Charge calculations in molecular mechanics. Part 8 Partial atomic charges from classical calculations

Summary The CHARGE2 programme, which involves the classical calculation of both the inductive and resonance contributions to the partial atomic charges in molecules is described, and the charges and electrostatic potentials obtained presented for some illustrative examples.In substituted methanes (CH₃X, CF₃X, CCl₃X) the effects of varying the electronegativity of the substituents and the - and -substituent contributions are clearly illustrated for a variety of substituent groups X.The problems involved in the inclusion of silicon into this scheme are detailed, together with the methods of overcoming them. The partial atomic charges ( and contributions) and electrostatic potentials for some silicon oxygen compounds are presented and discussed.The partial atomic charges from CHARGE2 for all the natural amino acids as their N-acetyl, N-methyl-amides are given and compared with those obtained from the AMBER and ECEPP/2 force fields. Considerable differences in these figures are observed, with the AMBER charges consistently much larger than those from the other two methods.The CHARGE2 partial atomic charges and electrostatic potentials for the four common nucleic acids, adenine, cytosine, guanine and thymine, are given and compared with those derived from other calculations. Again there is general similarity but also there are considerable differences, with those from the AMBER force field somewhat larger than the other methods.For previous parts in this series, see Refs. 1-7.     

Kinetics of the enzymatic saccharification of pretreated tapioca waste (Manihot esculenta) and water hyacinth (Eichhornia crassipes)

Studies were carried out on saccharification of pretreated tapioca waste and water hyacinth under two different conditions: using microbial enzymes (cellulase fromMyrothecium verrucaria, Coprinus comatus,Pleurotus florida, andCellulomonas sp.) and solid-state fermentation. The rate of saccharification was determined at different temperatures, pH, substrate concentration, and incubation period. It was found that as the source of the enzyme varies, the optimal temperature and pH for the saccharification varies. Among the two different treatments, enzymatic saccharification was found to be the most efficient. Among the various cellulase sources tested, M.verrucaria cellulase was found to be the most efficient one followed byC. comatus, P. florida, and finallyCellulomonas sp.     

Solvent dependent dimercaptothiadiazole monolayers on gold electrode for the simultaneous determination of uric acid and ascorbic acid

Dimercaptothiadiazole compound, 2,5-dimercapto-1,3,4-thiadiazole (DMcT) forms ‘thin’ monolayers on Au electrode when it was adsorbed from methanol, ethanol or DMSO solutions while it forms ‘thick’ layers on Au electrode from an aqueous solution under identical experimental conditions. Thick DMcT layers formed from aqueous solution effectively blocks the redox reaction of couple in contrast to thin DMcT monolayers. The monolayer thickness did not vary when structurally related DMcT compounds, 5-methyl-1,3,4-thiadiazole-2-thiol or 5-amino-1,3,4-thiadiazole-2-thiol was adsorbed from aqueous and non-aqueous solutions. This indicates that the presence of two thiol groups in DMcT plays a crucial role in the formation of thick and thin DMcT layers on Au electrode when it was adsorbed from aqueous and non-aqueous solutions. Methanol, ethanol, or DMSO solution of DMcT is considered as strong acid because these solvents are able to deprotonate DMcT into DMcT⁻ and thus thin monolayers formed on Au electrode. The deprotonating ability of these solvents was further verified from the observed absorption spectrum characteristic of DMcT⁻ species. On the other hand, an aqueous solution of DMcT is less acidic due to weak deprotonation of DMcT by water and thus DMcT forms thick layer on Au electrode. Interestingly, thin DMcT monolayers formed from non-aqueous solvents separates the voltammetric signals of uric acid and ascorbic acid while thick DMcT layers formed from aqueous solution fails to separate them.     

Molecular composites in thermosets

The synthesis of molecular composites where rigid polymer molecules are reinforcing elements in a thermoset bisimide matrix has been investigated. The approach has been designed to avoid phase separation by selecting systems where reaction of amine-terminated rigid and semiflexible oligomers with maleimide unsaturation occurs prior to crosslinking of the thermoset. This objective has been met for some compositions. The concentration and molecular weight of the rigid oligomers have been varied. The structure of the reinforcing polymer, the reactivity of the maleimide and the conditions for composite synthesis are variables of critical importance, and further work must determine the promise and limitations of this approach.     

Conformational analysis—II: A lanthanide-induced shift nmr and theoretical study of bicyclo [3.1.0] hexan-3-one and adamantanone

The solution conformation of bicyclo [3.1.0] hexan-3-one has been obtained by the use of the shifts induced in its ¹H and ¹³C NMR by Yb(fod)₃. Refinement of the angle of pucker, ∝, of the 5-membered ring indicates that the molecule adopts a flattened boat conformation with ∝ = 195°. This prediction is supported by ab initio, STO-3G, calculations on the isolated molecule. Use of a two- or four-site model for lanthanide-substrate complexing adequately reproduces the experimental data whereas a one-site binding model is unsatisfactory. The importance of multi-site binding is further emphasised by results for the C_2v-symmetric ketone, adamantanone, where only a four-site model gives satisfactory agreement between observed and calculated lanthanide-induced shifts.     

The formation of propylene fumarate oligomers for use in bioerodible bone cement composites

Poly(propylene fumarate) (PPF) oligomers were synthesized by step polymerization using bis(2-hydroxypropyl fumarate) or propylene bis(hydrogen maleate) as starting materials. Oligomers possessing identical degrees of polymerization (DP), but varying in their end group character (either hydroxyl or carboxyl) were first prepared and characterized, then used as part of a bone cement preparation consisting of oligomer, tricalcium phosphate, calcium carbonate, and methyl methacrylate. Compressive strength of the resulting composite appeared to be dependent on both the degree of polymerization of the PPF, and the nature of the oligomers' end groups.     

Micromethod for the analysis of the four commonly used antiepileptic drugs using a jet tube column

We describe a simple method for the determination of phenobarbital, diphenylhydantoin, carbamazepine, and primidone in serum, by use of gas-liquid chromatography with temperature programming. The methylated derivatives of these anticonvulsants were well resolved, as was 5-(p-methylphenyl)-5-phenylhydantoin, the internal standard. In this procedure we used the jet tube for separation of the drug from the serum. The proposed procedure requires only 100 μl of serum and can be done in less than 30 min. The lower limit of detection for each of the drugs is 0.5 mg/liter. Analytical recoveries of drug from serum were excellent and peak height and concentration were linearly related up to twice the toxic concentration for serum.