Journal of Computational Chemistry

doi: 10.1002/jcc.23432pmid: N/A

The cover depicts a Stone–Wales (SW) defective single‐walled carbon nanotube (SWNT) surrounded with several 1,3‐ dipoles such as azomethine ylide and nitrone. Using a two‐layered ONIOM method by Tao Yang, Xiang Zhao, and Shigeru Nagase on page 2223, 1,3–dipolar cycloadditions of several 1,3‐dipoles upon SW defective and defect‐free SWNTs are systematically studied. Compared with defect‐free SWNTs, the SW defective SWNTs exhibit the higher chemical reactivity. The larger the diameter of the SWNT, the lower chemical reactivity the SW defective SWNT shows.

doi: 10.1002/jcc.23431pmid: N/A

The cover shows an artistic rendering of some of the results obtained through the application of the program grcarma by Panagiotis Koukos and Nicholas Glykos on page 2310. The background surface is a color representation of the variance–covariance matrix of LmbE, a homohexameric protein. The molecular model in the foreground shows a dimer of the same protein colored according to its atomic root mean squared fluctuations.

Yang, Tao; Zhao, Xiang; Nagase, Shigeru

doi: 10.1002/jcc.23368pmid: 23832655

The presence of Stone‐Wales defects in single‐walled carbon nanotubes (SWNTs) not only leads to new interesting properties, but also provides opportunities for tailoring physical and chemical properties, and expands their novel potential applications. With a two‐layered ONIOM method, 1,3‐dipolar cycloadditions (1,3‐DCs) of a series of 1,3‐dipoles (azomethine ylide, nitrone, nitrile imine, nitrile ylide, nitrile oxide, and methyl azide) with Stone‐Wales defective SWNTs have been investigated theoretically for the first time. The calculated results demonstrate that the bond c, rather than the previously focused central bond a, exhibits the highest chemical reactivity among the defective sites. More interestingly, bond c is even more reactive thermodynamically and kinetically than the perfect CC bond in SWNTs, suggesting the feasibility of utilizing 1,3‐DC reactions to separate and purify perfect and defective SWNTs. The reactivity order for nonequivalent bonds in defective sites is different from that of (1+2) cycloaddition, indicating that the reactivity order for nonequivalent bonds depends on the kind of the chemical reactions. Except azomethine ylide, nitrile ylide and nitrile imine are found to be good candidates for 1,3‐DCs upon Stone‐Wales defective SWNTs. The SW‐A and SW‐B defective SWNTs show different chemical reactivity toward nitrile ylide, making it possible to purify and separate the SW‐A and SW‐B defective SWNTs. The SWNT diameters are found to moderately influence the 1,3‐DC reactivity of both perfect and Stone‐Wales defective SWNTs, implying that Stone‐Wales defective SWNTs with different diameter would be separated experimentally through 1,3‐DC chemistry. The above 1,3‐DC reactivity can be well understood in terms of the distortion/interaction theory, which means that instead of frontier molecular orbitals interaction energy, the distortion energy controls the chemical reactivity. © 2013 Wiley Periodicals, Inc.

Kim, Hyungjun; Park, Joungwon; Lee, Yoon Sup

doi: 10.1002/jcc.23380pmid: 23873702

Density functional theory calculation has been performed to calculate the redox potential and the correct ground spin state of iron complexes in acetonitrile. Widely used B3LYP functional is applied with the spin state corrected basis sets. The newly developed protocol for the set of 21 iron complexes is to optimize the structure at the level of the B3LYP/6‐31G* and to calculate the single point electronic energy with the same functional and the modified basis sets s6‐31G* for the iron atom and 6‐31+G* for other ligand atoms. The solvation energy is considered through the polarized continuum model and the cavity creation energy is included for the accurate spin state description. Modifying the cavity size by employing the different scaling factor according to the mean absolute value of the natural population analysis charge (MA‐NPA) is introduced. The molecule with the large MA‐NPA requires the cavity size smaller than the less polar one. This protocol gives only 1 wrong ground spin state among the 18 iron complexes for which experimental data are known. For the open circuit voltage (OCV) calculation, our protocol performs well yielding the mean absolute error of 0.112 V for the test set. The close correlation between the calculated and the experimental OCV are obtained. © 2013 Wiley Periodicals, Inc.

Bomble, Laetitia; Steinmann, Stephan N.; Perez‐Peralta, Nancy; Merino, Gabriel; Corminboeuf, Clemence

doi: 10.1002/jcc.23383pmid: 23897739

The multicenter bonding pattern of the intriguing hexa‐, hepta‐, and octacoordinate boron wheel series (e.g., CB62‐, CB7‐, B82‐, and SiB8 as well as the experimentally detected CB7‐ isomer) is revised using the block‐localized wave function analyzed by the localized orbital locator (BLW‐LOL). The more general implementation of BLW combined with the LOL scalar field is not restricted to the analysis of the out‐of‐plane π‐system but can also provide an intuitive picture of the σ‐radial delocalization and of the role of the central atom. The results confirm the presence of a π‐ring current pattern similar to that of benzene. In addition, the LOLπ isosurfaces along with the maximum intensity in the ΔLOL profiles located above and below the ring suggest that the central atom plays a minor role in the π‐delocalized bonding pattern. Finally, the analysis of the σ‐framework in these boron wheels is in line with a moderated inner cyclic rather than disk‐type delocalization. © 2013 Wiley Periodicals, Inc.

Anthopoulos, Athanasios; Grimstead, Ian; Brancale, Andrea

doi: 10.1002/jcc.23384pmid: 23861143

In this article, we describe an improved cell‐list approach designed to match the Kepler architecture of General‐purpose graphics processing units (GPGPU). We explain how our approach improves load balancing for the above algorithm and how warp intrinsics are used to implement Newton's third law for the nonbonded force calculations. We also talk through our approach to exclusions handling together with a method to calculate bonded forces and 1–4 electrostatic scaling using a single Cuda kernel. Performance benchmarks are included in the last sections to show the linear scaling of our implementation using a step minimization method. In addition, multiple performance benchmarks demonstrate the contribution of various optimizations we used for our implementations. © 2013 Wiley Periodicals, Inc.

Stachowicz, Anna; Korchowiec, Jacek

doi: 10.1002/jcc.23385pmid: 23878100

Charge sensitivity analysis in AMBER force‐field resolution has been used in quest for detectors of hydrogen bonds (HBs). The process of HB formation was investigated on ab initio classical trajectories (B3LYP/6‐31G*) of different nucleobase pairs. Several charge sensitivities, namely: electronegativity, hardness, Fukui function (FF), and polarization matrix, were analyzed. The global and constrained equilibria were considered. It was demonstrated that FF indices and polarization matrix elements are good detectors of HB formation. © 2013 Wiley Periodicals, Inc.

Kalyaanamoorthy, Subha; Chen, Yi‐Ping Phoebe

doi: 10.1002/jcc.23390pmid: 23893931

Exploring the molecular channels of class I histone deacetylases (HDACs) with buried active sites are important to understand their structures and functionalities. In this work, we perform hybrid classical molecular dynamics and random acceleration molecular dynamics simulations to explore the B3N (i.e., (4‐(dimethylamino)N‐(7(hydroxyamino)‐7‐oxoheptyle) benzamide)) exit channels in the x‐ray crystal structures of HDAC3 and HDAC8 enzymes. Our simulations identify B3N release through four different channels in HDAC3 (denoted as A1, A2, B1, and B2) and HDAC8 (referred as A1, B1, B2, and B3) enzymes, among which egression through channel A1 is more predominant in both the enzymes. This mechanism is similar to ligand release in HDAC1 and HDAC2 described in our previous study and can be the fingerprint ligand release mechanisms in class I HDACs. Ligand release events through B channels, on the other hand, are different among HDAC3 and HDAC8, highlighting the significances of substituted residues in controlling the access to these channels This study reveals a novel aromatic gating mechanism elicited by TYR154‐TRP141‐TYR111 that controls the B3N access to all the B channels in HDAC8. The TRP141 in HDAC8 is substituted by LEU133 in HDAC3, which do not hinder the access to B channels in HDAC3. However, two hydrogen bonded barricades formed as ARG28‐GLY297‐GLY295‐GLY131 and TRP129‐ARG28‐ALA130‐LEU29‐TRP129 obstruct the B3N from exploring the B channels in HDAC3. The structural and dynamical characterizations of molecular channels and ligand unbinding mechanisms reported in this study provide novel structural insights and atomic level perspectives on HDAC3 and HDAC8 enzymes, thereby potentially aiding in the design of more specific HDAC inhibitors.Copyright © 2013 Wiley Periodicals, Inc.

Kaliman, Ilya A.; Slipchenko, Lyudmila V.

doi: 10.1002/jcc.23375pmid: 24159627

A new high performance parallel implementation of the general Effective Fragment Potential (EFP) method in a form of a portable software library called libefp is presented. The libefp library was designed to provide developers of various quantum chemistry software packages with an easy way to add EFP functionality to the program of their choice. The general overview of the library is presented and various aspects of interfacing the library with third party quantum chemistry packages are considered. The reference implementation of common methods of computational chemistry such as geometry optimization and molecular dynamics on top of libefp is delivered in the form of efpmd program. Results of molecular dynamics simulation of liquid water using the developed software are described. © 2013 Wiley Periodicals, Inc.

Epifanovsky, Evgeny; Wormit, Michael; Kuś, Tomasz; Landau, Arie; Zuev, Dmitry; Khistyaev, Kirill; Manohar, Prashant; Kaliman, Ilya; Dreuw, Andreas; Krylov, Anna I.

doi: 10.1002/jcc.23377pmid: 24159628