Ab initio MO calculations and 17O NMR at natural abundance of para-substituted acetophenones

¹⁷O NMR chemical shifts and calculated (ab initio MO theory) electron densities are reported for a series of para-substituted acetophenones, X? C₄H₆? COCH₃, where X = NH₂, OCH₃, F, Cl, CH₃, H, COCH₃, CN, NO₂. The ¹⁷O shifts are very sensitive to the para substituent and cover a range of some 51 ppm. Donors induce upfield shifts and acceptors downfield shifts. The substituent chemical shifts (SCS) correlate precisely with σ_I and σ_R⁺ using the Dual Substituent Parameter (DSP) method. The derived transmission coefficients ρ_I and ρ_R indicate that polar and resonance mechanisms contribute approximately equally to the observed substituent effects. The shifts also correlate well with calculated π-electron densities (slope = 1500 ppm per electron) confirming their electronic origin. λ values are also reported, and the role of the average excitation energy, ΔE, in determining ¹⁷O SCS values is discussed. It is concluded that variations in ΔE are minor and that the local Δ-electron density is the dominant feature controlling ¹⁷O SCS values.     

A C-13 study of the reaction of 2,4,6-triarylpyrylium cations with amines

The reaction of primary and secondary amines with 2,4,6-triarylpyryliums is shown by C-13 NMR to proceed by fast ring opening to a vinylogous amide; in the case of primary amines this closes slowly to a pyridinium salt. The reaction in DMSO gives the pyridinium salt quantitatively when 2 moles of amines are used, with less amine significant quantities of a diketone intermediate are produced which results in slower conversion.     

Temperature dependence of 19F chemical shifts in substituted benzyl fluorides.

The ¹⁹F chemical shifts of substituted benzyl fluorides are shown to be temperature dependent and this is discussed in terms of conformational effects.     

Analysis of DNA restriction fragments and polymerase chain reaction products towards detection of the AIDS (HIV-1) virus in blood.

A high-performance capillary electrophoresis system with a polysiloxane-coated capillary and polymeric buffer additives was investigated for the analysis of DNA restriction fragments and polymerase chain reaction (PCR) products. Mobility data and Ferguson plots of the DNA fragments at different polymer (hydroxypropylmethylcellulose) concentrations indicated that effective molecular sieving was obtained consistent with existing data of conventional gel electrophoresis and with recent HPCE data. The precision and peak efficiency were excellent and the system was applied to the analysis of specific co-amplified DNA sequences (HIV-1 and HLA-DQ-alpha). After PCR, ultrafiltration was used in the sample preparation step to desalt the sample and to remove superfluous PCR reaction products. Electrokinetic injection was used for sample introduction into the capillary. The addition of ethidium bromide to the buffer resulted in longer migration times of DNA fragments and better peak resolution. During HPCE, an artifact associated with dilute DNA solutions leading to the appearance of extra peaks in the electropherogram was found.     

The calculation and accurate measurement of infrared band intensities: the v8 and v19 vibrations of monosubstituted benzenes

We report the results of calculations by the CNDO/2 molecular orbital method for the intensities of the v_19a and v_19b ring vibration of a series of mono-substituted benzenes and have repeated earlier calculations on the intensities of the corresponding v_8a and v_8b vibrations. These results are compared with intensity measurements in carbon tetrachloride solution made by improved techniques. Some gas phase measurements and results obtained for some deuterated compounds are included.     

The use of phased rays in very shallow water

Numerical predictions are studied of propagation in isovelocity water over a lossy bottom with the depth and frequency such that only one, two, or three normal modes exist. Comparison of the result from a new “Phased Ray” model with the normal mode result shows that it is the phase change upon reflection that is the major cause of the disagreement between the Phased Ray and Mode models. The possibility of controlling the phase of the plane wave reflection coefficient by tuning an overlying layer of silt, or whatever, is also demonstrated. The case is then put forward, when dealing with problems where the bottom has irregular contours or where the surface is rough, i.e., where there are no normal mode solutions, for modelling the propagation with rays corrected to agree in general properties with the normal mode solutions of nearly the same problems.     

Solvent affects the conformation of virginiamycin M1 (pristinamycin IIA, streptogramin A)

The streptogramins are antibiotics which act by binding two different components at separate nearby sites on the bacterial 50S ribosome, inhibiting protein synthesis. The first component, a macrolactone, is common to many of the streptogramin antibiotics and, thus, is referred to by many names including virginiamycin M1(VM1), pristinamycin IIA, ostreogrycin A and streptogramin A. X-Ray crystallographic studies of VM1 bound to ribosomes and to a deactivating enzyme show a different conformation to that of VM1 in chloroform solution. We now report the results of high resolution 2D NMR experiments that show that the conformation of VM1 in dimethyl sulfoxide and methanol differs from both that in chloroform solution and in the bound form. The 3D structure and the 1H NMR and 13C NMR chemical shifts of VM1 in dimethyl sulfoxide and methanol are described.     

Effect of atomic charge,solvation, entropy,and ligand protonation state on MM-PB(GB)SA binding energies of HIV protease

The molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) and MM-generalized-Born surface area (MM-GBSA) approaches are commonly used in molecular modeling and drug design. Four critical aspects of these approaches have been investigated for their effect on calculated binding energies: (1) the atomic partial charge method used to parameterize the ligand force field, (2) the method used to calculate the solvation free energy, (3) inclusion of entropy estimates, and (4) the protonation state of the ligand. HIV protease has been used as a test case with six structurally different inhibitors covering a broad range of binding strength to assess the effect of these four parameters. Atomic charge methods are demonstrated to effect both the molecular dynamics (MD) simulation and MM-PB(GB)SA binding energy calculation, with a greater effect on the MD simulation. Coefficients of determination and Spearman rank coefficients were used to quantify the performance of the MM-PB(GB)SA methods relative to the experimental data. In general, better performance was achieved using (i) atomic charge models that produced smaller mean absolute atomic charges (Gasteiger, HF/STO-3G and B3LYP/cc-pVTZ), (ii) the MM-GBSA approach over MM-PBSA, while (iii) inclusion of entropy had a slightly positive effect on correlations with experiment. Accurate representation of the ligand protonation state was found to be important. It is demonstrated that these approaches can distinguish ligands according to binding strength, underlining the usefulness of these approaches in computer-aided drug design. © 2012 Wiley Periodicals, Inc.