Global optimization of clusters using electronic structure methods

Over the past decade, there has been a significant growth in the development and application of methods for performing global optimization (GO) of cluster and nanoparticle structures using first‐principles electronic structure methods coupled to sophisticated search algorithms. This has in part been driven by the desire to avoid the use of empirical potentials (EPs), especially in cases where no reliable potentials exist to guide the search toward reasonable regions of configuration space. This has been facilitated by improvements in the reliability of the search algorithms, increased efficiency of the electronic structure methods, and the development of faster, multiprocessor high‐performance computing architectures. In this review, we give a brief overview of GO algorithms, though concentrating mainly on genetic algorithm and basin hopping techniques, first in combination with EPs. The major part of the review then deals with details of the implementation and application of these search methods to allow exploration for global minimum cluster structures directly using electronic structure methods and, in particular, density functional theory. Example applications are presented, ranging from isolated monometallic and bimetallic clusters to molecular clusters and ligated and surface supported metal clusters. Finally, some possible future developments are highlighted. © 2013 Wiley Periodicals, Inc.     

Investigation of surface topography, morphology and structure of amorphous carbon films by AFM and TEM

Morphology and structure of amorphous carbon films deposited with a pulsed arc source (LASER-ARC) have been studied using microscopical methods (SEM, TEM and AFM), electron diffraction and spectroscopical investigation (EELS). The parameters of the arc source and the deposition conditions (substrate temperature) influence morphology and structure of deposited amorphous carbon films. Especially the incorporation and growth of particles, embedded in the film have been investigated. By particle analysis using an optical microscope a majority of particles that is smaller than 500 nm has been determined. The morphology has been also demonstrated similar by AFM and TEM images. Their number and size of particles is strongly influenced by the deposition temperature. The structure of amorphous film is characterized by the EELS-spectra, but the particle structure was not detectable.     

Structure and cation ordering in spinel-type TcCo2O4. An example of a trivalent technetium oxide

The structure of TcCo(2)O(4) has been determined using a combination of synchrotron X-ray and neutron powder diffraction methods. It has an inverse spinel structure where the Tc occupies the octahedral sites. Both the refined Tc-O distance and X-ray absorption spectra suggest the Tc is predominantly trivalent.     

Structural studies of the Klebsiella type 57 capsular polysaccharide.

The structure of the capsular polysaccharide from Klebsiella type 57 has been investigated. Methylation analysis, uronic acid degradation, modified Smith degradation and graded acid hydrolysis were the principle methods used. Pure oligomeric fragments were isolated using the three methods of degradation and characterized by chemical and physical methods. These studies show the structure to consist of a tetrasaccharide repeating unit (all sugar residues have the D-configuration and are pyranosidic).     

A comparative study of various computational approaches in calculating the structure of pyridoxal 5'-phosphate (PLP)-dependent beta-lyase protein. The importance of protein environment

Various computational approaches, using molecular mechanics (Amber), semiempirical (AM1), density functional (B3LYP), and various ONIOM methods, have been comparatively investigated for the structure of Escherichia coli NifS CsdB protein. The structure of the entire monomer containing 407 amino acid residues and 579 surrounding water molecules has been optimized. The full geometry optimization in the "active site-only" approach (including only active site atoms) has been found to give the largest root-mean-square (RMS) deviation from the X-ray structure; a much better agreement has been achieved by keeping the atoms leading to the backbones of some amino acids frozen in their positions in the X-ray structure. The best agreement has been attained by including the surrounding protein in the calculations using the two-layer ONIOM (B3LYP:Amber) approach. The results presented in this study conclusively demonstrate the importance of the protein/active-site interaction on the active-site structure of the enzyme. The present theoretical study represents the largest system studied at the ONIOM level to date, containing 7992 atoms, including 84 atoms in the QM region and rest in the MM region.     

The molecular structure of [Sn(P2C2But2)] using gas-phase electron diffraction and DFT calculations

The molecular structure of 2,4-di-tert-butyl-eta4-1,3-diphosphacyclobutadiene tin has been determined in the gas phase by electron diffraction using both the DYNAMITE and SARACEN methods. The suitability of many different theoretical methods for the calculation of structures of half-sandwich main-group metal complexes has been investigated, and, by comparison of the results with the experimental structures, suggestions have been made as to the most suitable methods for this class of compound.     

Dynamic interaction of theory and experiment: total determination of the gas-phase molecular structure of tri-tert-butylphosphine oxide (OPBut3)

A new method to aid the determination of structures of sterically crowded molecules in the gas phase by dynamically linking the gas-phase electron diffraction (GED) refinement process with computational methods has been developed. The procedure involves refining the heavy-atom skeleton of the molecule using the GED data while continually updating the light-atom positions during the refinement using computational methods, in this case molecular mechanics. This removes errors associated with the assumption of local symmetry for the light-atom groups, which can affect the final values of the heavy-atom parameters. The refinement of the molecular structure of tri-tert-butyl phosphine oxide has been used to illustrate this new technique, which we call the DYNAMITE (DYNAMic Interaction of Theory and Experiment) method. Re-examination of the structure using this method has resulted in a shorter P-O distance than was found in a less sophisticated anaylsis, and is consistent with the molecule being regarded as O=PBut3, rather than O(-)-P+But3.     

Driving Curie temperature towards room temperature in the half-metallic ferromagnet K2Cr8O16 by soft redox chemistry

The half-metallic ferromagnet K(2)Cr(8)O(16) with the hollandite structure has been chemically modified using soft chemistry methods to increase the average oxidation state of chromium. The synthesis of the parent material has been performed under high pressure/high temperature conditions. Following this, different redox reactions have been carried out on K(2)Cr(8)O(16). Oxidation to obtain potassium-de-inserted derivatives, K(2-x)Cr(8)O(16) (0 ≤x≤ 1), has been investigated with electrochemical methods, while the synthesis of sizeable amounts was achieved chemically by using nitrosonium tetrafluoroborate as a highly oxidizing agent. The maximum amount of extracted K ions corresponds to x = 0.8. Upon oxidation the hollandite structure is maintained and the products keep high crystallinity. The de-insertion of potassium changes the Cr(3+)/Cr(4+) ratio, and therefore the magnetic properties. Interestingly, the Curie temperature increases from ca. 175 K to 250 K, getting therefore closer to room temperature.     

Analysis of pair interaction in a bipolar mesogen 4‐(4‐hydroxylbutyloxy)‐4′‐cyano‐biphenyl: A comparative study based on semiempirical and DFT methods

Structure of 4‐(4‐hydroxylbutyloxy)‐4′‐cyano‐biphenyl (H4CBP) molecule has been optimized using density functional B3LYP with 6‐31G (d) basis set taking crystallographic geometry as input. Using the optimized geometry, electronic structure of the H4CBP molecule has been evaluated on the basis of semiempirical methods and DFT calculations. Intermolecular interaction energy between a pair of H4CBP molecules has been evaluated by using Rayleigh–Schrodinger perturbation theory modified with multicentered multipole expansion method for the electrostatic part while dispersion and repulsion terms have been calculated using Kitaigorodskii formula. The results obtained through semiempirical and DFT calculations have been compared for various interacting conditions, viz.: (a) stacking, (b) in‐plane, and (c) terminal interactions. A comparative analysis of the results has been carried out with a view to examine suitability of different methods to study molecular aggregations in moderately large organic systems. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Protein structure prediction aided by geometrical and probabilistic constraints

Database-assisted ab initio protein structure prediction methods have exhibited considerable promise in the recent past, with several implementations being successful in community-wide experiments (CASP). We have employed combinatorial optimization techniques toward solving the protein structure prediction problem. A Monte Carlo minimization algorithm has been employed on a constrained search space to identify minimum energy configurations. The search space is constrained by using radius of gyration cutoffs, the loop backbone dihedral probability distributions, and various secondary structure packing conformations. Simulations have been carried out on several sequences and 1000 conformations have been initially generated. Of these, 50 best candidates have then been selected as probable conformations. The search for the optimum has been simplified by incorporating various geometrical constraints on secondary structural elements using distance restraint potential functions. The advantages of the reported methodology are its simplicity, and modifiability to include other geometric and probabilistic restraints.     

The structure of nitrosoacetylene by ab initio methods

The geometrical structure of HCCNO has been calculated using ab initio SCF and GVB methods. Since it has not yet been prepared, attempts are made to predict spectroscopic constants related to its microwave, infrared and visible absorption spectra.     

Electronic structure of the alpha and beta isomers of [Mo(8)O(26)](4-)

The structure and bonding in alpha and beta octamolybdate anions have been investigated using density functional methods. In general, good computational-experimental agreement for the geometrical parameters has been obtained. The electronic structure of the anions has been probed with molecular orbital and Mulliken-Mayer methods. All Mo-O interactions have been found to be predominantly d(Mo)-p(O) in character. Several multicentered molecular orbitals can be described as sigma or pi closed-loop structures, but the proposed connection with the stability of the polyanions is not completely supported by the calculations. Mayer indexes correspond to fractional multiple character for terminal bonds and approximately single or low-order character for bridging bonds, in accordance with structural and bond valence results. The valency analysis has yielded similar overall bonding capacity for the various oxygen atoms. A distribution of the negative charge over all types of oxygen sites and metal charges considerably smaller than the formal oxidation states have been obtained from the Mulliken analysis.     

Structure elucidation of the intermediate in triethylborane-mediated radical addition of oxime ethers with 2D- and 3D-DOSY NMR

The structures of the components in the triethylborane-mediated radical addition reaction of oxime ether were investigated by 1H- and 3D-DOSY NMR methods. It has been impossible to physically separate the unstable intermediates; therefore, the structures were thus far unidentified. It has been possible to elucidate the structures of these unstable intermediates using Diffusion-Ordered Spectroscopy (DOSY) methods for the reaction in an NMR tube. The DOSY methods resolved the spectra of each starting compound, intermediate and product having different diffusion coefficients. The structure of the intermediate was shown to be due to the bonding of diethylborane to the nitrogen atom of the alkoxyamino group.     

Electronic Structure of (8,0) Gold Nanotubes

The electronic structure of (8,0) gold nanotubes have been studied using quantum field theory methods in the framework of the Hubbard model. An expression for the Fourier transform of the anticommutator Green function, the poles of which determine the energy spectrum of the system under consideration, has been derived. The energy spectrum demonstrates that the (8,0) gold nanotube has metal-like electronic structure. The peaks of the calculated density of states correspond to Van Hove singularities. The optical absorption spectrum is presented, and the energy of the first direct optical transition is 0.55 eV.     

Probing the pore wall structure of nanoporous carbons using adsorption

Hitherto, adsorption has been traditionally used to study only the porous structure in disordered materials, while the structure of the solid phase skeleton has been probed by crystallographic methods such as X-ray diffraction. Here we show that for carbons density functional theory, suitably adapted to consider heterogeneity of the pore walls, can be reliably used to probe features of the solid structure hitherto accessibly only approximately even by crystallographic methods. We investigate a range of carbons and determine pore wall thickness distributions using argon adsorption, with results corroborated by X-ray diffraction.     

Modification of the chitosan structure and properties using high-energy chemistry methods

Literature on the modification of the natural polymer chitosan using high-energy chemistry methods (treatment by a low-temperature plasma, with an electron beam, energetic ions, or γ-iradiation) has been surveyed. The basic chitosan treatment procedures and facilities used in the processes have been described. The instrumental techniques used to study changes in the chemical structure and properties of modified chitosan have been considered. Data showing the possibility of using modified chitosan in medicine and biotechnology have been presented.     

Predicting solubility of anthracene in non-aqueous solvent mixtures using a combination of Jouyban-Acree and Abraham models

Quantitative structure property relationships were proposed to calculate the binary interaction terms of the Jouyban-Acree model using coefficients of Abraham solvational models. The applicability of the proposed methods for reproducing solubility data of anthracene in binary solvents has been evaluated using 56 solubility data sets collected from the literature. The mean percentage deviation (MPD) of experimental and calculated solubilities, using predicted mole fraction solubility of anthracene in solvents 1 and 2, has been computed as a measure of accuracy and the MPD of the proposed methods were 5.5 and 4.2%. The accuracy of the method was compared with that of a previously reported method where the MPD was 14.4% and the mean differences between proposed and previous methods was statistically significant. To provide a predictive model, solubility of anthracene was computed using Abraham solvational models and employed to predict the solubility in binary solvents using derived model constants of Jouyban-Acree model and the obtained MPDs were 37.9 and 22.2%, respectively.     

Chlorine--benzene complexes--the reliability of density functionals for non-covalent radical complexes

The structure of the chlorine atom-benzene complex has been a topic of significant controversy for more than 50 years. We have reexamined the structure of this complex with new density functional methods especially designed for non-covalent complexes, and compared the structures and energetics to those obtained using standard DFT and high accuracy composite methods. We find that the popular B3LYP functional fails to identify stationary points revealed by other functionals, and that the eta(1)-sigma complex appears to be more stable than the eta(1)-pi complex, contrary to other recent work, highlighting the careful selection of methods required in non-covalent radical systems.     

Characterizing slow state near Si-SiO2 in MOS structure

The Equilibrium Voltage Step (EVS) technique has been used for extraction of depth and energy concentration profile of traps situated in the oxide of a lightly stressed metal-oxide-semiconductor (MOS) structure. This has been achieved up to the very near Si-SiO₂ interface. The results are discussed and compared with those obtained using charge pumping (CP) technique. A good agreement is achieved between the trap densities extracted using the two methods even though differences in the shape of the profiles can be observed. The results also very well agree with those published previously using current deep level transient spectroscopy (C-DLTS).     

Density functional theory study on the structure and vibrational frequencies of glycylglycine

Eleven possible conformers of glycylglycine have been studied by using the BLYP, B3LYP methods of density functional theory and the HF method at the basis set of 6-311++G**. BLYP (using Becke's and Lee-Yang-Parr's correlation functionals), ab initio Hartree-Fock (HF) and hybrid DFT/HF B3LYP calculations have been carried out to study the structure and vibrational spectra of glycylglycine. Glycylglycine crystal structure has been determined by X-ray diffraction analysis. The title compound has been crystallizes in the orthorhombic space group C1, with Z=4. And the unit cell parameters are: a=8.1184(12)A, b=9.5542(14)A, c=7.8192(11)A and V=577.95(15)A(3). Molecular conformation calculations have got 11 possible conformers. In these possible conformers, the most stable one has been selected. The BLYP/6-311++G** and scaled HF/6-311++G** frequencies correspond well with available experimental assignments of the normal vibrational modes. Comparison of the observed fundamental vibrational frequencies of glycylglycine and calculated results by density functional B3LYP and Hartree-Fock (HF) methods indicates that B3LYP is superior to the scaled Hartree-Fock (HF) for molecular vibrational issues.