Journal of Computational Chemistry

doi: 10.1002/jcc.23480pmid: N/A

The reaction dynamics of ethylene adsorption onto the Si(001) surface is studied by Yung Ting Lee and Jyh Shing Lin on page 2697 by combining density functional theory (DFT)‐based molecular dynamics simulations with a molecular adsorption sampling scheme for investigating reaction pathways and corresponding populations. The major reaction pathway is indirect adsorption, in which ethylene forms the π‐bond with the Si dimer and then turns into di‐σ‐bonded C2H4(ads). The spectrogram, constructed by the short‐time Fourier transform of the structural coordinate autocorrelation function (STFT‐SCAF), illustrates that the CC stretching mode of π‐bonded C2H4(ads) shifts to the C–C stretching mode of di‐σ‐bonded C2H4(ads).

doi: 10.1002/jcc.23479pmid: N/A

By following the scheme of the grid empowered molecular simulator (GEMS), Leonardo Pacifici, Marco Verdicchio, Noelia Faginas Lago, Andrea Lombardi, and Alessandro Costantini on page 2668 calculate an extended set of high‐level abinitio electronic energy values. The calculated values are fitted using a many‐body expansion technique and a full‐dimensional N2 + N2 potential energy surface (PES), also allowing the N atom exchange to be produced. Plots of the obtained PES show the change of the intermediate geometry from reactants to products.

Pyykkö, Pekka

doi: 10.1002/jcc.23454pmid: 24122894

The RTAM bibliography is freely available at rtam.csc.fi and the Version 17.0 of August 22, 2013 now contains 16,566 items from the year 1916–2013. “Production works” were systematically covered until 1999. Since the year 2000, mainly methodological papers were included. The methods and principles behind RTAM are described. © 2013 Wiley Periodicals, Inc.

Pacifici, Leonardo; Verdicchio, Marco; Lago, Noelia Faginas; Lombardi, Andrea; Costantini, Alessandro

doi: 10.1002/jcc.23415pmid: 24037708

A new six‐dimensional (6D) global potential energy surface (PES) is proposed for the full range description of the interaction of the N2(1Σg+)+N2(1Σg+) system governing collisional processes, including N atom exchange. The related potential energy values were determined using high‐level ab initio methods. The calculations were performed at a coupled‐cluster with single and double and perturbative triple excitations level of theory in order to have a first full range picture of the PES. Subsequently, in order to accurately describe the stretching of the bonds of the two interacting N2 molecules by releasing the constraints of being considered as rigid rotors, for the same molecular geometries higher level of theory multi reference calculations were performed. Out of the calculated values a 6D 4‐atoms global PES was produced for use in dynamical calculations. The ab initio calculations were made possible by the combined use of High Throughput Computing and High Performance Computing techniques within the frame of a computing grid empowered molecular simulator. © 2013 Wiley Periodicals, Inc.

Zeng, Juan; Jia, Xiangyu; Zhang, John Z. H.; Mei, Ye

doi: 10.1002/jcc.23421pmid: 24000160

Recently, Baugh et al. discovered that a distal point mutation (F130L) in streptavidin causes no distinct variation to the structure of the binding pocket but a 1000‐fold reduction in biotin binding affinity. In this work, we carry out molecular dynamics simulations and apply an end‐state free energy method to calculate the binding free energies of biotin to wild type streptavidin and its F130L mutant. The absolute binding affinities based on AMBER charge are repulsive, and the mutation induced binding loss is underestimated. When using the polarized protein‐specific charge, the absolute binding affinities are significantly enhanced. In particular, both the absolute and relative binding affinities are in line with the experimental measurements. Further investigation indicates that polarization effect is indispensable in both the generation of structural ensembles and the calculation of interaction energies. This work verifies Baugh's conjecture that electrostatic polarization effect plays an essential role in modulating the binding affinity of biotin to the streptavidin through F130L mutation. © 2013 Wiley Periodicals, Inc.

Ćendić, Marina; Matović, Zoran D.; Deeth, Robert J.

doi: 10.1002/jcc.23437pmid: 24105618

A ligand field molecular mechanics (LFMM) force field (FF) has been developed for d9 copper(II) complexes of aminopolycarboxylate ligands. Training data were derived from density functional theory (DFT) geometry optimizations of 14 complexes comprising potentially hexadentate N2O4, tetrasubstituted ethylenediamine (ed), and propylenediamine cores with various combinations of acetate and propionate side arms. The FF was validated against 13 experimental structures from X‐ray crystallography including hexadentate N2O4 donors where the nitrogens donors are forced to be cis and bis‐tridentate ONO ligands which generate complexes with trans nitrogen donors. Stochastic conformational searches for (Cu{ed(acetate)n (propionate)4‐n})2−, n = 0–4, were carried out and the lowest conformers for each system reoptimized with DFT. In each case, both DFT and LFMM predict the same lowest‐energy conformer and the structures and energies of the higher‐energy conformers are also in satisfactory agreement. The relative interaction energies for n = 0, 2, and 4 computed by molecular mechanics correlate with the experimental log β binding affinities. Adding in the predicted log β values for n = 1 and 3 suggest for this set of complexes a monotonic decrease in log β as the number of propionate arms increases. © 2013 Wiley Periodicals, Inc.

Lee, Yung Ting; Lin, Jyh Shing

doi: 10.1002/jcc.23434pmid: 24105930

The reaction dynamics of ethylene adsorption onto the Si(001) surface have been studied by combining density functional theory‐based molecular dynamics simulations with molecular adsorption sampling scheme for investigating all kinds of reaction pathways and corresponding populations. Based on the calculated results, three possible reaction pathways—the indirect adsorption, the direct adsorption, and the repelling reaction—have been found. First, the indirect adsorption, in which the ethylene (C2H4(ads)) forms the π‐bonded C2H4(ads) with the buckled‐down Si atom to adsorb on the Si(001) surface and then turns into the di‐σ‐bonded C2H4(ads), is the major reaction pathway. The short‐time Fourier transform analysis of structural coordinate autocorrelation function is performed to further investigate the evolution of different vibrational modes along this indirect reaction pathway. This analysis illustrates that the Infrared (IR) inactive peak of the CC stretching mode of the π‐bonded C2H4(ads) shifts to the IR inactive peak of the CC stretching mode of di‐σ‐bonded C2H4(ads), which is in a good agreement with the IR inactive peak of the CC stretching mode vanished in the vibrational spectrum at 150 K (Nagao et al., J. Am. Chem. Soc. 2004, 126, 9922). Second, the direct adsorption, in which the di‐σ‐bonded C2H4(ads) is formed directly with the Si intradimer or the Si interdimer on the Si(001) surface, is the less significant reaction pathway. This reaction pathway leads to the CC stretching mode and the CH stretching mode of the di‐σ‐bonded C2H4(ads) appeared in the vibrational spectra at 48 and 150 K, respectively (Nagao et al., J. Am. Chem. Soc. 2004, 126, 9922). Finally, the repelling reaction, in which the C2H4(g) first interacts with the Si dimer and then is repelled by Si atoms, is the least important reaction pathway. Consequently, neither the π‐bonded C2H4(ads) nor the di‐σ‐bonded C2H4(ads) is formed on the Si(001) surface. © 2013 Wiley Periodicals, Inc.

Nickerson, Stella; Frost, Denzil S.; Phelan, Harrison; Dai, Lenore L.

doi: 10.1002/jcc.23443pmid: 24122780

We have studied the calculation of surface and interfacial tension for a variety of liquid–vapor and liquid–liquid interfaces using molecular dynamics (MD) simulations. Because of the inherently small scale of MD systems, large pressure fluctuations can cause imprecise calculations of surface tension using the pressure tensor route. The capillary wave method exhibited improved precision and stability throughout all of the simulated systems in this study. In order to implement this method, the interface was defined by fitting an error function to the density profile. However, full mapping of the interface from coordinate files produced enhanced accuracy. Upon increasing the system size, both methods exhibited higher precision, although the capillary wave method was still more reliable. © 2013 Wiley Periodicals, Inc.

Neumann, Tobias; Danilov, Denis; Lennartz, Christian; Wenzel, Wolfgang

doi: 10.1002/jcc.23445pmid: 24114652

Organic thin film devices are investigated for many diverse applications, including light emitting diodes, organic photovoltaic and organic field effect transistors. Modeling of their properties on the basis of their detailed molecular structure requires generation of representative morphologies, many of which are amorphous. Because time‐scales for the formation of the molecular structure are slow, we have developed a linear‐scaling single molecule deposition protocol which generates morphologies by simulation of vapor deposition of molecular films. We have applied this protocol to systems comprising argon, buckminsterfullerene, N,N‐Di(naphthalene‐1‐yl)‐N,N'‐diphenyl‐benzidine, mer‐tris(8‐hydroxy‐quinoline)aluminum(III), and phenyl‐C61‐butyric acid methyl ester, with and without postdeposition relaxation of the individually deposited molecules. The proposed single molecule deposition protocol leads to formation of highly ordered morphologies in argon and buckminsterfullerene systems when postdeposition relaxation is used to locally anneal the configuration in the vicinity of the newly deposited molecule. The other systems formed disordered amorphous morphologies and the postdeposition local relaxation step has only a small effect on the characteristics of the disordered morphology in comparison to the materials forming crystals. © 2013 Wiley Periodicals, Inc.

Grigoryan, Gevorg

doi: 10.1002/jcc.23448pmid: 24132787

Computing the absolute free energy of a macromolecule's structural state, F, is a challenging problem of high relevance. This study presents a method that computes F using only information from an unperturbed simulation of the macromolecule in the relevant conformational state, ensemble, and environment. Absolute free energies produced by this method, dubbed Valuation of Local Configuration Integral with Dynamics (VALOCIDY), enable comparison of alternative states. For example, comparing explicitly solvated and vaporous states of amino acid side‐chain analogs produces solvation free energies in good agreement with experiments. Also, comparisons between alternative conformational states of model heptapeptides (including the unfolded state) produce free energy differences in agreement with data from μs molecular‐dynamics simulations and experimental propensities. The potential of using VALOCIDY in computational protein design is explored via a small design problem of stabilizing a β‐turn structure. When VALOCIDY‐based estimation of folding free energy is used as the design metric, the resulting sequence folds into the desired structure within the atomistic force field used in design. The VALOCIDY‐based approach also recognizes the distinct status of the native sequence regardless of minor details of the starting template structure, in stark contrast with a traditional fixed‐backbone approach. © 2013 Wiley Periodicals, Inc.