Journal of Computational Chemistry

Mourik, Tanja Van

doi: 10.1002/jcc.20869pmid: 18000868

Palermo et al. have recently published a method to correct for intramolecular basis set superposition errors (J Comput Chem 2007, 28, 1208) in intramolecular interactions occurring in peptides. By considering the intermolecular equivalent of this method, it is shown that the method presented by Palermo et al. underestimates the magnitude of the intramolecular BSSE. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008

Csontos, József; Palermo, Nicholas Y.; Murphy, Richard F.; Lovas, Sándor

doi: 10.1002/jcc.20868pmid: N/A

In response to Van Mourik's comments on our paper (J Comput Chem 2007, 28, 1208.) we present an extended version of our rotation method. We also prove that intramolecular interaction energies as well the basis set superposition errors calculated with our rotation method are comparable with those obtained by the counterpoise method of Boys and Bernardi (Mol Phys 1970, 19, 533). In intramolecular interaction energy calculations, if the interacting groups are in proximity, our rotation method is recommended to avoid artificial interactions, which can be induced by fragmentation. © 2007 Wiley Periodicals, Inc.J Comput Chem, 2008

Feldmann, Michael T.; Cummings, Julian C.; Kent, David R.; Muller, Richard P.; Goddard, William A.

doi: 10.1002/jcc.20836pmid: 17918283

A manager–worker‐based parallelization algorithm for Quantum Monte Carlo (QMC‐MW) is presented and compared with the pure iterative parallelization algorithm, which is in common use. The new manager–worker algorithm performs automatic load balancing, allowing it to perform near the theoretical maximal speed even on heterogeneous parallel computers. Furthermore, the new algorithm performs as well as the pure iterative algorithm on homogeneous parallel computers. When combined with the dynamic distributable decorrelation algorithm (DDDA) (Feldmann et al., J Comput Chem 28, 2309 (2007)), the new manager–worker algorithm allows QMC calculations to be terminated at a prespecified level of convergence rather than upon a prespecified number of steps (the common practice). This allows a guaranteed level of precision at the least cost. Additionally, we show (by both analytic derivation and experimental verification) that standard QMC implementations are not “perfectly parallel” as is often claimed. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008

Song, Kun; Hornak, Viktor; De Los Santos, Carlos; Grollman, Arthur P.; Simmerling, Carlos

doi: 10.1002/jcc.20625pmid: 17551974

FapydG is a common oxidative DNA lesion involving opening of the imidazole ring. It shares the same precursor as 8‐oxodG and can be excised by the same enzymes as 8‐oxodG. However, the loss of the aromatic imidazole in FapydG results in a reduction of the double bond character between C5 and N7, with an accompanying increase in conformational flexibility. Experimental characterization of FapydG is hampered by high reactivity, and thus it is desirable to investigate structural details through computer simulation. We show that the existing Amber force field parameters for FapydG do not reproduce X‐ray structural data. We employed quantum mechanics energy profile calculations to derive new molecular mechanics parameters for the rotation of the dihedral angles in the eximidazole moiety. Using these parameters, all‐atom simulations in explicit water reproduce the nonplanar conformation of cFapydG in the crystal structure of the complex with L. lactis glycosylase Fpg. We note that the nonplanar structure is stabilized by an acidic residue that is not present in most Fpg sequences. Simulations of the E→S mutant, as present in E. coli, resulted in a more planar conformation, suggesting that the highly nonplanar form observed in the crystal structure may not have direct biological relevance for FapydG. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008

Rosso, Lula; Gould, Ian R.

doi: 10.1002/jcc.20675pmid: 17910006

Two fully hydrated pure‐species phospholipids bilayers, 1,2‐dimyristoyl‐sn‐glycero‐3‐phosphocholine (DMPC) and 1,2‐dioleoyl‐sn‐glycero‐3‐phosphorylcholine (DOPC), in the fluid phase and explicit solvent have been studied using molecular dynamics simulation. Atom interactions were modeled using recently developed force fields based on AMBER with full atomistic details. Several representative liquid phase properties for the structure and dynamics of lipids with different length of hydrocarbon chains and different level of saturation have been reproduced without artificially biasing the system in order to match experimental data. In particular, as the new GAFF (General Amber Force Field) has not been explicitly developed to reproduce lipid characteristics and is naturally compatible with standard AMBER nucleic acids and proteins parameters, it is here proven a promising tool to study mixed lipid–protein processes as protein activity dependence on membrane composition, permeation of solute across membranes, and other cellular processes. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008

Spiegel, Katrin; Magistrato, Alessandra; Maurer, Patrick; Ruggerone, Paolo; Rothlisberger, Ursula; Carloni, Paolo; Reedijk, Jan; Klein, Michael L.

doi: 10.1002/jcc.20739pmid: 17705162

Azole‐bridged diplatinum compounds are promising new anticancer drugs designed to induce small distortions upon DNA alkylation, able to circumvent resistance problems of existing platinum drugs. Hybrid quantum classical (QM/MM) molecular dynamics (MD) simulations of different azole‐bridged platinum drugs have recently revealed the nature of the local deformations at the DNA binding site. However, the description of global slow converging rearrangements cannot be addressed by QM/MM MD due to the short time scale accessible. Extensive classical MD simulations are therefore mandatory to describe accurately the structural distortions in the DNA double helix. This issue is now addressed by developing a new set of accurate force field parameters of the platinated moiety via a recently proposed force matching procedure of the classical forces to ab initio forces obtained from QM/MM trajectories. The accuracy of our force field parameters is validated by comparison of structural properties from classical MD and hybrid QM/MM simulations. The structural characteristics of the Pt‐lesion are well reproduced during classical MD compared with QM/MM simulations and available experimental data. The global distortions in the DNA duplex upon binding of dinuclear Pt‐compounds are very small and rather opposite to those induced by cisplatin. Thus, the force match approach significantly extends the potentialities of molecular simulations in the study of anticancer drugs and of the interactions with their biological targets. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008

Milgram, R. J.; Liu, Guanfeng; Latombe, J. C.

doi: 10.1002/jcc.20755pmid: 17542001

Loop closure in proteins requires computing the values of the inverse kinematics (IK) map for a backbone fragment with 2n ≥ 6 torsional degrees of freedom (dofs). It occurs in a variety of contexts, e.g., structure determination from electron‐density maps, loop insertion in homology‐based structure prediction, backbone tweaking for protein energy minimization, and the study of protein mobility in folded states. The first part of this paper analyzes the global structure of the IK map for a fragment of protein backbone with 6 torsional dofs for a slightly idealized kinematic model, called the canonical model. This model, which assumes that every two consecutive torsional bonds CαC and NCα are exactly parallel, makes it possible to separately compute the inverse orientation map and the inverse position map. The singularities of both maps and their images, the critical sets, respectively, decompose SO(3) × ℝ3 into open regions where the number of IK solutions is constant. This decomposition leads to a constructive proof of the existence of a region in ℝ3 × SO(3) where the IK of the 6‐dof fragment attains its theoretical maximum of 16 solutions. The second part of this paper extends this analysis to study fragments with more than 6 torsional dofs. It describes an efficient recursive algorithm to sample IK solutions for such fragments, by identifying the feasible range of each successive torsional dof. A numerical homotopy algorithm is then used to deform the IK solutions for a canonical fragment into solutions for a noncanonical fragment. Computational results for fragments ranging from 8 to 30 dofs are presented. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008

Rodríguez‐Ropero, Francisco; Casanovas, Jordi; Alemán, Carlos

doi: 10.1002/jcc.20763pmid: 17591719

π‐Stacked complexes formed by two, three, and four thiophene rings have been investigated using abinitio quantum mechanical calculations. The relative orientation between the rings was investigated for each complex by exploring the corresponding potential energy surface at the MP2/6‐31+G(d,p) level, the inter‐ring distance, and the degree of tilting being examined in each case. Interaction energies were calculated at the MP2, MP3, MP4, and CCSD, levels of theory. Negligible or even slightly positive n‐body effects have been predicted for the stacked thiophene arrangements studied in this work. This is consequence of the cancellation of favorable induction contribution by the destabilizing dispersion component. On the other hand analysis of the optimized geometries obtained for the trimer and tetramer revealed that the orientation of the rings presents a preferred degree of periodicity. Finally, we found that the lowest transition energy decreases when the size of the complex increases, this feature being attributed to desestabilization of the HOMO and stabilization of the LUMO that occur simultaneously. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008

Kovalyov, Evgenii V.; Elokhin, Vladimir I.; Myshlyavtsev, Aleksandr V.

doi: 10.1002/jcc.20766pmid: 17516426

The statistical lattice model has been proposed which permits one to take into account the change in the shape and surface morphology of the nanoparticle under the influence of the reaction media. The influence of monomolecular and dissociative adsorption on the particles equilibrium shape and surface morphology has been studied. It has been shown that by taking into account of attraction “adsorbate‐metal” the reshaping of the initial hemispheric particle into cone‐shaped one occurs induced by adsorption, similar to the experimentally observed reversible reshaping of active nanoparticles. The model reaction A+B2 has been studied taking into account the roughening of the active particle surface and the spillover phenomena of the adsorbed Aads species over the support surface. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008

Zhou, Y. C.; Feig, Michael; Wei, G. W.

doi: 10.1002/jcc.20769pmid: 17508411

Implicit solvent models based on the Poisson‐Boltzmann (PB) equation are frequently used to describe the interactions of a biomolecule with its dielectric continuum environment. A novel, highly accurate Poisson‐Boltzmann solver is developed based on the matched interface and boundary (MIB) method, which rigorously enforces the continuity conditions of both the electrostatic potential and its flux at the molecular surface. The MIB based PB solver attains much better convergence rates as a function of mesh size compared to conventional finite difference and finite element based PB solvers. Consequently, highly accurate electrostatic potentials and solvation energies are obtained at coarse mesh sizes. In the context of biomolecular electrostatic calculations it is demonstrated that the MIB method generates substantially more accurate solutions of the PB equation than other established methods, thus providing a new level of reference values for such models. Initial results also indicate that the MIB method can significantly improve the quality of electrostatic surface potentials of biomolecules that are frequently used in the study of biomolecular interactions based on experimental structures. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008