Showing papers in "Journal of Computational Chemistry in 2013"
TL;DR: The results show how the changes in the internal parameters associated with the peptide backbone via CMAP and the χ1 and χ2 dihedral parameters leads to improved treatment of the analyzed nonbond interactions.
Abstract: Protein structure and dynamics can be characterized on the atomistic level with both nuclear magnetic resonance (NMR) experiments and molecular dynamics (MD) simulations. Here, we quantify the ability of the recently presented CHARMM36 (C36) force field (FF) to reproduce various NMR observables using MD simulations. The studied NMR properties include backbone scalar couplings across hydrogen bonds, residual dipolar couplings (RDCs) and relaxation order parameter, as well as scalar couplings, RDCs, and order parameters for side-chain amino- and methyl-containing groups. It is shown that the C36 FF leads to better correlation with experimental data compared to the CHARMM22/CMAP FF and suggest using C36 in protein simulations. Although both CHARMM FFs contains the same nonbond parameters, our results show how the changes in the internal parameters associated with the peptide backbone via CMAP and the χ1 and χ2 dihedral parameters leads to improved treatment of the analyzed nonbond interactions. This highlights the importance of proper treatment of the internal covalent components in modeling nonbond interactions with molecular mechanics FFs. © 2013 Wiley Periodicals, Inc.
2,288 citations
TL;DR: A new program, PHI, with the ability to calculate the magnetic properties of large spin systems and complex orbitally degenerate systems, such as clusters of d‐block and f‐block ions, is presented.
Abstract: A new program, PHI, with the ability to calculate the magnetic properties of large spin systems and complex orbitally degenerate systems, such as clusters of d-block and f-block ions, is presented. The program can intuitively fit experimental data from multiple sources, such as magnetic and spectroscopic data, simultaneously. PHI is extensively parallelized and can operate under the symmetric multiprocessing, single process multiple data, or GPU paradigms using a threaded, MPI or GPU model, respectively. For a given problem PHI is been shown to be almost 12 times faster than the well-known program MAGPACK, limited only by available hardware.
1,429 citations
TL;DR: The NBO 6.0 as mentioned in this paper is a new version of the NBO that provides novel "link-free" interactivity with host electronic structure systems, improved search algorithms and labeling conventions, and new analysis options that significantly extend the range of chemical applications.
Abstract: We describe principal features of the newly released version, NBO 6.0, of the natural bond orbital analysis program, that provides novel “link-free” interactivity with host electronic structure systems, improved search algorithms and labeling conventions for a broader range of chemical species, and new analysis options that significantly extend the range of chemical applications. We sketch the motivation and implementation of program changes and describe newer analysis options with illustrative applications. © 2013 Wiley Periodicals, Inc.
1,154 citations
TL;DR: A novel computational technique is proposed by transferring the PW/PAW wavefunctions to a properly chosen local basis using analytically derived expressions that recovers the total and projected electronic DOS with a high degree of confidence, and yields a realistic chemical‐bonding picture in the framework of the projected COHP method.
Abstract: Quantum-chemical computations of solids benefit enormously from numerically efficient plane-wave (PW) basis sets, and together with the projector augmented-wave (PAW) method, the latter have risen to one of the predominant standards in computational solid-state sciences. Despite their advantages, plane waves lack local information, which makes the interpretation of local densities-of-states (DOS) difficult and precludes the direct use of atom-resolved chemical bonding indicators such as the crystal orbital overlap population (COOP) and the crystal orbital Hamilton population (COHP) techniques. Recently, a number of methods have been proposed to overcome this fundamental issue, built around the concept of basis-set projection onto a local auxiliary basis. In this work, we propose a novel computational technique toward this goal by transferring the PW/PAW wavefunctions to a properly chosen local basis using analytically derived expressions. In particular, we describe a general approach to project both PW and PAW eigenstates onto given custom orbitals, which we then exemplify at the hand of contracted multiple-ζ Slater-type orbitals. The validity of the method presented here is illustrated by applications to chemical textbook examples-diamond, gallium arsenide, the transition-metal titanium-as well as nanoscale allotropes of carbon: a nanotube and the C60 fullerene. Remarkably, the analytical approach not only recovers the total and projected electronic DOS with a high degree of confidence, but it also yields a realistic chemical-bonding picture in the framework of the projected COHP method.
1,103 citations
TL;DR: Results on crystal structures, cohesive energies, and solid‐state reaction enthalpies with the modified basis sets, denoted as pob‐TZVP, are compared with selected standard basis sets available from the CRYSTAL basis set database.
Abstract: Consistent basis sets of triple-zeta valence with polarization quality for main group elements and transition metals from row one to three have been derived for periodic quantum-chemical solid-state calculations with the crystalline-orbital program CRYSTAL. They are based on the def2-TZVP basis sets developed for molecules by the Ahlrichs group. Orbital exponents and contraction coefficients have been modified and reoptimized, to provide robust and stable self-consistant field (SCF) convergence for a wide range of different compounds. We compare results on crystal structures, cohesive energies, and solid-state reaction enthalpies with the modified basis sets, denoted as pob-TZVP, with selected standard basis sets available from the CRYSTAL basis set database. The average deviation of calculated lattice parameters obtained with a selected density functional, the hybrid method PW1PW, from experimental reference is smaller with pob-TZVP than with standard basis sets, in particular for metallic systems. The effects of basis set expansion by diffuse and polarization functions were investigated for selected systems.
832 citations
TL;DR: The Insubria Persistent Bioaccumulative and Toxic (PBT) Index model for the prediction of the cumulative behavior of new chemicals as PBTs is implemented and the user can validate single models, predeveloped using also different software.
Abstract: QSARINS (QSAR-INSUBRIA) is a new software for the development and validation of multiple linear regression Quantitative Structure-Activity Relationship (QSAR) models by Ordinary Least Squares method and Genetic Algorithm for variable selection. This program is mainly focused on the external validation of QSAR models. Various tools for explorative analysis of the datasets by Principal Component Analysis, prereduction of input molecular descriptors, splitting of datasets in training and prediction sets, detection of outliers and interpolated or extrapolated predictions, internal and external validation by different parameters, consensus modeling and various plots for visualizations are implemented. QSARINS is a user-friendly platform for QSAR modeling in agreement with the OECD Principles and for the analysis of the reliability of the obtained predicted data. The Insubria Persistent Bioaccumulative and Toxic (PBT) Index model for the prediction of the cumulative behavior of new chemicals as PBTs is implemented. Additionally, QSARINS allows the user to validate single models, predeveloped using also different software. © 2013 Wiley Periodicals, Inc.
479 citations
TL;DR: The Force Field Toolkit (ffTK), described herein, minimizes common barriers to ligand parameterization through algorithm and method development, automation of tedious and error‐prone tasks, and graphical user interface design.
Abstract: The inability to rapidly generate accurate and robust parameters for novel chemical matter continues to severely limit the application of molecular dynamics simulations to many biological systems of interest, especially in fields such as drug discovery. Although the release of generalized versions of common classical force fields, for example, General Amber Force Field and CHARMM General Force Field, have posited guidelines for parameterization of small molecules, many technical challenges remain that have hampered their wide-scale extension. The Force Field Toolkit (ffTK), described herein, minimizes common barriers to ligand parameterization through algorithm and method development, automation of tedious and error-prone tasks, and graphical user interface design. Distributed as a VMD plugin, ffTK facilitates the traversal of a clear and organized workflow resulting in a complete set of CHARMM-compatible parameters. A variety of tools are provided to generate quantum mechanical target data, setup multidimensional optimization routines, and analyze parameter performance. Parameters developed for a small test set of molecules using ffTK were comparable to existing CGenFF parameters in their ability to reproduce experimentally measured values for pure-solvent properties (<15% error from experiment) and free energy of solvation (±0.5 kcal/mol from experiment).
422 citations
TL;DR: A quantum chemical method based on a Hartree‐Fock calculation with a small Gaussian AO basis set with good results approaching large basis set DFT quality are obtained at a tiny fraction of computational cost.
Abstract: A quantum chemical method based on a Hartree-Fock calculation with a small Gaussian AO basis set is presented. Its main area of application is the computation of structures, vibrational frequencies, and noncovalent interaction energies in huge molecular systems. The method is suggested as a partial replacement of semiempirical approaches or density functional theory (DFT) in particular when self-interaction errors are acute. In order to get accurate results three physically plausible atom pair-wise correction terms are applied for London dispersion interactions (D3 scheme), basis set superposition error (gCP scheme), and short-ranged basis set incompleteness effects. In total nine global empirical parameters are used. This so-called Hartee-Fock-3c (HF-3c) method is tested for geometries of small organic molecules, interaction energies and geometries of noncovalently bound complexes, for supramolecular systems, and protein structures. In the majority of realistic test cases good results approaching large basis set DFT quality are obtained at a tiny fraction of computational cost.
362 citations
TL;DR: The present study reports that the web application can be easily used for computation of rm2 metrics provided observed and QSAR‐predicted data for a set of compounds are available and scaling of response data is recommended prior to rm2 calculation.
Abstract: Quantitative structure-activity relationship (QSAR) techniques have found wide application in the fields of drug design, property modeling, and toxicity prediction of untested chemicals. A rigorous validation of the developed models plays the key role for their successful application in prediction for new compounds. The r(m)(2) metrics introduced by Roy et al. have been extensively used by different research groups for validation of regression-based QSAR models. This concept has been further advanced here with introduction of scaling of response data prior to computation of r(m)(2). Further, a web application (accessible from http://aptsoftware.co.in/rmsquare/ and http://203.200.173.43:8080/rmsquare/) for calculation of the r(m)(2) metrics has been introduced here. The present study reports that the web application can be easily used for computation of r(m)(2) metrics provided observed and QSAR-predicted data for a set of compounds are available. Further, scaling of response data is recommended prior to r(m)(2) calculation.
360 citations
TL;DR: A critical analysis of the variables and components that maximize the accuracy of DHs is provided, and the quality of DSD‐DFT is only mildly dependent on the underlying DFT exchange and correlation components, with even D SD‐LDA yielding respectable performance.
Abstract: Following up on an earlier preliminary communication (Kozuch and Martin, Phys. Chem. Chem. Phys. 2011, 13, 20104), we report here in detail on an extensive search for the most accurate spin-component-scaled double hybrid functionals [of which conventional double hybrids (DHs) are a special case]. Such fifth-rung functionals approach the performance of composite ab initio methods such as G3 theory at a fraction of their computational cost, and with analytical derivatives available. In this article, we provide a critical analysis of the variables and components that maximize the accuracy of DHs. These include the selection of the exchange and correlation functionals, the coefficients of each component [density functional theory (DFT), exact exchange, and perturbative correlation in both the same spin and opposite spin terms], and the addition of an ad-hoc dispersion correction; we have termed these parametrizations "DSD-DFT" (Dispersion corrected, Spin-component scaled, Double-hybrid DFT). Somewhat surprisingly, the quality of DSD-DFT is only mildly dependent on the underlying DFT exchange and correlation components, with even DSD-LDA yielding respectable performance. Simple, nonempirical GGAs appear to work best, whereas meta-GGAs offer no advantage (with the notable exception of B95c). The best correlation components appear to be, in that order, B95c, P86, and PBEc, while essentially any good GGA exchange yields nearly identical results. On further validation with a wider variety of thermochemical, weak interaction, kinetic, and spectroscopic benchmarks, we find that the best functionals are, roughly in that order, DSD-PBEhB95, DSD-PBEP86, DSD-PBEPW91, and DSD-PBEPBE. In addition, DSD-PBEP86 and DSD-PBEPBE can be used without source code modifications in a wider variety of electronic structure codes. Sample job decks for several commonly used such codes are supplied as electronic Supporting Information.
271 citations
TL;DR: The QM‐ORSA protocol has been validated by comparison with experimental results, and its uncertainties have been proven to be no larger than those arising from experiments, which are expected to contribute increasing the kinetic data for free radical‐molecule reactions relevant to oxidative stress, which is currently rather scarce.
Abstract: The accurate prediction of rate constants for chemical reactions in solution, using computational methods, is a challenging task. In this work, a computational protocol designed to be a reliable tool in the study of radical-molecule reactions in solution is presented. It is referred to as quantum mechanics-based test for overall free radical scavenging activity (QM-ORSA) because it is mainly intended to provide a universal and quantitative way of evaluating the free radical scavenging activity of chemical compounds. That is, its primary antioxidant activity. However, it can also be successfully applied to obtain accurate kinetic data for other chemical reactions in solution. The QM-ORSA protocol has been validated by comparison with experimental results, and its uncertainties have been proven to be no larger than those arising from experiments. Further applications of QM-ORSA are expected to contribute increasing the kinetic data for free radical-molecule reactions relevant to oxidative stress, which is currently rather scarce.
TL;DR: It is shown that the accuracy of both methods is comparable, but that the fuzzy cells scheme is better suited for geometry optimization than the Voronoi space partitioning.
Abstract: In this article, we document a new implementation of the fuzzy cells scheme for numerical integration in polyatomic systems [Becke, J. Chem. Phys. 1998, 88, 2547] and compare its efficiency and accuracy with respect to an integration scheme based on the Voronoi space partitioning. We show that the accuracy of both methods is comparable, but that the fuzzy cells scheme is better suited for geometry optimization. For this method, we also introduce the locally dense grid concept and present a proof-of-concept application. © 2013 Wiley Periodicals, Inc.
TL;DR: A systematic approach is proposed for locating reaction paths that bypasses the required human effort and expands the reactive search space, all while maintaining low computational cost.
Abstract: Due to the significant human effort and chemical intuition required to locate chemical reaction pathways with quantum chemical modeling, only a small subspace of possible reactions is usually investigated for any given system. Herein, a systematic approach is proposed for locating reaction paths that bypasses the required human effort and expands the reactive search space, all while maintaining low computational cost. To achieve this, a range of intermediates are generated that represent potential single elementary steps away from a starting structure. These structures are then screened to identify those that are thermodynamically accessible, and then feasible reaction paths to the remaining structures are located. This strategy for elementary reaction path finding is independent of atomistic model whenever bond breaking and forming are properly described. The approach is demonstrated to work well for upper main group elements, but this limitation can easily be surpassed. Further extension will allow discovery of multistep reaction mechanisms in a single computation. The method is highly parallel, allowing for effective use of modern large-scale computational clusters.
TL;DR: An open‐source object‐oriented C++ library of classes and routines to perform tensor algebra to enable post‐Hartree–Fock electronic structure methods and offers a set of general tensor symmetry algorithms and a full implementation of tensor symmetries typically found in electronic structure theory.
Abstract: This article presents an open-source object-oriented C11 library of classes and routines to perform tensor algebra. The primary purpose of the library is to enable postHartree–Fock electronic structure methods; however, the code is general enough to be applicable in other areas of physical and computational sciences. The library supports tensors of arbitrary order (dimensionality), size, and symmetry. Implemented data structures and algorithms operate on large tensors by splitting them into smaller blocks, storing them both in core memory and in files on disk, and applying divide-and-conquer-type parallel algorithms to perform tensor algebra. The library offers a set of general tensor symmetry algorithms and a full implementation of tensor symmetries typically found in electronic structure theory: permutational, spin, and molecular point group symmetry. The Q-Chem electronic structure software uses this library to drive coupled-cluster, equation-of-motion, and algebraicdiagrammatic construction methods. V C 2013 Wiley Periodicals, Inc.
TL;DR: GALAMOST is a molecular simulation package designed to utilize the computational power of GPUs developed specially for the studies of self‐assembly, phase transition, and other properties of polymeric systems at mesoscopic scale by using some lately developed simulation techniques.
Abstract: GALAMOST [graphics processing unit (GPU)-accelerated large-scale molecular simulation toolkit] is a molecular simulation package designed to utilize the computational power of GPUs. Besides the common features of molecular dynamics (MD) packages, it is developed specially for the studies of self-assembly, phase transition, and other properties of polymeric systems at mesoscopic scale by using some lately developed simulation techniques. To accelerate the simulations, GALAMOST contains a hybrid particle-field MD technique where particle–particle interactions are replaced by interactions of particles with density fields. Moreover, the numerical potential obtained by bottom-up coarse-graining methods can be implemented in simulations with GALAMOST. By combining these force fields and particle-density coupling method in GALAMOST, the simulations for polymers can be performed with very large system sizes over long simulation time. In addition, GALAMOST encompasses two specific models, that is, a soft anisotropic particle model and a chain-growth polymerization model, by which the hierarchical self-assembly of soft anisotropic particles and the problems related to polymerization can be studied, respectively. The optimized algorithms implemented on the GPU, package characteristics, and benchmarks of GALAMOST are reported in detail.
TL;DR: An in‐depth insight into the nature of the involved excited states based on transition density matrix and charge density difference indicates that 7 may be superior to 1 and may act as a promising donor candidate for organic solar cell.
Abstract: To seek for high-performance small molecule donor materials used in heterojunction solar cell, six acceptor-donor-acceptor small molecules based on naphtho[2,3-b:6,7-b']dithiophene (NDT) units with different acceptor units were designed and characterized using density functional theory and time-dependent density functional theory. Their geometries, electronic structures, photophysical, and charge transport properties have been scrutinized comparing with the reported donor material NDT(TDPP)2 (TDPP = thiophene-capped diketopyrrolopyrrole). The open circuit voltage (V(oc)), energetic driving force(ΔE(L-L)), and exciton binding energy (E(b)) were also provided to give an elementary understanding on their cell performance. The results reveal that the frontier molecular orbitals of 3-7 match well with the acceptor material PC61 BM, and compounds 3-5 were found to exhibit the comparable performances to 1 and show promising potential in organic solar cells. In particular, comparing with 1, system 7 with naphthobisthiadiazole acceptor unit displays broader absorption spectrum, higher V(oc), lower E(b), and similar carrier mobility. An in-depth insight into the nature of the involved excited states based on transition density matrix and charge density difference indicates that all S1 states are mainly intramolecular charge transfer states with the charge transfer from central NDT unit to bilateral acceptor units, and also imply that the exciton of 7 can be dissociated easily due to its large extent of the charge transfer. In a word, 7 maybe superior to 1 and may act as a promising donor candidate for organic solar cell.
TL;DR: The Lattice Microbes software package for simulating cell models on HPC systems is introduced and the new algorithm efficiently samples the reaction‐diffusion master equation using NVIDIA graphics processing units and is shown to be two orders of magnitude faster than exact sampling for large systems while maintaining an accuracy of ∼0.1%.
Abstract: Spatial stochastic simulation is a valuable technique for studying reactions in biological systems. With the availability of high-performance computing (HPC), the method is poised to allow integration of data from structural, single-molecule and biochemical studies into coherent computational models of cells. Here, we introduce the Lattice Microbes software package for simulating such cell models on HPC systems. The software performs either well-stirred or spatially resolved stochastic simulations with approximated cytoplasmic crowding in a fast and efficient manner. Our new algorithm efficiently samples the reaction-diffusion master equation using NVIDIA graphics processing units and is shown to be two orders of magnitude faster than exact sampling for large systems while maintaining an accuracy of ∼0.1%. Display of cell models and animation of reaction trajectories involving millions of molecules is facilitated using a plug-in to the popular VMD visualization platform. The Lattice Microbes software is open source and available for download at http://www.scs.illinois.edu/schulten/lm © 2012 Wiley Periodicals, Inc.
TL;DR: This study evaluates the importance of electrostatic corrections to earlier quantum‐mechanically based methods to predict crystal densities of neutral and ionic molecular energetic materials and shows a significant improvement to the earlier method upon inclusion of electrostatically corrected methods.
Abstract: This study evaluates the importance of electrostatic corrections to earlier quantum-mechanically based methods to predict crystal densities of neutral and ionic molecular energetic materials. Our previous methods (B. M. Rice et al., J. Phys. Chem. A 2007, 111, 10874) use the molecular volumes of the isolated molecule or formula unit to estimate the crystal density; this volume is defined to be that inside the quantum-mechanically determined 0.001 a.u. isosurface of electron density surrounding the isolated molecule. The electrostatic corrections to these volumetric estimates are based on features of the electrostatic potential mapped onto this isosurface of electron density, and have been parameterized using information from 180 neutral and 23 ionic CHNO molecular systems. The quality of the electrostatically corrected methods was assessed through application to 38 neutral and 48 ionic compounds not used in the parameterization. The root mean square (rms) percent deviation and average absolute error of predictions for the 38 neutral species relative to experiment are 2.7% and 0.035 g/cm3, respectively, decreases of 0.9% and 0.015 g/cm3 from the earlier predictions (3.6% and 0.050 g/cm3, respectively). The rms percent deviation and average absolute error of predictions for the 48 ionic compounds relative to experiment are 3.7% and 0.045 g/cm3, respectively, decreases of 2.6% and 0.043 g/cm3 from the earlier predictions that used the formula unit volumes only. The results clearly show a significant improvement to the earlier method upon inclusion of electrostatic corrections. © 2013 Wiley Periodicals, Inc.
TL;DR: The results predict that M06L is the most trustworthy DFT method in Gaussian09 to study small non‐covalently interacting systems, and long‐range correction of Hirao and coworkers to exchange‐correlation functionals showed massive improvement in geometry and Eint.
Abstract: A benchmark study on all possible density functional theory (DFT) methods in Gaussian09 is done to locate functionals that agree well with CCSD/aug-cc-pVTZ geometry and Ave-CCSD(T)/(Q-T) interaction energy (Eint) for small non-covalently interacting molecular dimers in “dispersion-dominated” (class 1), “dipole-induced dipole” (class 2), and “dipole-dipole” (class 3) classes. A DFT method is recommended acceptable if the geometry showed close agreement to CCSD result (RMSD < 0.045) and Eint was within 80–120% accuracy. Among 382 tested functionals, 1–46% gave good geometry, 13–44% gave good Eint, while 1–33% satisfied geometry and energy criteria. Further screening to locate the best performing functionals for all the three classes was made by counting the acceptable values of energy and geometry given by each functionals. The meta-generalized gradient approximation (GGA) functional M06L was the best performer with total 14 hits; seven acceptable energies and seven acceptable geometries. This was the only functional “recommended” for at least two dimers in each class. The functionals M05, B2PLYPD, B971, mPW2PLYPD, PBEB95, and CAM-B3LYP gave 11 hits while PBEhB95, PW91B95, Wb97x, BRxVP86, BRxP86, HSE2PBE, HSEh1PBE, PBE1PBE, PBEh1PBE, and PW91TPSS gave 10 hits. Among these, M05, B971, mPW2PLYPD, Wb97x, and PW91TPSS were among the “recommended” list of at least one dimer from each class. Long-range correction (LC) of Hirao and coworkers to exchange-correlation functionals showed massive improvement in geometry and Eint. The best performing LC-functionals were LC-G96KCIS and LC-PKZBPKZB. Our results predict that M06L is the most trustworthy DFT method in Gaussian09 to study small non-covalently interacting systems. © 2013 Wiley Periodicals, Inc.
TL;DR: Assessment of the performance of a variety of exchange–correlation functionals and various basis sets in describing the noncovalent interactions in MH provides useful guidance for choosing appropriate methodology of first‐principles simulation of MH and related systems.
Abstract: Accurate description of hydrogen-bonding energies between water molecules and van der Waals interactions between guest molecules and host water cages is crucial for study of methane hydrates (MHs). Using high-level ab initio MP2 and CCSD(T) results as the reference, we carefully assessed the performance of a variety of exchange-correlation functionals and various basis sets in describing the noncovalent interactions in MH. The functionals under investigation include the conventional GGA, meta-GGA, and hybrid functionals (PBE, PW91, TPSS, TPSSh, B3LYP, and X3LYP), long-range corrected functionals (ωB97X, ωB97, LC-ωPBE, CAM-B3LYP, and LC-TPSS), the newly developed Minnesota class functionals (M06-L, M06-HF, M06, and M06-2X), and the dispersion-corrected density functional theory (DFT) (DFT-D) methods (B97-D, ωB97X-D, PBE-TS, PBE-Grimme, and PW91-OBS). We found that the conventional functionals are not suitable for MH, notably, the widely used B3LYP functional even predicts repulsive interaction between CH(4) and (H(2)O)(6) cluster. M06-2X is the best among the M06-Class functionals. The ωB97X-D outperforms the other DFT-D methods and is recommended for accurate first-principles calculations of MH. B97-D is also acceptable as a compromise of computational cost and precision. Considering both accuracy and efficiency, B97-D, ωB97X-D, and M06-2X functional with 6-311++G(2d,2p) basis set without basis set superposition error (BSSE) correction are recommended. Though a fairly large basis set (e.g., aug-cc-pVTZ) and BSSE correction are necessary for a reliable MP2 calculation, DFT methods are less sensitive to the basis set and BSSE correction if the basis set is sufficient (e.g., 6-311++G(2d,2p)). These assessments provide useful guidance for choosing appropriate methodology of first-principles simulation of MH and related systems. © 2012 Wiley Periodicals, Inc.
TL;DR: A new covalent docking package, the CovalentDock, built on the top of the source code of Autodock, which is compatible with existing scoring functions used in docking, while handling the molecular geometry constrains of the covalENT linkage with special atom types and directional grid maps.
Abstract: Covalent linkage formation is a very important mechanism for many covalent drugs to work. However, partly due to the limitations of proper computational tools for covalent docking, most covalent drugs are not discovered systematically. In this article, we present a new covalent docking package, the CovalentDock, built on the top of the source code of Autodock. We developed an empirical model of free energy change estimation for covalent linkage formation, which is compatible with existing scoring functions used in docking, while handling the molecular geometry constrains of the covalent linkage with special atom types and directional grid maps. Integrated preparation scripts are also written for the automation of the whole covalent docking workflow. The result tested on existing crystal structures with covalent linkage shows that CovalentDock can reproduce the native covalent complexes with significant improved accuracy when compared with the default covalent docking method in Autodock. Experiments also suggest that CovalentDock is capable of covalent virtual screening with satisfactory enrichment performance. In addition, the investigation on the results also shows that the chirality and target selectivity along with the molecular geometry constrains are well preserved by CovalentDock, showing great capability of this method in the application for covalent drug discovery.
TL;DR: An improved, mathematically rigorous method to determine an exact cone angle (θ°) by solving for the most acute right circular cone that contains the entire ligand is presented.
Abstract: Many properties of transition-metal complexes depend on the steric bulk of bound ligands, usually quantified by the Tolman (θ) and solid (θ) cone angles, which have proven utility but suffer from various limitations and coarse approximations. Here, we present an improved, mathematically rigorous method to determine an exact cone angle (θ°) by solving for the most acute right circular cone that contains the entire ligand. The procedure is applicable to any ligand, planar or nonplanar, monodentate or polydentate, bound to any metal center in any environment, and it is ideal for analyzing structures from quantum chemical computations as well as X-ray crystallography experiments. Exact cone angles were evaluated for a wide array of phosphine and amine ligands bound to palladium, nickel, or platinum by optimizing structures using B3LYP/6-31G* density functional theory with effective core potentials for the transition metals. The mean absolute deviations of the standard θ and θ parameters from the exact cone angles were 15–25°, mostly caused by distortions from the assumed idealized structures. © 2013 Wiley Periodicals, Inc.
TL;DR: Grcarma as discussed by the authors is a program encoding for a fully automated set of tasks aiming to simplify the analysis of molecular dynamics trajectories of biological macromolecules and is a cross-platform, Perl/Tk-based front-end to the program carma and is designed to facilitate the needs of the novice as well as those of the expert user, while at the same time maintaining a user-friendly and intuitive design.
Abstract: We report the availability of grcarma, a program encoding for a fully automated set of tasks aiming to simplify the analysis of molecular dynamics trajectories of biological macromolecules. It is a cross-platform, Perl/Tk-based front-end to the program carma and is designed to facilitate the needs of the novice as well as those of the expert user, while at the same time maintaining a user-friendly and intuitive design. Particular emphasis was given to the automation of several tedious tasks, such as extraction of clusters of structures based on dihedral and Cartesian principal component analysis, secondary structure analysis, calculation and display of root-mean-square deviation (RMSD) matrices, calculation of entropy, calculation and analysis of variance–covariance matrices, calculation of the fraction of native contacts, etc. The program is free-open source software available immediately for download. © 2013 Wiley Periodicals, Inc.
TL;DR: In the case of acetylene hydratase, a model with 408 QM atoms thus seems sufficient to achieve convergence in the computed relative energies to within 1–2 kcal/mol, and rather small variations in the relative energies from single‐point QM‐only and QM/MM calculations.
Abstract: We report systematic quantum mechanics-only (QM-only) and QM/molecular mechanics (MM) calculations on an enzyme-catalyzed reaction to assess the convergence behavior of QM-only and QM/MM energies with respect to the size of the chosen QM region. The QM and MM parts are described by density functional theory (typically B3LYP/def2-SVP) and the CHARMM force field, respectively. Extending our previous work on acetylene hydratase with QM regions up to 157 atoms (Liao and Thiel, J. Chem. Theory Comput. 2012, 8, 3793), we performed QM/MM geometry optimizations with a QM region M4 composed of 408 atoms, as well as further QM/MM single-point calculations with even larger QM regions up to 657 atoms. A charge deletion analysis was conducted for the previously used QM/MM model (M3a, with a QM region of 157 atoms) to identify all MM residues with strong electrostatic contributions to the reaction energetics (typically more than 2 kcal/mol), which were then included in M4. QM/MM calculations with this large QM region M4 lead to the same overall mechanism as the previous QM/MM calculations with M3a, but there are some variations in the relative energies of the stationary points, with a mean absolute deviation (MAD) of 2.7 kcal/mol. The energies of the two relevant transition states are close to each other at all levels applied (typically within 2 kcal/mol), with the first (second) one being rate-limiting in the QM/MM calculations with M3a (M4). QM-only gas-phase calculations give a very similar energy profile for QM region M4 (MAD of 1.7 kcal/mol), contrary to the situation for M3a where we had previously found significant discrepancies between the QM-only and QM/MM results (MAD of 7.9 kcal/mol). Extension of the QM region beyond M4 up to M7 (657 atoms) leads to only rather small variations in the relative energies from single-point QM-only and QM/MM calculations (MAD typically about 1–2 kcal/mol). In the case of acetylene hydratase, a model with 408 QM atoms thus seems sufficient to achieve convergence in the computed relative energies to within 1–2 kcal/mol.Copyright © 2013 Wiley Periodicals, Inc.
TL;DR: A fortran77 code based on an effective electrostatic model of point charges around a rare earth ion, designed for real systems that need not bear ideal symmetry, and able to determine the easy axis of magnetization is presented.
Abstract: This work presents a fortran77 code based on an effective electrostatic model of point charges around a rare earth ion. The program calculates the full set of crystal field parameters, energy levels spectrum, and wave functions, as well as the magnetic properties such as the magnetization, the temperature dependence of the magnetic susceptibility, and the Schottky contribution to the specific heat. It is designed for real systems that need not bear ideal symmetry and it is able to determine the easy axis of magnetization. Its systematic application to different coordination environments allows magneto-structural studies. The package has already been successfully applied to several mononuclear systems with single-molecule magnetic behavior. The determination of effective point charge parameters in these studies facilitates its application to new systems. In this article, we illustrate its usage with two example studies: (a) an ideal cubic structure coordinating a lanthanoid ion and (b) a system with slow relaxation of the magnetization, LiHo(x)Y((1-x))F(4).
TL;DR: In this paper, the authors employed GA to fit ReaxFF to SiOH data, using an in-house GA code that is parallelized across reference data items via the MPI.
Abstract: We have used unbiased global optimization to fit a reactive force field to a given set of reference data. Specifically, we have employed genetic algorithms (GA) to fit ReaxFF to SiOH data, using an in-house GA code that is parallelized across reference data items via the message-passing interface (MPI). Details of GA tuning turn-ed out to be far less important for global optimization efficiency than using suitable ranges within which the parameters are varied. To establish these ranges, either prior knowledge can be used or successive stages of GA optimizations, each building upon the best parameter vectors and ranges found in the previous stage. We have finally arrive-ed at optimized force fields with smaller error measures than those published previously. Hence, this optimization approach will contribute to converting force-field fitting from a specialist task to an everyday commodity, even for the more difficult case of reactive force fields. © 2013 Wiley Periodicals, Inc.
TL;DR: Fullerene (Version 4.4) is a general purpose open‐source program that can generate any fullerene isomer, perform topological and graph theoretical analysis, as well as calculate a number of physical and chemical properties.
Abstract: Fullerene (Version 44) is a general purpose open-source program that can generate any fullerene isomer, perform topological and graph theoretical analysis, as well as calculate a number of physical and chemical properties The program creates symmetric planar drawings of the fullerene graph and generates accurate molecular 3D geometries by way of force-field optimization, serving as a good starting point for further quantum theoretical treatments It includes a number of fullerene-to-fullerene transformations, such as Goldberg-Coxeter transforms, Stone-Wales transforms, Endo-Kroto, Yoshida-Fowler, and Brinkmann-Fowler vertex insertions The program is written in standard Fortran and C++ and can easily be installed in a Linux or UNIX environment
TL;DR: The free energy workflow (FEW) tool is introduced that facilitates setup and execution of binding free energy calculations with the AMBER suite for multiple ligands and it is demonstrated that the time needed for the preparation and analysis offree energy calculations is considerably reduced with FEW compared to a fully manual procedure.
Abstract: In the later stages of drug design projects, accurately predicting relative binding affinities of chemically similar compounds to a biomolecular target is of utmost importance for making decisions based on the ranking of such compounds. So far, the extensive application of binding free energy approaches has been hampered by the complex and time-consuming setup of such calculations. We introduce the free energy workflow (FEW) tool that facilitates setup and execution of binding free energy calculations with the AMBER suite for multiple ligands. FEW allows performing free energy calculations according to the implicit solvent molecular mechanics (MM-PB(GB)SA), the linear interaction energy, and the thermodynamic integration approaches. We describe the tool's architecture and functionality and demonstrate in a show case study on Factor Xa inhibitors that the time needed for the preparation and analysis of free energy calculations is considerably reduced with FEW compared to a fully manual procedure.
TL;DR: This study uses a robust metropolis Monte‐Carlo algorithm with simulated annealing to search for the optimum parameters for the ReaxFF force field in a high‐dimensional parameter space and optimization is done against a set of quantum chemical data for MgSO4 hydrates.
Abstract: Parameterization of a molecular dynamics force field is essential in realistically modeling the physicochemical processes involved in a molecular system. This step is often challenging when the equations involved in describing the force field are complicated as well as when the parameters are mostly empirical. ReaxFF is one such reactive force field which uses hundreds of parameters to describe the interactions between atoms. The optimization of the parameters in ReaxFF is done such that the properties predicted by ReaxFF matches with a set of quantum chemical or experimental data. Usually, the optimization of the parameters is done by an inefficient single-parameter parabolic-search algorithm. In this study, we use a robust metropolis Monte-Carlo algorithm with simulated annealing to search for the optimum parameters for the ReaxFF force field in a high-dimensional parameter space. The optimization is done against a set of quantum chemical data for MgSO4 hydrates. The optimized force field reproduced the chemical structures, the equations of state, and the water binding curves of MgSO4 hydrates. The transferability test of the ReaxFF force field shows the extend of transferability for a particular molecular system. This study points out that the ReaxFF force field is not indefinitely transferable.
TL;DR: The extension of the iterative Hirshfeld‐I method to periodic systems allows for easy calculation of atomic charges and charge transfer in periodic and bulk systems and shows that high‐quality results are obtained.
Abstract: In this work, a method is described to extend the iterative Hirshfeld-I method, generally used for molecules, to periodic systems. The implementation makes use of precalculated pseudo-potential based charge density distributions, and it is shown that high quality results are obtained for both molecules and solids, such as ceria, diamond, and graphite. The use of such grids makes the implementation independent of the solid state or quantum chemical code used for studying the system. The extension described here allows for easy calculation of atomic charges and charge transfer in periodic and bulk systems. PACS numbers: