Understanding binding affinity: a combined isothermal titration calorimetry/molecular dynamics study of the binding of a series of hydrophobically modified benzamidinium chloride inhibitors to trypsin

The binding of a series of p-alkylbenzamidinium chloride inhibitors to the serine proteinase trypsin over a range of temperatures has been studied using isothermal titration (micro)calorimetry and molecular dynamics simulation techniques. The inhibitors have small structural variations at the para position of the benzamidinium ion. They show small differences in relative binding affinity but large compensating differences in enthalpy and entropy. Binding affinity decreases with increased branching at the first carbon but increases with increasing the length of a linear alkyl substituent, suggesting that steric hindrance and hydrophobic interactions play dominant roles in binding. Structural analysis showed that the backbone of the enzyme was unaffected by the change of the para substituent. In addition, binding does not correlate strongly with octanol/water partition data. To further characterize this system, the change in the heat capacity on binding, the change in solvent-accessible surface area on binding, the effect of inhibitor binding on the hydration of the active site, the pK(a) of His57, and interactions within the catalytic triad have been investigated. Although the changes in inhibitor structure are small, it is demonstrated that simple concepts such as steric hindrance, hydrophobicity, and buried surface area are insufficient to explain the binding data. Other factors, such as access to the binding site and the cost of dehydration of the active site, are of equal or greater importance.     

A simplified synthesis of the hexamethylplatinate(IV) ion

Tetra-n-butylammonium hexachloroplatinate (IV) reacts with lithium methyl/lithium iodide in ether to give a solution containing lithium hexamethylplatinate (IV). With lithium methyl/lithium bromide in ether however, tetrabutylammonium hexamethylplatinate (IV) is precipitated together with lithium halides. Solid [Bu₄N)₂[Pt(Ch₃)₆] is stable under nitrogen at room temperature, but ether solutions of [Pt(Ch₃)₆]^2- decompose in a few minutes at room temperature in the absence of excess lithium methyl.     

A general and efficient synthesis of sulfonylbenzotriazoles from N-chlorobenzotriazole and sulfinic acid salts

One-pot reactions of sulfinic acid salts (produced from organometallic reagents with SO2) with N-chlorobenzotriazole gave the corresponding N-alkane-, N-arene-, and N-heteroenesulfonylbenzotriazoles 3a-j in 41-93% yields. Reagents 3a-j are efficient sulfonylating agents, reacting at 20-80 degrees C with various primary and secondary aliphatic amines to yield the corresponding sulfonamides in 64-100% yields.     

Flow-injection amperometric determination of oxalate with immobilized oxalate oxidase

Oxalate is immobilized on controlled-pore glass and is used on-line in a glass minicolumn (2.5×25 mm). The hydrogen peroxide formed is detected amperometrically. Oxalate (6×10^?6?9×10^?4 M) is determined in a flowing stream of pH 3.5 citrate (or succinate) buffer. As little as 20 ng (in 40 μl; 5.7×10^?6 M) of oxalate can be detected. Copper inhibition can be removed either by adding EDTA to the carrier stream or incorporating a chelating-resin minicolumn into the flow system prior to the enzyme column.     

Flow-injection determination of sulphite and assay of sulphite oxidase

Sulphite (1–80 × 10^?5 M) in formaldehyde-stabilized solutions is determined by injection into a flowing stream of pH 8.5 phosphate buffer, passing through a mini-column of sulphite oxidase immobilized on controlled-pore glass, with amperometric detection of the hydrogen peroxide produced. Sulphite oxidase (5–100 U l^?) is determined by injection into a flowing stream of formaldehyde-stabilized 2 × 10^?3 M sodium sulphite in pH 8.0 phosphate buffer; hydrogen peroxide is again monitored.     

The dimensions of the alternating polyesteramide 6NT6

The Flory-Williams rotational isomeric state models describing the conformational characteristics of polyesters and polyamides are combined to calculate the dimensions of the alternating polyesteramide (PEA) of the type 6NT6. The calculated ratio of unperturbed dimensions $\text{(〈r}{}^2\text{〉}{}_{\mathrm{o}}\text{/M}\text{)}{}^{\mathrm{<mtext>1</mtext><mtext>2</mtext>}}$ is $\text{1.03}\text{A}\text{?}\text{/gmole}{}^{\mathrm{<mtext>1</mtext><mtext>2</mtext>}}$ in excellent agreement with the value $\text{1.00}\text{A}\text{?}\text{/gmole}{}^{\mathrm{<mtext>1</mtext><mtext>2</mtext>}}$ recently obtained from an intrinsic viscosity-molecular weight study of PEA.     

Synthesis and characterisation of a series of alkylmagnesium amide and related oxygen-contaminated "alkoxy" compounds

Synthesised either by an unusual tert-butyl metathesis between tert-butyllithium and a n,s-butylmagnesium amide or by reaction of an alkyl Grignard reagent and a sodium amide, five tert-butylmagnesium amides, Bu(t)MgDBA (5)(DBA=dibenzylamide), Bu(t)MgDA (6)(DA=diisopropylamide), Bu(t)MgHMDS (7)(HMDS=1,1,1,3,3,3-hexamethyldisilazide), Bu(t)MgTMP (8)(TMP=2,2,6,6-tetramethylpiperidide) and Bu(t)MgNCy2 (9)(cy=cyclohexyl) have been isolated as crystalline solids. All five amides have been characterised by X-ray crystallography and solution NMR spectroscopic studies. The former studies reveal a common dimeric molecular structure with amido bridges in a planar (MgN)2 ring and terminal Bu(t) ligands on the Mg atoms. Also described is the dodecameric primary amide [Bu(n)MgN(H)Dipp]12 (10a) and its monomeric solvate Bu(n)MgN(H)Dipp.TMEDA (10b)(Dipp=2,6-diisopropylphenyl; TMEDA=N,N,N',N'-tetramethylethylenediamine). The crystal structures of the oxo-insertion products Bu(t)MgOBu(t).THF (11), Bu(t)Mg(mu-OBu(t))(mu-TMP)MgTMP (12) and Mg(OBu(n))HMDS.solv [solv=THF (13a) or Et2O (13b)], made fortuitously during the course of this work, are also presented.     

Some past achievements and future perspectives in main group chemistry

A survey of some recent developments and past achievements in low-valent main group chemistry is presented. Some emerging implications of this area of chemistry in materials science, catalysis and new reagent development are also discussed.     

Dependence of ion hydration on the sign of the ion's charge

The solvation of simple ions in water is studied using molecular dynamics simulations with a polarizable force field. Previous simulations using this potential demonstrated that anions are more favorably solvated in water than cations. The present work is an attempt to explain this result by examining the effects of ions on the surrounding water structure, with particular focus on the first solvation shell and its interactions with the surrounding water. We conclude that while the first solvation shell surrounding cations is frustrated by competition between ion-water and water-water interactions, solvation of anions is compatible with good water-water interactions.