Volume 135, Issue 11, 21 September 2011

We report the photoelectron spectrum of anionic Nacetylproline, (NAcPro)^{−}, measured with 3.49 eV photons. This spectrum, which consists of a band centered at an electron binding energy of 1.4 eV and a higher energy spectral tail, confirms that Nacetylproline forms a valence anion in the gas phase. The neutrals and anions of NAcPro were also studied computationally at the B3LYP/631++G(d,p) level. Based on the calculations, we conclude that the photoelectron spectrum is due to anions which originated from proton transfer induced by electron attachment to the π^{*} orbital localized at the acetyl group of NAcPro. We also characterized the energetics of reaction paths leading to pyrrolidine ring opening in the anionic NAcPro. These data suggest that electron induced decomposition of peptides/proteins comprising proline strongly depends on the presence of proton donors in the close vicinity to the proline residue.
 ARTICLES

 Theoretical Methods and Algorithms

Periodic force induced stabilization or destabilization of the denatured state of a protein
View Description Hide DescriptionWe have studied the effects of an external sinusoidal force in protein folding kinetics. The externally applied force field acts on the each amino acid residues of polypeptide chains. Our simulation results show that mean protein folding time first increases with driving frequency and then decreases passing through a maximum. With further increase of the driving frequency the mean folding time starts increasing as the noiseinduced hoping event (from the denatured state to the native state) begins to experience many oscillations over the mean barrier crossing time period. Thus unlike onedimensional barrier crossing problems, the external oscillating force field induces both stabilization or destabilization of the denatured state of a protein. We have also studied the parametric dependence of the folding dynamics on temperature, viscosity, nonMarkovian character of bath in presence of the external field.

Quantum and semiclassical theories for nonadiabatic transitions based on overlap integrals related to fast degrees of freedom
View Description Hide DescriptionAlternative treatments of quantum and semiclassical theories for nonadiabaticdynamics are presented. These treatments require no derivative couplings and instead are based on overlap integrals between eigenstates corresponding to fast degrees of freedom, such as electronic states. Derived from mathematical transformations of the Schrdinger equation, the theories describe nonlocal characteristics of nonadiabatic transitions. The idea that overlap integrals can be used for nonadiabatic transitions stems from an article by Johnson and Levine [Chem. Phys. Lett.13, 168 (1972)]10.1016/00092614(72)800691. Furthermore, overlap integrals in pathintegral form have been recently made available by Schmidt and Tully [J. Chem. Phys.127, 094103 (2007)]10.1063/1.2757170 to analyze nonadiabatic effects in thermal equilibrium systems. The present paper expands this idea to dynamic problems presented in pathintegral form that involve nonadiabatic semiclassical propagators. Applications to onedimensional nonadiabatic transitions have provided excellent results, thereby verifying the procedure. In principle these theories that are presented can be applied to multidimensional systems, although numerical costs could be quite expensive.

Coarsegraining Brownian motion: From particles to a discrete diffusion equation
View Description Hide DescriptionWe study the process of coarsegraining in a simple model of diffusion of Brownian particles. At a detailed level of description, the system is governed by a Brownian dynamics of noninteracting particles. The coarselevel is described by discrete concentration variables defined in terms of Delaunay cells. These coarse variables obey a stochastic differential equation that can be understood as a discrete version of a diffusionequation. We study different models for the two basic building blocks of this equation which are the free energy function and the diffusion matrix. The free energy function is shown to be nonadditive due to the overlapping of cells in the Delaunay construction. The diffusion matrix is state dependent in principle, but for nearequilibrium situations it is shown that it may be safely evaluated at the equilibrium value of the concentration field.

Generalized Langevin dynamics of a nanoparticle using a finite element approach: Thermostating with correlated noise
View Description Hide DescriptionA direct numerical simulation (DNS) procedure is employed to study the thermal motion of a nanoparticle in an incompressible Newtonian stationary fluid medium with the generalized Langevin approach. We consider both the Markovian (white noise) and nonMarkovian (OrnsteinUhlenbeck noise and MittagLeffler noise) processes. Initial locations of the particle are at various distances from the bounding wall to delineate wall effects. At thermal equilibrium, the numerical results are validated by comparing the calculated translational and rotational temperatures of the particle with those obtained from the equipartition theorem. The nature of the hydrodynamic interactions is verified by comparing the velocity autocorrelation functions and mean square displacements with analytical results. Numerical predictions of wall interactions with the particle in terms of mean square displacements are compared with analytical results. In the nonMarkovian Langevin approach, an appropriate choice of colored noise is required to satisfy the powerlaw decay in the velocity autocorrelation function at long times. The results obtained by using nonMarkovian MittagLeffler noise simultaneously satisfy the equipartition theorem and the longtime behavior of the hydrodynamiccorrelations for a range of memory correlation times. The OrnsteinUhlenbeck process does not provide the appropriate hydrodynamiccorrelations. Comparing our DNS results to the solution of an onedimensional generalized Langevin equation, it is observed that where the thermostat adheres to the equipartition theorem, the characteristic memory time in the noise is consistent with the inherent time scale of the memory kernel. The performance of the thermostat with respect to equilibrium and dynamic properties for various noise schemes is discussed.

A semiclassical study of the thermal conductivity of low temperature liquids
View Description Hide DescriptionThe conventional classical energy current autocorrelation function has been extended into a quantum mechanical version and then approximated by the linearized semiclassical initial value representation approach. Comparison of the thermal conductivity to simulation results shows that about 15% quantum correction to the classical molecular dynamics results for liquid neon are quantitatively predicted. For liquid parahydrogen the quantum effects are sufficiently large that the linearized semiclassical approach is only 20% accurate, while for both liquid He^{4} and He^{3} the thermal conductivity disagrees by a factor of 2, although exchange effects appear to play a minor role.

Zero field splitting of the chalcogen diatomics using relativistic correlated wavefunction methods
View Description Hide DescriptionThe spectrum arising from the (π*)^{2} configuration of the chalcogen dimers, namely, the X _{2}1, a2, and b0^{+} states, is calculated using wavefunction theory based methods. Twocomponent (2c) and fourcomponent (4c) multireference configuration interaction (MRCI) and Fockspace coupled cluster (FSCC) methods are used as well as twostep methods spinorbit complete active space perturbation theory at 2nd order (SOCASPT2) and spinorbit difference dedicated configuration interaction (SODDCI). The energy of the X _{2}1 state corresponds to the zerofield splitting of the ground state spin triplet. It is described with high accuracy by the 2 and 4component methods in comparison with experiment, whereas the twostep methods give about 80% of the experimental values. The b0^{+} state is well described by 4cMRCI, SOCASPT2, and SODDCI, but FSCC fails to describe this state and an intermediate Hamiltonian FSCC ansatz is required. The results are readily rationalized by a twoparameter model; Δε, the π* spinor splitting by spinorbit coupling and K, the exchange integral between the and the spinors with, respectively, angular momenta 1 and −1. This model holds for all systems under study with the exception of Po_{2}.

Comparing different protocols of temperature selection in the parallel tempering method
View Description Hide DescriptionParallel tempering Monte Carlo simulations have been applied to a variety of systems presenting rugged freeenergy landscapes. Despite this, its efficiency depends strongly on the temperature set. With this query in mind, we present a comparative study among different temperature selection schemes in three latticegas models. We focus our attention in the constant entropy method (CEM), proposed by Sabo et al. In the CEM, the temperature is chosen by the fixed difference of entropy between adjacent replicas. We consider a method to determine the entropy which avoids numerical integrations of the specific heat and other thermodynamic quantities. Different analyses for first and secondorder phase transitions have been undertaken, revealing that the CEM may be an useful criterion for selecting the temperatures in the parallel tempering.

Distributionfunction approach to free energy computation
View Description Hide DescriptionConnections are explored between the free energy difference of two systems and the microscopic distribution functions of the energy difference. On the basis of a rigorous relationship between the energy distribution functions and the free energy, the scheme of error minimization is introduced to derive accurate and simple methods of free energy computation. A set of distributionfunction approaches are then examined against model systems, and the newly derived methods exhibit stateofart performance. It is shown that the notion of error minimization is powerful to improve the free energy calculation using distribution functions.

Exploring the free energy surfaces of clusters using reconnaissance metadynamics
View Description Hide DescriptionA new approach is proposed for exploring the lowenergy structures of small to mediumsized aggregates of atoms and molecules. This approach uses the recently proposed reconnaissance metadynamics method [G. A. Tribello, M. Ceriotti, and M. Parrinello. Proc. Natl. Acad. Sci. U.S.A.107(41), 17509 (2010)10.1073/pnas.1011511107] in tandem with collective variables that describe the average structure of the coordination sphere around the atoms/molecules. We demonstrate this method on both LennardJones and waterclusters and show how it is able to quickly find the global minimum in the potential energy surface, while exploring the finite temperature free energysurface.

Multiple time scale molecular dynamics for fluids with orientational degrees of freedom. I. Microcanonical ensemble
View Description Hide DescriptionWe propose a new approach to eliminate the resonance instabilities inherent in multiple time step molecular dynamics simulations. The approach is developed within the microcanonical ensemble on the basis of an energyconstrained technique in the presence of orientational degrees of freedom. While the single and standard multiscale methods are restricted to small time steps of 5 and 8 fs, respectively, it is shown in simulations of water that the algorithms we have derived postpone the appearance of the instabilities to larger steps of about 16 fs. Such steps are close to the upper theoretical limit of 20 fs peculiar to the microcanonical ensemble and can be used without affecting static and dynamical properties.

Comparing ab initio densityfunctional and wave function theories: The impact of correlation on the electronic density and the role of the correlation potential
View Description Hide DescriptionThe framework of ab initio densityfunctional theory(DFT) has been introduced as a way to provide a seamless connection between the Kohn–Sham (KS) formulation of DFT and wavefunction based ab initio approaches [R. J. Bartlett, I. Grabowski, S. Hirata, and S. Ivanov, J. Chem. Phys.122, 034104 (2005)10.1063/1.1809605]. Recently, an analysis of the impact of dynamical correlation effects on the density of the neon atom was presented [K. Jankowski, K. Nowakowski, I. Grabowski, and J. Wasilewski, J. Chem. Phys.130, 164102 (2009)10.1063/1.3116157], contrasting the behaviour for a variety of standard density functionals with that of ab initio approaches based on secondorder MøllerPlesset (MP2) and coupled clustertheories at the singlesdoubles (CCSD) and singlesdoubles perturbative triples [CCSD(T)] levels. In the present work, we consider ab initiodensity functionals based on secondorder manybody perturbation theory and coupled clusterperturbation theory in a similar manner, for a range of small atomic and molecular systems. For comparison, we also consider results obtained from MP2, CCSD, and CCSD(T) calculations. In addition to this density based analysis, we determine the KS correlation potentials corresponding to these densities and compare them with those obtained for a range of ab initiodensity functionals via the optimized effective potential method. The correlation energies, densities, and potentials calculated using ab initioDFT display a similar systematic behaviour to those derived from electronic densities calculated using ab initiowave functiontheories. In contrast, typical explicit density functionals for the correlation energy, such as VWN5 and LYP, do not show behaviour consistent with this picture of dynamical correlation, although they may provide some degree of correction for already erroneous explicitly densitydependent exchangeonly functionals. The results presented here using orbital dependent ab initiodensity functionals show that they provide a treatment of exchange and correlation contributions within the KS framework that is more consistent with traditional ab initiowave function based methods.
 Advanced Experimental Techniques

Producing translationally cold, groundstate CO molecules
View Description Hide DescriptionCarbon monoxide molecules in their electronic, vibrational, and rotational ground state are highly attractive for trapping experiments. The optical or ac electric traps that can be envisioned for these molecules will be very shallow, however, with depths in the submilliKelvin range. Here, we outline that the required samples of translationally cold CO (X^{1}Σ^{+}, v′′ = 0, N′′ = 0) molecules can be produced after Stark deceleration of a beam of laserprepared metastable CO (a^{3}Π_{1}) molecules followed by optical transfer of the metastable species to the ground statevia perturbed levels in the A^{1}Π state. The optical transfer scheme is experimentally demonstrated and the radiative lifetimes and the electric dipole moments of the intermediate levels are determined.
 Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry

Valence anions of Nacetylproline in the gas phase: Computational and anion photoelectron spectroscopic studies
View Description Hide DescriptionWe report the photoelectron spectrum of anionic Nacetylproline, (NAcPro)^{−}, measured with 3.49 eV photons. This spectrum, which consists of a band centered at an electron binding energy of 1.4 eV and a higher energy spectral tail, confirms that Nacetylproline forms a valence anion in the gas phase. The neutrals and anions of NAcPro were also studied computationally at the B3LYP/631++G(d,p) level. Based on the calculations, we conclude that the photoelectron spectrum is due to anions which originated from proton transfer induced by electron attachment to the π^{*} orbital localized at the acetyl group of NAcPro. We also characterized the energetics of reaction paths leading to pyrrolidine ring opening in the anionic NAcPro. These data suggest that electron induced decomposition of peptides/proteins comprising proline strongly depends on the presence of proton donors in the close vicinity to the proline residue.

Efficient longrange collisional energy transfer between the E0_{ g } ^{+}(^{3} P _{2}) and D0_{ u } ^{+}(^{3} P _{2}) ionpair states of I_{2}, induced by H_{2}O, observed using highresolution Fourier transform emission spectroscopy
View Description Hide DescriptionUsing highresolution Fourier transform emission techniques, we have resolved rotational structure in the D0_{ u } ^{+}(^{3} P _{2}) → X0_{ g } ^{ + } emission following collisional transfer from the E0_{ g } ^{+}(^{3} P _{2}) state in I_{2}. The P:R branch ratios in the E0_{ g } ^{+}(^{3} P _{2}) → D0_{ u } ^{+}(^{3} P _{2}) transfer are found to vary enormously with v _{ E } and v _{ D }. We show that the observed intensities are all consistent with the transfer being dominated by longrange, nearresonant collisions with residual H_{2}O. Unequal P:R branch ratios in the E0_{ g } ^{+}(^{3} P _{2}) → A1_{ u } emission have been shown to result from mixing of the E0_{ g } ^{+}(^{3} P _{2}) and β1_{ g }(^{3} P _{2}) states via Ωuncoupling.

Spectral characterization in a supersonic beam of neutral chlorophyll a evaporated from spinach leaves
View Description Hide DescriptionThe observation of the light absorption of neutral biomolecules has been made possible by a method implemented for their preparation in the gas phase, in supersonically cooled molecular beams, based upon the work of Focsa et al.[C. Mihesan, M. Ziskind, B. Chazallon, E. Therssen, P. Desgroux, S. Gurlui, and C. Focsa, Appl. Surf. Sci.253, 1090 (2006)]10.1016/j.apsusc.2006.01.082. The biomolecules diluted in frozen water solutions are entrained in the gas plume of evaporated ice generated by an infrared optical parametric oscillators (OPO) laser tuned close to its maximum of absorption, at ∼3 μm. The biomolecules are then picked up in the flux of a supersonic expansion of argon. The method was tested with indole dissolved in water. The excitation spectrum of indole was found cold and large clusters of indole with water were observed up to n = 75. Frozen spinach leaves were examined with the same method to observe the chlorophyll pigments. The Q_{y} band of chlorophyll a has been observed in a pump probe experiment. The Q_{y} bands of chlorophyll a is centred at 647 nm, shifted by 18 nm from its position in toluene solutions. The ionization threshold could also be determined as 6.1 ± 0.05 eV.

Resonant twophoton ionization spectroscopy of jetcooled OsN: 520–418 nm
View Description Hide DescriptionThe optical transitions of supersonically cooled OsN have been investigated in the range from 19 200 to 23 900 cm^{−1} using resonant twophotonionization spectroscopy. More than 20 vibronic bands were observed, 17 of which were rotationally resolved and analyzed. The ground state is confirmed to be ^{2}Δ_{5/2}, deriving from the 1σ^{2} 2σ^{2} 1π^{4} 1δ^{3} 3σ^{2} electronic configuration. The X ^{2}Δ_{5/2}ground state rotational constant for ^{192}Os^{14}N was found to be B_{0} = 0.491921(34) cm^{−1}, giving r_{0} = 1.62042(6) Å (1σ error limits). The observed bands were grouped into three band systems with Ω^{′} = 7/2 and four with Ω^{′} = 3/2, corresponding to the three ^{2}Φ_{7/2} and four ^{2}Π_{3/2} states expected from the 1σ^{2} 2σ^{2} 1π^{4} 1δ^{3} 3σ^{1} 2π^{1} and 1σ^{2} 2σ^{2} 1π^{4} 1δ^{2} 3σ^{2} 2π^{1} electronic configurations. In addition, two interacting upper states with Ω^{′} = 5/2 were observed, one of which is thought to correspond to a 1σ^{2} 2σ^{2} 1π^{3} 1δ^{3} 3σ^{2} 2π^{1}, ^{2}Δ_{5/2} state. Spectroscopic constants are reported for all of the observed states, and comparisons to related molecules are made. The ionization energy of OsN is estimated as IE(OsN) = 8.80 ± 0.06 eV.

Consistent assignment of the vibrations of monosubstituted benzenes
View Description Hide DescriptionWe investigate the consistency of the labeling and assignments of the vibrations of the monosubstituted benzenes in the electronic ground state. In doing so, we also identify some inconsistencies in the labeling of the benzene modes. We commence by investigating the behavior of the benzene vibrations as one hydrogen is replaced by an artificial atomic substituent of increasing mass via quantum chemical calculations; the wavenumber variations with mass give insight into the assignments. We also examine how well the monohalobenzene vibrations can be described in terms of the benzene ones: consistent with some recent studies, we conclude that this is futile in a significant number of cases. We then show that “isotopic wavenumbers” obtained by artificially changing the mass of the fluorine atom in fluorobenzene are in very good agreement with the wavenumbers obtained via explicit calculation for the relevant monohalobenzene (chlorobenzene, bromobenzene, and iodobenzene) vibrations. As a consequence, we propose that the vibrations of monofluorobenzene be used as the basis for labelling the vibrational assignments of monosubstituted benzenes. As well as the four monohalobenzenes, we also apply this approach to the vibrations of aniline, toluene, benzonitrile, phenylacetylene, phenylphosphine, and nitrobenzene. This has allowed a much more consistent picture of the vibrational assignments to be obtained across ten monosubstituted benzenes.

Shattering dissociation in highenergy molecular collisions between nitrate esters
View Description Hide DescriptionWe present ab initiomolecular dynamics simulations of headon collisions between ethyl nitrate molecules at collisional energies from 200 to 1200 kJ/mol. Above a threshold energy, an increasing fraction of the collisions led to rapid dissociation on impact—“shattering.” The probability of the shattering dissociation was derived from the quasiclassical trajectories sampling the initial vibrational motion at T _{ vib } = 300 K. Even for the zero impact parameter and a fixed orientation considered, the observed dissociation probability exhibited a wide spread (much larger than kT _{ vib }) as a function of the collisionenergy. This is attributed to variations in the initial vibrational phase. We propose a closedform expression for the energydependent dissociation probability that captures the dependence on the phase and use it to analyze the probability of the shattering dissociation of a larger nitrate ester, pentaerythritol tetranitrate.

A quantum reaction dynamics study of the translational, vibrational, and rotational motion effects on the HD + reaction
View Description Hide DescriptionTimedependent, quantum reactiondynamics wavepacket approach is employed to investigate the impacts of the translational, vibrational, and rotational motion on the → H_{2}D^{+} + H_{2}reaction using the XieBraamsBowman potential energy surface [Z. Xie, B. J. Braams, and J. M. Bowman, J. Chem. Phys.122, 224307 (2005)]10.1063/1.1927529. We treat this five atom reaction with a sevendegreeoffreedom model by fixing one Jacobi and one torsion angle related to at the lowest saddle point geometry of the potential energy surface. The initial state selected reaction probabilities show that the rotational excitations of H^{+}H_{2} greatly enhance the reactivity with the reaction probabilities increased double at high rotational states compared to the ground state. However, the vibrational excitations of hinder the reactivity. The ground statereaction probability shows no reaction threshold for this exoergic reaction, and as the translational energy increases, the reaction probability decreases. Furthermore, reactive resonances and zero point energy play very important roles on the reactiondynamics. The obtained integral cross section has the character of an exoergic reaction without a threshold: it decreases with the translational energy increasing. The calculated thermal rate constants using this sevendegreeoffreedom model are in agreement with a later experiment measurement.

Nonadiabatic quantum dynamics of C(^{1} D)+H_{2}→CH+H: Coupledchannel calculations including RennerTeller and Coriolis terms
View Description Hide DescriptionThe RennerTeller (RT) coupledchanneldynamics for the reaction has been investigated for the first time, considering the first two singlet states and of CH_{2} dissociating into the products and RT couplings, evaluated through the ab initio matrix elements of the electronic angular momentum. We have obtained initialstateresolved probabilities, cross sections and thermal rate constants via the real wavepacket method for both coupled electronic states. In contrast to the system, RT effects tend to reduce probabilities, cross sections, and rate constants in the low energy range compared to BornOppenheimer (BO) ones, due to the presence of a repulsive RT barrier in the effective potentials and to longlived resonances. Furthermore, contrary to BO results, the rate constants have a positive temperature dependence in the 100–400 K range. The twostate RT rate constant at 300 K, lower than the BO one, remains inside the error bars of the experimental value.