Free energy perturbation study of water dimer dissociation kinetics

An efficient approach is described for using accurate ab initio calculations to determine the rates of elementary condensation and evaporation processes that lead to nucleation of aqueous aerosols. The feasibility of the method is demonstrated in an application to evaporation rates of water dimer at 230 K. The method, known as ABC-FEP (ab initio/classical free energy perturbation), begins with a calculation of the potential of mean force for the dissociation (evaporation) of small water clusters using a molecular dynamics (MD) simulation with a model potential. The free energy perturbation is used to calculate how changing from the model potential to a potential calculated from ab initio methods would alter the potential of mean force. The difference in free energy is the Boltzmann-weighted average of the difference between the ab initio and classical potential energies, with the average taken over a sample of configurations from the MD simulation. In principle, the method does not require a highly accurate model potential, though more accurate potentials require fewer configurations to achieve a small sampling error in the free energy perturbation step. To test the feasibility of obtaining accurate potentials of mean force from ab initio calculations at a modest number of configurations, the free energy perturbation method has been used to correct the errors when some standard models for bulk water (SPC, TIP4P, and TIP4PFQ) are applied to water dimer. To allow a thorough exploration of sampling issues, a highly accurate fit to results of accurate ab initio calculations, known as SAPT-5s, as been used a proxy for the ab initio calculations. It is shown that accurate values for a point on the potential of mean force can be obtained from any of the water models using ab initio calculations at only 50 configurations. Thus, this method allows accurate simulations of small clusters without the need to develop water models specifically for clusters.     

PHOTOCHEMICAL STUDIES ON THE ANTIINFLAMMATORY DRUG DICLOFENAC

Irradiation with UVA light of the anti-inflammatory drug diclofenac [2-(2,6-dichloroanilino)phenylacetic acid] in aqueous buffer or methanol solution leads to sequential loss of both chlorine substituents and ring closure to carbazole-1-acetic acid as the major product. Minor products result from substitution by the solvent. The photosensitizing properties of diclofenac and its major photoproduct were tested with singlet oxygen substrates and in the free radical polymerization of acrylamide. Although the major carbazole product is a weakly phototoxic agent, able to generate singlet oxygen more efficiently than diclofenac, the free radical photodechlorination process is postulated as the probable initiation step of in vivo photosensitivity responses.     

Linear quadrupoles with added octopole fields

Two methods of adding relatively small octopole fields to the main quadrupole field of quadrupoles and linear ion traps with cylindrical rods are investigated. The first, 'stretching' the quadrupole by moving two rods out from the axis, produces a combination of higher order fields with similar magnitudes in which the octopole field is not necessarily the greatest. The quadrupole field strength is changed significantly and a large potential appears on the axis. The second method uses rod pairs of different diameters. It adds octopole components of up to several percent while all other higher order fields remain small. An axis potential is also added, but it is only a few percent of the radio-frequency (RF) voltage and approximately equal to the strength of the octopole field. The axis potential can be removed by moving the larger rod pair out from the axis or applying unbalanced RF to the electrodes.     

Nickel(II) complexes of a thiosemicarbazone prepared from 2-Acetylpyridine

Summary The ligand 3-azabicyclo[3.2.2]nonane-3-thiocarboxylic acid 2-[1-(2-pyridinyl)ethylidene]hydrazide (HL), which is observed in an unusual tautomeric form in the solid state, and its selenium analogue (HLSe) have been used to prepare a series of nickel(II) complexes. Compounds of the general formula [NiLX] (X=Cl, Br, NCS, N₃, NO₂ or NCSe) as well as [Ni(LSe)Cl] have been found to be diamagnetic, planar complexes. A single crystal study of [NiL(NCS)] shows the deprotonated ligand bound in a tridentate mannervia its pyridyl nitrogen, imine nitrogen and the thione sulphur atom with the nitrogen atom of the thiocyanato-ligand occupying the fourth coordination position. The solids prepared from the nickel(II) salts having tetrafluoroborate, nitrate and iodide ions approximate to octahedral symmetry and have neutral HL ligands coordinated in a bidentate fashionvia the pyridine and imine nitrogens with the remaining coordination sites being occupied by the anions or water molecules. The [NiL₂] solid is also octahedral with the two deprotonated ligands bonding as tridentate groupsvia the same atoms as in the [NiLX] complexes.     

Controlling the outcome of an N-alkylation reaction by using N-oxide functional groups

Covalent modifiers of proteins are of importance in chemical proteomics, an emerging chemical technology used to assign protein function. In this study, high-field (1)H NMR techniques were used to analyze the reaction of the bioactive compound, 2,3-bis(bromomethyl)quinoxaline 1,4-dioxide, with amines (a model system for proteins containing nitrogen-based nucleophiles). Unexpectedly, the results show that a double nucleophilic substitution reaction involving 2 equiv of the amine is preferred to an intramolecular cyclization pathway. A direct comparison with the reaction carried out on a substrate lacking the N-oxide functional groups is also provided. X-ray crystal structures and computational studies are used to rationalize the observed differences in reactivity between the two systems.     

Gene expression analysis for high throughput screening applications

To meet growing needs for high throughput gene expression profiling, we established a new automated high throughput TaqMan RT-PCR method for quantitative mRNA expression analysis. In this method, the Allegro( trade mark ) (Zymark) system conducts all sample tracking and liquid handling steps, and ABI PRISM 7900 HT (Applied Biosystems) is used to conduct real-time determination of the C(t) value when amplification of PCR products is first detected and accumulation of inhibitory PCR products is unlikely to occur. The ABI PRISM 7900 HT Sequence Detection System features a real-time PCR instrument with 384-well-plate compatibility and robotic loading, and continuous wavelength detection, which enables the use of multiple fluorophores in a single reaction. The Allegro System offers an assembly line approach with a modular design that allows reconfiguration of the components to accommodate variations in the assay flow. In the present study, we have established and validated a new automated High Throughput (HT) TaqMan RT-PCR- based method for quantitative mRNA expression analysis. The data demonstrate that HT-Taqman PCR is a powerful tool that can be used for measuring low concentrations of mRNA, and is highly accurate, reproducible, and amenable to high throughput analysis. Results suggest that HT-TaqMan is a reliable method for the quantification of low-expression genes and a powerful tool with HT capability for target identification/validation, structure-activity relationship (SAR) study, compound selection for efficacy studies, and biomarker identification in drug discovery and development.     

Isoindole Cycloadditions. Part III: The Synthesis of "Windscreen Wiper" and Other N-Bridged Cavity Systems

The thermal addition of N-carbobenzyloxyisoindole (N-Z isoindole) 11a, generated by the reaction of 3,6-di(2-pyridyl)-s-tetrazine 9 with N-Z 7-azabenzonorbornadiene 8a, onto dimethyl tricyclo[4.2.1.0^2.5]nona-3,7-diene-3,4-dicarboxylate 17 occurred site selectively at the cyclobutene -bond to form a stereoisomeric mixture of 1 : 1-adducts 18 and 19, in which the bent-frame isomer 19 was dominant (ratio 5 : 1). In contrast, N-benzyl tetrafluoroisoindole 11c reacted with 17 only under high-pressure conditions (14 kbar, RT, 4 days) to afford 1 : 1-adducts at the cyclobutene site, in which the extended-frame isomer 18c was dominant and the accompanying bent-frame product 19c reverted to starting materials soon after isolation. These same stereoselectivities were used to prepare "windscreen wiper" compound 28c having two mobile N-benzyl substituents attached to a rigid scaffold by the reaction of N-benzyl tetrafluoroisoindole 11c with tetramethyl tetracyclo[4.4.1.0.^2,5.0^7.10]undeca-3,8-diene-3,4,7,8-tetracarboxylate 23. Cavity bis-(cyclobutene-1,2-diester) 6 reacted with N-benzyl tetrafluoroisoindole 11c twice over to produce cavity structure 36 with two O- and two N-benzyl bridges on the inner face, whereas the narrower cavity bis-alkene 32 stopped at the 1 : 1-addition stage. The dynamics of the Z-group in the dual adducts 26a–28a are discussed briefly and key adducts and cavity systems have been structurally evaluated by X-ray crystallography, VT NMR, and molecular modeling.     

Synthesis and characterization of the new 22-π aromatic furan-containing macrocycle, “ozaphyrin”

The new 22-π, aromatic “pentaplanar” macrocycle, ozaphyrin ( 6 ), has been synthesized by a McMurry coupling of 5,5′-diformyl-4,4′-dipropyl-2,2′-bipyrrole ( 1 ) with 2,5-bis(5-formyl-4-propyl-2-pyrrolyl)furan ( 5 ). This synthetic pathway to ozaphyrin and its characterization by ¹H nmr spectroscopy, uv-visible spectroscopy, cyclic voltammetry, and X-ray crystallography are described. The structure consists of layers of planar, staggered macrocycles stacked perpendicular to the α-axis. Ozaphyrin crystallizes with four formula units in the monoclinic space group C⁵_2h-P2₁/n in a cell of dimensions a = 10.481(7) Å, b = 17.353(17) Å, c = 18.726(12) Å, and β = 102.84(5)° (108 K). The structure has been refined on F² (5171 unique reflections, 411 variables) to R_w(F_o²) = 0.165. The conventional agreement index R(F) is 0.074 for the 3289 reflections have F_o²>2o(F_o²).     

Determination of retinyl palmitate (vitamin A) in fortified fluid milk by liquid chromatography: collaborative study

A liquid chromatographic (LC) method was developed for fast and simple measurement of retinyl palmitate (vitamin A) in fortified milk. Retinyl acetate internal standard was added to a test portion of milk followed by extraction into hexane. The hexane extract was analyzed by LC using a normal-phase silica gel column equilibrated with mobile phase (conditioned hexane-isopropanol, 99.85 + 0.15, v/v) about 1 h before injections. The retinyl palmitate concentration was calculated by using a relative response factor determined with calibration standards. In the collaborative study, 11 laboratories analyzed 13 pairs of fluid milk materials in blind duplicate. Twelve of the materials were composed of skim milk (< 0.5% fat), 1% fat milk, 2% fat milk, and 1% fat chocolate milk. Each material was fortified at 3 concentrations of retinyl palmitate of approximately 581 microg/L (1000 IU/qt), 1163 microg/L (2000 IU/qt), and 2236 microg/L (4000 IU/qt). The 13th material, unfortified skim milk, served as a matrix blank. Repeatability standard deviations (RSDr) without outliers ranged from 1.5 to 5.7% and reproducibility standard deviations (RSDR) without outliers ranged from 5.0 to 22.7%. cis-Isomers co-eluted with the predominant trans-retinyl palmitate isomer and were included in the results reported by all the collaborative laboratories. Endogenous long-chain esters from milk fat were also measured with the retinyl palmitate additive. The Study Director recommends that this method for determination of retinyl palmitate in fluid milk by LC be adopted First Action.