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21 Feb 2012

Volume 136, Issue 7, Articles (07xxxx)

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J. Chem. Phys. 136, 074501 (2012); http://dx.doi.org/10.1063/1.3679662 (14 pages)

Vanessa Labet, Paulina Gonzalez-Morelos, Roald Hoffmann, and N. W. Ashcroft
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Communication: Variational many-body expansion: Accounting for exchange repulsion, charge delocalization, and dispersion in the fragment-based explicit polarization method

Jiali Gao and Yingjie Wang

J. Chem. Phys. 136, 071101 (2012); http://dx.doi.org/10.1063/1.3688232 (4 pages)

Online Publication Date: 17 February 2012

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A fragment-based variational many-body (VMB) expansion method is described to directly account for exchange repulsion, charge delocalization (charge transfer) and dispersion interactions in the explicit polarization (X-Pol) method. The present VMB/X-Pol approach differs from other fragment molecular orbital (FMO) techniques in two major aspects. First, the wave function for the monomeric system is variationally optimized using standard X-Pol method, as opposed to the iterative update procedure adopted in FMO. Second, the mutual polarizations in the dimeric terms are also variationally determined, whereas single-point energy calculations of the individual dimers embedded in a static monomer field are used in FMO. The second-order (two-body) VMB (VMB2) expansion method is illustrated on a series of water hexamer complexes and one decamer cluster, making use of Hartree-Fock theory, MP2, and the PBE1 and M06 density functionals to represent the monomer and dimer fragments. The computed binding energies are within 2 kcal/mol of the corresponding results from fully delocalized calculations. Energy decomposition analyses reveal specific dimeric contributions to exchange repulsion, charge delocalization, and dispersion. Since the wave functions for one-body and all two-body terms are variationally optimized in VMB2 and X-Pol, it is straightforward to obtain analytic gradient without the additional coupled-perturbed Hartree-Fock step. Thus, the method can be useful for molecular dynamics simulations.
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34.70.+e Charge transfer
82.30.Fi Ion-molecule, ion-ion, and charge-transfer reactions
31.15.E- Density-functional theory
31.15.xr Self-consistent-field methods
33.15.Ry Ionization potentials, electron affinities, molecular core binding energy
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Communication: Translational Brownian motion for particles of arbitrary shape

Bogdan Cichocki, Maria L. Ekiel-Jeżewska, and Eligiusz Wajnryb

J. Chem. Phys. 136, 071102 (2012); http://dx.doi.org/10.1063/1.3689842 (4 pages)

Online Publication Date: 21 February 2012

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A single Brownian particle of arbitrary shape is considered. The time-dependent translational mean square displacement W(t) of a reference point at this particle is evaluated from the Smoluchowski equation. It is shown that at times larger than the characteristic time scale of the rotational Brownian relaxation, the slope of W(t) becomes independent of the choice of a reference point. Moreover, it is proved that in the long-time limit, the slope of W(t) is determined uniquely by the trace of the translational-translational mobility matrix μtt evaluated with respect to the hydrodynamic center of mobility. The result is applicable to dynamic light scattering measurements, which indeed are performed in the long-time limit.
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05.40.Jc Brownian motion
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back to top Theoretical Methods and Algorithms

Unraveling rotation-vibration mixing in highly fluxional molecules using diffusion Monte Carlo: Applications to H3+ and H3O+

Andrew S. Petit, Bethany A. Wellen, and Anne B. McCoy

J. Chem. Phys. 136, 074101 (2012); http://dx.doi.org/10.1063/1.3681391 (12 pages)

Online Publication Date: 15 February 2012

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A thorough examination of the use of fixed-node diffusion Monte Carlo for the study of rotation-vibration mixing in systems that undergo large amplitude vibrational motions is reported. Using H3+ as a model system, the overall accuracy of the method is tested by comparing the results of these calculations with those from converged variational calculations. The effects of the presence of a large amplitude inversion mode on rotation-vibration mixing are considered by comparing the H3+ results with those for H3O+. Finally, analysis of the results of the fixed-node diffusion Monte Carlo calculations performed in different nodal regions is found to provide clear indications of when some of the methodology's underlying assumptions are breaking down as well as provide physical insights into the form of the rotation-vibration coupling that is most likely responsible.
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33.20.Vq Vibration-rotation analysis
33.20.Wr Vibronic, rovibronic, and rotation-electron-spin interactions
31.15.xt Variational techniques
33.15.Mt Rotation, vibration, and vibration-rotation constants
33.20.Tp Vibrational analysis

Bi-fidelity fitting and optimization

Ryan L. Miller, Lawrence B. Harding, Michael J. Davis, and Stephen K. Gray

J. Chem. Phys. 136, 074102 (2012); http://dx.doi.org/10.1063/1.3684884 (11 pages)

Online Publication Date: 16 February 2012

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A common feature in computations of chemical and physical properties is the investigation of phenomena at different levels of computational accuracy. Less accurate computations are used to provide a relatively quick understanding of the behavior of a system and allow a researcher to focus on regions of initial conditions and parameter space where interesting phenomena are likely to occur. These inexpensive calculations are often discarded when more accurate calculations are performed. This paper demonstrates how computations at different levels of accuracy can be simultaneously incorporated to study chemical and physical phenomena with less overall computational effort than the most expensive level of computation. A smaller set of computationally expensive calculations is needed because the set of expensive calculations is correlated with the larger set of less expensive calculations. We present two applications. First, we demonstrate how potential energy surfaces can be fit by simultaneously using results from two different levels of accuracy in electronic structure calculations. In the second application, we study the optical response of metallic nanostructures. The optical response is generated with calculations at two different grid resolutions, and we demonstrate how using these two levels of computation in a correlated fashion can more efficiently optimize the response.
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82.20.Kh Potential energy surfaces for chemical reactions
31.50.-x Potential energy surfaces

A generalized solid-state nudged elastic band method

Daniel Sheppard, Penghao Xiao, William Chemelewski, Duane D. Johnson, and Graeme Henkelman

J. Chem. Phys. 136, 074103 (2012); http://dx.doi.org/10.1063/1.3684549 (8 pages)

Online Publication Date: 16 February 2012

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A generalized solid-state nudged elastic band (G-SSNEB) method is presented for determining reaction pathways of solid–solid transformations involving both atomic and unit-cell degrees of freedom. We combine atomic and cell degrees of freedom into a unified description of the crystal structure so that calculated reaction paths are insensitive to the choice of periodic cell. For the rock-salt to wurtzite transition in CdSe, we demonstrate that the method is robust for mechanisms dominated either by atomic motion or by unit-cell deformation; notably, the lowest-energy transition mechanism found by our G-SSNEB changes with cell size from a concerted transformation of the cell coordinates in small cells to a nucleation event in large cells. The method is efficient and can be applied to systems in which the force and stress tensor are calculated using density functional theory.
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64.70.K- Solid-solid transitions
81.30.Hd Constant-composition solid-solid phase transformations: polymorphic, massive, and order-disorder
64.60.Q- Nucleation
62.20.D- Elasticity
81.40.Jj Elasticity and anelasticity, stress-strain relations
61.66.Fn Inorganic compounds

A rare event sampling method for diffusion Monte Carlo using smart darting

K. Roberts, R. Sebsebie, and E. Curotto

J. Chem. Phys. 136, 074104 (2012); http://dx.doi.org/10.1063/1.3685453 (9 pages)

Online Publication Date: 17 February 2012

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We identify a set of multidimensional potential energy surfaces sufficiently complex to cause both the classical parallel tempering and the guided or unguided diffusion Monte Carlo methods to converge too inefficiently for practical applications. The mathematical model is constructed as a linear combination of decoupled Double Wells [(DDW)n]. We show that the set (DDW)n provides a serious test for new methods aimed at addressing rare event sampling in stochastic simulations. Unlike the typical numerical tests used in these cases, the thermodynamics and the quantum dynamics for (DDW)n can be solved deterministically. We use the potential energy set (DDW)n to explore and identify methods that can enhance the diffusion Monte Carlo algorithm. We demonstrate that the smart darting method succeeds at reducing quasiergodicity for n ≫ 100 using just 1 × 106 moves in classical simulations (DDW)n. Finally, we prove that smart darting, when incorporated into the regular or the guided diffusion Monte Carlo algorithm, drastically improves its convergence. The new method promises to significantly extend the range of systems computationally tractable by the diffusion Monte Carlo algorithm.
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05.10.Ln Monte Carlo methods
05.60.-k Transport processes
02.50.Fz Stochastic analysis

Efficient simultaneous reverse Monte Carlo modeling of pair-distribution functions and extended x-ray-absorption fine structure spectra of crystalline disordered materials

Károly Németh, Karena W. Chapman, Mahalingam Balasubramanian, Badri Shyam, Peter J. Chupas, Steve M. Heald, Matt Newville, Robert J. Klingler, Randall E. Winans, Jonathan D. Almer, Giselle Sandi, and George Srajer

J. Chem. Phys. 136, 074105 (2012); http://dx.doi.org/10.1063/1.3684547 (10 pages)

Online Publication Date: 21 February 2012

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An efficient implementation of simultaneous reverse Monte Carlo (RMC) modeling of pair distribution function (PDF) and EXAFS spectra is reported. This implementation is an extension of the technique established by Krayzman et al. [J. Appl. Cryst. 42, 867 (2009)] in the sense that it enables simultaneous real-space fitting of x-ray PDF with accurate treatment of Q-dependence of the scattering cross-sections and EXAFS with multiple photoelectron scattering included. The extension also allows for atom swaps during EXAFS fits thereby enabling modeling the effects of chemical disorder, such as migrating atoms and vacancies. Significant acceleration of EXAFS computation is achieved via discretization of effective path lengths and subsequent reduction of operation counts. The validity and accuracy of the approach is illustrated on small atomic clusters and on 5500–9000 atom models of bcc-Fe and α-Fe2O3. The accuracy gains of combined simultaneous EXAFS and PDF fits are pointed out against PDF-only and EXAFS-only RMC fits. Our modeling approach may be widely used in PDF and EXAFS based investigations of disordered materials.
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78.70.Dm X-ray absorption spectra
02.50.Ng Distribution theory and Monte Carlo studies
61.72.jd Vacancies
79.60.-i Photoemission and photoelectron spectra

Approaching the bulk limit with finite cluster calculations using local increments: The case of LiH

Hermann Stoll and Klaus Doll

J. Chem. Phys. 136, 074106 (2012); http://dx.doi.org/10.1063/1.3687003 (7 pages)

Online Publication Date: 21 February 2012

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Finite-cluster calculations employing high-level wavefunction-based ab initio methods and extended atomic-orbital basis sets are used to determine local energy increments for bulk LiH. It is shown that these increments can be converged with respect to cluster size and point-charge embedding so as to yield bulk cohesive energies with an accuracy of better than 1 mEh, both at the Hartree-Fock and at correlated levels. Instrumental for the efficiency of the scheme is the introduction of non-orthogonal orbitals, at an intermediate stage.
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31.15.A- Ab initio calculations
33.15.Ry Ionization potentials, electron affinities, molecular core binding energy
36.40.-c Atomic and molecular clusters
31.15.xr Self-consistent-field methods
back to top Advanced Experimental Techniques

Electronic states of cyclophanes with small bridges

H. Dodziuk, V. Vetokhina, H. Hopf, R. Luboradzki, P. Gaweł, and J. Waluk

J. Chem. Phys. 136, 074201 (2012); http://dx.doi.org/10.1063/1.3683454 (9 pages) | Cited 1 time

Online Publication Date: 15 February 2012

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Electronic absorption and magnetic circular dichroism were recorded for five cyclophanes with ethano bridges: [2.2]paracyclophane, (1,2,4)[2.2.2]cyclophane, (1,2,4;1,2,5)[2.2.2]cyclophane, (1,2,3,4,5,6)(1,2,3,4,5,6)cyclophane, and trans-[2.2]metacyclophane. Spectral and structural analyses were based on geometry optimization and calculations of transition energies, carried out using density functional theory methods. The assignments have been proposed for several electronic transitions observed in the region below 52 000 cm−1. The observation of transitions which should be forbidden in the high D2h symmetry [2.2]paracyclophane suggests a twisted ground state structure of D2 symmetry, although the former structure with large amplitude vibrations at room temperature cannot be excluded. The PBE0 functional turned out to appropriately reproduce the inter-ring distances and electronic transition energies.
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31.15.es Applications of density-functional theory (e.g., to electronic structure and stability; defect formation; dielectric properties, susceptibilities; viscoelastic coefficients; Rydberg transition frequencies)
33.55.+b Optical activity and dichroism
back to top Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry

Scattering resonances in slow NH3–He collisions

Koos B. Gubbels, Sebastiaan Y. T. van de Meerakker, Gerrit C. Groenenboom, Gerard Meijer, and Ad van der Avoird

J. Chem. Phys. 136, 074301 (2012); http://dx.doi.org/10.1063/1.3683219 (15 pages)

Online Publication Date: 15 February 2012

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We theoretically study slow collisions of NH3 molecules with He atoms, where we focus in particular on the observation of scattering resonances. We calculate state-to-state integral and differential cross sections for collision energies ranging from 10−4 cm−1 to 130 cm−1, using fully converged quantum close-coupling calculations. To describe the interaction between the NH3 molecules and the He atoms, we present a four-dimensional potential energy surface, based on an accurate fit of 4180 ab initio points. Prior to collision, we consider the ammonia molecules to be in their antisymmetric umbrella state with angular momentum j = 1 and projection k = 1, which is a suitable state for Stark deceleration. We find pronounced shape and Feshbach resonances, especially for inelastic collisions into the symmetric umbrella state with j = k = 1. We analyze the observed resonant structures in detail by looking at scattering wavefunctions, phase shifts, and lifetimes. Finally, we discuss the prospects for observing the predicted scattering resonances in future crossed molecular beam experiments with a Stark-decelerated NH3 beam.
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34.50.-s Scattering of atoms and molecules
34.20.Gj Intermolecular and atom-molecule potentials and forces
31.15.A- Ab initio calculations

B80 and B101–103 clusters: Remarkable stability of the core-shell structures established by validated density functionals

Fengyu Li, Peng Jin, De-en Jiang, Lu Wang, Shengbai B. Zhang, Jijun Zhao, and Zhongfang Chen

J. Chem. Phys. 136, 074302 (2012); http://dx.doi.org/10.1063/1.3682776 (8 pages) | Cited 1 time

Online Publication Date: 15 February 2012

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Prompted by the very recent claim that the volleyball-shaped B80 fullerene [X. Wang, Phys. Rev. B 82, 153409 (2010)10.1103/PhysRevB.82.153409] is lower in energy than the B80 buckyball [N. G. Szwacki, A. Sadrzadeh, and B. I. Yakobson, Phys. Rev. Lett. 98, 166804 (2007)10.1103/PhysRevLett.98.166804] and core-shell structure [J. Zhao, L. Wang, F. Li, and Z. Chen, J. Phys. Chem. A 114, 9969 (2010)10.1021/jp1018873], and inspired by the most recent finding of another core-shell isomer as the lowest energy B80 isomer [S. De, A. Willand, M. Amsler, P. Pochet, L. Genovese, and S. Goedecher, Phys. Rev. Lett. 106, 225502 (2011)10.1103/PhysRevLett.106.225502], we carefully evaluated the performance of the density functional methods in the energetics of boron clusters and confirmed that the core-shell construction (stuffed fullerene) is thermodynamically the most favorable structural pattern for B80. Our global minimum search showed that both B101 and B103 also prefer a core-shell structure and that B103 can reach the complete core-shell configuration. We called for great attention to the theoretical community when using density functionals to investigate boron-related nanomaterials.
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36.40.Mr Spectroscopy and geometrical structure of clusters
31.15.E- Density-functional theory
33.15.Hp Barrier heights (internal rotation, inversion, rotational isomerism, conformational dynamics)

A femtosecond velocity map imaging study on B-band predissociation in CH3I. II. The 201 and 301 vibronic levels

G. Gitzinger, M. E. Corrales, V. Loriot, R. de Nalda, and L. Bañares

J. Chem. Phys. 136, 074303 (2012); http://dx.doi.org/10.1063/1.3683252 (16 pages)

Online Publication Date: 16 February 2012

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Femtosecond time-resolved velocity map imaging experiments are reported on several vibronic levels of the second absorption band (B-band) of CH3I, including vibrational excitation in the ν2 and ν3 modes of the bound 3R1(E) Rydberg state. Specific predissociation lifetimes have been determined for the 201 and 301 vibronic levels from measurements of time-resolved I*(2P1/2) and CH3 fragment images, parent decay, and photoelectron images obtained through both resonant and non-resonant multiphoton ionization. The results are compared with our previously reported predissociation lifetime measurements for the band origin 000 [Gitzinger et al., J. Chem. Phys. 132, 234313 (2010)10.1063/1.3455207]. The result, previously reported in the literature, where vibrational excitation to the C-I stretching mode (ν3) of the CH3I 3R1(E) Rydberg state yields a predissociation lifetime about four times slower than that corresponding to the vibrationless state, whereas predissociation is twice faster if the vibrational excitation is to the umbrella mode (ν2), is confirmed in the present experiments. In addition to the specific vibrational state lifetimes, which were found to be 0.85 ± 0.04 ps and 4.34 ± 0.13 ps for the 201 and 301 vibronic levels, respectively, the time evolution of the fragment anisotropy and the vibrational activity of the CH3 fragment are presented. Additional striking results found in the present work are the evidence of ground state I(2P3/2) fragment production when excitation is produced specifically to the 301 vibronic level, which is attributed to predissociation via the A-band 1Q1 potential energy surface, and the indication of a fast adiabatic photodissociation process through the repulsive A-band 3A1(4E) state, after direct absorption to this state, competing with absorption to the 301 vibronic level of the 3R1(E) Rydberg state of the B-band.
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33.80.Gj Diffuse spectra; predissociation, photodissociation
33.80.Rv Multiphoton ionization and excitation to highly excited states (e.g., Rydberg states)
33.80.Eh Autoionization, photoionization, and photodetachment
33.60.+q Photoelectron spectra
33.15.Mt Rotation, vibration, and vibration-rotation constants
31.50.-x Potential energy surfaces

Structure and dynamics of the electronically excited C 1 and D 0+ states of ArXe from high-resolution vacuum ultraviolet spectra

Lorena Piticco, Martin Schäfer, and Frédéric Merkt

J. Chem. Phys. 136, 074304 (2012); http://dx.doi.org/10.1063/1.3682770 (15 pages)

Online Publication Date: 16 February 2012

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Vacuum ultraviolet spectra of the C 1 ← X 0+ and D 0+ ← X 0+ band systems of ArXe have been recorded at high resolution. Analysis of the rotational structure of the spectra of several isotopomers, and in the case of Ar129Xe and Ar131Xe also of the hyperfine structure, has led to the derivation of a complete set of spectroscopic parameters for the C 1 and D 0+ states. The rovibrational energy level structure of the C 1 state reveals strong homogeneous perturbations with neighboring Ω = 1 electronic states. The analysis of isotopic shifts led to a reassignment of the vibrational structure of the C 1 state. The observation of electronically excited Xe fragments following excitation to the C state rotational levels of f parity indicates that the C state is predissociated by the electronic state of 0− symmetry associated with the Ar(1S0) + Xe(6s′[1/2]0o) dissociation limit. The observed predissociation dynamics differ both qualitatively and quantitatively from the behavior reported in previous investigations. An adiabatic two-state coupling model has been derived which accounts for the irregularities observed in the rovibronic and hyperfine level structure of the C 1 state. The model predicts the existence of a second state of Ω = 1 symmetry, supporting several tunneling/predissociation resonances located ∼200 cm−1 above the C 1 state.
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33.20.Ni Vacuum ultraviolet spectra
33.20.Sn Rotational analysis
33.20.Tp Vibrational analysis
33.20.Vq Vibration-rotation analysis
33.80.Gj Diffuse spectra; predissociation, photodissociation
31.30.Gs Hyperfine interactions and isotope effects

Recoil frame photoelectron angular distributions of BF3: A sensitive probe of the shape resonance in the F 1s continuum

T. Mizuno, J. Adachi, N. Miyauchi, M. Kazama, M. Stener, P. Decleva, and A. Yagishita

J. Chem. Phys. 136, 074305 (2012); http://dx.doi.org/10.1063/1.3687006 (11 pages)

Online Publication Date: 21 February 2012

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Recoil frame photoelectron angular distributions (RFPADs) of BF3 molecules are presented over the energy region of the shape resonance in the F 1s continuum. Time-dependent density functional theory calculations are also given to understand the shape resonance dynamics. The RFPADs have been compared with the theoretical calculations. It is found that the RFPADs calculated by the localized core-hole model are in better agreement with the experimental, compared with those by the delocalized core hole. Dipole matrix elements and dipole prepared continuum wavefunctions show that the shape resonance in the F 1s ionization continuum of BF3 is induced by p-partial waves as previously reported by Swanson et al. [J. Chem. Phys. 75, 619 (1981)10.1063/1.442078]. However, due to the couplings with the other partial waves the feature characteristic of the p-partial waves has not been observed in the RFPADs.
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31.15.E- Density-functional theory
33.80.Eh Autoionization, photoionization, and photodetachment
33.70.Jg Line and band widths, shapes, and shifts
33.60.+q Photoelectron spectra
back to top Condensed Phase Dynamics, Structure, and Thermodynamics: Spectroscopy, Reactions, and Relaxation

A fresh look at dense hydrogen under pressure. I. An introduction to the problem, and an index probing equalization of H–H distances

Vanessa Labet, Paulina Gonzalez-Morelos, Roald Hoffmann, and N. W. Ashcroft

J. Chem. Phys. 136, 074501 (2012); http://dx.doi.org/10.1063/1.3679662 (14 pages) | Cited 3 times

Online Publication Date: 15 February 2012

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In the first of a series of four papers on hydrogen under pressure, and its transitions from an initiating molecular state, we begin by defining carefully the problem, and setting the distance scale of interactions of protons and electrons in molecular aggregates of the first of the elements. Following a review of the experimental situation, in particular the phase diagram of hydrogen, in as much as it is known, and the behavior of its vibrons and rotons, we move onto the setting up of a numerical laboratory for probing the underlying physics and chemistry of interactions in hydrogen as the pressure increases. The laboratory consists of the preferred static structures emerging from calculations on the system in the range of 1 atm to 500 GPa, those of Pickard and Needs. The intermolecular (inter-pair) H···H separations naturally decrease with increasing pressure, first rapidly so, then more slowly. The intramolecular (intra-pair) H–H distances vary over a much smaller scale (0.05 Å) as the pressure increases, first decreasing, then increasing, and finally decreasing. We define an equalization function to gauge the approach to equality of the first neighbor and shortest next neighbor H (proton) separations in this numerical laboratory. And we find that metallization is likely to occur before bond equalization.
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33.15.Mt Rotation, vibration, and vibration-rotation constants
33.15.Bh General molecular conformation and symmetry; stereochemistry
33.20.Tp Vibrational analysis

A fresh look at dense hydrogen under pressure. II. Chemical and physical models aiding our understanding of evolving H–H separations

Vanessa Labet, Roald Hoffmann, and N. W. Ashcroft

J. Chem. Phys. 136, 074502 (2012); http://dx.doi.org/10.1063/1.3679736 (10 pages) | Cited 3 times

Online Publication Date: 15 February 2012

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In order to explain the intricate dance of intramolecular (intra-proton-pair) H–H separations observed in a numerical laboratory of calculationally preferred static hydrogen structures under pressure, we examine two effects through discrete molecular models. The first effect, we call it physical, is of simple confinement. We review a salient model already in the literature, that of LeSar and Herschbach, of a hydrogen molecule in a spheroidal cavity. As a complement, we also study a hydrogen molecule confined along a line between two helium atoms. As the size of the cavity/confining distance decreases (a surrogate for increasing pressure), in both models the equilibrium proton separation decreases and the force constant of the stretching vibration increases. The second effect, which is an orbital or chemical factor, emerges from the electronic structure of the known molecular transition metal complexes of dihydrogen. In these the H–H bond is significantly elongated (and the vibron much decreased in frequency) as a result of depopulation of the σg bonding molecular orbital of H2, and population of the antibonding σu* MO. The general phenomenon, long known in chemistry, is analyzed through a specific molecular model of three hydrogen molecules interacting in a ring, a motif found in some candidate structures for dense hydrogen.
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33.15.Bh General molecular conformation and symmetry; stereochemistry
31.15.ae Electronic structure and bonding characteristics
33.20.Tp Vibrational analysis
33.15.Mt Rotation, vibration, and vibration-rotation constants
33.15.Fm Bond strengths, dissociation energies

A fresh look at dense hydrogen under pressure. III. Two competing effects and the resulting intra-molecular H-H separation in solid hydrogen under pressure

Vanessa Labet, Roald Hoffmann, and N. W. Ashcroft

J. Chem. Phys. 136, 074503 (2012); http://dx.doi.org/10.1063/1.3679749 (10 pages) | Cited 3 times

Online Publication Date: 15 February 2012

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A preliminary discussion of the general problem of localization of wave functions, and the way it is approached in theoretical condensed matter physics (Wannier functions) and theoretical chemistry (localized or fragment orbitals) is followed by an application of the ideas of Paper II in this series to the structures of hydrogen as they evolve under increasing pressure. The idea that emerges is that of simultaneously operative physical (reduction of available space by an increasingly stiff wall of neighboring molecules) and chemical (depopulation of the σg bonding molecular orbital of H2, and population of the antibonding σu* MO) factors. The two effects work in the same direction of reducing the intermolecular separation as the pressure increases, but compete, working in opposite directions, in their effect on the intramolecular (nearest neighbor, intra-pair) distance. We examine the population of σg and σu* MOs in our numerical laboratory, as well as the total electron transfer (small), and polarization (moderate, where allowed by symmetry) of the component H2 molecules. From a molecular model of two interacting H2 molecules we find a linear relationship between the electron transfer from σg to σu* of a hydrogen molecular fragment and the intramolecular H-H separation, and that, in turn, allows us to estimate the expected bond lengths in H2 under pressure if the first effect (that of simple confinement) was absent. In essence, the intramolecular H-H separations under pressure are much shorter than they would be, were there no physical/confinement effect. We then use this knowledge to understand how the separate E and PV terms contribute to hydrogen phase changes with increasing pressure.
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71.15.Ap Basis sets (LCAO, plane-wave, APW, etc.) and related methodology (scattering methods, ASA, linearized methods, etc.)
62.50.-p High-pressure effects in solids and liquids

A fresh look at dense hydrogen under pressure. IV. Two structural models on the road from paired to monatomic hydrogen, via a possible non-crystalline phase

Vanessa Labet, Roald Hoffmann, and N. W. Ashcroft

J. Chem. Phys. 136, 074504 (2012); http://dx.doi.org/10.1063/1.3679751 (10 pages) | Cited 2 times

Online Publication Date: 15 February 2012

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In this paper, we examine the transition from a molecular to monatomic solid in hydrogen over a wide pressure range. This is achieved by setting up two models in which a single parameter δ allows the evolution from a molecular structure to a monatomic one of high coordination. Both models are based on a cubic Bravais lattice with eight atoms in the unit cell; one belongs to space group Pamath, the other to space group Rmathm. In Pamath one moves from effective 1-coordination, a molecule, to a simple cubic 6-coordinated structure but through a very special point (the golden mean is involved) of 7-coordination. In Rmathm, the evolution is from 1 to 4 and then to 3 to 6-coordinate. If one studies the enthalpy as a function of pressure as these two structures evolve (δ increases), one sees the expected stabilization of minima with increased coordination (moving from 1 to 6 to 7 in the Pamath structure, for instance). Interestingly, at some specific pressures, there are in both structures relatively large regions of phase space where the enthalpy remains roughly the same. Although the structures studied are always higher in enthalpy than the computationally best structures for solid hydrogen – those emerging from the Pickard and Needs or McMahon and Ceperley numerical laboratories – this result is suggestive of the possibility of a microscopically non-crystalline or “soft” phase of hydrogen at elevated pressures, one in which there is a substantial range of roughly equi-enthalpic geometries available to the system. A scaling argument for potential dynamic stabilization of such a phase is presented.
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61.66.Bi Elemental solids
61.50.Lt Crystal binding; cohesive energy

The structure of liquid N-methyl pyrrolidone probed by x-ray scattering and molecular simulations

Lorenzo Gontrani and Ruggero Caminiti

J. Chem. Phys. 136, 074505 (2012); http://dx.doi.org/10.1063/1.3684988 (9 pages)

Online Publication Date: 15 February 2012

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The structural properties of liquid N-methyl pyrrolidone have been investigated by combining energy dispersive x-ray diffraction experiments and molecular dynamics simulations with generalized AMBER force field. A very good agreement between theoretical and experimental diffraction patterns was achieved. The analysis of the radial distribution functions shows that the methyl-carbonyl H-bond network observed in the crystal structure is partly preserved in the liquid structure.
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61.25.Em Molecular liquids
78.70.Ck X-ray scattering
61.20.Ja Computer simulation of liquid structure

Two-point approximation to the Kramers problem with coloured noise

Daniel Campos and Vicenç Méndez

J. Chem. Phys. 136, 074506 (2012); http://dx.doi.org/10.1063/1.3685418 (8 pages)

Online Publication Date: 15 February 2012

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We present a method, founded on previous renewal approaches as the classical Wilemski-Fixman approximation, to describe the escape dynamics from a potential well of a particle subject to non-Markovian fluctuations. In particular, we show how to provide an approximated expression for the distribution of escape times if the system is governed by a generalized Langevin equation (GLE). While we show that the method could apply to any friction kernel in the GLE, we focus here on the case of power-law kernels, for which extensive literature has appeared in the last years. The method presented (termed as two-point approximation) is able to fit the distribution of escape times adequately for low potential barriers, even if conditions are far from Markovian. In addition, it confirms that non-exponential decays arise when a power-law friction kernel is considered (in agreement with related works published recently), which questions the existence of a characteristic reaction rate in such situations.
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31.50.Bc Potential energy surfaces for ground electronic states
31.15.bt Statistical model calculations (including Thomas-Fermi and Thomas-Fermi-Dirac models)
05.40.Ca Noise

Microscopic probing of the size dependence in hydrophobic solvation

Ningdong Huang, Daniel Schlesinger, Dennis Nordlund, Congcong Huang, Tolek Tyliszczak, Thomas M. Weiss, Yves Acremann, Lars G. M. Pettersson, and Anders Nilsson

J. Chem. Phys. 136, 074507 (2012); http://dx.doi.org/10.1063/1.3684893 (7 pages) | Cited 1 time

Online Publication Date: 16 February 2012

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We report small angle x-ray scattering data demonstrating the direct experimental microscopic observation of the small-to-large crossover behavior of hydrophobic effects in hydrophobic solvation. By increasing the side chain length of amphiphilic tetraalkyl-ammonium (CnH2n+1)4N+ (R4N+) cations in aqueous solution we observe diffraction peaks indicating association between cations at a solute size between 4.4 and 5 Å, which show temperature dependence dominated by hydrophobic attraction. Using O K-edge x-ray absorption we show that small solutes affect hydrogen bonding in water similar to a temperature decrease, while large solutes affect water similar to a temperature increase. Molecular dynamics simulations support, and provide further insight into, the origin of the experimental observations.
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82.30.Nr Association, addition, insertion, cluster formation
33.20.Rm X-ray spectra
82.30.Rs Hydrogen bonding, hydrophilic effects
82.20.Yn Solvent effects on reactivity
33.15.Fm Bond strengths, dissociation energies
31.15.xv Molecular dynamics and other numerical methods

Rotational dynamics of benzene and water in an ionic liquid explored via molecular dynamics simulations and NMR T1 measurements

Yoshiro Yasaka, Michael L. Klein, Masaru Nakahara, and Nobuyuki Matubayasi

J. Chem. Phys. 136, 074508 (2012); http://dx.doi.org/10.1063/1.3685100 (12 pages)

Online Publication Date: 16 February 2012

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The rotational dynamics of benzene and water in the ionic liquid (IL) 1-butyl-3-methylimidazolium chloride are studied using molecular dynamics (MD) simulation and NMR T1 measurements. MD trajectories based on an effective potential are used to calculate the 2H NMR relaxation time, T1 via Fourier transform of the relevant rotational time correlation function, C2R(t). To compensate for the lack of polarization in the standard fixed-charge modeling of the IL, an effective ionic charge, which is smaller than the elementary charge is employed. The simulation results are in closest agreement with NMR experiments with respect to the temperature and Larmor frequency dependencies of T1 when an effective charge of ±0.5e is used for the anion and the cation, respectively. The computed C2R(t) of both solutes shows a bi-modal nature, comprised of an initial non-diffusive ps relaxation plus a long-time ns tail extending to the diffusive regime. Due to the latter component, the solute dynamics is not under the motional narrowing condition with respect to the prevalent Larmor frequency. It is shown that the diffusive tail of the C2R(t) is most important to understand frequency and temperature dependencies of T1 in ILs. On the other hand, the effect of the initial ps relaxation is an increase of T1 by a constant factor. This is equivalent to an “effective” reduction of the quadrupolar coupling constant (QCC). Thus, in the NMR T1 analysis, the rotational time correlation function can be modeled analytically in the form of aexp (−t/τ) (Lipari-Szabo model), where the constant a, the Lipari-Szabo factor, contains the integrated contribution of the short-time relaxation and τ represents the relaxation time of the exponential (diffusive) tail. The Debye model is a special case of the Lipari-Szabo model with a = 1, and turns out to be inappropriate to represent benzene and water dynamics in ILs since a is as small as 0.1. The use of the Debye model would result in an underestimation of the QCC by a factor of 2–3 as a compensation for the neglect of the Lipari-Szabo factor.
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76.60.Es Relaxation effects
81.05.Lg Polymers and plastics; rubber; synthetic and natural fibers; organometallic and organic materials
61.20.Ja Computer simulation of liquid structure
61.25.Em Molecular liquids
66.10.C- Diffusion and thermal diffusion

Molecular dynamics approach to water structure of HII mesophase of monoolein

Vesselin Kolev, Anela Ivanova, Galia Madjarova, Abraham Aserin, and Nissim Garti

J. Chem. Phys. 136, 074509 (2012); http://dx.doi.org/10.1063/1.3685509 (11 pages)

Online Publication Date: 16 February 2012

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The goal of the present work is to study theoretically the structure of water inside the water cylinder of the inverse hexagonal mesophase (HII) of glyceryl monooleate (monoolein, GMO), using the method of molecular dynamics. To simplify the computational model, a fixed structure of the GMO tube is maintained. The non-standard cylindrical geometry of the system required the development and application of a novel method for obtaining the starting distribution of water molecules. A predictor-corrector schema is employed for generation of the initial density of water. Molecular dynamics calculations are performed at constant volume and temperature (NVT ensemble) with 1D periodic boundary conditions applied. During the simulations the lipid structure is kept fixed, while the dynamics of water is unrestrained. Distribution of hydrogen bonds and density as well as radial distribution of water molecules across the water cylinder show the presence of water structure deep in the cylinder (about 6 Å below the GMO heads). The obtained results may help understanding the role of water structure in the processes of insertion of external molecules inside the GMO/water system. The present work has a semi-quantitative character and it should be considered as the initial stage of more comprehensive future theoretical studies.
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87.15.ap Molecular dynamics simulation
02.60.-x Numerical approximation and analysis
87.15.R- Reactions and kinetics
31.15.xv Molecular dynamics and other numerical methods

Crystal nucleation and the solid–liquid interfacial free energy

Vladimir G. Baidakov and Azat O. Tipeev

J. Chem. Phys. 136, 074510 (2012); http://dx.doi.org/10.1063/1.3678214 (9 pages)

Online Publication Date: 16 February 2012

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We present the results of molecular dynamics simulation of crystal nucleation in a supercooled Lennard–Jones liquid. Temperature and baric dependences of the nucleation rate, the Zeldovich factor, nucleus size diffusion coefficient, the radius, and the pressure in a critical crystal nucleus are defined in computer simulation. The data obtained have been used in the framework of classical nucleation theory to calculate the effective surface energy of crystal nuclei γe. It is shown that the value of γe at T = const exceeds the value of the interfacial free energy at a flat crystal–liquid interface γ∞ and γe < γ∞ at p = const.
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65.20.Jk Studies of thermodynamic properties of specific liquids

Theory and simulations of quantum glass forming liquids

Thomas E. Markland, Joseph A. Morrone, Kunimasa Miyazaki, B. J. Berne, David R. Reichman, and Eran Rabani

J. Chem. Phys. 136, 074511 (2012); http://dx.doi.org/10.1063/1.3684881 (10 pages)

Online Publication Date: 17 February 2012

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A comprehensive microscopic dynamical theory is presented for the description of quantum fluids as they transform into glasses. The theory is based on a quantum extension of mode-coupling theory. Novel effects are predicted, such as reentrant behavior of dynamical relaxation times. These predictions are supported by path integral ring polymer molecular dynamics simulations. The simulations provide detailed insight into the factors that govern slow dynamics in glassy quantum fluids. Connection to other recent work on both quantum glasses as well as quantum optimization problems is presented.
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64.70.pm Liquids
61.20.Ja Computer simulation of liquid structure
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