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The crucial roles of MgCl2 as a non-innocent additive in the Ni-catalyzed carboxylation of benzyl halide with CO2.
Chem. Commun. (Camb.)
PUBLISHED: 09-17-2014
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Ni-catalyzed carboxylation of the C(sp(3))-Cl bond with CO2 in the presence of MgCl2 was theoretically investigated. MgCl2 plays three crucial roles in stabilization of a Ni(I)-CO2 adduct and acceleration of the CO2 insertion as a non-innocent additive and the one-electron reduction process as one kind of reagent.
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Nickel-catalyzed double carboxylation of alkynes employing carbon dioxide.
Org. Lett.
PUBLISHED: 09-08-2014
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The nickel-catalyzed double carboxylation of internal alkynes employing carbon dioxide (CO2) has been developed. The reactions proceed under CO2 (1 atm) at room temperature in the presence of a nickel catalyst, Zn powder as a reducing reagent, and MgBr2 as an indispensable additive. Various internal alkynes could be converted to the corresponding maleic anhydrides in good to high yields. DFT calculations disclosed the indispensable role of MgBr2 in the second CO2 insertion.
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Proton transfers in the Strecker reaction revealed by DFT calculations.
Beilstein J Org Chem
PUBLISHED: 08-01-2014
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The Strecker reaction of acetaldehyde, NH3, and HCN to afford alanine was studied by DFT calculations for the first time, which involves two reaction stages. In the first reaction stage, the aminonitrile was formed. The rate-determining step is the deprotonation of the NH3 (+) group in MeCH(OH)-NH3 (+) to form 1-aminoethanol, which occurs with an activation energy barrier (?E (?)) of 9.6 kcal/mol. The stereochemistry (R or S) of the aminonitrile product is determined at the NH3 addition step to the carbonyl carbon of the aldehyde. While the addition of CN(-) to the carbon atom of the protonated imine 7 appears to scramble the stereochemistry, the water cluster above the imine plane reinforces the CN(-) to attack the imine group below the plane. The enforcement hinders the scrambling. In the second stage, the aminonitrile transforms to alanine, where an amide Me-CH(NH2)-C(=O)-NH2 is the key intermediate. The rate-determining step is the hydrolysis of the cyano group of N(amino)-protonated aminonitrile which occurs with an ?E (?) value of 34.7 kcal/mol. In the Strecker reaction, the proton transfer along the hydrogen bonds plays a crucial role.
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Generation of dihydrogen molecule and hydrosilylation of carbon dioxide catalyzed by zinc hydride complex: theoretical understanding and prediction.
Inorg Chem
PUBLISHED: 07-30-2014
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Generation of H2 from methanol/water and hydrosilylation of CO2 catalyzed by [tris(2-pyridylthio)methyl]zinc hydride [?(3)-Tptm]ZnH 1 were investigated with DFT and MP2 methods. The hydrosilylation of CO2 occurs via the CO2 insertion into the Zn-H bond of 1 followed by the metathesis of a Zn-(?(1)-OCOH) bond with hydrosilane to yield silyl formate and regenerate 1. The CO2 insertion easily occurs, but the metathesis is difficult because of the formation of a very stable Zn-(?(2)-O2CH) species before the metathesis. The ?G°(‡) value of the metathesis with triethoxysilane is much smaller than that with phenylsilane because electronegative methoxy groups stabilize the transition state bearing hypervalent Si center, which is consistent with the experimental result that triethoxysilane is used in the hydrosilylation of CO2. It is theoretically predicted here that hydrosilane with two electronegative OEt groups or one to three F groups can be applied to this reaction. In the generation of H2 from methanol/water by 1, the first step is the metathesis of 1 with the O-H bond of methanol/water to produce [?(3)-Tptm]Zn(OMe)/[k(3)-Tptm]Zn(OH) and dihydrogen molecule. The next step is the metathesis of the Zn-OMe/Zn-OH bond with hydrosilane to yield silyl ether and regenerate 1. The first metathesis is rate-determining but the second one occurs with very small activation energy, indicating that various hydrosilanes can be applied to this reaction.
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A DFT study on proton transfers in hydrolysis reactions of phosphate dianion and sulfate monoanion.
J Comput Chem
PUBLISHED: 07-01-2014
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B3LYP calculations were carried out on hydrolysis reactions of monosubstituted(R) phosphate dianion and sulfate monoanion. In the reacting system, water clusters (H2 O)22 and (H2 O)35 are included to trace reaction paths. For both P and S substrates with R?=?methyl group, elementary processes were calculated. While the phosphate undergoes the substitution at the phosphorus, the sulfate does at the methyl carbon. For the S substrate with R?=?neopentyl group, the product tert-amyl alcohol was found to be formed via a dyotropic rearrangement from the neopentyl alcohol intermediate. For R?=?aryl groups, transition-state geometries were calculated to be similar between P and S substrates. Calculated activation energies are in good agreement with experimental values. After the rate-determining transition state of the substitution, the hydronium ion H3 O(+) is formed at the third water molecule. It was suggested that alkyl and aryl substrates are of the different reactivity of the hydrolysis. © 2014 Wiley Periodicals, Inc.
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?-Bond activation of small molecules and reactions catalyzed by transition-metal complexes: theoretical understanding of electronic processes.
Inorg Chem
PUBLISHED: 04-30-2014
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?-Bond activations of R1-R2 and R1-X1 (R1, R2 = H, alkyl, aromatics, etc.; X1 = electronegative group) by transition-metal complexes are classified into two main categories: ?-bond activation by a metal (M) center and that by a metal-ligand bond. The former is classified into two subcategories: concerted oxidative addition to M and stepwise oxidative addition via nucleophilic attack of M. The latter is also classified into two subcategories: heterolytic activaton by M-X2 (X2 = anion ligand) and oxidative addition to M-L (L = neutral ligand). In the concerted oxidative addition, charge transfer (CT) occurs from the M d orbital to the ?* antibonding orbital of R1-R2, the clear evidence of which is presented here. The concerted oxidative additions of Ph-CN, Me-CN, and Ph-Cl to a nickel(0) complex are discussed as examples. The stepwise oxidative addition occurs through nucleophilic attack of M to R1-X1 to form an ion-pair intermediate. In the nucleophilic attack, CT occurs from the M d? to either the ?* orbital or empty p? orbital of R1-X1. Solvation plays a crucial role in stabilizing the transition state and ion-pair intermediate. The oxidative addition reactions of Ph-I, CH3-Br, and Br2B(OSiH3) to platinum(0), platinum(II), and palladium(0) complexes are discussed. In the heterolytic activation of R1-R2 by an M-X2 bond, R1 and R2 are bound with M and X2, respectively, indicating that R1 becomes anion-like and R2 becomes cation-like. CT mainly occurs from the X2 ligand to the ?* antibonding orbital of R1-R2 and also from R1 to the M empty d orbital. In the oxidative addition to an M-L moiety, R1 is bound with M, R2 is bound with L, and thus-formed L-R2 is bound with M. The oxidative addition reaction of the Si-H bond of silane to Cp2Zr(C2H4) and that of the H-H bond of H2 to Ni[MesB(o-Ph2PC6H4)2] are discussed as examples. The importance of the ?-bond activation in such catalytic reactions as nickel(0)-catalyzed phenylcyanation of alkyne, nickel(0)-catalyzed carboxylation of phenyl chloride, ruthenium(II)-catalyzed hydrogenation of carbon dioxide, and the Hiyama cross-coupling reaction is discussed based on theoretical studies.
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The important role of the Mo-Mo quintuple bond in catalytic synthesis of benzene from alkynes. A theoretical study.
Dalton Trans
PUBLISHED: 04-07-2014
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The Mo-Mo quintuple bond was recently applied to catalytic synthesis of benzene from alkynes, which is the first example of the catalytic reaction of the metal-metal multiple bond. This new reaction was studied using DFT and CASSCF/CASPT2 methods. The entire catalytic cycle consists of four steps: [2 + 2], [4 + 2], and [6 + 2] cycloadditions, and reductive elimination of benzene. The symmetry-forbidden [2 + 2] cycloaddition and asymmetric [2 + 2] cycloaddition are two possible pathways for the reaction between an alkyne and the Mo-Mo quintuple bond. Though the barrier of the former pathway is moderate because of the presence of the multi-reference character of the Mo-Mo quintuple bond, the asymmetric pathway is much more favorable because of its symmetry-allowed feature. The C-C bond formation in the next [4 + 2] cycloaddition occurs through charge transfer (CT) from the ? orbital of the incoming alkyne to the ?* orbital of another alkyne coordinating with the Mo center to afford a novel dimolybdenacyclic species 3. In 3, the ?(d(xz)) and ?(d(xz))* orbitals of the Mo-Mo moiety and four ? orbitals of the [C4H4] moiety construct the ? and ?* orbitals in the six-membered ring. The next [6 + 2] cycloaddition between 3 and one more alkyne affords an eight-membered ring compound 4 which has a Mo-Mo quadruple bond. This is the rate-determining step of the entire catalytic cycle, the ?G(0‡) value of which is 22.4 kcal mol(-1). The subsequent reductive elimination of benzene easily occurs to yield a ?2-?(2):?(2)-benzene dinuclear Mo complex with a Mo-Mo quintuple bond. On the other hand, further [8 + 2] cycloaddition between 4 and one more alkyne is much more unfavorable than the reductive elimination of benzene. The similar [4 + 2] process between alkyne and a Cr-Cr quadruple bond is calculated to be difficult, which is consistent with the experimental result that only the Mo-Mo quintuple bond was successfully applied to this reaction. It is likely that the crowded coordination environment and the much more stable ?(d(yz)) orbital in the Cr-Cr quadruple bond are responsible for the difficulty in the reaction.
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Catalytic transfer hydrogenation by a trivalent phosphorus compound: phosphorus-ligand cooperation pathway or P(III) /P(V) redox pathway?
Angew. Chem. Int. Ed. Engl.
PUBLISHED: 03-25-2014
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Main-group-element catalysts are a desirable alternative to transition-metal catalysts because of natural abundance and cost. However, the examples are very limited. Catalytic cycles involving a redox process and E-ligand cooperation (E=main-group element), which are often found in catalytic cycles of transition-metal catalysts, have not been reported. Herein theoretical investigations of a catalytic hydrogenation of azobenzene with ammonia-borane using a trivalent phosphorus compound, which was experimentally proposed to occur through P(III) /P(V) redox processes via an unusual pentavalent dihydridophosphorane, were performed. DFT and ONIOM(CCSD(T):MP2) calculations disclosed that this catalytic reaction occurs through a P-O cooperation mechanism, which resembles the metal-ligand cooperation mechanism of transition-metal catalysts.
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Interaction of various gas molecules with paddle-wheel-type open metal sites of porous coordination polymers: theoretical investigation.
Inorg Chem
PUBLISHED: 02-10-2014
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We theoretically evaluated binding energies (Eb's) between various gas molecules and the Cu center open metal site (Cu-OMS) of Cu paddle-wheel units, [Cu2(O2CR)4] (R = H, Me, or Ph) using density functional theory (DFT) and MP2-MP4. The optimized geometry of the model system [Cu2(O2CPh)4] agrees with the experimental structure. The Eb of CO with [Cu2(O2CH)4] is only slightly different between the open-shell singlet and triplet states. The calculated Eb decreases in the order MeNC > H2O > MeCN > C2H4 > C2H2 > CO > CO2 > N2 > CH4 > H2. The trend is discussed in terms of the electrostatic interaction energy (ES), exchange repulsion energy (EX), and charge-transfer (CT) + polarization (Pol) interaction energy at the Hartree-Fock level and the electron correlation effect. The ES increases linearly with an increase in Eb, while the EX decreases linearly with an increase in Eb. These relationships indicate that the ES compensates for the EX. In other words, the Eb does not depend on the sum of ES and EX, which corresponds to the static energy. The electron correlation effect contributes little to the above-mentioned decreasing order of Eb. The total Eb roughly increases with an increase in the CT+Pol term, suggesting that the CT+Pol term plays important roles in determining the trend of Eb. The shift of the stretching frequency of adsorbed gas molecules on the Cu-OMS is reproduced well by the DFT calculation with the model system [Cu2(O2CH)4(L)2] (L = gas molecule). We found that the positive charge on the Cu significantly contributes to the shift in the end-on coordination gas molecules such as CO, MeNC, MeCN, and N2. Although the shift has been generally discussed in terms of donation and back-donation, the present result indicates that the electrostatic potential field in the porous coordination polymer should be considered in the discussion of the frequency shift.
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CASPT2 study of inverse sandwich-type dinuclear Cr(I) and Fe(I) complexes of the dinitrogen molecule: significant differences in spin multiplicity and coordination structure between these two complexes.
J Phys Chem A
PUBLISHED: 02-10-2014
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Inverse sandwich-type complexes (ISTCs), (?-N2)[M(AIP)]2 (AIPH = (Z)-1-amino-3-imino-prop-1-ene; M = Cr and Fe), were investigated with the CASPT2 method. In the ISTC of Cr, the ground state takes a singlet spin multiplicity. However, the singlet to nonet spin states are close in energy to each other. The thermal average of effective magnetic moments (?eff) of these spin multiplicities is close to the experimental value. The ?(2)-side-on coordination structure of N2 is calculated to be more stable than the ?(1)-end-on coordination one. This is because the d-orbital of Cr forms a strong d?-?* bonding interaction with the ?* orbital of N2 in molecular plane. In the ISTC of Fe, on the other hand, the ground state takes a septet spin multiplicity, which agrees well with the experimentally reported ?eff value. The ?(1)-end-on structure of N2 is more stable than the ?(2)-side-on structure. In the ?(1)-end-on structure, two doubly occupied d-orbitals of Fe can form two d?-?* bonding interactions. The negative spin density is found on the bridging N2 ligand in the Fe complex but is not in the Cr complex. All these interesting differences between ISTCs of Cr and Fe are discussed on the basis of the electronic structure and bonding nature.
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S(N)1-S(N)2 and S(N)2-S(N)3 mechanistic changes revealed by transition states of the hydrolyses of benzyl chlorides and benzenesulfonyl chlorides.
J Comput Chem
PUBLISHED: 01-23-2014
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Hydrolysis reactions of benzyl chlorides and benzenesulfonyl chlorides were theoretically investigated with the density functional theory method, where the water molecules are explicitly considered. For the hydrolysis of benzyl chlorides (para-Z-C6H4-CH2-Cl), the number of water molecules (n) slightly influences the transition-state (TS) structure. However, the para-substituent (Z) of the phenyl group significantly changes the reaction process from the stepwise (S(N)1) to the concerted (S(N)2) pathway when it changes from the typical electron-donating group (EDG) to the typical electron-withdrawing one (EWG). The EDG stabilizes the carbocation (MeO-C6H4-CH2(+)), which in turn makes the S(N)1 mechanism more favorable and vice versa. For the hydrolysis of benzenesulfonyl chlorides (para-Z-C6H4-SO2-Cl), both the Z group and n influence the TS structure. For the combination of the large n value (n?>?9) and EDG, the S(N)2 mechanism was preferred. Conversely, for the combination of the small n value and EWG, the S(N)3 one was more favorable.
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Substrate dependent reaction channels of the Wolff-Kishner reduction reaction: A theoretical study.
Beilstein J Org Chem
PUBLISHED: 01-01-2014
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Wolff-Kishner reduction reactions were investigated by DFT calculations for the first time. B3LYP/6-311+G(d,p) SCRF=(PCM, solvent = 1,2-ethanediol) optimizations were carried out. To investigate the role of the base catalyst, the base-free reaction was examined by the use of acetone, hydrazine (H2N-NH2) and (H2O)8. A ready reaction channel of acetone ? acetone hydrazine (Me2C=N-NH2) was obtained. The channel involves two likely proton-transfer routes. However, it was found that the base-free reaction was unlikely at the N2 extrusion step from the isopropyl diimine intermediate (Me2C(H)-N=N-H). Two base-catalyzed reactions were investigated by models of the ketone, H2N-NH2 and OH(-)(H2O)7. Here, ketones are acetone and acetophenone. While routes of the ketone ? hydrazone ? diimine are similar, those from the diimines are different. From the isopropyl diimine, the N2 extrusion and the C-H bond formation takes place concomitantly. The concomitance leads to the propane product concertedly. From the (1-phenyl)ethyl substituted diimine, a carbanion intermediate is formed. The para carbon of the phenyl ring of the anion is subject to the protonation, which leads to a 3-ethylidene-1,4-cyclohexadiene intermediate. Its [1,5]-hydrogen migration gives the ethylbenzene product. For both ketone substrates, the diimines undergoing E2 reactions were found to be key intermediates.
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Self-Accelerating CO Sorption in a Soft Nanoporous Crystal.
Science
PUBLISHED: 12-12-2013
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Carbon monoxide (CO) produced in many large-scale industrial oxidation processes is difficult to separate from nitrogen (N2) and after it just further oxidized to CO2. We report a new soft nanoporous crystalline material that selectively adsorbs CO with adaptable pores, and present crystallographic evidence that CO molecules can coordinate with Cu(2+) ions. The unprecedented high selectivity was achieved by the synergetic effect of the local interaction between CO and accessible metal sites and a global transformation of the framework. This transformable crystalline material realized the separation of CO from mixtures with N2, a gas that is the most competitive to CO. The dynamic and efficient molecular trapping and releasing system is reminiscent of sophisticated biological systems such as heme proteins.
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Theoretical study of mononuclear nickel(I), nickel(0), copper(i), and cobalt(I) dioxygen complexes: new insight into differences and similarities in geometry and bonding nature.
Inorg Chem
PUBLISHED: 11-06-2013
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Geometries, bonding nature, and electronic structures of (N^N)Ni(O2) (N^N = ?-diketiminate), its cobalt(I) and copper(I) analogues, and (Ph3P)2Ni(O2) were investigated by density functional theory (DFT) and multistate restricted active space multiconfigurational second-order perturbation (MS-RASPT2) methods. Only (N^N)Ni(O2) takes a C(S) symmetry structure, because of the pseudo-Jahn-Teller effect, while all other complexes take a C(2V) structure. The symmetry lowering in (N^N)Ni(O2) is induced by the presence of the singly occupied ?(d(xy)-?(x)*) orbital. In all of these complexes, significant superoxo (O2-) character is found from the occupation numbers of natural orbitals and the O-O ?* bond order, which is independent of the number of d electrons and the oxidation state of metal center. However, this is not a typical superoxo species, because the spin density is not found on the O2 moiety, even in open-shell complexes, (N^N)Ni(O2) and (N^N)Co(O2). The M-O and O-O distances are considerably different from each other, despite the similar superoxo character. The M-O distance and the interaction energy between the metal and O2 moieties are determined by the d(yz) orbital energy of the metal moiety taking the valence state. The binding energy of the O2 moiety is understood in terms of the d(yz) orbital energy in the valence state and the promotion energy of the metal moiety from the ground state to the valence state. Because of the participations of various charge transfer (CT) interactions between the metal and O2 moieties, neither the d(yz) orbital energy nor the electron population of the O2 moiety are clearly related to the O-O bond length. Here, the ? bond order of the O2 moiety is proposed as a good measure for discussing the O-O bond length. Because the d electron configuration is different among these complexes, the CT interactions are different, leading to the differences in the ? bond order and, hence, the O-O distance among these complexes. The reactivity of dioxygen complex is discussed with the d(yz) orbital energy.
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The crucial role of a Ni(I) intermediate in Ni-catalyzed carboxylation of aryl chloride with CO2: a theoretical study.
Chem. Commun. (Camb.)
PUBLISHED: 10-09-2013
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In Ni(0)-catalyzed carboxylation reaction of aryl chloride with CO2, the formation of a Ni(I) species is crucial, because the CO2 insertion into the Ni(I)-Ph bond easily occurs but that into the Ni(II)-Ph bond cannot. This is a key point of this successful carboxylation reaction.
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Theoretical study of reactivity of Ge(II)-hydride compound: comparison with Rh(I)-hydride complex and prediction of full catalytic cycle by Ge(II)-hydride.
J. Am. Chem. Soc.
PUBLISHED: 06-06-2013
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The reaction of a Ge(II) hydride compound HC{CMeArN}2GeH (Ar = 2,6-iPr2C6H3) 1 with 2,2,2-trifluoroacetophenone (CF3PhCO) is theoretically investigated with density functional theory and spin-component-scaled second-order Møller-Plesset methods. This reaction easily occurs with moderate activation barrier and considerably large exothermicity, to afford a Ge(II) alkoxide 2 through a four-membered transition state. In the transition state, the charge transfer from the Ge-H ?-bonding molecular orbital (MO) to the C?O ?*-antibonding MO of CF3PhCO plays an important role. Acetone ((CH3)2CO) and benzophenone (Ph2CO) are not reactive for 1, because their ?*-antibonding MOs exist at higher energy than that of CF3PhCO. Though 2 is easily formed, the catalytic hydrogenation of CF3PhCO by 1 is difficult because the reaction of 2 with a dihydrogen molecule needs a large activation energy. On the other hand, our calculations clearly show that the catalytic hydrogenation of ketone by cis-RhH(PPh3)24 easily occurs, as expected. The comparison of catalytic cycle between 1 and 4 suggests that the strong Ge-O bond of 2 is the reason of the very large activation energy for the hydrogenation by 1. To overcome this defect, we investigated various reagents and found that the catalytic cycle can be completed with the use of SiF3H. The product is silylether CF3PhCHOSiF3, which is equivalent to alcohol because it easily undergoes hydrolysis to afford CF3PhCHOH. The similar catalytic cycles are also theoretically predicted for hydrosilylations of CO2 and imine. This is the first theoretical prediction of the full catalytic cycle with a heavier main-group element compound.
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Interest in new heterodinuclear transition-metal/main-group-metal complexes: DFT study of electronic structure and mechanism of fluoride sensing function.
Dalton Trans
PUBLISHED: 05-01-2013
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Systematic DFT calculations were carried out on a series of heterodinuclear complexes [(o-(Ph2P)C6H4)3M(1)M(2)Cl](+) (M(1) = As, Sb, or Bi; M(2) = Pd or Pt) to investigate the mechanism of colorimetric sensing function for the fluoride anion. The fluoride anion binds with the M(1) center to afford a hypervalent M(1) species with large stabilization energy. For instance, the stabilization energy by the fluoride adduct formation is -15.5 kcal mol(-1) for 3 (M(1) = Sb; M(2) = Pd) and -16.2 kcal mol(-1) for 6 (M(1) = Sb; M(2) = Pt), where a negative value represents stabilization. Interestingly, the allosteric coordination of the third phosphine with the M(2) center is induced by the fluoride adduct formation. For chloride, bromide, and thiocyanide anions, the binding energies are positive (~4.5 kcal mol(-1)), and the allosteric coordination does not occur. The allosteric coordination plays a crucial role in the absorption spectrum change induced by the fluoride adduct formation. For instance, the fluoride adduct formation quenches the absorption band of 3 around 400 nm and newly exhibits two absorption peaks at longer wavelength, 475 and 451 nm. These two peaks are assigned to ligand-field transitions (d(xy)? d(z(2)) and d(x(2)-y(2))? d(z(2))) including metal-to-ligand charge transfer character. We discussed the reasons why the allosteric coordination can occur only in the fluoride adduct and induces these two absorptions in the longer wavelength region. In addition, the Bi-Pd combination is also recommended for a fluoride sensing material, while the Sb-Pt combination is recommended for cyanide sensing.
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Levoglucosan formation from crystalline cellulose: importance of a hydrogen bonding network in the reaction.
ChemSusChem
PUBLISHED: 04-15-2013
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Levoglucosan (1,6-anhydro-?-D-glucopyranose) formation by the thermal degradation of native cellulose was investigated by MP4(SDQ)//DFT(B3LYP) and DFT(M06-2X)//DFT(B3LYP) level computations. The computational results of dimer models lead to the conclusion that the degradation occurs by a concerted mechanism similar to the degradation of methyl ?-D-glucoside reported in our previous study. One-chain models of glucose hexamer, in which the interchain hydrogen bonds of real cellulose crystals are absent, do not exhibit the correct reaction behavior of levoglucosan formation; for instance, the activation enthalpy (Ea =?38?kcal?mol(-1) ) is considerably underestimated compared to the experimental value (48-60?kcal?mol(-1) ). This problem is solved with the use of two-chain models that contain interchain hydrogen bonds. The theoretical study of this model clearly shows that the degradation of the internal glucosyl residue leads to the formation of a levoglucosan precursor at the chain end and levoglucosan is selectively formed from this levoglucosan end. The calculated Ea (56-62?kcal?mol(-1) ) agrees well with the experimental value. The computational results of three-chain models indicate that this degradation occurs selectively on the crystalline surface. All these computational results provide a comprehensive understanding of several experimental facts, the mechanisms of which have not yet been elucidated.
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A 3D-RISM-SCF method with dual solvent boxes for a highly polarized system: application to 1,6-anhydrosugar formation reaction of phenyl ?- and ?-D-glucosides under basic conditions.
Phys Chem Chem Phys
PUBLISHED: 03-26-2013
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One of the difficulties in application of the usual reference interaction site model self-consistent field (RISM-SCF) method to a highly polarized and bulky system arises from the approximate evaluation of electrostatic potential (ESP) with pure point charges. To improve this ESP evaluation, the ESP near a solute is directly calculated with a solute electronic wavefunction, that distant from a solute is approximately calculated with solute point charges, and they are connected with a switching function. To evaluate the fine solvation structure near the solute by incorporating the long-range solute-solvent Coulombic interaction with low computational cost, we introduced the dual solvent box protocol; one small box with the fine spacing is employed for the first and the second solvation shells and the other large box with the normal spacing is employed for long-range solute-solvent interaction. The levoglucosan formation from phenyl ?- and ?-d-glucosides under basic conditions is successfully inspected by this 3D-RISM-SCF method at the MP2 and SCS-MP2 levels, though the 1D-RISM-SCF could not be applied to this reaction due to the presence of highly polarized and bulky species. This 3D-RISM-SCF calculation reproduces the experimentally reported higher reactivity of the ?-anomer. The 3D-RISM-SCF-calculated activation free energy for the ?-anomer is closer to the experimental value than the PCM-calculated one. Interestingly, the solvation effect increases the difference in reactivity between these two anomers. The reason is successfully elucidated with 3D-RISM-SCF-calculated microscopic solvation structure and decomposition analysis of solute-solvent interaction.
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Absorption of CO2 and CS2 into the Hofmann-type porous coordination polymer: electrostatic versus dispersion interactions.
J. Am. Chem. Soc.
PUBLISHED: 03-14-2013
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Absorption of CO2 and CS2 molecules into the Hofmann-type three-dimensional porous coordination polymer (PCP) {Fe(Pz)[Pt(CN)4]}n (Pz = pyrazine) was theoretically explored with the ONIOM(MP2.5 or SCS-MP2:DFT) method, where the M06-2X functional was employed in the DFT calculations. The binding energies of CS2 and CO2 were evaluated to be -17.3 and -5.2 kcal mol(-1), respectively, at the ONIOM(MP2.5:M06-2X) level and -16.9 and -4.4 kcal mol(-1) at the ONIOM(SCS-MP2:M06-2X) level. It is concluded that CS2 is strongly absorbed in this PCP but CO2 is only weakly absorbed. The absorption positions of these two molecules are completely different: CO2 is located between two Pt atoms, whereas one S atom of CS2 is located between two Pz ligands and the other S atom is between two Pt atoms. The optimized position of CS2 agrees with the experimentally reported X-ray structure. To elucidate the reasons for these differences, we performed an energy decomposition analysis and found that (i) both the large binding energy and the absorption position of CS2 arise from a large dispersion interaction between CS2 and the PCP, (ii) the absorption position of CO2 is mainly determined by the electrostatic interaction between CO2 and the Pt moiety, and (iii) the small binding energy of CO2 comes from the weak dispersion interaction between CO2 and the PCP. Important molecular properties relating to the dispersion and electrostatic interactions, which are useful for understanding and predicting gas absorption into PCPs, are discussed in detail.
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Unexpected electronic process of H2 activation by a new nickel borane complex: comparison with the usual homolytic and heterolytic activations.
Inorg Chem
PUBLISHED: 03-06-2013
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H-H ?-bond activation promoted by Ni[MesB(o-Ph2PC6H4)2] (1(Mes)) was theoretically investigated with the density functional theory method. In 1(Mes), the nickel 3d, 4s, and 4p orbital populations are similar to those of the typical nickel(II) complex. First, one H2 molecule coordinates with the nickel center to form a dihydrogen complex, 2, which induces an increase in the nickel 3d and 4p orbital populations and thus a decrease in the nickel oxidation state. Then, the H-H ?-bond is cleaved under the unusual cooperation of the electron-rich nickel center and the electron-deficient borane ligand in a polarized manner, leading to an unprecedented trans-nickel(II) hydridoborohydrido complex, 3. In the transition state, charge transfer (CT) occuring from the H2 moiety to the 1(Mes) moiety (0.683 e) is much larger than the reverse CT (0.284 e). As a result, cleavage of the H-H ?-bond affords two positively charged hydrogen atoms. In this process, the boron atomic population and the nickel 4p orbital population increase, but the nickel 3d orbital population decreases. After cleavage of the H-H ?-bond, CT from the nickel 4p orbital to these positively charged hydrogen atoms occurs to afford 3, where the oxidation state of the nickel center increases to +2. These electronic processes are different from those of the usual homolytic and heterolytic H-H ?-bond activations. Regeneration of 1(Mes) and the role of the borane ligand in these reactions are also discussed in detail.
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Three competitive transition states at the glycosidic bond of sucrose in its acid-catalyzed hydrolysis.
J. Org. Chem.
PUBLISHED: 02-14-2013
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The acid-catalyzed hydrolysis of sucrose to glucose and fructose was investigated by DFT calculations. Protonations to three ether oxygen atoms of the sucrose molecule, A, B, and (C, D), were compared. Three (B, the fructosyl-ring oxygen protonation; C, protonation to the bridge oxygen of the glycosidic bond for the glucosyl-oxygen cleavage; and D, protonation to that for the fructosyl-oxygen cleavage) gave the fragmentation. Paths B, C, and D were examined by the use of the sucrose molecule and H3O(+)(H2O)13. The path B needs a large activation energy, indicating that it is unlikely. The fragmentation transition state (TS1) of path C needs almost the same activation energy as that of path D. The isomerization TS of Int(C) ? Int(D), TS(C ? D), was also obtained as a bypass route. The present calculations showed that the path via the fructosyl-oxygen cleavage (D) is slightly (not absolutely) more favorable than that via the glucosyl-oxygen cleavage (C).
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A theoretical study of luminescent vapochromic compounds including an AuCu2(NHC)2 core.
Dalton Trans
PUBLISHED: 01-31-2013
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Vapochromic complexes [Au(im(CH(2)py)(2))(2)(Cu(MeCN)(2))(2)](3+) 1, [Au(im(CH(2)py)(2))(2)(Cu(MeOH))(2)](3+) 2 and [Au(im(CH(2)py)(2))(2)(Cu(H(2)O))(2)](3+) 3 were theoretically investigated. The Au–Cu distances of 1 and 2 (4.631 Å and 2.767 Å, respectively) optimized by the SCS-MP2 method in this work agree with the literature experimental values (4.591 Å and 2.792 Å). Their structural features are explained by computational results: (i) in 1, two MeCN molecules coordinate with the Cu center, because of the strong coordination ability of MeCN, to afford a four-coordinate tetrahedral-like Cu center. This geometry needs a long Au–Cu distance. (ii) In 2 and 3, only one MeOH or H(2)O molecule coordinates with the Cu center because of their weak coordination abilities, to afford a three-coordinate planar Cu center. Because the three-coordinate Cu center is flexible, the Au–Cu distance becomes short due to the Au–Cu metallophilic interaction, the strength of which is 5.3 kcal mol(?1) at the SCS-MP2 level. The emission energies of 1, 2 and 3 (2.62, 2.40 and 2.38 eV, respectively) calculated here by the B3PW91 agree with their literature experimental values (2.68, 2.47, and 2.39 eV). The lowest energy triplet excited state (T(1)) is assigned as the excitation from the Cu d to the pyridine ?* orbital in 1 and that from the Au–Cu 5d–3d anti-bonding MO to the Au–Cu 6p–4sp bonding MO in 2 and 3. As a result, the emission energy from the T(1) to the ground state is different between these compounds. The difference in Au–Cu distance is one of the important factors for the differences in emission energy and assignment between 1 and others (2 and 3). The vapochromism of these compounds arises from the difference in Au–Cu distance which is determined by the balance between the strengths of the coordination of a gas molecule and the Au–Cu metallophilic interaction; in other words, the Au–Cu heterometallophilic interaction is important for the vapochromic activity of the complex.
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NMR shielding constants of CuX, AgX, and AuX (X = F, Cl, Br, and I) investigated by density functional theory based on the Douglas-Kroll-Hess Hamiltonian.
J Comput Chem
PUBLISHED: 01-19-2013
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Two-component relativistic density functional theory (DFT) with the second-order Douglas-Kroll-Hess (DKH2) one-electron Hamiltonian was applied to the calculation of nuclear magnetic resonance (NMR) shielding constant. Large basis set dependence was observed in the shielding constant of Xe atom. The DKH2-DFT-calculated shielding constants of I and Xe in HI, I2, CuI, AgI, and XeF2 agree well with those obtained by the four-component relativistic theory and experiments. The Au NMR shielding constant in AuF is extremely more positive than in AuCl, AuBr, and AuI, as reported recently. This extremely positive shielding constant arises from the much larger Fermi contact (FC) term of AuF than in others. Interestingly, the absolute values of the paramagnetic and the FC terms are considerably larger in CuF and AuF than in others. The large paramagnetic term of AuF arises from the large d-components in the Au d? -F p? and Au sd?-F p? molecular orbitals (MOs). The large FC term in AuF arises from the small energy difference between the Au sd? + F p? and Au sd?-F p? MOs. The second-order magnetically relativistic effect, which is the effect of DKH2 magnetic operator, is important even in CuF. This effect considerably improves the overestimation of the spin-orbit effect calculated by the Breit-Pauli magnetic operator.
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Presence or absence of a novel charge-transfer complex in the base-catalyzed hydrolysis of N-ethylbenzamide or ethyl benzoate.
Beilstein J Org Chem
PUBLISHED: 01-04-2013
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Reaction paths of base-catalyzed hydrolyses of isoelectronic substrates, Ph-C(=O)-X-Et [X = O (ethyl benzoate) and X = NH (N-ethylbenzamide)], were traced by DFT calculations. To simulate bond interchanges accompanied by proton transfers, a cluster model of Ph-C(=O)-X-Et + OH(-)(H(2)O)(16) was employed. For X = O, three elementary processes and for X = NH four ones were obtained. The rate-determining step of X = O is the first TS (TS1, the OH(-) addition step), while that of X = NH is TS2. TS2 of X = NH leads to a novel Mulliken charge-transfer complex, Ph-(OH)(O=)C???N(H(2))-Et. The superiority or inferiority between the direct nucleophilic process or the general base-catalyzed process for TS1 was examined with the model Ph-C(=O)-X-Et + OH(-)(H(2)O)(n), n = 3, 5, 8, 12, 16, 24 and 32. The latter process was calculated to be more favorable regardless of the number (n, except n = 3) of water molecules. The counter ion Na(+) works unfavorably on the ester hydrolysis, particularly on TS1. A minimal model of TS1 was proposed and was found to be insensitive to n.
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An aniline dication-like transition state in the Bamberger rearrangement.
Beilstein J Org Chem
PUBLISHED: 01-01-2013
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A Bamberger rearrangement of N-phenylhydroxylamine, Ph-N(OH)H, to p-aminophenol was investigated by DFT calculations for the first time. The nitrenium ion, C6H5-NH(+), suggested and seemingly established as an intermediate was calculated to be absent owing to the high nucleophilicity of the water cluster around it. First, a reaction of the monoprotonated system, Ph-N(OH)H + H3O(+)(H2O) n (n = 4 and 14) was examined. However, the rate-determining transition states involving proton transfers were calculated to have much larger activation energies than the experimental one. Second, a reaction of the diprotonated system, Ph-N(OH)H + (H3O(+))2(H2O)13, was traced. An activation energy similar to the experimental one was obtained. A new mechanism of the rearrangement including the aniline dication-like transition state was proposed.
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Theoretical study of magnesium fluoride in aqueous solution.
J Phys Chem B
PUBLISHED: 08-17-2011
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A series of magnesium fluorides (MgF(n)(2-n)), multiply charged anions, in the gas phase and in aqueous solution were theoretically studied with a hybrid approach of quantum chemistry and statistical mechanics, called RISM-SCF-SEDD theory. In the gas phase, MgF(3)(-) is the most stable species among the complexes (n = 1-6). In contrast, due to compensation between the intramolecular energy and solvation free energy, the stabilities of a number of complexes with different n are comparable in aqueous solution. Based on accurate evaluation of free energy change, the mole fraction of MgF(4)(2-) is the highest in the range from pF = 2.0 to 3.0 of aqueous solution. This is consistent with the available PDB data of the enzymes that catalyze the phosphoryl transfer reactions. The hydration structures of magnesium fluorides obtained by RISM-SCF-SEDD theory provide insight into their structural changes from the gas phase to aqueous solution.
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Theoretical study on aquation reaction of cis-platin complex: RISM-SCF-SEDD, a hybrid approach of accurate quantum chemical method and statistical mechanics.
Dalton Trans
PUBLISHED: 08-11-2011
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The ligand exchange process of cis-platin in aqueous solution was studied using RISM-SCF-SEDD (reference interaction site model-self-consistent field with spatial electron density distribution) method, a hybrid approach of quantum chemistry and statistical mechanics. The analytical nature of RISM theory enables us to compute accurate reaction free energy in aqueous solution based on CCSD(T), together with the microscopic solvation structure around the complex. We found that the solvation effect is indispensable to promote the dissociation of the chloride anion from the complex.
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Theoretical study of Pt(PR3)(2)(AlCl3) (R = H, Me, Ph, or Cy) including an unsupported bond between transition metal and non-transition metal elements: geometry, bond strength, and prediction.
J Phys Chem A
PUBLISHED: 07-13-2011
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The molecular structure and the binding energy of Pt(PR(3))(2)(AlCl(3)) (R = H, Me, Ph, or Cy) were investigated by DFT, MP2 to MP4(SDTQ), and CCSD(T) methods. The optimized structure of Pt(PCy(3))(2)(AlCl(3)) (Cy = cyclohexyl) by the DFT method with M06-2X and LC-BLYP functionals agrees well with the experimental one. The MP4(SDTQ) and CCSD(T) methods present similar binding energies (BE) of Pt(PH(3))(2)(AlCl(3)), indicating that these methods provide reliable BE value. The DFT(M06-2X)-calculated BE value is close to the MP4(SDTQ) and CCSD(T)-calculated values, while the other functionals present BE values considerably different from the MP4(SDTQ) and CCSD(T)-calculated values. All computational methods employed here indicate that the BE values of Pt(PMe(3))(2)(AlCl(3)) and Pt(PPh(3))(2)(AlCl(3)) are considerably larger than those of the ethylene analogues. The coordinate bond of AlCl(3) with Pt(PR(3))(2) is characterized to be the ? charge transfer (CT) from Pt to AlCl(3). This complex has a T-shaped structure unlike the well-known Y-shaped structure of Pt(PMe(3))(2)(C(2)H(4)), although both are three-coordinate Pt(0) complex. This T-shaped structure results from important participation of the Pt d(?) orbital in the ?-CT; because the Pt d(?) orbital energy becomes lower as the P-Pt-P angle decreases, the T-shaped structure is more favorable for the ?-CT than is the Y-shaped structure. [Co(alcn)(2)(AlCl(3))](-) (alcn = acetylacetoneiminate) is theoretically predicted here as a good candidate for the metal complex, which has an unsupported M-Al bond because its binding energy is calculated to be much larger than that of Pt(PCy(3))(2)(AlCl(3)).
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Noble reaction features of bromoborane in oxidative addition of B-Br ?-bond to [M(PMe3)2] (M=Pt or Pd): theoretical study.
Inorg Chem
PUBLISHED: 05-10-2011
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Through detailed calculations by density functional theory and second-order Møller-Plesset perturbation theory (MP2) to fourth-order Møller-Plesset perturbation theory including single, double, and quadruple excitations [MP4(SDQ)] methods, we investigated the oxidative addition of the B-Br bond of dibromo(trimethylsiloxy)borane [Br(2)B(OSiMe(3))] to Pt(0) and Pd(0) complexes [M(PMe(3))(2)] (M = Pt or Pd) directly yielding a trans bromoboryl complex trans-[MBr{BBr(OSiMe(3))}(PMe(3))(2)]. Two reaction pathways are found for this reaction: One is a nucleophilic attack pathway which directly leads to the trans product, and the other is a stepwise reaction pathway which occurs through successive cis oxidative addition of the B-Br bond to [M(PMe(3))(2)] and thermal cis-trans isomerization. In the Pt system, the former course occurs with a much smaller energy barrier (E(a) = 5.8 kcal/mol) than the latter one (E(a) = 20.7 kcal/mol), where the DFT-calculated E(a) value is presented hereafter. In the Pd system, only the latter course is found in which the rate-determining steps is the cis-trans isomerization with the E(a) of 15.1 kcal/mol. Interestingly, the thermal cis-trans isomerization occurs on the singlet potential energy surface against our expectation. This unexpected result is understood in terms of the strong donation ability of the boryl group. Detailed analyses of electronic processes in all these reaction steps as well as remarkable characteristic features of [Br(2)B(OSiMe(3))] are also provided.
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Theoretical study of photoinduced epoxidation of olefins catalyzed by ruthenium porphyrin.
J Phys Chem A
PUBLISHED: 04-15-2011
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Epoxidation of olefin by [Ru(TMP)(CO)(O)](-) (TMP = tetramesitylporphine), which is a key step of the photocatalyzed epoxidation of olefin by [Ru(TMP)(CO)], is studied mainly with the density functional theory (DFT) method, where [Ru(Por)(CO)] is employed as a model complex (Por = unsubstituted porphyrin). The CASSCF method was also used to investigate the electronic structure of important species in the catalytic cycle. In all of the ruthenium porphyrin species involved in the catalytic cycle, the weight of the main configuration of the CASSCF wave function is larger than 85%, suggesting that the static correlation is not very large. Also, unrestricted-DFT-calculated natural orbitals are essentially the same as CASSCF-calculated ones, here. On the basis of these results, we employed the DFT method in this work. Present computational results show characteristic features of this reaction, as follows: (i) The epoxidation reaction occurs via carboradical-type transition state. Neither carbocation-type nor concerted oxene-insertion-type character is observed in the transition state. (ii) Electron and spin populations transfer from the olefin moiety to the porphyrin ring in the step of the C-O bond formation. (iii) Electron and spin populations of the olefin and porphyrin moieties considerably change around the transition state. (iv) The atomic and spin populations of Ru change little in the reaction, indicating that the Ru center keeps the +II oxidation state in the whole catalytic cycle. (v) The stability of the olefin adduct [Ru(Por)(CO)(O)(olefin)](-) considerably depends on the kind of olefin, such as ethylene, n-hexene, and styrene. In particular, styrene forms a stable olefin adduct. And, (vi) interestingly, the difference in the activation barrier among these olefins is small in the quantitative level (within 5 kcal/mol), indicating that this catalyst can be applied to various substrates. This is because the stabilities and electronic structures of both the olefin adduct and the transition state are similarly influenced by the substituent of olefin.
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Multistate CASPT2 study of native iron(III)-dependent catechol dioxygenase and its functional models: electronic structure and ligand-to-metal charge-transfer excitation.
J Phys Chem B
PUBLISHED: 04-04-2011
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We theoretically investigated the ligand-to-metal charge-transfer (LMCT) excitation of the native iron(III)-dependent catechol dioxygenase and its functional model complexes with multistate complete active space second-order perturbation theory (MS-CASPT2) because the LMCT (catecholate-to-iron(III) charge-transfer) excitation energy is believed to relate to the reactivity of the native enzyme and its functional model complexes. The ground state calculated by the MS-CASPT2 method mainly consists of the iron(III)-catecholate electron configuration and moderately of the iron(II)-semiquinonate electron configuration for both of the enzyme active centers and the model complexes when the active center exists in the protein environment and the model complexes exist in the solution. However, the ground-state wave function mainly consists of the iron(II)-semiquinonate electron configuration for both the enzyme active site without a protein environment and the model complexes in vacuo. These results clearly show that the protein environment and solvent play important roles to determine the electronic structure of the catecholatoiron(III) complex. The LMCT excitation energy clearly relates to the weight of the iron(III)-catecholate configuration in the ground state. The reactivity and the LMCT excitation energy directly relate to the ionization potential of the catecholate (IP(CAT)) in the model complex. This is because the charge transfer from the catecholate moiety to the dioxygen molecule plays a key role to activate the dioxygen molecule. However, the reactivity of the native catechol dioxygenase is much larger than those of the model complexes, despite the similar IP(CAT) values, suggesting that other factors such as the coordinatively unsaturated iron(III) center of the native enzyme play a crucial role in the reactivity.
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Solvation structure of coronene-transition metal complex: a RISM-SCF study.
Phys Chem Chem Phys
PUBLISHED: 11-19-2010
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Coronene (C(24)H(12)) is a flat polyaromatic hydrocarbon consisting of seven peri-fused benzene rings and attracts lots of attention as a fragment of graphene. Using a hybrid method of quantum chemistry and statistical mechanics called RISM-SCF, which is an alternative to QM/MM, the electronic structure and solvation structure of a coronene-transition metal complex were computed in a self-consistent manner. The binding of a ruthenium complex ([C(5)H(5)Ru](+)) was extensively studied, especially the changing of the solvation structure.
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Theoretical study of 1,6-anhydrosugar formation from phenyl D-glucosides under basic condition: reasons for higher reactivity of ?-anomer.
J. Org. Chem.
PUBLISHED: 11-17-2010
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Degradation of anomeric phenyl d-glucosides to levoglucosan under basic condition is theoretically studied. MP4(SDQ)//DFT(B3LYP)-computational results indicate that the degradation of phenyl ?-glucoside (R(?)) occurs via the S(N)icB mechanism. In this mechanism, the oxyanion at the C6, which is formed through deprotonation of the OH group, directly attacks the anomeric carbon. On the other hand, the degradation of phenyl ?-glucoside (R(?)) occurs via the S(N)icB(2) mechanism. In this mechanism, the oxyanion at the C2 attacks the anomeric carbon in a nucleophilic manner to afford 1,2-anhydride intermediate and then the oxyanion at the C6 attacks the anomeric carbon to afford levoglucosan. The activation barrier is much lower in the reaction of R(?) (?G(0++) = 25.6 kcal/mol and E(a) = 26.5 kcal/mol) than in the reaction of R(?) (?G(0++) = 38.1 kcal/mol and E(a) = 37.2 kcal/mol), which is consistent with the experimental observation that ?-glucoside is generally much more reactive than the corresponding ?-glucoside. The lower activation barrier of the reaction of R(?) arises from the stereoelectronic effect, which is induced by the charge transfer from the ring oxygen to the anomeric carbon, and the staggered conformation around the C1-C2 bond. When the stereoelectronic effect is absent, the degradation needs larger activation energy; for instance, the degradation of phenyl 5a-carba-?-d-glucoside (R(C?)) occurs with large ?G(0++) and E(a) values like those of ?-glucosides, because the methylene group of R(C?) does not contribute to the stereoelectronic effect. Also, the conformation around the C1-C2 bond is staggered in the transition state of the R(?) reaction but eclipsed in that of the R(?) reaction, which also leads to the larger reactivity of R(?).
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Theoretical study of excited states of pyrazolate- and pyridinethiolate-bridged dinuclear platinum(II) complexes: relationship between geometries of excited states and phosphorescence spectra.
Inorg Chem
PUBLISHED: 09-01-2010
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Dinuclear platinum(II) complexes [Pt(2)(?-pz)(2)(bpym)(2)](2+) (1; pz = pyrazolate and bpym = 2,2-bipyrimidine) and [Pt(2)(?-pyt)(2)(ppy)(2)] (2; pyt = pyridine-2-thiolate and Hppy = 2-phenylpyridine) were theoretically investigated with density functional theory (DFT) to clarify the reasons why the phosphorescence of 1 is not observed in the acetonitrile (CH(3)CN) solution at room temperature (RT) but observed in the solid state at RT and why the phosphorescence of 2 is observed in both the CH(3)CN solution and the solid state at RT. The S(1) and T(1) states of 1 in the CH(3)CN solution are assigned as a metal-metal-to-ligand charge-transfer (MMLCT) excited state. Their geometries are C(2v) symmetrical, in which spin-orbit interaction between the S(1) and T(1) excited states is absent because the direct product of irreducible representations of the singly occupied molecular orbitals (SOMOs) of these excited states and the orbital angular momentum (l) operator involved in the Hamiltonian for spin-orbit interaction does not belong to the a(1) representation. As a result, the S(1) ? T(1) intersystem crossing hardly occurs, leading to the absence of T(1) ? S(0) phosphorescence in the CH(3)CN solution at RT. In the solid state, the geometry of the S(1) state does not reach the global minimum but stays in the C(1)-symmetrical local minimum. This S(1) excited state is assigned as a mixture of the ligand-centered ?-?* excited state and the metal-to-ligand charge-transfer excited state. Spin-orbit interaction between the S(1) and T(1) excited states operates to induce the S(1) ? T(1) intersystem crossing because the direct product of the irreducible representations of the SOMOs of these excited states and the l operator belongs to the "a" representation. As a result, T(1) ? S(0) phosphorescence occurs in the solid state. In 2, the S(1) and T(1) excited states are assigned as the MMLCT excited state. Their geometries are C(2)-symmetrical in both the CH(3)CN solution and the solid state, in which spin-orbit interaction between the S(1) and T(1) states operates to induce the S(1) ? T(1) intersystem crossing because the direct product of the irreducible representations of the SOMOs and the l operator belongs to the "a" representation. Thus, T(1) ? S(0) phosphorescence occurs in both the CH(3)CN solution and the solid state at RT, unlike 1.
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RISM-SCF-SEDD study on the symmetry breaking of carbonate and nitrate anions in aqueous solution.
J Phys Chem B
PUBLISHED: 08-25-2010
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The planarity of carbonate and nitrate anions was investigated in the gas and solution phases by means of the reference interaction site model self-consistent field spatial electron density distribution (RISM-SCF-SEDD) method. The computed optimized geometries and solvation structures are compared with the diffraction data. In the solution phase, the symmetry of carbonate anion is changed from D3h to C3v, whereas the planarity of nitrate anion is still retained. These are fully consistent with experimental knowledge. The classical electrostatic model was also utilized to elucidate the mechanism of the symmetry breaking. It should be emphasized that the symmetry breaking occurs not only by a specific solvent molecule attaching to the ion but by an overall electrostatic interaction between the infinite number of solvent molecules and the ion.
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Electronic structure of four-coordinate iron(I) complex supported by a bis(phosphaethenyl)pyridine ligand.
J. Am. Chem. Soc.
PUBLISHED: 07-03-2010
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A 15-electron iron complex with a formal Fe(I) center, [FeBr(BPEP)] (BPEP = 2,6-bis(1-phenyl-2-phosphaethenyl)pyridine), was prepared by one-electron reduction of the dibromide precursor [FeBr(2)(BPEP)]. The single-crystal diffraction analysis revealed a distorted trigonal monopyramidal arrangement around the iron center, and SQUID magnetometry established the S = 3/2 ground state. The Mossbauer isomer shift value (delta = 0.59 mm/s) was consistent with a high-spin Fe(I) center of [FeBr(BPEP)]. DFT calculations for a model complex revealed two highly delocalized molecular orbitals formed by bonding and antibonding interactions between the d(z(2)) (Fe) and pi* (BPEP) orbitals. Orbital occupancy analysis demonstrated the electronic structure with a high-spin Fe(I) center. The effective dpi-ppi interaction between iron and BPEP was concluded to be responsible for the highly distorted structure of [FeBr(BPEP)], with its rather uncommon trigonal monopyramidal configuration.
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An analysis of 3D solvation structure in biomolecules: application to coiled coil serine and bacteriorhodopsin.
J Phys Chem B
PUBLISHED: 05-18-2010
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Three-dimensional (3D) solvation structure around coiled coil serine (Coil-Ser) and inner 3D hydration structure in bacteriorhodopsin (bR) were studied using a recently developed method named multicenter molecular Ornstein-Zernike equation (MC-MOZ) theory. In addition, a procedure for analyzing the 3D solvent distribution was proposed. The method enables us to calculate the coordination number of solvent water as well as the strength of hydrogen bonding between the water molecule and the protein. The results for Coil-Ser and bR showed very good agreement with the experimental observations.
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Theoretical and computational studies of organometallic reactions: successful or not?
Chem Rec
PUBLISHED: 03-04-2010
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Theoretical and computational methods are powerful in studying transition metal complexes. Our theoretical studies of C-H sigma-bond activation of benzene by Pd(II)-formate complex and that of methane by Ti(IV)-imido complex successfully disclosed that these reactions are understood to undergo heterolytic sigma-bond activation and the driving force is the formation of strong O-H and N-H bonds in the former and the latter, respectively. Orbital interactions are considerably different from those of sigma-bond activation by oxidative addition. The transmetallation, which is a key process in the cross-coupling reaction, is understood to be heterolytic sigma-bond activation. Our theoretical study clarified how to accelerate this transmetallation. Also, we wish to discuss weak points in theoretical and computational studies of large systems including transition metal elements, such as the necessity to incorporate solvation effect and to present quantitatively correct numerical results. The importance of solvation effects is discussed in the oxidative addition of methyliodide to Pt(II) complex which occurs in a way similar to an S(N)2 substitution. To apply the CCSD(T) (coupled cluster singles and doubles with perturbative triples correction) method, which is the gold standard of electronic structure theory, to large system, we need to reduce the size of the system by employing a small model. But, such modeling induces neglects of electronic and steric effects of substituents which are replaced in the small model. Frontier-orbital-consistent quantum-capping potential (FOC-QCP) was recently proposed by our group to incorporate the electronic effects of the substituents neglected in the modeling. The CCSD(T) calculation with the FOC-QCP was successfully applied to large systems including transition metal elements.
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Pd(II)-promoted direct cross-coupling reaction of arenes via highly regioselective aromatic C-H activation: a theoretical study.
Dalton Trans
PUBLISHED: 02-13-2010
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The direct cross-coupling reaction of arenes promoted by Pd(OAc)(2) is synthetically very useful because the preparation of a haloarene as a substrate is not necessary. This reaction interestingly only occurs in the presence of benzoquinone (BQ). DFT, MP2 to MP4(SDQ), and CCSD(T) computations elucidated the whole mechanism of this cross-coupling reaction and the key roles of BQ. The first step is the heterolytic C-H activation of benzo[h]quinoline (HBzq) by Pd(OAc)(2) to afford Pd(Bzq)(OAc). The Pd center is more electron-rich in Pd(Bzq)(OAc) than in Pd(OAc)(2). Hence, BQ easily coordinates to Pd(Bzq)(OAc) with a low activation barrier to afford a distorted square planar complex Pd(Bzq)(OAc)(BQ) which is as stable as Pd(Bzq)(OAc). Then, the second C-H activation of benzene occurs with a moderate activation barrier and small endothermicity. The final step is the reductive elimination which occurs with little barrier. The rate-determining step of the overall reaction is the second C-H activation whose activation barrier is considerably higher than that of the first C-H activation. BQ plays a key role in accelerating this reaction; (i) the phenyl group must change its position a lot to reach the transition state in the reductive elimination from the square planar intermediate Pd(Ph)(Bzq)(OAc) but only moderately in the reaction from the trigonal bipyramidal intermediate Pd(Ph)(Bzq)(OAc)(BQ). This is because BQ suppresses the phenyl group to take a position at a distance from the Bzq. (ii) BQ stabilizes the transition state and the product complex by the back-donation interaction. In the absence of BQ, the reductive elimination step has a much higher activation barrier. Though it was expected that the BQ coordination accelerates the second C-H activation of benzene by decreasing the electron density of Pd in Pd(Bzq)(OAc), the activation barrier of this second C-H activation is little influenced by BQ.
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Ab initio study on SN2 reaction of methyl p-nitrobenzenesulfonate and chloride anion in [mmim][PF6].
Phys Chem Chem Phys
PUBLISHED: 01-05-2010
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A S(N)2 reaction of methyl p-nitrobenzenesulfonate (p-NBS) and chloride anion in ionic liquid ([mmim][PF(6)]) was studied using RISM-SCF-SEDD method coupled with a highly sophisticated ab initio electronic structure theory (CCSD). The solvation structure as well as the energy profile along the reaction were discussed through comparison with an ordinary solvent system, dichloromethane.
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Comparison of electronic structures and light-induced excited spin state trapping between [Fe(2-picolylamine)(3)](2+) and its iron(III) analogue.
Dalton Trans
PUBLISHED: 12-17-2009
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We investigated mer- and fac-[Fe(II)(2-pic)(3)](2+) (pic = picolylamine) and Fe(iii) analogue, mer-[Fe(III)(2-pic)(3)](3+), by the DFT method to clarify the mechanism of light-induced excited spin state trapping (LIESST). In mer-[Fe(II)(2-pic)(3)](2+), the potential energy surface (PES) of the triplet state is the least stable but it is close to the PESs of the singlet and quintet states at the equilibrium geometry of the triplet state within 5 kcal mol(-1). This indicates that intersystem crossing occurs from the triplet state to either the singlet state or the quintet state around the equilibrium geometry of the triplet state. The quintet state is as stable as the singlet state in their equilibrium geometries. All Fe-N bonds of the quintet state are longer than those of the singlet state by about 0.19 A. These are consistent with the general understanding that the Fe-ligand distances are considerably different but the relative stability is little different between the low spin and high spin states in LIESST complexes. Actually, a large activation barrier is calculated for the conversion between the singlet and quintet states, which is enough to suppress thermal spin transition and tunneling between them. The d-d transition energies are calculated with the TD-DFT method to be 2.05, 2.07, and 2.09 eV in the singlet state and 1.46 and 1.64 eV in the quintet state. Because of the significantly large difference in excitation energy between the singlet and quintet states, irradiation of visible light with different wavelengths selectively induces the excitation to the singlet excited state or the quintet one. All these results are consistent with the fact that both LIESST and reverse-LIESST are observed in mer-[Fe(II)(2-pic)(3)](2+). The fac-isomer is also useful for the LIESST/reverse-LIESST, though the mer-isomer is better. In the Fe(iii) analogue, mer-[Fe(III)(2-pic)(3)](3+), the DFT-computational results indicate small activation barriers and a large overlap of absorption spectra between the doublet and sextet states. Also, the Fe(III)-N bond distances are less different between the low spin and high spin states than the Fe(II)-N ones, leading to the narrow potential wall between the doublet and sextet states. As a result, the LIESST and reverse-LIESST cannot be observed in this Fe(iii) complex.
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Analytical energy gradient for reference interaction site model self-consistent field explicitly including spatial electron density distribution.
J Chem Phys
PUBLISHED: 12-09-2009
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Analytical energy gradient formula was derived for reference interaction site model self-consistent field explicitly including spatial electron density distribution (RISM-SCF-SEDD). RISM-SCF-SEDD is a combination method of ab initio electronic structure theory and statistical mechanics for molecular liquids [D. Yokogawa et al., J. Chem. Phys. 126, 244504 (2007)]. As shown previously, RISM-SCF-SEDD is numerically stable and has expanded the applicability of the solvation theory. The energy gradient is an indispensable tool to compute molecular geometry and its implementation further extends the capability of RISM-SCF-SEDD. The present method was applied to chemical systems in aqueous solution; hydration structure and geometry of phosphate anion PO(4) (3-) and tautomerization between 2-pyridone and 2-hydroxypyridine. Compared to available experimental data, the present method correctly reproduced the geometries and relative energies of solvated molecules with microscopic solvent distribution. It is clearly shown that highly sophisticated quantum chemical calculation such as coupled cluster with single and double and perturbative triple excitations coupled with solvation effect is a powerful tool to accurately evaluate molecular properties.
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Oxygen atom transfer reactions of iridium and osmium complexes: theoretical study of characteristic features and significantly large differences between these two complexes.
Inorg Chem
PUBLISHED: 08-13-2009
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Oxygen atom transfer reaction between ML(3)=O and ML(3) (L = 2,4,6-trimethylphenyl (Mes) for M = Ir and L = 2,6-diisopropylphenylimide (NAr) for M = Os) was theoretically investigated by DFT method. The optimized geometry of (Mes)(3)Ir-O-Ir(Mes)(3) agrees well with the experimental one, although those of (CH(3))(3)Ir-O-Ir(CH(3))(3) and Ph(3)Ir-O-IrPh(3) are much different from the experimental one of the Mes complex. These results indicate that the bulky ligand plays important roles to determine geometry of the mu-oxo dinuclear Ir complex. Theoretical study of the real systems presents clear pictures of these oxygen atom transfer reactions, as follows: In the Ir reaction system, (i) the mu-oxo bridged dinuclear complex is more stable than the infinite separation system in potential energy surface, indicating this is incomplete oxygen atom transfer reaction which does not occur at very low temperature, (ii) unsymmetrical transition state is newly found, in which one Ir-O distance is longer than the other one, (iii) unsymmetrical local minimum is also newly found between the transition state and the infinite separation system, and (iv) activation barrier (E(a)) is very small. In the Os reaction system, (v) the transition state is symmetrical, while no intermediate is observed unlike the Ir reaction system, and (vi) E(a) is very large. These results are consistent with the experimental results that the reaction rapidly occurs in the Ir system but very slowly in the Os system, and that the mu-oxo bridged dinuclear intermediate is detected in the Ir system but not in the Os system. To elucidate the reasons of these differences between Ir and Os systems, the E(a) value is decomposed into the nuclear and electronic factors. The former is the energy necessary to distort ML(3) and ML(3)=O moieties from their equilibrium geometries to those in the transition state. The latter depends on donor-acceptor interaction between ML(3)=O and ML(3). The nuclear factor is much larger in the Os system than in the Ir system and it contributes to about 70% of the difference in E(a). The energy gap between the donor orbital of ML(3) and the acceptor orbital of ML(3)=O is much larger in the Os system than in the Ir system, which also contributes to the lower E(a) value of the Ir system than that of the Os system.
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Thermal degradation of methyl beta-D-glucoside. a theoretical study of plausible reaction mechanisms.
J. Org. Chem.
PUBLISHED: 07-28-2009
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Thermal conversion of methyl beta-d-glucoside to levoglucosan was studied with the MP4//DFT(B3LYP) method. The first step is conformational change of the reactant to (1)C(4) from (4)C(1). The second step is intramolecular nucleophilic substitution at the anomeric C1, which occurs via one step without oxacarbenium ion intermediate. The DeltaG(0)() value (52.5 kcal/mol) is smaller than the C1-O1 bond energy, indicating the direct homolysis mechanism is clearly ruled out. Bimolecular reaction also occurs with smaller activation energy via the similar transition state.
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Carbon dioxide capture at the molecular level.
Phys Chem Chem Phys
PUBLISHED: 07-27-2009
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Carbon dioxide is recognized as a typical greenhouse gas and drastic reduction of CO2 emissions from industrial process is becoming more and more important in relation to global warming. In fact, the reaction between monoethanolamine (MEA) and CO2 in aqueous solution has been widely used for the removal from flue gases. In this study, the role of the interplay between solvent water and nitrogen (MEA)-carbon (CO2) bond formation is discussed based on the molecular theory using RISM-SCF-SEDD, which is the hybrid method of quantum chemistry of solute and statistical mechanics of solvent.
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New palladium(II) complex of P,S-containing hybrid calixphyrin. Theoretical study of electronic structure and reactivity for oxidative addition.
J. Am. Chem. Soc.
PUBLISHED: 07-16-2009
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The palladium complex of P,S-containing hybrid calixphyrin 1 was investigated with the DFT method. There are two kinds of valence tautomer in 1: one is a Pd(II) form in which the calixphyrin moiety possesses -2 charges and the Pd center takes +2 oxidation state, and the other is a Pd(0) form in which the calixphyrin is neutral and the Pd center takes zero oxidation state. Complex 1 takes the Pd(II) form in the ground state. Though the Pd center takes +2 oxidation state, DFT computations clearly show that the oxidative addition of phenyl bromide (PhBr) to 1 occurs with moderate activation enthalpy, as experimentally proposed. The first step of the oxidative addition is the coordination of PhBr with the Pd center to form intermediate 1INTa, in which the Pd center and the calixphyrin moiety are neutral; in other words, the valence tautomerization from the Pd(II) form to the Pd(0) form occurs in the palladium calixphyrin moiety. The activation enthalpy is 22.5 kcal/mol, and the enthalpy change of reaction is 20.3 kcal/mol. The next step is the C-Br sigma-bond cleavage of PhBr, which occurs with activation enthalpy of 2.0 kcal/mol relative to 1INTa. On the other hand, the oxidative additions of PhBr to palladium complex of P,S-containing hybrid porphyrin 2 and that of conventional porphyrin 3 need much larger activation enthalpies of 49.1 and 74.4 kcal/mol, respectively. The differences in the reactivity among 1, 2, and 3 were theoretically investigated; in 1, the valence tautomerization occurs with moderate activation enthalpy to afford the Pd(0) form which is reactive for the oxidative addition. In 2, the tautomerization from the Pd(II) form to the Pd(0) form needs very large activation enthalpy (43.3 kcal/mol). In 3, such valence tautomerization does not occur at all, indicating that the Pd(II) must change to the Pd(IV) in the oxidative addition of PhBr to 3, which is a very difficult process. These differences are interpreted in terms of the pi* orbital energies of P,S-containing hybrid calixphyrin, hybrid porphyrin, and conventional porphyrin and the flexibility of their frameworks.
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First principle theory for pKa prediction at molecular level: pH effects based on explicit solvent model.
J Phys Chem B
PUBLISHED: 07-04-2009
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pKa is one of the fundamental properties of molecules and its accurate prediction by theoretical method is indispensable in the current era. At present, the most common approach is based on the free energy difference evaluated in dielectric continuum model for pure water, epsilon=80, which completely ignores ionic influence, i.e., ionic strength. In the present paper, a molecular level theory to predict pKa is proposed based on the reference interaction site model, which is a statistical mechanics for molecular liquids. By regarding an acidic aqueous solution as a three component system including water, proton species (cation), and anion, aqueous solutions with desired pH can be theoretically realized by controlling the number density of the proton species. Using computed free energy changes on the deprotonation of glycine at various pH conditions, a titration curve and pKa can be obtained from the first principle, showing excellent agreement with experimental data. To our best knowledge, this is the first theoretical attempt to directly evaluate pKa under the condition where ionic influence is explicitly taken into account by using statistical molecular theory.
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A theoretical analysis of a Diels-Alder reaction in ionic liquids.
J Phys Chem B
PUBLISHED: 05-26-2009
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The Diels-Alder reaction of cyclopentadinene (CP) with methyl acrylate (MA) in room-temperature ionic liquids (RTILs) is theoretically examined. In the present study, quantum molecular orbital theory is combined with a multicomponent reference interaction site model (RISM). Because RISM is free from statistical error, it is possible to overcome the serious difficulty in the description of the strong Coulombic interaction in RTILs. We focused on the origin of the relatively moderate solvation effects of RTILs and the mechanism of endo-exo selectivity.
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Bidirectional chemo-switching of spin state in a microporous framework.
Angew. Chem. Int. Ed. Engl.
PUBLISHED: 03-19-2009
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The ins and outs of spin: Using the microporous coordination polymer {Fe(pz)[Pt(CN)(4)]} (1, pz=pyrazine), incorporating spin-crossover subunits, two-directional magnetic chemo-switching is achieved at room temperature. In situ magnetic measurements following guest vapor injection show that most guest molecules transform 1 from the low-spin (LS) state to the high-spin (HS) state, whereas CS(2) uniquely causes the reverse HS-to-LS transition.
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Theoretical study of dioxygen binding process in iron(III) catechol dioxygenase: "oxygen activation" vs "substrate activation".
J Phys Chem B
PUBLISHED: 03-17-2009
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Dioxygen binding process of nonheme iron(III) center in intradiol catechol dioxygenase was investigated with CASSCF/CASPT2 method to incorporate multiconfigurational character participating in Fe-O(2) interaction. In this process, two alternative mechanisms were proposed: one is called "oxygen activation" and the other is called "substrate activation". Our CASSCF/CASPT2-calculated results support the oxygen activation. Potential energy curves and electronic structure evaluated with SA(state-averaged)-CASSCF/CASPT2 method indicate that the charge transfer directly occurs from the catecholate moiety to the dioxygen moiety in the O(2) binding process, to produce eta(1)-end-on type iron(III)-superoxo complex. This is the key step of the dioxygen activation. Interestingly, the iron center always keeps high spin d(5) character during the O(2) binding process, indicating the iron(III) center does not receive charge transfer from the catecholate moiety. However, this does not mean that the iron(III) center is not necessary to the dioxygen activation. The important role which the iron(III) center plays in catechol dioxygenase is to adjust the energy level of O(2) to induce the charge transfer from the catecholate moiety to the dioxygen moiety. Besides the eta(1)-end-on iron(III)-superoxo complex, eta(2)-side-on type iron(III)-superoxo complex is also optimized. This species is more stable than the eta(1)-end-on type iron(III)-superoxo complex, suggesting that this is considered as a stable isomer in the early stage of the catalytic cycle.
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Luminescent heteropolynuclear complexes of 3,5-dimethylpyrazolate [Pt2Au2M2(Me2pz)8] (M = Ag, Cu) showing the synergistic effect of three transition elements in the excited state.
Chemistry
PUBLISHED: 03-14-2009
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Swap the coins! The Pt(2)Au(2), Pt(2)Au(2)Cu(2), and Pt(2)Au(2)Ag(2) complexes of 3,5-dimethylpyrazolate exhibit yellow-green, orange, and sky-blue luminescence, respectively (see figure). The emission energies of Pt(2)Au(2)M(2) complexes can be controlled by the change of the third coinage metal ions M. The Pt(2)Au(2)M(2) complexes take the cis configuration with respect to the Au(2)M(2) plane.
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Bonding nature of open-lantern-type dinuclear Cr(II) complexes. Theoretical study with the MRMP2 method.
J Phys Chem A
PUBLISHED: 03-11-2009
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Open-lantern-type dinuclear Cr(II) complex, [Cr(R(1)NC(R(2))NR(3))(2)](2) (R(1) = Et, R(2) = Me, and R(3) = (t)Bu), was theoretically investigated with DFT, CASSCF, and MRMP2 methods. The DFT-optimized Cr-Cr distance (1.757 A) is too short compared to the experimental value (1.960 A). The CASSCF method does not present the minimum in the range of the Cr-Cr distance from 1.75 to 2.05 A. The MRMP2 method presents the optimized Cr-Cr distance of 1.851 A, which is a little shorter than the experimental value. These results suggest that both nondynamical and dynamical correlations are considerably large in this complex. The Cr-Cr bond order is evaluated to be 2.40 with the CASSCF method, which is much smaller than the formal bond order of 4. In the Mo analogue, on the other hand, the DFT, CASSCF, and MRMP2 methods present almost the same Mo-Mo distance (2.151 A). The Mo-Mo bond order is evaluated to be 3.41, which is somewhat smaller than the formal value but much larger than the Cr-Cr bond order. These differences arise from the much larger d-d overlap integral of the Mo-Mo pair than that of the Cr-Cr pair. Though nondynamical correlation effect is very large in this dinuclear Cr(II) complex, the Cr-Cr distance of this complex was experimentally discussed to be short, based on formal shortness ratio (FSR). We wish to propose here orbital shortness ratio (OSR) based on the distance providing maximum overlap integral to discuss the M-M bond distance. According to the OSR, we understand that the Cr-Cr distance of 1.960 A is long but the Mo-Mo distance of 2.151 A is short. This understanding is consistent with much larger nondynamical correlation in the dinuclear Cr(II) complex than in the Mo(II) analogue. Interesting differences are also observed between M-M and Si-Si multiple bonds. The differences are discussed in terms of sigma- and pi-type overlap integrals and the participation of Si 3s orbital in the sigma-bonding orbital.
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A highly parallelizable integral equation theory for three dimensional solvent distribution function: application to biomolecules.
J Chem Phys
PUBLISHED: 02-19-2009
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Three dimensional (3D) hydration structure is informative to clarify the functions of hydrated waters around a protein. We develop a new approach to calculate 3D solvation structure with reasonable computational cost. In the present method, the total solvation structure is obtained using conventional one dimensional reference interaction site model (RISM) followed by integrating the 3D fragment data, which are evaluated around each atom (site) of solute. Thanks to this strategy, time-consuming 3D fast Fourier transformation, which is required in 3D-RISM theory, can be avoided and high-parallel performance is achieved. The method is applied to small molecular systems for comparison with 3D-RISM. The obtained results by the present method and by 3D-RISM show good agreement. The hydration structures for a large protein computed by the present method are also consistent with those obtained by x-ray crystallography.
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A systematic understanding of orbital energy shift in polar solvent.
J Chem Phys
PUBLISHED: 02-05-2009
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The orbital energy of molecule is significantly shifted upon going from gas phase to solution phase. Based on Koopmans theorem, the shift should be related to the change of ionization potential. However, the computed shift looks usually random and clear understanding has not been attained yet. Furthermore it is obtained only after solving complicated equations. In this study, we report a systematic framework for understanding the orbital energy shift by solvation effect and simple approximate formulae are presented.
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Evaluation procedure of electrostatic potential in 3D-RISM-SCF method and its application to hydrolyses of cis- and transplatin complexes.
J Phys Chem B
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In the three-dimensional reference interaction site model self-consistent field (3D-RISM-SCF) method, a switching function was introduced to evaluate the electrostatic potential (ESP) around the solute to smoothly connect the ESP directly calculated with the solute electronic wave function and that approximately calculated with solute point charges. Hydrolyses of cis- and transplatins, cis- and trans-PtCl(2)(NH(3))(2), were investigated with this method. Solute geometries were optimized at the DFT level with the M06-2X functional, and free energy changes were calculated at the CCSD(T) level. In the first hydrolysis, the calculated activation free energy is 20.8 kcal/mol for cisplatin and 20.3 kcal/mol for transplatin, which agrees with the experimental and recently reported theoretical results. A Cl anion, which is formed by the first hydrolysis, somehow favorably exists in the first solvation shell as a counteranion. The second hydrolysis occurs with a similar activation free energy (20.9 kcal/mol) for cisplatin but a somewhat larger energy (23.2 kcal/mol) for transplatin to afford cis- and trans-diaqua complexes. The Cl counteranion in the first solvation shell little influences the activation free energy but somewhat decreases the endothermicity in both cis- and transplatins. The present 3D-RISM-SCF method clearly displays the microscopic solvation structure and its changes in the hydrolysis, which are discussed in detail.
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How is the anionic tetrahedral intermediate involved in the isomerization of aspartyl peptides to iso-aspartyl ones? A DFT study on the tetra-peptide.
Org. Biomol. Chem.
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An isomerization reaction of a tetra-peptide, Ac-Gly-Asp-Gly-Gly-NHMe ? Ac-Gly-isoAsp-Gly-Gly-NHMe, was investigated by DFT calculations. Thirteen water molecules were added to the peptide for simulating proton transfers during the isomerization. As a starting analysis, the number (m) of water molecules participating in ready proton transfers was examined by the use of a small model system, H(3)C-NH-C(=O)-CH(2)-CH(2)-COOH and (H(2)O)(m). The m = 2 stepwise path was found to be of the smallest activation free energy. On the basis of this result, the first isomerization path of the tetra-peptide was obtained with four elementary processes. The m = 2 proton-transfer pattern is involved in them. A different proton transfer gives the second isomerization path with six elementary processes. The second path (with ionization) is more likely than the first one (without ionization). Formation of the five membered rings of the aminosuccinimidyl-residue and anionic tetrahedral intermediates enhances the encapsulation of H(3)O(+) through the wound tetra-peptide ring. The role of the hydrogen bonds on the encapsulation was discussed in terms of the optimized geometries of proton-transfer transition states and intermediates.
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Consistent scheme for computing standard hydrogen electrode and redox potentials.
J Comput Chem
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The standard hydrogen electrode (SHE) potential in aqueous solution was evaluated with new computational procedure that provides the Gibbs energy of a proton in aqueous solution from the experimental pK(a) value and the Gibbs energy change by deprotonation reactions of several neutral alcohol molecules. With our computational scheme, the CCSD(T)/aug-cc-pVDZ method provides the SHE potential of 4.52 V, which is almost the same as the experimental SHE potential. This scheme also reproduces well the redox potentials of several typical reactions within almost 0.1 V. B3LYP also gives excellent redox potentials of the same reactions with almost the same accuracy with our new computational scheme.
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Syntheses and luminescent properties of 3,5-diphenylpyrazolato-bridged heteropolynuclear platinum complexes. The influence of chloride ligands on the emission energy revealed by the systematic replacement of chloride ligands by 3,5-dimethylpyrazolate.
Inorg Chem
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Heteropolynuclear Pt(II) complexes with 3,5-diphenylpyrazolate [Pt(2)Ag(4)(?-Cl)(2)(?-Ph(2)pz)(6)] (3), [Pt(2)Ag(2)Cl(2)(?-Ph(2)pz)(4)(Ph(2)pzH)(2)] (4), [Pt(2)Cu(2)Cl(2)(?-Ph(2)pz)(4)(Ph(2)pzH)(2)] (5), [Pt(2)Ag(4)(?-Cl)(?-Me(2)pz)(?-Ph(2)pz)(6)] (7), and [Pt(2)Ag(4)(?-Me(2)pz)(2)(?-Ph(2)pz)(6)] (8) have been prepared and structurally characterized. These complexes are luminescent except for 5 in the solid state at an ambient temperature with emissions of red-orange (3), orange (4), yellow-orange (7), and green (8) light, respectively. Systematic red shift of the emission energies with the number of chloride ligands was observed for 3, 7, and 8. DFT calculations indicate that the highest occupied molecular orbital (HOMO) as well as HOMO-1 of the heterohexanuclear complexes, 3, 7, and 8, having Pt(2)Ag(4) core, mainly consist of d? orbital of Pt(II) and ? orbitals of Ph(2)pz ligands, while the lowest unoccupied molecular orbital (LUMO) of these complexes mainly consists of in-phase combination of 6p of two Pt(II) centers and 5p of four Ag(I) centers. It is likely that the emissions of 3, 7, and 8 are attributed to emissive states derived from the Pt(2)(d)/? ? Pt(2)Ag(4) transitions, the emission energy of which depends on the ratio of chloride ligands to pyrazolate ligands.
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A theoretical study of an unusual Y-shaped three-coordinate Pt complex: Pt(0) ?-disilane complex or Pt(II) disilyl complex?
J. Am. Chem. Soc.
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The unusual Y-shaped structure of the recently reported three-coordinate Pt complex Pt[NHC(Dip)(2)](SiMe(2)Ph)(2) (NHC = N-heterocyclic carbene; Dip = 2,6-diisopropylphenyl) was considered a snapshot of the reductive elimination of disilane. A density functional theory study indicates that this structure arises from the strong trans influence of the extremely ?-donating carbene and silyl ligands. Though this complex can be understood to be a Pt(II) disilyl complex bearing a distorted geometry due to the Jahn-Teller effect, its (195)Pt NMR chemical shift is considerably different from those of Pt(II) complexes but close to those of typical Pt(0) complexes. Its Si···Si bonding interaction is ~50% of the usual energy of a Si-Si single bond. The interaction between the Pt center and the (SiMe(2)Ph)(2) moiety can be understood in terms of donation and back-donation interactions of the Si-Si ?-bonding and ?*-antibonding molecular orbitals with the Pt center. Thus, we conclude that this is likely a Pt(0) ?-disilane complex and thus a snapshot after a considerable amount of the charge transfer from disilane to the Pt center has occurred. Phenyl anion (Ph(-)) and [R-Ar](-) [R-Ar = 2,6-(2,6-iPr(2)C(6)H(3))(2)C(6)H(3)] as well as the divalent carbon(0) ligand C(NHC)(2) also provide similar unusual Y-shaped structures. Three-coordinate digermyl, diboryl, and silyl-boryl complexes of Pt and a disilyl complex of Pd are theoretically predicted to have similar unusual Y-shaped structures when a strongly donating ligand coordinates to the metal center. In a trigonal-bipyramidal Ir disilyl complex [Ir{NHC(Dip)(2)}(PH(3))(2)(SiMe(3))(2)](+), the equatorial plane has a similar unusual Y-shaped structure. These results suggest that various snapshots can be shown for the reductive eliminations of the Ge-Ge, B-B, and B-Si ?-bonds.
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Theoretical study on the transition-metal oxoboryl complex: M-BO bonding nature, mechanism of the formation reaction, and prediction of a new oxoboryl complex.
Inorg Chem
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The Pt-BO bonding nature and the formation reaction of the experimentally reported platinum(II) oxoboryl complex, simplified to PtBr(BO)(PMe(3))(2), were theoretically investigated with the density functional theory method. The BO(-) ligand was quantitatively demonstrated to have extremely strong ?-donation but very weak d(?)-electron-accepting abilities. Therefore, it exhibits a strong trans influence. The formation reaction occurs through a four-center transition state, in which the B(?+)-Br(?-) polarization and the Br ? Si and O p(?) ? B p(?) charge-transfer interactions play key roles. The Gibbs activation energy (?G°(++)) and Gibbs reaction energy (?G°) of the formation reaction are 32.2 and -6.1 kcal/mol, respectively. The electron-donating bulky phosphine ligand is found to be favorable for lowering both ?G°(++) and ?G°. In addition, the metal effect is examined with the nickel and palladium analogues and MBrCl[BBr(OSiMe(3))](CO)(PR(3))(2) (M = Ir and Rh). By a comparison of the ?G°(++) and ?G° values, the M-BO (M = Ni, Pd, Ir, and Rh) bonding nature, and the interaction energy between [MBrCl(CO)(PR(3))(2)](+) and BO(-) with those of the platinum system, MBrCl(BO)(CO)(PR(3))(2) (M = Ir and Rh) is predicted to be a good candidate for a stable oxoboryl complex.
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Oscillator strength of symmetry-forbidden d-d absorption of octahedral transition metal complex: theoretical evaluation.
Inorg Chem
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The theoretical evaluation of the oscillator strength of a symmetry-forbidden d-d transition is not easy even nowadays. A new approximate method is proposed here and applied to octahedral complexes [Co(NH(3))(6)](3+) and [Rh(NH(3))(6)](3+) as an example. Our method incorporates the effects of geometry distortion induced by molecular vibration and the thermal distribution of such distorted geometries but does not need the Herzberg-Teller approximation. The calculated oscillator strengths of [Co(NH(3))(6)](3+) agree well with the experimental values in both (1)A(1g) ? (1)T(1g) and (1)A(1g) ? (1)T(2g) transitions. In the Rh analogue, though the calculated oscillator strengths are somewhat smaller than the experimental values, computational results reproduce well the experimental trends that the oscillator strengths of [Rh(NH(3))(6)](3+) are much larger than those of the Co analogue and the oscillator strength of the (1)A(1g) ? (1)T(1g) transition is larger than that of the (1)A(1g) ? (1)T(2g) transition. It is clearly shown that the oscillator strength is not negligibly small even at 0 K because the distorted geometry (or the uncertainty in geometry) by zero-point vibration contributes to the oscillator strength at 0 K. These results are discussed in terms of frequency of molecular vibration, extent of distortion induced by molecular vibration, and charge-transfer character involved in the d-d transition. The computational results clearly show that our method is useful in evaluating and discussing the oscillator strength of symmetry-forbidden d-d absorption of transition metal complex.
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Theoretical study of inverted sandwich type complexes of 4d transition metal elements: interesting similarities to and differences from 3d transition metal complexes.
J Phys Chem A
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Inverted sandwich type complexes (ISTCs) of 4d metals, (?-?(6):?(6)-C(6)H(6))[M(DDP)](2) (DDPH = 2-{(2,6-diisopropylphenyl)amino}-4-{(2,6-diisopropylphenyl)imino}pent-2-ene; M = Y, Zr, Nb, Mo, and Tc), were investigated with density functional theory (DFT) and MRMP2 methods, where a model ligand AIP (AIPH = (Z)-1-amino-3-imino-prop-1-ene) was mainly employed. When going to Nb (group V) from Y (group III) in the periodic table, the spin multiplicity of the ground state increases in the order singlet, triplet, and quintet for M = Y, Zr, and Nb, respectively, like 3d ISTCs reported recently. This is interpreted with orbital diagram and number of d electrons. However, the spin multiplicity decreases to either singlet or triplet in ISTC of Mo (group VI) and to triplet in ISTC of Tc (group VII), where MRMP2 method is employed because the DFT method is not useful here. These spin multiplicities are much lower than the septet of ISTC of Cr and the nonet of that of Mn. When going from 3d to 4d, the position providing the maximum spin multiplicity shifts to group V from group VII. These differences arise from the size of the 4d orbital. Because of the larger size of the 4d orbital, the energy splitting between two d(?) orbitals of M(AIP) and that between the d(?) and d(?) orbitals are larger in the 4d complex than in the 3d complex. Thus, when occupation on the d(?) orbital starts, the low spin state becomes ground state, which occurs at group VI. Hence, the ISTC of Nb (group V) exhibits the maximum spin multiplicity.
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Two-step evaluation of binding energy and potential energy surface of van der Waals complexes.
J Comput Chem
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Evaluation of intermolecular distance and binding energy (BE) of van der Waals complex/cluster at ab initio level of theory is computationally demanding when many monomers are involved. Starting from MP2 energy, we reached a two-step evaluation method of BE of van der Waals complex/cluster through reasonable approximations; BE = BE(HF) + sum Mi> Mj{BE (Mi- Mj)(MP2 or MP2.5) - BE(Mi-Mj)(HF)} where HF represents the Hartree-Fock calculation, Mi, Mj, etc. are interacting monomers, and MP2.5 represents the arithmetic mean of MP2 and MP3. The first term is the usual BE of the complex/cluster evaluated at the HF level. The second term is the sum of the difference in two-body BE between the correlated and HF levels of theory. This equation was applied to various van der Waals complexes consisting of up-to-four monomers at MP2 and MP2.5 levels of theory. We found that this method is capable of providing precise estimate of the BE and reproducing well the potential energy surface of van der Waals complexes/clusters; the maximum error of the BE is less than 1 kcal/mol and 1% in most cases except for several limited cases. The origins of error in these cases are discussed in detail.
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