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Journal of Chemical Theory and Computation

Reza Ghafarian Shirazi, Frank Neese, Dimitrios A Pantazis
A test set of twelve aryl carbenes (AC12) is compiled with the purpose of establishing their adiabatic singlet-triplet energy splittings using correlated wave function based methods. The set covers both singlet and triplet ground state aryl carbenes, as well as a range of magnitudes for the ground state to excited state gap. The performance of coupled cluster methods is examined with respect to the reference wave function, the basis set, and a number of additional methodological parameters that enter the calculation...
August 15, 2018: Journal of Chemical Theory and Computation
Georgi L Stoychev, Alexander A Auer, Frank Neese
Analytic calculation of nuclear magnetic resonance chemical shielding tensors, based on gauge-including atomic orbitals, is implemented for double-hybrid density functional theory (DHDFT), using the resolution of the identity (RI) approximation for its second order Møller-Plesset perturbation theory (MP2) correlation contributions. A benchmark set of 15 small molecules, containing 1 H, 13 C, 15 N, 17 O, 19 F, and 31 P nuclei, is used to assess the accuracy of the results in comparison to coupled cluster and empirical equilibrium reference data, as well as to calculations with MP2, Hartree-Fock, and commonly used pure and hybrid density functionals...
August 15, 2018: Journal of Chemical Theory and Computation
Hervé Hogues, Francis Gaudreault, Christopher R Corbeil, Christophe Deprez, Traian Sulea, Enrico O Purisima
Despite decades of development, protein-protein docking remains a largely unsolved problem. The main difficulties are the immense space spanned by the translational and rotational degrees of freedom and the prediction of the conformational changes of proteins upon binding. FFT is generally the preferred method to exhaustively explore the translation-rotation space at a fine grid resolution, albeit with the tradeoff of approximating force fields with correlation functions. This work presents a direct search alternative that samples the states in Cartesian space at the same resolution and computational cost as standard FFT methods...
August 14, 2018: Journal of Chemical Theory and Computation
Joseph P Heindel, Qi Yu, Joel M Bowman, Sotiris S Xantheas
We report extensive benchmark CCSD(T) Complete Basis Set (CBS) estimates of the binding energies, structures and harmonic frequencies of H3O+(H2O)n clusters, n=0-5, including all currently known low-lying energy isomers. These are used to test a previously reported many-body (up to 3-body interactions) CCSD(T)-based potential energy surface (PES) for the hydrated proton. A new 4-body term for the hydronium- water-water-water interactions is introduced. This term is aimed at rening the relative energies of isomers of the H3O+(H2O)n, n=4, 5 clusters...
August 13, 2018: Journal of Chemical Theory and Computation
Yuan Liu, Minsik Cho, Brenda Rubenstein
We present an ab initio auxiliary field quantum Monte Carlo method for studying the electronic structure of molecules, solids, and model Hamiltonians at finite temperature. The algorithm marries the ab initio phaseless auxiliary field quantum Monte Carlo algorithm known to produce high accuracy ground state energies of molecules and solids with its finite temperature variant, long used by condensed matter physicists for studying model Hamiltonian phase diagrams, to yield a phaseless, ab initio finite temperature method...
August 13, 2018: Journal of Chemical Theory and Computation
Zhen Luo, Yingjin Ma, Xicun Wang, Haibo Ma
The recent development of the density matrix renormalization group (DMRG) method in multireference quantum chemistry makes it practical to evaluate static correlation in a large active space, while dynamic correlation provides a critical correction to the DMRG reference for strong-correlated systems and is usually obtained using multireference perturbation (MRPT) or configuration interaction (MRCI) methods with internal contraction (ic) approximation. These methods can use an active space scalable to relatively larger size references than has previously been possible...
August 13, 2018: Journal of Chemical Theory and Computation
Bence Hégely, Péter R Nagy, Mihály Kállay
A dual basis (DB) approach is proposed which is suitable for the reduction of the computational expenses of the Hartree-Fock, Kohn-Sham, and wave function-based correlation methods. The approach is closely related to the DB approximation of Head-Gordon and co-workers [ J. Chem. Phys. 2006 , 125 , 074108 ] but specifically designed for embedding calculations. The new approach is applied to our variant of the projector-based embedding theory utilizing the Huzinaga-equation, multilevel local correlation methods, and combined density functional-multilevel local correlation approximations...
August 13, 2018: Journal of Chemical Theory and Computation
Luca Brugnoli, Anna Maria Ferrari, Bartolomeo Civalleri, Alfonso Pedone, Maria Cristina Menziani
CeO2 based materials are very attractive as catalytic component for industrial processes and environment friendly technologies, therefore, a reliable and computationally affordable theoretical description of the main properties of ceria is needed. In particular, the description of the interconversion between the Ce(IV) and Ce(III) oxidation states, on which lies the main chemical features of the Cerium Oxide, results quite challenging at the Density Functional Theory level. Here, we tested several Density functional approximations, spanning from GGA to Hybrid (Global, Meta-Global and Range Separated Corrected) functionals, on the structural, vibrational, electronic and thermochemical properties of bulk CeO2 and Ce2O3...
August 10, 2018: Journal of Chemical Theory and Computation
Yanfei Guan, Victoria M Ingman, Benjamin J Rooks, Steven E Wheeler
We describe an open-source computational toolkit (AARON: An Automated Reaction Optimizer for New catalysts) that automates the quantum mechanical geometry optimization and characterization of the transition state and intermediate structures required to predict the activities and selectivities of asymmetric catalytic reactions. Modern computational quantum chemistry has emerged as a powerful tool for explaining the selectivity and activity of asymmetric catalysts. However, reliably predicting the stereochemical outcome of realistic reactions often requires the geometry optimization of hundreds of transition state and intermediate structures, which is a tedious process...
August 10, 2018: Journal of Chemical Theory and Computation
Frank Jensen
We investigate by explicit parameter optimization to what extent basis sets of polarized double-ζ quality can introduce compensating errors in five different density functional methods. It is shown that minor changes in the contraction coefficients of the valence functions in the basis sets can have a significant impact and allow different density functional methods to achieve very similar performances. This holds for nuclear magnetic shielding constants and for isomerization energies, barrier heights, and noncovalent interactions...
August 10, 2018: Journal of Chemical Theory and Computation
Lin Shen, Xiancheng Zeng, Hao Hu, Xiangqian Hu, Weitao Yang
Understanding the regulation mechanism and molecular determinants of the reduction potential of metalloprotein is a major challenge. An ab initio quantum mechanical/molecular mechanical (QM/MM) method combining the minimum free energy path (MFEP) and fractional number of electron (FNE) approaches has been developed in our group to simulate the redox processes of large systems. The FNE scheme provides an efficient unique description for the redox process, while the MFEP method provides improved conformational sampling on complex environments such as protein in the QM/MM calculations...
August 10, 2018: Journal of Chemical Theory and Computation
Alireza Marefat Khah, Sarah Karbalaei Khani, Christof Hättig
An implementation of a QM/MM embedding in a polarizable environment is presented for second-order Møller-Plesset perturbation theory, MP2, for ground state energies and molecular gradients and for the second-order Algebraic Diagrammatic Construction, ADC(2), for excitation energies and excited state molecular gradients. In this implementation of PE-MP2 and PE-ADC(2), the polarizable embedded Hartree-Fock wave function is used as uncorrelated reference state. The polarization-correlation cross terms for the ground and excited states are included in this model via an approximate coupling density...
August 10, 2018: Journal of Chemical Theory and Computation
Dorothea Golze, Jan Wilhelm, Michiel van Setten, Patrick Rinke
The GW method is routinely used to predict charged valence excitations in molecules and solids. However, the numerical techniques employed in the most efficient GW algorithms break down when computing core excitations as measured by X-ray photoelectron spectroscopy (XPS). We present a full-frequency approach on the real axis using a localized basis to enable the treatment of core levels in GW . Our scheme is based on the contour deformation technique and allows for a precise and efficient calculation of the self-energy, which has a complicated pole structure for core states...
August 9, 2018: Journal of Chemical Theory and Computation
Thomas Schnappinger, Marco Marazzi, Sebastian Mai, Antonio Monari, Leticia Gonzalez, Regina de Vivie-Riedle
We present a non-adiabatic dynamics study concerning the sub picosecond relaxation of excited states in dimeric and trimeric thiophene chains. The influence of the triplet states in the overall process is, for the first time, taken into account by explicitly including spin-orbit couplings and hence allowing intersystem crossing phenomena. We observe the fundamental role of the triplet state manifold in driving the full relaxation process. In particular we evidence the effect of both, inter-ring rotation and ringopening, in the process, as compared to the monomer, where the ring-opening process appears as the dominant one...
August 9, 2018: Journal of Chemical Theory and Computation
Yelena A Arnautova, Ruben Abagyan, Maxim Totrov
Protein-RNA interactions play an important role in many biological processes. Computational methods such as docking have been developed to complement existing biophysical and structural biology techniques. Computational prediction of protein-RNA complex structures includes two steps: generating candidate structures from the individual protein and RNA parts and scoring the generated poses to pick out the correct one. In this work, we considered three recently developed data sets of protein-RNA complexes to evaluate and improve the performance of the FFT-based rigid-body docking algorithm implemented in the ICM package...
August 9, 2018: Journal of Chemical Theory and Computation
Matthew Welborn, Lixue Cheng, Thomas F Miller
We present a machine learning (ML) method for predicting electronic structure correlation energies using Hartree-Fock input. The total correlation energy is expressed in terms of individual and pair contributions from occupied molecular orbitals, and Gaussian process regression is used to predict these contributions from a feature set that is based on molecular orbital properties, such as Fock, Coulomb, and exchange matrix elements. With the aim of maximizing transferability across chemical systems and compactness of the feature set, we avoid the usual specification of ML features in terms of atom- or geometry-specific information, such atom/element-types, bond-types, or local molecular structure...
August 8, 2018: Journal of Chemical Theory and Computation
Szymon Śmiga, Ireneusz Grabowski
A practical, accurate, and cost- and implementation-free method (ΔMP2-SOS(IP)) for the calculation of vertical ionization potentials is proposed. The simple method is based on a single-step, a diagonal, frequency-independent approximation to the second-order self-energy expression combined with the spin-component-scaled technique. The search for an optimal scaling factor is performed for a set of 50 moderately sized molecules, and the quality of the method is additionally assessed for a benchmark set of 24 organic acceptor molecules...
August 8, 2018: Journal of Chemical Theory and Computation
Maximilian Scheurer, Michael F Herbst, Peter Reinholdt, Jógvan Magnus Haugaard Olsen, Andreas Dreuw, Jacob Kongsted
We present a variant of the algebraic diagrammatic construction (ADC) scheme by combining ADC with the polarizable embedding (PE) model. The presented PE-ADC method is implemented through second and third order and is designed with the aim of performing accurate calculations of excited states in large molecular systems. Accuracy and large-scale applicability are demonstrated with three case studies, and we further analyze the importance of both state-specific and linear-response-type corrections to the excitation energies in the presence of the polarizable environment...
August 7, 2018: Journal of Chemical Theory and Computation
Johannes Heuser, Sebastian Hoefener
We report the derivation and implementation of analytical orbital-relaxed properties and nuclear gradients for excited states using the second-order approximate coupled-cluster singles and doubles (CC2) model combined with uncoupled frozen-density embedding (FDEu). An implementation of the algebraic diagrammatic construction through second order ADC(2), which arises from simplification of RICC2 FDEu, is also presented. In order to ensure a RICC2 FDEu Lagrange functional that is linear in the Lagrange multipliers the Hartree-Fock density is employed for the target subsystem in the embedding contributions...
August 7, 2018: Journal of Chemical Theory and Computation
Jan Řezáč, Chandler Greenwell, Gregory J O Beran
Non-covalent interactions govern many important areas of chemistry ranging from biomolecules to molecular crystals. Here, an accurate and computationally inexpensive dispersion-corrected second-order Moller-Plesset perturbation theory model (MP2D) is presented. MP2D recasts the highly successful dispersion-corrected MP2C model in a framework based on Grimme's D3 dispersion correction, combining Grimme's D3 dispersion coefficients with new analogous uncoupled Hartree-Fock ones and five global empirical parameters...
August 7, 2018: Journal of Chemical Theory and Computation
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