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1.
Dalton Trans ; 39(40): 9684-95, 2010 Oct 28.
Artigo em Inglês | MEDLINE | ID: mdl-20830391

RESUMO

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 2.60 Å and 2.39 Å for Cd-S and Zn-S, in the MT clusters four characteristic terminal and bridging bonds are observed with average lengths 2.55 Å (Cd-S(t)); 2.35 Å (Zn-S(t)); 2.62 Å (Cd-S(b)); and 2.42 Å (Zn-S(b)). For each stoichiometry of Zn(2+) and Cd(2+), all possible isomers have been characterized and ranked according to relative free energy and metal ion selectivity. The most stable distribution at low Cd(2+) concentration is computed to be Zn(4) + CdZn(2), whereas at 2 : 1 Cd(2+) : Zn(2+) concentration, only heteroclusters are thermodynamically stable, explaining experimental data. The presence of two different clusters in MTs must and can be rationalized already in their intrinsic differences. The results indicate that the asymmetry allows for Zn(2+) transfer to various molecular targets having different thresholds for Zn(2+) binding, while maintaining detoxification sites.


Assuntos
Cádmio/química , Metalotioneína/química , Zinco/química , Humanos , Isomerismo , Modelos Químicos , Modelos Moleculares , Termodinâmica
2.
J Inorg Biochem ; 104(2): 136-45, 2010 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-19939457

RESUMO

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 (0.57-0.59mm/s) with experimental Mössbauer isomer shifts (0.55mm/s) and had low computed free energies. The weaker trans influence of histidine is shown to give rise to a bent O(2) coordination mode with O(2) pointing towards the cofactor and a more activated O-O bond (1.33A) than in O(glu) (1.30A). It is shown that the cofactor can hydrogen bond to O(2) and activate the O-O bond further (from 1.33 to 1.38A). The O(his) intermediate leads to a ferryl intermediate (F(his)) with an isomer shift of 0.34mm/s, also consistent with the experimental value (0.25mm/s) which we propose as the structure of the hydroxylating intermediate, with the tryptophan substrate well located for further reaction 3.5A from the ferryl group. Based on the optimized transition states, the activation barriers for the two paths (glu and his) are similar, so a two-state scenario involving O(his) and P(glu) is possible. A structure of the activated deoxy state which is high-spin implies that the valence electron count has been lowered from 18 to 16 (glutamate becomes bidentate), giving a "green light" that invites O(2)-binding. Our mechanism of oxygen activation in tryptophan hydroxylase does not require inversion of spin, which may be an important observation.


Assuntos
Modelos Químicos , Oxigênio/química , Triptofano Hidroxilase/química , Triptofano/química , Animais , Calibragem , Catálise , Domínio Catalítico , Simulação por Computador , Elétrons , Humanos , Cinética , Modelos Moleculares , Conformação Molecular , Estrutura Molecular , Oxigênio/metabolismo , Estrutura Terciária de Proteína , Especificidade por Substrato , Termodinâmica , Triptofano/metabolismo , Triptofano Hidroxilase/metabolismo
3.
J Am Chem Soc ; 131(34): 12155-71, 2009 Sep 02.
Artigo em Inglês | MEDLINE | ID: mdl-19663382

RESUMO

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. Our procedure identifies and characterizes various possible candidates for peroxo intermediates experimentally observed along the ribonucleotide reductase dioxygen activation reaction. The study explores how water or a proton can bind to the di-iron site of ribonucleotide reductase and facilitate changes that affect the electronic structure of the iron sites and activate the site for further reaction. Two potential reaction pathways are presented: one where water adds to Fe1 of the cis-mu-1,2 peroxo intermediate P causing opening of a bridging carboxylate to form intermediate P' that has an increased electron affinity and is activated for proton-coupled electron transfer to form the Fe(III)Fe(IV) intermediate X; and one that is more energetically favorable where the P to P' conversion involves addition of a proton to a terminal carboxylate ligand in the site which increases the electron affinity and triggers electron transfer to form X. Both pathways provide a mechanism for the activation of peroxy intermediates in binuclear non-heme iron enzymes for reactivity. The studies further show that water coordination can induce the conformational changes observed in crystal structures of the met state.


Assuntos
Ferro/metabolismo , Ribonucleotídeo Redutases/química , Ribonucleotídeo Redutases/metabolismo , Absorção , Simulação por Computador , Heme , Hidróxidos/química , Isomerismo , Modelos Moleculares , Conformação Molecular , Oxirredução , Oxigênio/química , Peróxidos/química , Prótons , Espectrofotometria Ultravioleta , Espectroscopia de Mossbauer , Termodinâmica , Vibração , Água/química
4.
J Phys Chem A ; 113(37): 10133-41, 2009 Sep 17.
Artigo em Inglês | MEDLINE | ID: mdl-19681590

RESUMO

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 0.03 A for the third row. TPSSh provides metal-ligand bond enthalpies with mean absolute errors of 37 and 44 kJ/mol for the second- and third-row molecules, respectively. Pathological cases (e.g., HgC and HgN) have errors of up to 155 kJ/mol, more than thrice the mean (observed with both functionals). Importantly, the systematic error component is negligible as measured by a coefficient of the linear regression line of 0.99. Equally important, TPSSh provides uniform accuracy across all three rows of the d-block, which is unprecedented and due to the 10% exact exchange, which is close to optimal for the d-block as a whole. This work provides an accurate and systematic prediction of electronic ground-state spins, characteristic metal-ligand bond lengths, and bond enthalpies for many as yet uncharacterized diatomics, of interest to researchers in the field of second- and third-row d-block chemistry. We stress that the success of TPSSh cannot be naively extrapolated to other special situations such as, e.g., metal-metal bonds. The high accuracy of the procedure further implies that the effective core functions used to model relativistic effects are necessary and sufficient for obtaining accurate geometries and bond enthalpies of second- and third-row molecular systems.

5.
J Phys Chem A ; 113(37): 10033-9, 2009 Sep 17.
Artigo em Inglês | MEDLINE | ID: mdl-19697914

RESUMO

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. TPSSh achieves an unprecedented mean absolute error of approximately 11 kJ/mol in spin transition energies, with the local functional M06L a distant second (25 kJ/mol). Other tested functionals give mean absolute errors of 40 kJ/mol or more. This work confirms earlier suggestions that 10% exact exchange is near-optimal for describing the electron correlation effects of first-row transition metal systems. Furthermore, it is shown that given an experimental structure of an iron complex, TPSSh can predict the electronic state corresponding to that experimental structure. We recommend this functional as current state-of-the-art for studying spin crossover and relative energies of close-lying electronic configurations in first-row transition metal systems.

6.
Inorg Chem ; 47(22): 10357-65, 2008 Nov 17.
Artigo em Inglês | MEDLINE | ID: mdl-18855376

RESUMO

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 0.99 upon linear fitting to experimental bond energies, whereas B3LYP and BP86, representing 20% and 0% exact exchange, respectively, give linear fits with slopes of 0.91 and 1.07. Thus, TPSSh eliminates the large systematic component of the error in other functionals, reducing rms errors from 46-57 to 34 kJ/mol. The nonhybrid version of the functional, TPSS, gives a slope of 1.08, similar to BP86, implying that using 10% exact exchange is the main reason for the success of TPSSh. Typical bioinorganic reactions were then investigated, including spin inversion and electron affinity in iron-sulfur clusters, and breaking or formation of bonds in iron proteins and cobalamins. The results show that differences in reaction energies due to exact exchange can be much larger than the usually cited approximately 20 kJ/mol, sometimes exceeding 100 kJ/mol. The TPSSh functional provides energies approximately halfway between nonhybrids BP86 and TPSS, and 20% exact exchange hybrid B3LYP: Thus, a linear correlation between the amount of exact exchange and the numeric value of the reaction energy is observed in all these cases. For these reasons, TPSSh stands out as a most promising density functional for use and further development within the field of bioinorganic chemistry.


Assuntos
Modelos Químicos , Elementos de Transição/química , Modelos Moleculares , Termodinâmica
7.
J Phys Chem A ; 112(50): 12829-41, 2008 Dec 18.
Artigo em Inglês | MEDLINE | ID: mdl-18610989

RESUMO

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. For those that have been characterized experimentally, very good agreement is obtained, implying that also the predicted structures and properties of new clusters are accurate. Mean absolute errors are 0.024 A for bond lengths ([Fe(4)S(4)], [NiFe(3)S(4)], [CoFe(3)S(4)]) and 0.09 V for shifts in reduction potentials relative to the [Fe(4)S(4)] cluster. All structures form cuboidal geometries similar to the all-iron clusters, except the Pd-substituted clusters, which instead form highly distorted trigonal and tetragonal local sites in compromised, pseudocuboidal geometries. In contrast to other electron-transfer sites, cytochromes, blue copper proteins, and smaller iron-sulfur clusters, we find that the [Fe(4)S(4)] clusters are very insensitive to metal substitution, displaying quite small changes in reorganization energies and reduction potentials upon substitution. Thus, the [Fe(4)S(4)] clusters have an evolutionary advantage in being robust to pollution from other metals, still retaining function. We analyze in detail the electronic structure of individual clusters and rationalize spin couplings and redox activity. Often, several configurations are very close in energy, implying possible use as spin-crossover systems, and spin states are predicted accurately in all but one case ([CuFe(3)S(4)]). The results are anticipated to be helpful in defining new molecular systems with catalytic and magnetic properties.

8.
Anal Chem ; 80(15): 5993-6000, 2008 Aug 01.
Artigo em Inglês | MEDLINE | ID: mdl-18553944

RESUMO

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). The 1:1 complex became the most abundant low molecular mass Sb(V) complex with dilution time. A novel mixed-mode chromatographic system was applied in order to separate complexes of various stoichiometry and isomers. Density functional theory was used to study the structure of the 1:1 Sb-gluconate complex with three or four solvent molecules bound. By computing the structures and the free energies of the various possible isomers in aqueous solvation models, the most likely structures of the species were deduced. Importantly, 6-coordination is always preferred over 5-coordination, and the species commonly adopt conformations involving tris-coordination of deprotonated hydroxyl groups from gluconate.


Assuntos
Gluconato de Antimônio e Sódio/química , Cromatografia Líquida de Alta Pressão , Estabilidade de Medicamentos , Leishmaniose/tratamento farmacológico , Espectrometria de Massas , Conformação Molecular , Peso Molecular , Preparações Farmacêuticas/química , Soluções
9.
J Phys Chem B ; 112(6): 1820-7, 2008 Feb 14.
Artigo em Inglês | MEDLINE | ID: mdl-18205348

RESUMO

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. It is shown that OPLS-AA free energies depend critically on the type of water model, TIP4P or TIP3P; i.e., each water model requires specific water-charged molecule interaction potentials. New models (models 1 and 3) are thus described for both water models. Uncertainties in relative free energies of charged residues are approximately 2 kcal/mol with the new parameters, due to variations in system setup (MAEs of ca. 1 kcal/mol) and noise from simulations (ca. 1 kcal/mol). The latter error of approximately 1 kcal/mol contrasts MAEs from standard OPLS-AA of up to 13 kcal/mol for the entire series of charged residues or up to 5 kcal/mol for the cationic series Lys, Arg, and Hip. The new parameters can be used directly in molecular simulations with no modification of neutral residues needed and are envisioned to be particular important in simulations where charged residues change environment.


Assuntos
Proteínas/química , Aminoácidos/química , Simulação por Computador , Eletroquímica , Transferência de Energia , Ligação de Hidrogênio , Modelos Químicos , Método de Monte Carlo
10.
J Inorg Biochem ; 102(1): 87-100, 2008 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-17723245

RESUMO

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 0.038A to 0.016A with this procedure. Four density functionals were compared, B3LYP, BP86, TPSS, and TPSSh. B3LYP and to a lesser extent TPSSh energies were inconsistent with experiment for the oxidized [Fe3S4]+ cluster. BP86 (and to a slightly lesser extent TPSS) was within expected theoretical and experimental uncertainties for all oxidation states, the only qualitative error being 5kJ/mol in favor of the M(S)=3/2 configuration for the [Fe3S4]+ cluster, so BP86 was used for quantitative results. Computed reorganization energies and reduction potentials point directly towards the [Fe3S4] cluster as the superior choice of electron carrier, with the [ZnFe2S4] cluster a close second. In addition, partially and fully Mo-substituted clusters were investigated and found to have very low reorganization energies but too negative reduction potentials. The results provide a direct rationale why any substitution weakens the cluster as an electron carrier, and thus why the [Fe3S4] composition is optimal in the biological clusters.


Assuntos
Proteínas Ferro-Enxofre/química , Ferro/química , Biologia Computacional , Simulação por Computador , Espectroscopia de Ressonância de Spin Eletrônica , Metais/química , Modelos Químicos , Estrutura Molecular , Oxirredução
11.
Inorg Chem ; 46(21): 8710-6, 2007 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-17880061

RESUMO

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 0.07 V. Using electrostatically screened geometries and large basis sets for expanding the wave functions gave quantitatively correct results, with errors of only 0.03 V. Correspondingly, only this approach predicted a change in the coordination mode of aspartate (i.e., a carboxylate shift) accompanying the reduction of the wild-type cluster, confirming results from synthetic models and explaining why electrostatic screening is necessary. Hence, the carboxylate shift appears to occur in the proteins from which data were collected. The results represent the most accurate predictions of shifts in reduction potentials for modified proteins, the success in part being due to the similar nature of the three amino acid ligands involved. The predicted carboxylate shift is expected to tune aspartate's degree of electron donation to the cluster's two oxidation states, thus making the reversible redox reaction feasible.


Assuntos
Química/métodos , Ferredoxinas/química , Proteínas Ferro-Enxofre/química , Pyrococcus furiosus/metabolismo , Ácido Aspártico/química , Ácidos Carboxílicos/química , Cristalografia por Raios X , Cisteína/química , Ligantes , Modelos Teóricos , Conformação Molecular , Oxirredução , Reprodutibilidade dos Testes , Software , Temperatura
12.
J Chem Phys ; 126(1): 014103, 2007 Jan 07.
Artigo em Inglês | MEDLINE | ID: mdl-17212486

RESUMO

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. However, on average, 58 of 63 spins are correctly predicted by any functional, with only small differences. BP86 and PBE are slightly better for obtaining geometries, with errors of only 0.020 A. Hybrid functionals tend to overestimate bond lengths by a few picometers and underestimate bond strengths by favoring open shells. Nonhybrid functionals usually overestimate bond energies. All functionals exhibit similar errors in bond energies, between 42 and 53 kJmol. Late transition metals are found to be better modeled by hybrid functionals, whereas nonhybrid functionals tend to have less of a preference. There are systematic errors in predicting certain properties that could be remedied. BLYP performs the best for ionization potentials studied here, PBE0 the worst. In other cases, errors are similar. Finally, there is a clear tendency for hybrid functionals to give larger dipole moments than nonhybrid functionals. These observations may be helpful in choosing and improving existing functionals for tasks involving transition metals, and for designing new, improved functionals.

13.
J Chem Theory Comput ; 3(6): 1987-1992, 2007 Nov 01.
Artigo em Inglês | MEDLINE | ID: mdl-21132092

RESUMO

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. The ab initio calculations reveal a 2.0-kcal/mol range in hydrogen-bond strengths for the XPhOH⋯OH(2) complexes in the order X = NO(2) > CN > CF(3) > Cl > F > H >OH >CH(3) > NH(2). The pattern is not well-reproduced with OPLS-AA, which also compresses the variation to 0.7 kcal/mol. However, the OPLS/CM1A results are in good accord with the ab initio findings for both the ordering and range, 2.3 kcal/mol. The hydrogen bonding is, of course, weaker with XPhOH as acceptor, the order for X is largely inverted, and the range is reduced to ca. 1.0 kcal/mol. The substituent effects are found to be much greater for the chloride ion complexes with a range of 11 kcal/mol. For quantitative treatment of such strong ion-molecule interactions the need for fully polarizable force fields is demonstrated.

14.
J Biol Inorg Chem ; 12(1): 49-61, 2007 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-16953415

RESUMO

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. Our results clearly show that the chlorophylls strongly prefer to be five-coordinate, in accordance with available crystal structures. The axial ligands decrease the reduction potentials, so they cannot explain the high potential of P680. They also redshift the Q band, but not enough to explain the occurrence of red chlorophylls. However, there is some relation between the axial ligands and their location in the various photosynthetic proteins. In particular, the intrinsic reduction potential of the second molecule in the electron transfer path is always lower than that of the third one, a feature that may prevent back-transfer of the electron.


Assuntos
Clorofila/química , Aminoácidos/química , Elétrons , Ligantes , Modelos Químicos , Conformação Molecular , Fosfatos/química , Fotossíntese , Proteínas/química , Água/química
15.
J Comput Chem ; 27(12): 1398-414, 2006 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-16802319

RESUMO

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. Likewise, we suggest that the conversion of O2- to H2O2 follows an at least a partly second-sphere pathway. There are small differences in the preferred oxidation and spin states, as well as in the geometries, of Fe and Mn, but these differences have little influence on the energetics, and therefore on the reaction mechanism of the two types of superoxide dismutases. For example, the two metals have very similar reduction potentials in the active-site models, although they differ by 0.7 V in water solution. The reaction mechanisms and spin states seem to have been designed to avoid spin conversions or to facilitate them by employing nearly degenerate spin states.


Assuntos
Superóxido Dismutase/química , Superóxido Dismutase/metabolismo , Sítios de Ligação , Simulação por Computador , Modelos Moleculares , Conformação Proteica
16.
J Inorg Biochem ; 100(8): 1436-9, 2006 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-16716401

RESUMO

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). This simple result provides an important, although partial, explanation why iron alone is used in this type of clusters. The results can be explained by simple orbital rules of electron transfer, which state that the occupation of anti-bonding orbitals should not change during the redox reactions. This rule immediately suggests good and poor electron carriers.


Assuntos
Ferro/química , Modelos Moleculares , Enxofre/química , Algoritmos , Cristalografia por Raios X , Elétrons , Ferro/metabolismo , Oxirredução , Teoria Quântica , Enxofre/metabolismo
17.
J Chem Theory Comput ; 2(6): 1499-509, 2006 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-26627020

RESUMO

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. 1 kcal/mol. For the halides, this is the first self-consistent set of parameters that has been optimized for aqueous-phase performance. The good results for relative free energies of hydration are particularly auspicious for use of the new parameters in a wide variety of liquid-phase simulations where halide and alkali cations are systematically varied.

18.
J Am Chem Soc ; 127(25): 9117-28, 2005 Jun 29.
Artigo em Inglês | MEDLINE | ID: mdl-15969590

RESUMO

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. This catalytic effect can be divided into four terms. First, the adenosine radical is kept within 4.2 angstroms of the Co ion in the enzyme, which decreases the BDE by 20 kJ/mol. Second, the surrounding enzyme stabilizes the dissociated state by 42 kJ/mol using electrostatic and van der Waals interactions. Third, the protein itself is stabilized by 11 kJ/mol in the dissociated state. Finally, the coenzyme is geometrically distorted by the protein, and this distortion is 61 kJ/mol larger in the Co(III) state. This deformation of the coenzyme is caused mainly by steric interactions, and it is especially the ribose moiety and the Co-C5'-C4' angle that are distorted. Without the polar ribose group, the catalytic effect is much smaller, e.g. only 42 kJ/mol for methyl cobalamin. The deformation of the coenzyme is caused mainly by the substrate, a side chain of the coenzyme itself, and a few residues around the adenosine part of the coenzyme.


Assuntos
Carbono/química , Cobalto/química , Cobamidas/química , Transferases Intramoleculares/química , Teoria Quântica , Cristalografia por Raios X , Ácido Glutâmico/química , Ligação de Hidrogênio , Modelos Moleculares , Conformação Molecular
19.
J Phys Chem B ; 109(20): 10505-12, 2005 May 26.
Artigo em Inglês | MEDLINE | ID: mdl-16852272

RESUMO

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 0.21 eV. Agreement is significantly better for CASPT2 than density functional theory (DFT), but DFT does surprisingly well. The correlated wave function implies that the ground state of Co(I) corrin is severely multiconfigurational, with only 67% of the d(8) reference configuration and prominent contributions of 20% from open-shell metal-to-ligand charge-transfer configurations. The ground state exhibits a fascinating degree of covalency between cobalt and the nitrogen orbitals, described by the bonding and antibonding orbital pair of a cobalt d-orbital and a delta-orbital linearly combined from nitrogen orbitals. Thus, the standard description of the d(8) supernucleophile is not completely valid. From a biological perspective, the mixing in of Co(II) configurations in cob(I)alamin may be an important reason for the redox accessibility of the formal Co(I) state of the cofactor, which again provides the catalytic power for one half-reaction of enzymes such as cobalamin-dependent methionine synthase.


Assuntos
Vitamina B 12/química , Modelos Moleculares , Estrutura Molecular
20.
J Inorg Biochem ; 99(1): 45-54, 2005 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-15598490

RESUMO

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%). Thus, the wavefunction is dominated by closed-shell configurations, as suggested by Pauling, whereas the Weiss 2FeIII-2O2- configuration is not encountered among the 10 most important configurations. However, many other states are also important for this multiconfigurational wavefunction. Moreover, the traditional view is based on an oversimplified picture of the atomic-orbital contributions to the molecular orbitals. Thus, the population analysis indicates that all five iron orbitals are significantly occupied (by 0.5-2.0 electrons) and that the total occupation is most similar to the 3FeII-3O2 picture. The net charge on O2 is small, -0.20 e. Thus, it is quite meaningless to discuss which is the best valence-bond description of this inherently multiconfigurational system. Finally, we have calculated the eleven lowest ligand-field excited states of oxyheme and assigned the experimental spectrum of oxyhemoglobin with an average error of 0.24 eV.


Assuntos
Elétrons , Heme , Oxigênio , Heme/química , Heme/metabolismo , Estrutura Molecular , Oxigênio/química , Oxigênio/metabolismo
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