Matrix merging arrangements for the study protein dynamics by time-resolved step-scan Fourier transform infrared spectroscopy and multivariate curve resolution

In this paper, we propose the construction of merging arrangements for combining the information from various runs as a powerful approach to improve the resolution. The bacteriorhodopsin (bR) photocycle has been chosen in this study as an example dealing with the protein dynamics monitored by means of time-resolved step-scan FT-IR spectroscopy. The possibilities of matrix merging are evaluated and results are compared with those from the analysis of individual and augmented matrices. As a conclusion, this strategy provides excellent results for the analysis of this type of time-resolved FT-IR data.     

Observation of triplet intraligand excited states through nanosecond step-scan Fourier transform infrared spectroscopy

Nanosecond step-scan Fourier transform infrared spectroscopy permits the observation of triplet intraligand ((3)IL) character in the excited states of [Ru(bpy)2(PNI-phen)]2+ and [Ru(PNI-phen)3]2+ where PNI is 4-piperidinyl-1,8-naphthalimide. After pulsed 355-nm laser excitation, the two ground-state imide C=O bands in each compound are bleached and two substantially lower energy vibrations are produced; the lower energy feature appears as two distinct bands split by an overlapping transient bleach. Model studies confirm that the time-resolved vibrational data are consistent with photoinduced sensitization of the 3IL excited state. Density functional theory calculations also support these assignments because localization of triplet electron density on the PNI moiety is expected to lead to red-shifted C=O vibrations of magnitude similar to those measured experimentally. The current results illustrate that triplet electron density can be directly tracked by time-resolved infrared measurements in metal-organic chromophores and that frequency shifts comparable to those observed in charge-transfer systems can be realized.     

Multichannel reaction of C2Cl3 + O2 studied by time-resolved Fourier transform infrared emission spectroscopy

The multichannel reaction of the C(2)Cl(3) radical with O(2) has been studied thoroughly by step-scan time-resolved Fourier transform infrared emission spectroscopy. Vibrationally excited products of Cl(2)CO, CO, and CO(2) are observed and three major reaction channels forming respectively ClCO + Cl(2)CO, CO + CCl(3)O, and CO(2) + CCl(3) are identified. The vibrational state distribution of the product CO is derived from the spectral fitting, and the nascent average vibrational energy of CO is determined to be 59.9 kJ/mol. A surprisal analysis is applied to evaluate the vibrational energy disposal, which reveals that the experimentally measured CO vibrational energy is much more than that predicted by statistical model. Combining previous ab initio calculation results, the nonstatistical dynamics and mechanism are characterized to be barrierless addition-elimination via short-lived reaction intermediates including the peroxy intermediate C(2)Cl(3)OO* and a crucial three-member-ring COO intermediate.     

Nature of water in nacre: a 2D Fourier transform infrared spectroscopic study

In this work, the interactions of aragonite and organic matrix in nacre with water are investigated using two-dimensional (2D) Fourier transform infrared (FTIR) spectroscopy. The 2D-FTIR analysis revealed four bands in the OH stretching region at around 3550, 3445, 3272 and 3074 cm(-1). Two additional bands were found at around 3616 and 3282 cm(-1) after deconvolution of the nacre spectrum. The bands at around 3616 and 3550 cm(-1) are assigned to asymmetric and symmetric OH stretching of partially hydrogen bonded water molecules. The bands at around 3445 and 3272 cm(-1) are assigned to asymmetric and symmetric OH stretching of water molecules fully hydrogen bonded with surrounding water molecules. Presence of above bands in the nacre spectrum suggests that water, in form of clusters, is present in protein matrix and aragonite pores. Water may also hydrogen bond with the organic matrix. The bands observed at 3282 and 3074 cm(-1) are assigned to asymmetric and symmetric OH stretching of water molecules, chemisorbed on surfaces of aragonite platelets. Polarization experiments suggest that H-O-H plane of water molecules is along to c-axis of aragonite platelets.     

Fourier transform infrared study of segmental orientation in polymer blends

The effect of the macromolecular plasticizer poly(-methyl--n-propyl--propiolactone), PMPPL, on the orientation of poly(vinyl chloride), PVC, has been studied by FTIR spectroscopy. The addition of PMPPL to PVC does not change significantly the degree of orientation of PVC segments. In blends, PMPPL chains are more oriented when the matrix is richer in PVC but the PMPPL orientation function always remains smaller than that of PVC segments.     

Fourier transform infrared study of uniaxially oriented atactic polystyrene

Infrared measurements of the dichroic ratio of atactic polystyrene absorption bands provide a valuable method of determination of the overall orientation of chains as well as the particular orientation of the trans conformational segments. The orientation process produces the alignment of the chains as well as an increase in the amount of trans conformational segments. A linear relationship is observed between birefringence and dichroic ratio for the absorption bands characteristic of overall orientation. A value of 35° ± 3° is obtained for the angle between the normal to the plane of the benzene ring and the chain axis from both infrared and birefringence determinations.     

Fourier transform infrared spectroscopy study of nanostructured nickel oxide

Nanostructured nickel oxide having different average particle sizes ranging from 3 to 16 nm were synthesized and Fourier transform infrared (FTIR) spectra of the samples were recorded in the far infrared (IR) region. The spectra were found to be dominated by surface mode absorptions with no distinct absorption corresponding to the bulk transverse optical mode. IR absorption coefficient, alpha, for the nanostructured NiO samples were calculated as a function of frequency using a macroscopic approach devised by Fuchs. The effects of crystalline geometry, numerical values of optical constants, filling factor and increased damping on the spectral features of the samples were analyzed. Though the simulations approximately reproduced the occurrence of a shoulder in the experimental spectra, the most intense peak in the simulated spectra was found to be about 50 cm(-1) above the corresponding experimentally observed peak. It was shown that the experimentally observed absorption maximum of all the samples were in close agreement with that determined using a microscopic theory based on the rigid ion model. The weak absorption peaks in the frequency region 60-100 cm(-1) appearing in the spectra of all the samples were identified as surface induced transverse acoustical modes, omegaTA, which became IR active due to the breakdown of translational symmetry in the nanocrystallites.     

Fourier transform infrared study of low-temperature CO adsorption on CuMgAl-hydrotalcite

Single-phase CuMgAl ternary hydrotalcite with (Cu+Mg)/Al atomic ratio of 3.0 and Cu/Mg atomic ratio of 1.0 was synthesized by coprecipitation. Thermoanalytical studies of this sample showed transformations in three stages in the temperature range up to ca. 900 K yielding mainly CuO phase. In situ diffuse reflectance infrared Fourier transform (DRIFT) spectroscopic measurements showed the presence of carbonates even after calcination of the sample at 973 K. The genesis of Cu+ sites during thermal treatment in vacuo at different temperatures for this sample was followed by IR spectroscopy of CO adsorbed at low temperature. Essentially no Cu+ sites are present on a sample calcined at 723 K, consistent with X-ray photoelectron spectroscopic (XPS) data. However, sample subjected to activation (1 h of O2 treatment at 723 K followed by 1 h of evacuation at the same temperature) upon CO adsorption at 85 K unambiguously showed the presence of Cu+ sites. 12CO-13CO coadsorption studies confirmed the presence of dicarbonyls, which are converted to linear Cu+-CO species during evacuation at 85 K. Concentration of the accessible Cu+ sites increased with the increase in activation temperature up to 873 K and decreased with a further temperature rise. The copper sites on the sample are heterogeneously distributed and their distribution depends on the activation temperature. Two routes of reduction of Cu2+ to Cu+ are proposed: (i) autoreduction during evacuation and (ii) reduction by CO.     

Fourier transform infrared study of two truxene-based discotic liquid crystals

We have used FTIR absorption to study the crystalline and liquid-crystalline phases of 2,3,7,8,12,13-hexa-n-tetradecanoyloxy-truxene (HATX) and 2,3,7,8,12,13-hexa(4-n-undecyloxybenzoyloxy)truxene (HBTX). Both materials show pronounced changes in the CH₂ stretching mode frequencies at their melting points. In addition, HATX shows a transition at about 20°C below the nominal melting point in which the alkyl tails gain significant disorder. Benzene stretching modes and the CH₂ deformation modes show subtle changes at the D_rd → N transition of HBTX and at the D_rd → D_hd transition of HATX.     

Applications of time-resolved step-scan Fourier-transform infrared spectroscopy in revealing the light-initiated reactions in condensed phases

Step-scan Fourier-transform infrared spectroscopy (ssFTIR) simultaneously provides the spectroscopic and kinetic information of a given reaction. ssFTIR has been extensively employed to acquire the transient absorption and emission spectra in gas phase for identifying unstable species, for example, various Criegee intermediates, and elucidating the dynamics and kinetics of the reaction, such as the molecular elimination dynamics of haloalkenes and the bimolecular reactions involving chlorine atoms and singlet oxygen atoms. In addition to gaseous studies, ssFTIR has been also utilized to record the time-resolved difference spectra of the photochemical reactions in condensed phases, such as the photolysis of metal–ligand complexes, photocycles of the retinal proteins, coordination capability of solvents to unstable transient species, chemical reactions of atmosphere-related molecules in aqua, and the exciplex dynamics of organic light emitting materials. Moreover, my group has pioneered the recording of the transient thermal infrared emission of gold nanostructures upon photoexcitation. The experimental setups and the working principles for probing the time-resolved infrared absorption and emission in condensed phases will be revealed and a number of studies on chemical, biological, and materials systems will be described. These reported results demonstrate that ssFTIR is a versatile tool for exploring the properties of novel materials and photoreactions in condensed phases.     

Depth profiling of SBS/PET layered materials using step-scan phase modulation Fourier transform infrared photoacoustic spectroscopy and two-dimensional correlation analysis

This paper demonstrates the application of step-scan phase modulation Fourier transform infrared photoacoustic spectroscopy(FTIR-PAS) in non-destructively depth profiling of styrene-butadiene-styrene block copolymer/polyethylene terephthalate(SBS/PET) layered materials.The surface thicknesses of three layered samples were determined to be 1.2,4.3 and 9.4μm by using phase difference analysis,overcoming the spatial detection limits of FTIR.Combined with generalized two-dimensional(G2D) FTIR correlation analys...     

A Fourier transform infrared study of Neurospora rhodopsin: similarities with archaeal rhodopsins

The NOP-1 gene from the eukaryote Neurospora crassa, a filamentous fungus, has recently been shown to encode an archaeal rhodopsin-like protein NOP-1. To explore the functional mechanism of NOP-1 and its possible similarities to archaeal and visual rhodopsins, static and time-resolved Fourier transform infrared difference spectra were measured from wild-type NOP-1 and from a mutant containing an Asp-->Glu substitution in the Schiff base (SB) counterion, Asp131 (D131E). Several conclusions could be drawn about the molecular mechanism of NOP-1: (1) the NOP-1 retinylidene chromophore undergoes an all-trans to 13-cis isomerization, which is typical of archaeal rhodopsins, and closely resembles structural changes of the chromophore in sensory rhodopsin II; (2) the NOP-1 SB counterion, Asp131, has a very similar environment and behavior compared with the SB counterions in bacteriorhodopsin (BR) and sensory rhodopsin II; (3) the O-H stretching of a structurally active water molecule(s) in NOP-1 is similar to water detected in BR and is most likely located near the SB and SB counterion in these proteins; and (4) one or more cysteine residues undergo structural changes during the NOP-1 photocycle. Overall, these results indicate that many features of the active sites of the archaeal rhodopsins are conserved in NOP-1, despite its eukaryotic origin.     

Matrix isolation Fourier transform infrared study of photodecomposition of formimidic acid

The UV isomerization of formamide (HCONH2) trapped in xenon, nitrogen, argon, and neon cryogenic matrices has been monitored by Fourier transform infrared (FT-IR) spectroscopy. Formamide monomer is the only species present in the matrices after deposition; when UV-selective irradiation was carried out at 240 nm, the n --> pi transition allowed us to observe the formation of several isomers of formimidic acid [H(OH)C=NH]. On these latter species, we carried out selective IR irradiation of their OH stretching mode and compared the experimental and theoretical (B3LYP/6-311+G(2d,2p)) sets of bands. This study allowed us to characterize for the first time all the isomers of formimidic acid. We have then studied the vacuum UV photodecomposition (lambda > 160 nm) of this molecule at 10 K in argon and xenon matrices. Several primary photoproducts such as HCN.H2O, HNC.H2O, and HNCO.H2 complexes, yielded by dehydration and dehydrogenation processes, were characterized.     

Fourier transform infrared study of the gel form of isotactic polystyrene

Infrared spectra of isotactic polystyrene gel films are observed to be significantly different from those of amorphous and crystalline polymer, indicating that the gel form is in a different conformation than the usual 3₁ helical crystal structure. Computer-assisted subtraction indicates that approximately 35% of the chains participate in the gel component, effectively ruling out structural defects as the origin of the ordered gel component.     

Fourier transform infrared study of the effects of irradiation on polyethylene

Fourier transform infrared spectra have been obtained for polyethylene irradiated in oxygen and nitrogen atmospheres. The spectra before and after irradiation have been compared by digital subtraction. The difference spectra are indicative of changes caused by irradiation. Crosslinking and chain scission reactions produce the observed changes.     

The study of a single BGC823 cell using Fourier transform infrared microspectroscopic imaging

In order to investigate gastric cancer at cellular and sub-cellular level, a single human gastric adenocarcinoma BGC823 cell was studied by an infrared microscope equipped with a focal plane array (FPA) detector. The spectra showed difference between the nucleus and the endoplasmic reticulum (ER) of the BGC823 cell. The peak of vasPO2- was shifted to a higher wavenumber at the nucleus compared with that at the ER. The height ratios of 2954 cm(-1)/2922 cm(-1) (CH3/CH2) and 1088 cm(-1)/1539 cm(-1) (DNA/amide II) of the nucleus were significantly higher than those of the ER. Furthermore, chemical images reveal the intensity distributions of lipids, proteins and DNA of the single BGC823 cell, and the intense absorptions of proteins and DNA were observed in the nuclear region of the cell while the intense absorption of lipids was found in the ER region of the cell. The Fourier transform infrared (FTIR) microspectroscopic imaging result indicates the study of the single gastric cancer cell at sub-cellular level can be beneficial for knowing gastric cancer more which will be of great importance for the study and diagnosis of gastric cancer. The result also suggests that FPA is a useful tool in the study of a single cell and may be a powerful tool for study and diagnosis of gastric cancer.     

Fourier transform infrared study of mercury interaction with carboxyl groups in humic acids

An interaction between humic acid, an organic part of soil and mercury was studied by Fourier transform infrared spectroscopy (FTIR) and by ICP-AES analysis under given pH and concentration conditions. First the spectroscopic model was validated on the interaction of simple molecules representing the structural components of humic acid such as benzoic acid, catechol and salicylic acid with mercury. The interaction of carboxylic parts of humic acid with mercury is very interesting and easily characterised by infrared spectroscopy, an ideal mean for molecular study. Under the salt form (commercial humic acid Fluka TM: FHA), humic acid reacts with mercury in a different way from its acid form (FHA purified noted PFHA) and the Leonardite (LHA). Because of the straightforward exchange between Na⁺, Ca²⁺ and Hg²⁺, fixation of the latter is much more important with the salt form (FHA). However, this reaction is reduced under the acid form (PFHA, LHA) because the exchange with protons is difficult. The effect of this exchange was studied by FTIR showing the intensity decrease of ν_CO (COOH), the carboxylic functional group band of the acid, and the shifting of ν_as (COO⁻), the carboxylate functional group band under given pH and mercury conditions. For the FHA salt form, the characteristic band ν_CO (COOH) represented by a shoulder did not evolute, whereas the corresponding band to ν_as (COO⁻) strongly shifted (40 cm⁻¹) for a maximum Hg²⁺ concentration (1 g l⁻¹). On the other hand, for the acid form (PFHA, LHA), the intense band of ν_CO (COOH) disappeared proportionally to the increase of Hg²⁺concentration and the ν_as (COO⁻) band moved for about 20 cm⁻¹. The same results were reached with pH variations. Our results were confirmed by ICP-AES mercury analysis. This study shows that humic acids react differently according to their chemical and structural state.     

Fourier transform infrared study of poly (2-hydroxyethyl methacrylate) PHEMA

 Fourier transform infrared spectra in the wave number range 450–4500 cm^-1 of poly (2-hydroxy-ethyl methacrylate) PHEMA have been studied as functions of water content in the range 38–2.6 wt% and of temperature in the range 300–373 K. The results show changes in the intensities of the stretching frequencies of the carbonyl band, H–O–H bending vibration and O–H stretching vibration with a change in water content and temperature. The results confirm two types of water in the hydrogel polymer system, tightly bound water and loosely bound water. At low concentrations, water is mainly hydrogen-bonded to the polymer and is described as tightly bound water. However, at water concentrations greater than 18% by weight, part of the water exists in a different form and behaves as loosely bound water. For concentrations over 30%, there is some evidence that excess water behaves more loosely bound somewhat like bulk water. Infrared spectroscopic results supplement those obtained by means of NMR by Smyth et al. and by dielectric spectroscopy. Our results also show that some of the water continues to be hydrogen bonded to the polymer until at least a temperature of 373 K when the bulk water should have evaporated. FTIR is found to yield greater site-specific insight into the local behaviour of water in hydrated PHEMA. Received: 22 August 1996 Accepted: 11 November 1996     

Fourier transform infrared spectroscopy as a tool for the study of rare earths carbohydrates complexes

FT-IR spectra of the mixtures of praseodymium chloride and glucose in glassy state were investigated. From the changes of relative intensity and shifts of the characteristic frequency of glucose and water, it is concluded that the coordinated water molecules of the praseodymium ions are partially substituted by glucose through O-H groups which coordinated with praseodymium ions to form chelate ions.