Computer simulation study of water using a fluctuating charge model

Hydrogen bonding in small water clusters is studied through computer simulation methods using a sophisticated, empirical model of interaction developed by Ricket al (S W Rick, S J Stuart and B J Berne 1994J. Chem. Phys. 101 6141) and others. The model allows for the charges on the interacting sites to fluctuate as a function of time, depending on their local environment. The charge flow is driven by the difference in the electronegativity of the atoms within the water molecule, thus effectively mimicking the effects of polarization of the charge density. The potential model is thus transferable across all phases of water. Using this model, we have obtained the minimum energy structures of water clusters up to a size often. The cluster structures agree well with experimental data. In addition, we are able to distinctly identify the hydrogens that form hydrogen bonds based on their charges alone, a feature that is not possible in simulations using fixed charge models. We have also studied the structure of liquid water at ambient conditions using this fluctuating charge model.     

Dipolar and electronic effects on charge transport through single transition metal complexes

Charge transport through single molecular neutral monoand di-cobalt(II) complexes with π-conjugated macromolecular wire was investigated.Scanning tunnelling spectroscopy (STS) studies revealed that the mono-cobalt(II) complex showed a pronounced rectifying effect with a large rectification ratio and finely featured NDR peaks,while the di-cobalt(II) complex showed a relatively symmetric electron transport without clear NDR peaks.Th     

Bending crystals. Solid state photomechanical properties of transition metal complexes containing semiquinonate ligands

The properties of transition metal complexes containing catecholate and radical semiquinonate ligands have often been found to be unusual and unexpected. Crystals of Rh(CO)₂(3,6-DBSQ), containing the 3,6-di-tert-butyl-1,2-semiquinonate ligand, form as long thin needles that are observed to bend reversibly upon irradiation with NIR light. Crystallographic characterization reveals a stacked solid state lattice with planar molecules aligned with metal atoms atop one another. Electronic spectra recorded in the solid state and in solution show an intense band at 1600 nm that maps the energy dependence of crystal bend angle. The transition is a property of the stacked assembly, rather than of an individual complex molecule, and appears associated with an MLCT process that transfers charge from an antibonding band formed by interacting Rhd _z ² orbitals to the vacant quinone π* orbital. Related observations have been made on the [Co(μ-pyz)(3,6-DBSQ)(3,6-DBCat)]_npolymer. Photomechanical properties appear associated with electronic transitions that lead to a physical change in axial length of a linear polymer, coupled with a soft solid state lattice that permits axial contraction/expansion without crystal fracture.     

Pyridine-type complexes of transition metal halides

Formation of nitrogen ligated complexes of types NiL₆X₂, NiL₄X₂, NiL₂X₂ and NiL₁X₂ (whereL=pyridine, 2-, 3- and 4-methyl-pyridine andX=F, Cl, Br, I) have been studied by traditional preparative methods, i.e. from solutions and by solid-gas phase chemisorption. Quaternary mixed complexes were obtained by chemisorption from heated intermediates. The complexes thus formed were further analysed by simultaneous TG-DTG-DTA. Effects of the ligands on stoichiometry and thermal properties of the complexes are discussed.     

Quantum mechanics/fluctuating charge calculations for absorption spectra of aqueous green fluorescent protein chromophore

We applied the quantum mechanics/fluctuating charges (QM/FQ) method to simulate the absorption spectra of three protonated forms of p-hydroxybenzylidene imidazolone (p-HBDI) in water. Configurations of solute-solvent were generated from molecular dynamics (MD) simulation within the context of a hybrid scheme in which solute and solvents were treated at QM and molecular mechanics, respectively. Nonperiodic spherical boundary condition was used. To examine the influence on simulated spectra coming from the geometrical relaxation of solute, the MD simulations were carried out for two cases: frozen and flexible molecular geometry of solute. As a result of our calculations, the simulations using the flexible solute's structure delivered vertical excitation energies closer to experimental data than those of a frozen solute, especially for the neutral case. For spectral broadening, changing from fixed geometry of solute to a flexible one led to a significant increase for both neutral and anionic forms of p-HBDI, but no effect happened for the cationic one.     

Application of the NDDO method to transition metal compounds

The NDDO method has been extended to include elements withd-orbitals. A parametrization for the first-row transition metals is given, which has been worked out to describe structural properties of transition metal complexes. Applications of the method to the Jahn-Teller distortions of tetrachloro complexes are presented. The NDDO results are compared with those from CNDO and INDO calculations. It turns out that the NDDO method seems to be the most sensitive among the ZDO procedures.     

Structures of large transition metal clusters

The present review surveys the results of X-ray diffraction studies of large stoichiometric transition metal clusters containing from 20 to 145 atoms in metal cores surrounded by ligand shells (72 compounds). Structures of such clusters have fragments of close packings (face-centered cubic (f.c.c.), hexagonal close (h.c.p.), and body-centered cubic (b.c.c.) packings) characteristic of crystalline bulk metals as well as mixed packings (f.c.c./h.c.p.), local close packings with pentagonal symmetry, and strongly distorted amorphous packings. The observed packing types, their distortions, and the relationship between the atomic structures of metal cores and the atomic radial distribution functions (RDF) are discussed. The structural principles established for the large clusters are applied to analysis of the experimental RDF for metal nanoparticles determined by X-ray diffraction and EXAFS spectroscopy.     

A comparison of bismuth- and antimony-containing transition metal cluster complexes

In recent years a number of transition metal clusters which incorporate bismuth and antimony have been reported. The structures and reaction chemistry of these complexes are compared.     

Valence charge concentrations, electron delocalization and beta-agostic bonding in d0 metal alkyl complexes

In this paper we describe a range of model d(0) metal ethyl compounds and related complexes, studied by DFT calculations and high resolution X-ray diffraction. The concept of ligand-opposed charge concentrations (LOCCs) for d(0) metal complexes is extended to include both cis-and trans-ligand-induced charge concentrations (LICCs) at the metal, which arise as a natural consequence of covalent metal-ligand bond formation in transition metal alkyl complexes. The interplay between locally induced sites of increased Lewis acidity and an ethyl ligand is crucial to the development of a beta-agostic interaction in d(0) metal alkyl complexes, which is driven by delocalization of the M-C bonding electrons. Topological analysis of theoretical and experimental charge densities reveals LICCs at the metal atom, and indicates delocalization of the M-C valence electrons over the alkyl fragment, with depletion of the metal-directed charge concentration (CC) at the alpha-carbon atom, and a characteristic ellipticity profile for the C(alpha)-C(beta) bond. These ellipticity profiles and the magnitude of the CC values at C(alpha) and C(beta) provide experimentally observable criteria for assessing quantitatively the extent of delocalization, with excellent agreement between experiment and theory. Finally, a concept is proposed which promises systematic control of the extent of C-H activation in agostic complexes.     

An Anderson impurity model for efficient sampling of adiabatic potential energy surfaces of transition metal complexes

We present a model intended for rapid sampling of ground and excited state potential energy surfaces for first-row transition metal active sites. The method is computationally inexpensive and is suited for dynamics simulations where (1) adiabatic states are required "on-the-fly" and (2) the primary source of the electronic coupling between the diabatic states is the perturbative spin-orbit interaction among the 3d electrons. The model Hamiltonian we develop is a variant of the Anderson impurity model and achieves efficiency through a physically motivated basis set reduction based on the large value of the d-d Coulomb interaction U(d) and a Lanczos matrix diagonalization routine to solve for eigenvalues. The model parameters are constrained by fits to the partial density of states obtained from ab initio density functional theory calculations. For a particular application of our model we focus on electron transfer occurring between cobalt ions solvated by ammonium, incorporating configuration interaction between multiplet states for both metal ions. We demonstrate the capability of the method to efficiently calculate adiabatic potential energy surfaces and the electronic coupling factor we have calculated compares well to previous calculations and experiment. (     

Crystal structures and Hirshfeld surface analysis of transition‐metal complexes of 1,3‐azolecarboxylic acids

The crystal structures of five new transition‐metal complexes synthesized using thiazole‐2‐carboxylic acid (2‐Htza), imidazole‐2‐carboxylic acid (2‐H₂ima) or 1,3‐oxazole‐4‐carboxylic acid (4‐Hoxa), namely diaquabis(thiazole‐2‐carboxylato‐κ²N,O)cobalt(II), [Co(C₄H₂NO₂S)₂(H₂O)₂], 1 , diaquabis(thiazole‐2‐carboxylato‐κ²N,O)nickel(II), [Ni(C₄H₂NO₂S)₂(H₂O)₂], 2 , diaquabis(thiazole‐2‐carboxylato‐κ²N,O)cadmium(II), [Cd(C₄H₂NO₂S)₂(H₂O)₂], 3 , diaquabis(1H‐imidazole‐2‐carboxylato‐κ²N³,O)cobalt(II), [Co(C₄H₂N₂O₂)₂(H₂O)₂], 4 , and diaquabis(1,3‐oxazole‐4‐carboxylato‐κ²N,O⁴)cobalt(II), [Co(C₄H₂NO₃)₂(H₂O)₂], 5 , are reported. The influence of the nature of the heteroatom and the position of the carboxyl group in relation to the heteroatom on the self‐assembly process are discussed based upon Hirshfeld surface analysis and used to explain the observed differences in the single‐crystal structures and the supramolecular frameworks and topologies of complexes 1 – 5 .     

Thermal analysis study of some transition metal complexes by TG and DSC methods

The thermodynamic and thermal properties of [Cu(L)₂·Cl₂], [Ni(L)₂]·Cl₂, [Co(L)₂·Cl₂]; L=1,2-bis(o-aminophenoxy)ethane (BAFE), complexes have been investigated. The thermal decomposition of the complexes took place in two distinct steps in endothermic reaction up to 700°C. The activation energy E, the entropy change S ^#, enthalpy H change and Gibbs free energy change G ^# were calculated from the results of thermogravimetry analysis (TG) and heat capacity from the results of differential scanning calorimetry (DSC). It was found that the thermal stabilities and activation energies of the complexes follow the order Ni(II)>Cu(II)>Co(II) and E _Co<E _Ni<E _Cu, respectively.This revised version was published online in November 2005 with corrections to the Cover Date.     

Valence state parameters of all transition metal atoms in metalloproteins—development of ABEEMσπ fluctuating charge force field

To promote accuracy of the atom‐bond electronegativity equalization method (ABEEMσπ) fluctuating charge polarizable force fields, and extend it to include all transition metal atoms, a new parameter, the reference charge is set up in the expression of the total energy potential function. We select over 700 model molecules most of which model metalloprotein molecules that come from Protein Data Bank. We set reference charges for different apparent valence states of transition metals and calibrate the parameters of reference charges, valence state electronegativities, and valence state hardnesses for ABEEMσπ through linear regression and least square method. These parameters can be used to calculate charge distributions of metalloproteins containing transition metal atoms (Sc‐Zn, Y‐Cd, and Lu‐Hg). Compared the results of ABEEMσπ charge distributions with those obtained by ab initio method, the quite good linear correlations of the two kinds of charge distributions are shown. The reason why the STO‐3G basis set in Mulliken population analysis for the parameter calibration is specially explained in detail. Furthermore, ABEEMσπ method can also quickly and quite accurately calculate dipole moments of molecules. Molecular dynamics optimizations of five metalloproteins as the examples show that their structures obtained by ABEEMσπ fluctuating charge polarizable force field are very close to the structures optimized by the ab initio MP2/6–311G method. This means that the ABEEMσπ/MM can now be applied to molecular dynamics simulations of systems that contain metalloproteins with good accuracy. © 2014 Wiley Periodicals, Inc.     

Electrochemical synthesis and properties of δ-fluoroacyl and δ-perfluoroalkyl transition metal complexes

The electrochemical synthesis of δ-fluoroacyl complexes [M]-δ-COR_f(M=C₅H₅(CO)₃W or (CO)₅Mn; R_f=CF₃ or C₄F₉) was performed according to two procedures: (1) the preliminary electrochemical synthesis of [M]⁻ from [M]₂ followed by reaction with a fluorine-containing compound and (2) the electrochemical synthesis of [M]⁻ in the presence of a fluorine-containing compound. Trifluoroacetic anhydride was demonstrated to be the best acylating agent in these reactions. The electrochemical properties of the resulting complexes were studied. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 2, pp. 373–375, February, 2000.     

Fast,efficient generation of high‐quality atomic charges. AM1‐BCC model: I. Method

The AM1‐BCC method quickly and efficiently generates high‐quality atomic charges for use in condensed‐phase simulations. The underlying features of the electron distribution including formal charge and delocalization are first captured by AM1 atomic charges for the individual molecule. Bond charge corrections (BCCs), which have been parameterized against the HF/6‐31G* electrostatic potential (ESP) of a training set of compounds containing relevant functional groups, are then added using a formalism identical to the consensus BCI (bond charge increment) approach. As a proof of the concept, we fit BCCs simultaneously to 45 compounds including O‐, N‐, and S‐containing functionalities, aromatics, and heteroaromatics, using only 41 BCC parameters. AM1‐BCC yields charge sets of comparable quality to HF/6‐31G* ESP‐derived charges in a fraction of the time while reducing instabilities in the atomic charges compared to direct ESP‐fit methods. We then apply the BCC parameters to a small “test set” consisting of aspirin, d ‐glucose, and eryodictyol; the AM1‐BCC model again provides atomic charges of quality comparable with HF/6‐31G* RESP charges, as judged by an increase of only 0.01 to 0.02 atomic units in the root‐mean‐square (RMS) error in ESP. Based on these encouraging results, we intend to parameterize the AM1‐BCC model to provide a consistent charge model for any organic or biological molecule. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 132–146, 2000     

Computational mechanistic studies of acceptorless dehydrogenation reactions catalyzed by transition metal complexes

Acceptorless dehydrogenation (AD) that uses non-toxic reagents and produces no waste is a type of catalytic reactions toward green chemistry. Acceptorless alcohol dehydrogenation (AAD) can serve as a key step in constructing new bonds such as C-C and C-N bonds in which alcohols need to be activated into more reactive ketones or aldehydes. AD reactions also can be utilized for hydrogen production from biomass or its fermentation products (mainly alcohols). Reversible hydrogenation/ dehy-drogenation with hydrogen uptake/release is crucial to realization of the potential organic hydride hydrogen storage. In this article, we review the recent computational mechanistic studies of the AD reactions catalyzed by various transition metal complexes as well as the experimental developments. These reactions include acceptorless alcohol dehydrogenations, reversible dehydrogenation/hydrogenation of nitrogen heterocycles, dehydrogenative coupling reactions of alcohols and amines to construct C-N bonds, and dehydrogenative coupling reactions of alcohols and unsaturated substrates to form C-C bonds. For the catalysts possessing metal-ligand bifunctional active sites (such as 28, 45, 86, 87, and 106 in the paper), the dehydrogenations prefer the "bifunctional double hydrogen transfer" mechanism rather than the generally accepted-H elimination mechanism. However, methanol dehydrogenation involved in the C-C coupling reaction of methanol and allene, catalyzed by the iridium complex 121, takes place via the-H elimination mechanism, because the Lewis basicity of either the-allyl moiety or the carboxyl group of the ligand is too weak to exert high Lewis basic reactivity. Unveiling the catalytic mechanisms of AD reactions could help to develop new catalysts.     

Interaction of vinylpyridines with 1,3-dienes catalyzed by transition metal complexes

The linear and cyclic cooligomerization of 2-vinyl-, 2-methyl-5-vinyl-, and 4-vinylpyridines with 1,3-dienes and trienes catalyzed by complexes of transition metals (Fe, Co, Ni, Mn, Cr, Pd, Ru, Rh, and Zr) was carried out to give unsaturated pyridines containing alkenyl and cycloalkenyl substituents.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 5, pp. 916–921, May, 1993.     

Designed synthesis for some transition metal clusters involving bridging-sulfido ligand

Designed synthesis for some transition metal clusters involving bridging-sulfido ligands is reviewed. The basic concept with the use of reactive fragments as building blocks is described. It is shown that the sulfido ligands with lone-pair electrons and the unsaturated coordination sites play important roles in this rational synthesis. The relationship between the metallic coordination types of the sulfido ligands and their assembling activity in the compounds is summarized. Examples of the six kinds of unit construction with reactive fragments as building blocks are shown, indicating clearly that the unit construction is a reasonable way in the synthesis of transition metal clusters involving bridging sulfido ligands. Finally, the potential application of the unit construction schemes in the synthesis of transition metal clusters involving other bridging ligands is presented.     

Electron correlation in weakly coupled transition metal dimers: Bimetallocenylenes and bimetallocenes

The Hartree-Fock (HF) instabilities in a series of bimetallocenes (1) and bimetallocenylenes (2) with Fe, Co, Ni and Cr as 3d centers have been investigated by means of a semiempirical INDO Hamiltonian. The HF picture is only valid in the case of the iron dimers. Strong correlation effects are encountered in the Co, Ni and Cr complexes. The necessary conditions for singlet, non-singlet (triplet) and non-real variations of the HF orbitals are discussed in detail. Singlet fluctuations are the result of intraatomic angular correlation (short-range) at each 3d center. The violation of the spin symmetry corresponds to a long-range interaction between the transition metal centers. Only for MOs with large 3d _xz amplitudes there exists a channel for the interatomic spin decoupling. Consequences for polymetallocenes are shortly discussed.