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21 Jun 2009

Volume 130, Issue 23, Articles (23xxxx)

Issue Cover Spotlight Figure

J. Chem. Phys. 130, 234101 (2009); http://dx.doi.org/10.1063/1.3149788 (14 pages)

Ruslan L. Davidchack, Richard Handel, and M. V. Tretyakov
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Approaching the Hartree–Fock limit by perturbative methods

Jia Deng, Andrew T. B. Gilbert, and Peter M. W. Gill

J. Chem. Phys. 130, 231101 (2009); http://dx.doi.org/10.1063/1.3152864 (4 pages) | Cited 14 times

Online Publication Date: 15 June 2009

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We describe perturbative methods for improving finite-basis Hartree–Fock calculations toward the complete-basis limit. The best method appears to offer quadratic error reduction and preliminary numerical applications demonstrate that remarkably accurate Hartree–Fock energies can be obtained.
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31.15.xr Self-consistent-field methods
31.15.xp Perturbation theory
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Controlling molecular rotational population by wave-packet interference

Chengyin Wu, Guiping Zeng, Yunan Gao, Nan Xu, Liang-You Peng, Hongbing Jiang, and Qihuang Gong

J. Chem. Phys. 130, 231102 (2009); http://dx.doi.org/10.1063/1.3155063 (4 pages) | Cited 10 times

Online Publication Date: 16 June 2009

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We propose a control scheme for selecting populations of molecular rotational states by wave-packet interference. A series of coherent rotational wave packets is created by nonadiabatic rotational excitation of molecules using two strong femtosecond laser pulses. By adjusting the time delay between the two laser pulses, constructive or destructive interference among these wave packets enables the population to be enhanced or suppressed for a specific rotational state. The evolution of the rotational wave packet with selected populations produces interference patterns with controlled spatial symmetries. This method provides an approach to prepare a molecular ensemble with selected quantum-state distributions and controlled spatial distributions under field-free condition.
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34.50.Ez Rotational and vibrational energy transfer
42.50.-p Quantum optics
33.15.Mt Rotation, vibration, and vibration-rotation constants
42.65.Re Ultrafast processes; optical pulse generation and pulse compression
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Auger recombination and excited state relaxation dynamics in Hgn− (n = 9–20) anion clusters

Graham B. Griffin, Oli T. Ehrler, Aster Kammrath, Ryan M. Young, Ori Cheshnovsky, and Daniel M. Neumark

J. Chem. Phys. 130, 231103 (2009); http://dx.doi.org/10.1063/1.3149562 (4 pages) | Cited 2 times

Online Publication Date: 17 June 2009

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Using femtosecond time-resolved photoelectron imaging, electron-hole pairs are created in size-selected Hgn− anion clusters (n = 9–20), and the subsequent decay dynamics are measured. These clusters eject electrons via Auger decay on time scales of 100–600 fs. There is an abrupt increase in the Auger decay time for clusters larger than Hg12−, coinciding with the onset of the transition from van der Waals to covalent bonding in mercury clusters. Our results also show evidence for subpicosecond excited state relaxation attributed to inelastic electron-electron and electron-hole scattering as well as hole-induced contraction of the cluster.
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36.40.Wa Charged clusters
33.80.Eh Autoionization, photoionization, and photodetachment
31.15.vj Electron correlation calculations for atoms and ions: excited states
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Strong fields induce ultrafast rearrangement of H atoms in H2O

F. A. Rajgara, A. K. Dharmadhikari, D. Mathur, and C. P. Safvan

J. Chem. Phys. 130, 231104 (2009); http://dx.doi.org/10.1063/1.3157234 (4 pages) | Cited 9 times

Online Publication Date: 17 June 2009

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H atoms in H2O are rearranged by strong optical fields generated by intense 9.3 fs laser pulses to form H2+. This atomic rearrangement is ultrafast: It occurs within a single laser pulse. Quantum-chemical calculations reveal that H2+ originates in the 1A state of H2O2+ when the O–H bond elongates to 1.15 a.u. and the H–O–H angle becomes 120°. Bond formation on the ultrafast time scale of molecular vibrations (10 fs for H2+) and in strong fields has hitherto not been reported.
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42.50.Hz Strong-field excitation of optical transitions in quantum systems; multiphoton processes; dynamic Stark shift
33.80.-b Photon interactions with molecules
33.15.Bh General molecular conformation and symmetry; stereochemistry
33.15.Dj Interatomic distances and angles
33.15.Mt Rotation, vibration, and vibration-rotation constants
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Formation of a dual hydrogen bond in the N–H⋯C = O moiety in the indole-(N-methylacetamide)1 cluster revealed by IR-dip spectroscopy with natural bond orbital analysis

Kenji Sakota, Yuiga Shimazaki, and Hiroshi Sekiya

J. Chem. Phys. 130, 231105 (2009); http://dx.doi.org/10.1063/1.3157254 (4 pages) | Cited 1 time

Online Publication Date: 17 June 2009

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IR-dip spectra in the NH stretch regions have been measured for the S0 state of the indole/N-methylacetamide 1:1 clusters (Ind-NMA1). We identified two structural isomers of Ind-NMA1 that possess an N–H⋯O = C hydrogen bond. The redshifts of the NH stretch fundamental of the indole moieties in Ind-NMA1 are larger than that for Ind-(H2O)1 [ Carney, Hagemeister, and Zweir, J. Chem. Phys. 108, 3379 (1998) ], indicating that the strength of the N–H⋯O = C hydrogen bond in Ind-NMA1 is stronger than that of the N–H⋯O–H hydrogen bond in Ind-(H2O)1. On the basis of the natural bond orbital analysis we suggest that two lone pair orbitals of the O atoms in the NMA moiety form a dual hydrogen bond with the NH group designated by N–H:::O = C. Owing to the dual nature of the N–H:::O = C hydrogen bond its strength in Ind-NMA1 is larger than that of the N–H⋯O–H hydrogen bond in Ind-(H2O)1.
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36.40.Mr Spectroscopy and geometrical structure of clusters
33.20.Ea Infrared spectra
33.20.Tp Vibrational analysis
33.15.Mt Rotation, vibration, and vibration-rotation constants
33.15.Fm Bond strengths, dissociation energies
33.15.Hp Barrier heights (internal rotation, inversion, rotational isomerism, conformational dynamics)
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back to top Theoretical Methods and Algorithms

Langevin thermostat for rigid body dynamics

Ruslan L. Davidchack, Richard Handel, and M. V. Tretyakov

J. Chem. Phys. 130, 234101 (2009); http://dx.doi.org/10.1063/1.3149788 (14 pages) | Cited 2 times

Online Publication Date: 15 June 2009

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We present a new method for isothermal rigid body simulations using the quaternion representation and Langevin dynamics. It can be combined with the traditional Langevin or gradient (Brownian) dynamics for the translational degrees of freedom to correctly sample the canonical distribution in a simulation of rigid molecules. We propose simple, quasisymplectic second-order numerical integrators and test their performance on the TIP4P model of water. We also investigate the optimal choice of thermostat parameters.
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05.40.Jc Brownian motion
02.70.Ns Molecular dynamics and particle methods

The initial and final states of electron and energy transfer processes: Diabatization as motivated by system-solvent interactions

Joseph E. Subotnik, Robert J. Cave, Ryan P. Steele, and Neil Shenvi

J. Chem. Phys. 130, 234102 (2009); http://dx.doi.org/10.1063/1.3148777 (14 pages) | Cited 13 times

Online Publication Date: 15 June 2009

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For a system which undergoes electron or energy transfer in a polar solvent, we define the diabatic states to be the initial and final states of the system, before and after the nonequilibrium transfer process. We consider two models for the system-solvent interactions: A solvent which is linearly polarized in space and a solvent which responds linearly to the system. From these models, we derive two new schemes for obtaining diabatic states from ab initio calculations of the isolated system in the absence of solvent. These algorithms resemble standard approaches for orbital localization, namely, the Boys and Edmiston–Ruedenberg (ER) formalisms. We show that Boys localization is appropriate for describing electron transfer [ Subotnik et al., J. Chem. Phys. 129, 244101 (2008) ] while ER describes both electron and energy transfer. Neither the Boys nor the ER methods require definitions of donor or acceptor fragments and both are computationally inexpensive. We investigate one chemical example, the case of oligomethylphenyl-3, and we provide attachment/detachment plots whereby the ER diabatic states are seen to have localized electron-hole pairs.
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82.30.Fi Ion-molecule, ion-ion, and charge-transfer reactions
61.20.Gy Theory and models of liquid structure
81.05.Lg Polymers and plastics; rubber; synthetic and natural fibers; organometallic and organic materials

A phase-field approach to no-slip boundary conditions in dissipative particle dynamics and other particle models for fluid flow in geometrically complex confined systems

Zhijie Xu and Paul Meakin

J. Chem. Phys. 130, 234103 (2009); http://dx.doi.org/10.1063/1.3152634 (8 pages) | Cited 3 times

Online Publication Date: 16 June 2009

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Dissipative particle dynamics (DPD) is an effective mesoscopic particle model with a lower computational cost than molecular dynamics because of the soft potentials that it employs. However, the soft potential is not strong enough to prevent the DPD particles that are used to represent the fluid from penetrating solid boundaries represented by stationary DPD particles. A phase-field variable, ϕ(x,t), is used to indicate the phase at point x and time t, with a smooth transition from −1 (phase 1) to +1 (phase 2) across the interface. We describe an efficient implementation of no-slip boundary conditions in DPD models that combines solid-liquid particle-particle interactions with reflection at a sharp boundary located with subgrid scale accuracy using the phase field. This approach can be used for arbitrarily complex flow geometries and other similar particle models (such as smoothed particle hydrodynamics), and the validity of the model is demonstrated by DPD simulations of flow in confined systems with various geometries.
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47.60.Dx Flows in ducts and channels
47.11.-j Computational methods in fluid dynamics

Computation of potential energy surfaces with the multireference correlation consistent composite approach

Benjamin Mintz, T. Gavin Williams, Levi Howard, and Angela K. Wilson

J. Chem. Phys. 130, 234104 (2009); http://dx.doi.org/10.1063/1.3149387 (10 pages) | Cited 11 times

Online Publication Date: 17 June 2009

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A multireference composite method that is based on the correlation consistent Composite Approach (ccCA) is introduced. The developed approach, multireference ccCA, has been utilized to compute the potential energy surfaces (PESs) of N2 and C2, which provide rigorous tests for multireference composite methods due to the large multireference character that must be correctly described as the molecules dissociate. As well, PESs provide a stringent test of a composite method because all components of the method must work in harmony for an appropriate, smooth representation across the entire surface.
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31.50.Bc Potential energy surfaces for ground electronic states
31.15.-p Calculations and mathematical techniques in atomic and molecular physics
31.50.Df Potential energy surfaces for excited electronic states

Simultaneous escaping of explicit and hidden free energy barriers: Application of the orthogonal space random walk strategy in generalized ensemble based conformational sampling

Lianqing Zheng, Mengen Chen, and Wei Yang

J. Chem. Phys. 130, 234105 (2009); http://dx.doi.org/10.1063/1.3153841 (10 pages) | Cited 14 times

Online Publication Date: 18 June 2009

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To overcome the pseudoergodicity problem, conformational sampling can be accelerated via generalized ensemble methods, e.g., through the realization of random walks along prechosen collective variables, such as spatial order parameters, energy scaling parameters, or even system temperatures or pressures, etc. As usually observed, in generalized ensemble simulations, hidden barriers are likely to exist in the space perpendicular to the collective variable direction and these residual free energy barriers could greatly abolish the sampling efficiency. This sampling issue is particularly severe when the collective variable is defined in a low-dimension subset of the target system; then the “Hamiltonian lagging” problem, which reveals the fact that necessary structural relaxation falls behind the move of the collective variable, may be likely to occur. To overcome this problem in equilibrium conformational sampling, we adopted the orthogonal space random walk (OSRW) strategy, which was originally developed in the context of free energy simulation [L. Zheng, M. Chen, and W. Yang, Proc. Natl. Acad. Sci. U.S.A. 105, 20227 (2008) ]. Thereby, generalized ensemble simulations can simultaneously escape both the explicit barriers along the collective variable direction and the hidden barriers that are strongly coupled with the collective variable move. As demonstrated in our model studies, the present OSRW based generalized ensemble treatments show improved sampling capability over the corresponding classical generalized ensemble treatments.
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05.70.Ce Thermodynamic functions and equations of state
02.50.-r Probability theory, stochastic processes, and statistics

Effective atomic orbitals for fuzzy atoms

I. Mayer and P. Salvador

J. Chem. Phys. 130, 234106 (2009); http://dx.doi.org/10.1063/1.3153482 (6 pages) | Cited 5 times

Online Publication Date: 18 June 2009

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The method of extracting effective atomic orbitals and effective minimal basis sets from molecular wave function characterizing the state of an atom in a molecule is developed in the framework of the “fuzzy” atoms. In all cases studied, there were as many effective orbitals that have considerable occupation numbers as orbitals in the classical minimal basis. That is considered to be of high conceptual importance.
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31.15.-p Calculations and mathematical techniques in atomic and molecular physics

The influence of dissipation on the quantum-classical correspondence: Stability of stochastic trajectories

Maksym Kryvohuz and Jianshu Cao

J. Chem. Phys. 130, 234107 (2009); http://dx.doi.org/10.1063/1.3154142 (10 pages) | Cited 2 times

Online Publication Date: 18 June 2009

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The quantum-classical correspondence in the presence of dissipation is studied. The semiclassical expression for the linear response function of an anharmonic system is expressed in a series containing classical stability matrix elements, which can diverge due to the chaotic behavior of stochastic trajectories. The presence of dissipation in most cases removes the divergence of higher-order correction terms, thus suppressing quantum effects and making the system more classical. The regime of system-bath coupling, which makes quantum dynamics completely classical, is obtained in terms of friction, temperature, and anharmonicity. Special cases when bath coupling may lead to enhancement of quantum effects are discussed.
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05.45.Mt Quantum chaos; semiclassical methods
03.65.Sq Semiclassical theories and applications
02.50.Ey Stochastic processes

On the determination of optimized, fully quadratic, coupled state quasidiabatic Hamiltonians for determining bound state vibronic spectra

Xiaolei Zhu and David R. Yarkony

J. Chem. Phys. 130, 234108 (2009); http://dx.doi.org/10.1063/1.3155392 (11 pages) | Cited 4 times

Online Publication Date: 18 June 2009

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The quasidiabatic, coupled electronic state, fully quadratic Hamiltonian (Hd), suitable for the simulation of spectra exhibiting strong vibronic couplings and constructed using a recently introduced pseudonormal equations approach, is studied. The flexibility inherent in the normal equations approach is shown to provide a robust means for (i) improving the accuracy of Hd, (ii) extending its domain of utility, and (iii) determining the limits of the fully quadratic model. The two lowest electronic states of pyrrolyl which are coupled by conical intersections are used as a test case. The requisite ab initio data are obtained from large multireference configuration interaction expansions comprised of 108.5×106 configuration state functions and based on polarized triple zeta quality atomic orbital bases.
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33.20.Wr Vibronic, rovibronic, and rotation-electron-spin interactions
31.15.am Relativistic configuration interaction (CI) and many-body perturbation calculations

Harmonic oscillator in presence of nonequilibrium environment

Jyotipratim Ray Chaudhuri, Pinaki Chaudhury, and Sudip Chattopadhyay

J. Chem. Phys. 130, 234109 (2009); http://dx.doi.org/10.1063/1.3155698 (7 pages) | Cited 5 times

Online Publication Date: 18 June 2009

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Based on a microscopic Hamiltonian picture where the system is coupled with the nonequilibrium environment, comprising of a set of harmonic oscillators, the Langevin equation with proper microscopic specification of Langevin force is formulated analytically. In our case, the reservoir is perturbed by an external force, either executing rapid or showing periodic fluctuations, hence the reservoir is not in thermal equilibrium. In the presence of external fluctuating force, using Shapiro–Loginov procedure, we arrive at the linear coupled first order differential equations for the two-time correlations and examine the time evolution of the same considering the system as a simple harmonic oscillator. We study the stochastic resonance phenomena of a Kubo-type oscillator (assumed to be the system) when the bath is modulated by a periodic force. The result(s) obtained here is of general significance and can be used to analyze the signature of stochastic resonance.
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03.65.Ge Solutions of wave equations: bound states

On the adequacy of the Redfield equation and related approaches to the study of quantum dynamics in electronic energy transfer

Akihito Ishizaki and Graham R. Fleming

J. Chem. Phys. 130, 234110 (2009); http://dx.doi.org/10.1063/1.3155214 (8 pages) | Cited 67 times

Online Publication Date: 18 June 2009

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The observation of long-lived electronic coherence in photosynthetic excitation energy transfer (EET) by Engel et al. [Nature (London) 446, 782 (2007)] raises questions about the role of the protein environment in protecting this coherence and the significance of the quantum coherence in light harvesting efficiency. In this paper we explore the applicability of the Redfield equation in its full form, in the secular approximation and with neglect of the imaginary part of the relaxation terms for the study of these phenomena. We find that none of the methods can give a reliable picture of the role of the environment in photosynthetic EET. In particular the popular secular approximation (or the corresponding Lindblad equation) produces anomalous behavior in the incoherent transfer region leading to overestimation of the contribution of environment-assisted transfer. The full Redfield expression on the other hand produces environment-independent dynamics in the large reorganization energy region. A companion paper presents an improved approach, which corrects these deficiencies [ A. Ishizaki and G. R. Fleming, J. Chem. Phys. 130, 234111 (2009) ].
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33.50.Hv Radiationless transitions, quenching
33.80.Be Level crossing and optical pumping
31.70.Dk Environmental and solvent effects

Unified treatment of quantum coherent and incoherent hopping dynamics in electronic energy transfer: Reduced hierarchy equation approach

Akihito Ishizaki and Graham R. Fleming

J. Chem. Phys. 130, 234111 (2009); http://dx.doi.org/10.1063/1.3155372 (10 pages) | Cited 94 times

Online Publication Date: 18 June 2009

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A new quantum dynamic equation for excitation energy transfer is developed which can describe quantum coherent wavelike motion and incoherent hopping in a unified manner. The developed equation reduces to the conventional Redfield theory and Förster theory in their respective limits of validity. In the regime of coherent wavelike motion, the equation predicts several times longer lifetime of electronic coherence between chromophores than does the conventional Redfield equation. Furthermore, we show quantum coherent motion can be observed even when reorganization energy is large in comparison to intersite electronic coupling (the Förster incoherent regime). In the region of small reorganization energy, slow fluctuation sustains longer-lived coherent oscillation, whereas the Markov approximation in the Redfield framework causes infinitely fast fluctuation and then collapses the quantum coherence. In the region of large reorganization energy, sluggish dissipation of reorganization energy increases the time electronic excitation stays above an energy barrier separating chromophores and thus prolongs delocalization over the chromophores.
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33.50.Dq Fluorescence and phosphorescence spectra
33.50.Hv Radiationless transitions, quenching
33.70.Ca Oscillator and band strengths, lifetimes, transition moments, and Franck-Condon factors
33.25.+k Nuclear resonance and relaxation
02.50.Ga Markov processes

Development and assessment of a short-range meta-GGA functional

Erich Goll, Matthias Ernst, Franzeska Moegle-Hofacker, and Hermann Stoll

J. Chem. Phys. 130, 234112 (2009); http://dx.doi.org/10.1063/1.3152221 (7 pages) | Cited 15 times

Online Publication Date: 18 June 2009

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Short-range DFT/long-range ab initio methods allow for a combination of the weak basis-set dependency of DFT with an accurate ab initio treatment of long-range effects like van der Waals interaction. In order to improve existing short-range LDA and GGA density functionals, we developed a TPSS-like short-range meta-GGA exchange-correlation functional and checked its performance in long-range CCSD(T) calculations for thermodynamical properties of the G2 set of molecules.
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31.15.eg Exchange-correlation functionals (in current density functional theory)
33.15.Ry Ionization potentials, electron affinities, molecular core binding energy
31.15.vq Electron correlation calculations for polyatomic molecules
31.15.A- Ab initio calculations
31.15.bw Coupled-cluster theory

Multiple coherent states for first-principles semiclassical initial value representation molecular dynamics

Michele Ceotto, Sule Atahan, Gian Franco Tantardini, and Alán Aspuru-Guzik

J. Chem. Phys. 130, 234113 (2009); http://dx.doi.org/10.1063/1.3155062 (11 pages) | Cited 10 times

Online Publication Date: 19 June 2009

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A multiple coherent states implementation of the semiclassical approximation is introduced and employed to obtain the power spectra with a few classical trajectories. The method is integrated with the time-averaging semiclassical initial value representation to successfully reproduce anharmonicity and Fermi resonance splittings at a level of accuracy comparable to semiclassical simulations of thousands of trajectories. The method is tested on two different model systems with analytical potentials and implemented in conjunction with the first-principles molecular dynamics scheme to obtain the power spectrum for the carbon dioxide molecule.
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78.30.-j Infrared and Raman spectra
68.43.-h Chemisorption/physisorption: adsorbates on surfaces
63.20.Ry Anharmonic lattice modes

High-performance ab initio density matrix renormalization group method: Applicability to large-scale multireference problems for metal compounds

Yuki Kurashige and Takeshi Yanai

J. Chem. Phys. 130, 234114 (2009); http://dx.doi.org/10.1063/1.3152576 (21 pages) | Cited 25 times

Online Publication Date: 19 June 2009

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This article presents an efficient and parallelized implementation of the density matrix renormalization group (DMRG) algorithm for quantum chemistry calculations. The DMRG method as a large-scale multireference electronic structure model is by nature particularly efficient for one-dimensionally correlated systems, while the present development is oriented toward applications for polynuclear transition metal compounds, in which the macroscopic one-dimensional structure of electron correlation is absent. A straightforward extension of the DMRG algorithm is proposed with further improvements and aggressive optimizations to allow its application with large multireference active space, which is often demanded for metal compound calculations. Special efficiency is achieved by making better use of sparsity and symmetry in the operator and wave function representations. By accomplishing computationally intensive DMRG calculations, the authors have found that a large number of renormalized basis states are required to represent high entanglement of the electron correlation for metal compound applications, and it is crucial to adopt auxiliary perturbative correction to the projected density matrix during the DMRG sweep optimization in order to attain proper convergence to the solution. Potential energy curve calculations for the Cr2 molecule near the known equilibrium precisely predicted the full configuration interaction energies with a correlation space of 24 electrons in 30 orbitals [denoted by (24e,30o)]. The energies are demonstrated to be accurate to 0.6mEh (the error from the extrapolated best value) when as many as 10 000 renormalized basis states are employed for the left and right DMRG block representations. The relative energy curves for [Cu2O2]2+ along the isomerization coordinate were obtained from DMRG and other correlated calculations, for which a fairly large orbital space (32e,62o) is modeled as a full correlation space. The DMRG prediction nearly overlaps with the energy curve from the coupled cluster with singles, doubles, and perturbative triple [CCSD(T)] calculations, while the multireference complete active space self-consistent field (CASSCF) calculations with the small reference configuration (8e,8o) are found to overestimate the biradical character of the electronic state of [Cu2O2]2+ according to the one-electron density matrix analysis.
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31.15.am Relativistic configuration interaction (CI) and many-body perturbation calculations
31.15.bw Coupled-cluster theory
31.15.xr Self-consistent-field methods
31.50.-x Potential energy surfaces

Car–Parrinello density matrix search with a first principles fictitious electron mass method for electronic wave function optimization

Xiaosong Li, Christopher L. Moss, Wenkel Liang, and Yong Feng

J. Chem. Phys. 130, 234115 (2009); http://dx.doi.org/10.1063/1.3155082 (5 pages) | Cited 4 times

Online Publication Date: 19 June 2009

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In spite of its success in molecular dynamics and the advantage of being a first order propagation technique, the Car–Parrinello method and its variations have not been successful in self-consistent-field (SCF) wave function optimization due to slow convergence. In this article, we introduce a first principles fictitious mass scheme to weigh each individual density element differently and instantaneously. As an alternative to diagonalization in SCF, the Car–Parrinello scheme is implemented as a density matrix search method. Not only does the fictitious mass scheme developed herein allow a very fast SCF convergence, but also the Car–Parrinello density matrix search (CP-DMS) exhibits linear scaling with respect to the system size for alanine helical chain test molecules. The excellent performance of CP-DMS holds even for very challenging compact three-dimensional quantum particles. While the conventional diagonalization based SCF method has difficulties optimizing electronic wave functions for CdSe quantum dots, CP-DMS shows both smooth and faster convergence.
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31.15.ae Electronic structure and bonding characteristics
31.15.xr Self-consistent-field methods
73.21.La Quantum dots

Measurement of work in single-molecule pulling experiments

Alessandro Mossa, Sara de Lorenzo, Josep Maria Huguet, and Felix Ritort

J. Chem. Phys. 130, 234116 (2009); http://dx.doi.org/10.1063/1.3155084 (10 pages) | Cited 6 times

Online Publication Date: 19 June 2009

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A main goal of single-molecule experiments is to evaluate equilibrium free energy differences by applying fluctuation relations to repeated work measurements along irreversible processes. We quantify the error that is made in a free energy estimate by means of the Jarzynski equality when the accumulated work expended on the whole system (including the instrument) is erroneously replaced by the work transferred to the subsystem consisting of the sole molecular construct. We find that the error may be as large as 100%, depending on the number of experiments and on the bandwidth of the data acquisition apparatus. Our theoretical estimate is validated by numerical simulations and pulling experiments on DNA hairpins using optical tweezers.
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87.15.Cc Folding: thermodynamics, statistical mechanics, models, and pathways
87.14.gk DNA
87.15.Ya Fluctuations
back to top Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry

A reanalysis of the math 1A″−math 1A′ transition of CFBr

Benjamin S. Truscott, Nicola L. Elliott, and Colin M. Western

J. Chem. Phys. 130, 234301 (2009); http://dx.doi.org/10.1063/1.3149785 (9 pages) | Cited 1 time

Online Publication Date: 15 June 2009

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The laser induced fluorescence spectrum of the math 1A″−math 1A′ transition of CFBr is presented, with selected bands recorded at sub-Doppler resolution, allowing the rotational constants to be fully determined. Analysis of dispersed fluorescence spectra and the pattern of 79Br/81Br isotope splittings indicate that the origin must be shifted from previous assignments in the literature to 23 271.0 cm−1. This implies that only the lowest four vibrational levels in the math state have significant quantum yields for fluorescence, with all other levels strongly predissociated. Comparison with photofragment measurements implies that the math state is metastable, with a barrier to dissociation of ∼ 1000 cm−1.
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33.50.Dq Fluorescence and phosphorescence spectra
33.15.Mt Rotation, vibration, and vibration-rotation constants
33.20.Sn Rotational analysis
33.20.Tp Vibrational analysis
33.80.Gj Diffuse spectra; predissociation, photodissociation

Symmetry-adapted density matrix renormalization group calculations of the primary excited states of poly(para-phenylene vinylene)

Robert J. Bursill and William Barford

J. Chem. Phys. 130, 234302 (2009); http://dx.doi.org/10.1063/1.3149536 (16 pages) | Cited 3 times

Online Publication Date: 16 June 2009

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The Pariser–Parr–Pople model of π-conjugated electrons is solved by a three-block, symmetry-adapted density matrix renormalization group (DMRG) method for the light emitting polymer, poly(para-phenylene vinylene). The energies of the primary excited states are calculated. There is excellent agreement between theory and experiment when solid state screening is incorporated into the model parameters, enabling us to make an identification of the origin of the key spectroscopic features. Appendices describe important technical aspects of the three-block DMRG approach: Local Hilbert space efficiency and its relation to the matrix product formulation of the DMRG; an efficient computational procedure for constructing symmetry-adapted states for DMRG calculations; and correct superblock state targeting to ensure good convergence of the method.
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61.41.+e Polymers, elastomers, and plastics
71.20.Rv Polymers and organic compounds

Coupled-surface investigation of the photodissociation of NH3(math): Effect of exciting the symmetric and antisymmetric stretching modes

David Bonhommeau, Rosendo Valero, Donald G. Truhlar, and Ahren W. Jasper

J. Chem. Phys. 130, 234303 (2009); http://dx.doi.org/10.1063/1.3132222 (17 pages) | Cited 3 times

Online Publication Date: 16 June 2009

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Using previously developed potential energy surfaces and their couplings, non-Born–Oppenheimer trajectory methods are used to study the state-selected photodissociation of ammonia, prepared with up to six quanta of vibrational excitation in the symmetric (ν1) or antisymmetric (ν3) stretching modes of NH3(math). The predicted dynamics is mainly electronically nonadiabatic (that is, it produces ground electronic state amino radicals). The small probability of forming the excited-state amino radical is found, for low excitations, to increase with total energy and to be independent of whether the symmetric or antisymmetric stretch is excited; however some selectivity with respect to exciting the antisymmetric stretch is found when more than one quantum of excitation is added to the stretches, and more than 50% of the amino radical are found to be electronically excited when six quanta are placed in the antisymmetric stretch. These results are in contrast to the mechanism inferred in recent experimental work, where excitation of the antisymmetric stretch by a single quantum was found to produce significant amounts of excited-state products via adiabatic dissociation at total energies of about 7.0 eV. Both theory and experiment predict a broad range of translational energies for the departing H atoms when the symmetric stretch is excited, but the present simulations do not reproduce the experimental translational energy profiles when the antisymmetric stretch is excited. The sensitivity of the predicted results to several aspects of the calculation is considered in detail, and the analysis leads to insight into the nature of the dynamics that is responsible for mode selectivity.
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82.50.Hp Processes caused by visible and UV light
82.30.Cf Atom and radical reactions; chain reactions; molecule-molecule reactions
33.15.Mt Rotation, vibration, and vibration-rotation constants
33.80.Gj Diffuse spectra; predissociation, photodissociation
82.20.Gk Electronically non-adiabatic reactions
82.20.Bc State selected dynamics and product distribution
82.20.Kh Potential energy surfaces for chemical reactions

A laboratory and theoretical study of protonated carbon disulfide, HSCS+

M. C. McCarthy, P. Thaddeus, Jeremiah J. Wilke, and Henry F. Schaefer, III

J. Chem. Phys. 130, 234304 (2009); http://dx.doi.org/10.1063/1.3137057 (6 pages) | Cited 1 time

Online Publication Date: 16 June 2009

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The rotational spectrum of protonated carbon disulfide, HSCS+, has been detected in the centimeter-wave band in a molecular beam by Fourier transform microwave spectroscopy. Rotational and centrifugal distortion constants have been determined from ten transitions in the Ka = 0 ladder of the normal isotopic species, HS13CS+, and DSCS+. The present assignment agrees well with high-level coupled cluster calculations of the HSCS+ structure, which, like earlier work, predict this isomer to be the ground state on the HCS2+ potential energy surface; HCSS+, an isomer with C2v symmetry, is predicted to lie more than 20 kcal/mol higher in energy. Other properties of HSCS+ including its dipole moment, anharmonic vibrational frequencies, and infrared intensities have also been computed at the coupled cluster level of theory with large basis sets. Because carbon disulfide possesses a fairly large proton affinity, and because this nonpolar molecule may plausibly exist in astronomical sources, HSCS+ is a good candidate for detection with radio telescopes in the submillimeter band where the stronger b-type transitions of this protonated cation are predicted to lie.
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33.20.Bx Radio-frequency and microwave spectra
33.20.Ea Infrared spectra
33.20.Sn Rotational analysis
33.20.Tp Vibrational analysis
33.15.Mt Rotation, vibration, and vibration-rotation constants
31.15.bw Coupled-cluster theory
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