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We have studied the photodissociation and recombination dynamics of diatomic anions in size-selected clusters by using simple model systems. The main purpose of the study is to provide a theoretical background for a better understanding of the salient features of the charge transfer and nonadiabatic transitions involved in the dynamics of solvated molecular ions. Calculations have been performed on the photodissociation and recombination of the model diatomic anion X2− embedded in N2O and CO2 clusters. The homonuclear diatomic anion is modeled as one-electron system consisting of two identical nuclei and an extra electron. The nuclear and electronic dynamics of X2− are treated quantum mechanically, while the motions of the solvent molecules are described by classical dynamics. Nonadiabatic theoretical calculations, in which the electronic and the nuclear dynamics are treated simultaneously, can reveal the importance of nonadiabatic effects by including intrinsically all electronic states. It is found that...

Previously we demonstrated the effectiveness of the recently developed q-jumping molecular dynamics simulation method (q-jumping MD) in vacuo for fast conformational searches and optimization purposes. In this work we attempt to further investigate the conformational searching capability of this new scheme by applying it to folding problems of helical peptides containing fully charged side chains in an implicit water. With a slightly modified q-jumping MD method using the all-atom empirical force field and its generalized Born solvation model, the current simulations at T=300 K all lead to fast helix folding with broad potential energy fluctuations, starting from their extended (linear) conformations. The present study demonstrates that this new MD scheme greatly enhances the rate of conformational changes, making it possible to explore low energy conformations of peptides in aqueous environments in a reasonably short time. Therefore, the all-atom based theoretical prediction of native solution structures of more challenging systems, such as helix bundles, β-sheets, and even small proteins may be a realistic possibility.

The structures and relaxation dynamics of I2− embedded in clusters of N2O molecules are studied by Monte Carlo and molecular dynamics simulations. The equilibrium structures of I2−(N2O)n clusters are obtained as a function of cluster size and the closing of the first solvation shell is found to occur at n=13, consistent with experimental observation. By comparing with the previous studies with different types of solvent molecules, it is found that differences in solvent polarity lead to noticeable changes in equilibrium structures and caging dynamics of clusters. N2O clusters tend to form more symmetric, spread-out solvent configurations, resulting in a weaker solvent electric field being exerted on the solute. The localization of the charge distribution for large internuclear separations happens for longer bond length and much more rapidly in I2−(N2O)16 than in I2−(CO2)16 clusters. Molecular dynamics simulations showed that I2− vibrational relaxation is very rapid, losing almost 90% of its internal energ...

Reaction dynamics on multiple electronic surfaces have been studied by performing quantum scattering calculations on a collinear A+BC→AB+C reaction. We propose model diabatic potentials with variable coupling potentials to examine the effect of the coupling between electronic states on the reaction. Time-independent quantum scattering theory based on diabatic representation provides a useful framework for treating reaction dynamics on coupled electronic states. Reaction probabilities calculated from the diabatic approach intrinsically include the effect of the presence of the excited state. We compared the results from the two-surface diabatic calculations with those using the single adiabatic surface alone. By varying the strength and the range of the diabatic coupling potential, we obtained a wide spectrum of reaction models. It is found that the reaction probabilities from the two-surface diabatic calculations showed noticeable differences from the single-surface adiabatic case. These results demonstra...

We report the results of molecular dynamics simulations of Langmuir monolayers of a semifluorinated hydrocarbon molecule F(CF2)12(CH2)18H. Our simulations show that highly ordered structures are formed at low temperature after quenching from a random structure at high temperature. The structural formation process of the monolayer is characterized by a decrease in the gauche defects of the hydrocarbon block and an increase in the global bond-orientational order throughout the chain molecules. It is also found that the monolayer structure consists of mixed orientations for the head-group-free F(CF2)12(CH2)18H molecule, with a slightly larger fraction for a hydrocarbon-down, fluorocarbon-up configuration.

A one-electron model for the photodissociation and recombination dynamics of a diatomic anion has been proposed. The main purpose of the study is to provide a simple model to better understand the effect of strong coupling between the solvent polarization and the extra charge in a system like I2−. The model diatomic anion consists of two identical nuclei and an extra electron whose dynamics are treated explicitly. The effect of solvent polarization is modeled by introducing an effective solvent field representing a nonequilibrium solvent configuration. Nonadiabatic theoretical calculations, in which the electronic and the nuclear dynamics are treated simultaneously, can reveal the importance of nonadiabatic effects by including intrinsically all the electronic states involved. It is found that a purely dissociative excited state can support recombination due to coupling of the anomalous charge distribution with the solvent polarization. The charge switching and the subsequent charge separation for the dis...

Numerical methods for solving kinetic equations for diffusion-influenced bimolecular reactions are presented for three cases. Finite difference method is used to solve diffusion-reaction equations for the pair distribution function. The kinetic equation for the concentration is evolved by the Runge–Kutta method with adaptive time step. The boundary doubling method is introduced to study long time dynamics, where the truncation problem of the infinite boundary is crucial. The above methods are applied, in the first case, to the classical Smoluchowski approach to a binary reaction with random initial condition and the results are compared with ones in two dimension. In the second case, an isolated pair recombination dynamics with a delta function initial condition is investigated and the results are compared with analytic expression in three dimension with spherical symmetry. A more complicated system with the hierarchical Smoluchowski approach with the Kirkwood superposition approximation is also investigated in the third case. The efficiency and the accuracy of the numerical calculations are examined against the asymptotic analytical solutions and a Monte Carlo simulation in one dimension.

A Monte Carlo (MC) simulation study of radical recombination dynamics in solution is presented. Random walks on a three‐dimensional lattice are used to simulate the diffusion of radical pairs initially prepared by photolysis. The survival probability as a function of time is calculated by the dynamical interpretation of the MC methods. For the dynamics of radical pairs, the interplay of the geminate and the bulk recombinations is important at high concentrations. In most previous simulations only the dynamics of isolated geminate pairs were considered. In our simulations such interplay is clearly demonstrated by studying the intermediate to long time dynamics of many radical pairs. We compare our results with the predictions of the diffusion and the kinetic theories to examine the validity of their approximations. For low concentrations, results of the simulations show good agreement with theoretical predictions and provide a microscopic basis for understanding the recombination process. But notable devia...

We report the results of molecular dynamics simulations of Langmuir monolayers of F(CF2)20F using both a united atom model and a recently developed anisotropic united atom model of the molecular force field. A comparison of our simulation results to experimental measures of the structure of Langmuir monolayers and lamellar crystals of F(CF2)20F indicates that the anisotropic united atom model provides the better representation. Simulations using the new model at 275 K generate an azimuthally disordered rotator phase monolayer, while simulations at 150 K generate a monolayer phase with azimuthal order. The relative intensities of peaks in the in‐plane structure function can be used to distinguish between the azimuthally ordered and disordered phases. Our simulations also predict, in agreement with experiment, that at large average areas per molecule the monolayer breaks up into islands that have a close‐packed structure at the center but are disordered at the periphery.

The potential energy surface for the Ar...CO van der Waals complex is calculated by the supermolecular approach using fourth‐order Mo/ller–Plesset perturbation theory (MP4) with a large basis set containing bond functions. The Hartree–Fock potentials are repulsive for all configurations considered. The second‐order correlation energy accounts for most of the dispersion interactions. The MP4 potential energy surface is characterized by a global minimum of −96.3 cm−1 at Re=3.743 A and θe=98° with the argon atom closer to the oxygen end. There are no local minima in the linear configurations. The linear configurations provide shallow barriers at both of the carbon and oxygen ends. The barrier height at the oxygen end is 13.6 cm−1 at R=4.04 A, while that at the carbon end is 28.0 cm−1 at R=4.58 A. The rovibrational energies of Ar...CO are calculated by the discrete variable representation method. The Ar...CO complex undergoes large amplitude hindered rotations in the ground state with a zero‐point energy of 2...

We use a minimal model to study the effects of the upper electronic states on the rate of a charge transfer reaction. The model consists of three ions and an electron, all strung on a line. The two ions at the ends of the structure are held fixed, but the middle ion and the electron are allowed to move in one dimension, along the line joining them. The system has two bound states, one in which the electron ties the movable ion to the fixed ion at the left, and the other in which the binding takes place to the fixed ion at the right. The transition between these bound states is a charge transfer reaction. We use the flux–flux correlation function theory to perform two calculations of the rate constant for this reaction. In one we obtain numerically the exact rate constant. In the other we calculate the exact rate constant for the case when the reaction proceeds exclusively on the ground adiabatic state. The difference between these calculations gives the magnitude of the nonadiabatic effects. We find that the nonadiabatic effects are fairly large even when the gap between the ground and the excited adiabatic state substantially exceeds the thermal energy. The rate in the nonadiabatic theory is always smaller than that of the adiabatic one. Both rate constants satisfy the Arrhenius formula. Their activation energies are very close but the nonadiabatic one is always higher. The nonadiabatic preexponential is smaller, due to the fact that the upper electronic state causes an early recrossing of the reactive flux. The description of this reaction in terms of two diabatic states, one for reactants and one for products, is not always adequate. In the limit when nonadiabaticity is small, we need to use a third diabatic state, in which the electron binds to the moving ion as the latter passes through the transition state; this is an atom transfer process. The reaction changes from an atom transfer to an electron transfer, as nonadiabaticity is increased.

We report calculations, based on the Cai–Rice theory [J. Chem. Phys. 96, 6229 (1992)], of the relative importance of chain–surface and chain–chain interactions for the occurrence of the tilting transition in expanded Langmuir monolayers. The interaction between amphiphile molecules, and that between an amphiphile molecule and the surface, are described by Lennard‐Jones potentials. It is found that for a reasonable set of interaction parameters the structure of the expanded monolayer supports a collective tilt, and that the existence of a nonzero amphiphile chain–surface interaction plays an important role in determining the collective tilt. However, over much of the range of surface density of interest, an expanded monolayer with nonzero collective tilt is unstable with respect to one with zero collective tilt and a smaller separation of the molecules. The existence or nonexistence of a collective tilt in the monolayer is very sensitive to the relative magnitude of the amphiphile chain–amphiphile chain an...

We report the results of new molecular dynamics simulations of liquid‐supported monolayers of perfluorinated and partially fluorinated amphiphiles such as F(CF2)11COOH and F(CF2)10CH2COOH. The new simulations include a representation of the superhelical structure of the perfluoroalkane portion of the amphiphile chain in the intramolecular potential energy; in addition, the calculation of the collective tilt angle of the monolayer is improved to include the effect of the azimuthal distribution of individual molecular tilt angles. The results of the simulations are in agreement with the available experimental data. In particular, the packing structure and the observed breakup of the homogeneous ordered monolayer into ordered islands with the same collective tilt of the molecules are correctly predicted as are the very small collective tilt angles. These new results remove the discrepancy between predicted and observed collective tilt angles reported in our previous papers [J. Chem. Phys. 96, 1352, 4735 (1992)].

We report the results of molecular‐dynamics simulations of monolayers of CF3(CF2)nCOOH supported on water, using a pseudoatom model for the amphiphile and a continuum model for the water surface. The calculations explore the influence of temperature, chain length and surface density on the packing structure of the monolayer. These fluorinated amphiphiles support a much lower gauche configuration concentration than do their corresponding hydrocarbon analogs and, of course, have different intermolecular interactions. The most striking results of the simulations are as follows. (i) Even and odd members of the series CF3(CF2)nCOOH, under the same external constraints (T=300 K, π=0.16 dyn cm−1), pack in monolayers in which the tilt is, respectively, towards next‐nearest neighbors and towards nearest neighbors. (ii) At constant surface pressure a monolayer of CF3(CF2)10COOH is predicted to undergo a transition between 325 and 350 K, in which the direction of the tilt changes from towards next‐nearest neighbors ...

We report the results of molecular dynamics simulations of liquid‐supported monolayers of three partially fluorinated amphiphile molecules, namely CF3(CF2)9CH2COOH, CF3(CF2)6CH2(CF2)3COOH, and CF3(CF2)6(CH2)4COOH. These studies were undertaken to provide information on the interplay between molecular flexibility and the packing structure in a monolayer so as to better interpret the results of recent experiments. The qualitative aspects of the predictions of the simulations are consistent with the recent experimental data for monolayers of CF3(CF2)9CH2COOH [S. W. Barton, A. Goudot, O. Boulassa, F. Rondelez, B. Lin, F. Novak, A. Acero, and S. A. Rice, J. Chem. Phys. 96, xxx (1992)]. In particular, the observed breakup of the homogeneous ordered monolayer into ordered islands with the same collective tilt of the molecules is correctly predicted, and the fact that the collective tilt angle is small is correctly predicted. However, the experimental and theoretical values of the tilt angles are not in quantitat...

We describe an extension of the generalized regular solution model of a liquid supported monolayer of long chain amphiphile molecules in which chain–chain interactions outside the surface layer are included as well as the effects of chain flexibility in the surface and in the space above the surface layer. Self‐consistent equations for the distribution of molecular configurations and the surface density and pressure are derived by using a model free energy expression. Two first order fluid–fluid phase transitions are predicted for three different models for the chain–chain interactions outside the surface. These transitions are identified as the observed gas‐to‐‘‘liquid‐expanded’’ and liquid‐expanded‐to‐‘‘liquid‐condensed’’ phase transitions in a monolayer, the first to be associated with the condensation of the in‐surface portions of the amphiphile chains and the second to be associated with the condensation of the out of surface portions of the amphiphile chains. This interpretation comes from the obser...

We propose a theoretical model, based on a free‐energy density‐functional formalism, for the uniaxial compression‐induced hexagonal‐to‐distorted‐hexagonal structural phase transition in Langmuir monolayers. It is shown that the experimentally observed distorted‐hexagonal structure is associated with collective tilting, relative to the normal to the surface, of the rod‐like molecules.

The non-relativistic and relativistic potential energy surfaces (PESs) of the symmetric and asymmetric reaction paths of Si(100)-2×1 oxidations by atomic oxygen were theoretically explored. Although only the singlet PES turned out to exist as a major channel leading to "on-dimer" product, both the singlet and triplet PESs leading to "on-top" products are attractive. The singlet PESs leading to the two surface products were found to be the singlet combinations (open-shell singlet) of the low-lying triplet state of surface silicon dimer and the ground (3)P state of atomic oxygen. The triplet state of the "on-top" product can also be formed by the ground singlet state of the surface silicon dimer and the same (3)P oxygen. The attractive singlet PESs leading to the "on-dimer" and "on-top" products made neither the intersystem crossings from triplet to singlet PES nor high energy (1)D of atomic oxygen necessary. Rather, the low-lying triplet state of surface silicon dimer plays an important role in the initial oxidations of silicon surface.

We propose and test numerically a scheme for controlling the bond distance in a diatomic molecule that requires the use of a single chirped pulse. The laser prepares a superposition state of both nuclear and electronic degrees of freedom, where the main character of the electronic wave function is that of an excited dissociative state. The main limitation of the scheme is the need of ultra broadband pulses, where the bandwidth must be of the order of the dissociation energy to achieve large bond elongations. The scheme can be used to deform the bond during the laser excitation to an arbitrary large and constant value, or to allow slow time-dependent bond elongations. Additionally, the scheme can be used to prepare highly excited vibrational wave packets in the ground potential after the pulse is switched off, at the expense of losing some population that dissociates. These wave packets are initially localized at the outer well of the potential, at energies controllable by the excitation process.

We study the photodissociation of ICl(-) under moderately strong (TW/cm(2)) and short (below picosecond) laser pulses. Using a single resonant pump pulse, the photodissociation spectra shows two barely overlapping bands corresponding to Frank-Condon excitation and dissociation in two electronic states. By adding a nonresonant stronger control pulse we show that (1) the photodissociation bands can be blueshifted and (2) the asymptotic state of the fragments depends on the chosen pulse sequence. If the pump pulse precedes the control pulse or the control pulse straddles the pump pulse, the outgoing wave packet has components in the two dissociation channels, whereas if the control pulse precedes the pump pulse, the photodissociation proceeds selectively in a single channel.

Selective population transfer in electronic states of dissociative molecular systems is illustrated by adopting a control scheme based on Stark-chirped rapid adiabatic passage (SCRAP). In contrast to the discrete N-level system, dynamical Stark shift is induced in a more complex manner in the molecular electronic states. Wavepacket dynamics on the light-induced potentials, which are determined by the detuning of the pump pulse, can be controlled by additional Stark pulse in the SCRAP scheme. Complete population transfer can be achieved by either lowering the energy barrier along the adiabatic passage or placing the initial wavepacket on a well-defined dressed state suitable for the control. The determination of the pulse sequence is sufficient for controlling population transfer to the target state.

We demonstrate that molecular dynamics simulations using the force scaling method with a Nose–Hoover-chain thermostat are capable of generating multicanonical ensembles. The frequency distribution of the Nose–Hoover-chain is broad enough to handle the energy dependent force scaling factor over a wide potential energy range, when three independent Nose–Hoover thermostats corresponding to the three orthogonal directions are attached to each particle. The performance of this method has been tested by reproducing various equilibrium properties of one-dimensional model potential, an Ar13 cluster, and a flexible water model.