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doi: 10.1002/jcc.26026pmid: 31301185
The accurate ground‐state potential energy function of aluminum monohydride (AlH) has been determined from ab initio calculations using the multireference averaged coupled‐pair functional (MR‐ACPF) method in conjunction with the correlation‐consistent core‐valence basis sets up to septuple‐zeta quality. The vibration‐rotation energy levels of the two isotopologues, AlH and AlD, were predicted to near the “spectroscopic” accuracy. The importance of electron correlation beyond the MR‐ACPF level of approximation, the scalar relativistic, spin‐orbit, adiabatic, and nonadiabatic effects was discussed. © 2019 Wiley Periodicals, Inc.
Daoudi, Syrine; Semmeq, Abderrahmane; Badawi, Michael; Assfeld, Xavier; Arfaoui, Youssef; Pastore, Mariachiara
doi: 10.1002/jcc.26027pmid: 31294857
Seven free base porphyrins employed in dye‐sensitized photoelectrosynthetic cells are investigated with the aim of benchmarking the ability of different density functional theory (DFT) and time‐dependent DFT approaches in reproducing their structure, vertical, and E0‐0 excitation energies and the energy levels alignment (red‐ox properties) at the interface with the TiO2. We find that both vertical and E0‐0 excitation energies are accurately reproduced by range‐separated functionals, among which the ωB97X‐D delivers the lowest absolute deviations from experiments. When the dye/TiO2 interface is modeled, the physical interfacial energetics is only obtained when the B3LYP functional is employed; on the other hand, M06‐2X (54% of exchange) and the two long‐range corrected approaches tested (CAM‐B3LYP and ωB97X‐D) excessively destabilize the semiconductor conduction band levels with respect to the dye's lowest unoccupied molecular orbitals (LUMOs), predicting no pathway for electron injection. © 2019 Wiley Periodicals, Inc.
Pei, Han‐Wen; Laaksonen, Aatto
doi: 10.1002/jcc.26028pmid: 31313339
A clustering framework is introduced to analyze the microscopic structural organization of molecular pairs in liquids and solutions. A molecular pair is represented by a representative vector (RV). To obtain RV, intermolecular atom distances in the pair are extracted from simulation trajectory as components of the key feature vector (KFV). A specific scheme is then suggested to transform KFV to RV by removing the influence of permutational molecular symmetry on the KFV as the predicted clusters should be independent of possible permutations of identical atoms in the pair. After RVs of pairs are obtained, a clustering analysis technique is finally used to classify all the RVs of molecular pairs into the clusters. The framework is applied to analyze trajectory from molecular dynamics simulations of an ionic liquid (trihexyltetradecylphosphonium bis(oxalato)borate ([P6,6,6,14][BOB])). The molecular pairs are successfully categorized into physically meaningful clusters, and their effectiveness is evaluated by computing the product moment correlation coefficient (PMCC). (Willett, Winterman, and Bawden, J. Chem. Inf. Comput. Sci. 1986, 26, 109–118; Downs, Willett, and Fisanick, J. Chem. Inf. Comput. Sci. 1994, 34, 1094–1102) It is observed that representative configurations of two clusters are related to two energy local minimum structures optimized by density functional theory (DFT) calculation, respectively. Several widely used clustering analysis techniques of both nonhierarchical (k‐means) and hierarchical clustering algorithms are also evaluated and compared with each other. The proposed KFV technique efficiently reveals local molecular pair structures in the simulated complex liquid. It is a method, which is highly useful for liquids and solutions in particular with strong intermolecular interactions. © 2019 Wiley Periodicals, Inc.
doi: 10.1002/jcc.26031pmid: 31301188
The unified term of trans‐philicity is proposed to cover the trans‐effect/trans‐influence concepts. NMR trans‐philicity ladders are built for a broad series of square planar trans‐Pt(NH3)2(Cl)L and trans‐Pt(CO)2(Cl)L complexes employing 35Cl NMR probe and quantified by calculation of NMR trans‐philicity indicators. The trans‐philicity is linearly correlated with the ligand electronic PL constant, a measure of the net donor power of the ligand. The nature of cis‐ligands does not affect trans‐philicity ladders but strongly affects trans‐philicity strength. Solvent has significant effect on the σcalcd 35Cl shielding constants, with the polar Dimethylformamide (DMF) solvent inducing downfield shifts relative to σcalcd 35Cl with nonpolar benzene solvent. Good correlations between σcalcd 35Cl shielding constants and the estimated R(Pt‐Cl) bond distances demonstrate the relation of trans‐philicity with trans‐influence and trans‐effect phenomena and put the grounds for the establishment of the new concept of trans‐philicity in the realm of square planar Pt(II) and other transition metal complexes. © 2019 Wiley Periodicals, Inc.
doi: 10.1002/jcc.26033pmid: 31322769
A full implementation of the analytical stress tensor for periodic systems is reported in the TURBOMOLE program package within the framework of Kohn–Sham density functional theory using Gaussian‐type orbitals as basis functions. It is the extension of the implementation of analytical energy gradients (Lazarski et al., Journal of Computational Chemistry 2016, 37, 2518–2526) to the stress tensor for the purpose of optimization of lattice vectors. Its key component is the efficient calculation of the Coulomb contribution by combining density fitting approximation and continuous fast multipole method. For the exchange‐correlation (XC) part the hierarchical numerical integration scheme (Burow and Sierka, Journal of Chemical Theory and Computation 2011, 7, 3097–3104) is extended to XC weight derivatives and stress tensor. The computational efficiency and favorable scaling behavior of the stress tensor implementation are demonstrated for various model systems. The overall computational effort for energy gradient and stress tensor for the largest systems investigated is shown to be at most two and a half times the computational effort for the Kohn–Sham matrix formation. © 2019 Wiley Periodicals, Inc.
Fujimoto, Kazushi; Payal, Rajadeep Singh; Hattori, Tomonori; Shinoda, Wataru; Nakagaki, Masayuki; Sakaki, Shigeyoshi; Okazaki, Susumu
doi: 10.1002/jcc.26034pmid: 31322762
A dissociative force field for all‐atomistic molecular dynamics calculations has been developed to investigate impact fracture of polymers accompanying dissociation of chemical bonds of polymer main chain. Energy of dimer molecules was evaluated as a function of both bond‐length b and bond‐angle θ by CASPT2 calculations, whose quality is enough to describe dissociation of chemical bonds. Because we found that the bond dissociation energy D decreases with increasing bond‐angle, we employed the Morse‐type function VBond(b, θ) = {D − VAngle(θ)}[1 − exp{−α(b − b0) − β(b − b0)2}] where a quartic function VAngle(θ) = k1(θ − θ0) + k2(θ − θ0)2 + k3(θ − θ0)3 + k4(θ − θ0)4. This function reproduced well the CASPT2 potential energy surface in a wide range of b and θ. The parameters have been obtained for four popular glassy polymers, polyethylene, poly(methyl methacrylate), poly(styrene), and polycarbonate. © 2019 Wiley Periodicals, Inc.
Chiba, Shuntaro; Okuno, Yasushi; Honma, Teruki; Ikeguchi, Mitsunori
doi: 10.1002/jcc.26035pmid: 31343749
We propose a novel force‐field‐parametrization procedure that fits the parameters of potential functions in a manner that the pair distribution function (DF) of molecules derived from candidate parameters can reproduce the given target DF. Conventionally, approaches to minimize the difference between the candidate and target DFs employ radial DFs (RDF). RDF itself has been reported to be insufficient for uniquely identifying the parameters of a molecule. To overcome the weakness, we introduce energy DF (EDF) as a target DF, which describes the distribution of the pairwise energy of molecules. We found that the EDF responds more sensitively to a small perturbation in the pairwise potential parameters and provides better fitting accuracy compared to that of RDF. These findings provide valuable insights into a wide range of coarse graining methods, which determine parameters using information obtained from a higher‐level calculation than that of the developed force field. © 2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.
Suma, Antonio; Poppleton, Erik; Matthies, Michael; Šulc, Petr; Romano, Flavio; Louis, Ard A.; Doye, Jonathan P. K.; Micheletti, Cristian; Rovigatti, Lorenzo
doi: 10.1002/jcc.26029pmid: 31301183
Simulations of nucleic acids at different levels of structural details are increasingly used to complement and interpret experiments in different fields, from biophysics to medicine and materials science. However, the various structural models currently available for DNA and RNA and their accompanying suites of computational tools can be very rarely used in a synergistic fashion. The tacoxDNA webserver and standalone software package presented here are a step toward a long‐sought interoperability of nucleic acids models. The webserver offers a simple interface for converting various common input formats of DNA structures and setting up molecular dynamics (MD) simulations. Users can, for instance, design DNA rings with different topologies, such as knots, with and without supercoiling, by simply providing an XYZ coordinate file of the DNA centre‐line. More complex DNA geometries, as designable in the cadnano, CanDo and Tiamat tools, can also be converted to all‐atom or oxDNA representations, which can then be used to run MD simulations. Though the latter are currently geared toward the native and LAMMPS oxDNA representations, the open‐source package is designed to be further expandable. TacoxDNA is available at http://tacoxdna.sissa.it. © 2019 Wiley Periodicals, Inc.
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