Volume 132, Issue 20, 28 May 2010

A systematic molecular dynamics (MD) study of zinc binding to a peptide that mimics the structural binding site of horse liver alcohol dehydrogenase (HLADH) has been conducted. The four zinc binding cysteines were successively mutated into alanines to study the stability, zinc coordination, and free energy of binding. The zinc ion is coordinated to four sulfurs in the native peptide as in xray structures of HLADH. When the cysteines are replaced by alanines, the zinc coordinating sulfurs are replaced by waters and/or polypeptide backbone carbonyl oxygens. With two or fewer cysteines, the coordination number increases from four to six, while the coordination number varies between four and six with three cysteines depending on which of the cysteines that is replaced by an alanine. The binding free energies of zinc to the proteins were calculated from MD free energy integration runs to which corrections from quantum mechanical cluster calculations were added. There is a reasonable correlation with experimental binding free energies [T. Bergman et al., Cell. Mol. Life Sci.65, 4019 (2008)]. For the chains with the lowest structural fluctuations and highest free energies lower coordination numbers for zinc are obtained. Finally, xrayabsorption fine structure spectra were calculated from the MD structures.
 COMMUNICATIONS


Communications: Evidence for proton tunneling from the microwave spectrum of the formic acidpropriolic acid dimer
View Description Hide DescriptionThe microwave spectrum of the formic acidpropriolic acid dimer was measured in the 5–13 GHz range using a pulsedbeam, Fourier transform spectrometer. 22 adipole rotational transitions and 3 bdipole rovibrational transitions were measured for the normal isotopomer. All of these observed transitions were split into doublets by the effects of the concerted tunneling of the two acidprotons. The smaller splittings of 1–1.5 MHz for the adipole transitions are due to the differences in rotational constants for the upper and lower tunneling states. The bdipole transitions are rovibrational (combination) transitions with a change in rotational state and tunneling state and provide direct information on the tunneling splittings since these observed splittings are the sum of the tunnelinglevel splittings for the two rotational states involved in the transition. The bdipole splittings are , , and . No similar splittings were observed when deuterium was substituted for either or both of the hydrogen bondingprotons. For the lower tunneling state , , , and . For the upper tunneling state , , , and . Using a simple model with potential function the splittings could be reproduced reasonably well with a barrier height of .
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 ARTICLES

 Theoretical Methods and Algorithms

Calculation of the interfacial free energy of a fluid at a static wall by Gibbs–Cahn integration
View Description Hide DescriptionThe interface between a fluid and a static wall is a useful model for a chemically heterogeneous solidliquid interface. In this work, we outline the calculation of the wallfluid interfacial free energy for such systems using molecular simulation combined with adsorptionequations based on Cahn’s extension of the surface thermodynamics of Gibbs. As an example, we integrate such an adsorptionequation to obtain as a function of pressure for a hardsphere fluid at a hard wall. The results so obtained are shown to be in excellent agreement in both magnitude and precision with previous calculations of this quantity, but are obtained with significantly lower computational effort.

Counterintuitive Coulomb hole around the bond midplane
View Description Hide DescriptionThe Coulomb hole does not have its largest depth around an electron in or near the bond midplane. It splits into two parts, localized on both nuclear sites forming the bond. Even counterintuitive positive values of the “hole” around such a position may be observed. This happens when the Fermi hole is deeper than the total exchangecorrelation hole at the reference electron position. This Coulomb “heap” is shown to arise from correlation effects on the oneelectron density rather than correlation effects in the pair density. Leftright correlation tends to enhance the effect of the nuclear attraction, contracting the electron density around the nuclear positions and depleting the bond center region. Possible alternative definitions of the Coulomb hole are discussed, including one based on the exact Kohn–Sham exchange hole. Approximate density functional theory methods (generalized gradient approximation) are not accurate enough to realize the advantages of this definition.

Input vector optimization of feedforward neural networks for fitting ab initio potentialenergy databases
View Description Hide DescriptionThe variation in the fitting accuracy of neural networks (NNs) when used to fit databases comprising potential energies obtained from ab initioelectronic structure calculations is investigated as a function of the number and nature of the elements employed in the input vector to the NN. Ab initiodatabases for , HONO, , and were employed in the investigations. These systems were chosen so as to include four, five, and sixbody systems containing first, second, third, and fourth row elements with a wide variety of chemical bonding and whose conformations cover a wide range of structures that occur under highenergy machining conditions and in chemical reactions involving cistransisomerizations, six different types of twocenter bond ruptures, and two different threecenter dissociationreactions. The ab initiodatabases for these systems were obtained using density functional theory/B3LYP, MP2, and MP4 methods with extended basis sets. A total of 31 input vectors were investigated. In each case, the elements of the input vector were chosen from interatomic distances, inverse powers of the interatomic distance, threebody angles, and dihedral angles. Both redundant and nonredundant input vectors were investigated. The results show that among all the input vectors investigated, the set employed in the Zmatrix specification of the molecular configurations in the electronic structure calculations gave the lowest NN fitting accuracy for both and vinyl bromide. The underlying reason for this result appears to be the discontinuity present in the dihedral angle for planar geometries. The use of trigometric functions of the angles as input elements produced significantly improved fitting accuracy as this choice eliminates the discontinuity. The most accurate fitting was obtained when the elements of the input vector were taken to have the form , where the are the interatomic distances. When the Levenberg–Marquardt procedure was modified to permit error minimization with respect to n as well as the weights and biases of the NN, the optimum powers were all found to lie in the range of 1.625–2.38 for the four systems studied. No statistically significant increase in fitting accuracy was achieved for vinyl bromide when a different value of n was employed and optimized for each bond type. The rate of change in the fitting error with n is found to be very small when n is near its optimum value. Consequently, good fitting accuracy can be achieved by employing a value of n in the middle of the above range. The use of interparticle distances as elements of the input vector rather than the Zmatrix variables employed in the electronic structure calculations is found to reduce the rms fitting errors by factors of 8.86 and 1.67 for and vinyl bromide, respectively. If the interparticle distances are replaced with input elements of the form with n optimized, further reductions in the rms error by a factor of 1.31 to 2.83 for the four systems investigated are obtained. A major advantage of using this procedure to increase NN fitting accuracy rather than increasing the number of neurons or the size of the database is that the required increase in computational effort is very small.

On the computation of fundamental measure theory in pores with cylindrical symmetry
View Description Hide DescriptionClassical density functional theories usually separate the formulation of the excess Helmholtz free energy in hardbody and energetic contributions. Fundamental measure theories (FMTs) have emerged as the preferred choice to account for the former contribution. The evaluation of geometrically weighted densities (convolutions) arisen in FMT for hard spheres in long cylindrical cavities is addressed in this paper. Previously, Malijevský [J. Chem. Phys.126, 134710 (2007)] reported expressions containing elliptic integrals for the kernels of the convolutions involving scalar and vectorial weights. Here, the set of kernels is extended to second and third order tensorial weights that introduce desirable dimensional crossover properties to the evaluation of the excess free energy. An alternative formulation for the convolutions, which greatly facilitates their computation, is also proposed. Integrals of the original kernels arise in this way and a set of expressions for them, again expressed in terms of elliptic integrals, is presented here. With the aim of providing a computationally simple framework to evaluate equilibrium density profile with cylindrical symmetry, a procedure based on direct minimization of the discretized grand potential energy, rather than employing the Euler–Lagrange equilibrium conditions, is discussed and used to identify differences between two FMT formulations, including or not second order tensorial kernels in very narrow cylindrical pores.

Cholesky decompositionbased definition of atomic subsystems in electronic structure calculations
View Description Hide DescriptionDecomposing the Hartree–Fock oneelectron density matrix and a virtual pseudodensity matrix, we obtain an orthogonal set of normalized molecular orbitals with local character to be used in postHartree–Fock calculations. The applicability of the procedure is illustrated by calculating CCSD(T) energies and CCSD molecular properties in reduced active spaces.

Doubly, triply, and multiply excited states from a constrained optimized effective potential method
View Description Hide DescriptionThis article further develops and applies a constrained optimized effective potential (COEP) approach for the practical calculations of doubly and multiply excited states of atoms and molecules. The COEP method uses the timeindependent theory of pure excited states and implements a simple asymptotic projection method to take orthogonality constraints into account. We show that, in contrast with the common timedependent density functional method, the COEP methodology is capable of treating doubly, triply, and multiply excited states and can be easily applied to both atoms and molecules. In particular, doubly excited energies of each state are calculated through a constrained minimization procedure including constraints that make its Slater determinantal functions orthogonal to those of the ground and all lowerlying doubly excited states. The performance of the proposed method is examined by calculations of doubly excited state energies for the He atom and molecule at exchangeonly and exchangecorrelation level of approximation.

Exponentially fitted open Newton–Cotes differential methods as multilayer symplectic integrators
View Description Hide DescriptionClassical open and closed Newton–Cotes differential methods possessing the characteristics of multilayer symplectic structures have been constructed in the past. In this paper, we study the exponentially fitted open Newton–Cotes differential methods of order two, four, and six. It is shown that these integrators, just as their classical counterparts, preserve the volume in the phase space of a Hamiltonian system. They can be converted into a multilayer symplectic structure so that volumepreserving integrators of a Hamiltonian system are obtained. A numerical example has been carried out to show the effectiveness of the present differential method.
 Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry

Lowenergy electron collisions with pyrrole
View Description Hide DescriptionWe report cross sections for lowenergy elastic electron scattering by pyrrole, obtained with the Schwinger multichannel method implemented with pseudopotentials. Our calculations indicate shape resonances in the and symmetries, and two resonances in the symmetry (the system belongs to the point group). The present assignments of resonances are very close to those previously reported for the isoelectronic furan molecule, in agreement with electron transmission spectra. The lowestlying anion is localized on the N–H bond and provides a dissociation coordinate similar to those found in the hydroxyl groups of organic acids and alcohols. This resonance overlaps the higherlying resonance (possibly both states) and could give rise to direct and indirect dissociation pathways, which arise from electron attachment to and orbitals, respectively. The photochemistry of pyrrole and 9H adenine is similar, in particular with respect to the photostability mechanism that allows for the dissipation of the photon energy, and we believe pyrrole would also be a suitable prototype for studies of dissociative electron attachment (DEA) to DNA bases. We point out the connection between the mechanisms of photostability and DEA since both arise from the occupation of and orbitals in neutral excited states and in anion states, respectively.

Dissociation of gaseous zwitterion glycinebetaine by slow electrons
View Description Hide DescriptionIn this work, we investigate dissociation processes induced by lowenergy electrons to gas phase trimethylglycine [glycinebetaine, ] molecules. Glycinebetaine represents a model system for zwitterions. All negative fragments are observed to be produced only at subelectronic excitation energies . With the exception of the loss of a neutral H atom that could arise from any bond breaking, we tentatively suggest that the zwitterion dissociates exclusively from the fragmentation of the cation site of the molecule, subsequent to the attachment of the excess electron. Within the context of radiation induced damage to biological systems, the present findings contribute to a more complete description of the fragmentation mechanism occurring to amino acids,peptides, and proteins since they adopt usually a zwitterion structure.

Neutral dissociation of the I, , and vibronic progressions of
View Description Hide DescriptionIt is suggested that the main mechanism for neutral dissociation of the I, , and vibronic progressions in is due to their interaction with the vibrational continuum of the Rydberg state (J state) leading to the formation of the fragments. In order to justify this, the O I fluorescence emission cross section following the neutral dissociation of the Rydberg states is simulated in the excitingphoton energy range of 14.636–16.105 eV. The results of highresolution measurements (H. Liebel et al., J. Phys. B34, 2581 (2001)) can be reproduced if a small adjustment of the computed potential curve of the J state is applied. NonFranck–Condon resonant intensity distributions of the I, , and progressions observed in the experiment are qualitatively explained by the presence of the perturber states. Present calculations allow to decide between two different assignments of the I, , and states available in literature.

Quantum Monte Carlo calculated potential energy curve for the helium dimer
View Description Hide DescriptionWe report on the results of both the diffusionquantum Monte Carlo (DMC) and reptationquantum Monte Carlo (RMC) methods on the potential energy curve of the helium dimer. We show that it is possible to obtain a highly accurate description of the helium dimer. An improved stochastic reconfiguration technique is employed to optimize the manybody wave function, which is the starting point for highly accurate simulations based on the DMC and RMC methods. We find that the results of these methods are in excellent agreement with the best theoretical results at short range, especially the recently developed RMC method, yield particularly accurate results with reduced statistical error, which gives very excellent agreement across the whole potential curve. For the equilibrium internuclear distance of 5.6 bohrs, the calculated total energy with RMC method is and the corresponding well depth is .

Ionion coincidence studies on multiple ionizations of and molecules irradiated by extreme ultraviolet freeelectron laser pulses
View Description Hide DescriptionWe have investigated multiple ionization of and molecules by 52 nm extremeultraviolet light pulses at the freeelectron laser facility SCSS in Japan. Coulomb breakup of parent ions with charge states up to is found by the ionion coincidence technique. The chargestate dependence of kinetic energy release distributions suggests that the electrons are emitted sequentially in competition with the elongation of the bond length.
 Condensed Phase Dynamics, Structure, and Thermodynamics: Spectroscopy, Reactions, and Relaxation

Dynamics simulation of scattering onto W(100,110) surfaces: A stringent test for the recently developed flexible periodic London–Eyring–Polanyi–Sato potential energy surface
View Description Hide DescriptionAn efficient method to construct the six dimensional global potential energy surface (PES) for two atoms interacting with a periodic rigid surface, the flexible periodic London–Eyring–Polanyi–Sato model, has been proposed recently. The main advantages of this model, compared to stateoftheart interpolatedab initio PESs developed in the past, reside in its global nature along with the small number of electronic structure calculations required for its construction. In this work, we investigate to which extent this global representation is able to reproduce the fine details of the scattering dynamics of onto W(100,110) surfaces reported in previous dynamics simulations based on locally interpolated PESs. The and systems are chosen as benchmarks as they exhibit very unusual and distinct dissociativeadsorptiondynamics although chemically similar. The reaction pathways as well as the role of dynamic trapping are scrutinized. Besides, elastic/inelastic scattering dynamics including internal state and angular distributions of reflected molecules are also investigated. The results are shown to be in fair agreement with previous theoretical predictions.

Manifestation of macroscopic correlations in elementary reaction kinetics. I. Irreversible reaction
View Description Hide DescriptionUsing an modern manyparticle method for the derivation of nonMarkovian binary kinetic equations, we have treated theoretically the applicability of the encounter theory (ET) (the prototype of the collision theory) concepts to the widely known diffusion assisted irreversible bulk reaction (for example, radical reaction) in dilute solutions. The method shows that the agreement with the ET is observed when the familiar integral ET is employed which in this method is just a step in the derivation of kinetic equations. It allows for twoparticle correlations only, but fails to take account of correlation of reactant simultaneously with the partner of the encounter and the reactant in the bulk. However, the next step leading to the modified ET under transformation of equations to the regular form both extends the time range of the applicability of ET rate equation (as it was for reactions proceeding with one of the reactants in excess), and gives the equation of the generalized ET. In full agreement with physical considerations, this theory reveals macroscopic correlations induced by the encounters in the reservoir of free walks. This means that the encounters of reactants in solution are correlated on a rather large time interval of the reaction. Though any nonstationary (nonMarkovian) effects manifest themselves rather weakly in the kinetics of the bimolecular reaction in question, just the existence of the revealed macroscopic correlations in the binary theory is of primary importance. In particular, it means that the wellknown phenomena which are generally considered to be associated solely with correlation of particles on the encounter (for example, chemically induced dynamic nuclear polarization) may be induced by correlation in the reservoir of free random walks of radicals in solution.

Effect of correlation of local fluctuations on exciton coherence
View Description Hide DescriptionRecent experimental studies have shown both oscillations of exciton populations and long lasting coherence in multichromophoric systems such as photosynthetic light harvesting systems and conjugated polymers. It has been suggested that this quantum effect is due to correlations of the fluctuations of site energies among the closely packed chromophores in the protein environment. In addition to these, there is the strong possibility of correlations between site energies and transfer matrix elements. In order to understand the role of such correlations we generalize the Haken–Strobl–Reineker (HSR) model to include the energetic correlations and the site diagonaloffdiagonal correlations in a systematic way. The extended HSR model in the exciton basis is also constructed and allows us to study the dynamics of the exciton populations and coherences. With the extended model, we can provide insight into how these correlations affect the evolution of the populations and coherences of excitons by comparing to the original HSR model with uncorrelated fluctuating environments.

Homogeneous water nucleation and droplet growth in methane and carbon dioxide mixtures at 235 K and 10 bar
View Description Hide DescriptionHomogeneous nucleation rates and droplet growth rates of water in pure methane and mixtures of methane and carbon dioxide were measured in an expansion wave tube at 235 K and 10 bar. The nucleation rate in pure methane is three orders of magnitude higher than literature nucleation rates of water in lowpressure helium or argon. Addition of carbon dioxide to the carrier gas mixture increases the rates even more. Specifically, rates in a mixture of methane and 3% carbon dioxide are a factor of 10 higher than the rates in pure methane. With 25% carbon dioxide, the rates are four orders of magnitude higher than the rates in pure methane. An application of the nucleation theorem shows that the critical cluster consists of 22 water molecules and 5 methane molecules, for nucleation in pure methane. Growth rates of waterdroplets were measured in methane and in methanecarbon dioxide mixtures at 243 K and 11.5 bar. At equal temperature, pressure and water vapor fraction, the growth rate of the squared droplet radius is about 20% lower in the mixture with 25% carbon dioxide than in pure methane. The lower growth rate is caused by a smaller diffusion coefficient of water in the mixture with carbon dioxide; the difference of the diffusion coefficients is qualitatively reproduced by the empirical Fuller correlation combined with Blanc’s law.

Infrared and Raman line shapes for ice Ih. I. Dilute HOD in and
View Description Hide DescriptionVibrational spectroscopy of ice Ih provides information about structure, dynamics, and vibrational coupling in this important substance. Vibrational spectra are simplified for HOD in either or , as in these instances the OD or OH stretch, respectively, functions as a local chromophore. As a first step in providing a theoretical treatment of the vibrational spectroscopy for the fully coupled system ( or ), herein we calculate the infrared and Raman spectra for the isotopically substituted systems. The calculation involves a classical molecular dynamics simulation using a new water model, an initial protondisordered ice configuration, and ab initio based transition frequency, dipole, and polarizability maps. Our theoretical results are in reasonable agreement with experiment, and from our results we provide molecular and physical interpretations for the spectral features.

Virial coefficients, thermodynamic properties, and fluidfluid transition of nonadditive hardsphere mixtures
View Description Hide DescriptionDifferent theoretical approaches for the thermodynamic properties and the equation of state for multicomponent mixtures of nonadditive hard spheres in dimensions are presented in a unified way. These include the theory by Hamad, our previous formulation, the original MIX1 theory, a recently proposed modified MIX1 theory, as well as a nonlinear extension of the MIX1 theory proposed in this paper. Explicit expressions for the compressibility factor, Helmholtz free energy, and second, third, and fourth virial coefficients are provided. A comparison is carried out with recent Monte Carlo data for the virial coefficients of asymmetric mixtures and with available simulation data for the compressibility factor, the critical consolute point, and the liquidliquid coexistence curves. The merits and limitations of each theory are pointed out.

Liquid crystalline phase in ethanol suspension of anisometric 4cyano4nhexylbiphenyl microcrystals: Witnessed by dielectric spectroscopy
View Description Hide DescriptionThe suspensions of 4cyano4nhexylbiphenyl (6CB) anisometric microcrystal were obtained by quenching homogeneous 6CB/ethanol mixtures with different 6CB concentrations. Such suspensions were strongly suggested from the differential scanning calorimetry examinations and the image observations of the samples during the quench and heating processes. The crystallization process for the mixtures with higher 6CB concentration looked like the isotropicnematic phase transition of bulk liquid crystal.Dielectricmeasurement was carried out on the mixtures during the heating process after quench. Distinct dielectric relaxation was observed in the frequency range between kHz and 100 kHz, which exhibited obvious dependence on temperature and 6CB concentration. Curve fitting on the complex conductivity spectra indicates that three Debye type relaxations exist in this narrow frequency range. Based on the dependences of relaxation parameters on temperature and 6CB concentration, the possible relaxation mechanisms and the phase conformation of the mixtures were discussed. It was concluded that the relaxations, from high to low relaxation frequency, originate from the Maxwell–Wagner polarization, the rotation of 6CB microcrystal around its long axis, and the reorientation of 6CB microcrystal around its short axis, respectively. It was also confirmed that the quenched 6CB/ethanol mixtures show isotropicnematic phase transition with the increase of 6CB concentration.