Showing papers in "Journal of Computational Chemistry in 2007"

Improved grid-based algorithm for Bader charge allocation.

Abstract: An improvement to the grid-based algorithm of Henkelman et al. for the calculation of Bader volumes is suggested, which more accurately calculates atomic properties as predicted by the theory of Atoms in Molecules. The CPU time required by the improved algorithm to perform the Bader analysis scales linearly with the number of interatomic surfaces in the system. The new algorithm corrects systematic deviations from the true Bader surface, calculated by the original method and also does not require explicit representation of the interatomic surfaces, resulting in a more robust method of partitioning charge density among atoms in the system. Applications of the method to some small systems are given and it is further demonstrated how the method can be used to define an energy per atom in ab initio calculations.

A semiempirical free energy force field with charge-based desolvation.

Abstract: The authors describe the development and testing of a semiempirical free energy force field for use in AutoDock4 and similar grid-based docking methods. The force field is based on a comprehensive thermodynamic model that allows incorporation of intramolecular energies into the predicted free energy of binding. It also incorporates a charge-based method for evaluation of desolvation designed to use a typical set of atom types. The method has been calibrated on a set of 188 diverse protein-ligand complexes of known structure and binding energy, and tested on a set of 100 complexes of ligands with retroviral proteases. The force field shows improvement in redocking simulations over the previous AutoDock3 force field.

Accelerating molecular modeling applications with graphics processors

Abstract: Molecular mechanics simulations offer a computational approach to study the behavior of biomolecules at atomic detail, but such simulations are limited in size and timescale by the available computing resources. State- of-the-art graphics processing units (GPUs) can perform over 500 billion arithmetic operations per second, a tremen- dous computational resource that can now be utilized for general purpose computing as a result of recent advances in GPU hardware and software architecture. In this article, an overview of recent advances in programmable GPUs is presented, with an emphasis on their application to molecular mechanics simulations and the programming techni- ques required to obtain optimal performance in these cases. We demonstrate the use of GPUs for the calculation of long-range electrostatics and nonbonded forces for molecular dynamics simulations, where GPU-based calculations are typically 10-100 times faster than heavily optimized CPU-based implementations. The application of GPU accel- eration to biomolecular simulation is also demonstrated through the use of GPU-accelerated Coulomb-based ion placement and calculation of time-averaged potentials from molecular dynamics trajectories. A novel approximation to Coulomb potential calculation, the multilevel summation method, is introduced and compared with direct Cou- lomb summation. In light of the performance obtained for this set of calculations, future applications of graphics processors to molecular dynamics simulations are discussed.

Density functional theory augmented with an empirical dispersion term. Interaction energies and geometries of 80 noncovalent complexes compared with ab initio quantum mechanics calculations

Abstract: Standard density functional theory (DFT) is augmented with a damped empirical dispersion term. The damping function is optimized on a small, well balanced set of 22 van der Waals (vdW) complexes and verified on a validation set of 58 vdW complexes. Both sets contain biologically relevant molecules such as nucleic acid bases. Results are in remarkable agreement with reference high-level wave function data based on the CCSD(T) method. The geometries obtained by full gradient optimization are in very good agreement with the best available theoretical reference. In terms of the standard deviation and average errors, results including the empirical dispersion term are clearly superior to all pure density functionals investigated-B-LYP, B3-LYP, PBE, TPSS, TPSSh, and BH-LYP-and even surpass the MP2/cc-pVTZ method. The combination of empirical dispersion with the TPSS functional performs remarkably well. The most critical part of the empirical dispersion approach is the damping function. The damping parameters should be optimized for each density functional/basis set combination separately. To keep the method simple, we optimized mainly a single factor, s(R), scaling globally the vdW radii. For good results, a basis set of at least triple-zeta quality is required and diffuse functions are recommended, since the basis set superposition error seriously deteriorates the results. On average, the dispersion contribution to the interaction energy missing in the DFT functionals examined here is about 15 and 100% for the hydrogen-bonded and stacked complexes considered, respectively.

Bond order and valence indices: a personal account.

Abstract: The paper accounts for the author's activity in developing bond order and valence indices since the early 80s. These indices represent an important conceptual link between the physical description of molecules as systems of electrons and nuclei and the chemical picture of molecules consisting of atoms kept together by bonds. They are also useful for a systematization and interpretation of the results obtained in the quantum chemical calculations, by permitting to extract from the wave function different pieces of information that may be assigned chemical significance. In some cases they can have some predictive power, too. Historically, the prototypes of such indices were introduced in the semiempirical quantum chemistry; the most important developments were Coulson's charge-bond order matrix in the simple Huckel theory and the Wiberg index in the CNDO framework. (Valence indices were also introduced in the semiempirical theory.) The definition of the ab initio bond order index emerged from the asymptotic term of the exchange energy component of the partitioning performed in the framework of the author's so-called "chemical Hamiltonian approach" using a "mixed" second quantization formalism for overlapping basis sets. They can also be introduced by studying the exchange part of the two-particle density (or of the second-order density matrix). Some properties of the bond order indices are discussed and the author's (until now unpublished) proof is also presented, showing the sufficient conditions under which the bond order index of a homonuclear diatomics is equal to the "chemist's bond order," i.e., the half of the difference between the number of electrons occupying bonding and antibonding orbitals. The ab initio valence indices are also introduced and discussed, and it is stressed that for correlated wave function the same "exchange only" definition of the bond order and valence indices should be used, which was introduced for the SCF case. The recent concept of the "atomic decomposition of identity" is also discussed and it is utilized for introducing bond orders and valences in the framework of the "3D analysis," when atoms are defined not by their basis orbitals but as regions of the three-dimensional (3D) physical space. Two versions of the 3D analysis are considered--the AIM (atoms in molecules)-type decomposing the space into disjunct atomic domains and the "fuzzy atoms" scheme in which there are no sharp boundaries between the atoms but they exhibit a continuous transition from one to another.

Pair interaction energy decomposition analysis

Abstract: The energy decomposition analysis (EDA) by Kitaura and Morokuma was redeveloped in the framework of the fragment molecular orbital method (FMO). The proposed pair interaction energy decomposition analysis (PIEDA) can treat large molecular clusters and the systems in which fragments are connected by covalent bonds, such as proteins. The interaction energy in PIEDA is divided into the same contributions as in EDA: the electrostatic, exchange-repulsion, and charge transfer energies, to which the correlation (dispersion) term was added. The careful comparison to the ab initio EDA interaction energies for water clusters with 2-16 molecules revealed that PIEDA has the error of at most 1.2 kcal/mol (or about 1%). The analysis was applied to (H2O)1024, the alpha helix, beta turn, and beta strand of polyalanine (ALA)10, as well as to the synthetic protein (PDB code 1L2Y) with 20 residues. The comparative aspects of the polypeptide isomer stability are discussed in detail.

PSI3: An open‐source Ab Initio electronic structure package

Abstract: PSI3 is a program system and development platform for ab initio molecular electronic structure computations. The package includes mature programming interfaces for parsing user input, accessing commonly used data such as basis-set information or molecular orbital coefficients, and retrieving and storing binary data (with no software limitations on file sizes or file-system-sizes), especially multi-index quantities such as electron repulsion integrals. This platform is useful for the rapid implementation of both standard quantum chemical methods, as well as the development of new models. Features that have already been implemented include Hartree-Fock, multiconfigurational self-consistent-field, second-order Moller-Plesset perturbation theory, coupled cluster, and configuration interaction wave functions. Distinctive capabilities include the ability to employ Gaussian basis functions with arbitrary angular momentum levels; linear R12 second-order perturbation theory; coupled cluster frequency-dependent response properties, including dipole polarizabilities and optical rotation; and diagonal Born-Oppenheimer corrections with correlated wave functions. This article describes the programming infrastructure and main features of the package. PSI3 is available free of charge through the open-source, GNU General Public License.

Ultrafast shape recognition to search compound databases for similar molecular shapes.

Abstract: Finding a set of molecules, which closely resemble a given lead molecule, from a database containing potentially billions of chemical structures is an important but daunting problem. Similar molecular shapes are particularly important, given that in biology small organic molecules frequently act by binding into a defined and complex site on a macromolecule. Here, we present a new method for molecular shape comparison, named ultrafast shape recognition (USR), capable of screening billions of compounds for similar shapes using a single computer and without the need of aligning the molecules before testing for similarity. Despite its extremely fast comparison rate, USR will be shown to be highly accurate at describing, and hence comparing, molecular shapes.

Computational alanine scanning mutagenesis--an improved methodological approach.

Abstract: Alanine scanning mutagenesis of protein-protein interfacial residues can be applied to a wide variety of protein complexes to understand the structural and energetic characteristics of the hot-spots. Binding free energies have been estimated with reasonable accuracy with empirical methods, such as Molecular Mechanics/Poisson-Boltzmann surface area (MM-PBSA), and with more rigorous computational approaches like Free Energy Perturbation (FEP) and Thermodynamic Integration (TI). The main objective of this work is the development of an improved methodological approach, with less computational cost, that predicts accurately differences in binding free energies between the wild-type and alanine mutated complexes (DeltaDeltaG(binding)). The method was applied to three complexes, and a mean unsigned error of 0.80 kcal/mol was obtained in a set of 46 mutations. The computational method presented here achieved an overall success rate of 80% and an 82% success rate in residues for which alanine mutation causes an increase in the binding free energy > 2.0 kcal/mol (warm- and hot-spots). This fully atomistic computational methodological approach consists in a computational Molecular Dynamics simulation protocol performed in a continuum medium using the Generalized Born model. A set of three different internal dielectric constants, to mimic the different degree of relaxation of the interface when different types of amino acids are mutated for alanine, have to be used for the proteins, depending on the type of amino acid that is mutated. This method permits a systematic scanning mutagenesis of protein-protein interfaces and it is capable of anticipating the experimental results of mutagenesis, thus guiding new experimental investigations.

Comprehensive analysis of chemical bonding in boron clusters.

Abstract: We present a comprehensive analysis of chemical bonding in pure boron clusters. It is now established in joint experimental and theoretical studies that pure boron clusters are planar or quasi-planar at least up to twenty atoms. Their planarity or quasi-planarity was usually discussed in terms of pi-delocalization or pi-aromaticity. In the current article, we demonstrated that one cannot ignore sigma-electrons and that the presence of two-center two-electron (2c--2e) peripheral B--B bonds together with the globally delocalized sigma-electrons must be taken into consideration when the shape of pure boron cluster is discussed. The global aromaticity (or global antiaromaticity) can be assigned on the basis of the 4n+2 (or 4n) electron counting rule for either pi- or sigma-electrons in the planar structures. We showed that pure boron clusters could have double (sigma- and pi-) aromaticity (B3-, B4, B5+, B6(2+), B7+, B7-, B8, B(8)2-, B9-, B10, B11+, B12, and B13+), double (sigma- and pi-) antiaromaticity (B6(2-), B15), or conflicting aromaticity (B5-,sigma-antiaromatic and pi-aromatic and B14, sigma-aromatic and pi-antiaromatic). Appropriate geometric fit is also an essential factor, which determines the shape of the most stable structures. In all the boron clusters considered here, the peripheral atoms form planar cycles. Peripheral 2c--2e B--B bonds are built up from s to p hybrid atomic orbitals and this enforces the planarity of the cycle. If the given number of central atoms (1, 2, 3, or 4) can perfectly fit the central cavity then the overall structure is planar. Otherwise, central atoms come out of the plane of the cycle and the overall structure is quasi-planar.

Interfacing Q‐Chem and CHARMM to perform QM/MM reaction path calculations

Abstract: A hybrid quantum mechanical/molecular mechanical (QM/MM) potential energy function with Hartree-Fock, density functional theory (DFT), and post-HF (RIMP2, MP2, CCSD) capability has been implemented in the CHARMM and Q-Chem software packages In addition, we have modified CHARMM and Q-Chem to take advantage of the newly introduced replica path and the nudged elastic band methods, which are powerful techniques for studying reaction pathways in a highly parallel (ie, parallel/parallel) fashion, with each pathway point being distributed to a different node of a large cluster To test our implementation, a series of systems were studied and comparisons were made to both full QM calculations and previous QM/MM studies and experiments For instance, the differences between HF, DFT, MP2, and CCSD QM/MM calculations of H2O···H2O, H2O···Na+, and H2O···Cl− complexes have been explored Furthermore, the recently implemented polarizable Drude water model was used to make comparisons to the popular TIP3P and TIP4P water models for doing QM/MM calculations We have also computed the energetic profile of the chorismate mutase catalyzed Claisen rearrangement at various QM/MM levels of theory and have compared the results with previous studies Our best estimate for the activation energy is 820 kcal/mol and for the reaction energy is −231 kcal/mol, both calculated at the MP2/6-31+G(d)//MP2/6-31+G(d)/C22 level of theory © 2007 Wiley Periodicals, Inc J Comput Chem, 2007

Unicorns in the world of chemical bonding models

Abstract: The appearance and the significance of heuristically developed bonding models are compared with the phenomenon of unicorns in mythical saga. It is argued that classical bonding models played an essential role for the development of the chemical science providing the language which is spoken in the territory of chemistry. The advent and the further development of quantum chemistry demands some restrictions and boundary conditions for classical chemical bonding models, which will continue to be integral parts of chemistry. © 2006 Wiley Periodicals, Inc. J Comput Chem 2007

Recent advances in planar tetracoordinate carbon chemistry

Abstract: We summarize our contributions on the quest of new planar tetracoordinate carbon entities (new carbon molecules with exotic chemical structures and strange bonding schemes). We give special emphasis on the rationalization why in this type of molecules the planar configuration is favored over the tetrahedral one. We will concentrate on the latter and will show that molecules containing planar tetracoordinate carbons have a stabilizing system of delocalized pi electrons, which shows similar properties as pi systems in aromatic molecules.

Using pseudo amino acid composition to predict protein structural class: approached by incorporating 400 dipeptide components.

Abstract: The proteins structure can be mainly classified into four classes: all-alpha, all-beta, alpha/beta, and alpha + beta protein according to their chain fold topologies. For the purpose of predicting the protein structural class, a new predicting algorithm, in which the increment of diversity combines with Quadratic Discriminant analysis, is presented to study and predict protein structural class. On the basis of the concept of the pseudo amino acid composition (Chou, Proteins: Struct Funct Genet 2001, 43, 246; Erratum: Proteins Struct Funct Genet 2001, 44, 60), 400 dipeptide components and 20 amino acid composition are, respectively, selected as parameters of diversity source. Total of 204 nonhomologous proteins constructed by Chou (Chou, Biochem Biophys Res Commun 1999, 264, 216) are used for training and testing the predictive model. The predicted results by using the pseudo amino acids approach as proposed in this paper can remarkably improve the success rates, and hence the current method may play a complementary role to other existing methods for predicting protein structural classification.

Global minimum structure searches via particle swarm optimization.

Abstract: Novel implementation of the evolutionary approach known as particle swarm optimization (PSO) capable of finding the global minimum of the potential energy surface of atomic assemblies is reported. This is the first time the PSO technique has been used to perform global optimization of minimum structure search for chemical systems. Significant improvements have been introduced to the original PSO algorithm to increase its efficiency and reliability and adapt it to chemical systems. The developed software has successfully found the lowest-energy structures of the LJ26 Lennard-Jones cluster, anionic silicon hydride Si2H, and triply hydrated hydroxide ion OH− (H2O)3. It requires relatively small population sizes and demonstrates fast convergence. Efficiency of PSO has been compared with simulated annealing, and the gradient embedded genetic algorithm. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007

An Improved Algorithm for Analytical Gradient Evaluation in Resolution-of-the-Identity Second-Order Møller-Plesset Perturbation Theory: Application to Alanine Tetrapeptide Conformational Analysis

Abstract: We present a new algorithm for analytical gradient evaluation in resolution-of-the-identity second-order Moller-Plesset perturbation theory (RI-MP2) and thoroughly assess its computational performance and chemical accuracy. This algorithm addresses the potential I/O bottlenecks associated with disk-based storage and access of the RI-MP2 t-amplitudes by utilizing a semi-direct batching approach and yields computational speed-ups of approximately 2-3 over the best conventional MP2 analytical gradient algorithms. In addition, we attempt to provide a straightforward guide to performing reliable and cost-efficient geometry optimizations at the RI-MP2 level of theory. By computing relative atomization energies for the G3/99 set and optimizing a test set of 136 equilibrium molecular structures, we demonstrate that satisfactory relative accuracy and significant computational savings can be obtained using Pople-style atomic orbital basis sets with the existing auxiliary basis expansions for RI-MP2 computations. We also show that RI-MP2 geometry optimizations reproduce molecular equilibrium structures with no significant deviations (>0.1 pm) from the predictions of conventional MP2 theory. As a chemical application, we computed the extended-globular conformational energy gap in alanine tetrapeptide at the extrapolated RI-MP2/cc-pV(TQ)Z level as 2.884, 4.414, and 4.994 kcal/mol for structures optimized using the HF, DFT (B3LYP), and RI-MP2 methodologies and the cc-pVTZ basis set, respectively. These marked energetic discrepancies originate from differential intramolecular hydrogen bonding present in the globular conformation optimized at these levels of theory and clearly demonstrate the importance of long-range correlation effects in polypeptide conformational analysis.

Chemical fragments in real space: definitions, properties, and energetic decompositions.

Abstract: The physical and chemical meaning of real space molecular fragments resulting from arbitrary partitions of the density is reviewed under a common unifying formalism. Both fuzzy (interpenetrating) and non-fuzzy (exhaustive) decompositions are treated on an equal basis. Density decompositions are consistently generalized to compatible density matrix partitions by using Li and Parr's ideas (Li and Parr J Chem Phys 1986, 84, 1704), and these are carried onto an energy partition. It is argued that the merits of a given decomposition should be judged against both the charge and the energetic image it provides. Atomic partitions are used to show how the interacting quantum atoms approach (IQA) allows us to cope with the most important energy cancellations of quantum chemistry. Binding results from a trade-off between atomic (or fragment) energy deformations with respect to a reference and interatomic (interfragment) interactions. Deformation energies are divided into charge transfer and redistribution terms and their relative roles are analyzed. A number of systems are compared against the fuzziness of different density decompositions. The results consistently show that fuzzy partitions tend to give low atomic net charges and enhanced covalency, while exhaustive partitions generate larger net charges and smaller covalencies, across a wide range of bonding regimes. © 2006 Wiley Periodicals, Inc. J Comput Chem, 2007

Valence bond theory for chemical dynamics.

Abstract: This essay provides a perspective on several issues in valence bond theory: the physical significance of semilocal bonding orbitals, the capability of valence bond concepts to explain systems with multireferences character, the use of valence bond theory to provide analytical representations of potential energy surfaces for chemical dynamics by the method of semiempirical valence bond potential energy surfaces (an early example of specific reaction parameters), by multiconfiguration molecular mechanics, by the combined valence bond-molecular mechanics method, and by the use of valence bond states as coupled diabatic states for describing electronically nonadiabatic processes (photochemistry). The essay includes both ab initio and semiempirical approaches. © 2006 Wiley Periodicals, Inc. J Comput Chem, 2007

SODOCK: swarm optimization for highly flexible protein-ligand docking.

Abstract: Protein-ligand docking can be formulated as a parameter optimization problem associated with an accurate scoring function, which aims to identify the translation, orientation, and conformation of a docked ligand with the lowest energy. The parameter optimization problem for highly flexible ligands with many rotatable bonds is more difficult than that for less flexible ligands using genetic algorithm (GA)-based approaches, due to the large numbers of parameters and high correlations among these parameters. This investigation presents a novel optimization algorithm SODOCK based on particle swarm optimization (PSO) for solving flexible protein-ligand docking problems. To improve efficiency and robustness of PSO, an efficient local search strategy is incorporated into SODOCK. The implementation of SODOCK adopts the environment and energy function of AutoDock 3.05. Computer simulation results reveal that SODOCK is superior to the Lamarckian genetic algorithm (LGA) of AutoDock, in terms of convergence performance, robustness, and obtained energy, especially for highly flexible ligands. The results also reveal that PSO is more suitable than the conventional GA in dealing with flexible docking problems with high correlations among parameters. This investigation also compared SODOCK with four state-of-the-art docking methods, namely GOLD 1.2, DOCK 4.0, FlexX 1.8, and LGA of AutoDock 3.05. SODOCK obtained the smallest RMSD in 19 of 37 cases. The average 2.29 A of the 37 RMSD values of SODOCK was better than those of other docking programs, which were all above 3.0 A.

Implementation of divide-and-conquer method including Hartree-Fock exchange interaction.

Abstract: The divide-and-conquer (DC) method, which is one of the linear-scaling methods avoiding explicit diagonalization of the Fock matrix, has been applied mainly to pure density functional theory (DFT) or semiempirical molecular orbital calculations so far. The present study applies the DC method to such calculations including the Hartree-Fock (HF) exchange terms as the HF and hybrid HF/DFT. Reliability of the DC-HF and DC-hybrid HF/DFT is found to be strongly dependent on the cut-off radius, which defines the localization region in the DC formalism. This dependence on the cut-off radius is assessed from various points of view: that is, total energy, energy components, local energies, and density of states. Additionally, to accelerate the self-consistent field convergence in DC calculations, a new convergence technique is proposed. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007

New six-site acetonitrile model for simulations of liquid acetonitrile and its aqueous mixtures

Abstract: A new six site flexible acetonitrile molecular model is developed. The AMBER force field was used for description of intramolecular parameters, the atomic charges were calculated from a high level ab initio theory and finally the Lennard-Jones parameters were tuned to fit the experimental density and evaporation heat. The obtained in this way model reproduces correctly densities of water-acetonitrile mixtures as well as provides qualitative description of the dielectric permittivity and self-diffusion coefficients.

Performance of the general amber force field in modeling aqueous POPC membrane bilayers.

Abstract: The aim of this work was to answer the question of whether the general amber force field (GAFF) is good enough to simulate fully hydrated POPC membrane bilayers. The test system contained 128 POPC and 2985 TIP3P water molecules. The equilibration was carried out in a nonarbitrary manner to reach the stable liquid-crystalline phase. The simulations were performed by using particle mesh Ewald electrostatics implemented in molecular dynamics packages Amber8 (NPT ensembles) and NAMD2 (NPgammaT ensembles). The computational results were assessed against the following experimental membrane properties: (i) area per lipid, (ii) area compressibility modulus, (iii) order parameter, (iv) gauche conformations per acyl chain, (v) lateral diffusion coefficients, (vi) electron density profile, and (vii) bound water at the lipid/water interface. The analyses revealed that the tested force field combination approximates the experimental values at an unexpectedly good level when the NPgammaT ensemble is applied with a surface tension of 60 mN m(-1) per bilayer. It is concluded that the GAFF/TIP3P combination can be utilized for aqueous membrane bilayer simulations, as it provides acceptable accuracy for biomolecular modeling.

Backbone building from quadrilaterals: a fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinates.

Abstract: In this contribution, we present an algorithm for protein backbone reconstruction that comprises very high computational efficiency with high accuracy. Reconstruction of the main chain atomic coordinates from the α carbon trace is a common task in protein modeling, including de novo structure prediction, comparative modeling, and processing experimental data. The method employed in this work follows the main idea of some earlier approaches to the problem. The details and careful design of the present approach are new and lead to the algorithm that outperforms all commonly used earlier applications. BBQ (Backbone Building from Quadrilaterals) program has been extensively tested both on native structures as well as on near-native decoy models and compared with the different available existing methods. Obtained results provide a comprehensive benchmark of existing tools and evaluate their applicability to a large scale modeling using a reduced representation of protein conformational space. The BBQ package is available for downloading from our website at http://biocomp.chem.uw.edu.pl/services/BBQ/. This webpage also provides a user manual that describes BBQ functions in detail.

Speeding up parallel GROMACS on high-latency networks

Abstract: We investigate the parallel scaling of the GROMACS molecular dynamics code on Ethernet Beowulf clusters and what prerequisites are necessary for decent scaling even on such clusters with only limited bandwidth and high latency. GROMACS 3.3 scales well on supercomputers like the IBM p690 (Regatta) and on Linux clusters with a special interconnect like Myrinet or Infiniband. Because of the high single-node performance of GROMACS, however, on the widely used Ethernet switched clusters, the scaling typically breaks down when more than two computer nodes are involved, limiting the absolute speedup that can be gained to about 3 relative to a single-CPU run. With the LAM MPI implementation, the main scaling bottleneck is here identified to be the all-to-all communication which is required every time step. During such an all-to-all communication step, a huge amount of messages floods the network, and as a result many TCP packets are lost. We show that Ethernet flow control prevents network congestion and leads to substantial scaling improvements. For 16 CPUs, e.g., a speedup of 11 has been achieved. However, for more nodes this mechanism also fails. Having optimized an all-to-all routine, which sends the data in an ordered fashion, we show that it is possible to completely prevent packet loss for any number of multi-CPU nodes. Thus, the GROMACS scaling dramatically improves, even for switches that lack flow control. In addition, for the common HP ProCurve 2848 switch we find that for optimum all-to-all performance it is essential how the nodes are connected to the switch's ports. This is also demonstrated for the example of the Car-Parinello MD code.

Electrostatic energy in the effective fragment potential method: Theory and application to benzene dimer

Abstract: Evaluation of the electrostatic energy within the effective fragment potential (EFP) method is presented. The performance of two variants of the distributed multipole analysis (DMA) together with two different models for estimating the charge penetration energies was studied using six homonuclear dimers. The importance of damping the higher order multipole terms, i.e. charge dipole, was also investigated. Damping corrections recover more than 70% of the charge penetration energy in all dimers, whereas higher order damping introduces only minor improvement. Electrostatic energies calculated by the numerical DMA are less accurate than those calculated by the analytic DMA. Analysis of bonding in the benzene dimer shows that EFP with inclusion of the electrostatic damping term performs very well compared to the high-level coupled cluster singles, doubles, and perturbative triples method. The largest error of 0.4 kcal/mol occurs for the sandwich dimer configuration. This error is about half the size of the corresponding error in second order perturbation theory. Thus, EFP in the current implementation is an accurate and computationally inexpensive method for calculating interaction energies in weakly bonded molecular complexes. © 2006 Wiley Periodicals, Inc. J Comput Chem 28: 276–291, 2007

Ab initio parametrized MM3 force field for the metal-organic framework MOF-5

Abstract: A new valence force field has been developed and validated for a particular class of coordination polymers known as nanoporous metal-organic frameworks (MOFs), introduced recently by the group of Yaghi. The experimental, structural, and spectroscopic data in combination with density functional theory calculations on several model systems were used to parametrize the bonded terms of the force field, which explicitly treats the metal-oxygen interactions as partially covalent as well as distinguishes different types of oxygens in the framework. Both the experimental crystal structure of MOF-5 and vibrational infrared spectrum are reproduced reasonably well. The proposed force field is believed to be useful in atomistic simulations of adsorption/diffusion of guest molecules inside the flexible pores of this important class of MOF materials.

σ and π contributions to the induced magnetic field: Indicators for the mobility of electrons in molecules

Abstract: The authors discuss the role of the sigma and pi contributions to the induced magnetic field for simple hydrocarbons containing a double or a triple bond, as well as for benzene and cyclobutadiene. While the magnetic field induced by the sigma electrons is short-ranged, the pi system is responsible for the formation of long-range cones. These cones influence the chemical shift of atoms by additional shielding (for aromatic) or deshielding (for antiaromatic molecules) contributions. While the hydrogen atoms of benzene are found to lie within the deshielded region of the magnetic field induced by the pi electrons, they are shielded by the total induced magnetic field. The induced magnetic field of the pi electrons support Pople's model on the basis of first-principles calculations.

Electronic structure of CO--an exercise in modern chemical bonding theory.

Abstract: This paper discusses recent progress that has been made in the understanding of the electronic structure and bonding situation of carbon monoxide which was analyzed using modern quantum chemical methods. The new results are compared with standard models of chemical bonding. The electronic charge distribution and the dipole moment, the nature of the HOMO and the bond dissociation energy are discussed in detail. © 2006 Wiley Periodicals, Inc. J Comput Chem, 2006

Nearest-neighbor nonparametric method for estimating the configurational entropy of complex molecules.

Abstract: A method for estimating the configurational (i.e., non-kinetic) part of the entropy of internal motion in complex molecules is introduced that does not assume any particular parametric form for the underlying probability density function. It is based on the nearest-neighbor (NN) distances of the points of a sample of internal molecular coordinates obtained by a computer simulation of a given molecule. As the method does not make any assumptions about the underlying potential energy function, it accounts fully for any anharmonicity of internal molecular motion. It provides an asymptotically unbiased and consistent estimate of the configurational part of the entropy of the internal degrees of freedom of the molecule. The NN method is illustrated by estimating the configurational entropy of internal rotation of capsaicin and two stereoisomers of tartaric acid, and by providing a much closer upper bound on the configurational entropy of internal rotation of a pentapeptide molecule than that obtained by the standard quasi-harmonic method. As a measure of dependence between any two internal molecular coordinates, a general coefficient of association based on the information-theoretic quantity of mutual information is proposed. Using NN estimates of this measure, statistical clustering procedures can be employed to group the coordinates into clusters of manageable dimensions and characterized by minimal dependence between coordinates belonging to different clusters.

The role of radial nodes of atomic orbitals for chemical bonding and the periodic table.

Abstract: The role of radial nodes, or of their absence, in valence orbitals for chemical bonding and periodic trends is discussed from a unified viewpoint In particular, we emphasize the special role of the absence of a radial node whenever a shell with angular quantum number l is occupied for the first time (lack of “primogenic repulsion”), as with the 1s, 2p, 3d, and 4f shells Although the consequences of the very compact 2p shell (eg good isovalent hybridization, multiple bonding, high electronegativity, lone-pair repulsion, octet rule) are relatively well known, it seems that some of the aspects of the very compact 3d shell in transition-metal chemistry are less well appreciated, eg, the often weakened and stretched bonds at equilibrium structure, the frequently colored complexes, and the importance of nondynamical electron-correlation effects in bonding © 2006 Wiley Periodicals, Inc J Comput Chem 28: 320–325, 2006