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Timothy Clark

Publications and source records attributed to Timothy Clark.

At least 19 recordsLinked to original sources
PubMed2006

SCRF-DFT and NMR comparison of tetracycline and 5a,6-anhydrotetracycline in solution.

A combination of structures, energies, and spectral data calculated using density functional theory (DFT) with experimental NMR data has been used to assign conformational equilibria for tetracycline and 5a,6-anhydrotetracycline in water at pH 1, 7, and 10 and in chloroform (5a,6-anhydrotetracycline) and methanol (tetracycline). The results suggest that tetracycline always prefers the extended conformation but that 5a,6-anhydrotetracycline exists in water as a mixture of the two conformers and in chloroform exclusively in the twisted conformation. The conformational equilibria are also shown to be pH dependent.

Computer Simulation↗
PubMed2006

Nitrite impurities are responsible for the reaction observed between vitamin B12 and nitric oxide in acidic aqueous solution.

The reaction between aquacobalamin, Cbl(H2O), and NO was studied at low pH. As previously reported, the final product of the reaction is the same as that obtained in the reaction of NO and reduced Cbl(H2O), viz. Cbl(NO-). Nevertheless, this reductive nitrosylation is preceded by a faster reaction (accompanied by small absorbance changes) that depends on the HNO2 concentration but not on the NO concentration. Kinetic and UV-vis spectroscopic data show that Cbl(NO2-) is generated during this reaction. Spectroscopic data show that the dimethylbenzimidazole group trans to the NO2- ligand is protonated and partially dechelated at pH 1, by which a reaction with NO is induced. DFT calculations were performed to compare the ability of NO and NO2- to bind to cobalamin and their influence on the stability of the dimethylbenzimidazole group. The reductive nitrosylation reaction shows a quadratic dependence on the HNO2 concentration and an inverse dependence on the NO concentration. It also strongly depends on pH and is no longer observed at pH > 4. On the basis of earlier work performed on a series of Co(III) porphyrins, a mechanism is proposed that can quantitatively account for the HNO2 and NO dependencies. The reductive nitrosylation reaction is practically dominated by a back reaction, i.e., the reaction between Cbl(NO-) and HNO2, which accounts for the strange NO and HNO2 concentration dependencies observed.

Acids↗
PubMed2006

Lithium cation as radical-polymerization catalyst.

Density-functional theory (DFT) and ab initio (QCISD and CBS-RAD) calculations suggest that complexation of "naked" lithium cations to olefins favors the addition of alkyl radicals to the double bond over abstraction of an allyllic hydrogen atom. Thus, "naked" lithium cations in nonpolar solvents can catalyze the radical polymerization of olefins by favoring the chain-lengthening reaction over the competing hydrogen-atom extraction, which is competitive in the absence of metal ions. One putative initiation reaction, addition of triplet dioxygen to the double bond, is thermoneutral and has a very low barrier when the oxygen molecule is complexed to a lithium cation. An alternative process, abstraction of an allyllic hydrogen atom to generate the allyl and hydroperoxy radicals, is also strongly favored by complexation of the oxygen to the lithium cation but is less favorable than addition. These results support Michl's recent interpretation of experimentally observed alkene polymerization in the presence of lithium salts of hydrophobic carborane anions.

Journal Article↗
PubMed2006

Halogen bonding: the sigma-hole. Proceedings of "Modeling interactions in biomolecules II", Prague, September 5th-9th, 2005.

Halogen bonding refers to the non-covalent interactions of halogen atoms X in some molecules, RX, with negative sites on others. It can be explained by the presence of a region of positive electrostatic potential, the sigma-hole, on the outermost portion of the halogen's surface, centered on the R-X axis. We have carried out a natural bond order B3LYP analysis of the molecules CF(3)X, with X = F, Cl, Br and I. It shows that the Cl, Br and I atoms in these molecules closely approximate the [Formula: see text] configuration, where the z-axis is along the R-X bond. The three unshared pairs of electrons produce a belt of negative electrostatic potential around the central part of X, leaving the outermost region positive, the sigma-hole. This is not found in the case of fluorine, for which the combination of its high electronegativity plus significant sp-hybridization causes an influx of electronic charge that neutralizes the sigma-hole. These factors become progressively less important in proceeding to Cl, Br and I, and their effects are also counteracted by the presence of electron-withdrawing substituents in the remainder of the molecule. Thus a sigma-hole is observed for the Cl in CF(3)Cl, but not in CH(3)Cl.

Halogens↗
PubMed2006

Multipole electrostatic potential derived atomic charges in NDDO-methods with spd-basis sets.

The recently introduced multipole approach for computing the molecular electrostatic potential (MEP) within the semiempirical neglect of diatomic differential overlap (NDDO) framework [Horn AHC, Lin Jr-H., Clark T (2005) Theor Chem Acc 114:159-168] has been used to obtain atomic charges of nearly ab initio quality by scaling the semiempirical MEP. The parameterization set comprised a total of 797 compounds and included not only the newly parameterized AM1* elements Al, Si, P, S, Cl, Ti, Zr, and Mo but also the standard AM1 elements H, C, N, O and F. For comparison, the ZDO-approximated MEP was also calculated analytically in the spd-basis. For the AM1*-optimized structures, single-point calculations at the B3LYP, HF and MP2 levels with the 6-31G(d) and LanL2DZP basis sets were performed to obtain the MEP. The regression analysis of all 12 combinations of semiempirical and ab initio MEP data yielded correlation coefficients of at least 0.99 in all cases. Scaling the analytical and multipole-derived semiempirical MEP by the regression coefficients yielded mean unsigned errors below 2.6 and 1.9 kcal mol(-1), respectively. Subsequently, for 22 drug molecules from the World Drug Index, atomic charges were computed according to the RESP procedure using XX/6-31G(d) (XX=B3LYP, HF, MP2) and scaled AM1* multipole MEP; the correlation coefficients obtained are 0.83, 0.85 and 0.83, respectively.

Models, Chemical↗
PubMed2006

Fit for practice? An exploration of the development of newly qualified nurses using focus groups.

UNLABELLED: Previous research in the newly qualified has primarily focused upon their levels of competence at the time of registration rather than upon the way that this continues to develop over time. Though newly qualified nurses are expected to be competent and able to practice independently without direct supervision the reality is that, for most, their training has not equipped them with the knowledge, skills or confidence necessary for independent practice. This belief provided the foundations for this study designed to gain an understanding of the way that competence develops amongst nurses themselves and how this is seen by their managers and those working with them. It focused neither on what competencies nurses possessed nor on the level of overall competence but rather on the factors influencing the development of competence over time. RESEARCH DESIGN: This qualitative exploratory study relied upon a combination of focus groups and individual interviews to access information and perceptions not readily accessible through more quantitative means. DATA COLLECTION: Data was collected using focus groups involving newly qualified staff, including both those on a development programme and those in substantive posts, experienced qualified nurses (preceptors) and practice development nurses. A total of twelve focus groups were conducted yielding a purposive sample of 105 volunteer participants; groups were continued until no new data emerged and saturation was achieved. Ward managers (5) were interviewed individually and their data was added to that obtained from the focus groups. ANALYSIS: Content analysis of the transcripts enabled the material to be explored systematically to identify relevant themes and categories within the data thus helping to clarify descriptions of the major issues identified; these were returned to the participants to ensure validity in data interpretation. FINDINGS: Ward managers appear to have low expectations of the newly qualified while 'new' nurses themselves believe that they are expected to be able to fulfil tasks that they feel ill-equipped to undertake. This emphasises the need for appropriate support to enable them to develop their knowledge, skills and confidence and enable independent practice. While staff development programmes benefit some, others gain equal value from supportive preceptorship in helping them to develop the clinical and managerial skills necessary in today's healthcare climate.

Attitude of Health Personnel↗
PubMed2006

Structural changes and binding characteristics of the tetracycline-repressor binding site on induction.

The binding motif (pharmacophore) for induction and the changes in the structure of the binding site that accompany induction have been determined from molecular-dynamics simulations on the tetracycline-repressor signal-transduction protein. The changes and the induction mechanism are discussed and compared with conclusions drawn from earlier X-ray structures. The differences in inducer strength of tetracycline and 5a,6-anhydrotetracycline are discussed with respect to their interaction in the MD simulations.

Allosteric Regulation↗
PubMed2006

The structure of 5a,6-anhydrotetracycline and its Mg2+ complexes in aqueous solution.

Semiempirical molecular orbital theory has been used for a systematic scan of the binding positions for a Mg2+ ion with 5a,6-anhydrotetracycline taking both conformational flexibility and possible different tautomeric forms into account. The magnesium ion has been calculated alone and with four or five complexed water molecules in order to simulate the experimental situation more closely. The results are analyzed by comparing the behavior of the title compound with that of tetracycline itself and possible causes for the stronger induction of the Tetracycline Receptor (TetR) by 5a,6-anhydrotetracycline than by tetracycline are considered. Energetically favored 3D-structure of the zwitteranionic 5a,6-anhydrotetracycline magnesium complex in solution.

Magnesium↗
PubMed2006

Molecular dynamics simulations of the tetracycline-repressor protein: the mechanism of induction.

Molecular dynamics simulations on the tetracycline-repressor (TetR) protein, both in the absence of an inducer and complexed with the inducers tetracycline and 5a,6-anhydrotetracycline, show significant differences in the structures and dynamics of the induced and non-induced forms of the protein. Calpha-density-difference plots, low-frequency normal vibrations and inter-residue interaction energies all point to a common mechanism of induction. The inducer displaces Asp156 from the magnesium ion in the binding pocket, leading to a short cascade of rearrangements of salt bridges that results in the allosteric change. The increased flexibility of the induced form of the protein is suggested to contribute to the decrease in binding affinity to DNA on induction.

Aspartic Acid↗
PubMed2006

Simulating FRET from tryptophan: is the rotamer model correct?

We present a computational model study designed to simulate the results of time-resolved fluorescence spectra of tryptophan in proteins. In such measurements, the occurrence of more than one fluorescence lifetime is generally attributed to the existence of several tryptophan rotamers and/or structural conformations of the protein structure. The protein system we chose for this initial study is the tetracycline repressor (TetR), an interesting model system for the investigation of the mechanisms of transcriptional regulation. Fluorescence resonance energy transfer (FRET) from tryptophan to tetracycline is frequently observed in complexes of the TetR with the antibiotic tetracycline. We use a combined classical/quantum mechanical approach to model the structure and the spectroscopic properties of the TetR-tetracycline complex. A classical molecular dynamics simulation provides input geometries for semiempirical quantum mechanical/molecular mechanical (QM/MM) single-point configuration interaction (CI) calculations, which are used to calculate tryptophan vertical absorption and fluorescence energies and intensities as well as relative FRET rate constants. These rate constants together with the Einstein coefficients for spontaneous emission and an assumed rate for nonradiative deactivation allow us to simulate fluorescence decay curves with and without FRET and for the entire ensemble as well as for individual rotamers. Our results indicate that the classical "rotamer model", used to explain the multiexponential fluorescence-decay curves of time-resolved tryptophan emission spectra, can be extended to systems with FRET acceptors present in the protein matrix but that the interpretation of the fitted lifetimes is different to that usually used.

Journal Article↗
PubMed2006

The formation of endo-complexes between calixarenes and amines--a reinvestigation.

The formation of an endo-complex between p-allylcalix[4]arene and t-butylamine was described by Gutsche in 1985. However, for a comparable system, it has been shown using NOE methods that the amine does not reside inside the calix. Instead, an exo-calix complex is formed. A reevaluation suggests that the previous conclusion is an artifact due to improper NMR-data processing. DFT (RB3LYP/6-31G(d)) calculations confirm the higher stability of the exo-complex over its endo-counterpart.

Amines↗
PubMed2005

The ethylene/metal(0) and ethylene/metal(I) redox system: model ab initio calculations.

Ab initio calculations (coupled cluster with single and double excitations; CCSD) have been used to investigate the model redox systems ethylene:M(0) (M = Li, Na, K, Rb, Cs) and ethylene:M(I) (M = Be, Mg, Ca, Sr, Ba, Zn, Cd, Hg). Within C2v symmetry, the ground (2A1) states correspond to the charge distribution given in the title. The lowest (2B2) excited states correspond, somewhat counter intuitively, to the ethylene*-/=M(II)ion pair. These trends can be rationalized on the basis of simple electrostatic and configuration-mixing arguments that lead to two simple equations for predicting the electron-transfer energies for oxidation or reduction of the ethylene. The electron-transfer energies to the 2B2 ion pairs are dominated by the electrostatic ion-pairing energies.

Boron↗
PubMed2005

AM1* parameters for aluminum, silicon, titanium and zirconium.

Our extension of the AM1 semiempirical molecular orbital technique, AM1*, has been parameterized for the elements Al, Si, Ti and Zr. The basis sets for all four metals contain a set of d-orbitals. Thus, AM1* parameters are now available for H, C, N, O and F (which use the original AM1 parameters), Al, Si, P, S, Cl, Ti, Mo and Zr. Special attention was paid to reproducing homolytic and heterolytic bond-dissociation energies correctly. Such bond-energy data help to avoid eccentricities in the parameterization caused by inaccurate experimental heats of formation. The performance and typical errors of AM1* for the newly parameterized elements are discussed. Generally, the new method performs less well than established techniques for heats of formation but considerably better for the heats of reaction.

Aluminum↗
PubMed2005

Regression formulae for ab initio and density functional calculated chemical shifts.

Linear regression formulae are given for converting 1H and 13C magnetic shielding constants calculated at common ab initio and density functional theory levels of calculation into chemical shifts relative to tetramethylsilane. Accuracies of roughly +/-2.2 ppm (13C) and +/-0.15 ppm (1H) or better are found for the training set for most levels. The highest level calculations do not always give better results than economical standard calculations.

Carbon Isotopes↗