Volume 135, Issue 6, 14 August 2011

By using a generic coarse grained polypeptide model, we perform multicanonical molecular dynamics simulations for determining the equilibrium conformation state diagram of a single homopolypeptide chain as a function of the chain length and temperature. The state diagram highlights the thermal regimes of stability for various conformational patterns in polypeptides, including swollen, random and collapsed coils, globular structures, extended and bended α helices, and compact β bundles. Remarkably, at low temperatures we observe a sharp transition from extended α helix to compact β bundles as the chain length increases. This finding indicates that the chain length is one of the intrisic factors that can trigger αβ transformations in a broad class of polypeptides.
 COMMUNICATIONS


Communication: Conformation state diagram of polypeptides: A chain length induced αβ transition
View Description Hide DescriptionBy using a generic coarse grained polypeptide model, we perform multicanonical molecular dynamics simulations for determining the equilibrium conformation state diagram of a single homopolypeptide chain as a function of the chain length and temperature. The state diagram highlights the thermal regimes of stability for various conformational patterns in polypeptides, including swollen, random and collapsed coils, globular structures, extended and bended α helices, and compact β bundles. Remarkably, at low temperatures we observe a sharp transition from extended α helix to compact β bundles as the chain length increases. This finding indicates that the chain length is one of the intrisic factors that can trigger αβ transformations in a broad class of polypeptides.

Communication: Where does the first water molecule go in imidazole?
View Description Hide DescriptionSupersonic jet FTIRspectroscopy supplemented by ^{18}O substitution shows unambiguously that water prefers to act as an O−H⋅⋅⋅N hydrogen bond donor towards imidazole, instead of acting as a N−H⋅⋅⋅O acceptor. Previous matrix isolation, helium droplet, and aromatic substitution experiments had remained ambiguous, as are standard quantum chemical calculations. The finding is supported by a study of the analogous methanol complexes and by higher level quantum chemical calculations.

Communication: Iterationfree, weighted histogram analysis method in terms of intensive variables
View Description Hide DescriptionWe present an iterationfree weighted histogram method in terms of intensive variables that directly determines the inverse statistical temperature, β_{ S } = ∂S/∂E, with S the microcanonical entropy. The method eliminates iterative evaluations of the partition functions intrinsic to the conventional approach and leads to a dramatic acceleration of the posterior analysis of combining statistically independent simulations with no loss in accuracy. The synergistic combination of the method with generalized ensemble weights provides insights into the nature of the underlying phase transitions via signatures in β_{ S }characteristic of finite size systems. The versatility and accuracy of the method is illustrated for the Ising and Potts models.
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 ARTICLES

 Theoretical Methods and Algorithms

Using a pruned basis, a nonproduct quadrature grid, and the exact Watson normalcoordinate kinetic energy operator to solve the vibrational Schrödinger equation for C_{2}H_{4}
View Description Hide DescriptionIn this paper we propose and test a method for computing numerically exact vibrational energy levels of a molecule with six atoms. We use a pruned product basis, a nonproduct quadrature, the Lanczos algorithm, and the exact normalcoordinate kinetic energy operator (KEO) with the π^{t}μπ term. The Lanczos algorithm is applied to a Hamiltonian with a KEO for which μ is evaluated at equilibrium. Eigenvalues and eigenvectors obtained from this calculation are used as a basis to obtain the final energy levels. The quadrature scheme is designed, so that integrals for the most important terms in the potential will be exact. The procedure is tested on C_{2}H_{4}. All 12 coordinates are treated explicitly. We need only ∼1.52 × 10^{8} quadrature points. A product Gauss grid with which one could calculate the same energy levels has at least 5.67 × 10^{13} points.

Effective Hamiltonian of liquidvapor curved interfaces in mean field
View Description Hide DescriptionWe analyze a onecomponent simple fluid in a liquidvapor coexistence state, which forms an arbitrarily curved interface. By using an approach based on density functional theory, we obtain an exact and simple expression for the grand potential at the level of mean field approximation that depends on the density profile and the shortrange interaction potential. By introducing the stepfunction approximation for the density profile, and using general geometric arguments, we expand the grand potential in powers of the principal curvatures of the surface and find consistency with the Helfrich phenomenological model in the second order approximation.

The relationship between double excitation amplitudes and Z vector components in some postHartreeFock correlation methods
View Description Hide DescriptionThe relationship between Z vector components and excitation amplitudes is analyzed for several postHartreeFock correlation methods limited to double excitation amplitudes. An analytical formula approximating the Z vector for the coupled cluster doubles method is presented and shown to be quite accurate. This approximation is also used to determine the prefactor of the norm of doubly excited states in averaged coupled pair functionaltype energy functionals selfconsistently leading to better agreement with coupled cluster results.

Improving the convergence of closed and open path integral molecular dynamics via higher order Trotter factorization schemes
View Description Hide DescriptionHigher order factorization schemes are developed for path integral molecular dynamics in order to improve the convergence of estimators for physical observables as a function of the Trotter number. The methods are based on the TakahashiImada and Susuki decompositions of the Boltzmann operator. The methods introduced improve the averages of the estimators by using the classical forces needed to carry out the dynamics to construct a posteriori weighting factors for standard path integral molecular dynamics. The new approaches are straightforward to implement in existing path integral codes and carry no significant overhead. The Suzuki higher order factorization was also used to improve the endtoend distance estimator in open path integral molecular dynamics. The new schemes are tested in various model systems, including an ab initio path integral molecular dynamics calculation on the hydrogen molecule and a quantum water model. The proposed algorithms have potential utility for reducing the cost of path integral molecular dynamics calculations of bulk systems.

A method for treating the passage of a charged hard sphere ion as it passes through a sharp dielectric boundary
View Description Hide DescriptionIn the implicit solvent models of electrolytes (such as the primitive model (PM)), the ions are modeled as point charges in the centers of spheres (hard spheres in the case of the PM). The surfaces of the spheres are not polarizable which makes these models appropriate to use in computer simulations of electrolyte systems where these ions do not leave their host dielectrics. The same assumption makes them inappropriate in simulations where these ions cross dielectric boundaries because the interaction energy of the point charge with the polarization charge induced on the dielectric boundary diverges. In this paper, we propose a procedure to treat the passage of such ions through dielectric interfaces with an interpolation method. Inspired by the “bubble ion” model (in which the ion's surface is polarizable), we define a spacedependent effective dielectric coefficient, , for the ion that overlaps with the dielectric boundary. Then, we replace the “bubble ion” with a point charge that has an effective charge and remove the portion of the dielectric boundary where the ion overlaps with it. We implement the interpolation procedure using the induced charge computation method [D. Boda, D. Gillespie, W. Nonner, D. Henderson, and B. Eisenberg, Phys. Rev. E69, 046702 (2004)]. We analyze the various energy terms using a spherical ion passing through an infinite flat dielectric boundary as an example.

A practical integral equation for the structure and thermodynamics of hard sphere Coulomb fluids
View Description Hide DescriptionA closure for the OrnsteinZernike equation is presented, applicable for fluids of charged, hard spheres. From an exact, but intractable closure, we derive the radial distribution function of nonlinearized DebyeHückel theory by subsequent approximations, and use the information to formulate a new closure by an extension of the mean spherical approximation. The radial distribution functions of the new closure, coined DebyeHückelextended mean spherical approximation, are in excellent agreement with those resulting from the hypernetted chain approximation and molecular dynamics simulations, in the regime where the latter are applicable, except for moderately dilute systems at low temperatures where the structure agrees at most qualitatively. The method is numerically more efficient, and more important, convergent in the entire temperaturedensity plane. We demonstrate that the method is accurate under many conditions for the determination of the structural and thermodynamic properties of homogeneous, symmetric hardsphere Coulomb systems, and estimate it to be a valuable basis for the formulation of density functional theories for inhomogeneous or highly asymmetric systems.
 Advanced Experimental Techniques

High purity chemical etching and thermal passivation process for Ge(001) as nanostructure template
View Description Hide DescriptionAn advanced twostep cleaning process of the Ge(001) surface for nanoscience requirements is presented. First, wetchemical etching with a variant of the Piranha solution (H_{2}SO_{4}, H_{2}O_{2}, H_{2}O) is used to remove contaminants as well as the native oxide layer. Second, passivation of the surface is achieved by a rapid thermal oxidation step, leading to a homogeneous protective oxide layer. The thickness of the oxide layer is tuned to be thick enough to protect the surface, yet thin enough to be completely removed by thermal treatment in ultrahigh vacuum. The application of this recipe results in an outstandingly clean and atomically flat surface, with carbon contamination at the detection limit of xray photoelectron spectroscopy. Scanning tunneling microscopy and electron diffraction reveal a long range ordered surface with typical terrace diameters of ∼100 nm, suitable for the growth of atomicscale nanostructures.
 Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry

Dynamical regimes on the Cl + H_{2} collisions: Inelastic rainbow scattering
View Description Hide DescriptionWhile Cl + H_{2} reactive collisions have been a subject of numerous experimental and theoretical studies, inelastic collisions leading to rotational energy transfer and/or vibrational excitation have been largely ignored. In this work, extensive quantum mechanical calculations covering the 0.5–1.5 eV total energy range and various initial rovibrational states have been carried out and used to perform a joint study of inelastic and reactive Cl + H_{2}collisions.Quasiclassical trajectories calculations complement the quantum mechanical results. The analysis of the inelastic transition probabilities has revealed the existence of two distinct dynamical regimes that correlate with low and high impact parameters, b, and are neatly separated by glory scattering. It has been found that while highbcollisions are mainly responsible for Δj = 2 transitions which dominate the inelastic scattering, they are very inefficient in promoting higher Δj transitions. The effectiveness of this type of collision also drops with rotational excitation of H_{2}. In contrast, reactive scattering, that competes with 2 inelastic transitions, is exclusively caused by lowbcollisions, and it is greatly favored when the reactants get rotationally excited. Previous studies focusing on the reactivity of the Cl + H_{2} system established that the van der Waals well located in the entrance channel play a key role in determining the mechanism of the collisions. Our results prove this to be also a case for inelastic processes, where the origin of the double dynamical regime can be traced back to the influence exerted by this well that shapes the topology of the entrance channel of the Cl–H_{2} system.

Polycyclic aromatic hydrocarbonisomer fragmentation pathways: Case study for pyrene and fluoranthene molecules and clusters
View Description Hide DescriptionWe report on measurements of the ionization and fragmentation of polycyclic aromatic hydrocarbon(PAH) targets in Xe^{20 +} + C_{16}H_{10} and Xe^{20 +} + [C_{16}H_{10}]_{ k } collisions and compare results for the two C_{16}H_{10} isomers: pyrene and fluoranthene. For both types of targets, i.e., for single PAH molecules isolated in vacuum or for isomerically pure clusters of one of the molecules, the resulting fragment spectra are surprisingly similar. However, we do observe weak but significant isomer effects. Although these are manifested in very different ways for the monomer and cluster targets, they both have at their roots small differences (<2.5 eV) between the total binding energies of neutral, and singly and multiply charged pyrene and fluoranthene monomers. The results will be discussed in view of the density functional theory calculations of ionization and dissociation energies for fluoranthene and pyrene. A simple classical overthebarrier model is used to estimate cross sections for single and multipleelectron transfer between PAHs and ions. Calculated single and multiple ionizationenergies, and the corresponding model PAHionization cross sections, are given.

Dissociative double ionization of 1bromo2chloroethane irradiated by an intense femtosecond laser field
View Description Hide DescriptionThe dissociative double ionization and multiphoton ionization of 1bromo2chloroethane (BCE) irradiated by the 800 nm femtosecond laser field have been investigated by dcslice imaging technology. The charged parent ion ratio [BCE^{2+}]/[BCE^{+}] was measured, and the corresponding ionization process including nonsequential double ionization and sequential double ionization was analyzed. The sliced images of different photodissociated ions were detected, and the corresponding kinetic energy release (KER) distributions were calculated and extracted. Furthermore, the dissociative double ionization channels, attributed to the cleavage of the C–C, C–Br, and C–Cl bonds by the Coulombic repulsive forces, were discussed, and the revised equilibrium distance , the energy ratio E _{exp}/E _{ coul }, and the value were calculated.

Quantifying cooperative intermolecular interactions for improved carbon dioxide capture materials
View Description Hide DescriptionWe have optimized the geometry and calculated interaction energies for over 100 different complexes of CO_{2} with various combinations of electron accepting (Lewis acid) and electron donating (Lewis base) molecules. We have used the recently developed explicitly correlated coupled cluster singles doubles and perturbative triples [CCSD(T)F12] methods and the associated VXZF12 (where X = D,T,Q) basis sets. We observe only modest changes in the geometric parameters of CO_{2} upon complexation, which suggests that the geometry of CO_{2} adsorbed in a nanoporous material should be similar to that of CO_{2} in gas phase. When CO_{2} forms a complex with two Lewis acids via the two electron rich terminal oxygen atoms, the interaction energy is less than twice what would be expected for the same complex involving a single Lewis acid. We consider a series of complexes that exhibit simultaneous CO_{2}Lewis acid and CO_{2}Lewis base intermolecular interactions, with total interaction energies spanning 14.1–105.9 kJ mol^{−1}. For these cooperative complexes, we find that the total interaction energy is greater than the sum of the interaction energies of the constituent complexes. Furthermore, the intermolecular distances of the cooperative complexes are contracted as compared to the constituent complexes. We suggest that metalorganicframework or similar nanoporous materials could be designed with adsorption sites specifically tailored for CO_{2} to allow cooperative intermolecular interactions, facilitating enhanced CO_{2}adsorption.

Structure of the alkalimetalatom + strontium molecular ions: Towards photoassociation and formation of cold molecular ions
View Description Hide DescriptionThe potential energy curves, permanent and transition dipole moments, and the static dipolar polarizability, of molecular ions composed of one alkalimetal atom and a strontium ion are determined with a quantum chemistry approach. The molecular ions are treated as effective twoelectron systems and are treated using effective core potentials including core polarization, large gaussian basis sets, and full configuration interaction. In the perspective of upcoming experiments aiming at merging cold atom and cold ion traps, possible paths for radiative charge exchange, photoassociation of a cold lithium or rubidium atom and a strontium ion are discussed, as well as the formation of stable molecular ions.

Theoretical investigation of rotationally inelastic collisions of the methyl radical with helium
View Description Hide DescriptionRotationally inelastic collisions of the CH_{3} molecule in its ground electronic state have been investigated. We have determined a potential energy surface (PES) for the interaction of rigid CH_{3}, frozen at its equilibrium geometry, with a helium atom, using a coupledcluster method that includes all single and double excitations, as well as perturbative contributions of connected triple excitations [RCCSD(T)]. The anisotropy of the PES is dominated by repulsion of the helium by the hydrogen atoms. The dissociation energy D _{ e } was computed to equal 27.0 cm^{−1}. At the global minimum, the helium atom lies in the CH_{3} plane between two C–H bonds at an atommolecule separation R = 6.52 bohr. Cross sections for collisioninduced rotational transitions have been determined through quantum scattering calculations for both nuclear spin modifications. Rotationally inelastic collisions can cause a change in the rotational angular momentumn and its bodyframe projection k. Because of the anisotropy of the PES due to the hydrogen atoms, there is a strong propensity for Δk = ±3 transitions. Thermal rate constants for statespecific total collisional removal have also been determined.

The study for the incipient solvation process of NaCl in water: The observation of the NaCl–(H_{2}O)_{ n } (n = 1, 2, and 3) complexes using Fouriertransform microwave spectroscopy
View Description Hide DescriptionPure rotational spectra of the sodium chloridewater complexes, NaCl–(H_{2}O)_{ n } (n = 1, 2, and 3), in the vibronic ground state have been observed by a Fourier transform microwave spectrometer coupled with a laser ablation source. The ^{37}Clisotopic species and a few deuterated species have also been observed. From the analyses of the spectra, the rotational constants, the centrifugal distortion constants, and the nuclear quadrupole coupling constants of the Na and Cl nuclei were determined precisely for all the species. The molecular structures of NaCl–(H_{2}O)_{ n } were determined using the rotational constants and the molecular symmetry. The charge distributions around Na and Cl nuclei in NaCl are dramatically changed by the complex formation with H_{2}O. Prominent dependences of the bond lengths r(Na–Cl) on the number of H_{2}O were also observed. By a comparison with results of theoretical studies, it is shown that the structure of NaCl–(H_{2}O)_{3} is approaching to that of the contact ionpair, which is considered to be an intermediate species in the incipient solvation process.

The airbroadened, nearinfrared CO_{2} line shape in the spectrally isolated regime: Evidence of simultaneous Dicke narrowing and speed dependence
View Description Hide DescriptionFrequencystabilized cavity ringdown spectroscopy (FSCRDS) was employed to measure airbroadened CO_{2}line shape parameters for transitions near 1.6 μm over a pressure range of 6.7–33 kPa. The high sensitivity of FSCRDS allowed for the first measurements in this wavelength range of airbroadened line shape parameters on samples with CO_{2} mixing ratios near those of the atmosphere. The measured airbroadening parameters show several percent deviations (0.9%–2.7%) from values found in the HITRAN 2008 database. Spectra were fit with a variety of models including the Voigt, Galatry, NelkinGhatak, and speeddependent NelkinGhatak line profiles. Clear evidence of line narrowing was observed, which if unaccounted for can lead to several percent biases. Furthermore, it was observed that only the speeddependent NelkinGhatak line profile was able to model the spectra to within the instrumental noise level because of the concurrent effects of collisional narrowing and speed dependence of collisional broadening and shifting.

The identification of a solvated electron pair in the gaseous clusters of Na^{−}(H_{2}O)_{ n } and Li^{−}(H_{2}O)_{ n }
View Description Hide DescriptionBy first principles calculations, we explore the possibility that Na^{−}(H_{2}O)_{ n } and Li^{−}(H_{2}O)_{ n } clusters, which have been measured previously by photoelectron experiments, could serve as gasphase molecular models for the solvation of two electrons. Such models would capture the electronelectron interaction in a solution environment, which is missed in the wellknown anionic water clusters . Our results show that by n = 10, the two loosely bound selectrons in Li^{−}(H_{2}O)_{ n } are indeed detached from lithium, and they could exist in either the singlet (spinparing) or the triplet (spincoupling) state. In contrast, the two electrons would prefer to stay on the sodium atom in Na^{−}(H_{2}O)_{ n } and on the surface of the cluster. The formation of a solvated electron pair and the variation in solvation structures make these two cluster series interesting subjects for further experimental investigation.

Rotational spectrum of asymmetric top molecules in combined static and laser fields
View Description Hide DescriptionWe examine the impact of the combination of a static electric field and a nonresonant linearly polarized laser field on an asymmetric top molecule. Within the rigid rotor approximation, we analyze the symmetries of the Hamiltonian for all possible field configurations. For each irreducible representation, the Schrödinger equation is solved by a basis set expansion in terms of a linear combination of symmetric top eigenfunctions respecting the corresponding symmetries, which allows us to distinguish avoided crossings from genuine ones. Using the fluorobenzene and pyridazine molecules as prototypes, the rotational spectra and properties are analyzed for experimentally accessible static field strengths and laser intensities. Results for energy shifts, orientation, alignment, and hybridization of the angular motion are presented as the field parameters are varied. We demonstrate that a proper selection of the fields gives rise to a constrained rotational motion in three Euler angles, the wave function being oriented along the electrostatic field direction, and aligned in other two angles.