Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

6.2.2. Definition of Effective Properties 3064 6.3. Response Properties to Magnetic Fields 3066 6.3.1. Nuclear Shielding 3066 6.3.2. Indirect Spin−Spin Coupling 3067 6.3.3. EPR Parameters 3068 6.4. Properties of Chiral Systems 3069 6.4.1. Electronic Circular Dichroism (ECD) 3069 6.4.2. Optical Rotation (OR) 3069 6.4.3. VCD and VROA 3070 7. Continuum and Discrete Models 3071 7.1. Continuum Methods within MD and MC Simulations 3072

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Quantum mechanical continuum solvation models.

6. Rehybridization of the Acceptor (RICT) 3908 7. Planarization of the Molecule (PICT) 3909 III. Fluorescence Spectroscopy 3909 A. Solvent Effects and the Model Compounds 3909 1. Solvent Effects on the Spectra 3909 2. Steric Effects and Model Compounds 3911 3. Bandwidths 3913 4. Isoemissive Points 3914 B. Dipole Moments 3915 C. Radiative Rates and Transition Moments 3916 1. Quantum Yields and Radiationless Deactivation Processes 3916

Structural Changes Accompanying Intramolecular Electron Transfer: Focus on Twisted Intramolecular Charge-Transfer States and Structures

▪ Abstract Proton-coupled electron transfer (PCET) is an important mechanism for charge transfer in a wide variety of systems including biology- and materials-oriented venues. We review several are...

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Proton-Coupled Electron Transfer

Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics.

Time-resolved emission measurements of the solute coumarin 153 (C153) are used to probe the time dependence of solvation in 24 common solvents at room temperature. Significant improvements in experimental time resolution ({approx}100 fs instrument response) as well as corresponding improvements in analysis methods provide confidence that all of the spectral evolution (including both the inertial and the diffusive parts of the response) are observed in these measurements. Extensive data concerning the steady-state solvatochromism of C153, coupled to an examination of the effects of vibrational relaxation, further demonstrate that the spectral dynamics being observed accurately monitor the dynamics of nonspecific solvation. Comparisons to theoretical predictions show that models based on the dielectric response of the pure solvent provide a semiquantitative understanding of the dynamics observed. 156 refs., 26 figs., 5 tabs.

Subpicosecond Measurements of Polar Solvation Dynamics: Coumarin 153 Revisited

THE timescale of the response of solvent molecules to electronic rearrangement of solute molecules has a critical influence on the rates of chemical reactions in liquids1–10. In particular, if the solvent cannot adapt quickly enough to this rearrangement as the reactants pass through the transition state, the evolving products may recross the free-energy barrier, reducing the reaction rate. Computer simulations have shown11–18 that the response of a solvent to a change in solute charge distribution is strongly bimodal: there is an initial ultrafast response owing to inertial (mainly libra-tional) motions of the solvent molecules, followed by a slow component owing to diffusive motions. Water seems to be by far the 'fastest' solvent studied so far: simulations predict that well over half of the solvation response for atomic solutes is inertial, happening on a timescale of about 20 femtoseconds12,13. The presence of this ultrafast component implies that solvent friction plays an important role in many aqueous charge-transfer processes9,10,19–21. Experimental verification of this prediction has been lacking, however, in part because of the difficulty of obtaining sufficient time resolution. Here we present experimental measurements of the ultrafast solvation dynamics of a coumarin salt in water. When considered in conjunction with computer simulations, our results demonstrate that a solvent response on a timescale faster than 50 fs can dominate aqueous solvation dynamics.

Femtosecond solvation dynamics of water

Solvation dynamics in polar liquids have been examined using the probe molecule coumarin 153 (Cu153) and picosecond spectroscopic techniques. Steady‐state absorption and fluorescence spectra of Cu153 as a function of solvent show that the frequency of the electronic spectrum of this probe provides a convenient measure of solvation energetics. Both nonspecific dipolar and to a smaller degree H‐bonding solute–solvent interactions are involved. Time‐correlated single photon counting was used to observe time‐dependent shifts of the fluorescence spectrum of Cu153 in a variety of alcohols, propylene carbonate, and N‐methylpropionamide solvents as a function of temperature. These time‐dependent spectral shifts provide a direct measure of the time dependence of the solvation process. Theoretical models that treat the solvent as a dielectric continuum do not adequately account for the observed solvation dynamics. In the solvents studied, such theories predict a single exponential shift of the fluorescence spectrum...

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Picosecond solvation dynamics of coumarin 153: The importance of molecular aspects of solvation

The dynamics of solvation in polar liquids

Two of the more fundamental ways in which molecules change their behavior when they are dissolved are that they can begin to exchange energy with the surrounding liquid and they can induce their surroundings to rearrange so as to provide a significant stabilizing influence. The first of these is typified by the process of vibrational population relaxation of a vibrationally hot species. The second conceptcritical to solution chemistryis what is known as solvation. Both of these processes are sufficiently fundamental that one would really like to know, at the most mechanical and molecular level possible, just what events are required in order to make them happen. But how difficult is it going to be to extract such molecular detail from the complicated many-body dynamics? The most microscopic level of understanding one could ever hope to possess might seem far removed from the finely detailed dynamical information which is available routinely for individual isolated molecules and for molecule−molecule colli...

Mark Maroncelli

Papers

Subpicosecond Measurements of Polar Solvation Dynamics: Coumarin 153 Revisited

Femtosecond solvation dynamics of water

Picosecond solvation dynamics of coumarin 153: The importance of molecular aspects of solvation

The dynamics of solvation in polar liquids

Nonreactive Dynamics in Solution: The Emerging Molecular View of Solvation Dynamics and Vibrational Relaxation