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.     

Fundamental role of the fostriecin unsaturated lactone and implications for selective protein phosphatase inhibition

Key derivatives and analogues of fostriecin were prepared and examined that revealed a fundamental role for the unsaturated lactone and confirmed the essential nature of the phosphate monoester. Thus, an identical 200-fold reduction in protein phosphatase 2A (PP2A) inhibition is observed with either the saturated lactone (7) or with an analogue that lacks the entire lactone (15). This 200-fold increase in PP2A inhibition attributable to the unsaturated lactone potentially may be due to reversible C269 alkylation within the PP beta12-beta13 active site loop accounting for PP2A/4 potency and selectivity.     

Evidence of a phase transition of RbHCO3 from high-resolution solid-state 13C and 87Rb NMR by comparison with KHCO3

A variable-temperature high-resolution 13C and 87Rb solid-state NMR study of powder rubidium hydrogencarbonate, RbHCO3, is presented for the first time. At ambient temperature, RbHCO3 is formed by centrosymmetric dimers linked by hydrogen bonds, but almost no information is available on this compound concerning proton disorder and the low-temperature phase. However, potassium hydrogencarbonate, KHCO3, which has an isomorphic structure for the high temperature phase, was well studied: it undergoes a non-ferroic, non-ferroelectric phase transition at Tc = 318 K between two monoclinic structures. The protons are disordered in an asymmetric double-well potential in the low-temperature phase, and the double-well potential becomes symmetric in the high-temperature phase. By comparison with recent solid-state NMR experimental results on KHCO3, we show that RbHCO3 undergoes a phase transition at Tc approximately 245 K, and give evidence that the proton dynamic disorder in both compounds is very similar.     

Exploring the free-energy landscape of a short peptide using an average force

The reversible folding of deca-alanine is chosen as a test case for characterizing a method that uses an adaptive biasing force (ABF) to escape from the minima and overcome the barriers of the free-energy landscape. This approach relies on the continuous estimation of a biasing force that yields a Hamiltonian in which no average force is exerted along the ordering parameter xi. Optimizing the parameters that control how the ABF is applied, the method is shown to be extremely effective when a nonequivocal ordering parameter can be defined to explore the folding pathway of the peptide. Starting from a beta-turn motif and restraining xi to a region of the conformational space that extends from the alpha-helical state to an ensemble of extended structures, the ABF scheme is successful in folding the peptide chain into a compact alpha helix. Sampling of this conformation is, however, marginal when the range of xi values embraces arrangements of greater compactness, hence demonstrating the inherent limitations of free-energy methods when ambiguous ordering parameters are utilized.     

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.     

Structural, textural, and electronic properties of a nanosized mesoporous ZnxTi1-xO2-) solid solution prepared by a supercritical drying route

Mesoporous nanosized TiO2 and Zn(x)Ti(1-x)O(2-x) solid solution having a Zn content below 10 mol % with a particles size between 13 and 17 nm are prepared by a template-free sol-gel method followed by high-temperature supercritical drying in 2-propanol. The structural, textural, and electronic properties of the obtained nanomaterials are methodically investigated by using XRD, SEM, TEM, ED, HREM, EDX, ICP-OES, N(2) adsorption-desorption, Raman spectroscopy, and diffuse reflectance UV-vis spectroscopy. It is shown that the proposed synthesis technique leads to the formation of a Zn(x)Ti(1-x)O(2-x) solid solution based on the anatase crystal structure rather than a two-phase sample. High-resolution electron microscopy and electron diffraction indicate that the distribution of zinc atoms over the anatase structure does not lead to a considerable deformation of the crystal structure.     

Reactivity differences between molecular and surface silanols in the preparation of homogeneous and heterogeneous olefin metathesis catalysts

The reaction of Mo(N)(CH₂tBu)₃ (1) and SiO_2-(700) generates (SiO)Mo(NH)(CHtBu)(CH₂tBu) (2) when performed in C₆H₆ (material [1/SiO_2-(700)]_C6H6). The grafting occurs presumably by protonation of the nitrido ligand to form an intermediate (SiO)Mo(NH)(CH₂tBu)₃ (3), a pentacoordinated complex, which decomposes into 2 and 2,2-dimethylpropane. While [1/SiO_2-(700)]_C6H6 is highly active in olefin metathesis, [1/SiO_2-(700)]_CH2Cl2 and [1/SiO_2-(700)]_THF are poorly active or inactive catalysts respectively. In contrast, when Mo(N)(CH₂tBu)₃ reacts with a molecular silanol derivative, a soluble model of the surface of SiO_2-(700), it yields a very stable complex, (c-C₅H₉)₇Si₇O₁₂SiO-Mo(NH)(CH₂tBu)₃ (3m), which does not spontaneously generate 2,2-dimethylpropane and an alkylidene complex in contrast to the surface complex. Moreover, 3m does not catalyse olefin metathesis at room temperature as it does not already contain the initiating carbene ligand, and it is necessary to heat up the reaction mixture to 110 °C to obtain low catalytic activity. Nevertheless, the complex 3m generates well-defined metallocarbenes when heated in the presence of PMe₃: (c-C₅H₉)₇Si₇O₁₂SiO-Mo(N)(CHtBu)(P(CH₃)₃)₂ (4m) as a 10:1 mixture of its syn and anti rotamers with the loss of 2 equiv. of 2,2-dimethylpropane.     

Synthesis of C-3' methyl taxotere (docetaxel)

Protected (3R,4S)-N-Boc-3-hydroxy-4-methyl-4-phenylazetidin-2-one has been synthesized stereoselectively and used to esterify protected 10-desacetylbaccatin III to give, following removal of the protecting groups, novel C-3' methyl taxotere (docetaxel).