IR Probes Research Articles

Nitrile and thiocyanate IR probes: Molecular dynamics simulation studies

Nitrile- and thiocyanate-derivatized amino acids have been found to be useful IR probes for investigating their local electrostatic environments in proteins. To shed light on the CN stretch frequency shift and spectral lineshape change induced by interactions with hydrogen-bonding solvent molecules, we carried out both classical and quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations for MeCN and MeSCN in water. These QM/MM and conventional force field MD simulation results were found to be inconsistent with the experimental results as well as with the high-level ab initio calculation results of MeCN-water and MeSCN-water potential energies. Thus, a new set of atomic partial charges of MeCN and MeSCN is obtained. By using the MD simulation trajectories and the electrostatic potential model recently developed, the CN and SCN stretching mode frequency trajectories were obtained and used to simulate the IR spectra. The C[Triple Bond]N frequency blueshifts of MeCN and MeSCN in water are estimated to be 9.0 and 1.9 cm(-1), respectively, in comparison with those of gas phase values. These values are found to be in reasonable agreement with the experimentally measured IR spectra of MeCN, MeSCN, beta-cyano-L-alanine, and cyanylated cysteine in water and other polar solvents.

Nitrile and thiocyanate IR probes: Quantum chemistry calculation studies and multivariate least-square fitting analysis

Hydration effects on the C[Triple Bond]N stretching mode frequencies of MeCN and MeSCN are investigated by carrying out ab initio calculations for a number of MeCN-water and MeSCN-water complexes with varying number of water molecules. It is found that the CN frequency shift induced by the hydrogen-bonding interactions with water molecules originate from two different ways to form hydrogen bonds with the nitrogen atom of the CN group. Considering the MeCN- and MeSCN-water cluster calculation results as databases, we first examined the validity of vibrational Stark effect relationship between the CN frequency and the electric field component parallel to the CN bond and found no strong correlation between the two. However, taking into account of additional electric field vector components is a simple way to generalize the vibrational Stark theory for the nitrile chromophore. Also, the electrostatic potential calculation method has been proposed and examined in detail. It turned out that the interactions of water molecules with nitrogen atom's lone pair orbital and with nitrile pi orbitals can be well described by the electrostatic potential calculation method. The present computational results will be of use to quantitatively simulate various linear and nonlinear vibrational spectra of nitrile compounds in solutions.

Effect of surface coverage on the conformation and mobility of C18-modified silica gels

C18-modified silica gels with surface coverages of 2 to 8.2 micromol m(-2), were prepared by different synthetic pathways and characterized by Fourier Transform infrared spectroscopy (FTIR), solid-state nuclear magnetic resonance (NMR) spectroscopy, and chromatographic measurements. The effects of temperature and bonding density on the conformational order of C18-modified silica gels were studied in detail by FTIR spectroscopy. The silane functionality and degree of cross-linking of silane ligands on the silica surface were evaluated by 29Si cross-polarization magic-angle spinning (CP/MAS) NMR and the structural order and mobility of the alkyl chains were investigated by 13C CP/MAS NMR spectroscopy. CH2 symmetric and anti-symmetric stretching bands and CH2 wagging bands were used as IR probes to monitor the conformational order and flexibility of the alkyl chains in the C18 phases. Qualitative information about the conformational order was obtained from frequency shifts of the CH2 symmetric and anti-symmetric stretching bands. The relative amounts of kink/gauche-trans-gauche, double-gauche, and end-gauche conformers in the alkyl chains were determined by analysis of CH2 wagging bands. These results indicate that surface coverage plays a dominant role in the conformational order of C18-modified silica gels. The FTIR and NMR data are discussed in the context of the chromatographic shape-selectivity differences.

FT-IR study of CO and NO adsorption on a VSiBEA zeolite

A VSiBEA zeolite containing 2.1 wt.% V has been prepared by a two-step post-synthesis method, which consists of first creating vacant T-sites by dealumination of the BEA zeolite with nitric acid and then impregnation of the SiBEA zeolite with an aqueous solution of ammonium metavanadate (NH 4VO 3), used as V 5+ precursor. The sample has been studied by XRD analysis, FT-IR, TPR and diffuse reflectance UV–Visible spectroscopy. The disappearance of the IR band near 3520 cm −1 after impregnation of NH 4VO 3 indicates that a specific reaction has occurred between the vanadium precursor and silanol groups of vacant T-sites. As a result, tetrahedral V 5+ ions connected with OH groups are incorporated in the framework. In addition, weakly bound extraframework V 5+ species (tetrahedral and octahedral) exists. CO and NO were used as IR probes for establishing the state of reduced vanadium sites. It was found that NO was a better probe for this purpose, but CO provided valuable complementary information on the coordination state of the reduced vanadium sites. As expected, adsorption of both, CO and NO, was negligible on non-reduced sample. However, sample reduced with hydrogen at 673 K is characterised by a high concentration of V 4+ and V 3+ sites produced by the reduction of the extraframework sites. NO was found to form dinitrosyls with both V 4+ and V 3+ cations. The V 4+(NO) 2 species are characterised by ν s at 1902 cm −1 and ν as at 1755 cm −1. The dinitrosyls of V 3+ were registered at 1830 ( ν s) and 1687 cm −1 ( ν as). Reduction at 773 K led to increase in amount of the V 3+ species and formation of framework V 4+ cations (respective dinitrosyl bands at 1900 and 1729 cm −1). The spectra of CO adsorbed on the reduced sample are complex. Evidence of tricarbonyl species was found. It was concluded that CO is a better probe than NO for testing the coordination state of V 4+ and V 3+ sites.

13C‐Labeled Tyrosine Residues as Local IR Probes for Monitoring Conformational Changes in Peptides and Proteins

¹³C‐Labeled Tyrosine Residues as Local IR Probes for Monitoring Conformational Changes in Peptides and Proteins

Preparation and characterization of poly(amidoamine) dendrimers functionalized with a rhenium carbonyl complex and PEG as new IR probes for carbonyl metallo immunoassay

The first poly(amidoamine) (PAMAM) dendrimers tethered with both (η 5-cyclopentadienyl) rhenium tricarbonyl (CpRe(CO) 3) units and polyethylene glycol (PEG) chains were prepared and characterized by combining NMR spectroscopy and Fourier-transform IR spectroscopy. Grafting of CpRe(CO) 3 units was achieved by reductive amination of formyl-CpRe(CO) 3 with the peripheral amines of generation 3 and 4 PAMAMs to yield dendrimers labeled with a variable number of CpRe(CO) 3 units, ranging from 8 to 14 for PAMAM-G3 and 17–30 for PAMAM-G4. PEG chains of different lengths were then attached to some of the remaining peripheral amines, and their respective ability to improve the solubility of the metallodendrimers in aqueous buffered media was evaluated. These metallodendrimers represent new infrared probes designed to be coupled to immunological reagents for the amplification of the IR signal in carbonyl metallo immunoassay (CMIA).

Submicron resolution infrared microscopy by use of a near-field scanning optical microscope with an apertured cantilever

We extend the spectral range of near-field infrared microscopy attaining submicron resolution by using tunable infrared radiation generated by difference frequency generation and an apertured cantilever. The custom-built cantilever has a hollow tip with a wide opening angle and offers two orders of magnitude higher optical throughput than that of other IR probes. In near-field observation of a line/space structured poly(methylmethacrylate) film at a 5.78 μm wavelength corresponding to absorption band of the C=O bonds, the microscope achieved a λ/7 spatial resolution, less than 1 μm. This shows the possibility of submicron resolution infrared microscopy in the fingerprint region.

NO + ions as IR probes for the location of OH groups and Na + ions in main channels and side pockets of mordenite

NO +, generated from NO and O 2, is an infrared probe for the differentiation of Brønsted sites in the main channels and side pockets of mordenites, and for the location and accessibility of sodium ions in the structure. Na + ions in cationic positions in the main channels are replaced by NO +, and sodium nitrate is formed. The band assignment was checked by isotopic experiments.

Identification of the basic sites on nitrided mixed galloaluminophosphates “AlGaPON” catalysts used for the Knoevenagel condensation between benzaldehyde and malononitrile

This work deals with the identification of the basic sites on nitrided mixed galloaluminophosphates “AlGaPON”, active in the Knoevenagel condensation between benzaldehyde and malononitrile. The strategy was to compare the properties of five samples, one oxide and four oxynitrides obtained by heating an amorphous Al0.5Ga0.5PO4 precursor under ammonia flow at 750°C for various periods of time. Two acidic molecules, sulfur dioxide and deuterated chloroform were used as IR probes of the basic sites. By comparing the IR spectra recorded before and after adsorption it has been evidenced that the probes interacted specifically with surface –NH2 groups. It was then concluded that those –NH2 groups present at the “ AlGaPON” surface were the basic sites responsible for the “AlGaPON” basic catalytic properties. In addition, on untreated oxynitrides, ammonia chemisorbed on Brönsted and for Lewis acid sites influences the course of the Knoevenagel reaction.

Accurate Measurement of Extrudate Temperature and Heat Loss On A Twin‐Screw Extruder

ABSTRACTInfrared (IR), extended melt and flush thermocouple probes were used to measure bulk temperatures of extrudates. Good agreement was obtained between IR and extended probes. However, substantial differences were observed between IR and flush mounted probes and between extended and flush mounted probes. A response surface methodology was used to study effects of moisture screw speed, and barrel temperature on measured temperature differences between IR and flush probes. The standard flush probe may not accurately measure bulk temperature of the extrudate. The heat flux from the surfaces (top, bottom, and side) of a twin‐screw extruder barrel was also measured. Total heat loss from the surface varied between 2–19% of the total heat input.

Methylene wagging modes of unsaturated acyl chains as IR probes of conformational order in methyl alkenoates and phospholipid bilayers

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMethylene wagging modes of unsaturated acyl chains as IR probes of conformational order in methyl alkenoates and phospholipid bilayersNian Cherng Chia and Richard MendelsohnCite this: J. Phys. Chem. 1992, 96, 25, 10543–10547Publication Date (Print):December 1, 1992Publication History Published online1 May 2002Published inissue 1 December 1992https://doi.org/10.1021/j100204a076RIGHTS & PERMISSIONSArticle Views206Altmetric-Citations38LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (668 KB) Get e-Alerts

Methylene wagging progressions as IR probes of slightly disordered phospholipid acyl chain states

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMethylene wagging progressions as IR probes of slightly disordered phospholipid acyl chain statesLaurence Senak, David Moore, and Richard MendelsohnCite this: J. Phys. Chem. 1992, 96, 6, 2749–2754Publication Date (Print):March 1, 1992Publication History Published online1 May 2002Published inissue 1 March 1992https://doi.org/10.1021/j100185a064RIGHTS & PERMISSIONSArticle Views233Altmetric-Citations89LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (778 KB) Get e-Alerts

Chelating phosphines on silica gel: I. carbonyl complexes as a mean to probe chelating ligand sites

Two methods for the preparation of the silica-bound chelating phosphine ligand bis(diphenylphosphino)maleimide have been studied. In the first a silica surface with bound amine groups is treated with bis(diphenylphosphino)maleic acid anhydride. By use of different Group VI carbonyl complexes M(CO) 6, M(CO) 4L (M  Cr, Mo, W; L  norbnornadiene) and M(CO) 5Cl − as IR probes it is shown that this method yields two different types of metal-binding sites on the gel, involving amine groups and bidentate phosphine groups, respectively. In the second method bis(diphenylphosphino)maleic acid anhydride is treated with 3-aminopropyltriethoxysilane and the imide formed by this reaction is, without isolation, further condensed on the silica surface. Use of the same type of IR probes as in the first route shows that the silica gel in this case contains the bidentate phosphine group as the sole metal-binding site. The preparations of new metal tetracarbonyl complexes for Cr, Mo and W bound to silica via bidentate phosphino groups are described.