Journal of Computational Chemistry

Cover image for Vol. 36 Issue 32

Early View (Online Version of Record published before inclusion in an issue)

Edited By: Charles L. Brooks III, Masahiro Ehara, Gernot Frenking, and Peter R. Schreiner

Impact Factor: 3.589

ISI Journal Citation Reports © Ranking: 2014: 36/157 (Chemistry Multidisciplinary)

Online ISSN: 1096-987X

Associated Title(s): International Journal of Quantum Chemistry, Wiley Interdisciplinary Reviews: Computational Molecular Science


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  1. Software News and Updates

    1. Accelerating electrostatic interaction calculations with graphical processing units based on new developments of ewald method using non-uniform fast fourier transform

      Sheng-Chun Yang, Yong-Lei Wang, Gui-Sheng Jiao, Hu-Jun Qian and Zhong-Yuan Lu

      Article first published online: 19 NOV 2015 | DOI: 10.1002/jcc.24250

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      By using graphical processing units and developing new algorithms both for real-space and reciprocal-space computations, the computational efficiency of the ENUF method used to evaluate electrostatic interactions in particle-based simulations is extraordinarily improved. A procedure for the selection of the optimal parameters with controlled accuracies is proposed. With this method, the same computational precision as the standard Ewald method is achieved, but with dramatically higher computational efficiency.

  2. Full Papers

    1. The barrier to the methyl rotation in Cis-2-butene and its isomerization energy to Trans-2-butene, revisited

      Chérif F. Matta, SeyedAbdolreza Sadjadi, Dale A. Braden and Gernot Frenking

      Article first published online: 18 NOV 2015 | DOI: 10.1002/jcc.24223

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      Atomic origin of the locally stabilizing H⋯H contact in cis-2-butene from virial QTAIM atomic energies along the potential energy surface of methyl rotation, i.e., in terms of atomic sub-potential energy surfaces.

    2. A highly efficient hybrid method for calculating the hydration free energy of a protein

      Hiraku Oshima and Masahiro Kinoshita

      Article first published online: 17 NOV 2015 | DOI: 10.1002/jcc.24253

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      Although the hydration free energy (HFE) is one of the most important factors in studies on the structural stability of a protein, its calculation is significantly difficult in computational cost and accuracy. We develop a new method for calculating the HFE by combining the generalized Born model and the morphometric approach. Our method gives almost the same result as that from the three-dimensional reference interaction site model (3D-RISM) theory with drastic reduction of computational cost.

    3. Shift-and-invert parallel spectral transformation eigensolver: Massively parallel performance for density-functional based tight-binding

      Murat Keçeli, Hong Zhang, Peter Zapol, David A. Dixon and Albert F. Wagner

      Article first published online: 17 NOV 2015 | DOI: 10.1002/jcc.24254

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      Massively parallel supercomputers can extend the size of systems that we can study with quantum chemistry methods. However, the eigenvalue problem remains the bottleneck of scalability for density-functional based tight-binding (DFTB) or semi-empirical molecular orbital methods. We present a sparse eigensolver that enables DFTB calculations for systems with more than 100,000 atoms utilizing more than 200,000 CPU cores.

    4. Revisiting the concept of the (a)synchronicity of diels-alder reactions based on the dynamics of quasiclassical trajectories

      Miguel A. F. de Souza, Elizete Ventura, Silmar A. do Monte, José M. Riveros and Ricardo L. Longo

      Article first published online: 17 NOV 2015 | DOI: 10.1002/jcc.24245

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      Model Diels-Alder cycloaddition reactions were studied by static and dynamics approaches to establish the (a)synchronous character of the concerted mechanism. The use of static criteria, such as the asymmetry of the TS geometry, for classifying and quantifying the (a)synchronicity of the concerted reaction mechanism provides contradictory results and conclusions when compared to the dynamics approach.

  3. Rapid Communication

    1. Self-consistent field for fragmented quantum mechanical model of large molecular systems

      Yingdi Jin, Neil Qiang Su, Xin Xu and Hao Hu

      Article first published online: 17 NOV 2015 | DOI: 10.1002/jcc.24252

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      Fragment-based, linear-scaling, quantum chemistry methods hold great potential for application in accurate simulations of complex molecular systems. Because of the coupled inter-fragment interactions, however, conventional fragment methods often employ a dual-layer SCF scheme to converge both the intra- and inter-fragment interactions. The total number of fragment SCF iterations displays a size-dependence to the target molecule. A new global SCF scheme developed here shows excellent performance over a broad range of molecular sizes and is applicable to other fragment methods.

  4. Full Papers

    1. 18-electron rule and the 3c/4e hyperbonding saturation limit

      C. R. Landis and F. Weinhold

      Article first published online: 14 NOV 2015 | DOI: 10.1002/jcc.24001

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      Electronic iconography of the 18e rule, illustrating how a normal-valent (12e) transition metal MX3 species (using s and d orbitals at M to accommodate three M[BOND]X bonds, blue dots, and three lone pairs, red dots) achieves the maximally stabilizing eM = 18 “count” (all dots) by adding three L donor ligands (green dots) that participate in all possible 3c/4e hyperbonding interactions (nL[RIGHTWARDS ARROW]σ*MX) with M[BOND]X bonds.

  5. Software News and Updates

    1. Molcas 8: New capabilities for multiconfigurational quantum chemical calculations across the periodic table

      Francesco Aquilante, Jochen Autschbach, Rebecca K. Carlson, Liviu F. Chibotaru, Mickaël G. Delcey, Luca De Vico, Ignacio Fdez. Galván, Nicolas Ferré, Luis Manuel Frutos, Laura Gagliardi, Marco Garavelli, Angelo Giussani, Chad E. Hoyer, Giovanni Li Manni, Hans Lischka, Dongxia Ma, Per Åke Malmqvist, Thomas Müller, Artur Nenov, Massimo Olivucci, Thomas Bondo Pedersen, Daoling Peng, Felix Plasser, Ben Pritchard, Markus Reiher, Ivan Rivalta, Igor Schapiro, Javier Segarra-Martí, Michael Stenrup, Donald G. Truhlar, Liviu Ungur, Alessio Valentini, Steven Vancoillie, Valera Veryazov, Victor P. Vysotskiy, Oliver Weingart, Felipe Zapata and Roland Lindh

      Article first published online: 12 NOV 2015 | DOI: 10.1002/jcc.24221

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      The Molcas quantum chemistry program package has a long history, and with the release of Molcas 8 in 2014, it continues to offer state-of-the-art tools for computational chemistry. This article summarizes some of the most significant additions and improvements included in the package in the last 6 years. There are sections on electron correlation methods, relativistic features, molecular dynamics, gradients and optimizations, and technical features.

  6. Full Papers

    1. DIRECT-ID: An automated method to identify and quantify conformational variations—application to β2-adrenergic GPCR

      Sirish Kaushik Lakkaraju, Justin A. Lemkul, Jing Huang and Alexander D. MacKerell Jr

      Article first published online: 12 NOV 2015 | DOI: 10.1002/jcc.24231

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      Characterizing changes in conformational dynamics of a macromolecule is important for understanding its function. To rapidly quantify the change and identify structural features that contribute most significantly to the conformational changes, a covariance matrix-based method, called DIRECT-ID, is presented. Ligand-modulated conformational changes in the β2-adrenergic GPCR are quantified using DIRECT-ID and both previously known and new ligand-specific microswitches are identified using the method.

    2. Free energies of solvation in the context of protein folding: Implications for implicit and explicit solvent models

      Alexander Cumberworth, Jennifer M. Bui and Jörg Gsponer

      Article first published online: 12 NOV 2015 | DOI: 10.1002/jcc.24235

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      We compare changes in solvation free energy upon folding provided by several implicit solvent models and the TIP3P explicit solvent model. Inconsistencies of an unexpected magnitude were found across the models, which could only be corrected by using settings that were nonphysical or system-specific.

    3. Moment expansion of the linear density-density response function

      Arne Scherrer and Daniel Sebastiani

      Article first published online: 12 NOV 2015 | DOI: 10.1002/jcc.24248

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      Intermolecular interactions lead to changes of the electronic charge density. We provide an efficient scheme to express these changes for an arbitrary interaction with an universal yet low-rank tensor. To that extend, we transform the linear density–density response function from its spectral decomposition to a more condensed representation, separating the contributions to the electronic response density from different multipole moments of the perturbation.

    4. You have full text access to this OnlineOpen article
      Attracting cavities for docking. Replacing the rough energy landscape of the protein by a smooth attracting landscape

      Vincent Zoete, Thierry Schuepbach, Christophe Bovigny, Prasad Chaskar, Antoine Daina, Ute F. Röhrig and Olivier Michielin

      Article first published online: 12 NOV 2015 | DOI: 10.1002/jcc.24249

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      A new algorithm called Attracting Cavities, which allows molecular docking to be performed by only simple energy minimizations, is presented. The approach consists in transiently replacing the rough protein potential energy landscape by a smooth attracting landscape driving the ligands into protein cavities. The actual protein energy landscape is ultimately reintroduced to refine the ligand pose. The approach achieved a success rate of 80% on the Astex diverse set starting from completely randomized ligand conformers.

    5. Hierarchical atom type definitions and extensible all-atom force fields

      Zhao Jin, Chunwei Yang, Fenglei Cao, Feng Li, Zhifeng Jing, Long Chen, Zhe Shen, Liang Xin, Sijia Tong and Huai Sun

      Article first published online: 5 NOV 2015 | DOI: 10.1002/jcc.24244

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      A hierarchical definition of atom type is proposed to solve the problem of “missing parameters”. The extensible atom type definitions make the force field extensible. Two general force fields are parameterized for some common organic molecules. Parameters are derived from ab initial data and experimental liquid data. Calculation results show good accuracy of the parameters.

    6. Revision of the GROMOS 56A6CARBO force field: Improving the description of ring-conformational equilibria in hexopyranose-based carbohydrates chains

      Wojciech Plazinski, Alice Lonardi and Philippe H. Hünenberger

      Article first published online: 3 NOV 2015 | DOI: 10.1002/jcc.24229

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      A revised version 56A6CARBO_R of the GROMOS 56A6CARBO force field for hexopyranose-based carbohydrates is proposed. The revision significantly improves the description of ring-conformational properties for residues within chains. In the revised force field, the 4C1 chair is the most stable conformation for all d-hexopyranose residues, irrespective of the linkage type and anomery, and of the position of the residue along the chain. Additionally, the influence of the functionalization type (alkylation or glycosylation) of the anomeric oxygen atom on the ring-inversion properties is discussed.

    7. The hydration properties of carboxybetaine zwitterion brushes

      Hongbo Du and Xianghong Qian

      Article first published online: 31 OCT 2015 | DOI: 10.1002/jcc.24234

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      The average pair distribution functions (g(r)) correlates the C atoms on the hydrocarbon chains between the cationic and anionic groups and the O atoms in water as a function of the carbon spacer chain length (CSL) on a carboxybetaine trimer. The sudden decrease in the g(r) function correlates to the hydrophilic-to-hydrophobic transition when the CSL increases from 12 to 14.

    8. Diffusive dynamics of DNA unzipping in a nanopore

      Anna Stachiewicz and Andrzej Molski

      Article first published online: 31 OCT 2015 | DOI: 10.1002/jcc.24236

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      When an electric field is applied to an insulating membrane, movement of charged particles through a nanopore is induced. In this work, the kinetics of DNA unzipping in a nanopore is explored using a coarse-grained model. Dependence of the translocation mode on the pore diameter is examined, and the threshold voltages are estimated. The potential of mean force, position-dependent diffusion coefficient and position-dependent effective charge are determined for the DNA unzipping.

  7. Editorial

    1. Paul Von Ragué Schleyer (1930–2014)

      Article first published online: 31 OCT 2015 | DOI: 10.1002/jcc.24240

  8. Full Papers

    1. Buckybowls as adsorbents for CO2, CH4, and C2H2: Binding and structural insights from computational study

      M. Althaf Hussain, Dolly Vijay and G. Narahari Sastry

      Article first published online: 31 OCT 2015 | DOI: 10.1002/jcc.24242

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      Computational studies reveal that monolayer carbonaceous surfaces, such as sumanene, corannulene and coronene, are optimal for adsorption of small gas molecules such as CO2, CH4 and C2H2. The concave surface of the buckybowl is preferred over the convex alternative for the adsorption as well as the selective binding of small molecules. Dispersion is largely responsible for binding of small molecules, buckybowls and coronene.

    2. Application of zone-folding approach to the first-principles estimation of thermodynamic properties of carbon and ZrS2-based nanotubes

      Andrei V. Bandura, Vitaly V. Porsev and Robert A. Evarestov

      Article first published online: 31 OCT 2015 | DOI: 10.1002/jcc.24243

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      In the case of nanotubes rolled up from the layers of layered compounds (such as graphite, ZrS2, or V2O5) the phonon contributions to the heat capacity and internal energy calculated directly and estimated with using the appropriate 2D layer supercell (within the zone-folding approach) remain very close to each other for temperatures up to 600 K.

    3. Re-evaluation of the bond length–bond strength rule: The stronger bond is not always the shorter bond

      Elfi Kraka, Dani Setiawan and Dieter Cremer

      Article first published online: 29 OCT 2015 | DOI: 10.1002/jcc.24207

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      Reverse bond length/bond strength relations have been reported in the literature, in particular for chemical bonds between electron rich atoms, e.g. N[BOND]F or O[BOND]F bonds. In this work, a comprehensive rational is derived covering all electronic and electrostatic factors that may lead to shorter but weaker bonds. A key feature is the use of a qualified bond strength measure based on vibrational spectroscopy.

    4. Surface chemistry of oxygen on aluminum—Performance of the density functionals: PBE, PBE0, M06, and M06-L

      Cláudio M. Lousada and Pavel A. Korzhavyi

      Article first published online: 29 OCT 2015 | DOI: 10.1002/jcc.24233

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      Within density functional theory (DFT), different functionals produce very large differences in the description of the molecular and dissociative adsorption of O2 at pure and doped aluminum surfaces. These differences are here reported and discussed in view of the type of physical descriptors of the electron density incorporated in each functional.

    5. Nontotally symmetric trifurcation of an SN2 reaction pathway

      Yu Harabuchi, Yuriko Ono, Satoshi Maeda, Tetsuya Taketsugu, Kristopher Keipert and Mark S. Gordon

      Article first published online: 29 OCT 2015 | DOI: 10.1002/jcc.24241

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      A new type of reaction pathway which involves a nontotally symmetric trifurcation was found and investigated for the SN2-type reaction, NC- + CH3X [RIGHTWARDS ARROW] NC[BOND]CH3 + X- (X = F, Cl). A nontotally symmetric valley-ridge inflection (VRI) point was located along the C3v reaction path. The branching path from the VRI point to the lower symmetry minima was determined. The possibility of a nontotally symmetric n-furcation is discussed.

    6. Catenanes: A molecular mechanics analysis of the (C13H26)2 Structure 13-13 D2

      Jenn-Huei Lii, Norman L. Allinger, Ching-Han Hu and Henry F. Schaefer Iii

      Article first published online: 29 OCT 2015 | DOI: 10.1002/jcc.24193

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      Catenanes have become important molecular units for the design of new materials for 21st century technology. The origins of strain in the simplest viable saturated hydrocarbon knots is investigated here. The combination of quantum chemistry with molecular mechanics provides many new insights.

    7. Spin-orbit ZORA and four-component Dirac–Coulomb estimation of relativistic corrections to isotropic nuclear shieldings and chemical shifts of noble gas dimers

      Marzena Jankowska, Teobald Kupka, Leszek Stobiński, Rasmus Faber, Evanildo G. Lacerda Jr. and Stephan P. A. Sauer

      Article first published online: 27 OCT 2015 | DOI: 10.1002/jcc.24228

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      The amount of relativistic contribution to nuclear shielding is the same for noble gas dimers and free atoms. For Ne to Xe, the relativistic contribution is more important than both electron correlation and vibrational corrections. However, for the chemical shifts the relativistic corrections almost cancel, so that ZPVC become more important than relativistic corrections for Ne2, Kr2, and Ar2.

    8. Protein:Ligand binding free energies: A stringent test for computational protein design

      Karen Druart, Zoltan Palmai, Eyaz Omarjee and Thomas Simonson

      Article first published online: 27 OCT 2015 | DOI: 10.1002/jcc.24230

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      A computational protein design method is extended to allow Monte Carlo simulations where two ligands are titrated into a protein binding pocket, yielding binding free energy differences. These provide a stringent test of the physical model, including the energy surface and sidechain rotamer definition. As a test, tyrosyl-tRNA synthetase and its specificity for its substrate l-Tyr, compared to d-Tyr, p-acetyl-, and p-azido-phenylalanine is considered.

    9. Protein folds recognized by an intelligent predictor based-on evolutionary and structural information

      Ngaam J. Cheung, Xue-Ming Ding and Hong-Bin Shen

      Article first published online: 27 OCT 2015 | DOI: 10.1002/jcc.24232

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      As an outstanding issue in protein science, protein-fold recognition is highly important for determining the tertiary structure of a protein from its primary sequence. How to correctly recognize the protein folds from sequences? Accordingly, a swarm-optimized predictor—a data-driven predicting method—is proposed to solve this scientific problem. Without manually tuning parameters, it avoids laborious work on finding an appropriate predictor for the problem and exhibits a good performance, even on different protein datasets.

    10. Cost and sensitivity of restricted active-space calculations of metal L-edge X-ray absorption spectra

      Rahul V. Pinjari, Mickaël G. Delcey, Meiyuan Guo, Michael Odelius and Marcus Lundberg

      Article first published online: 27 OCT 2015 | DOI: 10.1002/jcc.24237

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      With an appropriate choice of active space, basis set, and computational procedure, the restricted active space approach can be used to simulate metal L-edge X-ray absorption spectra with reasonable accuracy and computational cost. The sensitivity of the simulated results with respect to geometrical changes opens up for analysis of dynamical processes.

    11. Free energy simulations with the AMOEBA polarizable force field and metadynamics on GPU platform

      Xiangda Peng, Yuebin Zhang, Huiying Chu and Guohui Li

      Article first published online: 23 OCT 2015 | DOI: 10.1002/jcc.24227

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      The free energy calculation library PLUMED has been incorporated into the OpenMM simulation toolkit, with the purpose to perform enhanced sampling molecular dynamics simulations using the AMOEBA polarizable force field on GPU platform. Two examples show that the implementation in the work is reliable and would be utilized to study more complicated biological phenomena in both an accurate and efficient way

    12. DOX: A new computational protocol for accurate prediction of the protein–ligand binding structures

      Li Rao, Bo Chi, Yanliang Ren, Yongjian Li, Xin Xu and Jian Wan

      Article first published online: 13 OCT 2015 | DOI: 10.1002/jcc.24217

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      The detailed knowledge of the protein–ligand binding structures is always important for the deep understanding of protein-ligand interactions. The new computational protocol DOX, which takes the advantage of molecular Docking method's efficiency and QM methods' (ONIOM and eXtended ONIOM) accuracy, can be used to predict the accurate binding structures for the protein–ligand complexes of interest, as an effective alternative to the costly experimental methods.

    13. Assessment of the extended Koopmans' theorem for the chemical reactivity: Accurate computations of chemical potentials, chemical hardnesses, and electrophilicity indices

      Dilan Yildiz and Uğur Bozkaya

      Article first published online: 13 OCT 2015 | DOI: 10.1002/jcc.24225

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      The first benchmarking study to investigate the performance of the EKT methods for predictions of chemical potentials (μ) (hence electronegativities), chemical hardnesses (η), and electrophilicity indices (ω) is presented.

    14. Glucose transformation to 5-hydroxymethylfurfural in acidic ionic liquid: A quantum mechanical study

      Arifin, Maneeporn Puripat, Daisuke Yokogawa, Vudhichai Parasuk and Stephan Irle

      Article first published online: 10 OCT 2015 | DOI: 10.1002/jcc.24214

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      A combination of quantum mechanics and statistical mechanics, called reference interaction site model self-consistent field spatial electron density distribution, is used to investigate the transformation reaction of glucose to 5-hydroxymethylfurfural in aqueous and ionic liquids (ILs). The cyclic mechanism is more favorable in the aqueous solutions. Conversely, open chain mechanism is preferable in ILs.

    15. Schleyer hyperconjugative aromaticity and Diels–Alder reactivity of 5-substituted cyclopentadienes

      Brian J. Levandowski, Lufeng Zou and K. N. Houk

      Article first published online: 7 OCT 2015 | DOI: 10.1002/jcc.24191

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      Quantum chemical calculations are used to investigate the effect of substituents at the 5-position of cyclopentadiene on the stabilities and the activation energies (Ea) for the Diels–Alder reactions. Acceptors induce antiaromatic character by Schleyer's negative hyperconjugative aromaticity; donors have the opposite effect. The interaction energies (red) are nearly constant, and the differences in Ea arise mainly through changes in the distortion energies of the diene (blue) and dienophile (green). (Values reported in kcal/mol)

    16. Substituent effects on the optical properties of naphthalenediimides: A frontier orbital analysis across the periodic table

      Joshua R. Mulder, Célia Fonseca Guerra, J. Chris Slootweg, Koop Lammertsma and F. Matthias Bickelhaupt

      Article first published online: 7 OCT 2015 | DOI: 10.1002/jcc.24197

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      It is shown through TDDFT explorations that naphthalenediimide's (NDI's) strong S0–S1 transition offers excellent opportunities for tuning its absorption frequency through substituents. Kohn–Sham MO analyses reveal that the S0–S1 gap can be reduced by pushing the overall HOMO up in energy using a more electropositive substituent. The S0–S1 transition can be pushed beyond the “700 nm barrier” which is crucial for developing antenna molecules absorbing near-infrared photons in the solar spectrum.

    17. Isomerization and fragmentation pathways of 1,2-azaborine

      Klara Edel, Reinhold F. Fink and Holger F. Bettinger

      Article first published online: 29 SEP 2015 | DOI: 10.1002/jcc.24189

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      Very recently, the isolation of 1,2-azaborine was achieved in a cryogenic matrix. The possible isomerization, ring opening, and fragmentation pathways of 1,2-azaborine are investigated computationally and compared with available experimental and theoretical results for the all-carbon system.

    18. Computational design of organometallic oligomers featuring 1,3-metal-carbon bonding and planar tetracoordinate carbon atoms

      Xue-Feng Zhao, Cai-Xia Yuan, Xiang Wang, Jia-Jia Li, Yan-Bo Wu and Xiaotai Wang

      Article first published online: 24 SEP 2015 | DOI: 10.1002/jcc.24185

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      Organometallic complexes with the TiE2 (E=OH and SH) decoration on the edge of aromatic hydrocarbons have been computationally designed, which feature 1,3-metal-carbon (1,3-MC) bonding between titanium and planar tetracoordinate β-carbon. Condensation of these di-functional monomers by eliminating small molecules (H2O and H2S) produce chain-like oligomers. The HOMO-LUMO gaps of the oligomers decreases with growing oligomer chain, a trend that suggests possible semi-conductor properties for oligomers with longer chains.

    19. Cyclization of an α, β-Unsaturated hydrazone catalyzed by a BINOL-phosphoric acid: Pericyclic or not?

      Berit Heggen, Mahendra Patil and Walter Thiel

      Article first published online: 16 SEP 2015 | DOI: 10.1002/jcc.24044

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      Density functional theory is used to answer the question whether the cyclization of the unsaturated hydrazone proceeds in a pericyclic or pseudopericyclic manner. As reference for a 6π-electrocyclization, the isoelectronic pentadienyl anion is taken into account as well.

    20. d-AO spherical aromaticity in Ce6O8

      Xiaohu Yu, Artem R. Oganov, Ivan A. Popov and Alexander I. Boldyrev

      Article first published online: 18 AUG 2015 | DOI: 10.1002/jcc.24049

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      A highly stable bare Ce6O8 cluster of a spherical shape is predicted using evolutionary algorithm and DFT + U calculations. Natural bond orbital analysis, adaptive natural density partitioning algorithm, electron localization function, and partial charge plots demonstrate that the bare Ce6O8 cluster exhibits a unique 6c[BOND]2e chemical bonding, thus, explaining its exotic geometry and stability.

    21. Aromaticity, quantum multimolecular polyhedra, and quantum QSPR fundamental equation

      Ramon Carbó-Dorca

      Article first published online: 18 AUG 2015 | DOI: 10.1002/jcc.24021

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      A concise description of the Kekulé's historical origin of aromaticity and the current state of the field is given. Still, space is left for a discussion about the existence of aromaticity's quantum mechanical foundation. Quantum multimolecular polyhedra (QMP), based on density functions sets attached to QMP vertices, collective QMP distances, QSPR fundamental equation, and aromaticity descriptors are proposed as a way to construct an equation, able to estimate aromaticity via expectation values of Hermitian operators. Image created by Pep Camps, Girona.

    22. Breaking a bottleneck: Accurate extrapolation to “gold standard” CCSD(T) energies for large open shell organic radicals at reduced computational cost

      Arkajyoti Sengupta, Raghunath O. Ramabhadran and Krishnan Raghavachari

      Article first published online: 17 AUG 2015 | DOI: 10.1002/jcc.24050

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      Highly accurate extrapolated coupled-cluster with single and double and perturbative triple (CCSD(T)) energies were obtained using the Connectivity-Based Hierarchy method for medium to large sized radicals. A careful assessment was performed with a robust test set comprised of 49 diverse radicals including challenging systems with high ring strain and spin contamination. The most expensive calculation is MP2 on the entire radical, thereby breaking the existing bottleneck for calculating CCSD(T) energies of large open-shell organic molecules.

    23. Continuum in the X-Z---Y weak bonds: Z= main group elements

      Jyothish Joy, Anex Jose and Eluvathingal D. Jemmis

      Article first published online: 17 AUG 2015 | DOI: 10.1002/jcc.24036

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      Red- and blue- shift in the X-Z bonds during the X-Z---Y complex formation has been analyzed. A continuum in the X-Z bond length is observed for various classes of weak bonds such as H-bonds, halogen-bonds, chalcogen-bonds, and pnicogen-bonds. The balance between negative hyperconjugation within the X-Z molecule and charge transfer from Y-group provides a working model to explain the observations. The definition of the continuum in the weak (X-Z---Y) interactions is profitably extended to include strong (Z-Y) chemical bonds as well.

    24. Electron transfer pathways in mixed-valence paracyclophane-bridged bis-triarylamine radical cations

      Martin Kaupp, Simon Gückel, Manuel Renz, Sascha Klawohn, Kolja Theilacker, Matthias Parthey and Christoph Lambert

      Article first published online: 12 AUG 2015 | DOI: 10.1002/jcc.24038

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      Electron transfer through the π-stacked faces of paracyclophane bridge units in bis-triarylamine mixed-valence systems has been studied using a previously established quantum-chemical protocol. Pseudo-meta and pseudo-para connected systems exhibit very similar electronic couplings and thermal electron-transfer barriers, explained by resonant hole transfer. Through-space electron transfer through the π-stack dominates over through-bond transfer through the linkers.

    25. Simulations of thermodynamics and kinetics on rough energy landscapes with milestoning

      Juan M. Bello-Rivas and Ron Elber

      Article first published online: 12 AUG 2015 | DOI: 10.1002/jcc.24039

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      We compute, using the Milestoning method, the stationary flux (shown), the mean first passage time of Brownian trajectories, and the free energy (not shown) on a large ensemble of random energy landscapes with varying degrees of roughness and at a wide range of temperatures. We find two different behaviors: a diffusive regime for high temperatures and an Arrhenius-like regime for low temperatures.

    26. Coupled folding and binding with 2D Window-Exchange Umbrella Sampling

      Alex Dickson, Logan S. Ahlstrom and Charles L. Brooks III

      Article first published online: 6 AUG 2015 | DOI: 10.1002/jcc.24004

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      Intrinsically disordered proteins often fold in conjunction with binding to their partner. Sampling configurations corresponding to the transition between unfolded and bound conformational ensembles presents a complex sampling problem. A two-dimensional sampling method, Window-Exchange Umbrella Sampling using contact fractions, is developed to address this issue.

    27. Beyond static structures: Putting forth REMD as a tool to solve problems in computational organic chemistry

      Riccardo Petraglia, Adrien Nicolaï, Matthew D. Wodrich, Michele Ceriotti and Clemence Corminboeuf

      Article first published online: 31 JUL 2015 | DOI: 10.1002/jcc.24025

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      Replica-exchange molecular dynamics (REMD) is combined with density functional tight binding (DFTB) and applied to organic chemical problems. REMD@DFTB permits thorough exploration of the potential energy surface and reveals new insights and chemistry that likely would be missed using static electronic structure computations.

    28. Bis(azulene) “submarine” metal dimer sandwich compounds (C10H8)2M2 (M = Ti, V, Cr, Mn, Fe, Co, Ni): Parallel and opposed orientations

      Hongyan Wang, Hui Wang, R. Bruce King and Henry F. Schaefer III

      Article first published online: 27 JUL 2015 | DOI: 10.1002/jcc.24013

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      The lowest energy (C10H8)2M2 submarine sandwich structures of the early transition metals Ti, V, Cr, and Mn have the azulene units functioning as bis(pentahapto) ligands to each metal atom. For the later transition metals Fe, Co, and Ni the lowest energy (C10H8)2M2 structures contain pentahapto-trihapto azulene ligands with an uncomplexed C[DOUBLE BOND]C double bond

    29. Linear, planar, and tubular molecular structures constructed by double planar tetracoordinate carbon D2h C2(BeH)4 species via hydrogen-bridged [BOND]BeH2Be[BOND] bonds

      Xue-Feng Zhao, Haixia Li, Cai-Xia Yuan, Yan-Qin Li, Yan-Bo Wu and Zhi-Xiang Wang

      Article first published online: 22 JUL 2015 | DOI: 10.1002/jcc.24018

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      D2h C2(BeH)4 has been computationally characterized to be a species featuring double planar tetracoordinate carbons. Because of the electron deficiency nature of the BeH bonds, the species can serves as building blocks to construct nano-size structures via the intermolecular hydrogen-bridged -BeH2Be- bonds (HBB), as exemplified by our reported molecular chains, planar sheets, and tubes. Formation of a HBB is exothermic by more than 30.0 kcal/mol, implying a possibility to synthesize these nano-size molecules.

    30. Projected CAP/SAC-CI method with smooth Voronoi potential for calculating resonance states

      Masahiro Ehara, Ryoichi Fukuda and Thomas Sommerfeld

      Article first published online: 21 JUL 2015 | DOI: 10.1002/jcc.24010

      Thumbnail image of graphical abstract

      The complex absorbing potential (CAP)/symmetry-adapted cluster-configuration interaction method with a smooth Voronoi potential (example shown in the inset of the figure) has been developed. The method is applied to the π* resonance states of small- to medium-size molecules with double-bond and heteroaromatic structures. The corrected η-trajectory provides a stable resonance energy and width for all the resonances studied. Generally, the stabilization of the trajectories is clearer for the CAPs with relatively large cavity size.

    31. Ab initio/GIAO-CCSD(T) 13C NMR study of the rearrangement and dynamic aspects of rapidly equilibrating tertiary carbocations, C6 H13+ and C7 H15+

      George A. Olah, G. K. Surya Prakash and Golam Rasul

      Article first published online: 20 JUL 2015 | DOI: 10.1002/jcc.24019

      Thumbnail image of graphical abstract

      The rearrangement pathways of the equilibrating tertiary carbocations such as 2,3-dimethyl-2-butyl cation were calculated by the ab initio/GIAO-CCSD(T) method.

    32. Molybdatricarbaboranes as examples of isocloso metallaborane deltahedra with three carbon vertices

      Alexandru Lupan and R. Bruce King

      Article first published online: 16 JUL 2015 | DOI: 10.1002/jcc.23995

      Thumbnail image of graphical abstract

      The lowest energy CpMoC3Bn−4Hn−1 (n = 8, 9, 10, 11) structures are based on isocloso or similar MoC3Bn−4 deltahedra with the molybdenum atom at the unique degree 6 vertex, the carbon atoms at the lowest degree vertices (typically degree 4 vertices), no pairs of adjacent carbon atoms (i.e., no C-C edges), and the maximum number of Mo-C edges.

    33. Self-guided Langevin dynamics via generalized Langevin equation

      Xiongwu Wu, Bernard R. Brooks and Eric Vanden-Eijnden

      Article first published online: 16 JUL 2015 | DOI: 10.1002/jcc.24015

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      Self-guided Langevin dynamics (SGLD) is a molecular simulation method that enhances conformational search and sampling via acceleration of the low frequency motions of the molecular system. To eliminate the need of reweighting, the SGLD-generalized Langevin equation (GLE) method is proposed, which samples exact ensemble distribution and has enhanced conformational sampling. Using an alanine dipeptide and liquid argon, SGLD-GLE can produce correct NVT and NPT ensemble distributions while achieving enhanced conformational sampling.

    34. Noncatalytic bromination of benzene: A combined computational and experimental study

      Andrey V. Shernyukov, Alexander M. Genaev, George E. Salnikov, Henry S. Rzepa and Vyacheslav G. Shubin

      Article first published online: 14 JUL 2015 | DOI: 10.1002/jcc.23985

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      The noncatalytic bromination of benzene is shown experimentally to require high concentrations of bromine, proceeding at ambient temperatures to form predominantly bromobenzene and exhibiting a measured inverse deuterium isotope effect. Computed transition states models reveal an ionic concerted but asynchronous transition state involving a Br7 or Br9 cluster which acts as a Br+ donor, as a proton base and as a stabilizing arm forming weak dispersion interactions with benzene C[BOND]H hydrogens.

  9. Full PaperS

    1. Atomic-resolution dissection of the energetics and mechanism of isomerization of hydrated ATP-Mg2+ through the SOMA string method

      Davide Branduardi, Fabrizio Marinelli and José D. Faraldo-Gómez

      Article first published online: 7 JUL 2015 | DOI: 10.1002/jcc.23991

      Thumbnail image of graphical abstract

      The mechanisms of isomerization of ATP-Mg2+ in solution are examined with three complementary enhanced-sampling simulation methods. The recently developed String Method with Optimal Molecular Alignment is used to identify and characterize the minimum free-energy paths for the major conformational transitions of the complex, in a 48-dimensional space. This analysis reveals the driving forces controlling these isomerization mechanisms at single-atom resolution.

  10. Full Papers

    1. Structure and stability of noble gas bound EX3+ compounds (E = C, Ge, Sn, Pb; X = H, F, Cl, Br)

      Sudip Pan, Diego Moreno, Sreyan Ghosh, Pratim K. Chattaraj and Gabriel Merino

      Article first published online: 1 JUL 2015 | DOI: 10.1002/jcc.23986

      Thumbnail image of graphical abstract

      Making a bond: inline image (E = C-Pb; X = H, F-Br) could bind noble gas atoms, particularly Ar to Rn, quite effectively. The π back-bonding causing X [RIGHTWARDS ARROW] E electron transfer plays an important role in deciding their noble gas binding ability.

    2. On the inclusion of post-MP2 contributions to double-Hybrid density functionals

      Bun Chan, Lars Goerigk and Leo Radom

      Article first published online: 1 JUL 2015 | DOI: 10.1002/jcc.23972

      Thumbnail image of graphical abstract

      Double-hybrid density functionals (DHDFs) use MP2-type correlation to significantly improve the accuracy of DFT approximations. The inclusion of higher-order MP3, MP4, CCSD, and CCSD(T) terms is explored. DHDFs are not as systematically improvable as their wave-function counterparts, and the use of MP2 represents a near-optimal balance of accuracy and efficiency. These findings provide valuable insights for future research in DHDF development.

    3. Comparative exploration of hydrogen sulfide and water transmembrane free energy surfaces via orthogonal space tempering free energy sampling

      Chao Lv, Erick W. Aitchison, Dongsheng Wu, Lianqing Zheng, Xiaolin Cheng and Wei Yang

      Article first published online: 29 JUN 2015 | DOI: 10.1002/jcc.23982

      Thumbnail image of graphical abstract

      The orthogonal space tempering simulation shows that hydrogen sulfide is amphipathic, and thus is favorably localized at the interface between the head-group and acyl chain regions. Because the membrane binding affinity of H2S is mainly governed by its small hydrophobic moiety and the barrier height inbetween the interfacial region and the membrane center is largely determined by its moderate polarity, the trans-membrane free energy barriers to encounter by this toxic molecule are very small.

    4. Hydrogen bond–aromaticity cooperativity in self-assembling 4-pyridone chains

      Megha Anand, Israel Fernández, Henry F. Schaefer III and Judy I-Chia Wu

      Article first published online: 23 JUN 2015 | DOI: 10.1002/jcc.23976

      Thumbnail image of graphical abstract

      Hydrogen bonding interactions can polarize the π-systems of 4-pyridones to increase cyclic (4n+2) π electron delocalization. The resulting H-bonded six-membered rings exhibit enhanced π-aromaticity and the corresponding N[BOND]H···O[DOUBLE BOND]C interactions are strengthened. Extended H-bonded 4-pyridone chains exhibit high degrees of such cooperativity, even when each of the neighboring 4-pyridone rings are twisted to preclude direct π-overlap between the H-bonded units.

    5. Saturn Systems

      Habib U. Rehman, Nida A. McKee and Michael L. McKee

      Article first published online: 19 JUN 2015 | DOI: 10.1002/jcc.23979

      Thumbnail image of graphical abstract

      Nanohoops, such as cycloparaphenylenes [10]CPP, can bind to C60 and [Li@C60)]+ through noncovalent interactions with free energies of binding greater than 10 kcal/mol in nonpolar solvents. With the right size, the hoops bind around the equator of the fullerene and resemble the ring around Saturn. Density functional calculations can predict the binding constants and suggest new nanohoops as targets for synthesis. The graphic image is the HOMO of C60@(C6H4)10.

    6. Accurately modeling nanosecond protein dynamics requires at least microseconds of simulation

      Gregory R. Bowman

      Article first published online: 16 JUN 2015 | DOI: 10.1002/jcc.23973

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      This article assesses whether modern simulations accurately capture ps-ns timescales—as judged by their ability to predict order parameters—or if force fields are now a limiting factor. The results show microseconds of simulation with any of three force fields and a proper method for calculating order parameters are required for accuracy and precision. This has important implications for the extent of simulations required for slower processes and the utility of enhanced sampling methods.

    7. Heats of formation of platonic hydrocarbon cages by means of high-level thermochemical procedures

      Amir Karton, Peter R. Schreiner and Jan M. L. Martin

      Article first published online: 12 JUN 2015 | DOI: 10.1002/jcc.23963

      Thumbnail image of graphical abstract

      This work determines total atomization energies and heats of formation for platonic and prismatic polycyclic hydrocarbon cages by means of the W1-F12 and W2-F12 thermochemical protocols. Using these accurate reference data, the performance of computationally economical theoretical methods (e.g., density functional theory and composite ab initio methods) was evaluated via atomization and bond separation reactions for the calculation of these challenging thermochemical quantities.

    8. Nucleus-independent chemical shift analysis of the electronic states of the (CO)4, (CS)4, and (CSe)4 molecules

      Yunfei Zhou, Xiaoguang Bao and Weston Thatcher Borden

      Article first published online: 8 JUN 2015 | DOI: 10.1002/jcc.23962

      Thumbnail image of graphical abstract

      The occupancy of the a2u MOs of (CO)4, (CS)4, and (CSe)4 control the NICS(1) values that are computed for these compounds.

    9. Multiscale enhanced sampling of intrinsically disordered protein conformations

      Kuo Hao Lee and Jianhan Chen

      Article first published online: 6 JUN 2015 | DOI: 10.1002/jcc.23957

      Thumbnail image of graphical abstract

      Multiscale enhanced sampling (MSES) uses efficient coarse-grained (CG) models to accelerate sampling of atomistic protein conformations. The efficacy of MSES for simulating intrinsically disordered proteins (IDPs) is investigated, and refined MSES Hamiltonian/temperature replica exchange protocols are developed that involve additional parameters in the MSES coupling restraint potential. The refined protocols drive more conformational transitions to improve the convergence of simulated ensembles. Nonetheless, further improvement of MSES for simulating IDPs likely requires more detailed CG models.

    10. The Reaction between Bromine and the Water Dimer and the Highly Exothermic Reverse Reaction

      Guoliang Li, Hui Wang, Qian-Shu Li, Yaoming Xie and Henry F. Schaefer III

      Article first published online: 4 JUN 2015 | DOI: 10.1002/jcc.23951

      Thumbnail image of graphical abstract

      The entrance complex, transition state, and exit complex for the Br + (H2O)2 [RIGHTWARDS ARROW] HBr + (H2O)OH reaction have been investigated using the CCSD(T) method with correlation consistent basis sets up to cc-pVQZ-PP. Both zero-point vibrational energies and spin-orbit coupling effects are found to be important. The potential energy surface for the Br + (H2O)2 reaction is compared with the related Br + H2O, Cl + (H2O)2 and F + (H2O)2 reactions.

    11. The origins of the directionality of noncovalent intermolecular interactions#

      Changwei Wang, Liangyu Guan, David Danovich, Sason Shaik and Yirong Mo

      Article first published online: 25 MAY 2015 | DOI: 10.1002/jcc.23946

      Thumbnail image of graphical abstract

      The block-localized wavefunction method, which can derive hypothetical structures without the charge transfer effect and conduct intermolecular energy decomposition analysis, is used to probe the origins of the directionality of weak noncovalent bonds. While the overall steric energy exhibits certain angular dependency, in all cases the charge transfer exhibits the strongest directionality, suggesting that the linearity or near linearity of noncovalent bonds is largely governed by the charge-transfer interaction whose magnitude determines the bond covalency.

    12. A comparative computationally study about the defined m(II) pincer hydrogenation catalysts (m = fe, ru, os)

      Haijun Jiao, Kathrin Junge, Elisabetta Alberico and Matthias Beller

      Article first published online: 17 MAY 2015 | DOI: 10.1002/jcc.23944

      Thumbnail image of graphical abstract

      DFT studies on the defined pincer-type catalysts M(H)2(CO)[NH(C2H4PiPr2)2] (1M) and M(H)(CO)[N(C2H4PiPr2)2] (2M) (M = Fe, Ru, Os) reveal remarkable differences in electronic structures and hydrogenation reactivity of nitriles, ester, and ketones. For acetonitrile hydrogenation, Fe- and Ru-based catalysts are best. For methyl benzoate hydrogenation and dehydrogenation of benzyl alcohol, Ru-based catalysts are best. In contrast, Os-based catalysts are least active.

    13. Inter- and intramolecular CF···c[DOUBLE BOND]o interactions on aliphatic and cyclohexane carbonyl derivatives

      Rodrigo A. Cormanich, Roberto Rittner, David O'Hagan and Michael Bühl

      Article first published online: 23 APR 2015 | DOI: 10.1002/jcc.23918

      Thumbnail image of graphical abstract

      Prototypical inter- and intramolecular CF···C[DOUBLE BOND]O interactions are assessed computationally at the B3LYP-D3 level. The interactions are noticeable in intermolecular complexes 1, where they can amount to stabilizations around about 1 kcal mol, however, they are not strong enough to dominate conformational preferences in organofluorine derivatives such as 2 - 4.

    14. Theoretical and experimental investigation of crown/ammonium complexes in solution

      Andreas J. Achazi, Larissa K. S. von Krbek, Christoph A. Schalley and Beate Paulus

      Article first published online: 13 APR 2015 | DOI: 10.1002/jcc.23914

      Thumbnail image of graphical abstract

      Gibbs energies of association inline image of monovalent crown/ammonium complexes in solution are calculated with DFT-D3(BJ) and the continuum solvation model COSMO-RS. For comparison, experimental data are obtained by isothermal titration calorimetry. Calculated and measured Gibbs energies of association inline image in solution agree well.

    15. From small fullerenes to the graphene limit: A harmonic force-field method for fullerenes and a comparison to density functional calculations for Goldberg–Coxeter fullerenes up to C980

      Lukas N. Wirz, Ralf Tonner, Andreas Hermann, Rebecca Sure and Peter Schwerdtfeger

      Article first published online: 26 MAR 2015 | DOI: 10.1002/jcc.23894

      Thumbnail image of graphical abstract

      A general force field is introduced which works for all fullerene isomers. It leads to structures and zero-point vibrational energy contributions in very good agreement to more expensive quantum theoretical calculations. The graphene limit is well represented by the growth of Goldberg-Coxeter transforms of C20.

    16. Prediction of the crystal packing of di-tetrazine-tetroxide (DTTO) energetic material

      Jose L. Mendoza-Cortes, Qi An, William A. Goddard III, Caichao Ye and Sergey Zybin

      Article first published online: 18 MAR 2015 | DOI: 10.1002/jcc.23893

      Thumbnail image of graphical abstract

      The two most stable isomers of Di-tetrazine-tetroxide (DTTO), c1 and c2, were used to predict the most stable polymorphs of DTTO. For the c1 isomer, the most stable polymorph has P212121 space group with a density of 1.96 g/cm3. Conversely, for the c2 isomer, the most stable polymorph has Pbca space group with a density of 1.98 g/cm3. These predicted densities are among the highest of current energetic materials.


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