Showing papers by "James Alexis Platts published in 2005"

Synthesis, characterisation and theoretical studies of amidinato-indium(I) and thallium(I) complexes: isomers of neutral group 13 metal(I) carbene analogues.

Abstract: The synthesis and characterisation of the monomeric amidinato-indium(I) and thallium(I) complexes, [M(Piso)]·PisoH, M = In or Tl, Piso− = [ArNC(But)NAr]−, Ar = C6H3Pri2-2,6, are reported. These complexes, in which the metal centre is chelated by the amidinate ligand in an N,η3-arene-fashion, can be considered as isomers of four-membered group 13 metal(I) carbene analogues. Theoretical studies have compared the relative energies of both isomeric forms of a model complex, [In{PhNC(H)NPh}].

Hydrogen Bonding and Covalent Effects in Binding of Cisplatin to Purine Bases: Ab Initio and Atoms in Molecules Studies

Abstract: Ab initio and density functional calculations are employed to investigate the role of hydrogen bonding in the binding of cisplatin to the purine bases guanine and adenine. Through the use of the theory of atoms in molecules (AIM), it is shown that hydrogen bonds are ubiquitous in such systems, with N-H...N and N-H...Cl interactions present in addition to the expected N-H...O. This in turn means that the known stability of cisplatin-guanine complexes cannot be ascribed solely to hydrogen bonding and allows decomposition of total binding energy into contributions from covalent and hydrogen bonds. To do so, a new method for predicting hydrogen bond energies from bond critical point properties is proposed, employing partial least-squares analysis to remove the family dependence of simple models. Still more hydrogen bond motifs are found in bifunctional complexes of the general type purine-[Pt(NH(3))(2)](2+)-purine, including purine...purine contacts, though again the energetics of these are insufficient to explain the observed trends in stability. Finally, the effect of platination on the pairing of guanine with cytosine is studied in a similar manner, revealing large redistributions of hydrogen bonding but surprisingly small overall changes in pairing energy.

Binding of transition metal complexes to guanine and guanine-cytosine: hydrogen bonding and covalent effects.

Abstract: Density functional calculations and Atoms in Molecules analysis are used to investigate the role of covalent and hydrogen bondings in determining the binding of transition metal complexes to guanine, and the subsequent effect on pairing with cytosine Hydrogen bonding is ubiquitous, and typically contributes ca 10% to overall binding, a value that varies with the coordination site on guanine, as well as metal and ligands Early transition metals show a clear preference for the O6 position, while later ones prefer N7, the crossover point coming at the vanadium group Metallation at N7 causes a redistribution of hydrogen bonding strength between guanine and cytosine, but does not greatly affect the overall pairing energy In contrast, metallation at O6 strongly reduces the pairing energy, as may be expected given the role of O6 in pairing guanine with cytosine This effect can be quantified using electron density properties, and seems to be due to both electrostatic repulsion from the positive metal centre and a redistribution of electron density within guanine itself Qualitative agreement with experimental mass spectroscopic results is obtained

Structural requirements for binding of Myelin Basic Protein (MBP) Peptides to MHC II: effects on immune regulation

Abstract: Confronting Multiple Sclerosis requires as an underlying step the manipulation of immune response through modification of Myelin Basic Protein peptides. The aim is to design peptidic or nonpeptidic molecules that compete for recognition of self-antigens at the level of antigen presentation. The rational approach is to substitute residues that serve as anchors for the T-Cell Receptor with others that show no binding at all, and those that serve as Major Histocompatibility Complex II anchors with others that present increased binding affinity. The resulting structure, hence, retains normal or increased MHC II binding properties, but fails to activate disease-inducing T-cells. This rational design can only be achieved by identifying the structural requirements for binding of the natural peptide to MHC II, and the anchor residues with their corresponding specific pockets in the binding groove. The peptide-MHC II complex then interacts with the TCR; thus, an additional way to trigger the desired immune response is to alter secondary anchor residues as well as primary ones. In this review, the structural requirements for binding of MBP peptides to MHC II are presented, as are the mechanism and key features for TCR recognition of the peptide-MHC II complex.

Quaternary Ammonium Arylspiroborate Esters as Organo-Soluble, Environmentally Benign Wood Protectants

Abstract: As part of a larger project aimed at the development of leach resistant boron-based wood preservatives, the anti-fungal and termiticidal activities, and the resistance to leaching from timber, of three related tetra-n-butylammonium spiroborates, tetra-n-butylammonium bis(ortho-hydroxymethylphenolato)borate 2, tetra-n-butylammonium bis[catecholato(2–)-O,O′]borate 3, and tetra-n-butylammonium bis[salicylato(2-)-O,O']borate 4, have been examined. All three borates are found to be active against test organisms, with the following orders of activity being observed: 2 > 3 > 4 > boric acid against wood decay fungi, and 2 > 3 ≈ 4 > boric acid against termites. The most active compound in both assays 2 also has the highest calculated lipophilicity. In a test for permanence in wood, the following order of leach resistance is observed: 4 >> 3 ≈ 2 > boric acid. This order appears to correlate more closely with the stability constants of the borate esters, as determined using 11B NMR spectroscopy, rather than calculated lipophilicities.

Properties of interatomic surfaces: Relation to bond energies

Abstract: A number of properties of interatomic surfaces, as defined by the quantum theory of atoms in molecules (QTAIM), are calculated for approximately 50 molecules. These integrated surface properties are then tested for their ability to correlate and predict bond energies from MP2 atomisation energies. Three surface properties, each with units of energy, are found to show strong correlations with bond energy: single parameter models work well for non-polar bonds, but fail for polar and ionic bonds, where multi-variate methods are required. The local curvature of the interatomic surface is found to be useful this respect, reflecting charge transfer effects.

Ab initio and DFT computer studies of complexes of trimethylphosphine and products of substituted phosphonium cations with hydroxide, chloride and fluoride anions: Phosphorus analogues of choline and acetylcholine

Abstract: Theoretical calculations (DFT, MP2) are reported for up to four sets of reaction products of trimethylphosphine, (CH 3 ) 3 P, each with H 2 O, HCl and HF together with DFT calculations on up to three sets of reaction products of substituted phosphonium cations, (CH 3 ) 3 P–R + . These products comprise (a) P(III) normal complexes (CH 3 ) 3 P⋯HY, (b) P(IV) ‘reverse’ complexes Y⋯(H–CH 2 ) 3 P–R, (c) P(IV) ylidic complexes YH⋯CH 2 (CH 3 ) 2 P–R and (d) P(V) covalent compounds Y–P(CH 3 ) 3 –R for Y=HO, Cl and F and R=H, CH 3 , C 2 H 5 , C 2 H 4 OH and C 2 H 4 OC:OCH 3 . Calculations are carried out at the B3LYP/6-31+G(d,p) level in all cases and also at the MP2/6-31+G(d,p) level for systems in which R=H. Minimum energy structures are determined for predicted complexes or structures and geometrical properties, harmonic vibrations and BSSE corrected binding energies are reported and compared with the limited experimental information available. Potential energy scans predict equilibria between covalent trigonal bipyramidal P(V) forms and reverse complexes comprising hydrogen bonded or ion pair, tetrahedral P(IV) forms separated by low potential energy barriers. Similar scans are also reported for equilibria between reverse complexes and ylidic complexes for Y=OH and R=CH 3 , C 2 H 5 , C 2 H 4 OH and C 2 H 4 OC:OCH 3 . Corrected binding energies, structures and values of harmonic modes are discussed in relation to bonding The names ‘pholine’ and ‘acetylpholine’ are suggested for phosphorus analogues to choline and acetylcholine.