PubMed Health⌕ Search

Biomedical subjects

Thomas R Cundari

Publications and source records attributed to Thomas R Cundari.

At least 19 recordsLinked to original sources
PubMed2006

Catalytic loop motion in human glutathione synthetase: A molecular modeling approach.

Conformational changes of three flexible loops (G, A, and S) in human glutathione synthetase (hGS) arise to accommodate the substrates inside the active site. The crystal structure of hGS, a member of the ATP-grasp superfamily, has been reported only for the product-enzyme complex. To study the function of the hGS loops, molecular dynamics simulations are performed on three different conformational models: unbound enzyme, reactant-enzyme, and product-enzyme complex of hGS. The conformational changes among the three models are analyzed and the roles of the loops during the catalytic process are described. The modeled structures of hGS show that the central portions of the G- and A-loop have a double role in the reactant complex conformation: they bind the substrates and simultaneously interact with each other through an extensive network of hydrogen bonds. The present study proposes that these favorable loop-ligand and loop-loop interactions are required for opening and closing of the active site of hGS. Additionally, this research identifies important amino acid residues and explains their function within the catalytic loops of hGS.

Amino Acid Sequence↗
PubMed2006

Chemistry surrounding monomeric copper(I) methyl, phenyl, anilido, ethoxide, and phenoxide complexes supported by N-heterocyclic carbene ligands: reactivity consistent with both early and late transition metal systems.

Monomeric copper(I) alkyl complexes that possess the N-heterocyclic carbene (NHC) ligands IPr, SIPr, and IMes [IPr = 1,3-bis(2,6-diisopropylphenyl)imidazol-2-ylidene, SIPr = 1,3-bis(2,6-diisopropylphenyl)imidazolin-2-ylidene, IMes = 1,3-bis(2,4,6-trimethylphenyl)imidazol-2-ylidene] react with amines or alcohols to release alkane and form the corresponding monomeric copper(I) amido, alkoxide, or aryloxide complexes. Thermal decomposition reactions of (NHC)Cu(I) methyl complexes at temperatures between 100 and 130 degrees C produce methane, ethane, and ethylene. The reactions of (NHC)Cu(NHPh) complexes with bromoethane reveal increasing nucleophilic reactivity at the anilido ligand in the order (SIPr)Cu(NHPh) < (IPr)Cu(NHPh) < (IMes)Cu(NHPh) < (dtbpe)Cu(NHPh) [dtbpe = 1,2-bis(di-tert-butylphosphino)ethane]. DFT calculations suggest that the HOMO for the series of Cu anilido complexes is localized primarily on the amido nitrogen with some ppi(anilido)-dpi(Cu) pi-character. [(IPr)Cu(mu-H)]2 and (IPr)Cu(Ph) react with aniline to quantitatively produce (IPr)Cu(NHPh)/dihydrogen and (IPr)Cu(NHPh)/benzene, respectively. Analysis of the DFT calculations reveals that the conversion of [(IPr)Cu(mu-H)]2 and aniline to (IPr)Cu(NHPh) and dihydrogen is favorable with DeltaH approximately -7 kcal/mol and DeltaG approximately -9 kcal/mol.

Journal Article↗
PubMed2006

The correlation-consistent composite approach: application to the G3/99 test set.

The correlation-consistent composite approach (ccCA), an ab initio composite technique for computing atomic and molecular energies, recently has been shown to successfully reproduce experimental data for a number of systems. The ccCA is applied to the G3/99 test set, which includes 223 enthalpies of formation, 88 adiabatic ionization potentials, 58 adiabatic electron affinities, and 8 adiabatic proton affinities. Improvements on the original ccCA formalism include replacing the small basis set quadratic configuration interaction computation with a coupled cluster computation, employing a correction for scalar relativistic effects, utilizing the tight-d forms of the second-row correlation-consistent basis sets, and revisiting the basis set chosen for geometry optimization. With two types of complete basis set extrapolation of MP2 energies, ccCA results in an almost zero mean deviation for the G3/99 set (with a best value of -0.10 kcal mol(-1)), and a 0.96 kcal mol(-1) mean absolute deviation, which is equivalent to the accuracy of the G3X model chemistry. There are no optimized or empirical parameters included in the computation of ccCA energies. Except for a few systems to be discussed, ccCA performs as well as or better than Gn methods for most systems containing first-row atoms, while for systems containing second-row atoms, ccCA is an improvement over Gn model chemistries.

Journal Article↗
PubMed2006

Accurate enthalpies of formation of alkali and alkaline earth metal oxides and hydroxides: assessment of the correlation consistent composite approach (ccCA).

Computing the enthalpies of formation for alkali metal and alkaline earth metal oxides (M(x)O) and hydroxides [M(OH)(n)] using the Gaussian-n (Gn) and Weismann-n (Wn) ab initio model chemistries is difficult due to an improper treatment of core-valence electron correlation effects. Using a new model chemistry called the correlation consistent Composite Approach (ccCA), enthalpies of formation were determined for eight different alkali/alkaline earth metal oxides and hydroxides. Unlike the Gn and Wn model chemistries, which must be modified to properly account for core-valence electron correlation, the standard implementations of the ccCA provide acceptable results, and all enthalpies of formation obtained with the ccCA are within the accepted range of recommended values.

Computer Simulation↗
PubMed2006

Disproportionation of Gold(II) complexes. A density functional study of ligand and solvent effects.

A computational study of gold(II) disproportionation is presented for the atomic ion as well as complexes with chloride and neutral ligands. The Au2+ atomic ion is stable to disproportionation, but the barrier is more than halved to 119 kcal/mol in an aqueous environment vs 283 kcal/mol in the gas phase. For dissociative disproportionation of chloride complexes, the loss of chlorine, either as an atom (Delta G(aq) = +20 kcal/mol) or as an anion (Delta G(aq) = +15 kcal/mol) represents the largest calculated barrier. The calculated transition state for associative disproportionation is only 9 kcal/mol above separated Au(II)Cl3(-) anions. For the disproportionation of Au(II)L3 complexes with neutral ligands, disproportionation is highly endergonic in the gas phase. Calculations imply that for synthesis of a monometallic Au(II) complex, a nonpolar solvent is preferred. With the exception of [Au(CO)3]2+, disproportionation of Au(II)L3 complexes to Au(I)L and Au(III)L3 is exergonic in solution phase for the ligands investigated. The driving force is provided by the very favorable solvation free energy of the trivalent gold complex. The solvation free energy contribution to the reaction (Delta G(solv)) is very large for small and polar ligands such as ammonia and water. Furthermore, calculations imply that choosing ligands that would yield neutral species upon disproportionation may provide an effective route to thwart this decomposition pathway for Au(II) complexes. Likewise, bulkier ligands that yield larger, more weakly solvated complex ions would appear to be desirable.

Journal Article↗
PubMed2006

Hydrogen-deuterium exchange between TpRu(PMe3)(L)X (L = PMe3 and X = OH, OPh, Me, Ph, or NHPh; L = NCMe and X = Ph) and deuterated arene solvents: evidence for metal-mediated processes.

At elevated temperatures (90-130 degrees C), complexes of the type TpRu(PMe3)2X (X = OH, OPh, Me, Ph, or NHPh; Tp = hydridotris(pyrazolyl)borate) undergo regioselective hydrogen-deuterium (H/D) exchange with deuterated arenes. For X = OH or NHPh, H/D exchange occurs at hydroxide and anilido ligands, respectively. For X = OH, OPh, Me, Ph, or NHPh, isotopic exchange occurs at the Tp 4-positions with only minimal deuterium incorporation at the Tp 3- or 5-positions or PMe3 ligands. For TpRu(PMe3)(NCMe)Ph, the H/D exchange occurs at 60 degrees C at all three Tp positions and the phenyl ring. TpRu(PMe3)2Cl, TpRu(PMe3)2OTf (OTf = trifluoromethanesulfonate), and TpRu(PMe3)2SH do not initiate H/D exchange in C6D6 after extended periods of time at elevated temperatures. Mechanistic studies indicate that the likely pathway for the H/D exchange involves ligand dissociation (PMe3 or NCMe), Ru-mediated activation of an aromatic C-D bond, and deuteration of basic nondative ligand (hydroxide or anilido) or Tp positions via net D+ transfer.

Cadmium Compounds↗
PubMed2006

Intertrimer and intratrimer metallophilic and excimeric bonding in the ground and phosphorescent States of trinuclear coinage metal pyrazolates: a computational study.

The interactions present in cyclic trinuclear coinage metal pyrazolates were studied computationally. Cuprophilic interaction was found to bind the singlet ground state of the dimer of trimers [[Cu(Pz)](3)](2), overcoming electrostatic repulsion. The large variation in intertrimer separations found in the literature for coinage metal pyrazolates is consistent with the relatively weak metallophilic interaction. The emissive triplet excited-state geometry of [[M(Pz)](3)](2) is predicted by density functional calculations to show major geometric distortion caused by Jahn-Teller instability and excimeric M-M bonding. Large calculated Stokes' shifts, which are also observed for experimental models, are consistent with significant excited-state distortions for these materials. The major finding derived from the present study is that the intertrimer M...M contraction in the emissive T(1) state is much more than the intratrimer contraction in all [[M(Pz)](3)](2) models, giving rise to a lower T(1) --> S(0) phosphorescence energy in these models than in analogous monomer-of-trimer models. The observations made here point to a great potential for rationally tuning the emission properties of trinuclear coinage metal complexes through choice of the metal and ligands.

Journal Article↗
PubMed2006

Oxygen atom transfer energetics: assessment of the effect of method and solvent.

Several density functional methods, the semiempirical methods AM1 and PM3, Hartree-Fock, and Gaussian3 theories were applied to compute the oxygen atom transfer enthalpies for 14 X/XO couples (inorganic and organic systems, charged and neutral species, light and heavy main group element containing molecules). The calculated reaction enthalpies were compared to available experimental data. The G3 method alone was found to perform within the experimental error, while the popular B3LYP and BLYP functionals provided inadequate results. Solvent effects were estimated for 19 neutral and anionic X/XO couples by using the conductor-like polarizable continuum model and several cavity models coupled with the B3LYP/6-31++G(2d,2p) level of theory. Surprisingly, the magnitude of the aqueous solvent correction was found to vary significantly for different solute cavity models, occasionally giving larger errors than the gas-phase calculation.

Computer Simulation↗
PubMed2006

The correlation consistent composite approach (ccCA): an alternative to the Gaussian-n methods.

An alternative to the Gaussian-n (G1, G2, and G3) composite methods of computing molecular energies is proposed and is named the "correlation consistent composite approach" (ccCA, ccCA-CBS-1, ccCA-CBS-2). This approach uses the correlation consistent polarized valence (cc-pVXZ) basis sets. The G2-1 test set of 48 enthalpies of formation (DeltaHf), 38 adiabatic ionization potentials (IPs), 25 adiabatic electron affinities (EAs), and 8 adiabatic proton affinities (PAs) are computed using this approach, as well as the DeltaHf values of 30 more systems. Equilibrium molecular geometries and vibrational frequencies are obtained using B3LYP density functional theory. When applying the ccCA-CBS method with the cc-pVXZ series of basis sets augmented with diffuse functions, mean absolute deviations within the G2-1 test set compared to experiment are 1.33 kcal mol(-1) for DeltaHf,0.81 kcal mol(-1) for IPs, 1.02 kcal mol(-1) for EAs, and 1.51 kcal mol(-1) for PAs, without including the "high-level correction" (HLC) contained in the original Gn methods. Whereas the HLC originated in the Gaussian-1 method as an isogyric correction, it evolved into a fitted parameter that minimized the error of the composite methods, eliminating its physical meaning. Recomputing the G1 and G3 enthalpies of formation without the HLC reveals a systematic trend where most DeltaHf values are significantly higher than experimental values. By extrapolating electronic energies to the complete basis set (CBS) limit and adding G3-like corrections for the core-valence and infinite-order electron correlation effects, ccCA-CBS-2 often underestimates the experimental DeltaHf, especially for larger systems. This is desired as inclusion of relativistic and atomic spin-orbit effects subsequently improves theoretical DeltaHf values to give a 0.81 kcal mol(-1) mean absolute deviation with ccCA-CBS-2. The ccCA-CBS method is a viable "black box" method that can be used on systems with at least 10-15 heavy atoms.

Journal Article↗
PubMed2006

The butterfly dimer [(tBu3SiO)Cr]2(mu-OSitBu3)2 and its oxidative cleavage to (tBu3SiO)2Cr(=N-N=CPh2)2 and (tBu3SiO)2Cr=N(2,6-Ph2-C6H3).

Treatment of CrCl2(THF)2 with NaOSitBu3 afforded the butterfly dimer [(tBu3SiO)Cr]2(mu-OSitBu3)2 (1(2)), whose d(CrCr) of 2.658(31) A and magnetism were indicative of strong antiferromagnetic coupling. A Boltzmann distribution of low-energy 1A1, 3B1, 5A1, 7B1, and 9A1 states obtained from calculations on [(HO)2Cr]2(muOH)2 (1'(2)) were used to provide a reasonable fit of the mu(eff) vs T data. Cleavage of 1(2) with various L (L = 4-picoline, p-tolunitrile, tBuCN, tBuNC, Ph2CO, and PMe3) generated (tBu3SiO)2CrL2 (1-L2). The dimer was oxidatively severed by Ph2CN2 to give (tBu3SiO)2Cr(N2CPh2)2 (2) and by RN3 at 23 degrees C to afford (silox)2Cr=NR (3-R) for bulky R (adamantyl (Ad), 2,6-iPr2-C6H3, 2,4,6-Me3-C6H2 = Mes, 2,6-Ph2-C6H3) and (tBu3SiO)2Cr(=NR)2 (4-R) for smaller substituents (R = 1-Naph, 2-Anth). X-ray structural studies were conducted on 1(2), square planar 1-(OCPh2)2, pseudo-Td 2 and pseudo-trigonal 3-(2,6-Ph2-C6H3), whose S = 1 ground state was discussed on the basis of calculations of (H3SiO)2Cr=NPh (3' '-Ph).

Journal Article↗
PubMed2006

Studies of low-coordinate iron dinitrogen complexes.

Understanding the interaction of N2 with iron is relevant to the iron catalyst used in the Haber process and to possible roles of the FeMoco active site of nitrogenase. The work reported here uses synthetic compounds to evaluate the extent of NN weakening in low-coordinate iron complexes with an FeNNFe core. The steric effects, oxidation level, presence of alkali metals, and coordination number of the iron atoms are varied, to gain insight into the factors that weaken the NN bond. Diiron complexes with a bridging N2 ligand, L(R)FeNNFeL(R) (L(R) = beta-diketiminate; R = Me, tBu), result from reduction of [L(R)FeCl]n under a dinitrogen atmosphere, and an iron(I) precursor of an N2 complex can be observed. X-ray crystallographic and resonance Raman data for L(R)FeNNFeL(R) show a reduction in the N-N bond order, and calculations (density functional and multireference) indicate that the bond weakening arises from cooperative back-bonding into the N2 pi orbitals. Increasing the coordination number of iron from three to four through binding of pyridines gives compounds with comparable N-N weakening, and both are substantially weakened relative to five-coordinate iron-N2 complexes, even those with a lower oxidation state. Treatment of L(R)FeNNFeL(R) with KC8 gives K2L(R)FeNNFeL(R), and calculations indicate that reduction of the iron and alkali metal coordination cooperatively weaken the N-N bond. The complexes L(R)FeNNFeL(R) react as iron(I) fragments, losing N2 to yield iron(I) phosphine, CO, and benzene complexes. They also reduce ketones and aldehydes to give the products of pinacol coupling. The K2L(R)FeNNFeL(R) compounds can be alkylated at iron, with loss of N2.

Crystallography, X-Ray↗
PubMed2005

Metal effect on the supramolecular structure, photophysics, and acid-base character of trinuclear pyrazolato coinage metal complexes.

Varying the coinage metal in cyclic trinuclear pyrazolate complexes is found to significantly affect the solid-state packing, photophysics, and acid-base properties. The three isoleptic compounds used in this study are [[3,5-(CF3)2Pz]M]3 with M = Cu, Ag, and Au (i.e., Cu3, Ag3, and Au3, respectively). They form isomorphous crystals and exist as trimers featuring nine-membered M3N6 rings with linear two-coordinate metal sites. On the basis of the M-N distances, the covalent radii of two-coordinate Cu(I), Ag(I), and Au(I) were estimated as 1.11, 1.34, and 1.25 angstroms, respectively. The cyclic [[3,5-(CF3)2Pz]M]3 complexes pack as infinite chains of trimers with a greater number of pairwise intertrimer M...M interactions upon proceeding to heavier coinage metals. However, the intertrimer distances are conspicuously short in Ag3 (3.204 angstroms) versus Au3 (3.885 angstroms) or Cu3 (3.813 angstroms) despite the significantly larger covalent radius of Ag(I). Remarkable luminescence properties are found for the three M3 complexes, as manifested by the appearance of multiple unstructured phosphorescence bands whose colors and lifetimes change qualitatively upon varying the coinage metal and temperature. The multiple emissions are assigned to different phosphorescent excimeric states that exhibit enhanced M...M bonding relative to the ground state. The startling luminescence thermochromic changes in crystals of each compound are related to relaxation between the different phosphorescent excimers. The trend in the lowest energy phosphorescence band follows the relative triplet energy of the three M(I) atomic ions. DFT calculations indicate that [[3,5-(R)2Pz]M]3 trimers with R = H or Me are bases with the relative basicity order Ag << Cu < Au while fluorination (R = CF3) renders even the Au trimer acidic. These predictions were substantiated experimentally by the isolation of the first acid-base adduct, [[Au3]2:toluene]infinity, in which a trinuclear Au(I) complex acts as an acid.

Journal Article↗
PubMed2005

Synthesis of the five-coordinate ruthenium(II) complexes [(PCP)Ru(CO)(L)][BAr'4] [PCP = 2,6-(CH2P(t)Bu2)2C6H3, BAr'4 = 3,5-(CF3)2C6H3, L = eta1-ClCH2Cl, eta1-N2, or mu-Cl-Ru(PCP)(CO)]: reactions with phenyldiazomethane and phenylacetylene.

Reaction of (PCP)Ru(CO)(Cl) (1) with NaBAr'4 yields the bimetallic product [[(PCP)Ru(CO)](2)(mu-Cl)][BAr'4] (2). The monomeric five-coordinate complexes [(PCP)Ru(CO)(eta1-ClCH2Cl)][BAr'4] (3) and [(PCP)Ru(CO)(eta1-N2)][BAr'4] (4) are synthesized upon reaction of (PCP)Ru(CO)(OTf) (6) with NaBAr'4 in CH2Cl2 or C6H5F, respectively. The solid-state structures of 2, 3, and 4 have been determined by X-ray diffraction studies of single crystals. The reaction of 3 with PhCHN2 or PhCCH affords carbon-carbon coupling products involving the aryl group of the PCP ligand in transformations that likely proceed via the formation of Ru carbene or vinylidene intermediates. Density functional theory and hybrid quantum mechanics/molecular mechanics calculations were performed to investigate the bonding of weak bases to the 14-electron fragment [(PCP)Ru(CO)]+ and the energetics of different isomers of the product carbene and vinylidene complexes.

Journal Article↗
PubMed2005

A T-shaped three-coordinate nickel(I) carbonyl complex and the geometric preferences of three-coordinate d9 complexes.

A three-coordinate diketiminate-nickel(I) complex with a carbonyl ligand has been characterized using EPR and IR spectroscopies and X-ray crystallography. The T geometry (bending from the sterically favored C(2)(v)() structure) contrasts with that of isosteric d(9) copper(II) complexes. DFT calculations on a truncated model reproduce experimental geometries, implying that the geometric differences are electronic in nature. Analysis of the charge distribution in the complexes shows that the geometry of the three-coordinate d(9) complexes is affected by differential charge donation of the ligands to the metal center.

Journal Article↗
PubMed2005

Evidence for the net addition of arene C-H bonds across a Ru(II)-hydroxide bond.

TpRu(PMe3)2(OH) (1) reacts with C6D6 to initiate H/D exchange between the hydroxide ligand and the deuterated benzene. In addition, complex 1 catalyzes H/D exchange between H2O and C6D6. Mechanistic and computational studies suggest that a likely reaction pathway for the H/D exchange involves loss of PMe3 to produce {TpRu(PMe3)(OH)}, followed by the net addition of a benzene C-H(D) bond across the Ru-OH bond to form the putative complex TpRu(PMe3)(OH2)(Ph).

Crystallography, X-Ray↗