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Journal of Chemical Theory and Computation

Fabian Zeller, Manuel P Luitz, Rainer Bomblies, Martin Zacharias
A detailed understanding of the drug-receptor association process is of fundamental importance for drug design. Due to the long timescales of typical binding kinetics, the atomistic simulation of the ligand traveling from bulk solution into the binding site is still computationally challenging. In this work, we apply a multi-scale approach of combined molecular dynamics (MD) and Brownian dynamics (BD) simulations to investigate association pathway ensembles for the two prominent H1N1 neuraminidase inhibitors oseltamivir and zanamivir...
August 18, 2017: Journal of Chemical Theory and Computation
B Scott Fales, Edward G Hohenstein, Benjamin G Levine
The limited precision of floating point arithmetic can lead to the qualitative and even catastrophic failure of quantum chemical algorithms, especially when high accuracy solutions are sought. For example, numerical errors accumulated while solving for determinantal configuration interaction wave functions via Davidson diagonalization may lead to spin contamination in the trial subspace. This spin contamination may cause the procedure to converge to roots with undesired ⟨Ŝ(2)⟩, wasting computer time in the best case and leading to incorrect conclusions in the worst...
August 18, 2017: Journal of Chemical Theory and Computation
Tommaso Giovannini, Marta Olszówka, Franco Egidi, James R Cheeseman, Giovanni Scalmani, Chiara Cappelli
We present an analytical formulation and implementation of Raman and Raman Optical Activity (ROA) spectra within a three-layer fully polarizable Quantum Mechanical (QM)/ Molecular Mechanics (MM)/Polarizable Continuum Model (PCM) approach. Polarization effects in the MM layer are modeled by exploiting the Fluctuating Charges (FQ) method, in which MM solvent atoms are endowed with electric charges that can be mutually polarized by the solute QM density. Because of its fully polarizable atomistic description, QM/FQ/PCM is able to account for specific solvent effects like those due to hydrogen bonds, providing a physical picture for protic solvents such as water...
August 18, 2017: Journal of Chemical Theory and Computation
Jigneshkumar Dahyabhai Prajapati, Carlos José Fernández Solano, Mathias Winterhalter, Ulrich Kleinekathöfer
The rapid spreading of antimicrobial resistance in Gram-negative bacteria has become a major threat for humans as well as animals. As one of the main factors involved, the permeability of the outer membrane has attracted quite some attention recently. However, the knowledge regarding the translocation mechanisms for most available antibiotics is so far rather limited. Here, a theoretical study concerning the diffusion route of ciprofloxacin across the outer membrane porin OmpC from E. coli is presented. To this end, we establish a protocol to characterize meaningful permeation pathways by combining metadynamics with the zero-temperature string method...
August 17, 2017: Journal of Chemical Theory and Computation
Hoi Ling Luk, Johannes Feist, J Jussi Toppari, Gerrit Groenhof
When photoactive molecules interact strongly with confined light modes as found in plasmonic structures or optical cavities, new hybrid light-matter states can form, the so-called polaritons. These polaritons are coherent superpositions (in the quantum mechanical sense) of excitations of the molecules and of the cavity photon or surface plasmon. Recent experimental and theoretical works suggest that access to these polaritons in cavities could provide a totally new and attractive paradigm for controlling chemical reactions that falls in between traditional chemical catalysis and coherent laser control...
August 17, 2017: Journal of Chemical Theory and Computation
Xiaojing Wu, Jean-Marie Teuler, Fabien Cailliez, Carine Clavaguéra, Dennis R Salahub, Aurélien de la Lande
We propose a methodology for simulating attosecond electron dynamics in large molecular systems. Our approach is based on the combination of real time time-dependent-density-functional theory (RT-TDDFT) and polarizable Molecular Mechanics (MMpol) with the point-charge-dipole model of electrostatic induction. We implemented this methodology in the software deMon2k that relies heavily on auxiliary fitted densities. In the context of RT-TDDFT/MMpol simulations, fitted densities allow the cost of the calculations to be reduced drastically on three fronts: (i) the Kohn-Sham potential, (ii) the electric field created by the (fluctuating) electron cloud which is needed in the QM/MM interaction, and (iii) the analysis of the fluctuating electron density on-the-fly...
August 17, 2017: Journal of Chemical Theory and Computation
Soumen Ghosh, Amity Andersen, Laura Gagliardi, Christopher J Cramer, Niranjan Govind
We present an implementation of a time-dependent semiempirical method (INDO/S) in NWChem using real-time (RT) propagation to address, in principle, the entire spectrum of valence electronic excitations. Adopting this model, we study the UV-visible spectra of medium-sized systems like P3B2, f-coronene, and in addition much larger systems like ubiquitin in the gas phase and the betanin chromophore in the presence of two explicit solvents (water and methanol). RT-INDO/S provides qualitatively and indeed often quantitatively accurate results when compared with RT- TDDFT or experimental spectra...
August 16, 2017: Journal of Chemical Theory and Computation
Anita de Ruiter, Anton A Polyansky, Bojan Zagrovic
In order to fully understand the microscopic origins of binding specificity between nucleic acids and proteins, it is imperative to study the dependence of the binding preferences between nucleobases and protein side chains on the properties of the environment. Here, we employ molecular dynamics simulations and umbrella sampling to derive the potentials of mean force and the associated absolute binding free energies between the four standard RNA nucleobases and the side chains of aspartic acid and tryptophan in water/methanol mixtures exhibiting a wide range of dielectric constants...
August 16, 2017: Journal of Chemical Theory and Computation
Tobias Schwabe, Lars Goerigk
For the first time, we combine time-dependent double-hybrid density functional approximations (TD-DHDFAs) for the calculation of electronic excitation energies with the concepts of spin-component and spin-opposite scaling (SCS/SOS) of electron-pair contributions to their nonlocal correlation components. Different flavors of this idea, ranging from standard SCS parameters to fully fitted parameter sets, are presented and tested on six different parent DHDFAs. For cross-validation, we assess those methods on three benchmark sets that cover small- to medium-sized chromophores (up to 78 atoms) and different excitation types...
August 16, 2017: Journal of Chemical Theory and Computation
Samuel M Greene, Victor S Batista
We introduce the "tensor-train split-operator Fourier transform" (TT-SOFT) method for simulations of multidimensional nonadiabatic quantum dynamics. TT-SOFT is essentially the grid-based SOFT method implemented in dynamically adaptive tensor-train representations. In the same spirit of all matrix product states, the tensor-train format enables the representation, propagation, and computation of observables of multidimensional wave functions in terms of the grid-based wavepacket tensor components, bypassing the need of actually computing the wave function in its full-rank tensor product grid space...
August 16, 2017: Journal of Chemical Theory and Computation
Sergei N Yurchenko, Andrey Yachmenev, Roman I Ovsyannikov
We present a general, numerically motivated approach to the construction of symmetry-adapted basis functions for solving ro-vibrational Schrödinger equations. The approach is based on the property of the Hamiltonian operator to commute with the complete set of symmetry operators and, hence, to reflect the symmetry of the system. The symmetry-adapted ro-vibrational basis set is constructed numerically by solving a set of reduced vibrational eigenvalue problems. In order to assign the irreducible representations associated with these eigenfunctions, their symmetry properties are probed on a grid of molecular geometries with the corresponding symmetry operations...
August 16, 2017: Journal of Chemical Theory and Computation
Siri C van Keulen, Alicia Solano, Ursula Rothlisberger
Rhodopsin is a photoactive G-protein-coupled receptor (GPCR) that converts dim light into a signal for the brain, leading to eyesight. Full activation of this GPCR is achieved after passing through several steps of the protein's photoactivation pathway. Key events of rhodopsin activation are the initial cis-trans photoisomerization of the covalently bound retinal moiety followed by conformational rearrangements and deprotonation of the chromophore's protonated Schiff base (PSB), which ultimately lead to full activation in the meta II state...
August 15, 2017: Journal of Chemical Theory and Computation
Daoling Peng, Shaopeng Li, Liang Peng, Feng Long Gu, Weitao Yang
Time-dependent coupled perturbed Hartree-Fock/Density-Functional-Theory (TDHF/TDDFT) approach has been reformulated based on non-orthogonal localized molecular orbitals (NOLMOs). Based on the NOLMO Fock equation, we have derived the corresponding NOLMO-TDHF/TDDFT equations up to the third order, and the formula for the frequency dependent (hyper)polarizabilities have been given. Our approach has been applied to calculate both static and dynamic (hyper)polarizabilities of molecules varying from small molecules to large molecules...
August 14, 2017: Journal of Chemical Theory and Computation
Davide Mercadante, Johannes Andreas Wagner, Iker Valle Aramburu, Edward A Lemke, Frauke Gräter
Molecular dynamics simulations have valuably complemented experiments describing the dynamics of intrinsically disordered proteins (IDPs), particularly since the proposal of models to solve the artificial collapse of IDPs in silico. Such models suggest redefining non-bonded interactions, by either increasing water dispersion forces or adopting the Kirkwood-Buff force field. These approaches yield extended conformers that better comply with experiments, but it is unclear if they all sample the same intra-chain dynamics of IDPs...
August 14, 2017: Journal of Chemical Theory and Computation
Daniele Loco, Louis Lagardère, Stefano Caprasecca, Filippo Lipparini, Benedetta Mennucci, Jean-Philip Piquemal
We present the implementation of a Born-Oppenheimer (BO) hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) strategy using density functional theory (DFT) and the polarizable AMOEBA force field. This approach couples the Gaussian and Tinker suite of programs through a variational formalism allowing for a full self-consistent relaxation of both the AMOEBA induced dipoles and the DFT electron density at each MD step. As the DFT SCF cycles are the limiting factor in terms of computational efforts and MD stability, we focus on the latter aspect and compare the time-reversible BO (TR-BO) and the extended BO Lagrangian approaches (XL-BO) to the MD propagation...
August 14, 2017: Journal of Chemical Theory and Computation
Qianyi Cheng, InSuk Joung, Jooyoung Lee
Improving the quality of a given protein structure can serve as the ultimate solution for accurate protein structure prediction, and seeking such a method is currently a challenge in computational structural biology. In order to promote and encourage much needed such efforts, CASP (Critical Assessment of Structure Prediction) has been providing an ideal computational experimental platform, where it was reported only recently (since CASP10) that systematic protein structure refinement is possible by carrying out extensive (∼ms) MD simulations with proper restraints generated from the given structure...
August 11, 2017: Journal of Chemical Theory and Computation
Jeffrey R Wagner, Jesper Sørensen, Nathan Hensley, Celia Wong, Clare Zhu, Taylor Perison, Rommie E Amaro
We present a substantial update to the open-source POVME binding pocket analysis software. New capabilities of POVME 3.0 include a flexible chemical coloring scheme for feature identification, post-analysis tools for comparing large ensembles of pockets (e.g., from molecular dynamics simulations), and the introduction of scripts and methods that facilitate binding pocket comparison and analysis. We envision the use of this software for visualization of binding pocket dynamics, selection of representative structures for ensemble docking, and incorporation of molecular dynamics results into ligand design efforts...
August 11, 2017: Journal of Chemical Theory and Computation
Glen M Hocky, Thomas Dannenhoffer-Lafage, Gregory A Voth
Many free-energy sampling and quantum mechanics/molecular mechanics (QM/MM) computations on protein complexes have been performed where, by necessity, a single component is studied isolated in solution while its overall configuration is kept in the complex-like state by either rigid restraints or harmonic constraints. A drawback in these studies is that the system's native fluctuations are lost, both due to the change of environment and the imposition of the extra potential. Yet, we know that having both accurate structure and fluctuations is likely crucial to achieving correct simulation estimates for the subsystem within its native larger protein complex context...
August 11, 2017: Journal of Chemical Theory and Computation
Ying Li, Hui Li, Frank C Pickard, Badri Narayanan, Fatih Sen, Maria K Y Chan, Subramanian Sankaranarayanan, Bernard R Brooks, Benoît Roux
Machine learning (ML) techniques with the genetic algorithm (GA) have been applied to explore a polarizable force field parameters using only ab initio data from quantum mechanics (QM) calculations of molecular clusters at the MP2/6-31G(d,p), DFMP2(fc)/jul-cc-pVDZ, and DFMP2(fc)/jul-cc-pVTZ levels to predict experimental condensed phase properties (i.e., density and heat of vaporization). The performance of this ML/GA approach is demonstrated on 4,943 dimers electrostatic potentials and 1,250 clusters interaction energies for methanol...
August 11, 2017: Journal of Chemical Theory and Computation
Jake D Holmes, Alberto Otero-de-la-Roza, Gino A DiLabio
The ability of atom-centered potential (ACPs) to improve the modeling of water clusters using density-functional methods is explored. Water-specific ACPs were developed using accurate ab initio reference data to correct the deficiencies of the BHandHLYP density functional in the calculation of absolute and relative binding energies of water clusters. In conjunction with aug-cc-pVTZ basis sets and with or without dispersion corrections, it is possible to obtain absolute binding energies for water clusters containing up to 10 H2O molecules to within 0...
August 11, 2017: Journal of Chemical Theory and Computation
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