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Journal of Computational Chemistry

Chuancai Sun, Lijuan Zhu, Chao Zhang, Ce Song, Cuihong Wang, Meiling Zhang, Yaoming Xie, Henry F Schaefer
The conformational structures and properties of the anticancer drug docetaxel (DTX) are studied theoretically. A total of 3888 trial structures were initially generated by all combinations of internal single-bond rotamers and screened with the B3LYP/3-21G* method. A total of 31 unique conformers were further optimized at the B3LYP/6-311G* method. Their relative energies, dipole moments, rotational constants, and harmonic vibrational frequencies were predicted. Single-point relative energies were then determined at the M06-L/6-311G(2df,p) level...
January 12, 2018: Journal of Computational Chemistry
Bai Amutha Anjali, Cherumuttathu H Suresh
The influence of mono- and multiple substituent effect on the reduction potential (E0 ) of 1,3,6-triphenyl fulvenes is investigated using B3LYP-SMD/6-311+G(d,p) level density functional theory. The molecular electrostatic potential (MESP) minimum at the fulvene π-system (Vmin ) and the change in MESP at any of the fulvene carbon atoms (ΔVC ) for both neutral and reduced forms are used as excellent measures of substituent effect from the para and meta positions of the 1,3 and 6-phenyl moieties. Substitution at 6-phenyl para position has led to significant change in E0 than any other positions...
January 10, 2018: Journal of Computational Chemistry
Jan P Unsleber, Thomas Dresselhaus, Kevin Klahr, David Schnieders, Michael Böckers, Dennis Barton, Johannes Neugebauer
We present the new quantum chemistry program Serenity. It implements a wide variety of functionalities with a focus on subsystem methodology. The modular code structure in combination with publicly available external tools and particular design concepts ensures extensibility and robustness with a focus on the needs of a subsystem program. Several important features of the program are exemplified with sample calculations with subsystem density-functional theory, potential reconstruction techniques, a projection-based embedding approach and combinations thereof with geometry optimization, semi-numerical frequency calculations and linear-response time-dependent density-functional theory...
January 10, 2018: Journal of Computational Chemistry
Federica Maschietto, Marco Campetella, Michael J Frisch, Giovanni Scalmani, Carlo Adamo, Ilaria Ciofini
With the aim of investigating qualitatively and quantitatively the impact of using excited state relaxed or unrelaxed density for the estimation of nature and characteristic of electronic excited states, we analyzed the behavior of 52 exchange correlation functionals for the prediction of density-based indexes such as those recently introduced in literature to evaluate the charge transfer distance (DCT ) (Le Bahers et al. J. Chem. Theory Comput. 2011, 7, 2498) in the case of a prototype family of push-pull dyes...
January 10, 2018: Journal of Computational Chemistry
Paul L A Popelier
Atomic multipole moments associated with a spherical volume fully residing within a topological atom (i.e., the β sphere) can be obtained analytically. Such an integration is thus free of quadrature grids. A general formula for an arbitrary rank spherical harmonic multipole moment is derived, for an electron density comprising Gaussian primitives of arbitrary angular momentum. The closed expressions derived here are also sufficient to calculate the electrostatic potential, the two types of kinetic energy, as well as the potential energy between atoms...
January 10, 2018: Journal of Computational Chemistry
Sarah N Johnson, Gregory S Tschumper
The ClH⋯FH and FH⋯ClH configurations of the mixed HF/HCl dimer (where the donor⋯acceptor notation indicates the directionality of the hydrogen bond) as well as the transition state connecting the two configurations have been optimized using MP2 and CCSD(T) with correlation consistent basis sets as large as aug-cc-pV(5 + d)Z. Harmonic vibrational frequencies confirmed that both configurations correspond to minima and that the transition state has exactly one imaginary frequency. In addition, anharmonic vibrational frequencies computed with second-order vibrational perturbation theory (VPT2) are within 6 cm-1 of the available experimental values and deviate by no more than 4 cm-1 for the complexation induced HF frequency shifts...
January 9, 2018: Journal of Computational Chemistry
James S M Anderson, Paul W Ayers
Generalizing our recent work on relativistic generalizations of the quantum theory of atoms in molecules, we present the general setting under which the principle of stationary action for a region leads to open quantum subsystems. The approach presented here is general and works for any Hamiltonian, and when a reasonable Lagrangian is selected, it often leads to the integral of the Laplacian of the electron density on the region vanishing as a necessary condition for the zero-flux surface. Alternatively, with this method, one can design a Lagrangian that leads to a surface of interest (though this Lagrangian may not be, and indeed probably will not be, "reasonable")...
January 9, 2018: Journal of Computational Chemistry
Łukasz Szeleszczuk, Dariusz Maciej Pisklak, Monika Zielińska-Pisklak
Glycine is a common amino acid with relatively complex chemistry in solid state. Although several polymorphs (α, β, δ, γ, ε) of crystalline glycine are known, for NMR spectroscopy the most important is a polymorph, which is used as a standard for calibration of spectrometer performance and therefore it is intensively studied by both experimental methods and theoretical computation. The great scientific interest in a glycine results in a large number of crystallographic information files (CIFs) deposited in Cambridge Structural Database (CSD)...
January 5, 2018: Journal of Computational Chemistry
Giovanni Macetti, Leonardo Lo Presti, Carlo Gatti
Magnetic properties of open-shell systems depend on their unpaired electron density distribution. Accurate spin density (SD) is difficult to retrieve, both from polarized neutron diffraction (PND) data and from quantum approaches, and its interpretation is not trivial. The Source Function is a useful tool to interpret SD distributions and their accuracy. It is here applied to analyze and compare the theoretical SD in a weakly ferromagnetically coupled end-end azido dicopper complex with that in a strongly-coupled end-on complex...
January 5, 2018: Journal of Computational Chemistry
Rasmus Fonseca, Dominik Budday, Henry van den Bedem
The function of protein, RNA, and DNA is modulated by fast, dynamic exchanges between three-dimensional conformations. Conformational sampling of biomolecules with exact and nullspace inverse kinematics, using rotatable bonds as revolute joints and noncovalent interactions as holonomic constraints, can accurately characterize these native ensembles. However, sampling biomolecules remains challenging owing to their ultra-high dimensional configuration spaces, and the requirement to avoid (self-) collisions, which results in low acceptance rates...
January 5, 2018: Journal of Computational Chemistry
Minh Khoa Nguyen, Léonard Jaillet, Stéphane Redon
This article proposes a method to efficiently generate approximate ligand unbinding pathways. It combines an efficient tree-based exploration method with a morphing technique from Computer Graphics for dimensionality reduction. This method is computationally cheap and, unlike many existing approaches, does not require a reaction coordinate to guide the search. It can be used for finding pathways with known or unknown directions beforehand. The approach is evaluated on several benchmarks and the obtained solutions are compared with the results from other state-of-the-art approaches...
January 5, 2018: Journal of Computational Chemistry
Min Zheng, Mark P Waller
Herein, we describe the implementation details of our interaction-based partitioning API (application programming interface) called Yoink for QM/MM modeling and fragment-based quantum chemistry studies. Interactions are detected by computing density descriptors such as reduced density gradient, density overlap regions indicator, and single exponential decay detector. Only molecules having an interaction with a user-definable QM core are added to the QM region of a hybrid QM/MM calculation. Moreover, a set of molecule pairs having density-based interactions within a molecular system can be computed in Yoink, and an interaction graph can then be constructed...
January 5, 2018: Journal of Computational Chemistry
Torsten Sachse, Todd J Martínez, Benjamin Dietzek, Martin Presselt
Not only the molecular structure but also the presence or absence of aggregates determines many properties of organic materials. Theoretical investigation of such aggregates requires the prediction of a suitable set of diverse structures. Here, we present the open-source program EnergyScan for the unbiased prediction of geometrically diverse sets of small aggregates. Its bottom-up approach is complementary to existing ones by performing a detailed scan of an aggregate's potential energy surface, from which diverse local energy minima are selected...
January 3, 2018: Journal of Computational Chemistry
Mikhail S Bukharov, Valery G Shtyrlin, Edward M Gilyazetdinov, Nikita Yu Serov, Timur I Madzhidov
Hydration of the copper(II) bis-complexes with glycine, serine, lysine, and aspartic acid was studied by DFT and MD simulation methods. The distances between copper(II) and water molecules in the 1st and 2nd coordination shells, the average number of water molecules and their mean residence times in the hydration shells were calculated. Good agreement was observed between the values obtained and those found by DFT and NMR relaxation methods. Influence of the functional groups of the ligands and the cis-trans isomerism of the complexes on the structural and dynamical parameters of the hydration shells was displayed and explained...
December 28, 2017: Journal of Computational Chemistry
Sankar Ghorai, Pinaki Chaudhury
We have used a replica exchange Monte-Carlo procedure, popularly known as Parallel Tempering, to study the problem of Coulomb explosion in homogeneous Ar and Xe dicationic clusters as well as mixed Ar-Xe dicationic clusters of varying sizes with different degrees of relative composition. All the clusters studied have two units of positive charges. The simulations reveal that in all the cases there is a cutoff size below which the clusters fragment. It is seen that for the case of pure Ar, the value is around 95 while that for Xe it is 55...
December 28, 2017: Journal of Computational Chemistry
Ximena Zarate, Mario Saavedra-Torres, Angela Rodriguez-Serrano, Tatiana Gomez, Eduardo Schott
The possibility of dye charge recombination in DSSCs remains a challenge for the field. This consists of: (a) back-transfer from the TiO2 to the oxidized dye and (b) intermolecular electron transfer between dyes. The latter is attributed to dye aggregation due to dimeric conformations. This leads to poor electron injection which decreases the photocurrent conversion efficiency. Most organic sensitizers are characterized by an Acceptor-Bridge-Donor (A-Bridge-D) arrangement that is commonly employed to provide charge separation and, therefore, lowering the unwanted back-transfer...
December 28, 2017: Journal of Computational Chemistry
Nivedita Rajendiran, Jacob D Durrant
Molecular dynamics (MD) simulations provide critical insights into many biological mechanisms. Programs such as VMD, Chimera, and PyMOL can produce impressive simulation visualizations, but they lack many advanced rendering algorithms common in the film and video-game industries. In contrast, the modeling program Blender includes such algorithms but cannot import MD-simulation data. MD trajectories often require many gigabytes of memory/disk space, complicating Blender import. We present Pyrite, a Blender plugin that overcomes these limitations...
December 26, 2017: Journal of Computational Chemistry
Beibei An, Keke Wen, Songyan Feng, Xiao Pan, Wenpeng Wu, Xugeng Guo, Jinglai Zhang
Discotic liquid crystal (DLC) materials have attracted considerable attention mainly due to their high charge carrier mobilities in quasi-one-dimensional columns. In this article, five hexaazatrinaphthylene-based DLC molecules were investigated theoretically, and their frontier molecular orbital energy levels, crystal structures, and electron/hole drift mobilities were calculated by combination of density functional theory (DFT) and semiclassical Marcus charge transfer theory. The systems studied in this work include three experimentally reported molecules (1, 2, and 3) and two theoretically designed molecules (4 and 5)...
December 26, 2017: Journal of Computational Chemistry
Alexey V Odinokov, Nikita O Dubinets, Alexander A Bagaturyants
We present an open source tool able to describe intermolecular electrostatic interactions within the framework of the effective fragment potential (EFP) method. Complex molecular structure is subdivided into compact rigid fragments and parameters of their interactions are obtained from ab initio calculations. Automatic procedure allows for searching of these parameters into the existing database and merge new fragments into it. A set of standard fragments useful for the studies of organic semiconductors is also provided...
December 26, 2017: Journal of Computational Chemistry
Suranjan Shil, Carmen Herrmann
The prediction of magnetic behavior is important for the design of new magnetic materials. Kohn-Sham density functional theory is popular for this purpose, although one should be careful about choosing the right exchange-correlation functional. Here, we perform a statistical analysis to test different range-separated hybrid density functionals for the calculation of magnetic exchange coupling constants J of fourteen organic diradicals. Our analysis suggests that in absolute terms the MN12SX functional performs best among the series of twelve functionals studied here (including the popular B3LYP), followed by N12SX functionals along with Scuseria's HSE series of functionals...
December 26, 2017: Journal of Computational Chemistry
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