are established in terms of polyamide backbone carbonyl group orientation from analyses of residue junction conformers in experimentally determined peptide nucleic acid (PNA) complexes. Two types of interresidue hydrogen bonding are identified in PNA conformers in heteroduplexes with nucleic acids that adopt A-like basepair stacking. Quantum chemical calculations on the binding of a water molecule to an O2 base atom in glycine-based PNA thymine dimers indicate that junctions modeled with P-form backbone conformations are lower in energy than a dimer comprising the predominant conformation observed in A-like helices. It is further shown in model systems that PNA analogs based on D-lysine are better able to preorganize in a conformation exclusive to P-form helices than is glycine-based PNA. An intrinsic preference for this conformation is also exhibited by positively charged chiral PNA dimers carrying 3-amino-D-alanine or 4-aza-D-leucine residue units that provide for additional rigidity by side-chain hydrogen bonding to the backbone carbonyl oxygen. Structural modifications stabilizing P-form helices may obviate the need for large heterocycles to target DNA pyrimidine bases via PNA.DNA-PNA triplex formation. Quantum chemical modeling methods are used to propose candidate PNA Hoogsteen strand designs.

Amides↗