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Journal of Chemical Theory and Computation

Heiner Schröder, Tobias Schwabe
An extension of the Polarizable Embedding (PE) approach for the computation of perichromatic shifts within linear response theory, termed corrected PE, is presented. It covers the change in induction effects in addition to contributions from electrostatics and non-resonant excitonic coupling and thereby presents a combination of the corrected Linear Response and the PE method. Using this method, we analyzed the individual contributions for six different excitations from four molecules in different solvents to clarify the question, which effects should be accounted for by a polarizable solvation model...
December 15, 2017: Journal of Chemical Theory and Computation
Justin Provazza, Francesco Segatta, Marco Garavelli, David F Coker
Computation of nonlinear optical response functions allows for an in-depth connection between theory and experiment. Experimentally recorded spectra provide a high density of information, but to objectively disentangle overlapping signals and to reach a detailed and reliable understanding of the system dynamics, measurements must be integrated with theoretical approaches. Here, we present a new, highly accurate and efficient trajectory based semiclassical path integral method for computing higher-order nonlinear optical response functions for non-Markovian open quantum systems...
December 15, 2017: Journal of Chemical Theory and Computation
Jun Zhang
A new library called LIBRETA for the evaluation of electron repulsion integrals (ERIs) and their first and second derivatives over segmented and contracted Gaussian functions is developed. Our LIBRETA is optimized from three aspects: (1) The Obara-Saika, Dupuis-Rys-King, and McMurchie-Davidson method are all employed. The recurrence relations involved are optimized by tree-search for each combination of angular momenta, and in the best case, 50% of the intermediates can be eliminated to reduce the computational cost...
December 14, 2017: Journal of Chemical Theory and Computation
Julius Philipp Paul Zauleck, Regina de Vivie-Riedle
A challenge for molecular quantum dynamics (QD) calculations is the curse of dimensionality with respect to the nuclear degrees of freedom. A common approach that works especially well for fast reactive processes is to reduce the dimensionality of the system to a few most relevant coordinates. Identifying these can become a very difficult task, since they often are highly unintuitive. We present a machine learning approach that utilizes an autoencoder that is trained to find a low-dimensional representation of a set of molecular configurations...
December 13, 2017: Journal of Chemical Theory and Computation
Quan Van Vuong, Jissy Akkarapattiakal Kuriappan, Maximilian Kubillus, Julian Kranz, Thilo Mast, Thomas A Niehaus, Stephan Irle, Marcus Elstner
We present the parametrization and benchmark of long-range corrected second-order DFTB, LC-DFTB2, for organic and biological molecules. The LC-DFTB2 model not only improves fundamental orbital energy gaps, but also ameliorates the DFT self-interaction error and overpolarization problem, and further improves charge-transfer excited states significantly. Electronic parameters for the construction of the DFTB2 Hamiltonian as well as repulsive potentials were optimized for molecules containing C, H, N, and O chemical elements...
December 12, 2017: Journal of Chemical Theory and Computation
Hui Li, Christopher Paolucci, William F Schneider
The ability of metal-exchanged-zeolites to chemisorb small gas molecules is key to their performance as heterogeneous catalysts and gas-separating-agents. Here we propose and evaluate an ab initio potential of mean force (PMF) method for computing adsorption free energies of representative small molecules to Cu-exchanged sites in SSZ-13 zeolite. We show that Cu ions are mobilized by adsorbates and, as a result, computed free energies are significantly more negative than those obtained from a conventional harmonic oscillator model...
December 12, 2017: Journal of Chemical Theory and Computation
Shane M Parker, Dmitrij Rappoport, Filipp Furche
We report on the efficient Turbomole implementation of quadratic response properties within the time-dependent density functional theory (TDDFT) context that includes the static and dynamic dipole hyperpolarizability, ground-to-excited-state two-photon absorption amplitudes (through a single residue) and state-to-state one-photon absorption amplitudes (through a double residue). Our implementation makes full use of arbitrary (including non-Abelian) point-group symmetry as well as permutational symmetry and enables the calculation of nonlinear properties with hybrid density functionals for molecules with hundreds of atoms and thousands of basis functions at a cost that is a fixed multiple of the cost of the corresponding linear properties...
December 12, 2017: Journal of Chemical Theory and Computation
Kevin Reiter, Fabian Mack, Florian Weigend
We present a highly efficient implementation for density functional calculations of chemical shielding constants. It employs the multipole-accelerated resolution of the identity for the calculation of the Coulomb part, which complements the usage of low order scaling routines for the evaluation of the exchange-correlation part and the Hartree-Fock exchange part. Introduced errors for shifts of chemical shielding constants of H, C, F and P are evaluated for respective test sets of molecules and are related to the accuracy of shifts obtained with hybrid and non-hybrid functionals of the generalized gradient approximation type as well as for meta-GGA functionals themselves, also considering solvation effects...
December 12, 2017: Journal of Chemical Theory and Computation
Pedro Borlido, Miguel A L Marques, Silvana Botti
Hybrid functionals are by now the state-of-the-art for the calculation of electronic properties of solids within density functional theory. The key to their performance is how a part of Fock exchange is mixed with a semi-local exchange-correlation functional. The choice of the mixing parameter is particularly critical in non-homogeneous systems, such as an interface between two solid phases. In this work we propose a local mixing function that is a functional of the electron density through an estimator of the local dielectric function...
December 11, 2017: Journal of Chemical Theory and Computation
Tianyu Zhu, Piotr de Silva, Troy Van Voorhis
Chemical bonding plays a central role in the description and understanding of chemistry. Many methods have been proposed to extract information about bonding from quantum chemical calculations, majority of them resorting to molecular orbitals as basic descriptors. Here, we present a method called Self-Attractive Hartree (SAH) decomposition, to unravel pairs of electrons directly from electron density, which unlike molecular orbitals, is a well defined observable that can be accessed experimentally. The key idea is to partition the density into a sum of one-electron fragments which simultaneously maximize self-repulsion and maintain regular shapes...
December 11, 2017: Journal of Chemical Theory and Computation
Edwin Argueta, Jeena Shaji, Arun Gopalan, Peilin Liao, Randall Q Snurr, Diego A Gomez-Gualdron
Metal-organic frameworks (MOFs) are porous crystalline materials with attractive properties for gas separation and storage. Their remarkable tunability makes it possible to create millions of MOF variations, but creates the need for fast material screening to identify promising structures. Computational high-throughput screening (HTS) is a possible solution, but its usefulness is tied to accurate predictions of MOF adsorption properties. Accurate adsorption simulations often require an accurate description of electrostatic interactions, which depend on the electronic charges of the MOF atoms...
December 11, 2017: Journal of Chemical Theory and Computation
Andrew M Sand, Chad E Hoyer, Kamal Sharkas, Katherine Marie Kidder, Roland Lindh, Donald G Truhlar, Laura Gagliardi
Analytic gradient routines are a desirable feature for quantum mechanical meth- ods, allowing for efficient determination of equilibrium and transition state structures and several other molecular properties. In this work, we present analytical gradients for multiconfiguration pair-density functional theory (MC-PDFT) when used with a state-specific complete active space self-consistent field reference wave function. Our approach constructs a Lagrangian that is variational in all wave function parameters. We find that MC-PDFT locates equilibrium geometries for several small- to medium- sized organic molecules that are similar to those located by complete active space second-order perturbation theory but that are obtained with decreased computational cost...
December 6, 2017: Journal of Chemical Theory and Computation
Qianli Ma, Hans-Joachim Werner
A well-parallelized perturbative triples correction implementation for the pair natural orbital based coupled cluster method PNO-LCCSD(T)-F12 is presented. A composite approach is adopted in addressing the coupling due to off-diagonal Fock matrix elements, in which the local triples amplitudes are iteratively solved using small domains of triples natural orbitals, and a semicanonical (T0) domain correction with larger domains is applied to the reduce the domain errors. This treatment adds only about 20% to the computational cost of (T0) calculations with large domains, and the errors due to the use of small domains in the iterations are very small...
December 6, 2017: Journal of Chemical Theory and Computation
Michael Roemelt, Vera Krewald, Dimitrios A Pantazis
The accurate description of magnetic level energetics in oligonuclear exchange-coupled transition metal complexes remains a formidable challenge for quantum chemistry. The density matrix renormalization group (DMRG) brings such systems for the first time easily within reach of multireference wave function methods by enabling the use of unprecedentedly large active spaces. But does this guarantee systematic improvement in predictive ability, and if so, under which conditions? We identify operational parameters in the use of DMRG using as a test system an experimentally characterized mixed valence bis-μ-oxo/μ-acetato Mn(III,IV) dimer, a model for the oxygen-evolving complex of photosystem II...
December 6, 2017: Journal of Chemical Theory and Computation
Hussien Helmy Osman, Miguel Angel Salvadó, Pilar Pertierra, Joshua Engelkemier, Daniel C Fredrickson, J Manuel Recio
The characterization of bonding interactions in molecules and materials is one of the major applications of quantum mechanical calculations. Numerous schemes have been devised to identify and visualize chemical bonds, including the electron localization function, quantum theory of atoms in molecules, and natural bond orbital analysis, whereas the energetics of bond formation are generally analyzed in qualitative terms through various forms of energy partitioning schemes. In this article, we illustrate how the Chemical Pressure (CP) approach recently developed for analyzing atomic size effects in solid state compounds provides a basis for merging these two approaches, in which bonds are revealed through the forces of attraction and repulsion acting between the atoms...
December 6, 2017: Journal of Chemical Theory and Computation
Hamza M Ruzayqat, Tim P Schulze
We introduce a new kinetic Monte Carlo (KMC) algorithm for off-lattice simulation. In off-lattice KMC one needs to calculate the rates for all possible moves from the current state by searching the energy landscape for index-1 saddle points surrounding the current basin of attraction. We introduce a rejection scheme where the true rates are replaced by rate estimates. This is done by first associating each saddle point with the atom that would move the most if that transition were to take place, then constructing an estimate for the total rate associated with each atom by using a nearest-neighbor bond count...
December 6, 2017: Journal of Chemical Theory and Computation
James L McDonagh, Arnaldo F Silva, Mark A Vincent, Paul L A Popelier
We present an innovative method for predicting the dynamic electron correlation energy of an atom or a bond in a molecule utilizing topological atoms. Our approach uses the machine learning method Kriging (Gaussian Process Regression with a non-zero mean function) to predict these dynamic electron correlation energy contributions. The true energy values are calculated by partitioning the MP2 two-particle density-matrix via the Interacting Quantum Atoms (IQA) procedure. To our knowledge, this is the first time such energies have been predicted by a machine learning technique...
December 6, 2017: Journal of Chemical Theory and Computation
Javier Cerezo, Yanli Liu, Na Lin, Xian Zhao, Roberto Improta, Fabrizio Santoro
We present a novel mixed quantum classical dynamical method to include solvent effects on internal conversion (IC) processes. All the solute degrees of freedom are represented by a wavepacket moving according to nonadiabatic quantum dynamics, while the motion of an explicit solvent model is described by an ensemble of classical trajectories. The mutual coupling of the solute and solvent dynamics is included within a mean-field framework and the quantum and classical equations of motions are solved simultane ously...
December 5, 2017: Journal of Chemical Theory and Computation
Daniel Hollas, Lukáš Šištík, Edward G Hohenstein, Todd J Martínez, Petr Slavicek
We show that the Floating Occupation Molecular Orbital Complete Active Space Configuration Interaction (FOMO-CASCI) method is a promising alternative to the widely used Complete Active Space Self Consistent Field (CASSCF) method in direct non-adiabatic dynamics simulations. We have simulated photodynamics of three archetypal molecules in photodynamics: ethylene, methaniminium cation and malonaldehyde. We compared the time evolution of electronic populations and reaction mechanisms as revealed by the FOMO-CASCI and CASSCF approaches...
December 5, 2017: Journal of Chemical Theory and Computation
Lorenzo Boninsegna, Ralf Banisch, Cecilia Clementi
Macromolecular systems are composed of a very large number of atomic degrees of freedom. There is strong evidence suggesting that structural changes occurring in large biomolecular systems at long timescale dynamics may be captured by models coarser than atomistic, although a suitable or optimal coarse-graining is a priori unknown. Here we propose a systematic approach to learning a coarse representation of a macromolecule from microscopic simulation data. In particular, the definition of effective coarse variables is achieved by partitioning the degrees of freedom both in the structural (physical) space, and in the conformational space...
December 5, 2017: Journal of Chemical Theory and Computation
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