Journal of Computational Chemistry

Salehzadeh, Sadegh; Bayat, Mehdi

doi: 10.1002/jcc.21530pmid: 20340102

DFT(B3LYP) studies on first protonation step of a series of Cu(II) complexes of some tripodal tetraamines with general formula N[(CH2)nNH2][(CH2)mNH2][(CH2)pNH2] (n = m = p = 2, tren; n = 3, m = p = 2, pee; n = m = 3, p = 2, ppe; n = m = 3, tpt; n = 2, m = 3, p = 4, epb; and n = m = 3, p = 4; ppb) are reported. First, the gas‐phase proton macroaffinity of all latter complexes was calculated with considering following simple reaction: [Cu(L)]2+(g) + H+(g) → [Cu(HL)]3+(g). The results showed that there is a good correlation between the calculated proton macroaffinities of all complexes with their stability constants in solution. Then, we tried to determine the possible reliable structures for microspecies involved in protonation process of above complexes. The results showed that, similar to the solid state, the [Cu(L)(H2O)]2+ and [Cu(HL)(H2O)2]3+ are most stable species for latter complexes and their protonated form, respectively, at gas phase. We found that there are acceptable correlations between the formation constants of above complexes with both the −$\overline {\Delta E}$ and −$\overline {\Delta G}$ of following reaction: [Cu(L)(H2O)]2+(g) + H+(g) + H2O(g) → [Cu(HL)(H2O)2]3+(g). The −$\overline {\Delta E}$ of the latter reaction can be defined as a theoretically solvent–proton macroaffinity of reactant complexes because they have gained one proton and one molecule of the solvent. The unknown formation constant of [Cu(epb)]2+ complex was also predicted from the observed correlations. In addition, the first proton affinity of all complexes was studied in solution using DPCM and CPCM methods. It was shown that there is an acceptable correlation between the solvent–proton affinities of [Cu(L)(H2O)]2+ complexes with formation constants of [Cu(HL)(H2O)2]3+ complexes in solution. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010

Umeda, Hiroaki; Inadomi, Yuichi; Watanabe, Toshio; Yagi, Toru; Ishimoto, Takayoshi; Ikegami, Tsutomu; Tadano, Hiroto; Sakurai, Tetsuya; Nagashima, Umpei

doi: 10.1002/jcc.21531pmid: 20652982

A parallel Fock matrix construction program for FMO‐MO method has been developed with the distributed shared memory model. To construct a large‐sized Fock matrix during FMO‐MO calculations, a distributed parallel algorithm was designed to make full use of local memory to reduce communication, and was implemented on the Global Array toolkit. A benchmark calculation for a small system indicates that the parallelization efficiency of the matrix construction portion is as high as 93% at 1,024 processors. A large FMO‐MO application on the epidermal growth factor receptor (EGFR) protein (17,246 atoms and 96,234 basis functions) was also carried out at the HF/6‐31G level of theory, with the frontier orbitals being extracted by a Sakurai‐Sugiura eigensolver. It takes 11.3 h for the FMO calculation, 49.1 h for the Fock matrix construction, and 10 min to extract 94 eigen‐components on a PC cluster system using 256 processors. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010

Casanova, David; Alemany, Pere; Alvarez, Santiago

doi: 10.1002/jcc.21532pmid: 20652983

In this communication we define electronic symmetry operation and symmetry group measures, eSOM and eSGM, respectively, develop the basic algorithms to obtain them, and give some examples of the possible applications of these new computational tools. These new symmetry measures based on the electron density have been tested in an analysis of (a) the inversion symmetry for heteronuclear diatomic molecules, for the eclipsed and staggered conformations of ethane and tetrafluoroethane, and for a series of octahedral sulfur halides; (b) the reflection symmetry of three different conformers of tetrafluoroethene; and (c) the loss of C6 symmetry along the B2u distortion mode of benzene and an analysis of rotational symmetry for different six‐member ring heterocycles. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010

Rahalkar, Anuja P.; Katouda, Michio; Gadre, Shridhar R.; Nagase, Shigeru

doi: 10.1002/jcc.21533pmid: 20652984

Many Divide‐and‐Conquer based approaches are being developed to overcome the high scaling problem of the ab initio methods. In this work, one such method, Molecular Tailoring Approach (MTA) has been interfaced with recently developed efficient Møller‐Plesset second order perturbation theory (MP2) codes viz. IMS‐MP2 and RI‐MP2 to reap the advantage of both. An external driver script is developed for implementing MTA at the front‐end and the MP2 codes at the back‐end. The present version of the driver script is written only for a single point energy evaluation of a molecular system at a fixed geometry. The performance of these newly developed MTA‐IMS‐MP2 and MTA‐RI‐MP2 codes is extensively benchmarked for a variety of molecular systems vis‐à‐vis the corresponding actual runs. In addition to this, the performance of these programs is also critically compared with Fragment Molecular Orbital (FMO), another popular fragment‐based method. It is observed that FMO2/2 is superior to FMO3/2 and MTA with respect to time advantage; however, the errors of FMO2 are much beyond chemical accuracy. However, FMO3/2 is a highly accurate method for biological systems but is unsuccessful in case of water clusters. MTA produces estimates with errors within 1 kcal/mol uniformly for all systems with reasonable time advantage. Analysis carried out employing various basis sets shows that FMO gives its optimum performance only for basis sets, which does not include diffuse functions. On the contrary, MTA performance is found to be similar for any basis set used. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010

Lin, Zhixiong; Liu, Haiyan; van Gunsteren, Wilfred F.

doi: 10.1002/jcc.21534pmid: 20652985

Computer simulation using molecular dynamics is increasingly used to simulate the folding equilibria of peptides and small proteins. Yet, the quality of the obtained results depends largely on the quality of the force field used. This comprises the solute as well as the solvent model and their energetic and entropic compatibility. It is, however, computational very expensive to perform test simulations for each combination of force‐field parameters. Here, we use the one‐step perturbation technique to predict the change of the free enthalpy of folding of a β‐peptide in methanol solution due to changing a variety of force‐field parameters. The results show that changing the solute backbone partial charges affects the folding equilibrium, whereas this is relatively insensitive to changes in the force constants of the torsional energy terms of the force field. Extending the cut‐off distance for nonbonded interactions beyond 1.4 nm does not affect the folding equilibrium. The same result is found for a change of the reaction‐field permittivity for methanol from 17.7 to 30. The results are not sensitive to the criterion, e.g., atom‐positional RMSD or number of hydrogen bonds, that is used to distinguish folded and unfolded conformations. Control simulations with perturbed Hamiltonians followed by backward one‐step perturbation indicated that quite large perturbations still yield reliable results. Yet, perturbing all solvent molecules showed where the limitations of the one‐step perturbation technique are met. The evaluated methodology constitutes an efficient tool in force‐field development for molecular simulation by reducing the number of required separate simulations by orders of magnitude. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010

Scott, Gregory; Gruebele, Martin

doi: 10.1002/jcc.21535pmid: 20652986

Reaction kinetics on free energy surfaces with small activation barriers can be computed directly with the Smoluchowski equation. The procedure is computationally expensive even in a few dimensions. We present a propagation method that considerably reduces computational time for a particular class of problems: when the free energy surface suddenly switches by a small amount, and the probability distribution relaxes to a new equilibrium value. This case describes relaxation experiments. To achieve efficient solution, we expand the density matrix in a basis set obtained by singular value decomposition of equilibrium density matrices. Grid size during propagation is reduced from (100–1000)N to (2–4)N in N dimensions. Although the scaling with N is not improved, the smaller basis set nonetheless yields a significant speed up for low‐dimensional calculations. To demonstrate the practicality of our method, we couple Smoluchowsi dynamics with a genetic algorithm to search for free energy surfaces compatible with the multiprobe thermodynamics and temperature jump experiment reported for the protein α3D. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010

Grauffel, Cédric; Stote, Roland H.; Dejaegere, Annick

doi: 10.1002/jcc.21536pmid: 20652987

We describe the development of force field parameters for methylated lysines and arginines, and acetylated lysine for the CHARMM all‐atom force field. We also describe a CHARMM united‐atom force field for modified sidechains suitable for use with fragment‐based docking methods. The development of these parameters is based on results of ab initio quantum mechanics calculations of model compounds with subsequent refinement and validation by molecular mechanics and molecular dynamics simulations. The united‐atom parameters are tested by fragment docking to target proteins using the MCSS procedure. The all‐atom force field is validated by molecular dynamics simulations of multiple experimental structures. In both sets of calculations, the computational predictions using the force field were compared to the corresponding experimental structures. We show that the parameters yield an accurate reproduction of experimental structures. Together with the existing CHARMM force field, these parameters will enable the general modeling of post‐translational modifications of histone tails. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010

Carbó‐Dorca, R.; Besalú, E.

doi: 10.1002/jcc.21537pmid: 20652988

The so‐called holographic electron density theorem (HEDT) is analyzed from an algebraic perspective, and a brief analytical point of view is also given. The connection of the HEDT with quantum similarity measures (QSM) over electronic density functions (DF) is studied using GTO functions, atomic ASA DF, and promolecular ASA DF. Restricted integration of QSM over a box of finite side length is discussed for all this DF. This work emphasizes the geometric aspects of HEDT, but for the sake of completeness, some analytical insight based on a general Taylor series expansion is also given at the end. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010

Venkatesan, Santhosh Kannan; Shukla, Anil Kumar; Dubey, Vikash Kumar

doi: 10.1002/jcc.21538pmid: 20340105

Visceral leishmaniasis, most lethal form of Leishmaniasis, is caused by Leishmania infantum in the Old world. Current therapeutics for the disease is associated with a risk of high toxicity and development of drug resistant strains. Thiol‐redox metabolism involving trypanothione and trypanothione reductase, key for survival of Leishmania, is a validated target for rational drug design. Recently published structure of trypanothione reductase (TryR) from L. infantum, in oxidized and reduced form along with Sb(III), provides vital clues on active site of the enzyme. In continuation with our attempts to identify potent inhibitors of TryR, we have modeled binding modes of selected tricyclic compounds and quinone derivatives, using AutoDock4. Here, we report a unique binding mode for quinone derivatives and 9‐aminoacridine derivatives, at the FAD binding domain. A conserved hydrogen bonding pattern was observed in all these compounds with residues Thr335, Lys60, His461. With the fact that these residues aid in the orientation of FAD towards the active site forming the core of the FAD binding domain, designing selective and potent compounds that could replace FAD in vivo during the synthesis of Trypanothione reductase can be deployed as an effective strategy in designing new drugs towards Leishmaniasis. We also report the binding of Phenothiazine and 9‐aminoacridine derivatives at the Z site of the protein. The biological significance and possible mode of inhibition by quinone derivatives, which binds to FAD binding domain, along with other compounds are discussed. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010

Kalita, Bulumoni; Deka, Ramesh C.

doi: 10.1002/jcc.21541pmid: 20652989

We present the results of a density functional calculation on adsorption of O2, CO, and their coadsorption at various sites of neutral, cationic, and anionic Pd4 clusters. For all the clusters, the dissociative adsorption of oxygen sitting on Pd bridge sites is found to be preferable. Both O2 and CO binding energies are found to be higher for the anionic Pd4 cluster followed by cationic and neutral cluster. However, binding energies of O2 or CO in the coadsorption complexes follow the trend: anionic > neutral > cationic. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010