Biomedical subjects

Jan M L Martin

Publications and source records attributed to Jan M L Martin.

At least 19 recordsLinked to original sources

PubMed2006

W4 theory for computational thermochemistry: In pursuit of confident sub-kJ/mol predictions.

In an attempt to improve on our earlier W3 theory [A. D. Boese et al., J. Chem. Phys. 120, 4129 (2004)] we consider such refinements as more accurate estimates for the contribution of connected quadruple excitations (T4), inclusion of connected quintuple excitations (T5), diagonal Born-Oppenheimer corrections (DBOC), and improved basis set extrapolation procedures. Revised experimental data for validation purposes were obtained from the latest version of the Active Thermochemical Tables thermochemical network. The recent CCSDT(Q) method offers a cost-effective way of estimating T4, but is insufficient by itself if the molecule exhibits some nondynamical correlation. The latter considerably slows down basis set convergence for T4, and anomalous basis set convergence in highly polar systems makes two-point extrapolation procedures unusable. However, we found that the CCSDTQ-CCSDT(Q) difference converges quite rapidly with the basis set, and that the formula 1.10[CCSDT(Q)cc-pVTZ+CCSDTQcc-pVDZ-CCSDT(Q)cc-pVDZ] offers a very reliable as well as fairly cost-effective estimate of the basis set limit T4 contribution. The T5 contribution converges very rapidly with the basis set, and even a simple double-zeta basis set appears to be adequate. The largest T5 contribution found in the present work is on the order of 0.5 kcal/mol (for ozone). DBOCs are significant at the 0.1 kcal/mol level in hydride systems. Post-CCSD(T) contributions to the core-valence correlation energy are only significant at that level in systems with severe nondynamical correlation effects. Based on the accumulated experience, a new computational thermochemistry protocol for first- and second-row main-group systems, to be known as W4 theory, is proposed. Its computational cost is not insurmountably higher than that of the earlier W3 theory, while performance is markedly superior. Our W4 atomization energies for a number of key species are in excellent agreement (better than 0.1 kcal/mol on average, 95% confidence intervals narrower than 1 kJ/mol) with the latest experimental data obtained from Active Thermochemical Tables. Lower-cost variants are proposed: the sequence W1-->W2.2-->W3.2-->W4lite-->W4 is proposed as a converging hierarchy of computational thermochemistry methods. A simple a priori estimate for the importance of post-CCSD(T) correlation contributions (and hence a pessimistic estimate for the error in a W2-type calculation) is proposed.

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PubMed2006

The lowest singlet-triplet excitation energy of BN: A converged coupled cluster perspective.

The notoriously small X 3Pi-a 1Sigma+ excitation energy of the BN diatomic has been calculated using high-order coupled cluster methods. Convergence has been established in both the one-particle basis set and the coupled cluster expansion. Explicit inclusion of connected quadruple excitations T4 is required for even semiquantitative agreement with the limit value, while connected quintuple excitations T5 still have an effect of about 60 cm(-1). Still higher excitations only account for about 10 cm(-1). Inclusion of inner-shell correlation further reduces Te by about 60 cm(-1) at the CCSDT, and 85 cm(-1) at the CCSDTQ level. Our best estimate, Te = 183+/-40 cm(-1), is in excellent agreement with earlier calculations and experiment, albeit with a smaller (and conservative) uncertainty. The dissociation energy of BN(X 3Pi) is De = 105.74+/-0.16 kcal/mol and D0 = 103.57+/-0.16 kcal/mol.

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PubMed2006

Selective sp3 C-H activation of ketones at the beta position by Ir(I). Origin of regioselectivity and water effect.

The reaction of the cationic (PNP)Ir(I)(cyclooctene) complex (1) (PNP = 2,6-bis-(di-tert-butylphosphinomethyl)pyridine) with 2-butanone or 3-pentanone results in the selective, quantitative activation of a beta C-H bond, yielding O,C-chelated complexes. Calculations show that the selectivity is both kinetically (because of steric reasons in the rate determingin step (RDS)) and thermodynamically controlled, the latter as a result of carbonyl oxygen coordination in the product. The RDS is formation of the eta2-C,H intermediates from the complexed ketone intermediates. Water has a strong influence on the regioselectivity, and in its presence, reaction of 1 with 2-butanone gives also the alpha terminal C-H activation product. Computational studies suggest that water can stabilize the terminal alpha C-H activation product by hydrogen bonding, forming a six-membered ring with the ketone, as experimentally observed in the X-ray structure of the acetonyl hydride aqua complex.

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PubMed2006

Rozen's epoxidation reagent, CH3CN.HOF: a theoretical study of its structure, vibrational spectroscopy, and reaction mechanism.

Rozen's epoxidation reagent, CH(3)CN.HOF, and a prototype epoxidation reaction employing it, have been subjected to an extensive ab initio and density functional study. Its anharmonic force field reveals a very strong red shift for the OH stretch and a strong blue shift for the HOF bend, in semiquantitative agreement with experiment. The very strong hydrogen bond (8.20 kcal/mol at the W1 level) not only serves to stabilize the reactant but also considerably lowers the barrier height for epoxidation of ethylene. Moreover, the reaction byproduct HF is found to act autocatalytically. The OH moiety acquires HO(+) character in the transition state. Our W1 benchmark data for the reaction profile allow the performance of various DFT functionals to be assessed. In general, "kinetics" functionals overestimate barrier heights, the BMK functional less so than the others. The B1B95 and TPSS33B95 meta-GGA functionals both perform very well, whereas general-purpose hybrid GGAs underestimate barrier heights. The simple PBE0 functional does reasonably well.

Acetonitriles↗

PubMed2006

Benchmark study of DFT functionals for late-transition-metal reactions.

The performance of a wide variety of DFT exchange-correlation functionals for a number of late-transition-metal reaction profiles has been considered. Benchmark ab-initio reference data for the prototype reactions Pd + H2, Pd + CH4, Pd + C2H6 (both C-C and C-H activation), and Pd + CH3Cl are presented, while ab-initio data of lesser quality were obtained for the catalytic hydrogenation of acetone and for the low-oxidation-state and high-oxidation-state mechanisms of the Heck reaction. "Kinetics" functionals such as mPW1K, PWB6K, BB1K, and BMK clearly perform more poorly for late-transition-metal reactions than for main-group reactions, as well as compared to general-purpose functionals. There is no single "best functional" for late-transition-metal reactions, but rather a cluster of several functionals (PBE0, B1B95, PW6B95, and TPSS25B95) that perform about equally well; if main-group thermochemical performance is additionally considered, then B1B95 and PW6B95 emerge as the best performers. TPSS25B95 and TPSS33B95 offer attractive performance compromises if weak interactions and main-group barrier heights, respectively, are also important. In the ab-initio calculations, basis set superposition errors (BSSE) can be greatly reduced by ensuring that the metal spd shell has sufficient radial flexibility in the high-exponent range. Optimal HF percentages in hybrid functionals depend on the class of systems considered, increasing from anions to neutrals to cations to main-group barrier heights; transition-metal barrier heights represent an intermediate situation. The use of meta-GGA correlation functionals appears to be quite beneficial.

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PubMed2005

Structures and thermochemistry of calcium-containing molecules.

A variety of theoretical procedures, including the high-level ab initio methods G3, G3[CC](dir,full), and W2C//ACQ, have been used to predict the structures and heats of formation of several small calcium-containing molecules (CaH, CaH2, CaO, CaOH, Ca(OH)2, CaF, CaF2, CaS, CaCl, and CaCl2). B3-LYP and CCSD(T) with both the (aug-)cc-pWCVQZ and (aug-)cc-pWCVQ+dZ basis sets are found to give molecular geometries that agree well with the experimental results. The CCSD(T)(riv)/(aug-)cc-pWCVQ+dZ results are found to be the most accurate, with a mean absolute deviation from experiment of just 0.008 angstroms. Zero-point vibrational energies (ZPVEs) and thermochemical corrections are found to be relatively insensitive to the level of theory, except in the case of molecules with highly anharmonic calcium-centered bending modes (CaH2, Ca(OH)2, CaF2, CaCl2), where special procedures need to be employed in order to obtain satisfactory results. Several potential improvements to the W2C method were investigated, most of which do not produce significant changes in the heats of formation. It was observed, however, that for CaO and CaS the scalar relativistic corrections are unexpectedly large and highly basis set dependent. In these cases, Douglas-Kroll CCSD(T)/(aug-)cc-pWCV5Z calculations appear to give a converged result. The G3[CC](dir,full) and best W2C-type heats of formation are both found generally to agree well with experimental values recommended in recent critical compendia. However, in some cases (CaO, Ca(OH)2, and CaF2), they differ from one another by more than their predicted error margins. The available experimental data are not sufficiently precise to distinguish definitively between the two sets of results although, in general, when discrepancies exist the W2C heats of formation are lower in energy and tend to be in better agreement with experiment. In the case of CaO, the W2C heat of formation (20.7 kJ mol(-1)) is approximately 20 kJ mol(-1) lower than the G3[CC](dir, full) result and most of the experimental data. Extensive investigation of possible refinements of the W2C method has failed to reveal any weaknesses that could account for this discrepancy. We therefore believe that the heat of formation of CaO is likely to lie closer to the more recent direct experimental determination of 27 kJ mol(-1) than to the value of approximately 40 kJ mol(-1) recommended in recent thermochemical reviews.

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PubMed2005

Platinum stilbazoles: ring-walking coupled with aryl-halide bond activation.

The reaction between tetrakis(triethylphosphine)platinum(0) and 4-[trans-2-(4-bromophenyl)vinyl]pyridine (1) is examined. Initially, the metal center coordinates to the bridging double bond of 1. Complexes 2 and 3 were fully characterized, and their X-ray crystallography structures are presented. Upon heating, either in solution or in the solid state, complex 2 undergoes C-Br oxidative addition to give complex 3. Kinetic studies revealed that this conversion is unimolecular and does not involve dissociation of the metal center from the double bond. Density functional studies show that a plausible mechanism involves the metal center "walking" around the pi-system from the bridging C=C double bond to the C-Br bond.

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PubMed2005

NLO properties of metallabenzene-based chromophores: a time-dependent density functional study.

The static and dynamic first hyperpolarizabilities for a series of substituted metallabenzene-based nonlinear optical (NLO) chromophores were determined by time-dependent density functional theory (TDDFT). The electronic excitation contributions to the first hyperpolarizability are rationalized in terms of the two-level model. The effects on the hyperpolarizabilities of (a) the metal center (Os, Ir, Pt); (b) the ligand environment (PH3, CO, Cl); (c) various donor and acceptor substituents (NH2, OH, Me, H, Cl, Br, I, COOMe, COOH, CN, NO2); and (d) the length of pi-conjugation were studied. Our calculations predict that metallabenzenes have significant second-order NLO susceptibilities, ranging from = 1.0 x 10(-29) to 5.6 x 10(-28) esu and from mu = 3.0 x 10(-47) to 1.1 x 10(-44) esu, that can be tuned by changing the metal center and/or ligand environment.

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PubMed2005

Pi-accepting-pincer rhodium complexes: an unusual coordination mode of PCP-type systems.

The novel pi-accepting, pincer-type ligand, dipyrrolylphoshinoxylene (DPyPX), is introduced. This ligand has the strongest pi-accepting phosphines used so far in the PCP family of ligands and this results in some unusual coordination chemistry. The rhodium(I) complex, [(DPyPX)Rh(CO)(PR3)] (4, R=Ph, Et, pyrrolyl) is prepared by treating the relevant [(DPyPX)Rh(PR3)] (3) complex with CO and is remarkably resistant to loss of either ligand. X-ray crystallographic analysis of complex 4 b (R=Et) reveals an unusual cisoid coordination of the PCP phosphine ligands. These observations are supported by density functional theory (DFT) calculations.

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PubMed2004

The mechanism of aluminum-catalyzed Meerwein-Schmidt-Ponndorf-Verley reduction of carbonyls to alcohols.

The mechanistic details of the Meerwein-Schmidt-Ponndorf-Verley (MSPV) reduction of ketones to the corresponding alcohols were investigated both experimentally and computationally. Density functional theory (DFT) was used to assess the energetics of several proposed pathways (direct hydrogen transfer, hydridic, and radical). Our results demonstrate that a direct hydrogen transfer mechanism involving a concerted six-membered ring transition state is the most favorable pathway for all calculated systems starting from a small model system and concluding with the experimentally investigated BINOLate/Al/(i)PrOH/MePhC=O system. Experimental values for the activation parameters of acetophenone reduction using the BINOLate/Al/(i)PrOH system (DeltaG# = 21.8 kcal/mol, DeltaH# = 18.5 kcal/mol, DeltaS# = -11.7 au) were determined on the basis of kinetic investigation of the reaction and are in good agreement with the computational findings for this system. Calculated and experimental kinetic isotope effects support the concerted mechanism.

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PubMed2004

A computational foray into the formation and reactivity of metallabenzenes.

Various metallabenzene complexes, analogues of benzene where one CH unit has been replaced by an organometallic fragment, have been reported in the literature. A detailed theoretical investigation on the chemistry of these complexes is presented here. This includes an evaluation of their aromaticity, the mechanisms of formation of osmium, iridium, and platinum metallabenzene complexes, and one intriguing aspect of their chemistry, the formation of cyclopentadienyl (Cp) complexes. X-ray photoelectron spectroscopy (XPS) measurements on two osmabenzene examples are also presented. In addition, diffuse functions for use with the SDD and SDB-cc-pVDZ basis set-RECP combinations are presented for the transition metals.

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PubMed2004

Development of density functionals for thermochemical kinetics.

A density functional theory exchange-correlation functional for the exploration of reaction mechanisms is proposed. This functional, denoted BMK (Boese-Martin for Kinetics), has an accuracy in the 2 kcal/mol range for transition state barriers but, unlike previous attempts at such a functional, this improved accuracy does not come at the expense of equilibrium properties. This makes it a general-purpose functional whose domain of applicability has been extended to transition states, rather than a specialized functional for kinetics. The improvement in BMK rests on the inclusion of the kinetic energy density together with a large value of the exact exchange mixing coefficient. For this functional, the kinetic energy density appears to correct "back" the excess exact exchange mixing for ground-state properties, possibly simulating variable exchange.

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PubMed2004

W3 theory: robust computational thermochemistry in the kJ/mol accuracy range.

We are proposing a new computational thermochemistry protocol denoted W3 theory, as a successor to W1 and W2 theory proposed earlier [Martin and De Oliveira, J. Chem. Phys. 111, 1843 (1999)]. The new method is both more accurate overall (error statistics for total atomization energies approximately cut in half) and more robust (particularly towards systems exhibiting significant nondynamical correlation) than W2 theory. The cardinal improvement rests in an approximate account for post-CCSD(T) correlation effects. Iterative T3 (connected triple excitations) effects exhibit a basis set convergence behavior similar to the T3 contribution overall. They almost universally decrease molecular binding energies. Their inclusion in isolation yields less accurate results than CCSD(T) nearly across the board: It is only when T4 (connected quadruple excitations) effects are included that superior performance is achieved. T4 effects systematically increase molecular binding energies. Their basis set convergence is quite rapid, and even CCSDTQ/cc-pVDZ scaled by an empirical factor of 1.2532 will yield a quite passable quadruples contribution. The effect of still higher-order excitations was gauged for a subset of molecules (notably the eight-valence electron systems): T5 (connected quintuple excitations) contributions reach 0.3 kcal/mol for the pathologically multireference X 1Sigmag+ state of C2 but are quite small for other systems. A variety of avenues for achieving accuracy beyond that of W3 theory were explored, to no significant avail. W3 thus appears to represent a good compromise between accuracy and computational cost for those seeking a robust method for computational thermochemistry in the kJ/mol accuracy range on small systems.

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PubMed2003

Metallabenzene versus Cp complex formation: a DFT investigation.

One common reaction that metallabenzene complexes undergo is the formation of cyclopentadienyl (Cp) complexes. Density functional theory (DFT) was used here to investigate the reaction mechanism. It was found that the reaction can proceed via a carbene migratory insertion class of C-C coupling. Cp complexes are found to be thermodynamically favored, except for the case of (C5H5Ir)(PH3)2Cl2 (1j) where the metallabenzene was favored. Isolation a rhodiabenzene of the type (C5H5Rh)(PH3)2Cl2 (1m) and a palladiabenzene, such as (C5H5Pd)Cp (1p), may be possible.

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PubMed2003

Cycloaddition reactions of metalloaromatic complexes of iridium and rhodium: a mechanistic DFT investigation.

The mechanistic details of 1,2- and 1,4-cycloaddition reactions of acetone, CO(2), and CS(2) to isostructural iridiabenzene, iridiapyrylium, and iridiathiabenzene complexes, as well as their rhodium analogues, were elucidated by density functional theory (DFT) at the PCM/mPW1K/SDB-cc-pVDZ//mPW1K/SDD level of theory. The calculated reaction profiles concur with reported experimental observations. It was found that the first complex reacts via a concerted reaction mechanism, while the latter two react by a stepwise mechanism. Several factors affecting the reaction mechanisms and outcome were identified. They include the composition and size of the metal-aromatic ring, the length of the substrate C=X (X = O, S) bond, the geometry of the product, the symmetry of the frontier molecular orbitals, and the type of reaction mechanism involved.

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PubMed2003

Catalytic reduction of acetone by [(bpy)Rh]+: a theoretical mechanistic investigation and insight into cooperativity effects in this system.

Lahav, Milstein, and co-workers reported that the complex [(bpy)Rh(hd)](+)PF(6)(-) (bpy = substituted bipyridine ligand, hd = 1,5-hexadiene) shows catalytic activity in the hydrogenation of acetone (Töllner, K. et al. Science 1997, 278, 2100). The activity in an ordered monolayer was found to be dramatically greater than in solution. We used the DFT functional mPW1K (Lynch, B. J. et al. J. Phys. Chem. A 2000, 104, 4811) to investigate the mechanism of the homogenous reaction. The suitability of the mPW1K functional was verified by coupled cluster calculations on a model system. Bulk solvent effects were considered. Various alternative catalytic cycles were evaluated, and we found that one potential mechanism involves metal-catalyzed keto-enol tautomerization to form [(bpy)Rh(enol)](+) that adds hydrogen yielding a complex with axial and equatorial hydride ligands. The reaction continues via transfer of the hydrides to the enolic C=C bond thereby forming 2-propanol and regenerating the catalyst. Another potential catalytic cycle involves formation of [(bpy)Rh(acetone)(2)(H)(2)](+), which has a spectator solvent ligand, and initial transfer of the equatorial hydride to the carbonyl carbon of acetone. Other mechanisms involving hydrogen transfer to the acetone tautomer involved higher barriers. With an eye toward modeling multi-center catalysis, various model systems for the bpy ligand were considered. It was found that diimine (HN=CH-CH=NH) compares very well with bpy, whereas cis-1,2-diiminoethylene (H(2)C=N-CH=CH-N=CH(2)) yields a reaction profile very close to that of bpy. Finally, the system with two rhodium centers, [(diimine)Rh](2)(2+), was investigated. The results strongly suggest that an enol-type catalytic cycle occurs and that cooperativity between the two metal centers is responsible for the acceleration of the reaction in the monolayer system.

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PubMed2003

Aromatic vs aliphatic C-H bond activation by rhodium(I) as a function of agostic interactions: catalytic H/D exchange between olefins and methanol or water.

The aryl-PC type ligand 3, benzyl(di-tert-butyl)phosphane, reacts with [Rh(coe)(2)(solv)(n)()]BF(4) (coe = cyclooctene, solv = solvent), producing the C-H activated complexes 4a-c (solv = (a). acetone, (b). THF, (c). methanol). Complexes 4a-c undergo reversible arene C-H activation (observed by NMR spin saturation transfer experiments, SST) and H/D exchange into the hydride and aryl ortho-H with ROD (R = D, Me). They also promote catalytic H/D exchange into the vinylic C-H bond of olefins, with deuterated methanol or water utilized as D-donors. Unexpectedly, complex 2, based on the benzyl-PC type ligand 1 (analogous to 3), di-tert-butyl(2,4,6-trimethylbenzyl)phosphane, shows a very different reversible C-H activation pattern as observed by SST. It is not active in H/D exchange with ROD and in catalytic H/D exchange with olefins. To clarify our observations regarding C-H activation/reductive elimination in both PC-Rh systems, density functional theory (DFT) calculations were performed. Both nucleophilic (oxidative addition) and electrophilic (H/D exchange) C-H activation proceed through eta(2)-C,H agostic intermediates. In the aryl-PC system the agostic interaction causes C-H bond acidity sufficient for the H/D exchange with water or methanol, which is not the case in the benzyl PC-Rh system. In the latter system the C-H coordination pattern of the methyl controls the reversible C-H oxidative addition leading to energetically different C-H activation processes, in accordance with the experimental observations.

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PubMed2003

Metallacarbenes from diazoalkanes: an experimental and computational study of the reaction mechanism.

PCP ligand (1,3-bis-[(diisopropyl-phosphanyl)-methyl]-benzene), and PCN ligand ([3-[(di-tert-butyl-phosphanyl)-methyl]-benzyl]-diethyl-amine) based rhodium dinitrogen complexes (1 and 2, respectively) react with phenyl diazomethane at room temperature to give PCP and PCN-Rh carbene complexes (3 and 5, respectively). At low temperature (-70 degrees C), PCP and PCN phenyl diazomethane complexes (4 and 6, respectively) are formed upon addition of phenyl diazomethane to 1 and 2. In these complexes, the diazo moiety is eta(1) coordinated through the terminal nitrogen atom. Decomposition of complexes 4 and 6 at low temperatures leads only to a relatively small amount of the corresponding carbene complexes, the major products of decomposition being the dinitrogen complexes 1 and 2 and stilbene. This and competition experiments (decomposition of 6 in the presence of 1) suggests that phenyl diazomethane can dissociate under the reaction conditions and attack the metal center through the diazo carbon producing a eta(1)-C bound diazo complex. Computational studies based on a two-layer ONIOM model, using the mPW1K exchange-correlation functional and a variety of basis sets for PCP based systems, provide mechanistic insight. In the case of less bulky PCP ligand bearing H-substituents on the phosphines, a variety of mechanisms are possible, including both dissociative and nondissociative pathways. On the other hand, in the case of i-Pr substituents, the eta(1)-C bound diazo complex appears to be a critical intermediate for carbene complex formation, in good agreement with the experimental results. Our results and the analysis of reported data suggest that the outcome of the reaction between a diazoalkane and a late transition metal complex can be anticipated considering steric requirements relevant to eta(1)-C diazo complex formation.

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