The building blocks of metallothioneins: heterometallic Zn(2+) and Cd(2+) clusters from first-principles calculations.

Electronic structures of Zn(2+) and Cd(2+) thiolate clusters found in metallothioneins (MT) have been obtained using density functional theory. We have found that the inherent asymmetry of cluster architectures gives rise to seven distinct metal sites. Whereas the non-strained bond lengths of such tetrathiolate complexes are found to be 2.

Experimentally calibrated computational chemistry of tryptophan hydroxylase: trans influence, hydrogen-bonding, and 18-electron rule govern O2-activation.

Insight into the nature of oxygen activation in tryptophan hydroxylase has been obtained from density functional computations. Conformations of O(2)-bound intermediates have been studied with oxygen trans to glutamate and histidine, respectively. An O(2)-adduct with O(2)trans to histidine (O(his)) and a peroxo intermediate with peroxide trans to glutamate (P(glu)) were found to be consistent (0.

Accurate computed enthalpies of spin crossover in iron and cobalt complexes.

Despite their importance in many chemical processes, the relative energies of spin states of transition metal complexes have so far been haunted by large computational errors. By the use of six functionals, B3LYP, BP86, TPSS, TPSSh, M06, and M06L, this work studies nine complexes (seven with iron and two with cobalt) for which experimental enthalpies of spin crossover are available. It is shown that such enthalpies can be used as quantitative benchmarks of a functional's ability to balance electron correlation in both the involved states.

Metal-ligand bonds of second- and third-row d-block metals characterized by density functional theory.

This paper presents systematic data for 200 neutral diatomic molecules ML (M is a second- or third-row d-block metal and L = H, F, Cl, Br, I, C, N, O, S, or Se) computed with the density functionals TPSSh and BP86. With experimental structures and bond enthalpies available for many of these molecules, the computations first document the high accuracy of TPSSh, giving metal-ligand bond lengths with a mean absolute error of approximately 0.01 A for the second row and 0.

Peroxo-type intermediates in class I ribonucleotide reductase and related binuclear non-heme iron enzymes.

We have performed a systematic study of chemically possible peroxo-type intermediates occurring in the non-heme di-iron enzyme class Ia ribonucleotide reductase, using spectroscopically calibrated computational chemistry. Density functional computations of equilibrium structures, Fe-O and O-O stretch frequencies, Mossbauer isomer shifts, absorption spectra, J-coupling constants, electron affinities, and free energies of O(2) and proton or water binding are presented for a series of possible intermediates. The results enable structure-property correlations and a new rationale for the changes in carboxylate conformations occurring during the O(2) reaction of this class of non-heme iron enzymes.

Bioinorganic chemistry modeled with the TPSSh density functional.

In this work, the TPSSh density functional has been benchmarked against a test set of experimental structures and bond energies for 80 transition-metal-containing diatomics. It is found that the TPSSh functional gives structures of the same quality as other commonly used hybrid and nonhybrid functionals such as B3LYP and BP86. TPSSh gives a slope of 0.

Computational chemistry of modified [MFe3S4] and [M2Fe2S4] clusters: assessment of trends in electronic structure and properties.

The aim of this work is to understand the molecular evolution of iron-sulfur clusters in terms of electronic structure and function. Metal-substituted models of biological [Fe(4)S(4)] clusters in oxidation states [M(x)Fe(4-x)S(4)](3+/2+/1+) have been studied by density functional theory (M = Cr, Mn, Fe, Co, Ni, Cu, Zn, and Pd, with x = 1 or 2). Most of these clusters have not been characterized before.

Characterization of sodium stibogluconate by online liquid separation cell technology monitored by ICPMS and ESMS and computational chemistry.

High-performance liquid chromatography (HPLC), mass spectrometry (MS), and computational chemistry has been applied to resolve the composition and structure of the Sb species present in dilutions of Pentostam, a first-line treatment drug against Leishmania parasites. Using HPLC-inductively coupled plasma-MS and electrospray-MS, it was shown that the original drug consists of large Sb(V)-glyconate complexes of polymeric nature that degrade upon dilution. In dilution solution, the drug is a mixture of noncomplexed Sb(V), large polymeric complexes as well as several low molecular mass Sb(V)-glyconate complexes of various stoichiometry (1:1, 1:2, 1:3, 2:2, 2:3, 2:4, 3:3, 3:4).

Improved interaction potentials for charged residues in proteins.

Electrostatic interactions dominate the structure and free energy of biomolecules. To obtain accurate free energies involving charged groups from molecular simulations, OPLS-AA parameters have been reoptimized using Monte Carlo free energy perturbation. New parameters fit a self-consistent, experimental set of hydration free energies for acetate (Asp), propionate (Glu), 4-methylimidazolium (Hip), n-butylammonium (Lys), and n-propylguanidinium (Arg), all resembling charged residue side chains, including beta-carbons.

Polarization Effects for Hydrogen-Bonded Complexes of Substituted Phenols with Water and Chloride Ion.

Variations in hydrogen-bond strengths are investigated for complexes of nine para-substituted phenols (XPhOH) with a water molecule and chloride ion. Results from ab initio HF/6-311+G(d, p) and MP2/6-311+G(d, p)//HF/6-311+G(d, p) calculations are compared with those from the OPLS-AA and OPLS/CM1A force fields. In the OPLS-AA model, the partial charges on the hydroxyl group of phenol are not affected by the choice of para substituent, while the use of CM1A charges in the OPLS/CM1A approach does provide charge redistribution.

Accurate computation of reduction potentials of 4Fe-4S clusters indicates a carboxylate shift in Pyrococcus furiosus ferredoxin.

This work describes the computation and accurate reproduction of subtle shifts in reduction potentials for two mutants of the iron-sulfur protein Pyrococcus furiosus ferredoxin. The computational models involved only first-sphere ligands and differed with respect to one ligand, either acetate (aspartate), thiolate (cysteine), or methoxide (serine). Standard procedures using vacuum optimization gave qualitatively wrong results and errors up to 0.

Computational studies of modified [Fe3S4] clusters: why iron is optimal.

This work reports density functional computations of metal-substituted models of biological [Fe3S4] clusters in oxidation states [MFe2S4](+/0/-1) (M=Mn, Fe, Co, Ni, Cu, Zn, and Mo). Geometry optimization with a dielectric screening model is shown to provide a substantial improvement in structure, compared to earlier used standard procedures. The error for average Fe-S bonds decreased from 0.

Performance of density functionals for first row transition metal systems.

This article investigates the performance of five commonly used density functionals, B3LYP, BP86, PBE0, PBE, and BLYP, for studying diatomic molecules consisting of a first row transition metal bonded to H, F, Cl, Br, N, C, O, or S. Results have been compared with experiment wherever possible. Open-shell configurations are found more often in the order PBE0>B3LYP>PBE approximately BP86>BLYP.

Halide, Ammonium, and Alkali Metal Ion Parameters for Modeling Aqueous Solutions.

A complete set of Lennard Jones parameters for the halide ions, F(-), Cl(-), Br(-), and I(-), ammonium ion, and the alkali metal ions is reported. The parameters have been optimized using Monte Carlo simulations and free energy perturbation theory with the TIP4P water model to reproduce experimental free energies of hydration and locations of the first maxima of the ion-oxygen radial distribution functions, to provide water coordination numbers consistent with experimental ranges, and to exhibit gas-phase monohydrate energies in reasonable agreement with ab initio values. Average errors for absolute and relative free energies of hydration for the ions are ca.

The role of axial ligands for the structure and function of chlorophylls.

We have studied the effect of axial ligation of chlorophyll and bacteriochlorophyll using density functional calculations. Eleven different axial ligands have been considered, including models of histidine, aspartate/glutamate, asparagine/glutamine, serine, tyrosine, methionine, water, the protein backbone, and phosphate. The native chlorophylls, as well as their cation and anion radical states and models of the reaction centres P680 and P700, have been studied and we have compared the geometries, binding energies, reduction potentials, and absorption spectra.

Electronic structure of Cob(I)alamin: the story of an unusual nucleophile.

The electronic structure and the ligand-field spectrum of cobalt(I) corrin is reported using complete active space multiconfigurational perturbation theory (CASPT2) to address some inconsistencies and the nature of the cobalt(I) "supernucleophile", cob(I)alamin. An assignment of six of the seven intense lines in the experimental spectrum is obtained at a root-mean-square accuracy of 0.14 eV and largest error of 0.

The reaction mechanism of iron and manganese superoxide dismutases studied by theoretical calculations.

We have studied the detailed reaction mechanism of iron and manganese superoxide dismutase with density functional calculations on realistic active-site models, with large basis sets and including solvation, zero-point, and thermal effects. The results indicate that the conversion of O2- to O2 follows an associative mechanism, with O2- directly binding to the metal, followed by the protonation of the metal-bound hydroxide ion, and the dissociation of 3O2. All these reaction steps are exergonic.

Iron-sulfur clusters: why iron?

This communication addresses a simple question by means of density functional calculations: Why is iron used as the metal in iron-sulfur clusters? While there may be several answers to this question, it is shown here that one feature - the well-defined inner-sphere reorganization energy of self-exchange electron transfer - is very much favored in iron-sulfur clusters as opposed to metal substituted analogues of Mn, Co, Ni, and Cu. Furthermore, the conclusion holds for both 1Fe and 2Fe type iron-sulfur clusters. The results show that only iron provides a small inner-sphere reorganization energy of 21 kJ/mol in 1Fe (rubredoxin) and 46 kJ/mol in 2Fe (ferredoxin) models, whereas other metal ions exhibit values in the range 57-135 kJ/mol (1Fe) and 94-140 kJ/mol (2Fe).

How the Co-C bond is cleaved in coenzyme B12 enzymes: a theoretical study.

The homolytic cleavage of the organometallic Co-C bond in vitamin B12-dependent enzymes is accelerated by a factor of approximately 10(12) in the protein compared to that of the isolated cofactor in aqueous solution. To understand this much debated effect, we have studied the Co-C bond cleavage in the enzyme glutamate mutase with combined quantum and molecular mechanics methods. We show that the calculated bond dissociation energy (BDE) of the Co-C bond in adenosyl cobalamin is reduced by 135 kJ/mol in the enzyme.

O2-binding to heme: electronic structure and spectrum of oxyheme, studied by multiconfigurational methods.

We have studied the ground state of a realistic model of oxyheme with multiconfigurational second-order perturbation theory (CASPT2). Our results show that the ground-state electronic structure is strongly multiconfigurational in character. Thus, the wavefunction is a mixture of many different configurations, of which the three most important ones are approximately 1FeII-1O2 (70%), FeIV-2O2(2-) (12%) and 3FeII-3O2 (3%).

How O2 binds to heme: reasons for rapid binding and spin inversion.

We have used density functional methods to calculate fully relaxed potential energy curves of the seven lowest electronic states during the binding of O(2) to a realistic model of ferrous deoxyheme. Beyond a Fe-O distance of approximately 2.5 A, we find a broad crossing region with five electronic states within 15 kJ/mol.

Conversion of homocysteine to methionine by methionine synthase: a density functional study.

This communication reports a theoretical study of the conversion of homocysteine to methionine by methionine synthase. The reaction pathway is based on density functional calculations with large basis sets, including thermodynamic, relativistic, and solvent effects. We find that the suggested SN2 mechanism explains well the experimentally observed reaction rate.

Comparison of the chemical properties of iron and cobalt porphyrins and corrins.

Density functional calculations have been used to compare various geometric, electronic and functional properties of iron and cobalt porphyrin (Por) and corrin (Cor) species. The investigation is focussed on octahedral M(II/III) complexes (where M is the metal) with two axial imidazole ligands (as a model of b and c type cytochromes) or with one imidazole and one methyl ligand (as a model of methylcobalamin). However, we have also studied some five-coordinate M(II) complexes with an imidazole ligand and four-coordinate M(I/II) complexes without any axial ligands as models of other intermediates in the reaction cycle of coenzyme B12.

Metal ion enhanced binding of AMD3100 to Asp262 in the CXCR4 receptor.

The affinity of AMD3100, a symmetrical nonpeptide antagonist composed of two 1,4,8,11-tetraazacyclotetradecane (cyclam) rings connected through a 1,4-dimethylene(phenylene) linker to the CXCR4 chemokine receptor was increased 7, 36, and 50-fold, respectively, by incorporation of the following: Cu(2+), Zn(2+), or Ni(2+) into the cyclam rings of the compound. The rank order of the transition metal ions correlated with the calculated binding energy between free acetate and the metal ions coordinated in a cyclam ring. Construction of AMD3100 substituted with only a single Cu(2+) or Ni(2+) ion demonstrated that the increase in binding affinity of the metal ion substituted bicyclam is achieved through an enhanced interaction of just one of the ring systems.