Derivation of class II force fields. VIII. Derivation of a general quantum mechanical force field for organic compounds

A class II valence force field covering a broad range of organic molecules has been derived employing ab initio quantum mechanical "observables." The procedure includes selecting representative molecules and molecular structures, and systematically sampling their energy surfaces as described by energies and energy first and second derivatives with respect to molecular deformations. In this article the procedure for fitting the force field parameters to these energies and energy derivatives is briefly reviewed. The application of the methodology to the derivation of a class II quantum mechanical force field (QMFF) for 32 organic functional groups is then described. A training set of 400 molecules spanning the 32 functional groups was used to parameterize the force field. The molecular families comprising the functional groups and, within each family, the torsional angles used to sample different conformers, are described. The number of stationary points (equilibria and transition states) for these molecules is given for each functional group. This set contains 1324 stationary structures, with 718 minimum energy structures and 606 transition states. The quality of the fit to the quantum data is gauged based on the deviations between the ab initio and force field energies and energy derivatives. The accuracy with which the QMFF reproduces the ab initio molecular bond lengths, bond angles, torsional angles, vibrational frequencies, and conformational energies is then given for each functional group. Consistently good accuracy is found for these computed properties for the various types of molecules. This demonstrates that the methodology is broadly applicable for the derivation of force field parameters across widely differing types of molecular structures. Copyright 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1782-1800, 2001     

Lipid modifications of a Ras peptide exhibit altered packing and mobility versus host membrane as detected by 2H solid-state NMR

The human N-ras protein binds to cellular membranes by insertion of two covalently bound posttranslational lipid modifications, which is crucial for its function in signal transduction and cell proliferation. Mutations in ras may lead to unregulated cell growth and eventually cancer, making it an important therapeutic target. Here we have investigated the molecular details of the membrane binding mechanism. A heptapeptide derived from the C-terminus of the human N-ras protein was synthesized including two hexadecyl modifications. Solid-state 2H NMR was used to determine the packing and molecular dynamics of the ras lipid chains as well as the phospholipid matrix. Separately labeling the chains of the peptide and the phospholipids with 2H enabled us to obtain atomically resolved parameters relevant to their structural dynamics. While the presence of ras only marginally affected the packing of DMPC membranes, dramatically lower order parameters (S(CD)) were observed for the ras acyl chains indicating modified packing properties. Essentially identical projected lengths of the 16:0 ras chains and the 14:0 DMPC chains were found, implying that the polypeptide backbone is located at the lipid-water interface. Dynamical properties of both the ras and phospholipid chains were determined from spin-lattice 2H relaxation (R1Z) measurements. Plots of R1Z rates versus the corresponding squared segmental order parameters revealed striking differences. We propose the ras peptide is confined to microdomains containing DMPC chains which are in exchange with the bulk bilayer on the 2H NMR time scale (approximately 10(-5) s). Compared to the host DMPC matrix, the ras lipid modifications are extremely flexible and undergo relatively large amplitude motions. It is hypothesized that this flexibility is a requirement for the optimal anchoring of lipid-modified proteins to cellular membranes.     

Spectroscopic characterization of alkaline earth uranyl carbonates

A series of alkaline uranyl carbonates, M[UO₂(CO₃)₃]·nH₂O (M=Mg₂, Ca₂, Sr₂, Ba₂, Na₂Ca, and CaMg) was synthesized and characterized by inductively coupled plasma mass spectrometry (ICP-MS) and atomic absorption spectrometry (AAS) after nitric acid digestion, X-ray powder diffraction (XRD), and thermal analysis (TGA/DTA). The molecular structure of these compounds was characterized by extended X-ray absorption fine-structure (EXAFS) spectroscopy and X-ray photoelectron spectroscopy (XPS). Crystalline Ba₂[UO₂(CO₃)₃]·6H₂O was obtained for the first time. The EXAFS analysis showed that this compound consists of (UO₂)(CO₃)₃ clusters similar to the other alkaline earth uranyl carbonates. The average U-Ba distance is 3.90±0.02 Å.Fluorescence wavelengths and life times were measured using time-resolved laser-induced fluorescence spectroscopy (TRLFS). The U-O bond distances determined by EXAFS, TRLFS, XPS, and Raman spectroscopy agree within the experimental uncertainties. The spectroscopic signatures observed could be useful for identifying uranyl carbonate species adsorbed on mineral surfaces.     

Mass Spectrometric Decomposition Processes in Labelled 1-Heptenes

The 70 eV mass spectra of a number of ¹³C- and D-labelled analogs of 1-heptene have been measured, as well as the metastable transitions in the non-labelled compound. Isotopic distributions in the major fragment ions have been calculated from the high and low resolution data. The results show that considerable skeletal rearrangement must take place before formation of most of the fragment ions. Loss of methyl and ethyl radicals occurs mainly from the two ends of the molecule. Ethylene fragments come primarily from the unsaturated end of the molecule, but show evidence of significant prior skeletal rearrangement. The predicted McLafferty rearrangement accounts for only 2/3 of the C₄H₈⁺ ions formed, less for the C₃H₆⁺ ions. At least 80% of C₄H₉⁺ ions appear to be formed by allylic cleavage, as expected, but this mechanism can only account for a maximum of 20% of the formation of the complementary ion C₃H₅⁺. Both, this latter ion and C₃H₆⁺, are probably generated by loss of hydrogen from C₃H₇⁺. Figures obtained for label retention in 1-[¹³C]- and 1-D-labelled analogs were nearly identical for most fragment ions, probably indicating that the hydrogen atoms in position 1 remain on C(1) even following skeletal rearrangement. A similar result was found for the 7-[¹³C]- and 7-D-labelled compounds. The main exceptions in the case of the products labelled in position 1 (C₄H₇⁺, C₃H₃⁺) seem to be due to initial loss of an hydrogen atom from this position followed by further fragmentation.     

High performance liquid chromatographic-mass spectrometric assay for the quantitation of BMS-204352 in dog K(3)EDTA plasma

A high performance liquid chromatographic-mass spectrometric (LC/MS) assay was developed and validated for the determination of BMS-204352 in dog K(3)EDTA plasma. A 0.5 mL aliquot of control plasma was spiked with BMS-204352 and internal standard (IS) and buffered with 1 mL of 5 mM ammonium acetate. The mixture was then extracted with 3 mL of toluene. After separation and evaporation of the organic phase to dryness using nitrogen at 40 degrees C, the residue was reconstituted in the mobile phase and 25 microL of the sample were injected onto a Hypersil C(18) column (2 x 50 mm; 3 microm) at a flow rate of 0.5 mL/min. The mobile phase was consisted of two solvent mixtures (A and B). Solvent A was composed of 5 mM ammonium acetate and 0.1% triethylamine in 75:25 v/v water:methanol, pH adjusted to 5.5 with glacial acetic acid, and solvent B was 5 mM ammonium acetate in methanol. A linear gradient system was used to elute the analytes. The mass spectrometer was programmed to admit the de-protonated molecules at m/z 352.7 (IS) and m/z 357.9 (BMS-204352). Standard curves of BMS-204352 were linear (r(2) > or = 0.998) over the concentration range of 0.5-1000 ng/mL. The mean predicted quality control (QC) concentrations deviated less than 5.1% from the corresponding nominal values (ie 4, 80, 400 and 2000 ng/mL); the within- and between-assay precision of the assay were within 5.5% relative standard deviation. Stability of BMS-204352 was confirmed after at least three freeze/thaw cycles and BMS-204532 was stable in dog plasma when stored frozen at or below -20 degrees C for at least 16 weeks in spiked QC samples and for at least 4 1/2 weeks for in vivo study samples. BMS-204352 and IS were stable in the injection solvent at room temperature for at least 24 h. The assay was applied to delineate the pharmacokinetic disposition of BMS-204352 in dogs following a single intravenous dose administration. In conclusion, the assay is accurate, precise, specific, sensitive and reproducible for the pharmacokinetic analysis of BMS-204532 in dog plasma.     

Chiral separation of halogenated amino acids by ligand-exchange capillary electrophoresis

The chiral separation of halogenated amino acids by ligand-exchange CE is described. Halogenated amino acids attracted increasing interest in recent years because of their physiological activities. Different chiral selectors, as there are L-4-hydroxyproline, L-histidine, and N-alkyl derivatives of L-4-hydroxyproline in form of their copper(II) complexes, are compared for their chiral recognition ability for halogenated amino acids. The influence of various parameters, such as selector concentration, pH, organic modifier, and field strength, on the resolution was investigated. All halogenated amino acids investigated were baseline-separated under optimized conditions.     

Preparation of perhydroisoquinolines via the intramolecular Diels-Alder reaction of N-3,5-hexadienoyl ethyl acrylimidates: a formal synthesis of (+/-)-reserpine

The intramolecular Diels-Alder reaction of N-3,5-hexadienoyl ethyl acrylimidates provides an efficient method for the synthesis of cis-fused hexahydroisoquinolones. As a demonstration of the stereochemical control offered by this cycloaddition, two approaches to the construction of the DE rings of reserpine are reported. In the second entry, N-((4-(trimethylsilyl)ethoxymethoxy)methyl-6-benzyloxy-3Z,5E-hexadienoyl)-1-aza-2-ethoxy-1,3-butadiene (40) undergoes cycloaddition to produce as the major product (4aS,7R,8aS)-7-benzyloxy-5-((2-trimethylsilyl)ethoxymethoxy)methyl-3,4,4a,7,8,8a-hexahydroisoquinol-3-one (41). Cycloadduct 41 is then stereospecifically elaborated to (4aS,5S,6R,7R,8aR)-6-methoxy-5-methoxycarbonyl-7-(3,4,5-trimethoxy)benzoyldecahydroisoquinoline-2-carboxylic acid methyl ester (3), a key intermediate previously transformed to reserpine.