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Keiji Morokuma

Publications and source records attributed to Keiji Morokuma.

At least 19 recordsLinked to original sources

Electronic reorganization: origin of sigma trans promotion effect.

Binding of two ligands trans to each other by some transition metal complexes may be cooperative [Khoroshun et al., Mol Phys 2002, 100, 523]. Several interesting consequent effects include (i) inverse relationship between bond strength and binding affinity; (ii) smaller coordination barriers to formation of weaker bonds; (iii) enhancement of Lewis acidity with increased number of ligands. We describe a simple model, sigma trans promotion effect (TPE), which considers electronic reorganization between two Lewis structures, and predicts the above-mentioned effects. The applied result of present study is the unified perspective on several facts of heme chemistry. Particularly, we reiterate an important but often overlooked notion, developed previously within the spin pairing model [Drago and Corden, Acc Chem Res 1980, 13, 353], that, in hemoproteins, the proximal histidine and the distal ligand such as O2 or CO cooperate in promoting electronic reorganization. As a result, depopulation of dz2 orbital upon ligand binding contributes to the phenomenon of hemoglobin cooperativity. The presented density functional (B3LYP) calculations on realistic models, the processes of carbon monoxide binding by Fe(II) porphyrins and dinitrogen binding by triamido/triamidoamine Mo(III) complexes, particularly the evaluation of the coordination barriers due to spin-state change by location of the minima on seams of crossing, support the TPE model predictions. From a broader theoretical perspective, the present study would hopefully stimulate the development of much needed frameworks and tools for facile comparisons of wave functions and their properties between different geometries, species, and electronic states. Advancement of practical wave function comparisons may yield fresh qualitative perspectives on chemical reactivity, and promote better understanding of related concepts such as electronic reorganization.

Journal Article↗

Modeling carbon nanostructures with the self-consistent charge density-functional tight-binding method: vibrational spectra and electronic structure of C(28), C(60), and C(70).

The self-consistent charge density-functional tight-binding (SCC-DFTB) method is employed for studying various molecular properties of small fullerenes: C(28), C(60), and C(70). The computed bond distances, vibrational infrared and Raman spectra, vibrational densities of states, and electronic densities of states are compared with experiment (where available) and density-functional theory (DFT) calculations using various basis sets. The presented DFT benchmark calculations using the correlation-consistent polarized valence triple zeta basis set are at present the most extensive calculations on harmonic frequencies of these species. Possible limitations of the SCC-DFTB method for the prediction of molecular vibrational and optical properties are discussed. The presented results suggest that SCC-DFTB is a computationally feasible and reliable method for predicting vibrational and electronic properties of such carbon nanostructures comparable in accuracy with small to medium size basis set DFT calculations at the computational cost of standard semiempirical methods.

Journal Article↗

Origin of the linear relationship between CH2/NH/O-SWNT reaction energies and sidewall curvature: armchair nanotubes.

The origin of the linear relationship between the reaction energy of the CH2/NH/O exo and endo additions to armchair (n, n) single-walled carbon nanotubes (SWNTs) and the inverse tube diameter (1/d) measuring sidewall curvature was elucidated using density functional theory and density functional tight binding methods for finite-size SWNT models with n = 3, 4, ..., 13. A nearly perfect linear relationship between DeltaE and 1/d all through exohedral (positive curvature) and endohedral (negative curvature) additions is due to cancellation between the quadratic contributions of the SWNT deformation energy and the interaction energy (INT) between the deformed SWNT and CH2/NH/O adducts. Energy decomposition analysis shows that the quadratic contributions in electrostatic, exchange, and orbital terms mostly cancel each other, making INT weakly quadratic, and that the linear 1/d dependence of INT, and therefore of DeltaE, is a reflection of the 1/d dependence of the back-donative orbital interaction of b1 symmetry from the occupied CH2/NH/O p pi orbital to the vacant C=C pi* LUMO of the SWNT. We also discuss the origin of the two isomers (open and three-membered ring) of the exohedral addition product and explain the behavior of their associated minima on the C-C potential energy surfaces with changing d.

Journal Article↗

Does dinitrogen hydrogenation follow different mechanisms for [(eta5-C5Me4H)2Zr]2(mu2,eta2,eta2-N2) and {[PhP(CH2SiMe2NSiMe2CH2)PPh]Zr}2(mu2,eta2,eta2-N2) complexes? A computational study.

The mechanisms of dinitrogen hydrogenation by two different complexes--[(eta(5)-C(5)Me(4)H)(2)Zr](2)(mu(2),eta(2),eta(2)-N(2)), synthesized by Chirik and co-workers [Nature 2004, 427, 527], and {[P(2)N(2)]Zr}(2)(mu(2),eta(2),eta(2)-N(2)), where P(2)N(2) = PhP(CH(2)SiMe(2)NSiMe(2)CH(2))(2)PPh, synthesized by Fryzuk and co-workers [Science 1997, 275, 1445]--are compared with density functional theory calculations. The former complex is experimentally known to be capable of adding more than one H(2) molecule to the side-on coordinated N(2) molecule, while the latter does not add more than one H(2). We have shown that the observed difference in the reactivity of these dizirconium complexes is caused by the fact that the former ligand environment is more rigid than the latter. As a result, the addition of the first H(2) molecule leads to two different products: a non-H-bridged intermediate for the Chirik-type complex and a H-bridged intermediate for the Fryzuk-type complex. The non-H-bridged intermediate requires a smaller energy barrier for the second H(2) addition than the H-bridged intermediate. We have also examined the effect of different numbers of methyl substituents in [(eta(5)-C(5)Me(n)H(5)(-)(n))(2)Zr](2)(mu(2),eta(2),eta(2)-N(2)) for n = 0, 4, and 5 (n = 5 is hypothetical) and [(eta(5)-C(5)H(2)-1,2,4-Me(3))(eta(5)-C(5)Me(5))(2)Zr](2)(mu(2),eta(2),eta(2)-N(2)) and have shown that all complexes of this type would follow a similar H(2) addition mechanism. We have also performed an extensive analysis on the factors (side-on coordination of N(2) to two Zr centers, availability of the frontier orbitals with appropriate symmetry, and inflexibility of the catalyst ligand environment) that are required for successful hydrogenation of the coordinated dinitrogen.

Journal Article↗

The true nature of the Di-iron(III) gamma-Keggin structure in water: catalytic aerobic oxidation and chemistry of an unsymmetrical trimer.

The complex [gamma(1,2)-SiW(10){Fe(OH(2))}(2)O(38)](6)(-) (1) has been reported to catalyze the much sought reductant-free selective O(2)-based epoxidation of alkenes (Nishiyama, Y.; Nakagawa, Y.; Mizuno, N. Angew. Chem. Int. Ed. 2001, 40, 3639-3641) in chlorocarbon-acetonitrile solution. The challenge of reproducing catalysis by 1 led us to examine this chemistry in detail. In H(2)O, a desirable solvent for catalysis, 1, does not exist in the proposed organic-medium form in which the two iron atoms are in the binding pocket defined by the equatorial oxygens and, importantly, by two oxygens bound to the central Si heteroatom. Instead, 1 in H(2)O initially forms an unusual trimer [{Fe(2)(OH)(3)(H(2)O)(2)}(3)(gamma-SiW(10)O(36))(3)](15)(-) (2). The X-ray structure of 2 shows that the Fe-O(Si) bonds are cleaved and new bonds (mu-hydroxo bridges) form between these Fe centers and those of the neighboring [gamma(1,2)-SiW(10)Fe(2)] units. Structural, physical, and computational evidence indicate that if the bonds between the d-electron center, M (Fe in the case of 1 and 2), and the terminal ligands on M are stronger than the M-O(x)() bonds, then the out-of-pocket form is more stable and is the one observed. Significantly, 2 in H(2)O forms an intermediate that catalyzes the effective aerobic oxidation of sulfur compounds (mercaptoethanol is oxidized to the corresponding disulfide by O(2) at ambient pressure and temperature). All experimental findings are consistent with dissociation of a gamma-SiW(10) Keggin unit from the trimer, 2, to form the catalytically active species.

Journal Article↗

The C60 formation puzzle "solved": QM/MD simulations reveal the shrinking hot giant road of the dynamic fullerene self-assembly mechanism.

The dynamic self-assembly mechanism of fullerene molecules is an irreversible process emerging naturally under the nonequilibrium conditions of hot carbon vapor and is a consequence of the interplay between the dynamics and chemistry of polyyne chains, pi-conjugation and corresponding stabilization, and the dynamics of hot giant fullerene cages. In this feature article we briefly present an overview of experimental findings and past attempts to explain fullerene formation and show in detail how our recent quantum chemical molecular dynamics simulations of the dynamics of carbon vapor far from thermodynamic equilibrium have assisted in the discovery of the combined size-up/size-down "shrinking hot giant" road that leads to the formation of buckminsterfullerene C60, C70, and larger fullerenes. This formation mechanism is the first reported case of order created out of chaos where a distinct covalent bond network of an entire molecule is spontaneously self-assembled to a highly symmetric structure and fully explains the fullerene formation process consistently with all available experimental observations a priori. Experimental evidence suggests that it applies universally to all fullerene formation processes irrespective of the carbon source.

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Theory and experiment agree: single-walled carbon nanotube caps grow catalyst-free with chirality preference on a SiC surface.

High-temperature quantum chemical molecular dynamics simulations have been performed on model systems of thin SiC crystal surfaces with two graphene sheets placed on top of either C or Si face. In agreement with experiment, we find that (a) the C-face-attached graphene layer warps readily to form small diameter, stable nanocaps, suitable for further perpendicular growth of nanotubes, (b) the Si-face-attached graphene sheet does not readily wrap and forms more volatile Si-graphene bonds, and (c) C face nanocaps appear to anneal to dome-shape structures with zigzag chirality.

Journal Article↗

Is the protein surrounding the active site critical for hydrogen peroxide reduction by selenoprotein glutathione peroxidase? An ONIOM study.

In this ONIOM(QM:MM) study, we evaluate the role of the protein surroundings in the mechanism of H2O2 reduction catalyzed by the glutathione peroxidase enzyme, using the whole monomer (3113 atoms in 196 amino acid residues) as a model. A new optimization scheme that allows the full optimization of transition states for large systems has been utilized. It was found that in the presence of the surrounding protein the optimized active site structure bears a closer resemblance to the one in the X-ray structure than that without the surrounding protein. H2O2 reduction occurs through a two-step mechanism. In the first step, the selenolate anion (E-Se(-)) formation occurs with a barrier of 16.4 kcal/mol and is endothermic by 12.0 kcal/mol. The Gln83 residue plays the key role of the proton abstractor, which is in line with the experimental suggestion. In the second step, the O-O bond is cleaved, and selenenic acid (R-Se-OH) and a water molecule are formed. The calculated barrier for this process is 6.0 kcal/mol, and it is exothermic by 80.9 kcal/mol. The overall barrier of 18.0 kcal/mol for H2O2 reduction is in reasonable agreement with the experimentally measured barrier of 14.9 kcal/mol. The protein surroundings has been calculated to exert a net effect of only 0.70 kcal/mol (in comparison to the "active site only" model including solvent effects) on the overall barrier, which is most likely due to the active site being located at the enzyme surface.

Binding Sites↗

Structure and reaction pathway of TMP-Zincate: amido base or alkyl base?

The novel directed ortho metalation (DoM) reagents for functionalized aromatic rings, TMP-Zn-ates (R2Zn(TMP)Li (R = Me, 1; tBu, 2)), have been reported to be synthetically useful for the chemo- and regioselective construction of multi-functionalized aromatic compounds. Here, we present the first comprehensive structural and mechanistic investigation by means of X-ray, NMR, and DFT studies on the DoM reaction employing our original TMP-Zn-ate base. The structures of TMP-Zn-ates in solution and in the solid state were determined. The DFT study strongly suggested that the deprotonation involving the TMP ligand on the TMP-Zn-ate is kinetically more favorable than that involving the alkyl ligand, and this view was supported by monitoring of the 13C NMR spectrum of the reaction mixture.

Crystallography, X-Ray↗

Insights into the mechanism of selective olefin epoxidation catalyzed by [gamma-(SiO4)W10O32H4]4-. A computational study.

A mechanism for the H2O2-based epoxidation of olefins catalyzed by the lacunary polyoxometalate (POM) [gamma-(SiO4)W10O32H4]4- (1) has been investigated at the DFT level. In this study, for the first time a "hydroperoxy" mechanism for this important process has been proposed. It is divided into two steps and investigated using the whole lacunary compound as a model. In the first step, a hydroperoxy (W-OOH) species and a water molecule are generated. The formation of this nonradical oxidant (W-OOH), consistent with the experimental suggestions, occurs with a barrier of 4.4 (7.2) kcal/mol (the number without parenthesis includes solvent effects in benzene, while the one with parenthesis is in the gas phase). In the second step, the O-O bond of the W-OOH species is cleaved, and an epoxide is formed. This step has a barrier of 38.7 (40.0) kcal/mol. It was found that the presence of one and two (CH3)4N+ countercations significantly reduces the rate-limiting barrier by 7.6 (8.3) and 11.9 (12.6) kcal/mol, respectively, and makes this lacunary POM a very efficient catalyst for epoxidation of olefins by hydrogen peroxide. It was demonstrated that the lacunary polyoxometalate basically acts as a mononuclear W(VI) complex in activating the oxidant, a conceptually noteworthy finding.

Journal Article↗

The heat of formation of chlorine-isocyanate and the relative stability of isoelectronic molecules: an experimental and theoretical study.

Accurate thermochemical data of small molecules are invaluable to the progress of every aspect of chemistry, especially in the atmosphere, combustion and industry. In this work, photofragmentation translational spectroscopy and 1st principles electronic structure theory reveal the literature value of the heat of formation of chlorine-isocyanate to be in error by more than 40 kcalmol. We report a revised experimental value for D0(Cl-NCO) = 51+/-3 kcal/mol which leads to a Delta Hf (ClNCO) = 8.5+/-3 kcal/mol. High level ab initio (CCSD(T)) electronic structure calculations extrapolated to the complete basis set limit give D0(Cl-NCO) = 6.3 kcal/mol, in good agreement with experiment. In light of the present results, the destabilization of azides relative to isoelectronic isocyanates has been evaluated empirically for three pairs of related molecules. It is found to be 90-110 kcal/mol, and has been attributed mainly to the weakening of the N-NN bond relative to the N-CO bond. Electronic structure calculations employing decomposition analysis suggest that, compared to homopolar N2, the (+delta)CO(-delta) pi polarity provides better orbital interaction (charge transfer) and electrostatic attraction and results in a closer encounter and larger stabilization between the fragments and that this is the origin of isoelectronic destabilization of azides relative to the isocyanates.

Journal Article↗

Computational studies of nucleophilic attack and protonation of electron-deficient benzoheterocycle triosmium clusters.

The density functional theory method has been applied to gain insights into the regioselectivity of nucleophilic attack and protonation of electron-deficient benzoheterocycle triosmium clusters. We report our computational results on the reaction of the green 46-electron triosmium clusters Os3(CO)(9)(mu3-eta2-(LH))(mu-H) (L = benzoxazole, 1a; benzothiazole, 1b; dihydroquinoline, 1c; 1,3-dehydroindoline, 1d; 4H-3,1-benzoxazine, 1e) with hydride (H-) and proton (H+) in order to elucidate factors affecting the observed differences in the structure of the kinetic products of these reactions. Transition-state calculations for the interconversion of the anionic tautomers resulting from H- attack on the clusters 1a-e show that the activation energies of these anionic clusters are considerably lower than the previously reported barriers for related neutral clusters. Calculations also reveal that the structures of the kinetic products resulting from sequential H-/H+ attack are determined by the protonation process.

Journal Article↗

Peroxynitrite reductase activity of selenoprotein glutathione peroxidase: a computational study.

The peroxynitrite reductase activity of selenoprotein glutathione peroxidase (GPx) has been investigated using density functional theory calculations for peroxynitrite/peroxynitrous acid (ONOO-/ONOOH) substrates through two different "oxidation" and "nitration" pathways. In the oxidation pathway for ONOO-, the oxidation of GPx and the subsequent formation of the selenenic acid (E-Se-OH) occur through a concerted mechanism with an energy barrier of 4.7 (3.7) kcal/mol, which is in good agreement with the computed value of 7.1 kcal/mol for the drug ebselen and the experimentally measured barrier of 8.8 kcal/mol for both ebselen and GPx. For ONOOH, the formation of the E-Se-OH prefers a stepwise mechanism with an overall barrier of 6.9 (11.3) kcal/mol, which is 10.2 (11.2) kcal/mol lower than that for hydrogen peroxide (H2O2), indicating that ONOOH is a more efficient substrate for GPx oxidation. It has been demonstrated that the active site Gln83 residue plays a critical role during the oxidation process, which is consistent with the experimental suggestions. The nitration of GPx by ONOOH produces a nitro (E-Se-NO2) product via either of two different mechanisms, isomerization and direct, having almost the same barrier heights. A comparison between the rate-determining barriers of the oxidation and nitration pathways suggests that the oxidation of GPx by ONOOH is more preferable than its nitration. It was also shown that the rate-determining barriers remain the same, 21.5 (25.5) kcal/mol, in the peroxynitrite reductase and peroxidase activities of GPx.

Computational Biology↗

Density functional study of the roles of chemical composition of di-transition-metal-substituted gamma-Keggin polyoxometalate anions.

The roles of chemical composition (X, M and M(FW)) of di-transition-metal-substituted gamma-Keggin polytungstates and polymolybdates, [(X(n)(+)O(4))M(2)(OH)(2)(M(FW))(10)O(32)]((8-n)-), on the geometry, electronic structure, and magnetic properties of these species have been investigated at the density functional level. It was shown that the change of the heteroatom X via Al(III)-Si(IV)-P(V)-S(VI) slightly stabilizes the broken-symmetry (BS) state over the high-spin (HS) state, increases the antiferromagnetic coupling constant, J, of these species, and lowers the energies of their highest-occupied molecular orbitals (HOMOs) and lowest-unoccupied molecular orbitals (LUMOs). The change of the redox-active center M from Mn to Fe slightly increases the M-(XO(4)) interaction, J-coupling constant, and energy gap between the HS and BS states. Meanwhile, the LUMOs are stabilized, indicating the stronger oxidant character of [(X(n)(+)O(4))M(2)(OH)(2)W(10)O(32)]((8-n)-) for M = Fe than Mn. It was shown that the change of addenda atom M(FW) from W to Mo makes (a) the geometry of Keggin "cage" slightly smaller, (b) the interaction of redox-active centers (Fe) with the central XO(4)-unit slightly stronger, and (c) the J-coupling constant, as well as the energy gap DeltaE(BS-HS), slightly larger.

Journal Article↗

A study of the reaction of N+ with O2: experimental quantification of NO+(a 3Sigma+) production (298-500 K) and computational study of the overall reaction pathways.

The product branching ratios for NO+(X 1Sigma+) and NO+(a 3Sigma+) produced from the reaction of N+ with O2 have been measured at 298 and 500 K in a selected ion flow tube. Approximately 0.5% of the total products are in NO+(a) at both temperatures, despite the fact that the reaction to form NO+(a) is 0.3 eV exothermic. High-level ab initio calculations of the potential energy surfaces for the N+ + O2 reaction show that the reaction from N+(3P) + O2(3Sigma(g)) reactants starts with an efficient early stage charge transfer to the N(2D) + O2+(X 2Pi) channel, which gives rise to the O2+(X 2Pi) product and, at the same time, serves as the starting point for all of the reaction channels leading to NO+ and O+ products. Pathways to produce NO+(a 3Sigma+) are found to be less favorable than pathways leading to the major product NO+(X 1Sigma+). Production of N(2D) has implications for the concentration of NO in the mesosphere.

Journal Article↗

An experimental and theoretical study of ring closing dynamics in HN3.

We report on an H(D)-atom Rydberg tagging experiment for H(D)N(3) photolysis providing detailed dynamical information on the wavelength dependence of the H(D) + N(3) channel. We observe subtle yet striking changes in the photochemical dynamics as the photolysis energy passes through approximately 5.6 eV. In addition to producing linear azide with an average of approximately 40% of available energy appearing as translation, a second H(D)-atom producing channel grows in above this energy releasing only about 15%. An observed (inverse) isotope effect suggests that statistical decomposition on S(0) is unimportant. High level ab initio quantum chemical calculations reveal a transition state to cyclization of the N(3) moiety in H(D)N(3) on the first excited singlet (S(1)) surface that is close in energy to the experimentally observed threshold energy for this "slow channel". Furthermore, the translational energy release of the "slow channel" is energetically consistent with cyclic-N(3) formation. This work provides the clearest presently available insights into how ring closure can occur in azide photochemistry.

Azides↗

Computational insights into the mechanism of radical generation in B12-dependent methylmalonyl-CoA mutase.

ONIOM calculations have provided novel insights into the mechanism of homolytic Co-C5' bond cleavage in the 5'-deoxyadenosylcobalamin cofactor catalyzed by methylmalonyl-CoA mutase. We have shown that it is a stepwise process in which conformational changes in the 5'-deoxyadenosine moiety precede the actual homolysis step. In the transition state structure for homolysis, the Co-C5' bond elongates by approximately 0.5 Angstroms from the value found in the substrate-bound reactant complex. The overall barrier to homolysis is approximately 10 kcal/mol, and the radical products are approximately 2.5 kcal/mol less stable than the initial ternary complex of enzyme, substrate, and cofactor. The movement of the deoxyadenosine moiety during the homolysis step positions the resulting 5'-deoxyadenosyl radical for the subsequent hydrogen atom transfer from the substrate, methylmalonyl-CoA.

Adenosine↗