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

I. Introduction: Conceptual vs Fundamental andComputational Aspects of DFT1793II. Fundamental and Computational Aspects of DFT 1795A. The Basics of DFT: The Hohenberg−KohnTheorems1795B. DFT as a Tool for Calculating Atomic andMolecular Properties: The Kohn−ShamEquations1796C. Electronic Chemical Potential andElectronegativity: Bridging Computational andConceptual DFT1797III. DFT-Based Concepts and Principles 1798A. General Scheme: Nalewajski’s ChargeSensitivity Analysis1798B. Concepts and Their Calculation 18001. Electronegativity and the ElectronicChemical Potential18002. Global Hardness and Softness 18023. The Electronic Fukui Function, LocalSoftness, and Softness Kernel18074. Local Hardness and Hardness Kernel 18135. The Molecular Shape FunctionsSimilarity 18146. The Nuclear Fukui Function and ItsDerivatives18167. Spin-Polarized Generalizations 18198. Solvent Effects 18209. Time Evolution of Reactivity Indices 1821C. Principles 18221. Sanderson’s Electronegativity EqualizationPrinciple18222. Pearson’s Hard and Soft Acids andBases Principle18253. The Maximum Hardness Principle 1829IV. Applications 1833A. Atoms and Functional Groups 1833B. Molecular Properties 18381. Dipole Moment, Hardness, Softness, andRelated Properties18382. Conformation 18403. Aromaticity 1840C. Reactivity 18421. Introduction 18422. Comparison of Intramolecular ReactivitySequences18443. Comparison of Intermolecular ReactivitySequences18494. Excited States 1857D. Clusters and Catalysis 1858V. Conclusions 1860VI. Glossary of Most Important Symbols andAcronyms1860VII. Acknowledgments 1861VIII. Note Added in Proof 1862IX. References 1865

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Conceptual density functional theory.

The halogen bond occurs when there is evidence of a net attractive interaction between an electrophilic region associated with a halogen atom in a molecular entity and a nucleophilic region in another, or the same, molecular entity. In this fairly extensive review, after a brief history of the interaction, we will provide the reader with a snapshot of where the research on the halogen bond is now, and, perhaps, where it is going. The specific advantages brought up by a design based on the use of the halogen bond will be demonstrated in quite different fields spanning from material sciences to biomolecular recognition and drug design.

The Halogen Bond

: The unpolarized absorption and circular dichroism spectra of the fundamental vibrational transitions of the chiral molecule, 4-methyl-2-oxetanone, are calculated ab initio. Harmonic force fields are obtained using Density Functional Theory (DFT), MP2, and SCF methodologies and a 5S4P2D/3S2P (TZ2P) basis set. DFT calculations use the Local Spin Density Approximation (LSDA), BLYP, and Becke3LYP (B3LYP) density functionals. Mid-IR spectra predicted using LSDA, BLYP, and B3LYP force fields are of significantly different quality, the B3LYP force field yielding spectra in clearly superior, and overall excellent, agreement with experiment. The MP2 force field yields spectra in slightly worse agreement with experiment than the B3LYP force field. The SCF force field yields spectra in poor agreement with experiment.The basis set dependence of B3LYP force fields is also explored: the 6-31G* and TZ2P basis sets give very similar results while the 3-21G basis set yields spectra in substantially worse agreements with experiment. jg

Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields

This article provides an up-to-date perspective on the use of anion-exchange membranes in fuel cells, electrolysers, redox flow batteries, reverse electrodialysis cells, and bioelectrochemical systems (e.g. microbial fuel cells). The aim is to highlight key concepts, misconceptions, the current state-of-the-art, technological and scientific limitations, and the future challenges (research priorities) related to the use of anion-exchange membranes in these energy technologies. All the references that the authors deemed relevant, and were available on the web by the manuscript submission date (30th April 2014), are included.

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Anion-exchange membranes in electrochemical energy systems

In the present study we have introduced a new scheme for chemical bond analysis by combining the Extended Transition State (ETS) method [Theor. Chim. Acta 1977, 46, 1] with the Natural Orbitals for Chemical Valence (NOCV) theory [J. Phys. Chem. A 2008, 112, 1933; J. Mol. Model. 2007, 13, 347]. The ETS-NOCV charge and energy decomposition scheme based on the Kohn−Sham approach makes it not only possible to decompose the deformation density, Δρ, into the different components (such as σ, π, δ, etc.) of the chemical bond, but it also provides the corresponding energy contributions to the total bond energy. Thus, the ETS-NOCV scheme offers a compact, qualitative, and quantitative picture of the chemical bond formation within one common theoretical framework. Although, the ETS-NOCV approach contains a certain arbitrariness in the definition of the molecular subsystems that constitute the whole molecule, it can be widely used for the description of different types of chemical bonds. The applicability of the ETS-...

A Combined Charge and Energy Decomposition Scheme for Bond Analysis

Two sets of orbitals are derived, directly connected to the Nalewajski-Mrozek valence and bond-multiplicity indices: Localized Orbitals from the Bond-Multiplicity Operator (LOBO) and the Natural Orbitals for Chemical Valence (NOCV). LOBO are defined as the eigenvectors of the bond-multiplicity operator. The expectation value of this operator is the corresponding bond index. Thus, the approach presented here allows for a discussion of localized orbitals and bond multiplicity within one common framework of chemical valence theory. Another set of orbitals discussed in the present work, NOCV, are defined as eigenvectors of the overall chemical valence operator. This set of orbitals can be especially useful for a description of bonding in transition metal complexes, as it allows for separation of the deformation density contributions originating from the ligand --> metal donation and metal --> ligand back-donation.

Bond orbitals from chemical valence theory

Natural orbitals for chemical valence (NOCV) are defined as the eigenvectors of the chemical valence operator defined by Nalewajski et al.; they decompose the deformation density (differential density, Deltarho) into diagonal contributions. NOCV were used in a description of the chemical bond between the organometallic fragment and the ligand in example transition-metal complexes: heme-CO ([FeN(5)C(20)H(15)]-CO), [Ni-diimine hydride]-ethylene ([N;N-Ni-H]-C(2)H(4), N;N = -NH-CH-CH-NH-), and [Ni(NH(3))(3)]-CO. DFT calculations were performed using gradient-corrected density functional theory (DFT) in the fragments resolution, using the fragment/ligand Kohn-Sham orbitals as a basis set in calculations for the whole fragment-ligand complex. It has been found that NOCV lead to a very compact description of the fragment-ligand bond, with only a few orbitals exhibiting non-zero eigenvalues. Results of NOCV analysis, compared with Mulliken populations analysis and Zigler-Rauk interaction-energy decomposition, demonstrate that the use of the natural valence orbitals allows for a separation of the sigma-donation and pi-back-donation contributions to the ligand-fragment bond. They can be also useful in comparison of these contributions in different complexes.

Natural orbitals for chemical valence as descriptors of chemical bonding in transition metal complexes

Donor–Acceptor Properties of Ligands from the Natural Orbitals for Chemical Valence

The recent Hartree-Fock (HF) difference approach to the chemical valence indices (ionic and covalent), formulated in the framework of the pair-density matrix, is implemented within the Kohn-Sham (KS) density functional theory (DFT). The valence numbers are quadratic in terms of displacements of the molecular spin-resolved charge-and-bond-order (CBO) matrix elements, relative to values in the separated atoms limit (SAL). It is shown that the global valence represents a generalized “distance” quantity measuring a degree of similarity between the two CBO matrices: the molecular and SAL. Numerical values for typical molecules exhibiting single and multiple bonds demonstrate that the KS orbitals give rise to these new bond valences in good agreement with both chemical and HF predictions. This KS bond multiplicity analysis is applied to the chemisorption system including the allyl radical and a model surface cluster of molybdenum oxide. It is concluded that the quadratic valence analysis represents a valuable procedure for extracting useful chemical information from standard DFT calculations. © 1997 John Wiley & Sons, Inc.

Artur Michalak

Papers

A Combined Charge and Energy Decomposition Scheme for Bond Analysis

Bond orbitals from chemical valence theory

Natural orbitals for chemical valence as descriptors of chemical bonding in transition metal complexes

Donor–Acceptor Properties of Ligands from the Natural Orbitals for Chemical Valence

Two-electron valence indices from the Kohn-Sham orbitals