Infrared diffuse reflectance instrumentation and standards at NIST

A spectrophotometer system for spectral characterization of materials in the infrared has been built around a bench-top Fourier transform instrument. Its capabilities include the measurement of directional-hemispherical reflectance from 1 to 18 μm. The spectral reflectance measurement is performed with an integrating sphere with an incidence angle of 8°. Both relative and absolute measurements can be made. Several methods can be used to determine the absolute value of the directional-hemispherical reflectance of samples. The primary method used is independent of the integrating sphere theory and the requisite assumptions associated with its use. The calibration of a standard reference material (SRM) is described. This SRM has a reflectance value near 0.9 over the complete calibration range 2–18 μm. As part of the calibration procedure the spatial uniformity of the sphere throughput and the bi-directional reflectance distribution function (BRDF) of the SRM material are evaluated.     

A supramolecular assembly containing an unusually short n‐h…n hydrogen bond ‐ an x‐ray and neutron diffraction study

A supramolecular assembly formed between phthalimide and 2‐guanidinobenzimidazole, containing a short 2.692(4)AR N‐H…N hydrogen bond, is reported. The crystal structure of this species was determined by both X‐ray and neutron diffraction. The diffraction data reveal that the proton involved in the short hydrogen bond has been transferred from the phthalimide to the guanidinobenzimidazole to form an ion pair. There is also an interesting stacking interaction between the atoms involved in the short hydrogen bond and the π system of a phthalimide molecule that is approximately 3.3 Å away. The structure is compared with the structure of a similar assembly formed between 4‐nitrophthalimide and 2‐guanidinobenzimidazole.     

Ion Mobility Mass Spectrometry Measures the Conformational Landscape of p27 and its Domains and how this is Modulated upon Interaction with Cdk2/cyclin A

Intrinsically disordered proteins have been reported to undergo disorder‐to‐order transitions upon binding to their partners in the cell. The extent of the ordering upon binding and the lack of order prior to binding is difficult to visualize with classical structure determination methods. Binding of p27 to the Cdk2/cyclin A complex is accompanied by partial folding of p27 in the KID domain, with the retention of dynamic behavior for function, particularly in the C‐terminal half of the protein. Herein, native ion mobility mass spectrometry (IM‐MS) is employed to measure the intrinsic dynamic properties of p27, both in isolation and within the trimeric complex with Cdk2/cyclin A. The trimeric Cdk2/cyclin A/p27‐KID complex possesses significant structural heterogeneity compared to Cdk2/cyclin A. These findings support the formation of a fuzzy complex in which both the N‐ and C‐termini of p27 interact with Cdk2/cyclin A in multiple, closely associated states.     

Minimally corrected partial atomic charges for non-covalent electrostatic interactions

We develop a new scheme for determining molecular partial atomic charges (PACs) with external electrostatic potential (ESP) closely mimicking that of the molecule. The PACs are the ‘minimal corrections’ to a reference set of PACs necessary for reproducing exactly the tensor components of the Cartesian zero-, first- and second- molecular electrostatic multipoles. We evaluate the quality of ESP reproduction when ‘minimally correcting’ (MC) Mulliken, Hirshfeld or iterative-Hirshfeld reference PACs. In all these cases, the MC-PACs significantly improve the ESP while preserving the reference PACs’ invariance under the molecular symmetry operations. When iterative-Hirshfeld PACs are used as reference, the MC-PACs yield ESPs of comparable quality to those of the ChElPG charge fitting method.     

Effect of an aliphatic spacer group on the adsorption mechanism on the colloidal silver surface of L‐proline phosphonodipeptides

A comparative study of molecular structures of five L ‐proline (L ‐Pro) phosphonodipeptides: L ‐Pro‐NH‐C(Me,Me)‐PO₃H₂ (P1), L ‐Pro‐NH‐C(Me,iPr)‐PO₃H₂ (P2), L ‐Pro‐L ‐NH‐CH(iBu)‐PO₃H₂ (P3), L ‐Pro‐L ‐NH‐CH(PA)‐PO₃H₂ (P4) and L ‐Pro‐L ‐NH‐CH(BA)‐PO₃H₂ (P5) has been carried out using Raman and absorption infrared techniques of molecular spectroscopy. The interpretation of the obtained spectra has been supported by density functional theory calculations (DFT) at the B3LYP; 6–31 + + G** level using Gaussian 2003 software. The surface‐enhanced Raman scattering (SERS) on Ag‐sol in aqueous solutions of these phosphonopeptides has also been investigated. The surface geometry of these molecules on a silver colloidal surface has been determined by observing the position and relative intensity changes of the Pro ring, amide, phosphonate and so‐called spacer (−R) groups vibrations of the enhanced bands in their SERS spectra. Results show that P4 and P5 adsorb onto the silver as anionic molecules mainly via the amide bond (∼1630, ∼1533, ∼1248, ∼800 and ∼565 cm⁻¹), Pro ring (∼956, ∼907 and ∼876 cm⁻¹) and carboxylate group (∼1395 and ∼909 cm⁻¹). Coadsorption of the imine nitrogen atom and PO group with the silver surface, possibly by formation of a weaker interaction with the metal, is also suggested by the enhancement of the bands at 1158 and 1248 cm⁻¹. P1, P2 and P3 show two orientations of their main chain on the silver surface resulting from different interactions of the  C CH₃,  NH and  CONH fragments with this surface. Bonding to the Ag surface occurs mainly through the imino atom (1166 cm⁻¹) for P2, while for P1 and P3 it occurs via the methyl group(s) (1194–1208 cm⁻¹). The amide group functionality (CONH) is practically not involved in the adsorption process for P1 and P2, whereas the C_s P bonds do assist in the adsorption. Copyright © 2008 John Wiley & Sons, Ltd.     

Experimental and theoretical studies of the basicity and proton affinity of SiF4 and the structure of SiF4H+

A combined experimental and theoretical approach has been employed to establish the basicity and proton affinity of SiF₄ and the structure of SiF₄H⁺. The kinetics and energetics for the transfer of a proton between SiF₄, N₂, and Xe have been explored experimentally in helium at 0.35±0.02 torr and 297±3 K with a selected-ion flow tube apparatus. The results of equilibrium constant measurements are reported that provide a basicity and proton affinity for SiF₄ at 297±3 K of 111.4±1.0 and 117.7±1.2 kcal mol^?1, respectively. These values are more than 2.5 kcal mol^?1 lower than currently recommended values. The basicity order was determined to be GB(Xe)>GB(SiF₄)>GB(N₂), while the proton-affinity order was shown to be PA(Xe)>PA(N₂)>PA (SiF₄). Ab initio molecular orbital computations at MP4SDTQ(fc)/6-311++G(3df,3pd) using geometries from B3LYP/6-31+G(d,p) indicate a value for PA(SiF₄)=118.7 kcal mol^?1 that is in good agreement with experiment. Also, the most stable structure of SiF₄H⁺ is shown to correspond to a core SiF ₃ ⁺ cation solvated by HF with a binding energy of 43. 9 kcal mol^?1. Support for this structure is found in separate SIFT collision induced dissociation (CID) measurements that indicate exclusive loss of HF.     

Studies into the Early Degradation Stages of Cellulose by Different Iron Gall Ink Components

Selective fluorescence labelling of oxidized cellulose functionalities followed by GPC-MALLS was used to get a deeper insight into ink-induced degradation processes. As the method is very sensitive towards oxidation and molecular weight changes, slight variations at the very beginning of aging processes, e.g. during ink corrosion of cellulose, can be studied. Five different ink modifications were applied on model papers and underwent mild accelerated aging at 55 °C and cycling humidity (7 days) followed by a short period of static humid aging at 80 °C (2 days). Pure ink constituents like tannic acid or iron sulphate do not result in the same degree of oxidation or chain scission as complete inks. Balanced ink degrades paper more than single compounds, but less than unbalanced inks. Interestingly, some degradation occurs already during or shortly after the application process of unbalanced inks on paper. It could be demonstrated that this oxidation proceeded in a rather high Mw area, while the subsequent aging steps affected predominantly regions of shorter cellulose chains.