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Journal of Chemical Theory and Computation

Lindsey N Anderson, Maria Belen Oviedo, Bryan M Wong
The treatment of atomic anions with Kohn-Sham density functional theory (DFT) has long been controversial since the highest occupied molecular orbital (HOMO) energy, EHOMO, is often calculated to be positive with most approximate density functionals. We assess the accuracy of orbital energies and electron affinities for all three rows of elements in the periodic table (H-Ar) using a variety of theoretical approaches and customized basis sets. Among all of the theoretical methods studied here, we find that a non-empirically tuned range-separated approach (constructed to satisfy DFT-Koopmans' theorem for the anionic electron system) provides the best accuracy for a variety of basis sets - even for small basis sets where most functionals typically fail...
March 24, 2017: Journal of Chemical Theory and Computation
Jonathan S Mitchell, Jaroslaw Glowacki, Alexandre E Grandchamp, Robert S Manning, John H Maddocks
A Monte Carlo code applied to the cgDNA coarse-grain rigid-base model of B-form double-stranded DNA is used to predict a sequence-averaged persistence length of lF = 53.5 nm in the sense of Flory, and of lp = 160 bp or 53.5 nm in the sense of apparent tangent-tangent correlation decay. These estimates are slightly higher than the consensus experimental values of 150 bp or 50 nm, but we believe the agreement to be good given that the cgDNA model is itself parametrized from molecular dynamics simulations of short fragments of length 10-20 bp, with no explicit fit to persistence length...
March 24, 2017: Journal of Chemical Theory and Computation
Hui Liu, Fu Chen, Huiyong Sun, Dan Li, Tingjun Hou
By means of estimators based on non-equilibrium work, equilibrium free energy differences or potentials of mean force (PMFs) of a system of interest can be computed from biased molecular dynamics (MD) simulations. The approach, however, is often plagued by slow conformational sampling and poor convergence, especially when the solvent effects are taken into account. Here, as a possible way to alleviate the problem, several widely used implicit-solvent models, which are derived from the analytic generalized Born (GB) equation and implemented in the AMBER suite of programs, were employed in free energy calculations based on non-equilibrium work and evaluated for their abilities to emulate explicit water...
March 23, 2017: Journal of Chemical Theory and Computation
Sandeep Sharma, Adam A Holmes, Guillaume Jeanmairet, Ali Alavi, C J Umrigar
We extend the recently proposed heat-bath configuration interaction (HCI) method [Holmes, Tubman, Umrigar, J. Chem. Theory Comput. 2016, 12, 3674], by introducing a semistochastic algorithm for performing multireference Epstein-Nesbet perturbation theory, in order to completely eliminate the severe memory bottleneck of the original method. The proposed algorithm has several attractive features. First, there is no sign problem that plagues several quantum Monte Carlo methods. Second, instead of using Metropolis-Hastings sampling, we use the Alias method to directly sample determinants from the reference wave function, thus avoiding correlations between consecutive samples...
March 23, 2017: Journal of Chemical Theory and Computation
Johannes Flick, Heiko Appel, Michael Ruggenthaler, Angel Rubio
In this work, we illustrate the recently introduced concept of the cavity Born-Oppenheimer approximation [ Flick et al. PNAS 2017 , 10.1073/pnas.1615509114 ] for correlated electron-nuclear-photon problems in detail. We demonstrate how an expansion in terms of conditional electronic and photon-nuclear wave functions accurately describes eigenstates of strongly correlated light-matter systems. For a GaAs quantum ring model in resonance with a photon mode we highlight how the ground-state electronic potential-energy surface changes the usual harmonic potential of the free photon mode to a dressed mode with a double-well structure...
March 21, 2017: Journal of Chemical Theory and Computation
Jenna A Bilbrey, Andrea N Bootsma, Marcus A Bartlett, Jason Locklin, Steven E Wheeler, Wesley D Allen
While ring-walking is a critical step in transition metal catalyzed cross-coupling reactions, the associated metastable intermediates are often difficult to isolate and characterize. In this work, theoretical structures and energetics for ring-walking and oxidative addition of zerovalent nickel with 1-bromo-2-methylbenzene, 2-bromopyridine, 2-bromo-3-methyl-thiophene, and 2-bromopyrrole were computed at the B3LYP-D3/TZ2P-LANL2TZ(f)-LANL08d level. The mechanisms vary qualitatively with substrate ring size and type-the catalyst weaves along the edges of the benzene and pyridine rings, cuts through the interior of the thiophene ring, and arcs along the bond opposite the nitrogen atom in the pyrrole ring...
March 21, 2017: Journal of Chemical Theory and Computation
Julian J Kranz, Marcus Elstner, Bálint Aradi, Thomas Frauenheim, Vitalij Lutsker, Adriel Dominguez Garcia, Thomas A Niehaus
We present a consistent linear response formulation of the density functional based tight-binding method for long-range corrected exchange-correlation functionals (LC-DFTB). Besides a detailed account of derivation and implementation of the method, we also test the new scheme on a variety of systems considered to be problematic for conventional local/semilocal time-dependent density functional theory (TD-DFT). To this class belong the optical properties of polyacenes and nucleobases, as well as charge transfer excited states in molecular dimers...
March 21, 2017: Journal of Chemical Theory and Computation
Thomas J Piggot, Ángel Piñeiro, Syma Khalid
No abstract text is available yet for this article.
March 16, 2017: Journal of Chemical Theory and Computation
Karen Sargsyan, Cédric Grauffel, Carmay Lim
The root-mean-square deviation (RMSD) is a similarity measure widely used in analysis of macromolecular structures and dynamics. As increasingly larger macromolecular systems are being studied, dimensionality effects such as the "curse of dimensionality" (a diminishing ability to discriminate pairwise differences between conformations with increasing system size) may exist and significantly impact RMSD-based analyses. For such large bimolecular systems, whether the RMSD or other alternative similarity measures might suffer from this "curse" and lose the ability to discriminate different macromolecular structures had not been explicitly addressed...
March 16, 2017: Journal of Chemical Theory and Computation
Aliasghar Sepehri, Troy D Loeffler, Bin Chen
A new method, called Jacobian-Gaussian scheme, has been developed to overcome the challenge of bending angle generation for linear and branched molecules in configurational-bias Monte Carlo. This method is simple, general, fast, and robust which can yield high acceptance rates. Since there are several bending angles in a branched point and their energies are coupled to each other, generating one trial that is acceptable for all energetic terms is a difficult problem. In order to reach reasonable acceptance rates, traditional methods either generate many trials uniformly or use prepared tables to generate trials according to the expected distribution...
March 15, 2017: Journal of Chemical Theory and Computation
Mark S Miller, Wesley Kayser Lay, Shuxiang Li, William Charles Hacker, Jiadi An, Jianlan Ren, Adrian Hamilton Elcock
There is a small, but growing, body of literature describing the use of osmotic coefficient measurements to validate and reparameterize simulation force fields. Here we have investigated the ability of five very commonly used force field and water model combinations to reproduce the osmotic coefficients of seven neutral amino acids and five small molecules. The force fields tested include AMBER ff99SB-ILDN, CHARMM36, GROMOS54a7, and OPLS-AA, with the first of these tested in conjunction with the TIP3P and TIP4P-Ew water models...
March 15, 2017: Journal of Chemical Theory and Computation
Tanfeng Zhao, Haohao Fu, Tony Lelièvre, Xueguang Shao, Christophe Chipot, Wensheng Cai
Free-energy calculations in multiple dimensions constitute a challenging problem, owing to the significant computational cost incurred to achieve ergodic sampling. The generalized adaptive biasing force (gABF) algorithm calculates n one-dimensional lists of biasing forces to approximate the n-dimensional matrix by ignoring the coupling terms ordinarily taken into account in classical ABF simulations, thereby greatly accelerating sampling in the multidimensional space. This approximation may however occasionally lead to poor, incomplete exploration of the conformational space compared to classical ABF, especially when the selected coarse variables are strongly coupled...
March 15, 2017: Journal of Chemical Theory and Computation
Changwei Wang, David Danovich, Sason Shaik, Yirong Mo
Typical hydrogen and halogen bonds exhibit red-shifts of their vibrational frequencies upon the formation of hydrogen and halogen bonding complexes (denoted as D···Y-A, Y = H and X). The finding of blue-shifts in certain complexes is of significant interest, which has led to numerous studies of the origins of the phenomenon. Because charge transfer mixing (i.e., hyperconjugation in bonding systems) has been regarded as one of the key forces, it would be illuminating to compare the structures and vibrational frequencies in bonding complexes with the charge transfer effect "turned on" and "turned off"...
March 14, 2017: Journal of Chemical Theory and Computation
Casey Tyler Andrews, Brady A Campbell, Adrian Hamilton Elcock
Given the ubiquitous nature of protein-DNA interactions, it is important to understand the interaction thermodynamics of individual amino acid sidechains for DNA. One way to assess these preferences is to perform molecular dynamics (MD) simulations. Here we report MD simulations of twenty amino acid sidechain analogs interacting simultaneously with both a 70-base pair double-stranded DNA and with a 70-nucleotide single-stranded DNA. The relative preferences of the amino acid sidechains for dsDNA and ssDNA match well with values deduced from crystallographic analyses of protein-DNA complexes...
March 13, 2017: Journal of Chemical Theory and Computation
Florian Massuyeau, Eric Faulques, Camille Latouche
The present manuscript reports a thorough quantum investigation on the luminescence properties of three mono platinum(II) complexes. First, the simulated bond lengths at the ground state are compared to the observed ones and the simulated electronic transitions are compared to the reported ones in the literature in order to assess our methodology. In a second time we show that geometries from the first triplet excited state are similar to the ground state ones. Simulations of the phosphorescence spectra from the first triplet excited sates have been performed taking into account the vibronic coupling effects together with mode-mixing (Dushinsky) and solvent effects...
March 13, 2017: Journal of Chemical Theory and Computation
Dage Sundholm, Markus Rauhalahti, Nergiz Özcan, Raul Mera-Adasme, Jörg Kussmann, Arne Luenser, Christian Ochsenfeld
Nuclear magnetic shieldings have been calculated at the density functional theory (DFT) level for stacks of benzene, hexadehydro[12]annulene, dodecadehydro[18]annulene and hexabenzocoronene. The magnetic shieldings due to the ring currents in the adjacent molecules have been estimated by calculating nucleus independent molecular shieldings for the monomer in the atomic positions of neighbor molecules. The calculations show that the independent shielding model works reasonable well for the (1)H NMR shieldings of benzene and hexadehydro[12]annulene, whereas for the larger molecules and for the (13)C NMR shieldings the interaction between the molecules leads to shielding effects that are at least of the same size as the ring current contributions from the adjacent molecules...
March 13, 2017: Journal of Chemical Theory and Computation
Debarati Bhattacharya, Anael Ben-Asher, Idan Haritan, Mariusz Pawlak, Arie Landau, Nimrod Moiseyev
Resonances are metastable states that decay after a finite period of time. These states play a role in many physical processes. For example, in recent cold collision experiments, autoionization from a resonance state was observed. Complementing such observations with theory provide insight into the reaction dynamics under study. Theoretical investigation of autoionization processes is enabled via complex potential energy surfaces (CPESs), where the real and imaginary parts, respectively, provide the energy and decay rate of the system...
March 13, 2017: Journal of Chemical Theory and Computation
Abdallah Sayyed-Ahmad, Alemayehu A Gorfe
Membrane proteins represent a considerable fraction of pharmaceutical drug targets. A computational technique to identify ligand binding pockets in these proteins is therefore of great importance. We recently reported such a technique called pMD-membrane that utilizes small molecule probes to detect ligand binding sites and surface hotspots on membrane proteins based on probe-based molecular dynamics simulation. The current work extends pMD-membrane to a diverse set of small organic molecular species that can be used as cosolvents during simulation of membrane proteins...
March 13, 2017: Journal of Chemical Theory and Computation
Sukrit Singh, Gregory R Bowman
Allosteric (i.e. long-range) communication within proteins is crucial for many biological processes, such as the activation of signaling cascades in response to specific stimuli. However, the physical basis for this communication remains unclear. Existing computational methods for identifying allostery focus on the role of concerted structural changes, but recent experimental work demonstrates that disorder is also an important factor. Here, we introduce the Correlation of All Rotameric and Dynamical States (CARDS) framework for quantifying correlations between both the structure and disorder of different regions of a protein...
March 10, 2017: Journal of Chemical Theory and Computation
Dhabih V Chulhai, Jason D Goodpaster
Projection-based quantum embedding methodologies provide a framework for performing wave function-in-density functional theory (WF-in-DFT) calculations. The total WF-in-DFT energy is dependent on the partitioning of the total system and requires similar partitioning in each system for accurate energy differences. To achieve this, we enforce an absolute localization of the WF orbitals to basis functions only associated with the WF subsystem. This absolute localization, followed by iterative optimization of the subsystems' orbitals, provides improved energy differences for WF-in-DFT while simultaneously improving the computational efficiency...
March 9, 2017: Journal of Chemical Theory and Computation
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