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14 Aug 2011

Volume 135, Issue 6, Articles (06xxxx)

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J. Chem. Phys. 135, 061101 (2011); http://dx.doi.org/10.1063/1.3624928 (4 pages)

Piero Ricchiuto, Andrey V. Brukhno, Emanuele Paci, and Stefan Auer
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Communication: Conformation state diagram of polypeptides: A chain length induced α-β transition

Piero Ricchiuto, Andrey V. Brukhno, Emanuele Paci, and Stefan Auer

J. Chem. Phys. 135, 061101 (2011); http://dx.doi.org/10.1063/1.3624928 (4 pages)

Online Publication Date: 8 August 2011

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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 α-β transformations in a broad class of polypeptides.
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87.15.ap Molecular dynamics simulation
36.20.Ey Conformation (statistics and dynamics)
36.20.Fz Constitution (chains and sequences)
87.14.ef Peptides
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Communication: Where does the first water molecule go in imidazole?

Julia Zischang, Juhyon J. Lee, and Martin A. Suhm

J. Chem. Phys. 135, 061102 (2011); http://dx.doi.org/10.1063/1.3624841 (4 pages)

Online Publication Date: 8 August 2011

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Supersonic jet FTIR spectroscopy supplemented by 18O 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.
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82.30.Hk Chemical exchanges (substitution, atom transfer, abstraction, disproportionation, and group exchange)
82.30.Rs Hydrogen bonding, hydrophilic effects
31.15.-p Calculations and mathematical techniques in atomic and molecular physics
33.15.Fm Bond strengths, dissociation energies
33.20.Ea Infrared spectra
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Communication: Iteration-free, weighted histogram analysis method in terms of intensive variables

Jaegil Kim, Thomas Keyes, and John E. Straub

J. Chem. Phys. 135, 061103 (2011); http://dx.doi.org/10.1063/1.3626150 (4 pages) | Cited 1 time

Online Publication Date: 11 August 2011

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We present an iteration-free weighted histogram method in terms of intensive variables that directly determines the inverse statistical temperature, βS = ∂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 βS characteristic of finite size systems. The versatility and accuracy of the method is illustrated for the Ising and Potts models.
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05.70.Ce Thermodynamic functions and equations of state
05.70.Fh Phase transitions: general studies
05.50.+q Lattice theory and statistics (Ising, Potts, etc.)
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back to top Theoretical Methods and Algorithms

Using a pruned basis, a non-product quadrature grid, and the exact Watson normal-coordinate kinetic energy operator to solve the vibrational Schrödinger equation for C2H4

Gustavo Avila and Tucker Carrington, Jr.

J. Chem. Phys. 135, 064101 (2011); http://dx.doi.org/10.1063/1.3617249 (12 pages)

Online Publication Date: 8 August 2011

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In 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 non-product quadrature, the Lanczos algorithm, and the exact normal-coordinate kinetic energy operator (KEO) with the πtμπ 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 C2H4. All 12 coordinates are treated explicitly. We need only ∼1.52 × 108 quadrature points. A product Gauss grid with which one could calculate the same energy levels has at least 5.67 × 1013 points.
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33.20.Tp Vibrational analysis
31.15.-p Calculations and mathematical techniques in atomic and molecular physics

Effective Hamiltonian of liquid-vapor curved interfaces in mean field

José G. Segovia-López, Adolfo Zamora, and J. A. Santiago

J. Chem. Phys. 135, 064102 (2011); http://dx.doi.org/10.1063/1.3617414 (7 pages)

Online Publication Date: 8 August 2011

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We analyze a one-component simple fluid in a liquid-vapor 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 short-range interaction potential. By introducing the step-function 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.
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64.70.F- Liquid-vapor transitions

The relationship between double excitation amplitudes and Z vector components in some post-Hartree-Fock correlation methods

Christian Kollmar and Frank Neese

J. Chem. Phys. 135, 064103 (2011); http://dx.doi.org/10.1063/1.3618720 (10 pages)

Online Publication Date: 8 August 2011

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The relationship between Z vector components and excitation amplitudes is analyzed for several post-Hartree-Fock 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 functional-type energy functionals self-consistently leading to better agreement with coupled cluster results.
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31.15.xr Self-consistent-field methods
31.15.bw Coupled-cluster theory

Improving the convergence of closed and open path integral molecular dynamics via higher order Trotter factorization schemes

Alejandro Pérez and Mark E. Tuckerman

J. Chem. Phys. 135, 064104 (2011); http://dx.doi.org/10.1063/1.3609120 (17 pages)

Online Publication Date: 10 August 2011

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Higher 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 Takahashi-Imada 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 end-to-end 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.
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31.15.xv Molecular dynamics and other numerical methods
31.15.at Molecule transport characteristics; molecular dynamics; electronic structure of polymers

A method for treating the passage of a charged hard sphere ion as it passes through a sharp dielectric boundary

Dezső Boda, Douglas Henderson, Bob Eisenberg, and Dirk Gillespie

J. Chem. Phys. 135, 064105 (2011); http://dx.doi.org/10.1063/1.3622857 (12 pages)

Online Publication Date: 12 August 2011

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In 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 space-dependent effective dielectric coefficient, ε eff (r), for the ion that overlaps with the dielectric boundary. Then, we replace the “bubble ion” with a point charge that has an effective charge q/ε eff (r) 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. E 69, 046702 (2004)]. We analyze the various energy terms using a spherical ion passing through an infinite flat dielectric boundary as an example.
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77.22.Ch Permittivity (dielectric function)
77.22.Ej Polarization and depolarization
82.45.Gj Electrolytes

A practical integral equation for the structure and thermodynamics of hard sphere Coulomb fluids

Jos W. Zwanikken, Prateek K. Jha, and Monica Olvera de la Cruz

J. Chem. Phys. 135, 064106 (2011); http://dx.doi.org/10.1063/1.3624809 (7 pages) | Cited 1 time

Online Publication Date: 12 August 2011

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A closure for the Ornstein-Zernike equation is presented, applicable for fluids of charged, hard spheres. From an exact, but intractable closure, we derive the radial distribution function of nonlinearized Debye-Hückel 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 Debye-Hückel-extended mean spherical approximation, are in excellent agreement with those resulting from the hyper-netted 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 temperature-density plane. We demonstrate that the method is accurate under many conditions for the determination of the structural and thermodynamic properties of homogeneous, symmetric hard-sphere Coulomb systems, and estimate it to be a valuable basis for the formulation of density functional theories for inhomogeneous or highly asymmetric systems.
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61.20.Ja Computer simulation of liquid structure
82.45.-h Electrochemistry and electrophoresis
02.30.Rz Integral equations
back to top Advanced Experimental Techniques

High purity chemical etching and thermal passivation process for Ge(001) as nanostructure template

Christian Blumenstein, Sebastian Meyer, Andreas Ruff, Benjamin Schmid, Jörg Schäfer, and Ralph Claessen

J. Chem. Phys. 135, 064201 (2011); http://dx.doi.org/10.1063/1.3624902 (4 pages)

Online Publication Date: 12 August 2011

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An advanced two-step cleaning process of the Ge(001) surface for nanoscience requirements is presented. First, wet-chemical etching with a variant of the Piranha solution (H2SO4, H2O2, H2O) 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 ultra-high vacuum. The application of this recipe results in an outstandingly clean and atomically flat surface, with carbon contamination at the detection limit of x-ray 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 atomic-scale nanostructures.
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81.65.Cf Surface cleaning, etching, patterning
81.07.Bc Nanocrystalline materials
81.65.Mq Oxidation
79.60.Bm Clean metal, semiconductor, and insulator surfaces
back to top Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry

Dynamical regimes on the Cl + H2 collisions: Inelastic rainbow scattering

L. González-Sánchez, J. Aldegunde, P. G. Jambrina, and F. J. Aoiz

J. Chem. Phys. 135, 064301 (2011); http://dx.doi.org/10.1063/1.3618721 (10 pages)

Online Publication Date: 8 August 2011

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While Cl + H2 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 + H2 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 high-b collisions 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 H2. In contrast, reactive scattering, that competes with |Δj| > 2 inelastic transitions, is exclusively caused by low-b collisions, and it is greatly favored when the reactants get rotationally excited. Previous studies focusing on the reactivity of the Cl + H2 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–H2 system.
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82.30.Cf Atom and radical reactions; chain reactions; molecule-molecule reactions
31.15.-p Calculations and mathematical techniques in atomic and molecular physics
33.15.Mt Rotation, vibration, and vibration-rotation constants
33.70.Ca Oscillator and band strengths, lifetimes, transition moments, and Franck-Condon factors
34.20.Gj Intermolecular and atom-molecule potentials and forces
34.50.Ez Rotational and vibrational energy transfer

Polycyclic aromatic hydrocarbon-isomer fragmentation pathways: Case study for pyrene and fluoranthene molecules and clusters

F. Seitz, A. I. S. Holm, H. Zettergren, H. A. B. Johansson, S. Rosén, H. T. Schmidt, A. Ławicki, J. Rangama, P. Rousseau, M. Capron, R. Maisonny, A. Domaracka, L. Adoui, A. Méry, B. Manil, et al.

J. Chem. Phys. 135, 064302 (2011); http://dx.doi.org/10.1063/1.3622589 (8 pages)

Online Publication Date: 9 August 2011

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We report on measurements of the ionization and fragmentation of polycyclic aromatic hydrocarbon (PAH) targets in Xe20 + + C16H10 and Xe20 + + [C16H10]k collisions and compare results for the two C16H10 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 over-the-barrier model is used to estimate cross sections for single- and multiple-electron transfer between PAHs and ions. Calculated single and multiple ionization energies, and the corresponding model PAH ionization cross sections, are given.
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36.40.Wa Charged clusters
82.30.Qt Isomerization and rearrangement
31.15.E- Density-functional theory
33.15.Fm Bond strengths, dissociation energies
33.15.Hp Barrier heights (internal rotation, inversion, rotational isomerism, conformational dynamics)
33.15.Ry Ionization potentials, electron affinities, molecular core binding energy
34.70.+e Charge transfer
36.40.Mr Spectroscopy and geometrical structure of clusters

Dissociative double ionization of 1-bromo-2-chloroethane irradiated by an intense femtosecond laser field

Yan Yang, Lulu Fan, Shengzhi Sun, Jian Zhang, Yuting Chen, Shian Zhang, Tianqing Jia, and Zhenrong Sun

J. Chem. Phys. 135, 064303 (2011); http://dx.doi.org/10.1063/1.3620176 (7 pages)

Online Publication Date: 9 August 2011

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The dissociative double ionization and multi-photon ionization of 1-bromo-2-chloroethane (BCE) irradiated by the 800 nm femtosecond laser field have been investigated by dc-slice imaging technology. The charged parent ion ratio [BCE2+]/[BCE+] was measured, and the corresponding ionization process including non-sequential double ionization and sequential double ionization was analyzed. The sliced images of different photo-dissociated 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 Re*, the energy ratio Eexp/Ecoul, and the value a = math/(Eexp/Ecoul) were calculated.
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33.80.Eh Autoionization, photoionization, and photodetachment
33.80.Gj Diffuse spectra; predissociation, photodissociation
33.80.Rv Multiphoton ionization and excitation to highly excited states (e.g., Rydberg states)
33.15.Fm Bond strengths, dissociation energies

Quantifying cooperative intermolecular interactions for improved carbon dioxide capture materials

Katrina M. de Lange and Joseph R. Lane

J. Chem. Phys. 135, 064304 (2011); http://dx.doi.org/10.1063/1.3624363 (8 pages) | Cited 1 time

Online Publication Date: 11 August 2011

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We have optimized the geometry and calculated interaction energies for over 100 different complexes of CO2 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 VXZ-F12 (where X = D,T,Q) basis sets. We observe only modest changes in the geometric parameters of CO2 upon complexation, which suggests that the geometry of CO2 adsorbed in a nanoporous material should be similar to that of CO2 in gas phase. When CO2 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 CO2-Lewis acid and CO2-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 metal-organic-framework or similar nanoporous materials could be designed with adsorption sites specifically tailored for CO2 to allow cooperative intermolecular interactions, facilitating enhanced CO2 adsorption.
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31.15.bw Coupled-cluster theory
82.30.Cf Atom and radical reactions; chain reactions; molecule-molecule reactions

Structure of the alkali-metal-atom + strontium molecular ions: Towards photoassociation and formation of cold molecular ions

M. Aymar, R. Guérout, and O. Dulieu

J. Chem. Phys. 135, 064305 (2011); http://dx.doi.org/10.1063/1.3611399 (11 pages)

Online Publication Date: 11 August 2011

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The potential energy curves, permanent and transition dipole moments, and the static dipolar polarizability, of molecular ions composed of one alkali-metal atom and a strontium ion are determined with a quantum chemistry approach. The molecular ions are treated as effective two-electron 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.
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31.50.-x Potential energy surfaces
31.15.V- Electron correlation calculations for atoms, ions and molecules
33.15.Bh General molecular conformation and symmetry; stereochemistry
33.15.Kr Electric and magnetic moments (and derivatives), polarizability, and magnetic susceptibility
82.30.Nr Association, addition, insertion, cluster formation
82.50.-m Photochemistry

Theoretical investigation of rotationally inelastic collisions of the methyl radical with helium

Paul J. Dagdigian and Millard H. Alexander

J. Chem. Phys. 135, 064306 (2011); http://dx.doi.org/10.1063/1.3624525 (9 pages) | Cited 2 times

Online Publication Date: 11 August 2011

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Rotationally inelastic collisions of the CH3 molecule in its ground math2A2′′ electronic state have been investigated. We have determined a potential energy surface (PES) for the interaction of rigid CH3, frozen at its equilibrium geometry, with a helium atom, using a coupled-cluster 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 De was computed to equal 27.0 cm−1. At the global minimum, the helium atom lies in the CH3 plane between two C–H bonds at an atom-molecule separation R = 6.52 bohr. Cross sections for collision-induced 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 momentum n and its body-frame 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 state-specific total collisional removal have also been determined.
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34.50.-s Scattering of atoms and molecules
31.15.bw Coupled-cluster theory
33.15.Fm Bond strengths, dissociation energies
33.15.Mt Rotation, vibration, and vibration-rotation constants
34.20.Gj Intermolecular and atom-molecule potentials and forces

The study for the incipient solvation process of NaCl in water: The observation of the NaCl–(H2O)n (n = 1, 2, and 3) complexes using Fourier-transform microwave spectroscopy

Asao Mizoguchi, Yasuhiro Ohshima, and Yasuki Endo

J. Chem. Phys. 135, 064307 (2011); http://dx.doi.org/10.1063/1.3616047 (11 pages)

Online Publication Date: 12 August 2011

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Pure rotational spectra of the sodium chloride-water complexes, NaCl–(H2O)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 37Cl-isotopic 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–(H2O)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 H2O. Prominent dependences of the bond lengths r(Na–Cl) on the number of H2O were also observed. By a comparison with results of theoretical studies, it is shown that the structure of NaCl–(H2O)3 is approaching to that of the contact ion-pair, which is considered to be an intermediate species in the incipient solvation process.
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33.20.Bx Radio-frequency and microwave spectra
33.15.Mt Rotation, vibration, and vibration-rotation constants
33.20.Wr Vibronic, rovibronic, and rotation-electron-spin interactions
33.25.+k Nuclear resonance and relaxation
31.70.Dk Environmental and solvent effects
33.70.Jg Line and band widths, shapes, and shifts

The air-broadened, near-infrared CO2 line shape in the spectrally isolated regime: Evidence of simultaneous Dicke narrowing and speed dependence

David A. Long, Katarzyna Bielska, Daniel Lisak, Daniel K. Havey, Mitchio Okumura, Charles E. Miller, and Joseph T. Hodges

J. Chem. Phys. 135, 064308 (2011); http://dx.doi.org/10.1063/1.3624527 (7 pages) | Cited 2 times

Online Publication Date: 12 August 2011

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Frequency-stabilized cavity ring-down spectroscopy (FS-CRDS) was employed to measure air-broadened CO2 line shape parameters for transitions near 1.6 μm over a pressure range of 6.7–33 kPa. The high sensitivity of FS-CRDS allowed for the first measurements in this wavelength range of air-broadened line shape parameters on samples with CO2 mixing ratios near those of the atmosphere. The measured air-broadening 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, Nelkin-Ghatak, and speed-dependent Nelkin-Ghatak 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 speed-dependent Nelkin-Ghatak 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.
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33.70.Jg Line and band widths, shapes, and shifts
33.20.Ea Infrared spectra

The identification of a solvated electron pair in the gaseous clusters of Na−(H2O)n and Li−(H2O)n

Han Zhang and Zhi-Feng Liu

J. Chem. Phys. 135, 064309 (2011); http://dx.doi.org/10.1063/1.3622562 (11 pages) | Cited 1 time

Online Publication Date: 12 August 2011

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By first principles calculations, we explore the possibility that Na−(H2O)n and Li−(H2O)n clusters, which have been measured previously by photoelectron experiments, could serve as gas-phase molecular models for the solvation of two electrons. Such models would capture the electron-electron interaction in a solution environment, which is missed in the well-known anionic water clusters (H2O)n−. Our results show that by n = 10, the two loosely bound s electrons in Li−(H2O)n are indeed detached from lithium, and they could exist in either the singlet (spin-paring) or the triplet (spin-coupling) state. In contrast, the two electrons would prefer to stay on the sodium atom in Na−(H2O)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.
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36.40.Cg Electronic and magnetic properties of clusters
34.50.Fa Electronic excitation and ionization of atoms (including beam-foil excitation and ionization)
32.80.Gc Photodetachment of atomic negative ions

Rotational spectrum of asymmetric top molecules in combined static and laser fields

J. J. Omiste, R. González-Férez, and P. Schmelcher

J. Chem. Phys. 135, 064310 (2011); http://dx.doi.org/10.1063/1.3624774 (13 pages)

Online Publication Date: 12 August 2011

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We examine the impact of the combination of a static electric field and a non-resonant 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.
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33.20.Sn Rotational analysis
33.80.Gj Diffuse spectra; predissociation, photodissociation
31.15.ap Polarizabilities and other atomic and molecular properties
33.15.Kr Electric and magnetic moments (and derivatives), polarizability, and magnetic susceptibility
back to top Condensed Phase Dynamics, Structure, and Thermodynamics: Spectroscopy, Reactions, and Relaxation

Quantum molecular dynamic simulations of warm dense carbon monoxide

Yujuan Zhang, Cong Wang, Dafang Li, and Ping Zhang

J. Chem. Phys. 135, 064501 (2011); http://dx.doi.org/10.1063/1.3624920 (5 pages)

Online Publication Date: 11 August 2011

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Using quantum molecular dynamic simulations, we have studied the thermophysical properties of warm dense carbon monoxide under extreme conditions. The principal Hugoniot pressure up to 286 GPa, which is derived from the equation of state, is calculated and compared with available experimental and theoretical data. The chemical decomposition of carbon monoxide has been predicted at 8 GPa by means of pair correlation function and the charge density distribution. Based on Kubo-Greenwood formula, the dc electrical conductivity and the optical reflectivity are determined, and the nonmetal-metal transition for shock compressed carbon monoxide is observed around 40 GPa.
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31.15.xv Molecular dynamics and other numerical methods
64.30.-t Equations of state of specific substances
51.50.+v Electrical properties (ionization, breakdown, electron and ion mobility, etc.)
82.30.Lp Decomposition reactions (pyrolysis, dissociation, and fragmentation)
31.15.A- Ab initio calculations

Modeling the first stages of Cu precipitation in α-Fe using a hybrid atomistic kinetic Monte Carlo approach

N. Castin, M. I. Pascuet, and L. Malerba

J. Chem. Phys. 135, 064502 (2011); http://dx.doi.org/10.1063/1.3622045 (9 pages)

Online Publication Date: 11 August 2011

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We simulate the coherent stage of Cu precipitation in α-Fe with an atomistic kinetic Monte Carlo (AKMC) model. The vacancy migration energy as a function of the local chemical environment is provided on-the-fly by a neural network, trained with high precision on values calculated with the nudged elastic band method, using a suitable interatomic potential. To speed up the simulation, however, we modify the standard AKMC algorithm by treating large Cu clusters as objects, similarly to object kinetic Monte Carlo approaches. Seamless matching between the fully atomistic and the coarse-grained approach is achieved again by using a neural network, that provides all stability and mobility parameters for large Cu clusters, after training on atomistically informed results. The resulting hybrid algorithm allows long thermal annealing experiments to be simulated, within a reasonable CPU time. The results obtained are in very good agreement with several series of experimental data available from the literature, spanning over different conditions of temperature and alloy composition. We deduce from these results and relevant parametric studies that the mobility of Cu clusters containing one vacancy plays a central role in the precipitation mechanism.
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81.30.Mh Solid-phase precipitation
81.40.Gh Other heat and thermomechanical treatments
61.72.jd Vacancies

Molecular dynamics studies to understand the mechanism of heat accommodation in homogeneous condensing flow of carbon dioxide

Rakesh Kumar, Zheng Li, Adri van Duin, and Deborah Levin

J. Chem. Phys. 135, 064503 (2011); http://dx.doi.org/10.1063/1.3624335 (10 pages)

Online Publication Date: 12 August 2011

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Using molecular dynamics (MD), we have studied the mechanism of heat accommodation between carbon dioxide clusters and monomers for temperatures and cluster size conditions that exist in homogeneous condensing supersonic expansion plumes. The work was motivated by our meso-scale direct simulation Monte Carlo and Bhatnagar-Gross-Krook based condensation simulations where we found that the heat accommodation model plays a key role in the near-field of the nozzle expansion particularly as the degree of condensation increases [R. Kumar, Z. Li, and D. Levin, Phys. Fluids 23, 052001 (2011)]. The heat released by nucleation and condensation and the heat removed by cluster evaporation can be transferred or removed from either the kinetic or translational modes of the carbon dioxide monomers. The molecular dynamics results show that the time required for gas-cluster interactions to establish an equilibrium from an initial state of non-equilibrium is less than the time step used in meso-scale analyses [R. Kumar, Z. Li, and D. Levin, Phys. Fluids 23, 052001 (2011)]. Therefore, the good agreement obtained between the measured cluster and gas number density and gas temperature profiles with the meso-scale modeling using the second energy exchange mechanism is not fortuitous but is physically based. Our MD simulations also showed that a dynamic equilibrium is established by the gas-cluster interactions in which condensation and evaporation processes take place constantly to and from a cluster.
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47.55.Ca Gas/liquid flows
68.03.Fg Evaporation and condensation of liquids
47.60.Kz Flows and jets through nozzles
02.70.Ns Molecular dynamics and particle methods
47.11.Mn Molecular dynamics methods
47.40.Ki Supersonic and hypersonic flows

Accurate quantum-mechanical rate constants for a linear response Azzouz-Borgis proton transfer model employing the multilayer multiconfiguration time-dependent Hartree approach

Ian R. Craig, Michael Thoss, and Haobin Wang

J. Chem. Phys. 135, 064504 (2011); http://dx.doi.org/10.1063/1.3624342 (12 pages)

Online Publication Date: 12 August 2011

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The multilayer multiconfiguration time-dependent Hartree (ML-MCTDH) method is applied to simulate the quantum dynamics and thermal rate constant of the Azzouz-Borgis model of proton transfer in a polar solvent. To this end, the original atomistic potential is mapped to a system-bath model. Employing the flux correlation function formalism and importance sampling techniques, accurate quantum mechanical rate constants are obtained, which provide a benchmark for evaluating approximate approaches to study the quantum dynamics of condensed-phase chemical reactions. Furthermore, the validity of the mapping procedure is discussed based on the comparison of the classical dynamics of the original atomistic Azzouz-Borgis model and the mapped system-bath model.
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82.30.Hk Chemical exchanges (substitution, atom transfer, abstraction, disproportionation, and group exchange)
82.20.Pm Rate constants, reaction cross sections, and activation energies
82.20.Sb Correlation function theory of rate constants and its applications
82.20.Yn Solvent effects on reactivity

The mean reaction force: A method to study the influence of the environment on reaction mechanisms

Esteban Vöhringer-Martinez and Alejandro Toro-Labbé

J. Chem. Phys. 135, 064505 (2011); http://dx.doi.org/10.1063/1.3624388 (8 pages)

Online Publication Date: 12 August 2011

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The mean reaction force is introduced as the negative derivative of the free energy along a predefined reaction path. In analogy to the reaction force, this descriptor allows detailed characterization of different processes of the reaction mechanism and the assignment of electronic and structural free energy contributions to activation barriers. Due to its free energy dependence, the mean reaction force represents a new tool to study the influence of the environment on the reaction mechanism. Moreover, it enables the separation of catalytic effects in structural and electronic components responsible for the free energy barrier reduction of a reaction. To validate the method, the intramolecular proton transfer in tryptophan was studied in the gas phase, in aqueous solution and at the vacuum-water interface employing molecular dynamics simulation in combination with ab initio calculations and the quantum molecular/molecular mechanics (QM/MM) methodology. The obtained results were compared to static vacuum and continuum calculations. The mean reaction force distinguishes structural rearrangements as the dominant free energy component to reach the transition state from the neutral form, whereas electronic reorganization predominates the activation of the zwitterion in aqueous solution. In addition, it identifies the origin of the reduction of the activation barrier for desolvated functional groups at the water-vacuum interface as the absence of hydrogen bonds which stabilize charge delocalized species.
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82.30.Hk Chemical exchanges (substitution, atom transfer, abstraction, disproportionation, and group exchange)
82.20.Db Transition state theory and statistical theories of rate constants
82.20.Hf Product distribution
82.20.Pm Rate constants, reaction cross sections, and activation energies
82.20.Wt Computational modeling; simulation
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