Low-temperature NMR studies of the structure and dynamics of a novel series of acid-base complexes of HF with collidine exhibiting scalar couplings across hydrogen bonds

The low-temperature (1)H, (19)F, and (15)N NMR spectra of mixtures of collidine-(15)N (2,4,6-trimethylpyridine-(15)N, Col) with HF have been measured using CDF(3)/CDF(2)Cl as a solvent in the temperature range 94-170 K. Below 140 K, the slow proton and hydrogen bond exchange regime is reached where four hydrogen-bonded complexes between collidine and HF with the compositions 1:1, 2:3, 1:2, and 1:3 could be observed and assigned. For these complexes, chemical shifts and scalar coupling constants across the (19)F(1)H(19)F and (19)F(1)H(15)N hydrogen bridges have been measured which allowed us to determine the chemical composition of the complexes. The simplest complex, collidine hydrofluoride ColHF, is characterized at low temperatures by a structure intermediate between a molecular and a zwitterionic complex. Its NMR parameters depend strongly on temperature and the polarity of the solvent. The 2:3 complex [ColHFHCol](+)[FHF](-) is a contact ion pair. Collidinium hydrogen difluoride [ColH](+)[FHF](-) is an ionic salt exhibiting a strong hydrogen bond between collidinium and the [FHF](-) anion. In this complex, the anion [FHF](-) is subject to a fast reorientation rendering both fluorine atoms equivalent in the NMR time scale with an activation energy of about 5 kcal mol(-)(1) for the reorientation. Finally, collidinium dihydrogen trifluoride [ColH](+)[F(HF)(2)](-) is an ionic pair exhibiting one FHN and two FHF hydrogen bonds. Together with the [F(HF)(n)()](-) clusters studied previously (Shenderovich et al., Phys. Chem. Chem. Phys. 2002, 4, 5488), the new complexes represent an interesting model system where the evolution of scalar couplings between the heavy atoms and between the proton and the heavy atoms of hydrogen bonds can be studied. As in the related FHF case, we observe also for the FHN case a sign change of the coupling constant (1)J(FH) when the F.H distance is increased and the proton shifted to nitrogen. When the sign change occurs, that is, (1)J(FH) = 0, the heavy atom coupling constant (2)J(FN) remains very large, of the order of 95 Hz. Using the valence bond order model and hydrogen bond correlations, we describe the dependence of the hydrogen bond coupling constants, of hydrogen bond chemical shifts, and of some H/D isotope effects on the latter as a function of the hydrogen bond geometries.     

Calculations of the contribution of ring currents to the chemical shielding anisotropy

Ring currents can exert a large effect upon the chemical shielding of NMR resonances. The analytical expression developed by Waugh and Fessenden (Waugh, J. S.; Fessenden, R. W. J. Am. Chem. Soc. 1957, 79, 846) and Johnson and Bovey (Johnson, C. E.; Bovey, F. A. J. Chem. Phys. 1957, 29, 1012) only quantifies the contribution of ring currents to the isotropic component of the shielding tensor. In the work described here an additional analytical expression is developed so that the contribution of ring currents to the full shielding tensor can be calculated, allowing an estimate of the influence of ring currents upon the chemical shielding anisotropy (CSA, Deltasigma). To test that this pair of analytical expressions can provide a reasonable estimate of the contribution of ring currents to the full shielding tensor a series of density functional calculations (DFT) were carried out. A shielding tensor in a model compound was calculated in two distinct ways. For the first series, DFT shielding calculations of the model compound were carried out in the presence of a benzene ring. For the second series a ring current contribution to the shielding tensor was calculated via the new expressions, and this was added to the result of a DFT shielding calculation which used in place of benzene the nonaromatic analogue 1,3 cyclohexadiene. The two series of results proved to be in excellent agreement. The pair of analytical expressions are used to calculate ring current contributions to the CSA (Deltasigma) of 1H(N) backbone amide resonances in a structure of the second type 2 module from the protein fibronectin. Significant CSA variations are predicted in particular for the 1H(N) of G42 which is most likely involved in a N-H...tpi aromatic hydrogen bond.     

Approaches to understanding the searching behavior of CrossFire users

Due to the high costs of purchasing, supporting and training users of desktop chemical information systems, it is important to understand users' behavior in order that deficiencies in their search efficiency and effectiveness can be identified and addressed. CrossFire generates comprehensive log files that can be examined to determine the nature of search activity. At GSK (GlaxoSmithKline) a Log File Parser, CrossParse, has been developed in Visual Basic that enables analysis by individual user name, groups of users or the whole user population. Log files can be analyzed for occasions when specific structural features are built, specific types of search are done and how the results are manipulated. CrossParse produces output that can be saved and analyzed within Microsoft Excel. It also allows determination of numbers of active concurrent users on the CrossFire system. CrossParse has been used at GSK (ex-SmithKline Beecham sites) to examine the search behavior of medicinal and synthetic chemists. Additionally, it has been used by MIMAS (Manchester Information and Associated Services) to compare the search behavior of trained and untrained users in the higher education community and to identify any areas where improvements to training can be made. Use of CrossParse in both organizations has allowed identification of areas where users may have difficulties using CrossFire. This will provide valuable feedback to MDL Inc., the authors of the CrossFire application, and guide them in enhancing CrossFire.     

Structure of ions [ZnNCR]+ and [Zn(NCR)2]+ (R = H,CH3) in the gas phase

Structures of [ZnNCR]⁺ and [Zn(NCR)₂]⁺ ions (R = H, Me), which are abundant in the mass spectra of many types of coordination compounds, were studied by the MNDO method. In all cases the most stable isomers correspond to the zinc ion coordinated with the nitrogen(s) of the nitrile ligand. For [Zn(NCR)₂]⁺, the N-Zn-N angles are ～108°.     

A new spin probe of protein dynamics: nitrogen relaxation in 15N-2H amide groups

(15)N spin relaxation data have provided a wealth of information on protein dynamics in solution. Standard R(1), R(1)(rho), and NOE experiments aimed at (15)N[(1)H] amide moieties are complemented in this work by HA(CACO)N-type experiments allowing the measurement of nitrogen R(1) and R(1)(rho) rates at deuterated (15)N[(2)D] sites. Difference rates obtained using this approach, R(1)((15)N[(1)H]) - R(1)((15)N[(2)D]) and R(2)((15)N[(1)H]) - R(2)((15)N[(2)D]), depend exclusively on dipolar interactions and are insensitive to (15)N CSA and R(ex) relaxation mechanisms. The methodology has been tested on a sample of peptostreptococcal protein L (63 residues) prepared in 50% H(2)O-50% D(2)O solvent. The results from the new and conventional experiments are found to be consistent, with respect to both local backbone dynamics and overall protein tumbling. Combining several data sets permits evaluation of the spectral density J(omega(D) + omega(N)) for each amide site. This spectral density samples a uniquely low frequency (26 MHz at a 500 MHz field) and, therefore, is expected to be highly useful for characterizing nanosecond time scale local motions. The spectral density mapping demonstrates that, in the case of protein L, J(omega(D) + omega(N)) values are compatible with the Lipari-Szabo interpretation of backbone dynamics based on the conventional (15)N relaxation data.     

Crystal and molecular structure of 9-methyl-9-phenyl-9,10-dihydro-9-sila-3-azaanthrone

The crystal and molecular structure of 9-methyl-9-phenyl-9,10-dihydro-9-sila-3-azaanthrone has been determined from three-dimensional X-ray diffraction data. The title compound crystals are monoclinic, space group P2₁/b, a = 12.818(2), b = 16.508(2), c = 7.694(1) Å,γ = 105°, 34′(2), Z = 4 and D_cal = 1.278 g cm^?3. The structure was determined by direct methods and refined by full-matrix least-squares calculations in the block-diagonal anisotropic approximation for non-hydrogen atoms to R = 0.043 for 2190 independent reflections, registered at room temperature. This is the first crystal structure determination of a Si-dihydroanthracene derivative with two heterocycles and a planar carbon atom in the C10-position. The tricyclic fragment takes up a planar configuration, the silicon atom having a tetrahedral surrounding, with an endocyclic angle of 103.7(1)° and average bond length SiC, 1.862(1) Å. The CO, 1.220(2) Å, bond length in the carbonylic group exactly corresponds with the double bond length. Average distance NC is 1.335(3) Å, angle CNC, 116.5(2)°.     

Analysis of hot D2O emission using spectroscopically determined potentials

Fourier transform emission spectra of D2O vapor were recorded at a temperature of 1500 degrees C in the wavenumber range 380-1880 cm(-1). 15 346 lines were measured, of which the majority were identified as belonging to D2O. The spectrum was analyzed using variational nuclear motion calculations based on spectroscopically determined potential-energy surfaces. Initial assignments were made using a potential surface obtained by fitting a high accuracy ab initio potential. The new assignments were used to refine the potential surface, resulting in additional assignments. A total of 6400 D2O transitions were assigned and 2144 new D2O energy levels were obtained. Transitions involving the 4nu2 and 5nu2 bending states, with band origins of 4589.30 (+/-0.02) and 5679.6 (+/-0.1) cm(-1), respectively, were assigned for the first time.     

Drastic difference in lifetimes of the charge-separated state of the formanilide-anthraquinone dyad versus the ferrocene-formanilide-anthraquinone triad and their photoelectrochemical properties of the composite films with fullerene clusters

A long-lived charge-separated (CS) state, which can be observed even at 900 mus after laser excitation, has been attained in the formanilide-anthraquinone dyad (FA-AQ) in dimethyl sulfoxide, whereas the CS lifetime is shortened significantly to 20 ps in the ferrocene-formanilide-anthraquinone triad (Fc-FA-AQ). Such a drastic decrease in the CS lifetime by the addition of a ferrocene moiety to the FA-AQ dyad is ascribed to a decrease in the driving force of back electron transfer and an increase in the reorganization energy of electron transfer despite the longer charge-separation distance. The FA-AQ dyad and the Fc-FA-AQ triad have been employed as components of photovoltaic cells, where composite molecular nanoclusters of the FA-AQ dyad or the Fc-FA-AQ triad with fullerene (C60) are assembled onto a SnO2 electrode using an electrophoretic method. The composite films of the Fc-FA-AQ triad exhibit 10 times smaller values of an incident photon-to-photocurrent efficiency (IPCE) as compared with those of the FA-AQ dyad in accordance with a drastic decrease of the CS lifetime by addition of a ferrocene moiety to the FA-AQ dyad.     

Analysis of aqueous 2,4,6-trinitrotoluene (TNT) using a fluorescent displacement immunoassay

We report a rapid, simple, and sensitive assay that is potentially amenable to high throughput screening for analysis of 2,4,6-trinitrotoluene (TNT) present in aqueous solutions. The assay is based on the change in fluorescence emission intensity of a fluorescently labeled TNT analogue pre-bound to an anti-TNT antibody that occurs upon its competitive displacement by TNT. The assay can be performed in both cuvette- and 96-well plate-based formats. TNT at a level of 0.5 micro g L(-1) (0.5 ppb) was detected in phosphate buffered saline; detection improved to 0.05 micro g L(-1) (0.05 ppb) for TNT dissolved in artificial seawater.