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1.	Abraham, Mark J, et al. (författare) Optimization of parameters for molecular dynamics simulation using smooth particle-mesh Ewald in GROMACS 4.5 2011 Ingår i: Journal of Computational Chemistry. - : John Wiley & Sons. - 0192-8651 .- 1096-987X. ; 32:9 Tidskriftsartikel (refereegranskat)abstract Based on our critique of requirements for performing an efficient molecular dynamics simulation with the particle-mesh Ewald (PME) implementation in GROMACS 4.5, we present a computational tool to enable the discovery of parameters that produce a given accuracy in the PME approximation of the full electrostatics. Calculations on two parallel computers with different processor and communication structures showed that a given accuracy can be attained over a range of parameter space, and that the attributes of the hardware and simulation system control which parameter sets are optimal. This information can be used to find the fastest available PME parameter sets that achieve a given accuracy. We hope that this tool will stimulate future work to assess the impact of the quality of the PME approximation on simulation outcomes, particularly with regard to the trade-off between cost and scientific reliability in biomolecular applications.
2.	Abraham, Mark J (författare) Performance enhancements for GROMACS nonbonded interactions on BlueGene. 2011 Ingår i: Journal of Computational Chemistry. - : John Wiley & Sons. - 0192-8651 .- 1096-987X. ; 32:9 Tidskriftsartikel (refereegranskat)abstract Several improvements to the previously optimized GROMACS BlueGene inner loops that evaluate nonbonded interactions in molecular dynamics simulations are presented. The new improvements yielded an 11% decrease in running time for both PME and other kinds of GROMACS simulations that use nonbonded table look-ups. Some other GROMACS simulations will show a small gain.
3.	Almlöf, Martin, et al. (författare) Binding affinity prediction with different force fields : examination of the 2004 Ingår i: J Comput Chem. - 0192-8651. ; 25:10, s. 1242-54 Tidskriftsartikel (refereegranskat)
4.	Almlöf, Martin, et al. (författare) Binding Affinity Prediction with Different Force Fields: Examination of the Linear Interaction Energy Method 2004 Ingår i: Journal of Computational Chemistry. - 0192-8651. ; 25:10, s. 1242-1254 Tidskriftsartikel (refereegranskat)
5.	Andersson, Rasmus, 1990, et al. (författare) CHAMPION: Chalmers hierarchical atomic, molecular, polymeric and ionic analysis toolkit 2021 Ingår i: Journal of Computational Chemistry. - : Wiley. - 0192-8651 .- 1096-987X. ; 42:23, s. 1632-1642 Tidskriftsartikel (refereegranskat)abstract We present CHAMPION (Chalmers hierarchical atomic, molecular, polymeric, and ionic analysis toolkit): a software developed to automatically detect time-dependent bonds between atoms based on their dynamics, classify the local graph topology around them, and analyze the physicochemical properties of these topologies by statistical physics. In stark contrast to methodologies where bonds are detected based on static conditions such as cut-off distances, CHAMPION considers pairs of atoms to be bound only if they move together and act as a bound pair over time. Furthermore, the time-dependent global bond graph is possible to split into dynamically shifting connected components or subgraphs around a certain chemical motif and thereby allow the physicochemical properties of each such topology to be analyzed by statistical physics. Applicable to condensed matter and liquids in general, and electrolytes in particular, this allows both quantitative and qualitative descriptions of local structure, as well as dynamical processes such as speciation and diffusion. We present here a detailed overview of CHAMPION, including its underlying methodology, implementation, and capabilities.
6.	Andres, Juan, et al. (författare) Nine questions on energy decomposition analysis 2019 Ingår i: Journal of Computational Chemistry. - : Wiley. - 0192-8651 .- 1096-987X. ; 40:26, s. 2248-2283 Tidskriftsartikel (refereegranskat)abstract The paper collects the answers of the authors to the following questions: Is the lack of precision in the definition of many chemical concepts one of the reasons for the coexistence of many partition schemes? Does the adoption of a given partition scheme imply a set of more precise definitions of the underlying chemical concepts? How can one use the results of a partition scheme to improve the clarity of definitions of concepts? Are partition schemes subject to scientific Darwinism? If so, what is the influence of a community's sociological pressure in the “natural selection” process? To what extent does/can/should investigated systems influence the choice of a particular partition scheme? Do we need more focused chemical validation of Energy Decomposition Analysis (EDA) methodology and descriptors/terms in general? Is there any interest in developing common benchmarks and test sets for cross-validation of methods? Is it possible to contemplate a unified partition scheme (let us call it the “standard model” of partitioning), that is proper for all applications in chemistry, in the foreseeable future or even in principle? In the end, science is about experiments and the real world. Can one, therefore, use any experiment or experimental data be used to favor one partition scheme over another?
7.	Aquilante, Francesco, et al. (författare) Molcas 8 : New capabilities for multiconfigurational quantum chemical calculations across the periodic table 2016 Ingår i: Journal of Computational Chemistry. - : Wiley. - 0192-8651 .- 1096-987X. ; 37:5, s. 506-541 Tidskriftsartikel (refereegranskat)abstract In this report, we summarize and describe the recent unique updates and additions to the Molcas quantum chemistry program suite as contained in release version 8. These updates include natural and spin orbitals for studies of magnetic properties, local and linear scaling methods for the Douglas-Kroll-Hess transformation, the generalized active space concept in MCSCF methods, a combination of multiconfigurational wave functions with density functional theory in the MC-PDFT method, additional methods for computation of magnetic properties, methods for diabatization, analytical gradients of state average complete active space SCF in association with density fitting, methods for constrained fragment optimization, large-scale parallel multireference configuration interaction including analytic gradients via the interface to the Columbus package, and approximations of the CASPT2 method to be used for computations of large systems. In addition, the report includes the description of a computational machinery for nonlinear optical spectroscopy through an interface to the QM/MM package Cobramm. Further, a module to run molecular dynamics simulations is added, two surface hopping algorithms are included to enable nonadiabatic calculations, and the DQ method for diabatization is added. Finally, we report on the subject of improvements with respects to alternative file options and parallelization.
8.	Aquilante, Francesco, et al. (författare) Software news and update MOLCAS 7 : The Next Generation 2010 Ingår i: Journal of Computational Chemistry. - : Wiley. - 0192-8651 .- 1096-987X. ; 31:1, s. 224-247 Forskningsöversikt (refereegranskat)abstract Some of the new unique features of the MOLCAS quantum chemistry package version 7 are presented in this report. In particular, the Cholesky decomposition method applied to some quantum chemical methods is described. This approach is used both in the context of a straight forward approximation of the two-electron integrals and in the generation of so-called auxiliary basis sets. The article describes how the method is implemented for most known wave functions models: self-consistent field, density functional theory, 2nd order perturbation theory, complete-active space self-consistent field multiconfigurational reference 2nd order perturbation theory, and coupled-cluster methods. The report further elaborates on the implementation of a restricted-active space self-consistent field reference function in conjunction with 2nd order perturbation theory. The average atomic natural orbital basis for relativistic calculations, covering the whole periodic table, are described and associated unique properties are demonstrated. Furthermore, the use of the arbitrary order Douglas-Kroll-Hess transformation for one-component relativistic calculations and its implementation are discussed. This section especially focuses on the implementation of the so-called picture-change-free atomic orbital property integrals. Moreover, the ElectroStatic Potential Fitted scheme, a version of a quantum mechanics/molecular mechanics hybrid method implemented in MOLCAS, is described and discussed. Finally, the report discusses the use of the MOLCAS package for advanced studies of photo chemical phenomena and the usefulness of the algorithms for constrained geometry optimization in MOLCAS in association with such studies.
9.	Blomberg, Margareta R. A., et al. (författare) Improved free energy profile for reduction of NO in cytochrome c dependent nitric oxide reductase (cNOR) 2016 Ingår i: Journal of Computational Chemistry. - : Wiley. - 0192-8651 .- 1096-987X. ; 37:19, s. 1810-1818 Tidskriftsartikel (refereegranskat)abstract Quantum chemical calculations play an essential role in the elucidation of reaction mechanisms for redox-active metalloenzymes. For example, the cleavage and the formation of covalent bonds can usually not be described only on the basis of experimental information, but can be followed by the calculations. Conversely, there are properties, like reduction potentials, which cannot be accurately calculated. Therefore, computational and experimental data has to be carefully combined to obtain reliable descriptions of entire catalytic cycles involving electron and proton uptake from donors outside the enzyme. Such a procedure is illustrated here, for the reduction of nitric oxide (NO) to nitrous oxide and water in the membrane enzyme, cytochrome c dependent nitric oxide reductase (cNOR). A surprising experimental observation is that this reaction is nonelectrogenic, which means that no energy is conserved. On the basis of hybrid density functional calculations a free energy profile for the entire catalytic cycle is obtained, which agrees much better with experimental information on the active site reduction potentials than previous ones. Most importantly the energy profile shows that the reduction steps are endergonic and that the entire process is rate-limited by high proton uptake barriers during the reduction steps. This result implies that, if the reaction were electrogenic, it would become too slow when the gradient is present across the membrane. This explains why this enzyme does not conserve any of the free energy released.
10.	Blomgren, Fredrik, 1973, et al. (författare) Exploring the potential energy surface of retinal, a comparison of the performance of different methods 2005 Ingår i: Journal of Computational Chemistry. - : Wiley. - 0192-8651 .- 1096-987X. ; 26:7, s. 738-742 Tidskriftsartikel (refereegranskat)abstract The ground state structure of retinal has been investigated. We found that DFT and CASSCF produce different results for the bond length alternation in a model system of retinal. Quantum mechanics/molecular mechanics calculations including the closest surrounding amino acids have been performed, using DFT and CASSCF to calculate the structure of retinal in the protein cavity. The planarity of the retinal molecule is affected by the surrounding protein. DFT and CASSCF produce different twist angles. The difference between CASSCF and DFT appears to be related to the positively charged nitrogen of the Schiff base, which leads to different π-bond orders produced by the two methods.
11.	Bondesson, Laban, et al. (författare) Basis set dependence of solute-solvent interaction energy of benzene in water : a HF/DFT study 2008 Ingår i: Journal of Computational Chemistry. - : Wiley. - 0192-8651 .- 1096-987X. ; 29:11, s. 1725-1732 Tidskriftsartikel (refereegranskat)abstract Solute-solvent interaction energies for the benzene molecule dissolved in water are computed using Hartree-Fock and B3LYP density functional theories. Explicit solvent molecules up to 14-angstrom away from the dissolved benzene molecule are included in the calculation of interaction energies. Both basis set dependence and basis Set Superposition errors are carefully examined. It is found that the use of a larger basis set for the region near the solute together with a smaller basis set for the outer region gives results very close to what would have been obtained if the larger basis set had been used for the whole system. It is also shown that a correction for the basis Set superposition error is a necessary component in this kind of calculations. With this correction, results obtained with different tested basis sets converge to within 1 kcal/mol.
12.	Bondesson, Laban, et al. (författare) Erratum to : Basis set dependence of solute-solvent interaction energy of benzene in waterA HF/DFT study (vol 29, pg 1725, 2008) 2012 Ingår i: Journal of Computational Chemistry. - : WILEY-BLACKWELL. - 0192-8651 .- 1096-987X. ; 33:3, s. 354-354 Tidskriftsartikel (refereegranskat)
13.	Boomsma, Wouter, et al. (författare) PHAISTOS: A framework for Markov chain Monte Carlo simulation and inference of protein structure. 2013 Ingår i: Journal of Computational Chemistry. - : Wiley. - 1096-987X .- 0192-8651. ; 34:19, s. 1697-1705 Tidskriftsartikel (refereegranskat)abstract We present a new software framework for Markov chain Monte Carlo sampling for simulation, prediction, and inference of protein structure. The software package contains implementations of recent advances in Monte Carlo methodology, such as efficient local updates and sampling from probabilistic models of local protein structure. These models form a probabilistic alternative to the widely used fragment and rotamer libraries. Combined with an easily extendible software architecture, this makes PHAISTOS well suited for Bayesian inference of protein structure from sequence and/or experimental data. Currently, two force-fields are available within the framework: PROFASI and OPLS-AA/L, the latter including the generalized Born surface area solvent model. A flexible command-line and configuration-file interface allows users quickly to set up simulations with the desired configuration. PHAISTOS is released under the GNU General Public License v3.0. Source code and documentation are freely available from http://phaistos.sourceforge.net. The software is implemented in C++ and has been tested on Linux and OSX platforms. © 2013 Wiley Periodicals, Inc.
14.	Brooks, BR, et al. (författare) CHARMM: the biomolecular simulation program 2009 Ingår i: Journal of computational chemistry. - : Wiley. - 1096-987X .- 0192-8651. ; 30:10, s. 1545-1614 Tidskriftsartikel (refereegranskat)
15.	Bushnell, Eric A. C., et al. (författare) The first branching point in porphyrin biosynthesis : a systematic docking, molecular dynamics and quantum mechanical/molecular mechanical study of substrate binding and mechanism of uroporphyrinogen-III decarboxylase 2011 Ingår i: Journal of Computational Chemistry. - New York : John Wiley & Sons. - 0192-8651 .- 1096-987X. ; 32:5, s. 822-834 Tidskriftsartikel (refereegranskat)abstract In humans, uroporphyrinogen decarboxylase is intimately involved in the synthesis of heme, where the decarboxylation of the uroporphyrinogen-III occurs in a single catalytic site. Several variants of the mechanistic proposal exist; however, the exact mechanism is still debated. Thus, using an ONIOM quantum mechanical/molecular mechanical approach, the mechanism by which uroporphyrinogen decarboxylase decarboxylates ring D of uroporphyrinogen-III has been investigated. From the study performed, it was found that both Arg37 and Arg50 are essential in the decarboxylation of ring D, where experimentally both have been shown to be critical to the catalytic behavior of the enzyme. Overall, the reaction was found to have a barrier of 10.3 kcal mol−1 at 298.15 K. The rate-limiting step was found to be the initial protontransfer from Arg37 to the substrate before the decarboxylation. In addition, it has been found that several key interactions exist between the substrate carboxylate groups and backbone amides of various activesite residues as well as several other functional groups.
16.	Cammi, Roberto, et al. (författare) Analytical calculation of pressure for confined atomic and molecular systems using the eXtreme-Pressure Polarizable Continuum Model 2018 Ingår i: Journal of Computational Chemistry. - : Wiley. - 0192-8651 .- 1096-987X. ; 39:26, s. 2243-2250 Tidskriftsartikel (refereegranskat)abstract We show that the pressure acting on atoms and molecular systems within the compression cavity of the eXtreme-Pressure Polarizable Continuum method can be expressed in terms of the electron density of the systems and of the Pauli-repulsion confining potential. The analytical expression holds for spherical cavities as well as for cavities constructed from van der Waals spheres of the constituting atoms of the molecular systems. © 2018 Wiley Periodicals, Inc.
17.	Carlsson, P, et al. (författare) Improved precision and efficiency of free energy calculations for small systems using lambda-scaled atomic masses and separating conformational and transformational sampling 2003 Ingår i: Journal of computational chemistry. - : Wiley. - 0192-8651 .- 1096-987X. ; 24:12, s. 1383-1389 Tidskriftsartikel (refereegranskat)
18.	Cordomi, Arnau, et al. (författare) Effect of different treatments of long-range interactions and sampling conditions in molecular dynamic simulations of rhodopsin embedded in a dipalmitoyl phosphatidylcholine bilayer 2007 Ingår i: Journal of Computational Chemistry. - : Wiley. - 0192-8651 .- 1096-987X. ; 28:6, s. 1017-1030 Forskningsöversikt (refereegranskat)abstract The present study analyzes the effect of the simulation conditions on the results of molecular dynamics simulations of G-protein coupled receptors (GPCRs) performed with an explicit lipid bilayer. Accordingly, the present work reports the analysis of different simulations of bovine rhodopsin embedded in a dipalmitoyl phosphatidylcholine (DPPC) lipid bilayer using two different sampling conditions and two different approaches for the treatment of long-range electrostatic interactions. Specifically, sampling was carried out either by using the statistical ensembles NVT or NPT (constant number of atoms, a pressure of 1 arm in all directions and fixed temperature), and the electrostatic interactions were treated either by using a twin-cutoff, or the particle mesh Ewald summation method (PME). The results of the present study suggest that the use of the NPT ensemble in combination with the PME method provide more realistic simulations. The use of NPT during the equilibration avoids the need of an a priori estimation of the box dimensions, giving the correct area per lipid. However, once the system is equilibrated, the simulations are irrespective of the sampling conditions used. The use of an electrostatic cutoff induces artifacts on both lipid thickness and the ion distribution, but has no direct effect on the protein and water molecules.
19.	Delcey, Mickael G, et al. (författare) Efficient calculations of a large number of highly excited states for multiconfigurational wavefunctions 2019 Ingår i: Journal of Computational Chemistry. - : Wiley. - 0192-8651 .- 1096-987X. ; 40:19, s. 1789-1799 Tidskriftsartikel (refereegranskat)abstract Electronically excited states play important roles in many chemical reactions and spectroscopic techniques. In quantum chemistry, a common technique to solve excited states is the multiroot Davidson algorithm, but it is not designed for processes like X-ray spectroscopy that involves hundreds of highly excited states. We show how the use of a restricted active space wavefunction together with a projection operator to remove low-lying electronic states offers an efficient way to reach single and double-core-hole states. Additionally, several improvements to the stability and efficiency of the configuration interaction (CI) algorithm for a large number of states are suggested. When applied to a series of transition metal complexes the new CI algorithm does not only resolve divergence issues but also leads to typical reduction in computational time by 70%, with the largest savings for small molecules and large active spaces. Together, the projection operator and the improved CI algorithm now make it possible to simulate a wide range of single- and two-photon spectroscopies.
20.	Denning, EJ, et al. (författare) Impact of 2'-hydroxyl sampling on the conformational properties of RNA: update of the CHARMM all-atom additive force field for RNA 2011 Ingår i: Journal of computational chemistry. - : Wiley. - 1096-987X .- 0192-8651. ; 32:9, s. 1929-1943 Tidskriftsartikel (refereegranskat)
21.	Dias, Roberta P, et al. (författare) Modeling the Electrostatic Potential of Asymmetric Lipopolysaccharide Membranes 2014 Ingår i: Journal of Computational Chemistry. - : Wiley Periodicals. - 0192-8651 .- 1096-987X. ; 35:19, s. 1418-1429 Tidskriftsartikel (refereegranskat)abstract Four chemotypes of the rough lipopolysaccharides (LPS) membrane from Pseudomonas aeruginosa were investigated by a combined approach of explicit water molecular dynamics (MD) simulations and Poisson–Boltzmann continuum electrostatics with the goal to deliver the distribution of the electrostatic potential across the membrane. For the purpose of this investigation, a new tool for modeling the electrostatic potential profile along the axis normal to the membrane, MEMbrane POTential (MEMPOT), was developed and implemented in DelPhi. Applying MEMPOT on the snapshots obtained by MD simulations, two observations were made: (a) the average electrostatic potential has a complex profile but is mostly positive inside the membrane due to the presence of Ca2+ ions, which overcompensate for the negative potential created by lipid phosphate groups; and (b) correct modeling of the electrostatic potential profile across the membrane requires taking into account the water phase, while neglecting it (vacuum calculations) results in dramatic changes including a reversal of the sign of the potential inside the membrane. Furthermore, using DelPhi to assign different dielectric constants for different regions of the LPS membranes, it was investigated whether a single frame structure before MD simulations with appropriate dielectric constants for the lipid tails, inner, and the external leaflet regions, can deliver the same average electrostatic potential distribution as obtained from the MD-generated ensemble of structures. Indeed, this can be attained by using smaller dielectric constant for the tail and inner leaflet regions (mostly hydrophobic) than for the external leaflet region (hydrophilic) and the optimal dielectric constant values are chemotype-specific.
22.	Dias, R. S., et al. (författare) Stepwise Disproportionation in Polyelectrolyte Complexes 2011 Ingår i: Journal of Computational Chemistry. - : Wiley. - 1096-987X .- 0192-8651. ; 32:12, s. 2697-2707 Tidskriftsartikel (refereegranskat)abstract Structural properties and the topology of polyelectrolyte complexes (PECs) formed in solution have been investigated under different conditions by Monte Carlo simulations using a coarse-grained model. The extension of individual polyions has been characterized by their radius of gyration, whereas the composition of the complexes has been investigated by their net charge and their internal topological structure by a novel analysis describing how the shorter polycations link to monomers of the longer polyanion. Conditions have been found at which the polyanion and a given number of polycations form distinguishable complexes differing in (i) the polyanion conformation and (ii) the fraction of polycations being in extended and collapsed states. Thus, at equilibrium, these PECs display a stepwise variation of the degree of intrachain disproportionation within the polyanion (also referred to as intrachain segregation), concomitant with the interchain disproportionation of the polycations, which is in agreement with previous theoretical predictions. The coexistence of the different polyelectrolyte complex structures appears, generally, at mixing ratios close to but different from charge equivalence and, as a consequence, broad polyelectrolyte size distributions are commonly obtained. (C) 2011 Wiley Periodicals, Inc. J Comput Chem 32: 2697-2707, 2011
23.	Ding, Zongling, et al. (författare) The Finite-Size Effect on the Transport Properties in Edge-Modified Graphene Nanoribbon-Based Molecular Devices 2011 Ingår i: Journal of Computational Chemistry. - : Wiley. - 0192-8651 .- 1096-987X. ; 32:8, s. 1753-1759 Tidskriftsartikel (refereegranskat)abstract The size-dependence on the electronic and transport properties of the molecular devices of the edge-modified graphene nanoribbon (GNR) slices is investigated using density-functional theory and Green's function theory. Two edge-modifying functional group pairs are considered. Energy gap is found in all the GNR slices. The gap shows an exponential decrease with increasing the slice size of two vertical orientations in the two edge terminated cases, respectively. The tunneling probability and the number of conducting channel decreases with increasing the GNR-slices size in the junctions. The results indicate that the acceptor-donor pair edge modulation can improve the quantum conductance and decrease the finite-size effect on the transmission capability of the GNR slice-based molecular devices.
24.	Ding, Zongling, et al. (författare) Transport Properties of Graphene Nanoribbon-Based Molecular Devices 2011 Ingår i: Journal of Computational Chemistry. - : Wiley. - 0192-8651 .- 1096-987X. ; 32:4, s. 737-741 Tidskriftsartikel (refereegranskat)abstract The electronic and transport properties of an edge-modified prototype graphene nanoribbon (GNR) slice are investigated using density functional theory and Green's function theory. Two decorating functional group pairs are considered, such as hydrogen-hydrogen and NH2-NO2 with NO2 and NH2 serving as a donor and an acceptor, respectively. The molecular junctions consist of carbon-based GNR slices sandwiched between Au electrodes. Nonlinear I-V curves and quantum conductance have been found in all the junctions. With increasing the source-drain bias, the enhancement of conductance is quantized. Several key factors determining the transport properties such as the electron transmission probabilities, the density of states, and the component of Frontier molecular orbitals have been discussed in detail. It has been shown that the transport properties are sensitive to the edge type of carbon atoms. We have also found that the accepter-donor functional pairs can cause orders of magnitude changes of the conductance in the junctions.
25.	Dong, Hua, et al. (författare) The bergman cyclizations of the enediyne and its N-substituted analogs using multiconfigurational second-order perturbation theory 2012 Ingår i: Journal of Computational Chemistry. - : Wiley. - 0192-8651 .- 1096-987X. ; 33:5, s. 537-549 Tidskriftsartikel (refereegranskat)abstract The Bergman cyclizations of the enediyne and its four N-substituted analogs [(Z)-pent-2-en-4-ynenitrile, 3-azahex-3-en-1,5-diyne, malenotrile, and 3,4-azahex-3-en-1,5-diyne] have been studied using the complete active space self-consistent field and multiconfigurational second-order perturbation theory methods in conjunction with the atomic natural orbital basis sets. The geometries and energies of the reactants, transition states, and products along both the S0 (the ground state) and T1 (the lowest-lying triplet state) potential energy surfaces (PESs) were calculated. The calculated geometries are in good agreement with the available experimental data. The distance between two terminal carbons in enediyne, which was considered as an important parameter governing the Bergman cyclization, was predicted to be 4.319 angstrom, in agreement with the experimental value of 4.321 angstrom. Our calculations indicate that the replacements of the terminal C atom(s) or the middle C atom(s) in the C-C bond by the N atom(s) increase or decrease the energy barrier values, respectively. There exist stable ring biradical products on the T1 PESs for the five reactions. However, on the S0 PESs the ring biradical products exist only for the reactions of enediyne, (Z)-pent-2-en-4-ynenitrile, and 3-azahex-3-en-1,5-diyne.
26.	Eriksen, Janus J., et al. (författare) Computational Protocols for Prediction of Solute NMR Relative Chemical Shifts. A Case Study of L-Tryptophan in Aqueous Solution 2011 Ingår i: Journal of Computational Chemistry. - : Wiley. - 0192-8651 .- 1096-987X. ; 32:13, s. 2853-2864 Tidskriftsartikel (refereegranskat)abstract In this study, we have applied two different spanning protocols for obtaining the molecular conformations of L-tryptophan in aqueous solution, namely a molecular dynamics simulation and a molecular mechanics conformational search with subsequent geometry re-optimization of the stable conformers using a quantum mechanically based method. These spanning protocols represent standard ways of obtaining a set of conformations on which NMR calculations may be performed. The results stemming from the solute-solvent configurations extracted from the MD simulation at 300 K are found to be inferior to the results stemming from the conformations extracted from the MM conformational search in terms of replicating an experimental reference as well as in achieving the correct sequence of the NMR relative chemical shifts of L-tryptophan in aqueous solution. We find this to be due to missing conformations visited during the molecular dynamics run as well as inaccuracies in geometrical parameters generated from the classical molecular dynamics simulations.
27.	Falklöf, Olle, et al. (författare) Distinguishing Between Keto-Enol and Acid-Base Forms of Firefly Oxyluciferin Through Calculation of Excited-State Equilibrium Constants 2014 Ingår i: Journal of Computational Chemistry. - : Wiley: 12 months. - 0192-8651 .- 1096-987X. ; 35:30, s. 2184-2194 Tidskriftsartikel (refereegranskat)abstract Although recent years have seen much progress in the elucidation of the mechanisms underlying the bioluminescence of fireflies, there is to date no consensus on the precise contributions to the light emission from the different possible forms of the chemiexcited oxyluciferin (OxyLH(2)) cofactor. Here, this problem is investigated by the calculation of excited-state equilibrium constants in aqueous solution for keto-enol and acid-base reactions connecting six neutral, monoanionic and dianionic forms of OxyLH(2). Particularly, rather than relying on the standard Forster equation and the associated assumption that entropic effects are negligible, these equilibrium constants are for the first time calculated in terms of excited-state free energies of a Born-Haber cycle. Performing quantum chemical calculations with density functional theory methods and using a hybrid cluster-continuum approach to describe solvent effects, a suitable protocol for the modeling is first defined from benchmark calculations on phenol. Applying this protocol to the various OxyLH(2) species and verifying that available experimental data (absorption shifts and ground-state equilibrium constants) are accurately reproduced, it is then found that the phenolate-keto-OxyLH(-) monoanion is intrinsically the preferred form of OxyLH(2) in the excited state, which suggests a potential key role for this species in the bioluminescence of fireflies.
28.	Falklöf, Olle, et al. (författare) Modeling of phytochrome absorption spectra 2013 Ingår i: Journal of Computational Chemistry. - : John Wiley & Sons. - 0192-8651 .- 1096-987X. ; 34:16, s. 1363-1374 Tidskriftsartikel (refereegranskat)abstract Phytochromes constitute one of the six well-characterized families of photosensory proteins in Nature. From the viewpoint of computational modeling, however, phytochromes have been the subject of much fewer studies than most other families of photosensory proteins, which is likely a consequence of relevant high-resolution structural data becoming available only in recent years. In this work, hybrid quantum mechanics/molecular mechanics (QM/MM) methods are used to calculate UV-vis absorption spectra of Deinococcus radiodurans bacteriophytochrome. We investigate how the choice of QM/MM methodology affects the resulting spectra and demonstrate that QM/MM methods can reproduce the experimental absorption maxima of both the Q and Soret bands with an accuracy of about 0.15 eV. Furthermore, we assess how the protein environment influences the intrinsic absorption of the bilin chromophore, with particular focus on the Q band underlying the primary photochemistry of phytochromes.
29.	Farahani, Pooria, 1985-, et al. (författare) A Two-Scale Approach to Electron Correlation in Multiconfigurational Perturbation Theory 2014 Ingår i: Journal of Computational Chemistry. - : John Wiley & Sons. - 0192-8651 .- 1096-987X. ; 35:22, s. 1609-1617 Forskningsöversikt (refereegranskat)abstract We present a new approach for the calculation of dynamicelectron correlation effects in large molecular systems usingmulticonfigurational second-order perturbation theory(CASPT2). The method is restricted to cases where partitioningof the molecular system into an active site and an environment is meaningful. Only dynamic correlation effects derivedfrom orbitals extending over the active site are included at theCASPT2 level of theory, whereas the correlation effects of theenvironment are retrieved at lower computational costs. Forsufficiently large systems, the small errors introduced by thisapproximation are contrasted by the substantial savings inboth storage and computational demands compared to thefull CASPT2 calculation. Provided that static correlation effectsare correctly taken into account for the whole system, the proposed scheme represent a hierarchical approach to the electron correlation problem, where two molecular scales aretreated each by means of the most suitable level of theory.
30.	Gao, Bin, et al. (författare) An efficient first-principle approach for electronic structures calculations of nanomaterials 2008 Ingår i: Journal of Computational Chemistry. - : Wiley. - 0192-8651 .- 1096-987X. ; 29:3, s. 434-444 Tidskriftsartikel (refereegranskat)abstract An efficient parallel implementation has been realized for a recently proposed central insertion scheme (Jiang, Liu, Lu, Luo. J Chem Phys 2006,124,214711; J Chem Phys 2006,125, 149902) that allows to calculate electronic structures of nanomaterials at various density functional theory levels. It has adopted the sparse-matrix format for Fock/Kohn-Sham and overlap matrices, as well as a combination of implicitly restarted Arnoldi methods (IRAM) and spectral transformation for computing selected eigenvalues/eigenvectors. A systematic error analysis and control for the proposed method has been provided based on a strict mathematical basis. The efficiency and applicability of the new implementation have been demonstrated by calculations of electronic structures of two different nanomaterials consisting of one hundred thousand electrons.
31.	Genheden, Samuel, et al. (författare) A comparison of different initialization protocols to obtain statistically independent molecular dynamics simulations. 2011 Ingår i: Journal of Computational Chemistry. - : Wiley. - 1096-987X .- 0192-8651. ; 32:2, s. 187-195 Tidskriftsartikel (refereegranskat)abstract We study how the results of molecular dynamics (MD) simulations are affected by various choices during the setup, e.g., the starting velocities, the solvation, the location of protons, the conformation of His, Asn, and Gln residues, the protonation and titration of His residues, and the treatment of alternative conformations. We estimate the binding affinity of ligands to four proteins calculated with the MM/GBSA method (molecular mechanics combined with a generalized Born and surface area solvation energy). For avidin and T4 lysozyme, all variations gave similar results within 2 kJ/mol. For factor Xa, differences in the solvation or in the selection of alternative conformations gave results that are significantly different from those of the other approaches by 4-6 kJ/mol, whereas for galectin-3, changes in the conformations, rotations, and protonation gave results that differed by 10 kJ/mol, but only if residues close to the binding site were modified. This shows that the results of MM/GBSA calculations are reasonably reproducible even if the MD simulations are set up with different software. Moreover, we show that the sampling of phase space can be enhanced by solvating the systems with different equilibrated water boxes, in addition to the common use of different starting velocities. If different conformations are available in the crystal structure, they should also be employed to enhance the sampling. Protonation, ionization, and conformations of Asn, Gln, and His may also be used to enhance sampling, but great effort should be spent to obtain as reliable predictions as possible close to the active site.
32.	Genheden, Samuel, et al. (författare) Binding affinities by alchemical perturbation using QM/MM with a large QM system and polarizable MM model. 2015 Ingår i: Journal of Computational Chemistry. - : Wiley. - 1096-987X .- 0192-8651. ; 36:28, s. 2114-2124 Tidskriftsartikel (refereegranskat)abstract The most general way to improve the accuracy of binding-affinity calculations for protein-ligand systems is to use quantum-mechanical (QM) methods together with rigorous alchemical-perturbation (AP) methods. We explore this approach by calculating the relative binding free energy of two synthetic disaccharides binding to galectin-3 at a reasonably high QM level (dispersion-corrected density functional theory with a triple-zeta basis set) and with a sufficiently large QM system to include all short-range interactions with the ligand (744-748 atoms). The rest of the protein is treated as a collection of atomic multipoles (up to quadrupoles) and polarizabilities. Several methods for evaluating the binding free energy from the 3600 QM calculations are investigated in terms of stability and accuracy. In particular, methods using QM calculations only at the endpoints of the transformation are compared with the recently proposed non-Boltzmann Bennett acceptance ratio (NBB) method that uses QM calculations at several stages of the transformation. Unfortunately, none of the rigorous approaches give sufficient statistical precision. However, a novel approximate method, involving the direct use of QM energies in the Bennett acceptance ratio method, gives similar results as NBB but with better precision, ∼3 kJ/mol. The statistical error can be further reduced by performing a greater number of QM calculations. © 2015 Wiley Periodicals, Inc.
33.	Genheden, Samuel, et al. (författare) How to obtain statistically converged MM/GBSA results. 2010 Ingår i: Journal of Computational Chemistry. - : Wiley. - 1096-987X .- 0192-8651. ; 31:Online 13 Jul 2009, s. 837-846 Tidskriftsartikel (refereegranskat)abstract The molecular mechanics/generalized Born surface area (MM/GBSA) method has been investigated with the aim of achieving a statistical precision of 1 kJ/mol for the results. We studied the binding of seven biotin analogues to avidin, taking advantage of the fact that the protein is a tetramer with four independent binding sites, which should give the same estimated binding affinities. We show that it is not enough to use a single long simulation (10 ns), because the standard error of such a calculation underestimates the difference between the four binding sites. Instead, it is better to run several independent simulations and average the results. With such an approach, we obtain the same results for the four binding sites, and any desired precision can be obtained by running a proper number of simulations. We discuss how the simulations should be performed to optimize the use of computer time. The correlation time between the MM/GBSA energies is approximately 5 ps and an equilibration time of 100 ps is needed. For MM/GBSA, we recommend a sampling time of 20-200 ps for each separate simulation, depending on the protein. With 200 ps production time, 5-50 separate simulations are required to reach a statistical precision of 1 kJ/mol (800-8000 energy calculations or 1.5-15 ns total simulation time per ligand) for the seven avidin ligands. This is an order of magnitude more than what is normally used, but such a number of simulations is needed to obtain statistically valid results for the MM/GBSA method. (c) 2009 Wiley Periodicals, Inc. J Comput Chem 2009.
34.	Georgieva, Polina, et al. (författare) Quantum Chemical Modeling of Enzymatic Reactions : The Case of Histone Lysine Methyltransferase 2010 Ingår i: Journal of Computational Chemistry. - : Wiley. - 0192-8651 .- 1096-987X. ; 31:8, s. 1707-1714 Tidskriftsartikel (refereegranskat)abstract Quantum chemical cluster models of enzyme active sites are today an important and powerful tool in the study of various aspects of enzymatic reactivity. This methodology has been applied to a wide spectrum of reactions and many important mechanistic problems have been solved. Herein, we report a systematic study of the reaction mechanism of the histone lysine methyltransferase (HKMT) SET7/9 enzyme, which catalyzes the methylation of the N-terminal histone tail of the chromatin structure. In this study, HKMT SET7/9 serves as a representative case to examine the modeling approach for the important class of methyl transfer enzymes. Active site models of different sizes are used to evaluate the methodology. In particular, the dependence of the calculated energies on the model size, the influence of the dielectric medium, and the particular choice of the dielectric constant are discussed. In addition, we examine the validity of some technical aspects, such as geometry optimization in solvent or with a large basis set, and the use of different density functional methods.
35.	Hellström, Matti, et al. (författare) Treatment of Delocalized Electron Transfer in Periodic and Embedded Cluster DFT Calculations : The Case of Cu on ZnO (10(1)over-bar0) 2015 Ingår i: Journal of Computational Chemistry. - : Wiley. - 0192-8651 .- 1096-987X. ; 36:32, s. 2394-2405 Tidskriftsartikel (refereegranskat)abstract We assess the consequences of the interface model-embedded-cluster or periodic-slab model-on the ability of DFT calculations to describe charge transfer (CT) in a particularly challenging case where periodic-slab calculations indicate a delocalized charge-transfer state. Our example is Cu atom adsorption on ZnO(10 (1) over bar0), and in fact the periodic slab calculations indicate three types of CT depending on the adsorption site: full CT, partial CT, and no CT. Interestingly, when full CT occurs in the periodic calculations, the calculated Cu atom adsorption energy depends on the underlying ZnO substrate supercell size, since when the electron enters the ZnO it delocalizes over as many atoms as possible. In the embedded-cluster calculations, the electron transferred to the ZnO delocalizes over the entire cluster region, and as a result the calculated Cu atom adsorption energy does not agree with the value obtained using a large periodic supercell, but instead to the adsorption energy obtained for a periodic supercell of roughly the same size as the embedded cluster. Different density functionals (of GGA and hybrid types) and basis sets (local atom-centered and plane-waves) were assessed, and we show that embedded clusters can be used to model Cu adsorption on ZnO(10 (1) over bar0), as long as care is taken to account for the effects of CT.
36.	Hermida-Ramon, J M, et al. (författare) Inter- and intramolecular potential for the N-formylglycinamide-water system. A comparison between theoretical modeling and empirical force fields 2003 Ingår i: Journal of Computational Chemistry. - : Wiley. - 1096-987X .- 0192-8651. ; 24:2, s. 161-176 Tidskriftsartikel (refereegranskat)abstract An intramolecular NEMO potential is presented for the N-formylglycinamide molecule together with an intermolecular potential for the N-formylglycinamide-water system. The intramolecular N-formylglycinamide potential can be used as a building block for the backbone of polypeptides and proteins. Two intramolecular minima have been obtained. One, denoted as C5, is stabilized by a hydrogen bonded five member ring, and the other, denoted as C7, corresponds to a seven membered ring. The interaction between one water molecule and the N-formylglycinamide system is also studied and compared with Hartree-Fock SCF calculations and with the results obtained for some of the more commonly used force fields. The agreement between the NEMO and SCF energies for the complexes is in general superior to that of the other force fields. In the C7 region the surfaces obtained from the intramolecular part of the commonly used force fields are too flat compared to the NEMO potential and the ab initio calculations. We further analyze the possibility of using a charge distribution obtained from one conformation to describe the charge distribution of other conformations. We have found that the use of polarizabilities and generic dipoles can model most of the changes in charge density due to the different geometry of the new conformations, but that one can expect additional errors in the interaction energies that are of the order of 1 kcal/mol. © 2002 Wiley Periodicals, Inc. J Comput Chem 24: 161-176, 2003
37.	Holt, Asbjörn, et al. (författare) A NEMO potential that includes the dipole-quadrupole and quadrupole-quadrupole polarizability 2010 Ingår i: Journal of Computational Chemistry. - : Wiley. - 0192-8651 .- 1096-987X. ; 31:8, s. 1583-1591 Tidskriftsartikel (refereegranskat)abstract To increase the accuracy of molecular force fields a systematical and balanced improvement of the various terms included is needed. In this work, we have followed this strategy to improve the quality of the NEMO potential for the formaldehyde dimer by introducing local quadrupole moments and higher-order polarizabilities. It is found that inclusion of the quadrupole moment significantly improves the interaction potential. Furthermore, the inclusion of higher-order polarizabilities up to quadrupole-quadrupole polarizability is shown to give a better description of the intermolecular interaction. In addition, it is demonstrated that localized properties based on MP2 densities reproduces the BSSE corrected MP2 interaction energy at large intermolecular separations. This is not the case for HF-SCF based properties.
38.	Holt, Asbjörn, et al. (författare) An intramolecular induction correction model of the molecular dipole moment. 2008 Ingår i: Journal of Computational Chemistry. - : Wiley. - 1096-987X .- 0192-8651. ; 29:7, s. 1084-1091 Tidskriftsartikel (refereegranskat)abstract A model for intramolecular polarization is presented. It is used to describe the changes in the molecular charge distribution occurring as a response to changes of dihedral angles in the molecule. The model is based on a multicenter multipole distribution of the molecular charge distribution. The electric field from this charge distribution induce dipole moments in the same molecule. The model contains atom type parameters to describe the damping of the electric field. A total of four atom types are used. The parameters are fitted to a calibration set with various functional groups, and tested against a validation set. The error obtained for the calibration set is reduced by 92% and by 88% for the validation set, if compared to an accurate state-of-the-art force field. It is shown that rotating the non-polarizable multicenter multipole distribution for the equilibrium geometry gives too large dipole moments for dihedral angles deviating from the equilibrium geometry. This will lead to too large long-range attractions in simulations. This problem is overcome by using the dipole polarizability correction suggested here, which gives dipole moments very close to the Hartree-Fock dipole moments obtained from reference calculations. (c) 2007 Wiley Periodicals, Inc. J Comput Chem 2007.
39.	Holt, Asbjörn, et al. (författare) Inclusion of the quadrupole moment when describing polarization. The effect of the dipole-quadrupole polarizability. 2008 Ingår i: Journal of Computational Chemistry. - : Wiley. - 1096-987X .- 0192-8651. ; 29:12, s. 2033-2038 Tidskriftsartikel (refereegranskat)abstract A method to compute distributed dipole-quadrupole polarizabilities is suggested. The method is based on numerical differentiation of distributed quadrupole moments, using finite field perturbation calculations. It is tested using two different multicenter multipole expansions, and compared with results using polarizabilities obtained via the uncoupled Hartree-Fock approximation. The accuracy of these dipole-quadrupole polarizabilities are tested for different molecules and basis sets, by comparing the induced electrostatic potential of the Hartree-Fock density with the induced electrostatic potential of the polarization models. This is done by perturbing the molecules with an external homogeneous field and with an external dipole. It is found that inclusion of the dipole-quadrupole polarizability significantly improves the accuracy of the response of the molecule to these external perturbations. This suggests that inclusion of higher-order induced moments can be of importance when improving the description of intermolecular interactions using force fields. (c) 2008 Wiley Periodicals, Inc. J Comput Chem 2008.
40.	Holt, Asbjörn, et al. (författare) Induction correction model for rotation of two or three dihedral angles. 2008 Ingår i: Journal of Computational Chemistry. - : Wiley. - 1096-987X .- 0192-8651. ; 29:12, s. 1905-1911 Tidskriftsartikel (refereegranskat)abstract In a previous work we have introduced an intramolecular induction correction model. In this work we have used the model to calculate the total dipol moment of six molecules as a function of two or three dihedral angles that are simultaneously varied in the molecules. It is found that the induction model behaves very well for the systems studied when compared with a regular force field model where fixed charges and dipoles are rotated along with the atoms of the molecules. This suggests that the proposed induction correction model can be used to model systems containing several dihedral angles around which rotations are performed. (c) 2008 Wiley Periodicals, Inc. J Comput Chem, 2008.
41.	Hugosson, Håkan Wilhelm, et al. (författare) A comparative theoretical study of dipeptide solvation in water 2006 Ingår i: Journal of Computational Chemistry. - : Wiley. - 0192-8651 .- 1096-987X. ; 27:5, s. 672-684 Tidskriftsartikel (refereegranskat)abstract Molecular dynamics studies have been performed on the zwitterionic form of the dipeptide glycine-alanine in water, with focus oil the solvation and electrostatic properties using a range of theoretical methods, from purely classical force fields, through mixed quantum mechanical/molecular mechanical simulations, to fully quantum mechanical Car-Parrinello calculations. The results of these studies show that the solvation pattern is similar for all methods used for most atoms in the dipeptide, but call differ substantially for some groups; namely the carboxy and aminoterminii, and the backbone amid NH group. This might have implications in other theoretical studies of peptides and proteins, with charged -NH3+ and -CO2- side chains solvated in water. Hybrid quantum mechanical/molecular mechanical simulations successfully reproduce the solvation patterns from the fully quantum mechanical simulations (PACS numbers: 87.14.Ee, 87.15.Aa, 87.15.He. 71.15.Pd).
42.	Högberg, Carl-Johan, et al. (författare) Modification of the CHARMM force field for DMPC lipid bilayer 2008 Ingår i: Journal of Computational Chemistry. - : Wiley. - 0192-8651 .- 1096-987X. ; 29:14, s. 2359-2369 Tidskriftsartikel (refereegranskat)abstract The CHARMM force field for DMPC lipids was modified in order to improve agreement with experiment for a number of important properties of hydrated lipid bilayer. The modification consists in introduction of a scaling factor 0.83 for 1-4 electrostatic interactions (between atoms separated by three covalent bonds), which provides correct transgauche ratio in the alkane tails, and recalculation of the headgroup charges on the basis of HF/6-311(d,p) ab-initio computations. Both rigid TIP3P and flexible SPC water models were used with the new lipid model, showing similar results. The new model in a 75 ns simulation has shown a correct value of the area per lipid at zero surface tension, as well as good agreement with the experiment for the electron density, structure factor, and order parameters, including those in the headgroup part of lipids.
43.	Irbäck, Anders, et al. (författare) PROFASI: A Monte Carlo simulation package for protein folding and aggregation 2006 Ingår i: Journal of Computational Chemistry. - : Wiley. - 1096-987X .- 0192-8651. ; 27:13, s. 1548-1555 Tidskriftsartikel (refereegranskat)abstract We present a flexible and efficient program package written in C++, PROFASI, for simulating protein folding and aggregation. The systems are modeled using an all-atom description of the protein chains with only torsional degrees of freedom, and implicit water. The program package has a modular structure that makes the interaction potential easy to modify. The currently implemented potential is able to fold several peptides with about 20 residues, and has also been used to study aggregation and force-induced unfolding. The simulation methods implemented in PROFASI are Monte Carlo-based and include a semilocal move and simulated tempering. Adding new updates is easy. The code runs fast in both single- and multi-chain applications, as is illustrated by several examples. (C) 2006 Wiley Periodicals, Inc.
44.	Ivanov, Mikhail, 1995-, et al. (författare) Development of a bottom-up coarse-grained model for interactions of lipids with TiO2 nanoparticles 2024 Ingår i: Journal of Computational Chemistry. - 0192-8651 .- 1096-987X. ; 45:16, s. 1364-1379 Tidskriftsartikel (refereegranskat)abstract Understanding interactions of inorganic nanoparticles with biomolecules is important in many biotechnology, nanomedicine, and toxicological research, however, the size of typical nanoparticles makes their direct modeling by atomistic simulations unfeasible. Here, we present a bottom-up coarse-graining approach for modeling titanium dioxide (TiO2) nanomaterials in contact with phospholipids that uses the inverse Monte Carlo method to optimize the effective interactions from the structural data obtained in small-scale all-atom simulations of TiO2 surfaces with lipids in aqueous solution. The resulting coarse-grained models are able to accurately reproduce the structural details of lipid adsorption on different titania surfaces without the use of an explicit solvent, enabling significant computational resource savings and favorable scaling. Our coarse-grained simulations show that small spherical TiO2 nanoparticles (?=2 nm) can only be partially wrapped by a lipid bilayer with phosphoethanolamine headgroups, however, the lipid adsorption increases with the radius of the nanoparticle. The current approach can be used to study the effect of the size and shape of TiO2 nanoparticles on their interactions with cell membrane lipids, which can be a determining factor in membrane wrapping as well as the recently discovered phenomenon of nanoquarantining, which involves the formation of layered nanomaterial–lipid structures.
45.	Jayasinghe-Arachchige, Vindi M., et al. (författare) Hydrolysis of Chemically Distinct Sites of Human Serum Albumin by Polyoxometalate : A Hybrid QM/MM (ONIOM) Study 2019 Ingår i: Journal of Computational Chemistry. - : Wiley. - 0192-8651 .- 1096-987X. ; 40:1, s. 51-61 Tidskriftsartikel (refereegranskat)abstract In this study, mechanisms of hydrolysis of all four chemically diverse cleavage sites of human serum albumin (HSA) by [Zr(OH) (PW11O39)](4-)(ZrK) have been investigated using the hybrid two-layer QM/MM (ONIOM) method. These reactions have been proposed to occur through the following two mechanisms: internal attack (IA) and water assisted (WA). In both mechanisms, the cleavage of the peptide bond in the Cys392-Glu393 site of HSA is predicted to occur in the rate-limiting step of the mechanism. With the barrier of 27.5 kcal/mol for the hydrolysis of this site, the IA mechanism is found to be energetically more favorable than the WA mechanism (barrier = 31.6 kcal/mol). The energetics for the IA mechanism are in line with the experimentally measured values for the cleavage of a wide range of dipeptides. These calculations also suggest an energetic preference (Cys392-Glu393, Ala257-Asp258, Lys313-Asp314, and Arg114-Leu115) for the hydrolysis of all four sites of HSA. (C) 2018 Wiley Periodicals, Inc.
46.	Jämbeck, Joakim P. M., 1986-, et al. (författare) Partial Atomic Charges and Their Impact on the Free Energy of Solvation 2013 Ingår i: Journal of Computational Chemistry. - : Wiley. - 0192-8651 .- 1096-987X. ; 34:3, s. 187-197 Tidskriftsartikel (refereegranskat)abstract Free energies of solvation (Delta G) in water and n-octanol have been computed for common drug molecules by molecular dynamics simulations with an additive fixed-charge force field. The impact of the electrostatic interactions was investigated by computing the partial atomic charges with four methods that all fit the charges from the quantum mechanically determined electrostatic potential (ESP). Due to the redistribution of electron density that occurs when molecules are transferred from gas phase to condensed phase, the polarization impact was also investigated. By computing the partial atomic charges with the solutes placed in a conductor-like continuum, the charges were effectively polarized to take the polarization effects into account. No polarization correction term or similar was considered, only the partial atomic charges. Results show that free energies are very sensitive to the choice of atomic charges and that Delta G can differ by several k(B)T depending on the charge computing method. Inclusion of polarization effects makes the solutes too hydrophilic with most methods and in vacuo charges make the solutes too hydrophobic. The restrained-ESP methods together with effectively polarized charges perform well in our test set and also when applied to a larger set of molecules. The effect of water models is also highlighted and shows that the conclusions drawn are valid for different three-point models. Partitioning between an aqueous and a hydrophobic phase is also described better if the two environment's polarization is taken into account, but again the results are sensitive to the charge calculation method. Overall, the results presented here show that effectively polarized charges can improve the description of solvating a drug-like molecule in a solvent and that the choice of partial atomic charges is crucial to ensure that molecular simulations produce reliable results.
47.	Kikugawa, Gota, et al. (författare) Application of MDGRAPE-3, a Special Purpose Board for Molecular Dynamics Simulations, to Periodic Biomolecular Systems 2009 Ingår i: Journal of Computational Chemistry. - : Wiley. - 0192-8651 .- 1096-987X. ; 30:1, s. 110-118 Tidskriftsartikel (refereegranskat)abstract We describe the application of a special purpose board for molecular dynamics simulations, named MDGRAPE-3, to the problem of simulating periodic bio-molecular systems. MDGRAPE-3 is the latest board in a series of hardware accelerators designed to calculate the nonbonding long-range interactions much more rapidly than normal processors. So far, MDGRAPEs were mainly applied to isolated systems, where very many nonbonded interactions were calculated without any distance cutoff. However, in order to regulate the density and pressure during simulations of membrane embedded protein systems, one has to evaluate interactions under periodic boundary conditions. For this purpose, we implemented the Particle-Mesh Ewald (PME) method, and its approximation with distance cutoffs and charge neutrality as proposed by Wolf et al., using MDGRAPE-3. When the two methods were applied to simulations of two periodic biomolecular systems, a single MDGRAPE-3 achieved 30-40 times faster computation times than a single conventional processor did in the both cases. Both methods are shown to have the same molecular structures and dynamics of the systems.
48.	Kloo, Lars (författare) On closed-shell interactions between heavy main-group elements 2022 Ingår i: Journal of Computational Chemistry. - : Wiley. - 0192-8651 .- 1096-987X. ; 43:29, s. 1985-1996 Tidskriftsartikel (refereegranskat)abstract A series of di- and polymetal complexes involving closed-shell, heavy main-group atoms and ions shows a selection of special physical properties. These involve short metal-metal contacts, low entropies of formation and, most interestingly, strong Raman bands at low wavenumbers. These results together with the constitution of the coordination compounds, where the majority of electrons are assembled on the highly polarizable metal atoms and ions, experimental results have been interpreted in terms of direct, partial covalent metal-metal bonding. Previous theoretical studies have challenged this view and instead attributed the obvious attractive forces involved to secondary-type of interactions, such as dispersion. This study utilizes a multitude of theoretical tools, such as natural bond order (NBO) and natural energy decomposition analysis (NEDA), non-covalent interaction (NCI) analysis, electron localization functions (ELFs), and atoms-in-molecules (AIM) to characterize the interactions in models comprising closed-shell dimers, as well as experimentally studied ring and cage systems constituting the main reason for the hypotheses on metal-metal interactions. The results show that all experimental results can be attributed to the covalent interactions between the electron-rich, metal centers and the bridging anions in ring and cage coordination compounds of high symmetry, where the experimentally observed effects can be traced to the combination of covalent interactions between the metal centers and the anions along the edges of the ring and cage systems in combination with the cooperative effects generated by the high symmetry of these ring and cage systems.
49.	Kuttel, Michelle M., et al. (författare) CarbBuilder : Software for building molecular models of complex oligo- and polysaccharide structures 2016 Ingår i: Journal of Computational Chemistry. - : Wiley. - 0192-8651 .- 1096-987X. ; 37:22, s. 2098-2105 Tidskriftsartikel (refereegranskat)abstract CarbBuilder is a portable software tool for producing three-dimensional molecular models of carbohydrates from the simple text specification of a primary structure. CarbBuilder can generate a wide variety of carbohydrate structures, ranging from monosaccharides to large, branched polysaccharides. Version 2.0 of the software, described in this article, supports monosaccharides of both mammalian and bacterial origin and a range of substituents for derivatization of individual sugar residues. This improved version has a sophisticated building algorithm to explore the range of possible conformations for a specified carbohydrate molecule. Illustrative examples of models of complex polysaccharides produced by CarbBuilder demonstrate the capabilities of the software. CarbBuilder is freely available under the Artistic License 2.0.
50.	Kutzner, Carsten, et al. (författare) Best bang for your buck : GPU nodes for GROMACS biomolecular simulations 2015 Ingår i: Journal of Computational Chemistry. - : Wiley. - 0192-8651 .- 1096-987X. ; 36:26, s. 1990-2008 Tidskriftsartikel (refereegranskat)abstract The molecular dynamics simulation package GROMACS runs efficiently on a wide variety of hardware from commodity workstations to high performance computing clusters. Hardware features are well-exploited with a combination of single instruction multiple data, multithreading, and message passing interface (MPI)-based single program multiple data/multiple program multiple data parallelism while graphics processing units (GPUs) can be used as accelerators to compute interactions off-loaded from the CPU. Here, we evaluate which hardware produces trajectories with GROMACS 4.6 or 5.0 in the most economical way. We have assembled and benchmarked compute nodes with various CPU/GPU combinations to identify optimal compositions in terms of raw trajectory production rate, performance-to-price ratio, energy efficiency, and several other criteria. Although hardware prices are naturally subject to trends and fluctuations, general tendencies are clearly visible. Adding any type of GPU significantly boosts a node's simulation performance. For inexpensive consumer-class GPUs this improvement equally reflects in the performance-to-price ratio. Although memory issues in consumer-class GPUs could pass unnoticed as these cards do not support error checking and correction memory, unreliable GPUs can be sorted out with memory checking tools. Apart from the obvious determinants for cost-efficiency like hardware expenses and raw performance, the energy consumption of a node is a major cost factor. Over the typical hardware lifetime until replacement of a few years, the costs for electrical power and cooling can become larger than the costs of the hardware itself. Taking that into account, nodes with a well-balanced ratio of CPU and consumer-class GPU resources produce the maximum amount of GROMACS trajectory over their lifetime.

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