https://www.sandia.gov/~sjplimp/papers/jcompphys95.pdf

Fast parallel algorithms for short-range molecular dynamics

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.

Combined quantum-mechanics/molecular-mechanics (QM/MM) approaches have become the method of choice for modeling reactions in biomolecular systems. Quantum-mechanical (QM) methods are required for describing chemical reactions and other electronic processes, such as charge transfer or electronic excitation. However, QM methods are restricted to systems of up to a few hundred atoms. However, the size and conformational complexity of biopolymers calls for methods capable of treating up to several 100,000 atoms and allowing for simulations over time scales of tens of nanoseconds. This is achieved by highly efficient, force-field-based molecular mechanics (MM) methods. Thus to model large biomolecules the logical approach is to combine the two techniques and to use a QM method for the chemically active region (e.g., substrates and co-factors in an enzymatic reaction) and an MM treatment for the surroundings (e.g., protein and solvent). The resulting schemes are commonly referred to as combined or hybrid QM/MM methods. They enable the modeling of reactive biomolecular systems at a reasonable computational effort while providing the necessary accuracy.

QM/MM Methods for Biomolecular Systems

Colloidal nanoparticles are being intensely pursued in current nanoscience research. Nanochemists are often frustrated by the well-known fact that no two nanoparticles are the same, which precludes the deep understanding of many fundamental properties of colloidal nanoparticles in which the total structures (core plus surface) must be known. Therefore, controlling nanoparticles with atomic precision and solving their total structures have long been major dreams for nanochemists. Recently, these goals are partially fulfilled in the case of gold nanoparticles, at least in the ultrasmall size regime (1–3 nm in diameter, often called nanoclusters). This review summarizes the major progress in the field, including the principles that permit atomically precise synthesis, new types of atomic structures, and unique physical and chemical properties of atomically precise nanoparticles, as well as exciting opportunities for nanochemists to understand very fundamental science of colloidal nanoparticles (such as the s...

Atomically Precise Colloidal Metal Nanoclusters and Nanoparticles: Fundamentals and Opportunities

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

We investigated molecular interactions involved in the selective binding of several short peptides derived from phage-display techniques (8−12 amino acids, excluding Cys) to surfaces of Au, Pd, and Pd−Au bimetal. The quantitative analysis of changes in energy and conformation upon adsorption on even {111} and {100} surfaces was carried out by molecular dynamics simulation using an efficient computational screening technique, including 1000 explicit water molecules and physically meaningful peptide concentrations at pH = 7. Changes in chain conformation from the solution to the adsorbed state over the course of multiple nanoseconds suggest that the peptides preferably interact with vacant sites of the face-centered cubic lattice above the metal surface. Residues that contribute to binding are in direct contact with the metal surfaces, and less-binding residues are separated from the surface by one or two water layers. The strength of adsorption ranges from 0 to −100 kcal/(mol peptide) and scales with the s...

Nature of Molecular Interactions of Peptides with Gold, Palladium, and Pd-Au Bimetal Surfaces in Aqueous Solution

Density functional theory (DFT) electronic structure calculations were carried out to predict the structures and ground-state spectra for zinc complexes of porphyrin (ZnP), tetraazaporphyrin (ZnTAP), tetrabenzoporphyrin (ZnTBP), and phthalocyanine (ZnPc). All four porphyrins are found to have stable D4h structures. Structurally, meso-tetraaza substitutions significantly reduce the central hole in ZnTAP and ZnPc compared to ZnP. The excitation energies and oscillator strengths, computed by time-dependent DFT, provide a good account of the observed spectra of all four compounds. The TDDFT spectrum of ZnPc has a number of bands in the Soret region, in agreement with the experimental spectra that have been determined through spectral deconvolution. The low energy n→π* transition (Q′) reported for ZnPc, however, was not found in the computed spectrum. The effects of meso-tetraaza substitutions and tetrabenzo annulations on the spectrum of ZnP are discussed.

Ground state electronic structures and spectra of zinc complexes of porphyrin, tetraazaporphyrin, tetrabenzoporphyrin, and phthalocyanine: A density functional theory study

Although innumerable different ionic liquids are possible, even basic physical-property data, such as the density and melting point, exist only for relatively few. Derivation of melting point quantitative structure−property relationships (QSPRs) for energetic ionic liquids would therefore greatly aid in the molecular design of new compounds. A new class of ionic liquids, based on 1-substituted 4-amino-1,2,4-triazolium bromide and nitrate salts, were recently synthesized and their melting points and densities measured. We optimized the molecular geometries of the cations of the ionic liquids using ab initio quantum chemical methods. Melting point QSPRs were then derived from molecular orbital, thermodynamic, and electrostatic descriptors. Good correlations with the experimental data were found. The correlation coefficients for three-parameter melting point QSPRs and for one-parameter density QSPRs exceed 0.9. Although some of the descriptors that appear in our QSPRs were designed to describe chemical react...

Quantitative Structure-Property Relationships for Melting Points and Densities of Ionic Liquids

Simulated annealing methods have been used with the effective fragment potential to locate the lowest energy structures for the water clusters (H2O)n with n=6, 8, 10, 12, 14, 16, 18, and 20. The most successful method uses a local minimization on each Monte Carlo step. The effective fragment potential method yielded interaction energies in excellent agreement with those calculated at the ab initio Hartree–Fock level and was quite successful at predicting the same energy ordering as the higher-level perturbation theory and coupled cluster methods. Analysis of the molecular interaction energies in terms of its electrostatic, polarization, and exchange-repulsion/charge-transfer components reveals that the electrostatic contribution is the dominant term in determining the energy ordering of the minima on the (H2O)n potential energy surfaces, but that differences in the polarization and repulsion components can be important in some cases.

A study of water clusters using the effective fragment potential and Monte Carlo simulated annealing

Structure and properties of small quantum dots are of fundamental and practical interest due to a broad range of applications that exploit their optical tunability. Although previous experimental and theoretical investigation of very small semiconductor quantum dots have shown relative stability for clusters that deviate from the bulk, these materials have not been systematically characterized. In this work, structures of (CdSe)n (n = 1−37) clusters were studied using a combination of structure enumeration, Monte Carlo search, and local optimization. Binding energy (En and relative binding energy, ΔEn = n(En+1 − En), per CdSe unit) calculations using density functional theory (DFT) were carried out to identify the so-called magic size (MS, ΔEn > 0) quantum dots. (CdSe)n with n = 9, 12, 16, 18, 21, 24, 28, 32, 33, 35, and 36 were found to have high relative stability. MS structural motifs were investigated further for clusters up to (CdSe)54. In addition, time-dependent DFT calculations of one-photon absor...

Ruth Pachter

Papers

Nature of Molecular Interactions of Peptides with Gold, Palladium, and Pd-Au Bimetal Surfaces in Aqueous Solution

Ground state electronic structures and spectra of zinc complexes of porphyrin, tetraazaporphyrin, tetrabenzoporphyrin, and phthalocyanine: A density functional theory study

Quantitative Structure-Property Relationships for Melting Points and Densities of Ionic Liquids

A study of water clusters using the effective fragment potential and Monte Carlo simulated annealing

Understanding Structural and Optical Properties of Nanoscale CdSe Magic-Size Quantum Dots: Insight from Computational Prediction