Showing papers in "Journal of Chemical Theory and Computation in 2008"

GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation

Abstract: Molecular simulation is an extremely useful, but computationally very expensive tool for studies of chemical and biomolecular systems Here, we present a new implementation of our molecular simulation toolkit GROMACS which now both achieves extremely high performance on single processors from algorithmic optimizations and hand-coded routines and simultaneously scales very well on parallel machines The code encompasses a minimal-communication domain decomposition algorithm, full dynamic load balancing, a state-of-the-art parallel constraint solver, and efficient virtual site algorithms that allow removal of hydrogen atom degrees of freedom to enable integration time steps up to 5 fs for atomistic simulations also in parallel To improve the scaling properties of the common particle mesh Ewald electrostatics algorithms, we have in addition used a Multiple-Program, Multiple-Data approach, with separate node domains responsible for direct and reciprocal space interactions Not only does this combination of a

P-LINCS: A Parallel Linear Constraint Solver for Molecular Simulation

Abstract: By removing the fastest degrees of freedom, constraints allow for an increase of the time step in molecular simulations. In the last decade parallel simulations have become commonplace. However, up till now efficient parallel constraint algorithms have not been used with domain decomposition. In this paper the parallel linear constraint solver (P-LINCS) is presented, which allows the constraining of all bonds in macromolecules. Additionally the energy conservation properties of (P-)LINCS are assessed in view of improvements in the accuracy of uncoupled angle constraints and integration in single precision.

The MARTINI Coarse-Grained Force Field: Extension to Proteins

Abstract: Many biologically interesting phenomena occur on a time scale that is too long to be studied by atomistic simulations. These phenomena include the dynamics of large proteins and self-assembly of biological materials. Coarse-grained (CG) molecular modeling allows computer simulations to be run on length and time scales that are 2–3 orders of magnitude larger compared to atomistic simulations, providing a bridge between the atomistic and the mesoscopic scale. We developed a new CG model for proteins as an extension of the MARTINI force field. Here, we validate the model for its use in peptide-bilayer systems. In order to validate the model, we calculated the potential of mean force for each amino acid as a function of its distance from the center of a dioleoylphosphatidylcholine (DOPC) lipid bilayer. We then compared amino acid association constants, the partitioning of a series of model pentapeptides, the partitioning and orientation of WALP23 in DOPC lipid bilayers and a series of KALP peptides in dimyris...

Revised Basis Sets for the LANL Effective Core Potentials.

Abstract: We suggest a new contraction of the basis sets associated with the Hay-Wadt relativistic effective core potentials (RECPs) for the main group and transition metal atoms. These bases are more suitable for density functional theory investigations than the previous ‘double-ζ’ contractions based upon Hartree−Fock atomic results. The original Hay-Wadt primitives are now contracted [5s5p3d], [4s4p3d], and [4s4p3d] for the first, second, and third transition series, respectively, and denoted as LANL2TZ basis sets. For the main group atoms, we advocate using a completely uncontracted basis denoted LANL08. While modestly extending the size of the basis, the resulting sets should be suitable for both DFT and wave function based approaches. The valence bases for the transition metal atoms can be supplemented with the polarization functions determined by Frenking.

All-Electron Scalar Relativistic Basis Sets for Third-Row Transition Metal Atoms.

Abstract: A family of segmented all-electron relativistically contracted (SARC) basis sets for the elements Hf−Hg is constructed for use in conjunction with the Douglas−Kroll−Hess (DKH) and zeroth-order regular approximation (ZORA) scalar relativistic Hamiltonians. The SARC basis sets are loosely contracted and thus offer computational advantages compared to generally contracted relativistic basis sets, while their sufficiently small size allows them to be used in place of effective core potentials (ECPs) for routine studies of molecules. Practical assessments of the SARC basis sets in DFT calculations of atomic (ionization energies) as well as molecular properties (geometries and bond dissociation energies for MHn complexes) confirm that the basis sets yield accurate and reliable results, providing a balanced description of core and valence electron densities. CCSD(T) calculations on a series of gold diatomic compounds also demonstrate the applicability of the basis sets to correlated methods. The SARC basis sets ...

Exploring the Limit of Accuracy of the Global Hybrid Meta Density Functional for Main-Group Thermochemistry, Kinetics, and Noncovalent Interactions

Abstract: The hybrid meta density functionals M05-2X and M06-2X have been shown to provide broad accuracy for main group chemistry. In the present article we make the functional form more flexible and improve the self-interaction term in the correlation functional to improve its self-consistent-field convergence. We also explore the constraint of enforcing the exact forms of the exchange and correlation functionals through second order (SO) in the reduced density gradient. This yields two new functionals called M08-HX and M08-SO, with different exact constraints. The new functionals are optimized against 267 diverse main-group energetic data consisting of atomization energies, ionization potentials, electron affinities, proton affinities, dissociation energies, isomerization energies, barrier heights, noncovalent complexation energies, and atomic energies. Then the M08-HX, M08-SO, M05-2X, and M06-2X functionals and the popular B3LYP functional are tested against 250 data that were not part of the original training ...

Performance of B3LYP Density Functional Methods for a Large Set of Organic Molecules

Abstract: Testing of the commonly used hybrid density functional B3LYP with the 6-31G(d), 6-31G(d,p), and 6-31+G(d,p) basis sets has been carried out for 622 neutral, closed-shell organic compounds containing the elements C, H, N, and O. The focus is comparison of computed and experimental heats of formation and isomerization energies. In addition, the effect of an empirical dispersion correction term has been evaluated and found to improve agreement with the experimental data. For the 622 compounds, the mean absolute errors (MAE) in the heats of formation are 3.1, 2.6, 2.7, and 2.4 kcal/mol for B3LYP/6-31G(d), B3LYP/6-31G(d,p), B3LYP/6-31+G(d,p), and B3LYP/6-31+G(d,p) with the dispersion correction. A diverse set of 34 isomerizations highlights specific issues of general interest, such as performance on differences in steric effects, conjugation, and bonding. The corresponding MAEs for the isomerizations are 2.7, 2.4, 2.2, and 1.9 kcal/mol. Improvement is obtained for isomerizations of amines and alcohols when bot...

TD-DFT Performance for the Visible Absorption Spectra of Organic Dyes: Conventional versus Long-Range Hybrids

Abstract: The π → π* transitions of more than 100 organic dyes from the major classes of chromophores (quinones, diazo, ...) have been investigated using a Time-Dependent Density Functional Theory (TD-DFT) procedure relying on large atomic basis sets and the systematic modeling of solvent effects. These calculations have been performed with pure (PBE) as well as conventional (PBE0) and long-range (LR) corrected hybrid functionals (LC-PBE, LC-ωPBE, and CAM-B3LYP). The computed wavelengths are systematically guided by the percentage of exact exchange included at intermediate interelectronic distance, i.e., the λmax value always follows the PBE > PBE0 > CAM-B3LYP > LC-PBE > LC-ωPBE > HF sequence. The functional giving the best estimates of the experimental transition energies may vary, but PBE0 and CAM-B3LYP tend to outperform all other approaches. The latter functional is shown to be especially adequate to treat molecules with delocalized excited states. The mean absolute error provided by PBE0 is 22 nm (0.14 eV) wit...

Assessment of the Performance of the M05-2X and M06-2X Exchange-Correlation Functionals for Noncovalent Interactions in Biomolecules.

Abstract: The highly parametrized, empirical exchange-correlation functionals, M05−2X and M06−2X, developed by Zhao and Truhlar have been shown to describe noncovalent interactions better than density functionals which are currently in common use. However, these methods have yet to be fully benchmarked for the types of interactions important in biomolecules. M05−2X and M06−2X are claimed to capture “medium-range” electron correlation; however, the “long-range” electron correlation neglected by these functionals can also be important in the binding of noncovalent complexes. Here we test M05−2X and M06−2X for the nucleic acid base pairs in the JSCH-2005 database. Using the CCSD(T) binding energies as a benchmark, the performance of these functionals is compared to that of a nonempirical density functional, PBE, and also to that of PBE plus Grimme’s empirical dispersion correction, PBE-D. Due to the importance of “long-range” electron correlation in hydrogen-bonded and interstrand base pairs, PBE-D provides more accur...

Quantum Chemistry on Graphical Processing Units. 1. Strategies for Two-Electron Integral Evaluation

Abstract: Modern videogames place increasing demands on the computational and graphical hardware, leading to novel architectures that have great potential in the context of high performance computing and molecular simulation. We demonstrate that Graphical Processing Units (GPUs) can be used very efficiently to calculate two-electron repulsion integrals over Gaussian basis functionsthe first step in most quantum chemistry calculations. A benchmark test performed for the evaluation of approximately 106 (ss|ss) integrals over contracted s-orbitals showed that a naive algorithm implemented on the GPU achieves up to 130-fold speedup over a traditional CPU implementation on an AMD Opteron. Subsequent calculations of the Coulomb operator for a 256-atom DNA strand show that the GPU advantage is maintained for basis sets including higher angular momentum functions.

Investigations into the Nature of Halogen Bonding Including Symmetry Adapted Perturbation Theory Analyses.

Abstract: In recent years it has been recognized that, because of their unique properties, halogen bonds have tremendous potential in the development of new pharmaceutical compounds and materials. In this study we investigate the phenomenon of halogen bonding by carrying out ab initio calculations on the halomethane-formaldehyde complexes as well as the fluorine substituted FnH3-nCX···OCH2 dimers, where the halogen bonding halogens (X) are chlorine, bromine, and iodine. Coupled cluster (CCSD(T)/aug-cc-pVTZ) calculations indicate that the binding energies for these type of interactions lie in the range between −1.05 kcal/mol (H3CCl···OCH2) and −3.72 kcal/mol (F3CI···OCH2). One of the most important findings in this study is that, according to symmetry adapted perturbation theory (SAPT) analyses, halogen bonds are largely dependent on both electrostatic and dispersion type interactions. As the halogen atom involved in halogen bonding becomes larger the interaction strength for this type of interaction also gets large...

Cholesky Decomposition-Based Multiconfiguration Second-Order Perturbation Theory (CD-CASPT2): Application to the Spin-State Energetics of Co(III)(diiminato)(NPh).

Abstract: The electronic structure and low-lying electronic states of a Co-III(diiminato)(NPh) complex have been studied using mulficonfigurational wave function theory (CASSCF/CASPT2) The results have been compared to those obtained with density functional theory. The best agreement with ab initio results is obtained with a modified B3LYP functional containing a reduced amount (15%) of Hartree-Fock exchange. A relativistic basis set with 869 functions has been employed in the most extensive ab initio calculations, where a Cholesky decomposition technique was used to overcome problems arising from the large size of the two-electron integral matrix. It is shown that this approximation reproduces results obtained with the full integral set to a high accuracy, thus opening the possibility to use this approach to perform multiconfigurational wave-function-based quantum chemistry on much larger systems relative to what has been possible until now.

Accurate Spin-State Energies for Iron Complexes

Abstract: A critical assessment of the OPBE functional is made for its performance for the geometries and spin-states of iron complexes. In particular, we have examined its performance for the geometry of first-row transition-metal (di)halides (MnX2, FeX2, CoX2, NiX2, CuX, X=[F, Cl]), whose results were previously [J. Chem. Theory Comput. 2006, 2, 1282] found to be representative for a much larger and more diverse set of 32 metal complexes. For investigating the performance for spin ground-states of iron complexes, we examined a number of small iron complexes (Fe(II)Cl42−, Fe(III)Cl41−, Fe(II)Cl64−, Fe(III)Cl63−, Fe(II)CN64−, Fe(III)CN63−, Fe(VI)O42−, Fe(III)(NH3)63+), benchmark systems (Fe(II)(H2O)62+, Fe(II)(NH3)62+, Fe(II)(bpy)32+), and several challenging iron complexes such as the Fe(II)(phen)2(NCS)2 spin-crossover compound, the monopyridylmethylamine Fe(II)(amp)2Cl2 and dipyridylmethylamine Fe(II)(dpa)22+, and the bis complex of Fe(III)-1,4,7-triazacyclononane (Fe(III)(9aneN3)23+. In all these cases OPBE give...

Basis Set Convergence of Nuclear Magnetic Shielding Constants Calculated by Density Functional Methods

Abstract: The previously proposed polarization consistent basis sets, optimized for density functional calculations, are evaluated for calculating nuclear magnetic shielding constants. It is shown that the basis set convergence can be improved by adding a single p-type function with a large exponent and allowing for a slight decontraction of the p functions. The resulting pcS-n basis sets should be suitable for calculating nuclear magnetic shielding constants with density functional methods and are shown to perform significantly better than existing alternatives for a comparable computational cost.

Perspective on Free-Energy Perturbation Calculations for Chemical Equilibria

Abstract: An overview is provided on the computation of free energy changes in solution using perturbation theory, overlap sampling, and related approximate methods. As a specific application, extensive results are provided for free energies of hydration of substituted benzenes using the OPLS-AA force field in explicit TIP4P water. For a similar amount of computer time, the double-wide sampling and overlap sampling methods yield very similar results in the free-energy perturbation calculations. With standard protocols, the average statistical uncertainty in computed differences in free energies of hydration is 0.1 - 0.2 kcal/mol. Application of the power-series expansion in the Peierls equation was also tested. Use of the first-order term is generally reliable, while inclusion of the slowly-convergent, second-order fluctuation term causes deterioration in the results for strongly hydrogen-bonded solutes.

Parallel Calculation of CCSD and CCSD(T) Analytic First and Second Derivatives

Abstract: In this paper we present a parallel adaptation of a highly efficient coupled-cluster algorithm for calculating coupled-cluster singles and doubles (CCSD) and coupled-cluster singles and doubles augmented by a perturbative treatment of triple excitations (CCSD(T)) energies, gradients, and, for the first time, analytic second derivatives. A minimal-effort strategy is outlined that leads to an amplitude-replicated, communication-minimized implementation by parallelizing the time-determining steps for CCSD and CCSD(T). The resulting algorithm is aimed at affordable cluster architectures consisting of compute nodes with sufficient memory and local disk space and that are connected by standard communication networks like Gigabit Ethernet. While this scheme has disadvantages in the limit of very large numbers of compute nodes, it proves to be an efficient way of reducing the overall computational time for large-scale coupled-cluster calculations. In this way, CCSD(T) calculations of molecular properties such as vibrational frequencies or NMR-chemical shifts for systems with more than 1000 basis functions are feasible. A thorough analysis of the time-determining steps for CCSD and CCSD(T) energies, gradients, and second derivatives is carried out. Benchmark calculations are presented, proving that the parallelization of these steps is sufficient to obtain an efficient parallel scheme. This also includes the calculation of parallel CCSD energies and gradients using unrestricted (UHF) and restricted open-shell (ROHF) Hartree-Fock references, parallel UHF-CCSD(T) energies and gradients, parallel ROHF-CCSD(T) energies as well as parallel equation-of-motion CCSD energies and gradients for closed- and open-shell references. First applications to the calculation of the NMR chemical shifts of benzene using large basis sets and to the calculation of the equilibrium geometry of ferrocene as well as energy calculations with more than 1300 basis functions demonstrate the efficiency of the implementation.

Benzene Dimer: High-Level Wave Function and Density Functional Theory Calculations.

Abstract: High-level OVOS (optimized virtual orbital space) CCSD(T) interaction energy calculations (up to the aug-cc-pVQZ basis set) and various extrapolations toward the complete basis set (CBS) limit are presented for the most important structures on the benzene dimer potential energy surface. The geometries of these structures were obtained via an all-coordinate gradient geometry optimization using the DFT-D/BLYP method, covering the empirical dispersion correction fitted exclusively for this system. The fit was carried out against two estimated CCSD(T)/CBS potential energy curves corresponding to the distance variation between two benzene rings for the parallel-displaced (PD) and T-shaped (T) structures. The effect of the connected quadruple excitations on the interaction energy was estimated using the CCSD(TQf) method in a 6-31G*(0.25) basis set, destabilizing the T and T-shaped tilted (TT) structures by ≈0.02 kcal/mol and the PD structure by ≈0.04 kcal/mol. Our best CCSD(T)/CBS results show, within the error bars of the applied methodology, that the energetically lowest-lying structure is the TT structure, which is nearly 0.1 kcal/mol more stable than the almost isoenergetic PD and T structures. The specifically parametrized DFT-D/BLYP method leads to a correct energy ordering of the structures, with the errors being smaller by 0.2 kcal/mol with respect to the most accurate CCSD(T) values.

Development and Validation of the B3LYP/N07D Computational Model for Structural Parameter and Magnetic Tensors of Large Free Radicals.

Abstract: Extensive calculations on a large set of free radicals containing atoms of the second and third row show that the B3LYP/N07D computational model provides remarkably accurate structural parameters and magnetic tensors at reasonable computational costs. The key of this success is the optimization of core-valence s functions for hyperfine coupling constants, while retaining (and even improving) the good performances of the parent 6−31+G(d,p) basis set for valence properties through reoptimization of polarization and diffuse p functions.

Structural and Electronic Properties of Selected Rutile and Anatase TiO2 Surfaces: An ab Initio Investigation

Abstract: Five low-index stoichiometric TiO2 rutile and anatase surfaces, i.e., rutile (110), (100), and (001) as well as anatase (101) and (100), have been investigated using different Hamiltonians with all-electron Gaussian basis sets, within a periodic approach. Full-relaxations of the aforementioned surfaces have been essentially carried out at the Hartree-Fock (HF) level, but selected surfaces were treated also using pure and hybrid Density Functional Theory (DFT) models. Mulliken charges, band structures, and total and projected-densities of states have been computed both at the HF and the hybrid DFT (B3LYP and PBE0) levels. As regards DFT, the local density (LDA) and generalized gradient approximations (GGA) have been used. No matter which Hamiltonian is considered, as long as sufficiently thick slabs are taken into account, computed atomic relaxations show an overall excellent agreement with the most recent experimental reports. This is especially true when using hybrid functionals which enable the clarification of some conflicting results. Moreover, both at the LDA and HF levels, we were able to classify the surface relative energies in the following sequence: anatase (101) < rutile (110) < anatase (100) < rutile (100) ≪ rutile (001). Instead, when using PBE, B3LYP, or PBE0, the two most stable surfaces are reversed.

Computing the Heat of Adsorption using Molecular Simulations: The Effect of Strong Coulombic Interactions

Abstract: Molecular simulations are an important tool for the study of adsorption of hydrocarbons in nanoporous materials such as zeolites. The heat of adsorption is an important thermodynamic quantity that can be measured both in experiments and molecular simulations, and therefore it is often used to investigate the quality of a force field for a certain guest-host (g - h) system. In molecular simulations, the heat of adsorption in zeolites is often computed using either of the following methods: (1) using the Clausius-Clapeyron equation, which requires the partial derivative of the pressure with respect to temperature at constant loading, (2) using the energy difference between the host with and without a single guest molecule present, and (3) from energy/particle fluctuations in the grand-canonical ensemble. To calculate the heat of adsorption from experiments (besides direct calorimetry), only the first method is usually applicable. Although the computation of the heat of adsorption is straightforward for all-silica zeolites, severe difficulties arise when applying the conventional methods to systems with nonframework cations present. The reason for this is that these nonframework cations have very strong Coulombic interactions with the zeolite. We will present an alternative method based on biased interactions of guest molecules that suffers less from these difficulties. This method requires only a single simulation of the host structure. In addition, we will review some of the other important issues concerning the handling of these strong Coulombic interactions in simulating the adsorption of guest molecules. It turns out that the recently proposed Wolf method ( J. Chem. Phys. 1999, 110 , 8254 ) performs poorly for zeolites as a large cutoff radius is needed for convergence.

Torsional barriers and equilibrium angle of biphenyl: reconciling theory with experiment

Abstract: The barriers of internal rotation of the two phenyl groups in biphenyl are investigated using a combination of coupled cluster and density functional theory. The experimental barriers are for the first time accurately reproduced; our best estimates of the barriers are 8.0 and 8.3 kJ/mol around the planar and perpendicular conformations, respectively. The use of flexible basis sets of at least augmented quadruple-ζ quality is shown to be a crucial prerequisite. Further, to finally reconcile theory with experiment, extrapolations of both the basis set toward the basis set limit and electron correlation toward the full configuration-interaction limit are necessary. The minimum of the torsional angle is significantly increased by free energy corrections, which are needed to reach an agreement with experiment. The density functional B3LYP approach is found to perform well compared with the highest level ab initio results.

Performance of the Density Functional Theory/Multireference Configuration Interaction Method on Electronic Excitation of Extended π-Systems.

Abstract: The combined density functional theory/multireference configuration interaction (DFT/MRCI) method [Grimme and Waletzke. J. Chem. Phys. 1999, 111, 5645] has been employed to study the 1La and 1Lb states of linear polyacenes and the low-lying triplet and singlet states of linear polyenes and diphenyl-polyenes. We have systematically investigated the dependence of the electronic state properties on technical parameters of the calculations such as the atomic orbital basis set or the geometry optimization approach. The choice of basis set appears to be of minor importance whereas the excitation energies of the polyenes are quite sensitive to the ground-state geometry parameters. The DFT/MRCI energies at the B3-LYP optimized geometries systematically underestimate the experimental values, but we do not observe a bias toward one or the other type of state. The energy gaps between the electronically excited states are reproduced very well. In particular, this applies also to the first excited singlet 2 1Ag− and t...

Implementation and Performance of DFT-D with Respect to Basis Set and Functional for Study of Dispersion Interactions in Nanoscale Aromatic Hydrocarbons.

Abstract: The implementation, optimization, and performance of various DFT-D schemes have been tested on models for polar−π interactions between arenes spaced at van der Waals distances and on a series of functionalized corannulene derivatives and complexes. For DFT-D schemes involving a semiempirical correction, optimized parameters are proposed for several basis sets. Performance of the different DFT-D strategies is compared, where functionals include some of the most recently proposed, B97D, B2PLYP, BMK, and M06−2X functionals, together with several other well-known functionals. Semiempircally corrected dispersion functionals hold some promise as useful and affordable methods for studies involving large polynuclear aromatic molecules and molecules on metal surfaces.

Zn Coordination Chemistry: Development of Benchmark Suites for Geometries, Dipole Moments, and Bond Dissociation Energies and Their Use To Test and Validate Density Functionals and Molecular Orbital Theory

Abstract: We present nonrelativistic and relativistic benchmark databases (obtained by coupled cluster calculations) of 10 Zn-ligand bond distances, 8 dipole moments, and 12 bond dissociation energies in Zn coordination compounds with O, S, NH3, H2O, OH, SCH3, and H ligands. These are used to test the predictions of 39 density functionals, Hartree-Fock theory, and seven more approximate molecular orbital theories. In the nonrelativisitic case, the M05-2X, B97-2, and mPW1PW functionals emerge as the most accurate ones for this test data, with unitless balanced mean unsigned errors (BMUEs) of 0.33, 0.38, and 0.43, respectively. The best local functionals (i.e., functionals with no Hartree-Fock exchange) are M06-L and τ-HCTH with BMUEs of 0.54 and 0.60, respectively. The popular B3LYP functional has a BMUE of 0.51, only slightly better than the value of 0.54 for the best local functional, which is less expensive. Hartree-Fock theory itself has a BMUE of 1.22. The M05-2X functional has a mean unsigned error of 0.008 A for bond lengths, 0.19 D for dipole moments, and 4.30 kcal/mol for bond energies. The X3LYP functional has a smaller mean unsigned error (0.007 A) for bond lengths but has mean unsigned errors of 0.43 D for dipole moments and 5.6 kcal/mol for bond energies. The M06-2X functional has a smaller mean unsigned error (3.3 kcal/mol) for bond energies but has mean unsigned errors of 0.017 A for bond lengths and 0.37 D for dipole moments. The best of the semiempirical molecular orbital theories are PM3 and PM6, with BMUEs of 1.96 and 2.02, respectively. The ten most accurate functionals from the nonrelativistic benchmark analysis are then tested in relativistic calculations against new benchmarks obtained with coupled-cluster calculations and a relativistic effective core potential, resulting in M05-2X (BMUE = 0.895), PW6B95 (BMUE = 0.90), and B97-2 (BMUE = 0.93) as the top three functionals. We find significant relativistic effects (∼0.01 A in bond lengths, ∼0.2 D in dipole moments, and ∼4 kcal/mol in Zn-ligand bond energies) that cannot be neglected for accurate modeling, but the same density functionals that do well in all-electron nonrelativistic calculations do well with relativistic effective core potentials. Although most tests are carried out with augmented polarized triple-ζ basis sets, we also carried out some tests with an augmented polarized double-ζ basis set, and we found, on average, that with the smaller basis set DFT has no loss in accuracy for dipole moments and only ∼10% less accurate bond lengths.

Assessment of a Middle-Range Hybrid Functional

Abstract: While hybrid functionals are largely responsible for the utility of modern Kohn-Sham density functional theory, they are not without their weaknesses. In the solid state, the slow decay of their nonlocal Hartree-Fock-type exchange makes hybrids computationally demanding and can introduce unphysical effects. Both problems can be remedied by a screened hybrid which uses exact exchange only at short-range. Many molecular properties, in contrast, benefit from the inclusion of long-range exact exchange. Recently, the authors reconciled these two seemingly contradictory requirements by introducing the HISS functional [ J. Chem. Phys. 2007 , 127 , 221103 ], which uses exact exchange only in the middle range. In this paper, we expand upon our previous work, benchmarking the performance of the HISS functional for several simple properties and applying it to the dissociation of homonuclear diatomic cations and to the polarizability of linear H2 chains to determine the importance of middle-range exact exchange for these systems, which are expected to be sensitive to the asymptotic exchange potential.

Accelerating Density Functional Calculations with Graphics Processing Unit.

Abstract: An algorithm is presented for graphics processing units (GPUs), which execute single-precision arithmetic much faster than commodity microprocessors (CPUs), to calculate the exchange-correlation term in ab initio density functional calculations. The algorithm was implemented and applied to two molecules, taxol and valinomycin. The errors in the total energies were about 10(-5) a.u., which is accurate enough for practical usage. If the exchange-correlation term is split into a simple analytic model potential and the correction to it, and only the latter is calculated with the GPU, the energy error is decreased by an order of magnitude. The resulting time to compute the exchange-correlation term is smaller than it is on the latest CPU by a factor of 10, indicating that a GPU running the proposed algorithm accelerates the density functional calculation considerably.

Characterization of Chitin and Chitosan Molecular Structure in Aqueous Solution.

Abstract: Molecular dynamics simulations have been used to characterize the structure of single chitin and chitosan chains in aqueous solutions Chitin chains, whether isolated or in the form of a β-chitin nanoparticle, adopt the 2-fold helix with ϕ and φ values similar to its crystalline state In solution, the intramolecular hydrogen bond HO3(n)···O5(n+1) responsible for the 2-fold helical motif in these polysaccharides is stabilized by hydrogen bonds with water molecules in a well-defined orientation On the other hand, chitosan can adopt five distinct helical motifs, and its conformational equilibrium is highly dependent on pH The hydrogen bond pattern and solvation around the O3 atom of insoluble chitosan (basic pH) are nearly identical to these quantities in chitin Our findings suggest that the solubility and conformation of these polysaccharides are related to the stability of the intrachain HO3(n)···O5(n+1) hydrogen bond, which is affected by the water exchange around the O3-HO3 hydroxyl group

Multireference Model Chemistries for Thermochemical Kinetics.

Abstract: By combining the generalized valence bond ansatz of correlated participating orbitals (CPO) with the complete-active-space prescription for selecting configurations and with the use of multireference second order perturbation theory (MRMP2) for including dynamical correlation, we define three levels of multireference (MR) theoretical model chemistries for electronic structure calculations of chemical reaction energies and barrier heights. The three levels differ in their choice of which orbitals are considered to be participating; the choices are called nominal (nom-CPO), moderate (mod-CPO), and extended (ext-CPO). Combining any of these three choices with a method for treatment of dynamical correlation energy and a one-electron basis set yields a theoretical model chemistry. Unlike the full-valence choice of active orbitals, the CPO choices lead to active spaces that contain the orbitals needed to include important static correlation effects on chemical reactions but do not increase with the size of the nonparticipating portion of the system, and hence they remain viable computational options even for many large and complex reacting systems. The accuracies of the new levels, combined with the MG3S basis set (a partially augmented, multiply polarized valence triple-ζ basis with appropriately tight d functions for 3p-block elements) and with the fully augmented correlation-consistent aug-cc-pVTZ basis set, are assessed against a previously presented database of barrier heights for diverse reaction types. We find that nom-CPO level captures the bulk of the static correlation energy, and MRMP2/nom-CPO calculations have an average error of only 1.4 kcal/mol in barrier heights, which may be compared to 5.0 kcal/mol for single-reference MP2 theory, 2.5 kcal/mol for CCSD, and 4.1 and 1.0 kcal/mol for the B3LYP and M06-2X density functionals, respectively. The accuracy of MRMP2/CPO for transition structure bond lengths and donor-acceptor distances is excellent, with a mean unsigned error of only 0.007 A as compared to 0.018 A for CCSD, 0.019 A for M06-2X, and 0.039 A for MP2 and B3LYP. We also introduce a new multireference diagnostic, called the M diagnostic, that allows one to measure the importance of static correlation in a given reagent or transition state.

The pDynamo Program for Molecular Simulations using Hybrid Quantum Chemical and Molecular Mechanical Potentials.

Abstract: The pDynamo program has been developed for the simulation of molecular systems using hybrid quantum chemical (QC) and molecular mechanical (MM) potentials. pDynamo is written in a mixture of the computer languages Python and C and is a successor to the previous version of Dynamo, now denoted fDynamo, that was written in Fortran 90 (J. Comput. Chem. 2000, 21, 1088). The current version of Dynamo has a similar range of functionality to the older one but extends it in some significant ways, including the addition of a density functional theory QC capability. This paper gives a general description of pDynamo and outlines some of the advantages and disadvantages that have been encountered in switching computer languages. Some technical aspects of the implementation of pDynamo's algorithms are also discussed and illustrated with the results of example calculations. pDynamo is available on the Web at the address http://www.pdynamo.org and is released under the CeCILL license which is equivalent to the GNU general public license but conforms to the principles of French law.

The "Hot-Solvent/Cold-Solute" Problem Revisited.

Abstract: The temperature steers the equilibrium and nonequilibrium conformational dynamics of macromolecules in solution. Therefore, corresponding molecular dynamics simulations require a strategy for tempe...