Biomedical subjects

Djamaladdin G Musaev

Publications and source records attributed to Djamaladdin G Musaev.

36 records · Page 2Linked to original sources

PubMed2005

Cooperative pull and push effects on the O-O bond cleavage in acylperoxo complexes of [(Salen)MnIIIL]: ensuring formation of manganese(V) oxo species.

The acidity (pull) and the axial ligand (push) effects on the O-O bond cleavage in the [(Salen)Mn(III)(RCO(3))L] acylperoxo complexes, with model L = none, NH(3), and HCO(2)(-) (1), have been studied with B3LYP density functional calculations. The acidic conditions have been mimicked by explicit protonation of 1 to afford a variety of [(Salen)Mn(III)(RCO(3)H)L] (2) and [(SalenH)Mn(III)(RCO(3))L] (3) complexes in ground quintet states. The protonation assists the O-O bond heterolysis, thus primarily forming highly reactive Mn(V)(O) species, and consequently suppresses formation of the less reactive Mn(IV)(O) species through homolytic channel described earlier in 1 [Khavrutskii, I. V.; Rahim, R. R.; Musaev, D. G.; Morokuma, K. J. Phys. Chem. B 2004, 108, 3845-3854]. In addition to the qualitative change of the O-O bond cleavage mode, the protonation affects the rate of the O-O bond cleavage. Therefore, varying the acidity of the reaction media helps control the O-O bond cleavage mode and rate.

Journal Article↗

PubMed2004

Computational modeling of di-transition-metal-substituted gamma-keggin polyoxometalate anions. Structural refinement of the protonated divacant lacunary silicodecatungstate.

The B3LYP density functional method has been validated for the di-Mn-substituted gamma-Keggin polyoxometalate (POM) anion, [(SiO4)MnIII2(OH)2W10O32]4-, and for the divacant lacunary silicodecatungastate, gamma-[(SiO4)W10O32]8-. This approach was shown to adequately describe the geometries of [(SiO4)MnIII2(OH)2W10O32]4- and gamma-[(SiO4)W10O32]8. Three different geometrical models, "full", "medium", and "small", for Mn2-gamma-Keggin have also been validated. It was shown that the medium [(SiO4)MnIII2(OH)2W6O24H8]4- model, as well as small [(SiO4)MnIII2(OH)2W4O18H10]2- model, preserves structural features of the full system, [(SiO4)MnIII2(OH)2W10O32]4-. However, the small model distorts the charge distribution at the "active site" of the system and should be used with caution. The same computational approach was employed to elucidate the structure of the di-Fe-substituted gamma-Keggin POM. The structure of the acidic (tetra-protonated form) of lacunary POM, gamma-[(SiO4)W10O32H4]4-, was shown to be gamma-[(SiO4)W10O28(OH)4]4- with four terminal hydroxo ligands, rather than gamma-[(SiO4)W10O30(H2O)2]4- with two aqua and two oxo(terminal) ligands as reported by Mizuno and co-workers (Science 2003, 300, 964). The observed and calculated asymmetry in the W-O(terminal) bond distances of gamma-[(SiO4)W10O32H4]4- is explained in terms of the existence of O1H1...O2H2 and O4H4...O3H3 hydrogen-bonding patterns in the gamma-[(SiO4)W10O28(OH)4]4- structure.

Journal Article↗

PubMed2004

RETRACTED: A late-transition metal oxo complex: K7Na9[O=PtIV(H2O)L2], L = [PW9O34]9-.

Terminal mono-oxo complexes of the late transition metal elements have long been considered too unstable to synthesize because of repulsion between the oxygen electrons and the mostly filled metal d orbitals. A platinum(IV)-oxo compound flanked by two polytungstate ligands, K7Na9[O=Pt(H2O)L2], L = [PW9O34(9-)], has now been prepared and isolated at room temperature as air-stable brown crystals. X-ray and neutron diffraction at 30 kelvin revealed a very short [1.720(18) angstrom] Pt-O bond and no evidence of a hydrogen atom at the terminal oxygen, ruling out a better precedented Pt-OH complex. Density functional theory and spectroscopic data account for the stability of the Pt(IV)-oxo unit by electron withdrawal into delocalized orbitals of the polytungstates.

Chemical Phenomena↗

PubMed2004

Epoxidation of unfunctionalized olefins by Mn(salen) catalyst using organic peracids as oxygen source: a theoretical study.

The mechanism and origin of asymmetric induction in the Mn(III)(salen)-catalyzed epoxidation by peracetic acid have been elucidated by the density functional [Becke three-parameter hybrid functional combined with Lee-Yang-Parr correlation functional (B3LYP)] method in two different regimes: with and without an axial ligand. The acylperoxo complexes of Mn(II,III,IV) in cisON cisNO and trans geometrical configurations cannot compete with the catalyst-free Prilezhaev epoxidation. Instead, oxo species perform epoxidation following the O-O bond cleavage in the acylperoxo complexes. The epoxidation may proceed in a concerted and/or radical-mediated stepwise manner. The actual mechanism of the epoxidation depends on the electronic and oxidation state of the oxo species and the nature of the axial ligand. The olefin can approach the reactive MnO fragment of both cis and trans-l-isomers of the plain oxo species along multiple distinct directions: native approaches. The native approaches are used to rationalize the inversion of the absolute configuration of the product epoxide due to the axial ligand.

Journal Article↗

PubMed2003

Theoretical studies of the complex [(BPMEN)Fe(II)(NCCH3)2](2+), precursor of non-heme iron catalysts for olefin epoxidation and cis-dihydroxylation.

The density functional theory (DFT) was applied to elucidate the electronic structure of the BPMEN [N,N'-bis(6-R-2-pyridylmethyl)-1,2-diaminoethane] iron complex, [(BPMEN)Fe(NCCH3)2](2+), a precursor of catalysts that catalyze the stereospecific olefin oxidation. The low-lying high and low spin states of complex 1 (R=H) are nearly degenerate with a slight preference for the high spin state. For complexes with substituents (R) at the 6-positions of two pyridine rings of BPMEN, the ground state is the high spin (HS) state, with the low spin (LS) state higher in energy by 9.5, 5.3, 8.5, 6.3, and 5.1 kcal/mol for complexes 2 (R=CH3), 3 (R=SiH3), 4 (R=OH), 5 (R=F), and 6 (R=CN), respectively, with the B3LYP method. Our findings for complexes 1 and 2 are in good agreement with the experimental observations. The calculated LS-HS difference of 17.9 kcal/mol for complex 7 (R=t-Bu) clearly demonstrates that the steric effect causes the Fe-N bonds to stretch and favors the high spin state. Comparison of the B3LYP and B3PW91 results with experiments and ab initio MP2 and CCSD(T) as well as pure DFT results shows that hybrid DFT methods provide a qualitatively correct description of the relative energies of low-lying electronic states of a model of the [(BPMEN)Fe(NCCH3)2](2+) complex, while pure DFT methods underestimate the stability of the HS state.

Alkenes↗

PubMed2003

Insights into the structure and reactivity of acylperoxo complexes in the Kochi-Jacobsen-Katsuki catalytic system. A density functional study.

Structural properties of the acylperoxo complexes [(Salen)Mn(III)RCO(3)] (2) and [(Salen)Mn(IV)RCO(3)] (3), the critical intermediates in the Kochi-Jacobsen-Katsuki reaction utilizing organic peracids or O(2)/aldehydes as oxygen source, have been studied with the density functional theory. Four distinct isomers, cis(O,N), cis(N,O), cis(N,N), and trans, of these complexes have been located. The isomer 2-cis(O,N) in its quintet ground state, and nearly degenerate isomers 3-cis(O,N) and 3-cis(N,O) in their quartet ground states are found to be the lowest in energy among the other isomers. The O-O bond cleavage in the cis(O,N), cis(N,O), and trans isomers of 2 and 3 has been elucidated. In complex 3, the O-O bond is inert. On the contrary, in complex 2, the O-O bond cleaves via two distinct pathways. The first pathway occurs exclusively on the quintet potential energy surface (PES) and corresponds to heterolytic O-O bond scission coupled with insertion of an oxygen atom into an Mn-N(Salen) bond to form 2-N-oxo species; this pathway has the lowest barrier of 14.9 kcal/mol and is 15.6 kcal/mol exothermic. The second pathway is tentatively a spin crossover pathway. In particular, for 2-cis(O,N) and 2-cis(N,O) the second pathway proceeds through a crucial minimum on the seam of crossing (MSX) between the quintet and triplet PESs followed by heterolytic O-O cleavage on the triplet PES, and produces unusual triplet 2-cis(O,N)- and 2-cis(N,O)-oxo ([(Salen)Mn(V)(O)RCO(2)]) species; this pathway requires 12.8 kcal/mol and is 1.4 kcal/mol endothermic. In contrast, for the 2-trans isomer, spin crossing is less crucial and the O-O cleavage proceeds homolytically to generate 2-trans-oxo [(Salen)Mn(IV)(O)] species with RCO(2) radical; this pathway, however, cannot compete with that in 2-cis because it needs 21.9 kcal/mol for activation and is 15.3 kcal/mol endothermic. In summary, the O-O cleavage occurs predominantly in the 2-cis complexes, and may proceed either through pure high spin or spin crossover heterolytic pathway to produce 2-cis-oxo and 2-N-oxo species.

Journal Article↗

PubMed2003

Relationship between rate and distance.

The activation energies for four Smiles reactions vary with the distance squared between the nucleophilic and electrophilic atoms (consistent with theoretical considerations and pertinent to organic and enzymatic catalyses).

Journal Article↗

PubMed2003

Versatile and cooperative reactivity of a triruthenium polyhydride cluster. A computational study.

The reaction of a trinuclear polyhydride complex Ru3H5(C5H5)3 with cyclopentadiene, C5H6, has been studied computationally. A mechanism for the experimentally observed selective C-C bond activation is proposed. All three Ru centers participate in various steps of the mechanism. The catalytic involvement of two cluster hydrides in the transformation of the C5Hn fragment is emphasized.

Journal Article↗

PubMed2003

Computational study of the aminolysis of 2-benzoxazolinone.

Three possible mechanisms (zwitterionic, neutral stepwise, and neutral concerted) of the ring-opening reaction of 2-benzoxazolinone (BO) upon aminolysis with methylamine were studied at the B3LYP/6-31G* level. In the gas phase, the neutral concerted mechanism is shown to be most favorable, which proceeds via a rate-determining barrier of 28-29 kcal/mol. The transition state, CTS, associated with this barrier is a four-centered one, where 1,2-addition of the N[bond]H of methylamine to the C[bond]O of BO ring occurs. The rate-determining barrier of the neutral stepwise pathway is found to be ca. 42 kcal/mol. The inclusion of solvent effects by a polarizable continuum model (PCM) does not change the conclusions based on the gas-phase study; the barrier at CTS is reduced to 20, 20, and 22 kcal/mol in water, ethanol, and acetonitrile, respectively.

Journal Article↗

PubMed2003

Structure, stability, and electronic and NMR properties of various oxo- and nitrido-derivatives of [L(Salen)Mn(III)]+, where L = none and imidazole. A density functional study.

Structure, stability, and electronic and NMR properties of [(Salen)Mn(III)](+)-derived intermediates/reactants in the epoxidation/amination of unfunctionalized olefins, namely [(Salen)Mn(V)O](+) (1-oxo), [(Salen)Mn(IV)O] (2-oxo), and [(Salen)Mn(V)N] (3), have been studied with the B3LYP density functional method. It has been shown that the (1)A, (3)A, and (5)A states of cationic 1-oxo species are virtually degenerate, while for the neutral 2-oxo species the ground (4)A state lies 6.4 kcal/mol lower than (2)A. In the nitrido species 3, the (1)A state has been shown to be the ground state in agreement with experiment. We have investigated isomerization of 1-oxo and 2-oxo species into unusual [(OSalen)Mn(III)](+) (1-N-oxo and 1-peroxo) and [(OSalen)Mn(II)] (2-N-oxo and 2-peroxo) species, respectively. For cationic species 1, the 1-N-oxo isomers are more stable (by 10-12 kcal/mol) than the 1-oxo isomer and are separated from the latter by 21-22 kcal/mol barriers. On the other hand, 1-peroxo isomers are calculated to be 14-16 kcal/mol higher than the 1-oxo isomer. For neutral species 2, however, both 2-N-oxo and 2-peroxo isomers lie significantly higher in energy than the 2-oxo isomer. It has been shown that coordination of axial imidazole ligand alters relative energies of spin states for 1- and 2-oxo species, destabilizing low-spin states. For singlet states of H(2)Salen, 1-oxo, and 3, we have calculated (1)H, (13)C, (15)N, and (17)O NMR chemical shifts using the gauge-independent-atomic orbital (GIAO) approach.

Journal Article↗

PubMed2003

Can the ebselen derivatives catalyze the isomerization of peroxynitrite to nitrate?

The reaction of ebselen and its derivatives (1-7) with peroxynitrite anion (ONOO(-); PN) has been studied in gas phase and in aqueous, dichloromethane, benzene, and cyclohexane solutions using B3LYP/6-311+G(d,p)//B3LYP/6-311G(d,p) and PCM-B3LYP/6-311+G(d,p)//B3LYP/6-311G(d,p) approaches, respectively. It was shown that the reaction of 2 (R=H) with PN proceeds via 2 + PN --> 2-PN --> 2-TS1 (O-O activation) --> 2-O(NO(2)(-)()) --> 2-SeO + NO(2)(-) pathway with a rate-determining barrier of 25.3 (14.8) kcal/mol at the NO(2)(-) dissociation step (numbers presented without parentheses are enthalpies, and those in parentheses are Gibbs free energies). The NO(3)(-) formation process, starting from the complex 2-O(NO(2)(-)()), requires by (7.9) kcal/mol more energy than the NO(2)(-) dissociation process and is unlikely to compete with the latter. Thus, in the gas phase, the peroxynitrite --> nitrate isomerization catalyzed by complex 2 is unlikely to occur. It is shown that the NO(3)(-) formation process is slightly more favorably than the NO(2)(-) dissociation process for complex 4, with a strongest electron-withdrawing ligand R=CF(3). Therefore, complex 4 (as well as complex 6 with R=OH) is predicted to be a good catalyst for peroxynitrite <--> nitrite isomerization in the gas phase. Solvent effects (a) change the rate-determining step of the reaction 2 + PN from NO(2)(-) dissociation in the gas phase to O-O activation, which occurs with barriers of (13.9), (8.4), (8.4), and (8.2) kcal/mol in water, dichloromethane, benzene, and cyclohexane, respectively, and (b) significantly reduce the NO(2)(-) dissociation energy, while only slightly destabilizing the NO(3)(-) formation barrier, and make the peroxynitrite <--> nitrate isomerization process practically impossible, even for complex 4.

Anions↗

PubMed2003

Computational study of the aminolysis of esters. The reaction of methylformate with ammonia.

The aminolysis of esters is a basic organic reaction considered as a model for the interaction of carbonyl group with nucleophiles. In the present computational study the different possible mechanistic pathways of the reaction are reinvestigated by applying higher level electronic structure theory, examining the general base catalysis by the nucleophile, and a more comprehensive study the solvent effect. Both the ab initio QCISD/6-31(d,p) method and density functional theory at the B3LYP/6-31G(d) level were employed to calculate the reaction pathways for the simplest model aminolysis reaction between methylformate and ammonia. Solvent effects were assessed by the PCM method. The results show that in the case of noncatalyzed aminolysis the addition/elimination stepwise mechanism involving two transition states and the concerted mechanism have very similar activation energies. However, in the case of catalyzed aminolysis by a second ammonia molecule the stepwise mechanism has a distinctly lower activation energy. All transition states in the catalyzed aminolysis are 10-17 kcal/mol lower than those for the uncatalyzed process.

Journal Article↗

PubMed2003

Internal degrees of freedom, structural motifs, and conformational energetics of the 5'-deoxyadenosyl radical: implications for function in adenosylcobalamin-dependent enzymes. A computational study.

The potential energy surface of the free 5'-deoxyadenosyl radical in the gas phase is explored using density functional and second-order Møller-Plesset perturbation theories with 6-31G(d) and 6-31++G(d,p) basis sets and interpreted in terms of attractive and repulsive interactions. The 5',8-cyclization is found to be exothermic by approximately 20 kcal/mol but kinetically unfavorable; the lowest cyclization transition state (TS) lies about 7 kcal/mol higher than the highest TS for conversion between most of the open isomers. In open isomers, the two energetically most important attractive interactions are the hydrogen bonds (a) between the 2'-OH group and the N3 adenine center and (b) between the 2'-OH and 3'-OH groups. The relative ribose-adenine rotation about the C1'-N9 glycosyl bond in a certain range changes the energy by as much as 10-15 kcal/mol, the origin being (i) the repulsive 2'-H.H-C8 and O1'.N3 and (ii) the attractive 2'-OH.N3 ribose-adenine interactions. The hypothetical synergy between the glycosyl rotation and the Co-C bond scission may contribute to the experimentally established labilization of the Co-C bond in enzyme-bound adenosylcobalamin. The computational results are not inconsistent with the rotation about the C1'-N9 glycosyl bond being the principal coordinate for long-range radical migration in coenzyme B(12)-dependent enzymes. The effect of the protein environment on the model system results reported here remains an open question.

Adenine↗

PubMed2002

Theoretical study of the mechanism of alkane hydroxylation and ethylene epoxidation reactions catalyzed by diiron bis-oxo complexes. The effect of substrate molecules.

The hybrid density functional method B3LYP was used to study the mechanism of the hydrocarbon (methane, ethane, methyl fluoride, and ethylene) oxidation reaction catalyzed by the complexes cis-(H(2)O)(NH(2))Fe(mu-O)(2)(eta(2)-HCOO)(2)Fe(NH(2))(H(2)O), I, and cis-(HCOO)(Imd)Fe(mu-O)(2)(eta(2)-HCOO)(2)Fe(Imd)(HCOO) (Imd = Imidazole), I_m, the "small" and "medium" model of compound Q of the methane monooxygenase (MMO). The improvement of the model from "small" to "medium" did not change the qualitative conclusions but significantly changed the calculated energetics. As in the case of methane oxidation reported by the authors previously, the reaction of all the substrates studied here is shown to start by coordination of the substrate molecule to the bridging oxygen atom, O(1) of I, an Fe(IV)-Fe(IV) complex, followed by the H-atom abstraction at the transition state III leading to the bound hydroxy alkyl intermediate IV of Fe(III)-Fe(IV) core. IV undergoes a very exothermic coupling of alkyl and hydroxy groups to give the alcohol complex VI of Fe(III)-Fe(III) core, from which alcohol dissociates. The H(b)-atom abstraction (or C-H bond activation) barrier at transition state III is found to be a few kcal/mol lower for C(2)H(6) and CH(3)F than for CH(4). The calculated trend in the H(b)-abstraction barrier, CH(4) (21.8 kcal/mol) > CH(3)F (18.8 kcal/mol) > or = C(2)H(6) (18.5 kcal/mol), is consistent with the C-H(b) bond strength in these substrates. Thus, the weaker the C-H(b) bond, the lower is the H(b)-abstraction barrier. It was shown that the replacement of a H-atom in a methane molecule with a more electronegative group tends to make the H(b)-abstraction transition state less "reactant-like". In contrast, the replacement of the H-atom in CH(4) with a less electronegative group makes the H(b)-abstraction transition state more "reactant-like". The epoxidation of ethylene by complex I is found to proceed without barrier and is a highly exothermic process. Thus, in the reaction of ethylene with complex I the only product is expected to be ethylene oxide, which is consistent with the experiment.

Alkanes↗

PubMed2002

Computational studies of tungsten-catalyzed endo-selective cycloisomerization of 4-pentyn-1-ol.

Endo- and exo-cycloisomerizations of 4-pentyn-1-ol have been studied computationally with density functional theory, in conjunction with double-zeta and triple-zeta basis sets, both in the absence and in the presence of tungsten carbonyl catalyst. In the absence of the catalyst, both endo- and exo-cycloisomerizations have been calculated to have a very high activation barrier of approximately 50-55 kcal/mol and cannot take place. With tungsten pentacarbonyl catalyst, endo-cycloisomerization becomes a complex multiple-step reaction and proceeds with a rate-determining barrier of 26 kcal/mol at the C(alpha) --> C(beta) hydride migration step to form a vinylidene intermediate. The primary role of the tungsten catalyst is to stabilize the vinylidene intermediate, thus lowering the rate-determining barrier. The second important role of the tungsten catalyst in endo-cycloisomerization is to assist the OH hydride migration to C(alpha) by making it a multistep process with small activation barriers. The exo-cycloisomerization with the catalyst still has a high rate-determining barrier of 47 kcal/mol. These findings clearly explain the experimentally observed endo-selectivity in the cycloisomerization of 4-pentyn-1-ol derivatives and support the experimentally proposed mechanism.

Alkynes↗

PubMed2002

Vinyl-vinyl coupling on late transition metals through C-C reductive elimination mechanism. A computational study.

A detailed density functional study was performed for the vinyl-vinyl reductive elimination reaction from bis-sigma-vinyl complexes [M(CH=CH(2))(2)X(n)]. It was shown that the activity of these complexes decreases in the following order: Pd(IV), Pd(II) > Pt(IV), Pt(II), Rh(III) > Ir(III), Ru(II), Os(II). The effects of different ligands X were studied for both platinum and palladium complexes, which showed that activation barriers for C-C bond formation reaction decrease in the following order: X = Cl > Br, NH(3) > I > PH(3). Steric effects induced either by the ligands X or by substituents on the vinyl group were also examined. In addition, the major factors responsible for stereoselectivity control on the final product formation stage and possible involvement of asymmetric coupling pathways are reported. In all cases DeltaE, DeltaH, DeltaG, and DeltaG(aq) energy surfaces were calculated and analyzed. The solvent effect calculation shows that in a polar medium halogen complexes may undergo a reductive elimination reaction almost as easily as compounds with phosphine ligands.

Journal Article↗

PubMed2002

Effects of the protein environment on the structure and energetics of active sites of metalloenzymes. ONIOM study of methane monooxygenase and ribonucleotide reductase.

As the first application of our recently developed ONIOM2(QM:MM) and ONIOM3(QM:QM:MM) codes to the metalloenzymes with a large number of protein residues, two members of the non-heme protein family, methane monooxygenause and ribonucleotide reductase, have been chosen. The "active-site + four alpha-helical fragments" model was adopted which includes about 1000 atoms from 62 residues around the Fe-centered spheres. Comparison of the active-site geometries of MMOH and R2 units optimized with this model with those obtained with the "active site only" (with only 39-46 atoms) model and the X-ray results clearly demonstrates the crucial role of the active site-protein interaction in the enzymatic activities.

Binding Sites↗

PubMed2002

Computational studies of reaction mechanisms of methane monooxygenase and ribonucleotide reductase.

An overview of the computational efforts made by our group during the last few years in the field of nonheme diiron proteins is presented. Through application of ab initio methodology to a reasonable set of molecular models, significant progress is made in understanding how the soluble Methane Monooxygenase system achieves the hydroxylation of methane and how the catalytic cycle of Ribonucleotide Reductase is initiated. In particular, the current studies reveal in more detail (1) the nature of key intermediates in the reaction cycles of these two metalloenzymes, (2) details of how the iron centers regulate the systems, and (3) important aspects of how the carboxylate ligands in the active sites may tailor the enzymatic needs of the metalloprotein. This knowledge also leads to novel connections between the two enzymes. The coordinative unsaturation and carboxylate shifts investigated herein are two properties that are likely to be of more general impact in nonheme proteins. The control of the redox chemistry of the enzyme by the binuclear metal center, also analyzed here, should find common ground among other bimetallic systems as well.

Binding Sites↗