Chemistry and Biochemistry

The technique of molecular beam photofragment translational spectroscopy has been used to study the dissociation of acetone following S 1 ←S 0 ͑248 nm͒ and S 2 ←S 0 ͑193 nm͒ excitation. Excitation at 248 nm resulted in the production of CH 3 and CH 3 CO with 14.2Ϯ1.0 kcal/mole on average of the available energy appearing as translation of the photofragments. Comparison of the measured ͗E T ͘ with values reported at 266 nm suggest that the energy partitioning is dominated by the exit barrier caused by an avoided crossing on the potential energy surface. A substantial fraction ͑30Ϯ4%͒ of the nascent acetyl radicals from the primary dissociation contain sufficient energy to undergo spontaneous secondary decomposition. From the onset of the truncation of the CH 3 CO P(E T ) a threshold of 17.8Ϯ3.0 kcal/mole for the dissociation of the acetyl radical has been determined in agreement with recent results on the photodissociation of acetyl chloride. The translational energy release in the dissociation of CH 3 CO closely matches the experimentally determined exit barrier. At 193 nm the only observed dissociation pathway was the formation of two methyl radicals and carbon monoxide. On average ϳ38% of the available energy is found in product translation suggesting that significant internal energy resides in the nascent CH 3 fragments consistent with the results of Hall et al. ͓J. Chem. Phys. 94, 4182 ͑1991͔͒. We conclude that the dynamics and energy partitioning for dissociation at 193 nm is similar to that at 248 nm.

We investigate pairwise electrostatic interaction methods and show that there are viable computationally efficient ͑O͑N͒͒ alternatives to the Ewald summation for typical modern molecular simulations. These methods are extended from the damped and cutoff-neutralized Coulombic sum originally proposed by Wolf et al. ͓J. Chem. Phys. 110, 8255 ͑1999͔͒. One of these, the damped shifted force method, shows a remarkable ability to reproduce the energetic and dynamic characteristics exhibited by simulations employing lattice summation techniques. Comparisons were performed with this and other pairwise methods against the smooth particle-mesh Ewald summation to see how well they reproduce the energetics and dynamics of a variety of molecular simulations.

We discuss whether or not local information on the potential energy surface embodied by the distribution of unstable instantaneous normal modes can be used to predict the hopping rates and barrier heights for Zwanzig's model of self-diffusion ͓R. Zwanzig, J. Chem. Phys. 79, 4507 ͑1983͔͒ in simple liquids. Results from a set of simulations of Lennard-Jones particles done at multiple temperatures and densities are presented. These simulations show that the theories which predict diffusive barrier heights from the distribution of imaginary frequencies are questionable. This discrepancy is due to the presence of imaginary frequency instantaneous normal modes which persist into the solid phase. Model systems are used to show that imaginary frequency instantaneous normal modes ͑and even those at the top of the barrier along that mode͒ are not necessarily indicators of diffusive barrier crossing as used in Zwanzig's model. These false barriers are shown to be the cause of all of the imaginary frequency zero-force modes in the solid as well as many of the imaginary frequency modes in the high-density super-cooled liquid. We therefore dispute their utility as predictors of barrier heights or hopping rates in related liquid systems. We also show that attempts to separate the modes that are truly diffusive from those with false barriers using a frequency cutoff or local information on the potential energy surface are not successful at removing all of the non-barrier modes. © 1997 American Institute of Physics. ͓S0021-9606͑97͒50336-9͔

We present a method for estimating the hopping rate for Zwanzig's model of self-diffusion in liquids ͓R. Zwanzig, J. Chem. Phys. 79, 4507 ͑1983͔͒. To obtain this estimate, we introduce the cage correlation function which measures the rate of change of atomic surroundings, and associate the long-time decay of this function with the basin hopping rate for diffusion. Results from a set of simulations on Lennard-Jones particles are presented. A simple analytic model for the diffusion constant in supercooled and normal liquids that is based on estimates of the activation energy obtained via the cage correlation function is derived. We discuss the breakdown of Zwanzig's hopping mechanism for mass transport as well as the low temperature behavior of the self-diffusion constant on rough potential energy surfaces.

We report on the direct observation of stretched exponential relaxation in low-temperature monatomic Lennard-Jones systems which were cooled slowly from the liquid phase to form crystals with a large number of defects. We use the cage correlation function [ E. Rabani, J. D. Gezelter, and B. J. Berne, J. Chem. Phys. 107, 6867 (1997)] which measures changes in atomic surroundings to observe the stretched exponential relaxations. We obtain a distribution of hopping rates assuming that the origin of the Kohlrausch-Williams-Watts law is from static disorder in the distribution of barrier heights.

We have examined the effects on the fundamental behavior of the dynamics of applying constraints to control the aphysical flow of zero-point energy in classical trajectories of molecular systems. Test calculations on the popular Henon-Heiles potential surface show that these costraints can induce physically undesirable effects in the dynamics, e.g., changing quasiperiodic motion (characterized by a few discrete frequencies) into chaotic motion (characterized by a continuous distribution of frequencies).

We extend the cage correlation function method for calculating the hopping rate in Zwanzig's model of self-diffusion in liquids ͓R. Zwanzig, J. Chem. Phys. 79, 4507 ͑1983͔͒ to liquids composed of polyatomic molecules. We find that the hopping rates defined by the cage correlation function drop to zero below the melting transition and we obtain excellent agreement with the diffusion constants calculated via the Einstein relation in liquids, solids, and supercooled liquids of CS 2 . We also investigate the vibrational density of states of inherent structures in liquids which have rough potential energy surfaces, and conclude that the normal mode density of states at the local minima are not the correct vibrational frequencies for use in Zwanzig's model when it is applied to CS 2 .

Calculations of the microcanonical isomerization rates for vibrationally excited ketene are presented. The calculations utilize the quantum reactive scattering methodology of absorbing boundary conditions with a discrete variable representation to obtain the cumulative reaction probability for one form of ketene to isomerize via the oxirene intermediate, and were carried out with model 1-, 2-, and 3-degree-of-freedom potential energy surfaces constructed using ab initio data. Significant differences are seen in the energy dependent features of the microcanonical rate for the single mode and multi-mode potentials; e.g., the single mode potential exhibits tunneling resonances with widths of around 1 cm Ϫ1 , while the calculations involving more than one degree of freedom have additional resonant features that have widths around 10 cm Ϫ1 and also exhibit non-Breit-Wigner resonant line shapes. This suggests that many of the resonance features are best described as Feshbach ͑energy transfer, or dynamical͒ resonances that result because of a strongly bent region on the multi-mode potential energy surfaces. The calculated rates show reasonable qualitative agreement with the experimental results of Lovejoy and Moore ͓J. Chem. Phys. 98, 7846 ͑1993͔͒.

Calculations of the microcanonical dissociation rate for vibrationally excited ketene on the first excited triplet surface (T 1 ) are presented. The calculations utilize the quantum reactive scattering methodology of absorbing boundary conditions ͑ABC͒ with a discrete variable representation ͑DVR͒ to obtain the cumulative reaction probability for dissociation over the barrier. Model 1-and 2-degree of freedom potential energy surfaces for the T 1 surface were obtained by fitting to the best available ab initio structures, energies, and frequencies. The dissociation rates in these reduced-dimensionality calculations give good overall agreement with the experimentally measured rates, although the steplike features seen in the experiments are washed out by the tunneling through the narrow barrier predicted in the ab initio calculations. Further model calculations reveal that a barrier frequency of approximately 50-100i cm Ϫ1 is required to recover the step structure seen experimentally, which suggests that there is either another transition state region on the T 1 surface farther out towards the product channel, or that there is surface-hopping dynamics taking place between the T 1 and S 0 ketene potential energy surfaces, or that the ab initio barrier frequency is simply too large.

Preface OOPSE is a new molecular dynamics simulation program which is capable of efficiently integrating equations of motion for atom types with orientational degrees of freedom (e.g. "sticky" atoms and point dipoles). Transition metals can also be simulated using the embedded atom method (EAM) potential included in the code. Parallel simulations are carried out using the force-based decomposition method. Simulations are specified using a very simple C-based metadata language. A number of advanced integrators are included, and the basic integrator for orientational dynamics provides substantial improvements over older quaternion-based schemes.

The absolute free energies of several ice polymorphs were calculated using thermodynamic integration. These polymorphs are predicted by computer simulations using a variety of common water models to be stable at low pressures. A recently discovered ice polymorph that has as yet only been observed in computer simulations (Ice-i) was determined to be the stable crystalline state for all the water models investigated. Phase diagrams were generated, and phase coexistence lines were determined for all of the known low-pressure ice structures. Additionally, potential truncation was shown to play a role in the resulting shape of the free energy landscape.

We present calculations of the bulk modulus, heat capacity, and the period of the breathing mode for spherical nanoparticles following excitation by ultrafast laser pulses. The bulk modulus and heat capacities both exhibit clear transitions upon bulk melting of the particles. Equilibrium calculations of the heat capacity show that the melting transition is sharper and occurs at a lower temperature than one would observe from an ultrafast experiment. We also observe an intriguing splitting in the low-frequency spectra of the nanoparticles and analyze this splitting in terms of Lamb's classical theory of elastic spheres. We conclude that the particles either (1) melt during the observation period following laser excitation or (2) melt an outer shell while maintaining a crystalline core. Both mechanisms for melting are commensurate with our observations.

Radiofrequency pulses specifically tailored to generate a particular frequency profile are increasingly used in high-resolution NMR spectroscopy and magnetic resonance imaging. The search for these "designer" pulses makes use of an entire family of numerical techniques, ranging from the Fourier transform approximation (I, 2) through the standard gradient descent methods, linearization of the Bloch equations (3), average Hamiltonian theory (4). simulated annealing (5-7). and evolutionary methods (8). We propose here the use of neural networks (9-14) to address this important problem; this technique has already been successfully used in NMR for spectral recognition problems ( 15 ).

We present a new method for introducing stable nonequilibrium velocity and temperature gradients in molecular dynamics simulations of heterogeneous systems. This method extends earlier reverse nonequilibrium molecular dynamics ͑RNEMD͒ methods which use momentum exchange swapping moves. The standard swapping moves can create nonthermal velocity distributions and are difficult to use for interfacial calculations. By using nonisotropic velocity scaling ͑NIVS͒ on the molecules in specific regions of a system, it is possible to impose momentum or thermal flux between regions of a simulation while conserving the linear momentum and total energy of the system. To test the method, we have computed the thermal conductivity of model liquid and solid systems as well as the interfacial thermal conductivity of a metal-water interface. We find that the NIVS-RNEMD improves the problematic velocity distributions that develop in other RNEMD methods.

We have developed a new isobaric-isothermal (NPT) algorithm which applies an external pressure to the facets comprising the convex hull surrounding the system. A Langevin thermostat is also applied to the facets to mimic contact with an external heat bath. This new method, the "Langevin Hull", can handle heterogeneous mixtures of materials with different compressibilities. These systems are problematic for traditional affine transform methods. The Langevin Hull does not suffer from the edge effects of boundary potential methods, and allows realistic treatment of both external pressure and thermal conductivity due to the presence of an implicit solvent. We apply this method to several different systems including bare metal nanoparticles, nanoparticles in an explicit solvent, as well as clusters of liquid water. The predicted mechanical properties of these systems are in good agreement with experimental data and previous simulation work.

This review summarizes the development of monolithic materials, including both organic and inorganic polymers, according mainly to the papers published in the past two years. Due to their good permeability, fast mass transfer, high stability, and their ease of modification, such materials have been widely used in microcolumn separation systems, not only as stationary phases for CEC and capillary HPLC, but also as substances for sample concentration and enzyme reactor. All the research results demonstrate that monolithic materials in microseparation systems can be expected to play an increasingly important role in the analysis of complex samples.

Glycidyl methacrylate (GMA) and ethylene dimethacrylate (EDMA) were used to synthesize a monolithic capillary column containing reactive epoxy groups. Glutaraldehyde was introduced and linked to the monolith after a process of amination. An aqueous solution of commercial carrier ampholytes (CAs, Ampholine) was focused in such a polymer column. The primary amino groups of CAs reacted with glutaraldehyde along the capillary. CAs were immobilized at different positions in the column according to their isoelectric points (pI), resulting in a monolithic immobilized pH gradient (M-IPG). Isoelectric focusing (IEF) was performed without CAs in such an M-IPG column. Due to the covalent attachment of the CAs this M-IPG can be repeatedly used after its preparation. Good stability, linearity, and reproducibility were obtained.

Monolithic materials were prepared in capillaries by in situ polymerization of acrylamide, glycidyl methacrylate, and N,N'-methylenebisacrylamide in the presence of 1,4-butanediol, dodecanol, and DMSO as porogens. With Ampholine attached to the surface of the porous monolith via epoxide groups, a monolithic-IPG (M-IPG) was formed and showed good mechanical and chemical stability. With such a column immobilized by Ampholine 3.5-10, IEF-MIX 3.6-9.3 was separated and good linearity was obtained. The CIEF behavior of M-IPG was evinced by comparing the current with that in the open tubular capillary. In addition, the protein mixtures excreted from lung cancer cells of rats were analyzed with such a new M-IPG column.

Monolith with immobilized pH gradient (M-IPG) is a novel separation matrix for amphoteric substances, such as peptides and proteins. To improve the properties of the newly designed column, efforts were made to optimize the preparation procedure, including the concentrations of the monomers, glycidyl methacrylate (GMA) and ethylene glycol dimethacrylate (EDMA), as well as the kinds of porogens, which led to a monolith with improved permeability, uniformity and continuity. In addition, different diamines, including ethylenediamine, 1,3-diaminopropane, 1,4-diaminobutane and 1,5-diaminopentane, were subjected to aminate the polymer, and the last two exhibited excellent reactivity with epoxy on the polymer surface, which could obviously make the immobilization of pH gradient facilitated. Under the optimal conditions, a simple method to prepare M-IPG column with narrow pH gradient was developed with commercial carrier ampholytes (CAs) solution. Such columns were applied into the analysis of proteins and peptides, and showed the improved resolution compared to the traditional one with a wide pH distribution.