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

Molecular self-assembly is the spontaneous association of molecules under equilibrium conditions into stable, structurally well-defined aggregates joined by noncovalent bonds. Molecular self-assembly is ubiquitous in biological systems and underlies the formation of a wide variety of complex biological structures. Understanding self-assembly and the associated noncovalent interactions that connect complementary interacting molecular surfaces in biological aggregates is a central concern in structural biochemistry. Self-assembly is also emerging as a new strategy in chemical synthesis, with the potential of generating nonbiological structures with dimensions of 1 to 10(2) nanometers (with molecular weights of 10(4) to 10(10) daltons). Structures in the upper part of this range of sizes are presently inaccessible through chemical synthesis, and the ability to prepare them would open a route to structures comparable in size (and perhaps complementary in function) to those that can be prepared by microlithography and other techniques of microfabrication.

Molecular self-assembly and nanochemistry: A chemical strategy for the synthesis of nanostructures

Mean-field electronic structure methods like Hartree–Fock, semilocal density functional approximations, or semiempirical molecular orbital (MO) theories do not account for long-range electron correlation (London dispersion interaction). Inclusion of these effects is mandatory for realistic calculations on large or condensed chemical systems and for various intramolecular phenomena (thermochemistry). This Review describes the recent developments (including some historical aspects) of dispersion corrections with an emphasis on methods that can be employed routinely with reasonable accuracy in large-scale applications. The most prominent correction schemes are classified into three groups: (i) nonlocal, density-based functionals, (ii) semiclassical C6-based, and (iii) one-electron effective potentials. The properties as well as pros and cons of these methods are critically discussed, and typical examples and benchmarks on molecular complexes and crystals are provided. Although there are some areas for furthe...

Dispersion-Corrected Mean-Field Electronic Structure Methods.

Kohn-Sham density functional theory (DFT) has become established as an indispensable tool for investigating aqueous systems of all kinds, including those important in chemistry, surface science, biology, and the earth sciences. Nevertheless, many widely used approximations for the exchange-correlation (XC) functional describe the properties of pure water systems with an accuracy that is not fully satisfactory. The explicit inclusion of dispersion interactions generally improves the description, but there remain large disagreements between the predictions of different dispersion-inclusive methods. We present here a review of DFT work on water clusters, ice structures, and liquid water, with the aim of elucidating how the strengths and weaknesses of different XC approximations manifest themselves across this variety of water systems. Our review highlights the crucial role of dispersion in describing the delicate balance between compact and extended structures of many different water systems, including the liquid. By referring to a wide range of published work, we argue that the correct description of exchange-overlap interactions is also extremely important, so that the choice of semi-local or hybrid functional employed in dispersion-inclusive methods is crucial. The origins and consequences of beyond-2-body errors of approximate XC functionals are noted, and we also discuss the substantial differences between different representations of dispersion. We propose a simple numerical scoring system that rates the performance of different XC functionals in describing water systems, and we suggest possible future developments.

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Perspective: How good is DFT for water?

Silica Surface Features and Their Role in the Adsorption of Biomolecules: Computational Modeling and Experiments / Albert Rimola;Dominique Costa;Mariona Sodupe;Jean-François Lambert;Piero Ugliengo. In: CHEMICAL REVIEWS. ISSN 0009-2665. STAMPA. 113:6(2013), pp. 4216-4313. Original Citation: Silica Surface Features and Their Role in the Adsorption of Biomolecules: Computational Modeling and Experiments

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Silica Surface Features and Their Role in the Adsorption of Biomolecules: Computational Modeling and Experiments

B3LYP is the most widely used density-functional theory (DFT) approach because it is capable of accurately predicting molecular structures and other properties. However, B3LYP is not able to reliably model systems in which noncovalent interactions are important. Here we present a method that corrects this deficiency in B3LYP by using dispersion-correcting potentials (DCPs). DCPs are utilized by simple modifications to input files and can be used in any computational package that can read effective-core potentials. Therefore, the technique requires no programming. DCPs (developed for H, C, N, and O) produce the best results when used in conjunction with 6-31+G(2d,2p) basis sets. The B3LYP-DCP approach was tested on the S66, S22, and HSG-A benchmark sets of noncovalently interacting dimers and trimers and was found to, on average, significantly outperform almost all other DFT-based methods that were designed to treat van der Waals interactions. Users of B3LYP who wish to model systems in which noncovalent interactions (viz., steric repulsion, hydrogen bonding, π-stacking) are present, should consider B3LYP-DCP.

A (Nearly) Universally Applicable Method for Modeling Noncovalent Interactions Using B3LYP.

We recently showed that dispersion-correcting potentials (DCPs), atom-centered Gaussian-type functions developed for use with B3LYP (J. Phys. Chem. Lett. 2012, 3, 1738-1744) greatly improved the ability of the underlying functional to predict non-covalent interactions. However, the application of B3LYP-DCP for the {\beta}-scission of the cumyloxyl radical led a calculated barrier height that was over-estimated by ca. 8 kcal/mol. We show in the present work that the source of this error arises from the previously developed carbon atom DCPs, which erroneously alters the electron density in the C-C covalent-bonding region. In this work, we present a new C-DCP with a form that was expected to influence the electron density farther from the nucleus. Tests of the new C-DCP, with previously published H-, N- and O-DCPs, with B3LYP-DCP/6-31+G(2d,2p) on the S66, S22B, HSG-A, and HC12 databases of non-covalently interacting dimers showed that it is one of the most accurate methods available for treating intermolecular interactions, giving mean absolute errors (MAEs) of 0.19, 0.27, 0.16, and 0.18 kcal/mol, respectively. Additional testing on the S12L database of complexation systems gave an MAE of 2.6 kcal/mol, showing that the B3LYP-DCP/6-31+G(2d,2p) approach is one of the best-performing and feasible methods for treating large systems dominated by non-covalent interactions. Finally, we showed that C-C making/breaking chemistry is well-predicted using the newly developed DCPs. In addition to predicting a barrier height for the {\beta}-scission of the cumyloxyl radical that is within 1.7 kcal/mol of the high-level value, application of B3LYP-DCP/6-31+G(2d,2p) to 10 databases that include reaction barrier heights and energies, isomerization energies and relative conformation energies gives performance that is amongst the best of all available dispersion-corrected density-functional theory approaches.

Extension of the B3LYP - Dispersion-Correcting Potential Approach to the Accurate Treatment of both Inter- and Intramolecular Interactions

The structural and energetic effects due to gold adatoms and/or gold surface vacancies in ethylthiol/Au(111) self-assembled monolayers (SAMs) in the high-density regime have been studied The stability of these SAM structures was evaluated based on adsorption and surface energies that allow a direct comparison of structures with different compositions We have found another energetically more favorable $c(4\ifmmode\times\else\texttimes\fi{}2)$ structure that includes two adatoms These adatoms may initially be taken from the gold surface creating vacancies However our results indicate that the SAM may further stabilize by stepwise filling the surface vacancies A plausible mechanism for the formation of gold vacancy islands, as seen in experiments during the growth of high-density domains, arises from this stabilization process The best structure including two adatoms agrees with many structural data derived from the experiments In particular, the simulated scanning tunneling microscope (STM) image exhibits a zigzag modulation that is characteristic of the $\ensuremath{\delta}$ phase frequently found in STM experiments

Mechanism for phase transitions and vacancy island formation in alkylthiol/Au(111) self-assembled monolayers based on adatom and vacancy-induced reconstructions

We recently demonstrated that dispersion-correcting potentials (DCPs), which are atom-centered Gaussian-type functions that were developed for use with B3LYP (Torres and DiLabio in J Phys Chem Lett 3:1738–1744, 2012), greatly improved the ability of the underlying functional to predict non-covalent interactions. However, the recent application of the B3LYP–DCP approach to study the β-scission of the cumyloxyl radical led to a calculated barrier height that was over-estimated by ca. 8 kcal/mol. We demonstrate in the present work that the source of this error arises from the previously developed carbon atom DCPs, which erroneously alters the electron density in the C–C covalent-bonding region. In this work, we developed a new C-DCP with a form that was expected to less strongly influence the electron density in the covalent bonding region. Tests of the new C-DCP, in conjunction with previously published H-, N-, and O-DCPs, with B3LYP–DCP/6-31+G(2d,2p) on the S66, S22B, HSG-A, and HC12 databases of non-covalently interacting dimers showed that it is one of the most accurate methods available for treating intermolecular interactions, giving mean absolute errors (MAEs) of 0.19, 0.27, 0.16, and 0.18 kcal/mol, respectively. Additional testing on the S12L database of very large complexation systems gave an MAE of 2.6 kcal/mol, demonstrating that the B3LYP–DCP/6-31+G(2d,2p) approach to be one of the best-performing and most feasible methods for treating large systems containing significant non-covalent interactions. Finally, we showed that the modeling of C–C-making/C–C-breaking chemistry is well predicted using the newly developed DCPs. In addition to predicting a barrier height for the β-scission of the cumyloxyl radical, that is, within 1.7 kcal/mol of the high-level value, application of B3LYP–DCP/6-31+G(2d,2p) to 10 databases that include reaction barrier heights and energies, isomerization energies, and relative conformation energies gives performance that is among the best of all available dispersion-corrected density-functional theory approaches.

Extension of the B3LYP–dispersion-correcting potential approach to the accurate treatment of both inter- and intra-molecular interactions

The translational and orientational potential energy surfaces (PESs) of n-alkanethiols with up to four carbon atoms are studied for (√(3)×√(3))R30° self-assembled monolayers (SAMs). The PESs indicate that methanethiol may form SAM structures that are not accessible for long-chain thiols. The tilt of the thiol molecules is determined by a compromise between the preferred binding geometry at the sulfur atom and the steric requirements of the alkane chains. The Au-S bond lengths, offset from the bridge position (brg), and the Au-S-C bond angles result in tilt angles of the S-C bond in the range of 55-60°. As DFT/generalized gradient approximation systematically underestimates chain-chain interactions, the binding energies are corrected by comparison to MP2 interaction energies of alkane dimers in SAM-like configurations. The resulting thiol binding energies increase by approximately 1 kcal mol(-1) per CH(2) group, which results in a substantial stabilization of long-chain SAMs due to chain-chain interactions. Furthermore, as the chain length increases, the accessible range of backbone tilt angles is constrained due to steric effects. The combination of these two effects may explain why SAM structures with long-chain thiols exhibit higher order in experiments. For each thiol two favorable SAM structures are found with the sulfur head group at the fcc-brg and hcp-brg positions, respectively. These domains may coexist in thermal equilibrium. In combination with the symmetry of the gold (111) surface, this raises the possibility of up to six different domains on single-crystal terraces. Reconstructions by an adatom or vacancy of ethanethiol SAMs with (√(3)×√(3))R30° lattice are also studied using PES scans. The results indicate that adsorption of thiols next to a vacancy is favorable and may lead to point defects inside SAMs.

E. Torres

Papers

A (Nearly) Universally Applicable Method for Modeling Noncovalent Interactions Using B3LYP.

Extension of the B3LYP - Dispersion-Correcting Potential Approach to the Accurate Treatment of both Inter- and Intramolecular Interactions

Mechanism for phase transitions and vacancy island formation in alkylthiol/Au(111) self-assembled monolayers based on adatom and vacancy-induced reconstructions

Extension of the B3LYP–dispersion-correcting potential approach to the accurate treatment of both inter- and intra-molecular interactions

Steric and chain length effects in the (√(3)×√(3))R30° structures of alkanethiol self-assembled monolayers on Au(111).