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Journal of Chemical Theory and Computation

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https://www.readbyqxmd.com/read/29678106/uncertainty-quantification-in-alchemical-free-energy-methods
#1
Agastya P Bhati, Shunzhou Wan, Yuan Hu, Brad Sherborne, Peter Vivian Coveney
The alchemical free energy methods have gained much importance recently from several reports of improved ligand-protein binding affinity predictions based on their implementation using molecular dynamics simulation. A large number of variants of such methods implementing different accelerated sampling techniques and free energy estimators are available, each claimed to be better than the others in its own way. However, the key features of reproducibility and the quantification of the associated uncertainties in such methods have barely been discussed...
April 20, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29677446/classical-optimal-control-for-energy-minimization-based-on-diffeomorphic-modulation-under-observable-response-preserving-homotopy
#2
Micheline B Soley, Andreas Markmann, Victor S Batista
We introduce the so-called 'Classical Optimal Control Optimization' (COCO) method for global energy minimization based on the implementation of the diffeomorphic modulation under observable-response-preserving homotopy (DMORPH) gradient algorithm. A probe particle with time-dependent mass m(t;b) and dipole m(r; t;b) is evolved classically on the potential energy surface V(r) coupled to an electric field E(t;b), as described by the time-dependent density of states represented on a grid, or otherwise as a linear combination of Gaussians generated by the k-means clustering algorithm...
April 20, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29676906/relativistic-spin-orbit-heavy-atom-on-the-light-atom-nmr-chemical-shifts-general-trends-across-the-periodic-table-explained
#3
Jan Vícha, Stanislav Komorovsky, Michal Repisky, Radek Marek, Michal Straka
The importance of relativistic effects on the NMR parameters in heavy-atom (HA) compounds, particularly the SO-HALA (Spin-Orbit Heavy Atom on the Light Atom) effect on NMR chemical shifts, has been known for about 40 years. Yet, a general correlation between the electronic-structure and SO-HALA effect have been missing. By analyzing 1H NMR chemical shifts of the 6th-period hydrides (Cs-At) we discovered general electronic-structure principles and mechanisms that dictate the size and sign of the SO-HALA NMR chemical shifts...
April 20, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29652499/rapid-sampling-of-hydrogen-bond-networks-for-computational-protein-design
#4
Jack B Maguire, Scott E Boyken, David Baker, Brian Kuhlman
Hydrogen bond networks play a critical role in determining the stability and specificity of biomolecular complexes, and the ability to design such networks is important for engineering novel structures, interactions, and enzymes. One key feature of hydrogen bond networks that makes them difficult to rationally engineer is that they are highly cooperative and are not energetically favorable until the hydrogen bonding potential has been satisfied for all buried polar groups in the network. Existing computational methods for protein design are ill-equipped for creating these highly cooperative networks because they rely on energy functions and sampling strategies that are focused on pairwise interactions...
April 20, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29672048/propagators-for-the-time-dependent-kohn-sham-equations-multistep-runge-kutta-exponential-runge-kutta-and-commutator-free-magnus-methods
#5
Adrián Gómez Pueyo, Miguel A L Marques, Angel Rubio, Alberto Castro
We examine various integration schemes for the time-dependent Kohn-Sham equations. Contrary to the time-dependent Schrödinger's equation, this set of equations is non-linear, due to the dependence of the Hamiltonian on the electronic density. We discuss some of their exact properties, and in particular their symplectic structure. Four different families of propagators are considered, specifically the linear multistep, Runge-Kutta, exponential Runge-Kutta, and the commutator-free Magnus schemes. These have been chosen because they have been largely ignored in the past for time-dependent electronic structure calculations...
April 19, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29672042/reaxff-molecular-dynamics-simulation-for-the-graphitization-of-amorphous-carbon-a-parametric-study
#6
Kejiang Li, Hang Zhang, Guang-Yue Li, Jianliang Zhang, Mohammed Bouhadja, Zhengjian Liu, Adam A Skelton, Mansoor Barati
A parametric study of ReaxFF for molecular dynamics simulation of graphitization of amorphous carbon was conducted. The responses to different initial amorphous carbon configurations, simulation time steps, simulated temperatures, and ReaxFF parameter sets were investigated. The results showed that time step shorter than 0.2 fs is sufficient for the ReaxFF simulation of carbon using both Chenoweth 2008 and Srinivasan 2015 parameter sets. The amorphous carbon networks produced using both parameter sets at 300 K are similar to each other, with the first peak positions of pair distribution function curves located between the graphite sp2 bond peak position and the diamond sp3 bond peak position...
April 19, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29669201/simulation-of-ultra-fast-dynamics-effects-in-resonant-inelastic-x-ray-scattering-of-gas-phase-water
#7
Adam E A Fouda, Gregory I Purnell, Nicholas A Besley
Resonant inelastic soft x-ray scattering maps for the water molecule are simulated by combining quantum chemical calculations of x-ray spectroscopy with ab initio molecular dynamics. The resonant inelastic scattering intensity is computed using the Kramers-Heisenberg formalism which accounts for channel interference and polarisation anisotropy. Algebraic diagrammatic construction and density functional theory based approaches for the calculation of the x-ray transition energies and transition dipole moments of the absorption and emission processes are explored...
April 18, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29664633/finite-size-effects-of-binary-mutual-diffusion-coefficients-from-molecular-dynamics
#8
Seyed Hossein Jamali, Ludger Wolff, Tim M Becker, André Bardow, Thijs J H Vlugt, Othonas A Moultos
Molecular Dynamics simulations were performed for the prediction of the finite-size effects of Maxwell-Stefan diffusion coefficients of molecular mixtures and a wide variety of binary Lennard-Jones systems. A strong dependency of computed diffusivities on the system size was observed. Computed diffusivities were found to increase with the number of molecules. We propose a correction for the extrapolation of Maxwell-Stefan diffusion coefficients to the thermodynamic limit, based on the study by Yeh and Hummer (J...
April 17, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29660292/two-level-chebyshev-filter-based-complementary-subspace-method-pushing-the-envelope-of-large-scale-electronic-structure-calculations
#9
Amartya S Banerjee, Lin Lin, Phanish Suryanarayana, Chao Yang, John E Pask
We describe a novel iterative strategy for Kohn-Sham density functional theory calculations aimed at large systems (> 1000 electrons), applicable to metals and insulators alike. In lieu of explicit diagonalization of the Kohn-Sham Hamiltonian on every self-consistent field (SCF) iteration, we employ a two-level Chebyshev polynomial filter based complementary subspace strategy to: 1) compute a set of vectors that span the occupied subspace of the Hamiltonian; 2) reduce subspace diagonalization to just partially occupied states; and 3) obtain those states in an efficient, scalable manner via an inner Chebyshev-filter iteration...
April 16, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29660291/the-molecular-mechanism-underlying-ligand-binding-to-the-membrane-embedded-site-of-a-g-protein-coupled-receptor
#10
Xiao-Jing Yuan, Stefano Raniolo, Vittorio Limongelli, Yechun Xu
The crystal structure of P2Y1 receptor (P2Y1R), a class A GPCR, revealed a special extra-helical site for its antagonist, BPTU, which locates in between the membrane and the protein. However, due to the limitation of crystallization experiments, the membrane was mimicked by use of detergents and the information related to the binding of BPTU to the receptor in the membrane environment is rather limited. In the present work, we conducted a total of ~7.5 µs all-atom simulations in explicit solvent using conventional molecular dynamics and multiple enhanced sampling methods, with models of BPTU and a POPC bilayer, both in the absence and presence of P2Y1R...
April 16, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29660288/atomic-orbital-implementation-of-extended-symmetry-adapted-perturbation-theory-xsapt-and-benchmark-calculations-for-large-supramolecular-complexes
#11
Ka Un Lao, John M Herbert
We report an implementation of extended symmetry-adapted perturbation theory (XSAPT) in the atomic orbital basis, extending this method to systems where the monomers are large. In our "XSAPT(KS)" approach, monomers are described using range-separated Kohn-Sham (KS) density functionals whose asymptotic behavior is set by tuning the range-separation parameter, ω, in a monomer-specific way. This is accomplished either by conventional ionization potential (IP)-based tuning, in which ω is adjusted to satisfy the condition εHOMO (ω) = -IP(ω), or else using a so-called "global density-dependent" (GDD) condition, in which ω is fixed based on the size of the exchange hole...
April 16, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29660278/transient-charge-and-energy-flow-in-the-wide-band-limit
#12
Fabio Covito, Florian G Eich, Riku Tuovinen, Michael A Sentef, Angel Rubio
The wide-band limit is a commonly used approximation to analyze transport through nanoscale devices. In this work we investigate its applicability to the study of charge and heat transport through molecular break junctions exposed to voltage biases and temperature gradients. We find by comparative simulations that while the wide-band-limit approximation faithfully describes the long-time charge and heat transport, it fails to characterize the short-time behavior of the junction. In particular, we show that the charge current flowing through the device shows a discontinuity when a temperature gradient is applied, while the energy flow is discontinuous when a voltage bias is switched on and even diverges when the junction is exposed to both a temperature gradient and a voltage bias...
April 16, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29660274/plane-wave-implementation-and-performance-of-%C3%A3-la-carte-coulomb-attenuated-exchange-correlation-functionals-for-predicting-optical-excitation-energies-in-some-notorious-cases
#13
Martin Peter Bircher, Ursula Rothlisberger
Linear-response time-dependent density functional theory (LR-TDDFT) has become a valuable tool in the calculation of excited states of molecules of various sizes. However, standard generalised gradient approximation (GGA) and hybrid exchange-correlation (xc) functionals often fail to correctly predict charge-transfer (CT) excitations with low orbital overlap, thus limiting the scope of the method. The Coulomb-attenuation method (CAM) in the form of the CAM-B3LYP functional has been shown to reliably remedy this problem in many CT systems, making accurate predictions possible...
April 16, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29660273/rapid-calculation-of-molecular-kinetics-using-compressed-sensing
#14
Florian Litzinger, Lorenzo Boninsegna, Hao Wu, Feliks Nüske, Raajen Patel, Richard Baraniuk, Frank Noé, Cecilia Clementi
Recent methods for the analysis of molecular kinetics from massive molecular dynamics (MD) data rely on the solution of very large eigenvalue problems. Here we build upon recent results from the field of compressed sensing and develop the spectral oASIS method, a highly efficient approach to approximate the leading eigenvalues and eigenvectors of large generalized eigenvalue problems without ever having to evaluate the full matrices. The approach is demonstrated to reduce the dimensionality of the problem by one or two orders of magnitude, directly leading to corresponding savings in the computation and storage of the necessary matrices, and a speedup of two to four orders of magnitude in solving the eigenvalue problem...
April 16, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29660272/a-force-field-for-water-over-pt-111-development-assessment-and-comparison
#15
Stephan N Steinmann, Rodrigo Ferreira de Morais, Andreas W Götz, Paul Fleurat-Lessard, Marcella Iannuzzi, Philippe Sautet, Carine Michel
Metal/water interfaces are key in many natural and industrial processes, such as corrosion, atmospheric or environmental chemistry. Even today, the only practical approach to simulate large interfaces between a metal and water is to perform force field simulations. In this work, we propose a novel force field, GAL17, to describe the interaction of water and a Pt(111) surface. GAL17 builds on three terms: (i) a standard Lennard-Jones potential for the bonding interaction between the surface and water; (ii) a Gaussian term to improve the surface corrugation and (iii) two terms describing the angular dependence of the interaction energy...
April 16, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29658715/accurate-and-efficient-parallel-implementation-of-an-effective-linear-scaling-direct-random-phase-approximation-method
#16
Daniel Graf, Matthias Beuerle, Henry F Schurkus, Arne Luenser, Gökcen Savasci, Christian Ochsenfeld
An efficient algorithm for calculating the random phase approximation (RPA) correlation energy is presented that is as accurate as the canonical molecular orbital resolution-of-the-identity RPA (RI-RPA) with the important advantage of an effective linear-scaling behavior (instead of quartic) for large systems due to a formulation in the local atomic orbital space. The high accuracy is achieved by utilizing optimized minimax integration schemes and the local Coulomb metric attenuated by the complementary error function for the RI approximation...
April 16, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29648812/minimum-energy-paths-and-transition-states-by-curve-optimization
#17
Alain C Vaucher, Markus Reiher
Transition states and minimum energy paths are essential to understand and predict chemical reactivity. Double-ended methods represent a standard approach for their determination. We introduce a new double-ended method that optimizes reaction paths described by curves. Unlike other methods, our approach optimizes the curve parameters rather than distinct structures along the path. With molecular paths represented as continuous curves, the optimization can benefit from the advantages of an integral-based formulation...
April 12, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29634270/recovering-intrinsic-fragmental-vibrations-using-the-generalized-subsystem-vibrational-analysis
#18
Yunwen Tao, Chuan Tian, Niraj Verma, Wenli Zou, Chao Wang, Dieter Cremer, Elfi Kraka
Normal vibrational modes are generally delocalized over the molecular system, which makes it difficult to assign certain vibrations to specific fragments or functional groups. We introduce a new approach, the Generalized Subsystem Vibrational Analy- sis (GSVA), to extract the Intrinsic Fragmental Vibrations of any fragment/subsystem from the whole system via the evaluation of the corresponding effective Hessian matrix. The retention of the curvature information with regard to the potential energy surface for the effective Hessian matrix endows our approach with a concrete physical basis and enables the normal vibrational modes of different molecular systems to be legit- imately comparable...
April 10, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29630836/one-dimensional-projection-of-collective-variables-for-effective-sampling-of-complex-chemical-reaction-coordinates
#19
Yong Su Baek, Cheol Ho Choi
A one-dimensional projection (ODP) technique is introduced to overcome the challenges in multi-dimensional sampling. With the help of a projected "advancement of reaction (ξ)" control parameter, it was demonstrated that multi-dimensional samplings could be performed with a single parameter, thus dramatically reducing the computational overhead. In our test studies, the ODP technique successfully yielded the free energy surface of the double proton transfer reaction of the acetic acid dimer and the hydrolysis of the methyl diazonium ion...
April 9, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29630831/parametrization-of-molybdenum-cofactors-for-the-amber-force-field
#20
Pedro Ferreira, Nuno M F Sousa A Cerqueira, Natércia Fernandes Brás, Pedro A Fernandes, Maria João Ramos
Molybdenum containing enzymes have been receiving significant attention from the scientific community since they participate in important biological processes and in the global biogeochemical cycles of carbon, nitrogen and sulfur. Molecular modeling studies of these metalloproteins with classical force fields are however often hampered by the "missing parameter" problem. In this article, a set of parameters have been determined for the AMBER force field from nine different molybdenum cofactors. All of these cofactors were optimized and parametrized, using a bonded model approach...
April 9, 2018: Journal of Chemical Theory and Computation
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