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Thomas R Cundari

Publications and source records attributed to Thomas R Cundari.

31 records · Page 2Linked to original sources
PubMed2005

3-center-4-electron bonding in [(silox)2Mo=NtBu]2(mu-Hg) controls reactivity while frontier orbitals permit a dimolybdenum pi-bond energy estimate.

Na/Hg reduction of (silox)2Cl2Mo=NtBu (3) afforded C2h [(silox)2Mo=NtBu]2(mu-Hg) (12-Hg), which consists of two distorted trigonal monoprisms with Hg at the each apex (d(MoHg) = 2.6810(5) A). Calculations reveal 3c4e bonding in the linear MoHgMo linkage that renders 12-Hg susceptible to nucleophilic cleavage. Exposure to PMe3 and pyridine rapidly (<5 min) affords (silox)2(tBuN)MoLn (L = PMe3, n = 1 (1-PMe3); py, n = 2 (1-py2)), while poorer nucleophiles (L = C2H4, 2-butyne) yield adducts (e.g., 1-C2H4 and 1-C2Me2) after prolonged heating. The HOMO and LUMO of 12-Hg are "stretched" pi and pi* orbitals from which four states arise: 1Ag (GS), 3Bu, 1Bu, and 1Ag. DeltaE = E(1Bu) - E(3Bu) = 2K, where K is the exchange energy. Magnetic studies indicate E(3Bu) - E(1Ag) approximately 550 cm-1 (calcd 1744 cm-1), and a UV-vis absorption at 10 000 cm-1 is assigned to 1Ag --> 1Bu, permitting K to be evaluated as 4725 cm-1. With the pi --> pi* transition in Schrock's [Mo(NAr)(CH2tBu)(OC6F5)]2 (4) assigned at 528 nm, this estimation places its pi-bond energy as {E(pi2 --> pi1pi*1 in 4) - E(1Ag --> 1Bu in 12-Hg)} + E(1Ag --> 3Bu in 12-Hg) = 27 kcal/mol.

Journal Article↗
PubMed2005

Low-coordinate chromium siloxides: the "box" [Cr(mu-Cl)(mu-OSitBu3)]4, distorted trigonal [(tBu3SiO)3Cr][Na(benzene)] and [(tBu3SiO)3Cr][Na(dibenzo-18-c-6)], and trigonal (tBu3SiO)3Cr.

Treatment of CrCl(2)(THF)(2) with NaOSi(t)Bu(3) afforded the tetrameric "box" [Cr(mu-Cl)(mu-OSi(t)Bu(3))](4) (1, X-ray). THF cleaved 1 to provide trans-(silox)ClCr(THF)(2) (2), whereas degradation of 1 with 4-picoline caused disproportionation and the generation of trans-Cl(2)Cr(4-pic)(2) and trans-(silox)(2)Cr(4-pic)(x) (n = 2, 3; 3, 3-4-pic). Chromous centers in 1 were antiferromagnetically coupled, and density functional calculations on the high-spin (multiplicity = 17) model [Cr(mu-Cl)(mu-OH)](4) (1') revealed that its singly occupied 3d orbitals spanned an energy range of approximately 2 eV. The addition of 8 equiv of Na(silox) to 1 yielded [((t)Bu(3)SiO)Cr(mu-OSi(t)Bu(3))(2)]Na.C(6)H(6) (4, Y shaped, angle OCrO(Na) = 91.28(7) degrees), and treatment of 4 with dibenzo-18-crown-6 produced [(silox)(3)Cr][Na(dibenzo-18-crown-6)] (5, angle OCrO = approximately 120 degrees, (120 + alpha) degrees, (120 - alpha) degrees). Calculations of [((t)Bu(3)SiO)Cr(mu-OSi(t)Bu(3))(2)]Na (4') and Cr(silox)(3)(-) (5') provided reasonable matches with the experimental geometries (X-ray). The trigonal chromic derivative (silox)(3)Cr (6) was synthesized from CrCl(3)(THF)(3) for structural and calculational comparisons to the chromous derivatives.

Journal Article↗
PubMed2005

Thermodynamics, kinetics, and mechanism of (silox)3M(olefin) to (silox)3M(alkylidene) rearrangements (silox = tBu3SiO; M = Nb, Ta).

Olefin complexes (silox)(3)M(ole) (silox = (t)Bu(3)SiO; M = Nb (1-ole), Ta (2-ole); ole = C(2)H(4), C(2)H(3)Me, C(2)H(3)Et, C(2)H(3)C(6)H(4)-p-X (X = OMe, H, CF(3)), C(2)H(3)(t)Bu, (c)C(5)H(8), (c)C(6)H(10), (c)C(7)H(10) (norbornene)) rearrange to alkylidene isomers (silox)(3)M(alk) (M = Nb (1=alk), Ta (2=alk); alk = CHMe, CHEt, CH(n)Pr, CHCH(2)C(6)H(4)-p-X (X = OMe, H, CF(3) (Ta only)), CHCH(2)(t)Bu, (c)C(5)H(8), (c)C(6)H(10), (c)C(7)H(10) (norbornylidene)). Kinetics and labeling experiments suggest that the rearrangement proceeds via a delta-abstraction on a silox CH bond by the beta-olefin carbon to give (silox)(2)RM(kappa(2)-O,C-OSi(t)Bu(2)CMe(2)CH(2)) (M = Nb (4-R), Ta (6-R); R = Me, Et, (n)Pr, (n)Bu, CH(2)CH(2)C(6)H(4)-p-X (X = OMe, H, CF(3) (Ta only)), CH(2)CH(2)(t)Bu, (c)C(5)H(9), (c)C(6)H(11), (c)C(7)H(11) (norbornyl)). A subsequent alpha-abstraction by the cylometalated "arm" of the intermediate on an alpha-CH bond of R generates the alkylidene 1=alk or 2=alk. Equilibrations of 1-ole with ole' to give 1-ole' and ole, and relevant calculations on 1-ole and 2-ole, permit interpretation of all relative ground and transition state energies for the complexes of either metal.

Journal Article↗
PubMed2004

Function of conserved residues of human glutathione synthetase: implications for the ATP-grasp enzymes.

Glutathione synthetase is an enzyme that belongs to the glutathione synthetase ATP-binding domain-like superfamily. It catalyzes the second step in the biosynthesis of glutathione from gamma-glutamylcysteine and glycine in an ATP-dependent manner. Glutathione synthetase has been purified and sequenced from a variety of biological sources; still, its exact mechanism is not fully understood. A variety of structural alignment methods were applied and four highly conserved residues of human glutathione synthetase (Glu-144, Asn-146, Lys-305, and Lys-364) were identified in the binding site. The function of these was studied by experimental and computational site-directed mutagenesis. The three-dimensional coordinates for several human glutathione synthetase mutant enzymes were obtained using molecular mechanics and molecular dynamics simulation techniques, starting from the reported crystal structure of human glutathione synthetase. Consistent with circular dichroism spectroscopy, our results showed no major changes to overall enzyme structure upon residue mutation. However, semiempirical calculations revealed that ligand binding is affected by these mutations. The key interactions between conserved residues and ligands were detected and found to be essential for enzymatic activity. Particularly, the negatively charged Glu-144 residue plays a major role in catalysis.

Adenosine Triphosphate↗
PubMed2003

Jahn-Teller distortion in the phosphorescent excited state of three-coordinate Au(I) phosphine complexes.

DFT calculations were used to optimize the phosphorescent excited state of three-coordinate [Au(PR3)3]+ complexes. The results indicate that the complexes rearrange from their singlet ground-state trigonal planar geometry to a T-shape in the lowest triplet luminescent excited state. The optimized structure of the exciton contradicts the structure predicted based on the AuP bonding properties of the ground-state HOMO and LUMO. The rearrangement to T-shape is a Jahn-Teller distortion because an electron is taken from the degenerate e' (5dxy, 5dx2-y2) orbital upon photoexcitation of the ground-state D3h complex. The calculated UV absorption and visible emission energies are consistent with the experimental data and explain the large Stokes' shifts while such correlations are not possible in optimized models that constrained the exciton to the ground-state trigonal geometry.

Journal Article↗
PubMed2003

Symmetry and geometry considerations of atom transfer: deoxygenation of (silox)3WNO and R3PO (R = Me, Ph, (t)Bu) by (silox)3M (M = V, NbL (L = PMe3, 4-picoline), Ta; silox = (t)Bu3SiO).

Deoxygenations of (silox)(3)WNO (12) and R(3)PO (R = Me, Ph, (t)Bu) by M(silox)(3) (1-M; M = V, NbL (L = PMe(3), 4-picoline), Ta; silox = (t)Bu(3)SiO) reflect the consequences of electronic effects enforced by a limiting steric environment. 1-Ta rapidly deoxygenated R(3)PO (23 degrees C; R = Me (DeltaG degrees (rxn)(calcd) = -47 kcal/mol), Ph) but not (t)Bu(3)PO (85 degrees, >2 days), and cyclometalation competed with deoxygenation of 12 to (silox)(3)WN (11) and (silox)(3)TaO (3-Ta; DeltaG degrees (rxn)(calcd) = -100 kcal/mol). 1-V deoxygenated 12 slowly and formed stable adducts (silox)(3)V-OPR(3) (3-OPR(3)) with OPR(3). 1-Nb(4-picoline) (S = 0) and 1-NbPMe(3) (S = 1) deoxygenated R(3)PO (23 degrees C; R = Me (DeltaG degrees (rxn)(calcd from 1-Nb) = -47 kcal/mol), Ph) rapidly and 12 slowly (DeltaG degrees (rxn)(calcd) = -100 kcal/mol), and failed to deoxygenate (t)Bu(3)PO. Access to a triplet state is critical for substrate (EO) binding, and the S --> T barrier of approximately 17 kcal/mol (calcd) hinders deoxygenations by 1-Ta, while 1-V (S = 1) and 1-Nb (S --> T barrier approximately 2 kcal/mol) are competent. Once binding occurs, significant mixing with an (1)A(1) excited state derived from population of a sigma-orbital is needed to ensure a low-energy intersystem crossing of the (3)A(2) (reactant) and (1)A(1) (product) states. Correlation of a reactant sigma-orbital with a product sigma-orbital is required, and the greater the degree of bending in the (silox)(3)M-O-E angle, the more mixing energetically lowers the intersystem crossing point. The inability of substrates EO = 12 and (t)Bu(3)PO to attain a bent 90 degree angle M-O-E due to sterics explains their slow or negligible deoxygenations. Syntheses of relevant compounds and ramifications of the results are discussed. X-ray structural details are provided for 3-OPMe(3) (90 degree angle V-O-P = 157.61(9) degrees), 3-OP(t)Bu(3) ( 90 degree angle V-O-P = 180 degrees ), 1-NbPMe(3), and (silox)(3)ClWO (9).

Journal Article↗
PubMed2003

A priori assessment of the stereoelectronic profile of phosphines and phosphites.

This research has demonstrated the utility of a rigorously calibrated, molecular mechanics/semiempirical quantum mechanical protocol for developing stereoelectronic (Tolman) maps for phosphine ligands. A computational analysis of alkyl and aryl phosphines in common usage suggests that these ligands are quite similar stereoelectronically. A noticeable gap in the Tolman map for common phosphines is observed for large, electron-poor phosphines. Several candidates meeting these criteria were identified, the most promising of which is P(t-C(4)F(9))(3). Phosphines in which the phosphorus participates in a ring, which comprise a very small subset of reported phosphines, have very interesting stereoelectronic properties, particularly those in which the ligating phosphorus is part of a three-membered ring. In terms of steric properties, the symmetric deformation coordinate proposed by Orpen and co-workers on the basis of crystallographic studies is calculated with sufficient accuracy using PM3(tm) to allow good confidence in predictions of novel phosphines. For quantification of the electronic properties of phosphines, we analyzed changes in the CO stretching frequency upon changing the ancillary phosphine ligands.

Journal Article↗
PubMed2002

Electronically unsaturated three-coordinate chloride and methyl complexes of iron, cobalt, and nickel.

Three-coordinate organometallic complexes are rare, especially with the prototypical methyl ligand. Using a hindered, rigid bidentate ligand (L), it is possible to create 12-electron methyliron(II) and 13-electron methylcobalt(II) complexes. These complexes are thermally stable, and (1)H NMR spectra suggest that the low coordination number is maintained in solution. Attempts to create the 14-electron LNiCH(3) led instead to the three-coordinate nickel(I) complex LNi(THF). Single crystals of LMCH(3) are isomorphous with the new three-coordinate chloride complexes LNiCl and LCoCl. Along with the recently reported LFeCl (Smith, J. M.; Lachicotte, R. J.; Holland, P. L. Chem. Commun. 2001, 1542), these are the only examples of three-coordinate iron(II), cobalt(II), and nickel(II) complexes with terminal chloride ligands, enabling the systematic evaluation of the effect of coordination number and metal identity on M-Cl bond lengths. Electronic structure calculations predict the ground states of the trigonal complexes.

Journal Article↗
PubMed2002

De novo structural prediction of transition metal complexes: application to technetium.

De novo structural prediction of transition metal complexes is investigated. Technetium complexes are chosen given their importance in medical imaging and nuclear waste remediation and for the chemical diversity they display. A new conformational searching algorithm (LIGB) for transition metals is described that allows one to search for different conformational and geometric isomers within a single simulation. In the preponderance of cases, both conformational searching techniques (LIGB and high-temperature molecular dynamics/simulated annealing) provide comparable results, while LIGB is superior for macrocyclic complexes. A genetic algorithm-optimized PM3(tm) parametrization for Tc is compared with the standard implementation and found to yield a significant improvement in predictive ability for the most prevalent Tc structural motifs. The utility of a coupled molecular mechanics-semiempirical quantum mechanics protocol is demonstrated for very rapid, efficient, and effective de novo prediction of transition metal complex geometries.

Journal Article↗
PubMed2002

Carbon [bond] hydrogen bond activation by titanium imido complexes. Computational evidence for the role of alkane adducts in selective C [bond] H activation.

This paper reports calculations that probe the role of R (hydrocarbon) and R' (ligand substituent) effects on the reaction coordinate for C [bond] H activation: Ti(OR')(2)(=NR') + RH --> adduct --> transition state --> (OR')(2)Ti(N(H)R')(R). Compounds with R = H, Me, Et, Vy, cPr, Ph, Cy, Bz, and cubyl are studied using quantum (R' = H, SiH(3), SiMe(3)) and classical (R' = Si(t)Bu(3)) techniques. Calculated geometries are in excellent agreement with data for experimental models. There is little variability in the calculated molecular structure of the reactants, products, and most interestingly, transition states as R and R' are changed. Structural flexibility is greatest in the adducts Ti(OR')(2)(=NR')...HR. Despite the small structural changes observed for Ti(OR')(2)(double bond] NR') with different R', significant changes are manifested in calculated electronic properties (the Mulliken charge on Ti becomes more positive and the Ti [double bond] N bond order decreases with larger R'), changes that should facilitate C [bond] H activation. Substantial steric modification of the alkane complex is expected from R [bond] R' interactions, given the magnitude of Delta G(add) and the conformational flexibility of the adduct. Molecular mechanics simulations of Ti(OSi(t)Bu(3))(2)([double bond] NSi(t)Bu(3))...isopentane adducts yield an energy ordering as a function of the rank of the C [bond] H bond coordinated to Ti that is consistent with experimental selectivity patterns. Calculated elimination barriers compare very favorably with experiment; larger SiH(3) and TMS ligand substituents generally yield better agreement with experiment, evidence that the modeling of the major contributions to the elimination barrier (N [bond] H and C [bond] H bond making) is ostensibly correct. Calculations indicate that weakening the C [bond] H bond of the hydrocarbon yields a more strongly bound adduct. Combining the different conclusions, the present computational research points to the adduct, specifically the structure and energetics of the substrate/Ti-imido interaction, as the main factor in determining the selectivity of hydrocarbon (R) C [bond] H activation.

Journal Article↗
PubMedDate not supplied

Robust fuzzy principal component analysis (FPCA). A comparative study concerning interaction of carbon-hydrogen bonds with molybdenum-oxo bonds.

Principal component analysis (PCA) is a favorite tool in chemometrics for data compression and information extraction. PCA finds linear combinations of the original measurement variables that describe the significant variations in the data. However, it is well-known that PCA, as with any other multivariate statistical method, is sensitive to outliers, missing data, and poor linear correlation between variables due to poorly distributed variables. As a result data transformations have a large impact upon PCA. In this regard one of the most powerful approaches to improve PCA appears to be the fuzzification of the matrix data, thus diminishing the influence of outliers. In this paper we discuss a robust fuzzy PCA algorithm (FPCA). The new algorithm is illustrated on a data set concerning interaction of carbon-hydrogen bonds with transition metal-oxo bonds in molybdenum complexes. Considering, for example, a two component model, FPCA accounts for 97.20% of the total variance and PCA accounts only for 69.75%.

Journal Article↗
PubMedDate not supplied

Stability studies of transition-metal linkage isomers using quantum mechanical methods. Groups 11 and 12 transition metals.

Several hypotheses to elucidate the linkage isomer preference of the thiocyanate (SCN(-)) ion have been offered. For complexes with small coordination numbers (i.e., 1 and 2) and groups 11 (Cu-triad) and 12 (Zn-triad) metals, different levels of theory and a variety of basis sets have been employed to study linkage isomerism. Similar results are obtained for all density functionals tested, pure and hybrid. Overall, good agreement, vis-à-vis experimentally identified linkage isomers, is achieved for ab initio techniques, whereas semiempirical quantum mechanical methods show a bias toward S-ligated isomers. Despite the seeming ease for the a priori prediction of the most stable thiocyanate isomers using acid/base principles, this research highlights the sensitivity of quantitative calculations of transition-metal linkage isomerism to the choice of basis set and electron correlation, particularly with post-Hartree-Fock treatments.

Journal Article↗