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Timothy Clark

Publications and source records attributed to Timothy Clark.

At least 37 records · Page 2Linked to original sources
PubMed2004

Electron transfer within 2,7-dinitronaphthalene radical anion.

The optical spectrum of 2,7-dinitronaphthalene radical anion generated by Na(Hg) reduction in acetonitrile containing a large excess of cryptand[2.2.2] exhibits a Hush-type intervalence charge-transfer band at 1070 nm, estimated to correspond to an off-diagonal matrix coupling element of 310 cm(-)(1). The interpolated rate constant for intramolecular electron transfer at 293 K measured by ESR between 225 and 320 K for this solution is 3.1(+/-0.2) x 10(9) s(-)(1). Rate constants estimated in two ways from the optical parameters using the Marcus-Hush assumption that the diabatic surfaces should be parabolae are 1.0 and 0.11 x 10(9) s(-1), and those using diabatic surfaces that fit the observed charge-transfer band are 9.6 and 3.4 x 10(9) s(-)(1), when used with an electron-transfer distance on the adiabatic surfaces of 6.42 A. Similar measurements and comparisons were also carried out using dimethylformamide and butyronitrile as solvents. The success of simple, classical two-state Marcus-Hush theory precludes an electron-hopping mechanism. UHF calculations predict a planar unsymmetrical gas-phase structure for 1,3-dinitrobenzene radical anion but give serious spin contamination. Semiempirical AM1 calculations using singles excitation configuration interaction with an active space of 70 orbitals and the COSMO solvent model also give a planar unsymmetrical structure. These calculations make the internal vibrational component of the reorganization energy nearly constant, and much smaller than the solvent reorganizational component, and predict the transition energy to lie between that observed in acetonitrile (9360 cm(-1)) and those observed in dimethylformamide (8100 cm(-1)) and butyronitrile (8040 cm(-1)).

Journal Article↗
PubMed2004

Aeromonas proteolytica aminopeptidase: an investigation of the mode of action using a quantum mechanical/molecular mechanical approach.

The aminopeptidase of Aeromonas proteolytica (AAP) belongs to the group of metallo-hydrolases that require two divalent cations for full activity. Such binuclear metal centers are found in several aminopeptidases, raising the question whether a common mechanism, at least partly, is likely. We have used a quantum mechanical/molecular mechanical (QM/MM) approach to investigate the reaction mechanism of AAP. Among several possibilities, one reaction path was found to be clearly the most favorable. Beside the chemical transformation steps, effects of the enzyme environment and the influence of the solvent on the catalytic reaction were included in the study. The results are in good agreement with experimental studies and correspond to a high degree to our previous QM/MM calculations on the reaction mechanism of the related binuclear bovine lens leucine aminopeptidase (blLAP), which, although related to the AAP, has different Zn(2+)-coordination spheres and a different catalytic residue. The mechanisms of the two enzymes as suggested in the literature differ on the mode of coordination of the nucleophile and the identity of the general base. However, the results of this and our previous work on blLAP allow us to identify a common mechanism for the two enzymes. This mechanism is probably quite general for binuclear zinc enzymes.

Aeromonas↗
PubMed2004

NO binding to cobalamin: influence of the metal oxidation state.

Density functional and molecular orbital theory calculations on models for cobalamin suggest that NO binds similarly to the Co(II) and Co(III) oxidation states. However, Co(III) can bind water far more strongly than Co(II) as a sixth ligand, so that the competition between water and NO complexation strongly favors water for Co(III) in the gas phase. Although the Co(II) oxidation state is found to bind water slightly more strongly than NO in the gas phase, the inclusion of solvation effects via the polarizeable continuum model makes NO binding more favorable. Thus, the experimentally observed ability of cob(II)alamin to bind NO in aqueous solution is the result of its weak complexation with water and the relatively poor solvation of NO. Calculated vibrational frequencies support the interpretation of the cob(II)alamin-NO complex as being cob(III)alamin-NO-, although the DFT calculations underestimate the degree of charge transfer in comparison to Hartree-Fock calculations.

Binding Sites↗
PubMed2004

Enthalpies of formation from B3LYP calculations.

We have calculated the geometries, energies, and normal vibrations of 845 compounds containing the elements H, C, N, O, F, Al, Si, P, S, and Cl using hybrid density functional theory in order to investigate the accuracy of atom-additive schemes for predicting enthalpies of formation at 298 K. The results give a more realistic estimate of the accuracy of density functional calculations than some overoptimistic earlier correlations. We have also calculated atom-additive schemes for the zero-point energies and enthalpic corrections to the energies. Remarkably, it is not important to include the vibrational or rotational contributions, which can be estimated well within a purely Born-Oppenheimer regression model.

Journal Article↗
PubMed2004

QSAR and QSPR based solely on surface properties?

The use of descriptors based on local properties calculated at the molecular surface for QSPR models is discussed. It is suggested that descriptors should be related to the physical theory of intermolecular interactions and the relationship between established surface-based descriptors and the fundamental types of intermolecular interaction is discussed. Descriptors based on local properties that do not encode the chemical constitution of the molecule directly are likely to provide less local QSPR models and favor scaffold hopping. The major disadvantage for surface-based descriptors is that they are difficult to interpret in the sense of relating predictions to the chemical composition of the molecule. This disadvantage must be alleviated by suitable model-interrogation techniques.

Models, Molecular↗
PubMed2004

How does Mg(2+) affect the binding of anhydrotetracycline in the TetR protein?

The binding of anhydrotetracycline (atc) in wild-type TetR(D), TetR(B), and four single tryptophan mutants of TetR(B) was investigated by UV/vis absorption, steady state, and time-resolved fluorescence spectroscopy. From absorption titration experiments with Mg2+, we conclude that binding of one [atc-Mg]+ complex in the homodimer causes changes in the protein conformation around the second binding pocket. In the presence of absence of Mg2+, several different groups of atc-protein arrangements must exist, each with a characteristic atc fluorescence decay time. Taking into account the results of molecular dynamics (MD) simulations, we propose as one possible origin for such a differentiation teh extent of hydrogen bonding between atc and the surrounding amino acids. Binding of Mg2+ should change the arrangement of the surrounding amino acids such that some of the excited atc molecules do not undergo the relaxation process typical for free atc. The MD simulations also show that the pattern of intra- and intermolecular hydrogen bonding in the two monomeric units is no correlated, thereby leading to different fluorescence kinetics for atc in the two monomeric units. Furthermore, it is suggested that hydrogen bonding between Arg104 and O10 of anhydrotetracycline could regulate the relaxation processes of excited anhydrotetracycline.

Bacterial Proteins↗
PubMed2003

Systematic surface scan of the most favorable interaction sites of magnesium ions with tetracycline.

AM1 semiempirical molecular orbital calculations have been used to probe the complexation sites for naked and hydrated magnesium ions to the different conformations and protonation states of tetracycline. The calculations reveal a wealth of possible magnesium complexation sites within a small energy range, but also indicate that magnesium complexation does not change the conformational behavior of tetracycline significantly. A hitherto unknown solvated conformation is suggested for deprotonated tetracycline.

Cations, Divalent↗
PubMed2003

AM1* parameters for phosphorus, sulfur and chlorine.

An extension of the AM1 semiempirical molecular orbital technique, AM1*, is introduced. AM1* uses AM1 parameters and theory unchanged for the elements H, C, N, O and F. The elements P, S and Cl have been reparameterized using an additional set of d orbitals in the basis set and with two-center core-core parameters, rather than the Gaussian functions used to modify the core-core potential in AM1. Voityuk and Rösch's AM1(d) parameters have been adopted unchanged for AM1* with the exception that new core-core parameters are defined for Mo-P, Mo-S and Mo-Cl interactions. Thus, AM1* gives identical results to AM1 for compounds with only H, C, N, O, and F, AM1(d) for compounds containing Mo, H, C, N, O and F only, but differs for molybdenum compounds containing P, S or Cl. The performance and typical errors of AM1* are discussed.

Chlorine↗
PubMed2003

Local molecular properties and their use in predicting reactivity.

Expressions for the local electron affinity, electronegativity and hardness are derived in analogy to the local ionization energy introduced by Sjoberg, Murray and Politzer. The local polarizability is also defined based on an additive atomic orbital polarizability model that uses Rivail's variational technique. The characteristics of these local properties at molecular surfaces and their relevance to electrophilic aromatic substitution, to S(N)2 reactivity and to the nucleophilicity of enolate ions are discussed.

Bromine↗
PubMed2003

Does metal ion complexation make radical clocks run fast?

Ab initio molecular orbital and density functional calculations at the CBS-RAD(QCISD,B3-LYP) level for Li+ and at B3LYP for Na+, K+, Cu+,and Ag+ reveal that the barrier to ring-closure of the 1-hexen-6-yl ("Delta(5)-hexenyl") radical to the cyclopentylmethyl radical, a so-called radical clock reaction, is decreased very significantly by complexation of the double bond to metal cations. This barrier lowering should occur on complexation with many metal ions, as shown by calculations on all of the monovalent ions listed above. Additional density functional calculations including explicit solvation of the model system complexed to the lithium ion with tetrahydrofuran suggest that the effect found is not limited to the gas phase but may also be significant in experimental radical clock reactions in solution, even for lithium.

Journal Article↗
PubMed2002

Descriptors, physical properties, and drug-likeness.

We have investigated techniques for distinguishing between drugs and nondrugs using a set of molecular descriptors derived from semiempirical molecular orbital (AM1) calculations. The "drug" data set of 2105 compounds was derived from the World Drug Index (WDI) using a procedure designed to select real drugs. The "nondrug" data set was the Maybridge database. We have first investigated the dimensionality of physical properties space based on a set of 26 descriptors that we have used successfully to build absorption, distribution, metabolism, and excretion-related quantitative structure-property relationship models. We discuss the general nature of the descriptors for physical property space and the ability of these descriptors to distinguish between drugs and nondrugs. The third most significant principal component of this set of descriptors serves as a useful numerical index of drug-likeness, but no others are able to distinguish between drugs and nondrugs. We have therefore extended our set of descriptors to a total of 66 and have used recursive partitioning to identify the descriptors that can distinguish between drugs and nondrugs. This procedure pointed to two of the descriptors that play an important role in the principal component found above and one more from the set of 40 extra descriptors. These three descriptors were then used to train a Kohonen artificial neural net for the entire Maybridge data set. Projecting the drug database onto the map obtained resulted in a clear distinction not only between drugs and nondrugs but also, for instance, between hormones and other drugs. Projection of 42 131 compounds from the WDI onto the Kohonen map also revealed pronounced clustering in the regions of the map assigned as druglike.

Chemical Phenomena↗
PubMed2002

Solvation largely accounts for the effect of N-alkylation on the properties of nickel(II/I) and chromium(III/II) cyclam complexes.

The source of the effect of N-alkylation on the redox properties of Ni(II/I) and Cr(III/II) cyclam complexes has been investigated using DFT calculations. The structures of the anhydrous and hydrated complexes were optimized in the gas phase, and single point calculations were performed in a polarized continuum. The main results are the following: the decrease in outer sphere solvation upon N-alkylation is the major source of the relative stabilization of the lower oxidation state complexes by the tertiary amine ligands; tertiary amine nitrogen donors are stronger sigma-donors than the secondary amines, as predicted from the inductive effect of alkyls; steric strain elongates the metal-nitrogen bonds in the tertiary complexes and decreases the ligand strain energies; and the site of water binding to the complexes differs because of their different electronic structures (i.e., in the Ni complexes, the water molecules bind to the M[bond]N[bond]H sites, whereas in the Cr complexes they bind to the central metal cation). Outer sphere hydrogen bonding of water to the ligands in the coordination sphere lowers the ionization potentials by charge delocalization.

Journal Article↗
PubMed2002

Ionized bicyclo[2.2.2]oct-2-ene: a twisted olefinic radical cation showing vibronic coupling.

The bicyclo[2.2.2]oct-2-ene radical cation (1(.+)) exhibits matrix ESR spectra that have two very different types of gamma-exo hydrogens (those hydrogens formally in a W-plan with the alkene pi bond), a(2H) about 16.9 G and a(2H) about 1.9 G, instead of the four equivalent hydrogens as would be the case in an untwisted C(2v) structure. Moreover, deuterium substitution showed that the vinyl ESR splitting is not resolved (and under about 3.5 G); this is also a result of the twist. Enantiomerization of the C(2) structures is rapid on the ESR timescale above 110 K (barrier estimated at 2.0 kcalmol(-1)). Density functional theory calculations estimate the twist angle at the double bond to be 11-12 degrees and the barrier as 1.2-2.0 kcalmol(-1). Single-configuration restricted Hartree-Fock (RHF) calculations at all levels that were tried give untwisted C(2v) structures for 1(.+), while RHF calculations that include configuration interactions (CI) demonstrate that this system undergoes twisting because of a pseudo Jahn-Teller effect (PJTE). Significantly, twisting does not occur until the sigma-orbital of the predicted symmetry is included in the CI active space. UHF calculations at all levels that include electron correlation (even semiempirical) predict twisting at the alkene pi bond because they allow the filled alpha and the beta hole of the SOMO to have different geometries. The 2,3-dimethylbicyclo[2.2.2]oct-2-ene radical cation (2(.+)) is twisted significantly less than 1(.+), but has a similar temperature for maximum line broadening. Neither the 2,3-dioxabicyclo[2.2.2]octane radical cation (3(.+)) nor its 2,3-dimethyl-2,3-diaza analogue (5(.+)) shows any evidence of twisting. Calculations show that the orbital energy gap between the SOMO and PJTE-active orbitals for 3(.+) is too large for significant PJTE stabilization to occur.

Alkenes↗
PubMed2002

A QSPR-approach to the estimation of the pK(HB) of six-membered nitrogen-heterocycles using quantum mechanically derived descriptors.

Descriptors derived from semiempirical (AM1) molecular orbital calculations have been used to construct a quantitative structure-property relationship (QSPR) for the thermodynamic hydrogen-bond basicity, p K(HB), of a series of six-membered aromatic nitrogen-heterocycles. The resulting model uses four-descriptors (the Coulson charge on the nitrogen atom, the energy of the localized nitrogen lone-pair orbital, the p-orbital contribution to this MO and an accessibility angle). The model gives r2(cv)=0.95 for 51 compounds with a standard deviation between calculation and experiment of 0.13 log units.

Heterocyclic Compounds, 1-Ring↗
PubMed2002

Excited state conformational dynamics of semiflexibly bridged electron donor-acceptor systems: a semiempirical CI-study including solvent effects.

Semiempirical (AM1) molecular orbital theory with configuration interaction has been used to investigate the harpooning mechanism proposed from experimental studies on semiflexibly bridged electron donor-acceptor systems. Our calculations on the charge-transfer state of N-phenyl-4-(4-cyano-naphth-1-ylmethyl)-piperidine, 1, confirm the proposed harpooning mechanism including an intermediate loosely folded charge-transfer state and reproduce the thermodynamics obtained from our spectroscopic studies closely. The structural details of the extended (ECT), intermediate (ICT) and compact (CCT) charge-transfer states are discussed, as are the transition states connecting them. Solvent effects have been modeled using self-consistent reaction field (SCRF) calculations within the polarized continuum model. The effect of solvent polarity on the stabilities of the three charge-transfer states is discussed.

Computer Simulation↗
PubMed2002

Placement of a vena cava filter with an antecubital approach.

RATIONALE AND OBJECTIVES: The authors performed this study to evaluate the use of an antecubital venous approach for inferior vena cava (IVC) filter placement. MATERIALS AND METHODS: An IVC filter was placed in 26 patients (15 men, 11 women) in whom the antecubital vein was the preferred access site. An antecubital vein was accessed with ultrasound guidance and used for IVC filter placement. This same access site was used to place a peripherally inserted central catheter (PICC) in 17 of the 26 patients. Access was obtained via the basilic vein in 15 patients (58%), brachial vein in eight (31%), and cephalic vein in three (12%). RESULTS: The IVC filter was successfully placed in the infrarenal vena cava in all 26 patients (100%) by using an antecubital vein for access. All filters deployed appropriately without complication. No complications occurred during PICC placement. CONCLUSION: The IVC filter can be safely placed via an antecubital vein. When clinically necessary, this site can provide convenient access for the PICC placement.

Catheterization, Peripheral↗
PubMed2002

Outcomes of a pain management educational initiative at Baylor University Medical Center.

Baylor University Medical Center established a pain initiative group in 1996 to research the effectiveness of pain management throughout the hospital. After analyzing 300 patient surveys, the group undertook an intensive program to educate physicians, nurses, and patients regarding newer pain management techniques. The outcome of this educational initiative was reassessed in 2001 based on surveys completed by 100 patients after discharge. Results showed marked improvement in patient education regarding pain management. In 2001, 93% of patients were offered education and choices regarding pain management vs only 36% in 1996. Fewer patients were afraid to "bother" their nurses to ask for pain medication (3% in 2001 vs 14% in 1996). Waiting time for administration of analgesics decreased considerably. The number of patients reporting moderate to severe pain decreased significantly since 1996, yet the overall satisfaction with pain relief remained high and did not change significantly. The overall incidence of patients reporting moderate to severe pain was significantly less at Baylor than the national average. In conclusion, attitudes, misconceptions, and fears about pain management can be changed with intensive educational programs.

Journal Article↗