Molecular dynamics implementation in MSINDO: study of silicon clusters

Born-Oppenheimer molecular dynamics is implemented in the semiempirical self-consistent field molecular orbital method MSINDO. The method is employed for the investigation of the structure and dynamics of silicon clusters of various sizes. The reliability of the present parameterization for silicon compounds is demonstrated by a comparison of the results of simulated annealing and of density functional calculations of Si(n) clusters (n = 5-7). The melting behavior of the Si(7) cluster is investigated and the MSINDO results are compared to previous high-level calculations. The efficiency of the present approach for the treatment of large systems is demonstrated by an extensive simulated annealing study of the Si(45) and Si(60) clusters. New Si(45) and Si(60) structures are found and evaluated. The relative stability of various energy minimum structures is compared with density functional calculations and available literature data.     

Miscibility of zinc sulfide and zinc phosphide

Solid solutions in the system zinc sulfide/zinc phosphide (Zn(2+)(x)S(2-2xP(2x)) were investigated using the cyclic cluster model within the semiempirical MSINDO method. Results of cyclic cluster calculations for binding energies of the perfect ZnS and Zn(3)P(2) are presented and compared with the experimental data. The miscibility of ZnS and Zn(3)P(2) over the whole composition range of 0 < x < 1 was investigated by calculating the Gibbs free energy of mixing Delta(M)G for different values of x. A miscibility gap was found at both ends of the composition range and compared with experimental data.     

Assessment of quantum‐chemical methods for electronic properties and geometry of signaling biomolecules

A reasonable balance between accuracy and feasibility of quantum‐chemical methods depends on the complexity of the molecular system and the scientific goals. Six series of indole‐, naphthalene‐, phenol‐, benzoic‐, phenoxy‐, other auxin‐derivatives, and a test set of similar organic molecules have been chosen for an assessment of 13 density functional and semi‐empirical molecular orbital methods with respect to electronic and structural properties. The accuracy and precision of HOMO/LUMO calculations are determined by comparison with experimental ionization potentials and electron affinities. Further comparison was performed at atomic level by covariance analysis. The methods KMLYP, MSINDO, and PM3 are precise and accurate for the whole set of molecules. The method AM1 offers comparable accuracy with the exception of electron affinities of indole derivatives, where significant deviations from experiment were observed. Geometrical properties were best reproduced with the semi‐empirical method MSINDO. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

MSINDO parameterization for third‐row transition metals

The recently developed MSINDO version of the semiempirical SCF MO method SINDO1 has been parameterized for third‐row transition metals Sc to Zn. The set of reference data used for the previous parameterization of SINDO1 has been substantially increased by incorporating results of recent experiments and first‐principles calculations. A comparison of calculated heats of formation, geometries, ionization potentials, and dipole moments with literature values for more than 200 gas phase molecules is presented. The accuracy of the modified MSINDO version achieved for heats of formation and bond lengths has been considerably improved compared to SINDO1. Small clusters of transition metals and metal oxides were included in the parameterization to ensure accurate results for studies of larger systems. The application of the method to small transition metal complexes that were not included in the parameterization shows that the optimized parameters are transferable to other compounds. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 861–887, 2001     

Computational modeling of the adsorption and photodegradation of 4-chlorophenol on anatase TiO2 particles

In the present work, the adsorption and photodegradation of 4-chlorophenol (4-CP) on the (100) surface of TiO₂ anatase with semiempirical SCF MO method MSINDO has been investigated. The (100) surface is modeled with free clusters (TiO₂)_n, where n = 20–80. The surface lattice titanium atoms, which are Lewis acid sites, are considered as adsorption sites. Molecular dynamics (MD) simulations have been used for the investigation of 4-CP adsorption conformations and the surface reaction mechanism studies. The 4-CP molecule has revealed parallel adsorption upon optimization, whereas under excitation conditions the perpendicular configuration is dominant. The aromatic ring cleavage by atomic oxygen has been studied computationally and accordingly, the relevant mechanism was suggested. By comparison with experimental and other theoretical calculations, it is shown that MSINDO can reproduce literature data with acceptable accuracy.     

Periodic calculations of excited state properties for solids using a semiempirical approach

The semiempirical SCF MO method MSINDO (modified symmetrically orthogonalized intermediate neglect of differential overlap) [T. Bredow and K. Jug, Electronic Encyclopedia of Computational Chemistry, 2004] is extended to the calculation of excited state properties through implementation of the configuration interaction singles (CIS) approach. MSINDO allows the calculation of periodic systems via the cyclic cluster model (CCM) [T. Bredow et al., J. Comput. Chem., 2001, 22, 89] which is a direct-space approach and therefore can be in principle combined with all molecular quantum-chemical techniques. The CIS equations are solved for a cluster with periodic boundary conditions using the Davidson-Liu iterative block diagonalization approach. As a proof-of-principle, MSINDO-CCM-CIS is applied for the calculation of optical spectra of ZnO and TiO(2), oxygen-defective rutile, and F-centers in NaCl. The calculated spectra are compared to available experimental and theoretical literature data. After re-adjustment of the empirical parameters the quantitative agreement with experiment is satisfactory. The present approximate approach is one of the first examples of a quantum-chemical methodology for solids where excited states are correctly described as n-electron state functions. After careful benchmark testing it will allow calculation of photophysical and photochemical processes relevant to materials science and catalysis.     

Nucleation of CuGa Phases on the MgO(100) Surface

MSINDO calculations are presented for the coadsorption of Cu and Ga atoms as clusters and islands on the MgO(100) surface. The surface is simulated by a (8 × 8 × 3) Mg₉₆O₉₆ cyclic cluster. The relative number of Cu and Ga atoms was varied in order to understand the influence of copper rich and gallium rich phases. It was found that the copper atoms have a dominating influence on the structural arrangement in mixed phases. The adsorption sites of Cu and Ga atoms are preferably O atoms, but in mixed phases these sites are usually occupied by Cu atoms.     

Development of the cyclic cluster model formalism for Kohn-Sham auxiliary density functional theory methods

The development of the cyclic cluster model (CCM) formalism for Kohn-Sham auxiliary density functional theory (KS-ADFT) methods is presented. The CCM is a direct space approach for the calculation of perfect and defective systems under periodic boundary conditions. Translational symmetry is introduced in the CCM by integral weighting. A consistent weighting scheme for all two-center and three-center interactions appearing in the KS-ADFT method is presented. For the first time, an approach for the numerical integration of the exchange-correlation potential within the cyclic cluster formalism is derived. The presented KS-ADFT CCM implementation was applied to covalent periodic systems. The results of cyclic and molecular cluster model (MCM) calculations for trans-polyacetylene, graphene, and diamond are discussed as examples for systems periodic in one, two, and three dimensions, respectively. All structures were optimized. It is shown that the CCM results represent the results of MCM calculations in the limit of infinite molecular clusters. By analyzing the electronic structure, we demonstrate that the symmetry of the corresponding periodic systems is retained in CCM calculations. The obtained geometric and electronic structures are compared with available data from the literature.     

Analysis of the bond‐valence method for calculating 29Si and 31P magnetic shielding in covalent network solids

²⁹Si and ³¹P magnetic‐shielding tensors in covalent network solids have been evaluated using periodic and cluster‐based calculations. The cluster‐based computational methodology employs pseudoatoms to reduce the net charge (resulting from missing co‐ordination on the terminal atoms) through valence modification of terminal atoms using bond‐valence theory (VMTA/BV). The magnetic‐shielding tensors computed with the VMTA/BV method are compared to magnetic‐shielding tensors determined with the periodic GIPAW approach. The cluster‐based all‐electron calculations agree with experiment better than the GIPAW calculations, particularly for predicting absolute magnetic shielding and for predicting chemical shifts. The performance of the DFT functionals CA‐PZ, PW91, PBE, rPBE, PBEsol, WC, and PBE0 are assessed for the prediction of ²⁹Si and ³¹P magnetic‐shielding constants. Calculations using the hybrid functional PBE0, in combination with the VMTA/BV approach, result in excellent agreement with experiment. © 2016 Wiley Periodicals, Inc.     

MSINDO study of water adsorption on NiO surfaces

The dissociation of water adsorbed on the surface of NiO was investigated by using the semi-empirical SCF MO method MSINDO. Simulations were based on embedded cluster models representing the (100) surface, with and without a monatomic step. The angle formed between the metal adsorption site and the O–H bond associated with water has been found to be critical to the energetics of the dissociation process. Based on this criterion, it was shown that water dissociation is favorable on the stepped surface, but highly unlikely on the planar surface. In addition, the activation energy required for water dissociation in a monatomic NiO step was considerably lower than for dissociation at the planar surface. The high activation energy associated with water dissociation on the planar surface is attributed to the rigidity of the NiO lattice. Dedicated to Prof. K. Jug in honor of his 65th birthday     

Toward an understanding of the formation of vanadia-titania catalysts

Structures of hydrated vanadia species on the TiO2-anatase surfaces were investigated using the semiempirical molecular orbital method MSINDO. The (101), (001), and (100) surfaces of anatase were considered. They were modeled by appropriate two-dimensional cyclic clusters of TiO2. Monomeric and dimeric hydrated vanadia species on the anatase surfaces were simulated by adsorbing VO4H3 and V2O7H4 molecules, respectively. Different adsorption structures were considered, and their stabilities at 300 and 600 K were tested by constant-temperature Born-Oppenheimer molecular dynamics simulations in the framework of MSINDO. Structural features of the vanadia-titania catalysts found in extended X-ray absorption fine structure, secondary ion mass spectrometry, IR, Raman, and NMR spectroscopy and conductivity experiments can be explained by the present calculations.     

Theoretical analysis on TiO2(110)/V surface

Theoretical analysis based on the Hartree–Fock method were performed in order to study the stoichiometric TiO₂ (110) surface and the vanadium substituted system. The Pople with polarization 3‐21G* basis set level was used. The TiO₂ (110) surface was modeled using a (TiO₂)₁₅ cluster model. In order to take into account the finite size of the cluster, we have studied two different models: the point charge and the hydrogen saturated methodologies. The charge values used in the point charge calculations were optimized. The density of states, orbital self‐consistend field (SCF) energies, and Mulliken charge values were analyzed. The method and model's dependence on the analyzed results are discussed. The theoretical results are compared with available experimental data. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001     

Consistent modifications of SINDO1: I. Approximations and parameters

A consistent modification, MSINDO, of the semiempirical MO method SINDO1 is presented. Different basis sets are used for one- and two-center interactions. The treatment of the core matrix elements in the nonorthogonal basis is retained with changes only for hydrogen and 3d orbitals. Orthogonalization corrections are now restricted to nonvanishing core matrix elements in the INDO approximation. The set of atomic parameters is increased, but bond parameters are no longer used. An automatic nonlinear least-squares algorithm with a restricted step constraint is used for the optimization of parameters. Heats of formation are adjusted with inclusion of zero-point energies obtained by a scaling procedure of the force constant matrix. The present version MSINDO provides significant improvements over previous versions. A brief comparison for ground-state properties of the elements H, C, N, O, F, and Na to Cl is given. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 563–571, 1999     

Conductor‐like screening model for relaxed excited states: Implementation in the semiempirical method MSINDO

Two approaches to treat solvent polarization and reorientation effects for excited states of molecules and surfaces have been implemented in the recently developed MSINDO‐sCIS method (Gadaczek, Krause, Hintze, Bredow, J. Chem. Theory Comput. 2011, 7, 3675). They allow for an efficient calculation of analytical energy gradients and hence open the opportunity to investigate fluorescence effects or photochemical reactions in solution for large molecules that are difficult to treat with high‐level methods. Both approaches are based on the conductor‐like screening model (COSMO) (Klamt and Schüürmann, J. Chem. Soc., Perkin Trans. 1993, 2, 799) in combination with the configuration interaction singles (CIS) method (Foresman, Head‐Gordon, Pople, and Frisch, J. Phys. Chem. 1992, 96, 135). The paper gives a brief outline of the theoretical background. As a first application, solvent shifts of three well‐studied, environment‐sensitive fluorescent dyes (Kucherak, Didier, Mély, and Klymchenko, J. Phys. Chem. Lett. 2010, 1, 616) have been calculated and compared with experimental results and standard time‐dependent density functional theory. A statistical evaluation of MSINDO‐COSMO‐sCIS is provided for a set of 39 molecules suggested recently by Jacquemin et al. (Jacquemin, Planchat, Adamo, and Mennucci, J. Chem. Theory Comput. 2012, 8, 2359). Calculated vertical and adiabatic excitation energies and fluorescence energies are compared to experimental data. © 2014 Wiley Periodicals, Inc.     

Quasiclassical trajectory study of the O(3P) + CH4 --> OH + CH3 reaction with a specific reaction parameters semiempirical Hamiltonian

We present a theoretical study of the O(3P) + CH4 --> OH + CH3 reaction using electronic structure, kinetics, and dynamics calculations. We calculate a grid of ab initio points at the PMP2/AUG-cc-pVDZ level to characterize the potential energy surface in regions of up to 1.3 eV above reagents. This grid of ab initio points is used to derive a set of specific reaction parameters (SRP) for the MSINDO semiempirical Hamiltonian. The resulting SRP-MSINDO Hamiltonian improves the quality of the standard Hamiltonian, particularly in regions of the potential energy surface beyond the minimum-energy reaction path. Quasiclassical-trajectory calculations are used to study the reaction dynamics with the original and the improved MSINDO semiempirical Hamiltonians, and a prior surface. The SRP-MSINDO semiempirical Hamiltonian yields OH rotational distributions in agreement with experimental results, improving over the results of the other surfaces. Thermal rate constants estimated with Variational Transition State Theory using the SRP-MSINDO Hamiltonian are also in agreement with experiments. Our results indicate that reparametrized semiempirical Hamiltonians are a good alternative to generating potential energy surfaces for accurate dynamics studies of polyatomic reactions.     

Revisiting the calculation of (13)C chemical shift tensors in cadmium acetate dihydrate with EIM and EIM/cluster methods

The chemical shift tensors of the acetate anions in cadmium acetate dihydrate are calculated using a cluster approach, the embedded ion method (EIM), and a combination of the two in the EIM/cluster method. The results of these calculations are compared with those completed on the isolated acetate anion and show the need for the inclusion of intermolecular interactions. The RMS difference between experiment and theory improves from over 60 ppm when the calculation is completed on an isolated anion, to below 10 ppm when interactions to nearby atoms are included. The best cluster model includes three cadmium acetate dihydrate and gives an RMS result of 4.4 ppm. The EIM method, which uses point charges to account for the intermolecular effects, achieves an RMS of 7.7 ppm on individual anions alone. A combination of the two, the EIM/cluster method, shows that the only necessary atom to explicitly add is the nearest cadmium; this addition results in an RMS of 4.1 ppm. These results are also discussed in terms of the computational cost of the different calculations.     

Assessing Solvation Effects on Chemical Reactions with Globally Optimized Solvent Clusters

We have examined the influence of water solvent on the Menshutkin reaction of methyl chloride with ammonia by performing static, quantum chemical calculations. We have employed large, explicit, and globally structure‐optimized water clusters around the reaction center, in a mixed explicit/implicit solvent model. This approach deliberately deviates from attempts to capture the most likely solvent‐molecule distribution around a reaction center. Instead, it explores extremes on the scale of rearrangement speed in terms of the surrounding solvent cluster, relative to the reaction progress itself. A comparison to traditional theoretical and experimental results enables us to quantify the energy penalty that is induced by the inability of the water cluster to instantaneously and completely follow the reaction progress. In addition, the influence of water clusters on the reaction energy profile can be much larger than merely changing it somewhat. Certain clusters can completely annihilate the sizeable activation barrier of 23.5 kcal mol^?1.     

A Unique Tryptophan C‐Prenyltransferase from the Kawaguchipeptin Biosynthetic Pathway

Cyanobactins are a rapidly growing family of linear and cyclic peptides produced by cyanobacteria. Kawaguchipeptins A and B, two macrocyclic undecapeptides reported earlier from Microcystis aeruginosa NIES‐88, are shown to be products of the cyanobactin biosynthetic pathway. The 9 kb kawaguchipeptin (kgp) gene cluster was identified in a 5.26 Mb draft genome of Microcystis aeruginosa NIES‐88. We verified that this gene cluster is responsible for the production of the kawaguchipeptins through heterologous expression of the kgp gene cluster in Escherichia coli. The KgpF prenyltransferase was overexpressed and was shown to prenylate C‐3 of Trp residues in both linear and cyclic peptides in vitro. Our findings serve to further enhance the structural diversity of cyanobactins to include tryptophan‐prenylated cyclic peptides.     

Importance of structural motifs in liquid hydrogen fluoride

The investigation of liquid phases by means of accurate electronic structure methods is a demanding task due to the high computational effort. We applied second-order M?ller-Plesset perturbation theory and high-level quantum chemical calculations using the coupled-cluster method with single, double and perturbative triple excitations in combination with Dunnings correlation-consistent basis sets up to quintuple ζ quality. Based on these calculations, we extrapolated the correlation energy to the basis set limit in order to improve the results even further. For comparison to the correlated electronic structure methods, density functional calculations employing different functionals are presented as well. The investigated species are a cyclic pentamer as well as a set of branched structures. The quantum cluster equilibrium method is employed for the investigation of the liquid-phase structure of hydrogen fluoride. The pentamer is found to be present to a high extent and in the case of the MP2/QZVP data, its presence improves the results significantly. Accounting for branched structures slightly improves results, so that they are found to be present but not to dominate in liquid hydrogen fluoride. Concerning both the interaction energy and the result of the quantum cluster equilibrium calculation the basis set has a major influence, whereas the difference between M?ller-Plesset perturbation theory and coupled-cluster calculations is less pronounced.     

An ab initio study of water clusters in gas phase and bulk aqueous media: (H2O)n,n=1–12

Geometries of several clusters of water molecules including single minimum energy structures of n‐mers (n=1–5), several hexamers and two structures of each of heptamer to decamer derived from hexamer cage and hexamer prism were optimized. One structural form of each of 11‐mer and 12‐mer were also studied. The geometry optimization calculations were performed at the RHF/6‐311G* level for all the cases and at the MP2/6‐311++G** level for some selected cases. The optimized cluster geometries were used to calculate total energies of the clusters in gas phase employing the B3LYP density functional method and the 6‐311G* basis set. Frequency analysis was carried out in all the cases to ensure that the optimized geometries corresponded to total energy minima. Zero‐point and thermal free energy corrections were applied for comparison of energies of certain hexamers. The optimized cluster geometries were used to solvate the clusters in bulk water using the polarized continuum model (PCM) of the self‐consistent reaction field (SCRF) theory, the 6‐311G* basis set, and the B3LYP density functional method. For the cases for which MP2/6‐311++G** geometry optimization was performed, solvation calculations in water were also carried out using the B3LYP density functional method, the 6‐311++G** basis set, and the PCM model of SCRF theory, besides the corresponding gas‐phase calculations. It is found that the cage form of water hexamer cluster is most stable in gas phase among the different hexamers, which is in agreement with the earlier theoretical and experimental results. Further, use of a newly defined relative population index (RPI) in terms of successive total energy differences per water molecule for different cluster sizes suggests that stabilities of trimers, hexamers, and nonamers in gas phase and those of hexamers and nonamers in bulk water would be favored while those of pentamer and decamer in both the phases would be relatively disfavored. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 81: 90–104, 2001