Showing papers in "Journal of Chemical Theory and Computation in 2011"
TL;DR: The rules and parameters for one of the most commonly used empirical pKa predictors, PROPKA, are revised based on better physical description of the desolvation and dielectric response for the protein, and a new and consistent approach to interpolate the description between the previously distinct classifications into internal and surface residues is introduced.
Abstract: In this study, we have revised the rules and parameters for one of the most commonly used empirical pKa predictors, PROPKA, based on better physical description of the desolvation and dielectric response for the protein. We have introduced a new and consistent approach to interpolate the description between the previously distinct classifications into internal and surface residues, which otherwise is found to give rise to an erratic and discontinuous behavior. Since the goal of this study is to lay out the framework and validate the concept, it focuses on Asp and Glu residues where the protein pKa values and structures are assumed to be more reliable. The new and improved implementation is evaluated and discussed; it is found to agree better with experiment than the previous implementation (in parentheses): rmsd = 0.79 (0.91) for Asp and Glu, 0.75 (0.97) for Tyr, 0.65 (0.72) for Lys, and 1.00 (1.37) for His residues. The most significant advance, however, is in reducing the number of outliers and removing...
2,833 citations
TL;DR: The NCI computational algorithms and their implementation for the analysis and visualization of weak interactions, using both self-consistent fully quantum-mechanical, as well as promolecular, densities are described.
Abstract: Noncovalent interactions hold the key to understanding many chemical, biological, and technological problems. Describing these noncovalent interactions accurately, including their positions in real space, constitutes a first step in the process of decoupling the complex balance of forces that define noncovalent interactions. Because of the size of macromolecules, the most common approach has been to assign van der Waals interactions (vdW), steric clashes (SC), and hydrogen bonds (HBs) based on pairwise distances between atoms according to their vdW radii. We recently developed an alternative perspective, derived from the electronic density: the non-covalent interactions (NCI) index [J. Am. Chem. Soc. 2010, 132, 6498]. This index has the dual advantages of being generally transferable to diverse chemical applications and being very fast to compute, since it can be calculated from promolecular densities. Thus, NCI analysis is applicable to large systems, including proteins and DNA, where analysis of noncova...
2,596 citations
TL;DR: The Automated force field Topology Builder is a Web-accessible server that can provide topologies and parameters for a wide range of molecules appropriate for use in molecular simulations, computational drug design, and X-ray refinement.
Abstract: The Automated force field Topology Builder (ATB, http://compbio.biosci.uq.edu.au/atb) is a Web-accessible server that can provide topologies and parameters for a wide range of molecules appropriate for use in molecular simulations, computational drug design, and X-ray refinement. The ATB has three primary functions: (1) to act as a repository for molecules that have been parametrized as part of the GROMOS family of force fields, (2) to act as a repository for pre-equilibrated systems for use as starting configurations in molecular dynamics simulations (solvent mixtures, lipid systems pre-equilibrated to adopt a specific phase, etc.), and (3) to generate force field descriptions of novel molecules compatible with the GROMOS family of force fields in a variety of formats (GROMOS, GROMACS, and CNS). Force field descriptions of novel molecules are derived using a multistep process in which results from quantum mechanical (QM) calculations are combined with a knowledge-based approach to ensure compatibility (a...
1,328 citations
TL;DR: A novel algorithm is presented that identifies noncovalently coupled ionizable groups, where pKa prediction may be especially difficult, which is a general improvement to PROPKA and is applied to proteins with and without ligands.
Abstract: The new empirical rules for protein pKa predictions implemented in the PROPKA3.0 software package (Olsson et al. J. Chem. Theory Comput.2010, 7, 525–537) have been extended to the prediction of pKa shifts of active site residues and ionizable ligand groups in protein–ligand complexes. We present new algorithms that allow pKa shifts due to inductive (i.e., covalently coupled) intraligand interactions, as well as noncovalently coupled interligand interactions in multiligand complexes, to be included in the prediction. The number of different ligand chemical groups that are automatically recognized has been increased to 18, and the general implementation has been changed so that new functional groups can be added easily by the user, aided by a new and more general protonation scheme. Except for a few cases, the new algorithms in PROPKA3.1 are found to yield results similar to or better than those obtained with PROPKA2.0 (Bas et al. Proteins: Struct., Funct., Bioinf.2008, 73, 765–783). Finally, we present a n...
1,306 citations
TL;DR: An extended and improved version of the recently published database for general main group thermochemistry, kinetics, and noncovalent interactions is presented, and the PWPB95-D3 functional is recommended in general chemistry applications as the least basis set dependent and the best functional at the triple-ζ level.
Abstract: We present an extended and improved version of our recently published database for general main group thermochemistry, kinetics, and noncovalent interactions [J. Chem. Theory Comput. 2010, 6, 107], which is dubbed GMTKN30. Furthermore, we suggest and investigate two new double-hybrid-meta-GGA density functionals called PTPSS-D3 and PWPB95-D3. PTPSS-D3 is based on reparameterized TPSS exchange and correlation contributions; PWPB95-D3 contains reparameterized PW exchange and B95 parts. Both functionals contain fixed amounts of 50% Fock-exchange. Furthermore, they include a spin-opposite scaled perturbative contribution and are combined with our latest atom-pairwise London-dispersion correction [J. Chem. Phys. 2010, 132, 154104]. When evaluated with the help of the Laplace transformation algorithm, both methods scale as N(4) with system size. The functionals are compared with the double hybrids B2PLYP-D3, B2GPPLYP-D3, DSD-BLYP-D3, and XYG3 for GMTKN30 with a quadruple-ζ basis set. PWPB95-D3 and DSD-BLYP-D3 are the best functionals in our study and turned out to be more robust than B2PLYP-D3 and XYG3. Furthermore, PWPB95-D3 is the least basis set dependent and the best functional at the triple-ζ level. For the example of transition metal carbonyls, it is shown that, mainly due to the lower amount of Fock-exchange, PWPB95-D3 and PTPSS-D3 are better applicable than the other double hybrids. Finally, we discuss in some detail the XYG3 functional [Proc. Nat. Acad. Sci. U.S.A. 2009, 106, 4963], which makes use of B3LYP orbitals and electron densities. We show that it is basically a highly nonlocal variant of B2PLYP and that its partially good performance is mainly due to a larger effective amount of perturbative correlation compared to other double hybrids. We finally recommend the PWPB95-D3 functional in general chemistry applications.
999 citations
TL;DR: A large new database of interaction energies calculated using an accurate CCSD(T)/CBS scheme is presented, designed to cover the most common types of noncovalent interactions in biomolecules, while keeping a balanced representation of dispersion and electrostatic contributions.
Abstract: With numerous new quantum chemistry methods being developed in recent years and the promise of even more new methods to be developed in the near future, it is clearly critical that highly accurate, well-balanced, reference data for many different atomic and molecular properties be available for the parametrization and validation of these methods One area of research that is of particular importance in many areas of chemistry, biology, and material science is the study of noncovalent interactions Because these interactions are often strongly influenced by correlation effects, it is necessary to use computationally expensive high-order wave function methods to describe them accurately Here, we present a large new database of interaction energies calculated using an accurate CCSD(T)/CBS scheme Data are presented for 66 molecular complexes, at their reference equilibrium geometries and at 8 points systematically exploring their dissociation curves; in total, the database contains 594 points: 66 at equilib
822 citations
TL;DR: The present study combines earlier extensions and improves them consistently with, first, an improved Coulomb interaction between atomic partial charges, and second, the complete third-order expansion of the DFT total energy, leading to the next generation of theDFTB methodology called DFTB3, which substantially improves the description of charged systems containing elements C, H, N, O, and P.
Abstract: The self-consistent-charge density-functional tight-binding method (SCC-DFTB) is an approximate quantum chemical method derived from density functional theory (DFT) based on a second-order expansion of the DFT total energy around a reference density. In the present study we combine earlier extensions and improve them consistently with, first, an improved Coulomb interaction between atomic partial charges, and second, the complete third-order expansion of the DFT total energy. These modifications lead us to the next generation of the DFTB methodology called DFTB3, which substantially improves the description of charged systems containing elements C, H, N, O, and P, especially regarding hydrogen binding energies and proton affinities. As a result, DFTB3 is particularly applicable to biomolecular systems. Remaining challenges and possible solutions are also briefly discussed.
816 citations
TL;DR: A new index, evaluated only from the computed density for the ground and excited state, is derived and tested on a family of molecules that can be considered as prototypes of push-pull chromophores, to define the spatial extent associated to an electronic transition.
Abstract: With the aim of defining the spatial extent associated to an electronic transition, of particular relevance in the case of charge-transfer (CT) excitations, a new index, evaluated only from the computed density for the ground and excited state, is here derived and tested on a family of molecules that can be considered as prototypes of push–pull chromophores.The index (DCT) allows to define the spatial extent associated to a given transition as well as the associated fraction of electron transferred. By definition of centroids of charges associated to the density increase and depletion zones upon excitation, a qualitative and easy to visualize measure of the spatial extent of the donor and the acceptor moieties within a given molecular system is also given. Finally, an index (t) allowing to define the presence eventually pathologic CT transitions for time-dependent density functional theory treatment in conjunction with standard generalized gradient approximation or hybrid functional, that is through space...
800 citations
TL;DR: The parameters remove destabilization of the anti region found in the ff99 force field and thus prevent formation of spurious ladder-like structural distortions in RNA simulations, and improve the description of the syn region and the syn–anti balance as well as enhance MD simulations of various RNA structures.
Abstract: We report a reparameterization of the glycosidic torsion χ of the Cornell et al. AMBER force field for RNA, χOL. The parameters remove destabilization of the anti region found in the ff99 force field and thus prevent formation of spurious ladder-like structural distortions in RNA simulations. They also improve the description of the syn region and the syn–anti balance as well as enhance MD simulations of various RNA structures. Although χOL can be combined with both ff99 and ff99bsc0, we recommend the latter. We do not recommend using χOL for B-DNA because it does not improve upon ff99bsc0 for canonical structures. However, it might be useful in simulations of DNA molecules containing syn nucleotides. Our parametrization is based on high-level QM calculations and differs from conventional parametrization approaches in that it incorporates some previously neglected solvation-related effects (which appear to be essential for obtaining correct anti/high-anti balance). Our χOL force field is compared with sev...
798 citations
TL;DR: It is found that minimal augmentation is almost always enough for density functional theory (DFT) when applied to ionization potentials, electron affinities, atomization energies, barrier heights, and hydrogen-bond energies.
Abstract: We present a perspective on the use of diffuse basis functions for electronic structure calculations by density functional theory and wave function theory. We especially emphasize minimally augmented basis sets and calendar basis sets. We base our conclusions on our previous experience with commonly computed quantities, such as bond energies, barrier heights, electron affinities, noncovalent (van der Waals and hydrogen bond) interaction energies, and ionization potentials, on Stephens et al.’s results for optical rotation and on our own new calculations (presented here) of polarizabilities and of potential energy curves of van der Waals complexes. We emphasize the benefits of partial augmentation of the higher-zeta basis sets in preference to full augmentation at a lower ζ level. Benefits and limitations of the use of fully, partially, and minimally augmented basis sets are reviewed for different electronic structure methods and molecular properties. We have found that minimal augmentation is almost alway...
515 citations
TL;DR: Development of force-field parameters for monosaccharide derivatives and their covalent connections to proteins via O-linkages to serine or threonine sidechains and via N- linkages to asparagine sidechains are detailed.
Abstract: Monosaccharide derivatives such as xylose, fucose, N-acetylglucosamine (GlcNAc), N-acetylgalactosamine (GlaNAc), glucuronic acid, iduronic acid, and N-acetylneuraminic acid (Neu5Ac) are important components of eukaryotic glycans. The present work details development of force-field parameters for these monosaccharides and their covalent connections to proteins via O-linkages to serine or threonine sidechains and via N-linkages to asparagine sidechains. The force field development protocol was designed to explicitly yield parameters that are compatible with the existing CHARMM additive force field for proteins, nucleic acids, lipids, carbohydrates, and small molecules. Therefore, when combined with previously developed parameters for pyranose and furanose monosaccharides, for glycosidic linkages between monosaccharides, and for proteins, the present set of parameters enables the molecular simulation of a wide variety of biologically-important molecules such as complex carbohydrates and glycoproteins. Parametrization included fitting to quantum mechanical (QM) geometries and conformational energies of model compounds, as well as to QM pair interaction energies and distances of model compounds with water. Parameters were validated in the context of crystals of relevant monosaccharides, as well NMR and/or x-ray crystallographic data on larger systems including oligomeric hyaluronan, sialyl Lewis X, O- and N-linked glycopeptides, and a lectin:sucrose complex. As the validated parameters are an extension of the CHARMM all-atom additive biomolecular force field, they further broaden the types of heterogeneous systems accessible with a consistently-developed force-field model.
TL;DR: A semiclassical surface-hopping method which is able to treat arbitrary couplings in molecular systems including all degrees of freedom is presented, in very good agreement with those calculated from exact quantum dynamical simulations.
Abstract: We present a semiclassical surface-hopping method which is able to treat arbitrary couplings in molecular systems including all degrees of freedom. A reformulation of the standard surface-hopping scheme in terms of a unitary transformation matrix allows for the description of interactions like spin−orbit coupling or transitions induced by laser fields. The accuracy of our method is demonstrated in two systems. The first one, consisting of two model electronic states, validates the semiclassical approach in the presence of an electric field. In the second one, the dynamics in the IBr molecule in the presence of spin−orbit coupling after laser excitation is investigated. Due to an avoided crossing that originates from spin−orbit coupling, IBr dissociates into two channels: I + Br(2P3/2) and I + Br*(2P1/2). In both systems, the obtained results are in very good agreement with those calculated from exact quantum dynamical simulations.
TL;DR: An improved protocol for constructing Markov State Models from molecular dynamics simulations is described, which leads to significant increases in model accuracy, as assessed by the ability to recapitulate equilibrium and kinetic properties of reference systems.
Abstract: Markov state models provide a framework for understanding the fundamental states and rates in the conformational dynamics of biomolecules. We describe an improved protocol for constructing Markov state models from molecular dynamics simulations. The new protocol includes advances in clustering, data preparation, and model estimation; these improvements lead to significant increases in model accuracy, as assessed by the ability to recapitulate equilibrium and kinetic properties of reference systems. A high-performance implementation of this protocol, provided in MSMBuilder2, is validated on dynamics ranging from picoseconds to milliseconds.
TL;DR: The AMOEBA force field performs well across different environments and phases, and the key algorithms involved in the electrostatic model and a protocol for developing parameters are detailed to facilitate extension to additional molecular systems.
Abstract: An empirical potential based on permanent atomic multipoles and atomic induced dipoles is reported for alkanes, alcohols, amines, sulfides, aldehydes, carboxylic acids, amides, aromatics, and other small organic molecules. Permanent atomic multipole moments through quadrupole moments have been derived from gas phase ab initio molecular orbital calculations. The van der Waals parameters are obtained by fitting to gas phase homodimer QM energies and structures, as well as experimental densities and heats of vaporization of neat liquids. As a validation, the hydrogen bonding energies and structures of gas phase heterodimers with water are evaluated using the resulting potential. For 32 homo- and heterodimers, the association energy agrees with ab initio results to within 0.4 kcal/mol. The RMS deviation of the hydrogen bond distance from QM optimized geometry is less than 0.06 A. In addition, liquid self-diffusion and static dielectric constants computed from a molecular dynamics simulation are consistent wit...
TL;DR: The SAPT results confirm that the contribution of dispersion and induction are significant at and near equilibrium, although electrostatics dominate and among the DFT/DFT-D techniques, the best overall results are obtained.
Abstract: Noncovalent interactions such as hydrogen bonds, van der Waals forces, and π-π interactions play important roles influencing the structure, stability, and dynamic properties of biomolecules including DNA and RNA base pairs. In an effort to better understand the fundamental physics of hydrogen bonding (H-bonding), we investigate the distance dependence of interaction energies in the prototype bimolecular complexes of formic acid, formamide, and formamidine. Potential energy curves along the H-bonding dissociation coordinate are examined both by establishing reference CCSD(T) interaction energies extrapolated to the complete basis set limit and by assessing the performance of the density functional methods B3LYP, PBE, PBE0, B970, PB86, M05-2X, and M06-2X and empirical dispersion corrected methods B3LYP-D3, PBE-D3, PBE0-D3, B970-D2, BP86-D3, and ωB97X-D, with basis sets 6-311++G(3df,3pd), aug-cc-pVDZ, and aug-cc-pVTZ. Although H-bonding interactions are dominated by electrostatics, it is necessary to properly account for dispersion interactions to obtain accurate energetics. In order to quantitatively probe the nature of hydrogen bonding interactions as a function of distance, we decompose the interaction energy curves into physically meaningful components with symmetry-adapted perturbation theory (SAPT). The SAPT results confirm that the contribution of dispersion and induction are significant at and near equilibrium, although electrostatics dominate. Among the DFT/DFT-D techniques, the best overall results are obtained utilizing counterpoise-corrected ωB97X-D with the aug-cc-pVDZ basis set.
TL;DR: dDsC, presented herein, is constructed from dispersion coefficients computed on the basis of a generalized gradient approximation to Becke and Johnson's exchange-hole dipole moment formalism, making the approach especially valuable for modeling redox reactions and charged species in general.
Abstract: Standard density functional approximations cannot accurately describe interactions between nonoverlapping densities. A simple remedy consists in correcting for the missing interactions a posteriori, adding an attractive energy term summed over all atom pairs. The density-dependent energy correction, dDsC, presented herein, is constructed from dispersion coefficients computed on the basis of a generalized gradient approximation to Becke and Johnson’s exchange-hole dipole moment formalism. dDsC also relies on an extended Tang and Toennies damping function accounting for charge-overlap effects. The comprehensive benchmarking on 341 diverse reaction energies divided into 18 illustrative test sets validates the robust performance and general accuracy of dDsC for describing various intra- and intermolecular interactions. With a total MAD of 1.3 kcal mol–1, B97-dDsC slightly improves the results of M06-2X and B2PLYP-D3 (MAD = 1.4 kcal mol–1 for both) at a lower computational cost. The density dependence of both ...
TL;DR: The purpose of the toolkit is to simplify the workflow for charge transport simulations, provide a uniform error control for the methods and a flexible platform for their development, and eventually allow in silico prescreening of organic semiconductors for specific applications.
Abstract: Charge carrier dynamics in an organic semiconductor can often be described in terms of charge hopping between localized states. The hopping rates depend on electronic coupling elements, reorganization energies, and driving forces, which vary as a function of position and orientation of the molecules. The exact evaluation of these contributions in a molecular assembly is computationally prohibitive. Various, often semiempirical, approximations are employed instead. In this work, we review some of these approaches and introduce a software toolkit which implements them. The purpose of the toolkit is to simplify the workflow for charge transport simulations, provide a uniform error control for the methods and a flexible platform for their development, and eventually allow in silico prescreening of organic semiconductors for specific applications. All implemented methods are illustrated by studying charge transport in amorphous films of tris-(8-hydroxyquinoline)aluminum, a common organic semiconductor.
TL;DR: The use of the Tamm-Dancoff approximation (TDA) significantly improves the problematic triplet excitation energies, recovering the correct state ordering in benzoquinone; it also affects the corresponding singlet states, recover the correctState ordering in naphthalene.
Abstract: Singlet and triplet vertical excitation energies from time-dependent density functional theory (TDDFT) can be affected in different ways by the inclusion of exact exchange in hybrid or Coulomb-attenuated/range-separated exchange-correlation functionals; in particular, triplet excitation energies can become significantly too low. To investigate these issues, the explicit dependence of excitation energies on exact exchange is quantified for four representative molecules, paying attention to the effect of constant, short-range, and long-range contributions. A stability analysis is used to verify that the problematic TDDFT triplet excitations can be understood in terms of the ground state triplet instability problem, and it is proposed that a Hartree-Fock stability analysis should be used to identify triplet excitations for which the presence of exact exchange in the TDDFT functional is undesirable. The use of the Tamm-Dancoff approximation (TDA) significantly improves the problematic triplet excitation energies, recovering the correct state ordering in benzoquinone; it also affects the corresponding singlet states, recovering the correct state ordering in naphthalene. The impressive performance of the TDA is maintained for a wide range of molecules across representative functionals.
TL;DR: It is found that the semiempirical kinetic-energy-density dependence introduced in the M06 functionals mimics some of the nonlocal correlation needed to describe dispersion, however, long-range contributions are still missing.
Abstract: We present a comparative assessment of the accuracy of two different approaches for evaluating dispersion interactions: interatomic pairwise corrections and semiempirical meta-generalized-gradient-approximation (meta-GGA)-based functionals. This is achieved by employing conventional (semi)local and (screened-)hybrid functionals, as well as semiempirical hybrid and nonhybrid meta-GGA functionals of the M06 family, with and without interatomic pairwise Tkatchenko–Scheffler corrections. All of those are tested against the benchmark S22 set of weakly bound systems, a representative larger molecular complex (dimer of NiPc molecules), and a representative dispersively bound solid (hexagonal boron nitride). For the S22 database, we also compare our results with those obtained from the pairwise correction of Grimme (DFT-D3) and nonlocal Langreth–Lundqvist functionals (vdW-DF1 and vdW-DF2). We find that the semiempirical kinetic-energy-density dependence introduced in the M06 functionals mimics some of the nonloca...
TL;DR: In this paper, a segmented all-electron relativistically contracted (SARC) basis set for the complete actinide series 89Ac−103Lr, optimized for use with the popular Douglas−Kroll−Hess to the second order and zeroth-order regular approximation scalar relativistic Hamiltonians is presented.
Abstract: Increasing interest in the computational modeling of actinide compounds creates the need for alternative choices when in comes to fine tuning the computational methodology in order to best fit the problem at hand. All-electron scalar relativistic density functional theory can be a useful approach for a variety of actinide systems and would benefit from atomic basis sets geared to that level of theory. In this paper we present segmented all-electron relativistically contracted (SARC) basis sets for the complete actinide series 89Ac−103Lr, optimized for use with the popular Douglas−Kroll−Hess to the second order and zeroth-order regular approximation scalar relativistic Hamiltonians. The quality of the SARC basis sets is assessed in terms of their intrinsic incompleteness and contraction errors, with respect to total energies, orbital properties, and ionization energies. Calculations on diatomic Ac and Lr molecules confirm that the valence-space construction results in negligible basis set superposition err...
TL;DR: An efficient and massively parallel real-time real-space time-dependent density functional theory (RT-TDDFT) implementation in NWChem is presented and nonlinear excitation of green fluorescent protein is studied, which shows a blue-shift in the spectrum with increasing perturbation, as well as a saturation in absorption.
Abstract: The response of matter to external fields forms the basis for a vast wealth of fundamental physical processes ranging from light harvesting to nanoscale electron transport. Accurately modeling ultrafast electron dynamics in excited systems thus offers unparalleled insight but requires an inherently nonlinear time-resolved approach. To this end, an efficient and massively parallel real-time real-space time-dependent density functional theory (RT-TDDFT) implementation in NWChem is presented. The implementation is first validated against linear-response TDDFT and experimental results for a series of molecules subjected to small electric field perturbations. Second, nonlinear excitation of green fluorescent protein is studied, which shows a blue-shift in the spectrum with increasing perturbation, as well as a saturation in absorption. Next, the charge dynamics of optically excited zinc porphyrin is presented in real time and real space, with relevance to charge injection in photovoltaic devices. Finally, inte...
TL;DR: A fragment-based protocol for converting membrane simulation systems, comprising a membrane protein embedded in a phospholipid bilayer, from coarse-grained to atomistic resolution, for further refinement and analysis via atomistic simulations is described.
Abstract: Coarse-grained molecular dynamics provides a means for simulating the assembly and the interactions of membrane protein/lipid complexes at a reduced level of representation, allowing longer and larger simulations. We describe a fragment-based protocol for converting membrane simulation systems, comprising a membrane protein embedded in a phospholipid bilayer, from coarse-grained to atomistic resolution, for further refinement and analysis via atomistic simulations. Overall, this provides a method for generating an accurate and well equilibrated membrane protein/lipid complex. We exemplify the protocol using the acid-sensing/amiloride-sensitive ion channel protein (ASIC) channel protein, a trimeric integral membrane protein. The method is further evaluated using a test set of 10 different membrane proteins of differing size and complexity. Simulations are assessed in terms of protein conformational drift, lipid/protein interactions, and lipid dynamics.
TL;DR: The ability of the four families of basis sets to extrapolate SCF and correlation energies to the basis set limit has been investigated and the SCF energy extrapolation proposed by Petersson and co-workers is found to be effective.
Abstract: The performance of several families of basis sets for correlated wave function calculations on molecules is studied. The widely used correlation-consistent basis set family cc-pVXZ (n = D, T, Q, 5) is compared to a systematic series of atomic natural orbital basis sets (ano-pVXZ). These basis sets are built from the cc-pV6Z primitives in atomic multireference average coupled pair functional (MR-ACPF) calculations. Segmented basis sets optimized for self-consistent field calculations (def2-SVP, def2-TZVPP, and def2-QZVPP as well as “pc-n”, n = 1, 2, 3) were also tested. Reference Hartree−Fock energies are determined with the uncontracted aug-cc-pV6Z basis set for a set of 21 small molecules built from H, B, C, N, O, and F. Reference coupled cluster CCSD(T) correlation energies were determined from extrapolation at the cc-pV5Z/cc-pV6Z level. It is found that the ano-pVXZ basis sets outperform the other basis sets. The error in the SCF energies compared to cc-pVXZ basis sets is reduced by about a factor of 3...
TL;DR: It is shown that optimal tuning of a range-separated hybrid functional, so as to enforce the DFT version of Koopmans' theorem, restores the predictive power of TDDFT even for such difficult cases, without any external reference data and without any adjustable parameters.
Abstract: We address the conundrum posed by the well-known failure of time-dependent DFT (TDDFT) with conventional functionals for "charge-transfer-like" excitations in oligoacenes. We show that this failure is due to a small spatial overlap in orbitals obtained from the underlying single-electron orbitals by means of a unitary transformation. We further show that, as in true charge-transfer excitations, this necessarily results in failure of linear-response TDDFT with standard functionals. Range-separated hybrid functionals have been previously shown to mitigate such errors but at the cost of an empirically adjusted range-separation parameter. Here, we explain why this approach should succeed where conventional functionals fail. Furthermore, we show that optimal tuning of a range-separated hybrid functional, so as to enforce the DFT version of Koopmans' theorem, restores the predictive power of TDDFT even for such difficult cases, without any external reference data and without any adjustable parameters. We demonstrate the success of this approach on the oligoacene series and on related hydrocarbons. This resolves a long-standing question in TDDFT and extends the scope of molecules and systems to which TDDFT can be applied in a predictive manner.
TL;DR: The calculations show that the optimal value of Ueff required to match calculated and experimental values of the reaction energy are significantly different from those reported in the literature based on matching lattice parameters or electronic properties and that the use of these values can result in errors in the calculated redox energies.
Abstract: GGA+U calculation were performed for oxides of Ti, V, Mo, and Ce with the objective of establishing the best value of the parameter Ueff to use in order to match the calculated reduction and oxidation energies of each oxide with experimental values. In each case, the reaction involved the hydrogen reduction of an oxide to its next lower oxide and the formation of water. Our calculations show that the optimal value of Ueff required to match calculated and experimental values of the reaction energy are significantly different from those reported in the literature based on matching lattice parameters or electronic properties and that the use of these values of Ueff can result in errors in the calculated redox energies of over 100 kJ/mol. We also found that, when an element exhibits more than two oxidation states, the energy of redox reactions between different pairs of these states are described by slightly different values of Ueff.
TL;DR: The addition of the NL dispersion energy definitely improves the results of all tested functionals and DFT-NL can be recommended as a fully electronic, robust electronic structure method.
Abstract: The nonlocal van der Waals density functional VV10 (Vydrov, O. A.; Van Voorhis, T. J. Chem. Phys.2010, 133, 244103) is tested for the thermochemical properties of 1200+ atoms and molecules in the GMTKN30 database in order to assess its global accuracy. Five GGA and hybrid functionals in unmodified form are augmented by the nonlocal (NL) part of the VV10 functional (one parameter adjusted). The addition of the NL dispersion energy definitely improves the results of all tested functionals. On the basis of little empiricism and basic physical insight, DFT-NL can be recommended as a fully electronic, robust electronic structure method.
TL;DR: The tremendous reduction in computational time due to the GPU allows us to perform a systematic study of the energy-transfer efficiency in the Fenna-Matthews-Olson (FMO) light-harvesting complex at physiological temperature under full consideration of memory effects.
Abstract: Excitonic models of light-harvesting complexes, where the vibrational degrees of freedom are treated as a bath, are commonly used to describe the motion of the electronic excitation through a molecule. Recent experiments point toward the possibility of memory effects in this process and require one to consider time nonlocal propagation techniques. The hierarchical equations of motion (HEOM) were proposed by Ishizaki and Fleming to describe the site-dependent reorganization dynamics of protein environments ( J. Chem. Phys. 2009 , 130 , 234111 ), which plays a significant role in photosynthetic electronic energy transfer. HEOM are often used as a reference for other approximate methods but have been implemented only for small systems due to their adverse computational scaling with the system size. Here, we show that HEOM are also solvable for larger systems, since the underlying algorithm is ideally suited for the usage of graphics processing units (GPU). The tremendous reduction in computational time due to the GPU allows us to perform a systematic study of the energy-transfer efficiency in the Fenna-Matthews-Olson (FMO) light-harvesting complex at physiological temperature under full consideration of memory effects. We find that approximative methods differ qualitatively and quantitatively from the HEOM results and discuss the importance of finite temperature to achieving high energy-transfer efficiencies.
TL;DR: Řezac et al. as mentioned in this paper used a triple-ζ basis set for the CCSD(T) term in the CBS scheme, which allows for the extrapolation of this term to the complete basis set limit.
Abstract: We present two extensions of the recently published S66 data set [Řezac, Riley, Hobza; DOI: 10.1021/ct2002946]. Interaction energies for the equilibrium geometry complexes have been recalculated using a triple-ζ basis set for the CCSD(T) term in the CCSD(T)/CBS scheme. This allows for the extrapolation of this term to the complete basis set limit, improving accuracy by almost 1 order of magnitude compared to the scheme previously used for the S66 set. Now, we estimate the largest error in the set to be about 1%. Validation of several methods against the new data indicates the exceptional robustness and accuracy of the SCS-MI-CCSD method. The second extension improves the coverage of nonequilibrium geometries. We introduce a new data set, S66a8, that samples intermolecular angular degrees of freedom in the S66 complexes. For each of the 66 complexes, eight displaced geometries have been constructed, systematically sampling possible rotations of the monomers. Interaction energies in this set are calculated ...
TL;DR: An efficient strategy for partial augmentation is developed and tested and the advantages of using these partially augmented basis sets for Møller-Plesset second-order perturbation theory (MP2) are shown and recommend which basis sets offer the best accuracy for a given number of basis functions for calculations on large systems.
Abstract: We present sets of convergent, partially augmented basis set levels corresponding to subsets of the augmented “aug-cc-pV(n+d)Z” basis sets of Dunning and co-workers. We show that for many molecular properties a basis set fully augmented with diffuse functions is computationally expensive and almost always unnecessary. On the other hand, unaugmented cc-pV(n+d)Z basis sets are insufficient for many properties that require diffuse functions. Therefore, we propose using intermediate basis sets. We developed an efficient strategy for partial augmentation, and in this article, we test it and validate it. Sequentially deleting diffuse basis functions from the “aug” basis sets yields the “jul”, “jun”, “may”, “apr”, etc. basis sets. Tests of these basis sets for Moller−Plesset second-order perturbation theory (MP2) show the advantages of using these partially augmented basis sets and allow us to recommend which basis sets offer the best accuracy for a given number of basis functions for calculations on large syste...
TL;DR: For simulating proteins at work in millisecond time scale or longer, a coarse-grained molecular dynamics method and software, CafeMol, is developed that has various and flexible means to "switch" the energy functions that induce active motions of the proteins.
Abstract: For simulating proteins at work in millisecond time scale or longer, we develop a coarse-grained (CG) molecular dynamics (MD) method and software, CafeMol. At the resolution of one-particle-per-residue, CafeMol equips four structure-based protein models: (1) the off-lattice Go model, (2) the atomic interaction based CG model for native state and folding dynamics, (3) the multiple-basin model for conformational change dynamics, and (4) the elastic network model for quasiharmonic fluctuations around the native structure. Ligands can be treated either explicitly or implicitly. For mimicking functional motions of proteins driven by some external force, CafeMol has various and flexible means to "switch" the energy functions that induce active motions of the proteins. CafeMol can do parallel computation with modest sized PC clusters. We describe CafeMol methods and illustrate it with several examples, such as rotary motions of F1-ATPase and drug exports from a transporter. The CafeMol source code is available at www.cafemol.org .