Journal of Computational Chemistry

doi: 10.1002/jcc.23497pmid: N/A

A comprehensive study on the structural and optical properties of a guanidine–quinoline copper(I) bis(chelate) complex is reported by Sonja Herres‐Pawlis et al. on page 1. This complex displays interesting metal–ligand charge‐transfer behavior. In order to probe the applicability of timedependent density functional theory (TDDFT) to charge‐transfer excitations in these complexes, many‐body perturbation theory calculations are performed for a small model system. The TDDFT optical response agrees at least qualitatively with the spectrum obtained from the Bethe–Salpeter equation based on quasiparticle energies within the GW approximation. However, the TDDFT results strongly depend on the exchange and correlation functional, and need careful benchmarking.

doi: 10.1002/jcc.23496pmid: N/A

An extension of the VALBOND‐trans force field for iridium complexes is introduced by Franziska Hofmann, Michael Devereux, Andreas Pfaltz, and Markus Meuwly on page 18. Newly fitted, transferable parameters capture the structure and interactions of a chemically diverse set of ligands, depicted on the cover using the electrostatic potential of interacting species mapped onto their isodensity surfaces. A recently developed, “supervised” fitting approach is used to obtain the parameters, combining the efficiency of computational fitting with the crucial extra stability that human supervision can provide for highly correlated and nonlinear fitting problems.

Jesser, Anton; Rohrmüller, Martin; Schmidt, Wolf Gero; Herres‐Pawlis, Sonja

doi: 10.1002/jcc.23449pmid: 24122864

We report a comprehensive computational benchmarking of the structural and optical properties of a bis(chelate) copper(I) guanidine–quinoline complex. Using various (TD‐)DFT flavors a strong influence of the basis set is found. Moreover, the amount of exact exchange shifts metal‐to‐ligand bands by 1 eV through the absorption spectrum. The BP86/6‐311G(d) and B3LYP/def2‐TZVP functional/basis set combinations were found to yield results in best agreement with the experimental data. In order to probe the general applicability of TD‐DFT to excitations of copper bis(chelate) charge‐transfer (CT) systems, we studied a small model system that on the one hand is accessible to methods of many‐body perturbation theory (MBPT) but still contains simple guanidine and imine groups. These calculations show that large quasiparticle energies of the order of several electronvolts are largely offset by exciton binding energies for optical excitations and that TD‐DFT excitation energies deviate from MBPT results by at most 0.5 eV, further corroborating the reliability of our TD‐DFT results. The latter result in a multitude of MLCT bands ranging from the visible region at 3.4 eV into the UV at 5.5 eV for the bis(chelate) complex. Molecular orbital analysis provided insight into the CT within these systems but gave mixed transitions. A meaningful transition assignment is possible, however, by using natural transition orbitals. Additionally, we performed a thorough conformational analysis as the correct description of the copper coordination is crucial for the prediction of optical spectra. We found that DFT identifies the correct conformational minimum and that the MLCTs are strongly dependent on the torsion of the chelate angles at the copper center. From the results, it is concluded that extensive benchmarking allows for the quantitative analyses of the CT behavior of copper bis(chelate) complexes within TD‐DFT. © 2013 Wiley Periodicals, Inc.

Hofmann, Franziska D.; Devereux, Michael; Pfaltz, Andreas; Meuwly, Markus

doi: 10.1002/jcc.23460pmid: 24155105

The structural and energetic characterization of metal complexes is important in catalysis and photochemical applications. Unraveling their modes‐of‐action can be greatly assisted by computation, which typically is restricted to computationally demanding methods including electronic structure calculations with density functional theory. Here, we present an empirical force field based on valence bond theory applicable to a range of octahedral Ir(III) complexes with different coordinating ligands, including iridium complexes with a chiral P,N ligand. Using an approach applicable to metal‐containing complexes in general, it is shown that with one common parametrization 85% of the 116 diastereomers—all within 21 kcal/mol of the lowest energy conformation of each series—can be correctly ranked. For neutral complexes, all diastereomers are ranked correctly. This helps to identify the most relevant diastereomers which, if necessary, can be further investigated by more demanding computational methods. Furthermore, if one specific complex is considered, the root mean square deviation between reference data from electronic structure calculations and the force field is ≈1  kcal/mol . This, together with the possibility to carry out explicit simulations in solution paves the way for an atomistic understanding of iridium‐containing complexes in catalysis. © 2013 Wiley Periodicals, Inc.

Fracchia, Francesco; Filippi, Claudia; Amovilli, Claudio

doi: 10.1002/jcc.23461pmid: 24151051

We present here several novel features of our recently proposed Jastrow linear generalized valence bond (J‐LGVB) wave functions, which allow a consistently accurate description of complex potential energy surfaces (PES) of medium‐large systems within quantum Monte Carlo (QMC). In particular, we develop a multilevel scheme to treat different regions of the molecule at different levels of the theory. As prototypical study case, we investigate the decomposition of α‐hydroxy‐dimethylnitrosamine, a carcinogenic metabolite of dimethylnitrosamine (NDMA), through a two‐step mechanism of isomerization followed by a retro‐ene reaction. We compute a reliable reaction path with the quadratic configuration interaction method and employ QMC for the calculation of the electronic energies. We show that the use of multideterminantal wave functions is very important to correctly describe the critical points of this PES within QMC, and that our multilevel J‐LGVB approach is an effective tool to significantly reduce the cost of QMC calculations without loss of accuracy. As regards the complex PES of α‐hydroxy‐dimethylnitrosamine, the accurate energies computed with our approach allows us to confirm the validity of the two‐step reaction mechanism of decomposition originally proposed within density functional theory, but with some important differences in the barrier heights of the individual steps. © 2013 Wiley Periodicals, Inc.

Ikebe, Jinzen; Sakuraba, Shun; Kono, Hidetoshi

doi: 10.1002/jcc.23462pmid: 24166005

A novel, efficient sampling method for biomolecules is proposed. The partial multicanonical molecular dynamics (McMD) was recently developed as a method that improved generalized ensemble (GE) methods to focus sampling only on a part of a system (GEPS); however, it was not tested well. We found that partial McMD did not work well for polylysine decapeptide and gave significantly worse sampling efficiency than a conventional GE. Herein, we elucidate the fundamental reason for this and propose a novel GEPS, adaptive lambda square dynamics (ALSD), which can resolve the problem faced when using partial McMD. We demonstrate that ALSD greatly increases the sampling efficiency over a conventional GE. We believe that ALSD is an effective method and is applicable to the conformational sampling of larger and more complicated biomolecule systems. © 2013 Wiley Periodicals, Inc.

Ganguly Neogi, Soumya; Chaudhury, Pinaki

doi: 10.1002/jcc.23465pmid: 24272539

In this article, we propose a stochastic search‐based method, namely genetic algorithm (GA) and simulated annealing (SA) in conjunction with density functional theory (DFT) to evaluate global and local minimum structures of (TiO2)n clusters with n = 1–12. Once the structures are established, we evaluate the infrared spectroscopic modes, cluster formation energy, vertical excitation energy, vertical ionization potential, vertical electron affinity, highest occupied molecular orbital (HOMO)‐lowest unoccupied molecular orbital (LUMO) gaps, and so forth. We show that an initial determination of structure using stochastic techniques (GA/SA), also popularly known as natural algorithms as their working principle mimics certain natural processes, and following it up with density functional calculations lead to high‐quality structures for these systems. We have shown that the clusters tend to form three‐dimensional networks. We compare our results with the available experimental and theoretical results. The results obtained from SA/GA‐DFT technique agree well with available theoretical and experimental data of literature. © 2013 Wiley Periodicals, Inc.

Yang, Pei‐Kun

doi: 10.1002/jcc.23466pmid: 24129882

Gauss's law or Poisson's equation is conventionally used to calculate solvation free energy. However, the near‐solute dielectric polarization from Gauss's law or Poisson's equation differs from that obtained from molecular dynamics (MD) simulations. To mimic the near‐solute dielectric polarization from MD simulations, the first‐shell water was treated as two layers of surface charges, the densities of which are proportional to the electric field at the solvent molecule that is modeled as a hard sphere. The intermediate water was treated as a bulk solvent. An equation describing the solvation free energy of ions using this solvent scheme was derived using the TIP3P water model. © 2013 Wiley Periodicals, Inc.

Xu, Zhijun; Yang, Yang; Wang, Ziqiu; Mkhonto, Donald; Shang, Cheng; Liu, Zhi‐Pan; Cui, Qiang; Sahai, Nita

doi: 10.1002/jcc.23474pmid: 24272540

The unique, plate‐like morphology of hydroxyapatite (HAP) nanocrystals in bone lends to the hierarchical structure and functions of bone. Proteins enriched in phosphoserine (Ser‐OPO3) and glutamic acid (Glu) residues have been proposed to regulate crystal morphology; however, the atomic‐level mechanisms remain unclear. Previous molecular dynamics studies addressing biomineralization have used force fields with limited benchmarking, especially at the water/mineral interface, and often limited sampling for the binding free energy profile. Here, we use the umbrella sampling/weighted histogram analysis method to obtain the adsorption free energy of Ser‐OPO3 and Glu on HAP (100) and (001) surfaces to understand organic‐mediated crystal growth. The calculated organic‐water–mineral interfacial energies are carefully benchmarked to density functional theory calculations, with explicit inclusion of solvating water molecules around the adsorbate plus the Poisson–Boltzmann continuum model for long‐range solvation effects. Both amino acids adsorb more strongly on the HAP (100) face than the (001) face. Growth rate along the [100] direction should then be slower than in the [001] direction, resulting in plate‐like crystal morphology with greater surface area for the (100) than the (001) face, consistent with bone HAP crystal morphology. Thus, even small molecules are capable of regulating bone crystal growth by preferential adsorption in specific directions. Furthermore, Ser‐OPO3 is a more effective growth modifier by adsorbing more strongly than Glu on the (100) face, providing one possible explanation for the energetically expensive process of phosphorylation of some proteins involved in bone biomineralization. The current results have broader implications for designing routes for biomimetic crystal synthesis. © 2013 Wiley Periodicals, Inc.

Canneaux, Sébastien; Bohr, Frédéric; Henon, Eric

doi: 10.1002/jcc.23470pmid: 24190715

Kinetic and Statistical Thermodynamical Package (KiSThelP) is a cross‐platform free open‐source program developed to estimate molecular and reaction properties from electronic structure data. To date, three computational chemistry software formats are supported (Gaussian, GAMESS, and NWChem). Some key features are: gas‐phase molecular thermodynamic properties (offering hindered rotor treatment), thermal equilibrium constants, transition state theory rate coefficients (transition state theory (TST), variational transition state theory (VTST)) including one‐dimensional (1D) tunnelling effects (Wigner, and Eckart) and Rice‐Ramsperger‐Kassel‐Marcus (RRKM) rate constants, for elementary reactions with well‐defined barriers. KiSThelP is intended as a working tool both for the general public and also for more expert users. It provides graphical front‐end capabilities designed to facilitate calculations and interpreting results. KiSThelP enables to change input data and simulation parameters directly through the graphical user interface and to visually probe how it affects results. Users can access results in the form of graphs and tables. The graphical tool offers customizing of 2D plots, exporting images and data files. These features make this program also well‐suited to support and enhance students learning and can serve as a very attractive courseware, taking the teaching content directly from results in molecular and kinetic modelling. © 2013 Wiley Periodicals, Inc.