Strong Infrared Bands Research Articles

Quantifying Bound Proteins on Pegylated Gold Nanoparticles Using Infrared Spectroscopy.

Protein-nanoparticle (NP) complexes are nanomaterials that have numerous potential uses ranging from biosensing to biomedical applications such as drug delivery and nanomedicine. Despite their extensive use quantifying the number of bound proteins per NP remains a challenging characterization step that is crucial for further developments of the conjugate, particularly for metal NPs that often interfere with standard protein quantification techniques. In this work, we present a method for quantifying the number of proteins bound to pegylated thiol-capped gold nanoparticles (AuNPs) using an infrared (IR) spectrometer, a readily available instrument. This method takes advantage of the strong IR bands present in proteins and the capping ligands to quantify protein-NP ratios and circumvents the need to degrade the NPs prior to analysis. We show that this method is generalizable where calibration curves made using inexpensive and commercially available proteins such as bovine serum albumin (BSA) can be used to quantify protein-NP ratios for proteins of different sizes and structures.

Understanding the infrared and Raman spectra of ganoderic acid A: An experimental and DFT study.

Ganoderic Acids (GAs) are the major medicinal compounds in Ganoderma lucidum used as traditional Chinese medicine since ancient times. Ganoderic acid A (GAA) is the first discovered ganoderic acids reported in the literature, which is also one of most abundant triterpenoids of Ganoderma lucidum. Especially, GAA has been extensively investigated in recent decades for its positive medicinal activities. However, the vibrational properties of GAs have rarely been studied or reported. In this work, we focused on the typical GAA and studied the infrared (IR) and Raman spectra based on both experiments and DFT calculations. As such, we could not only achieve the assignments of the vibrational modes, but also from the IR and Raman spectra, we found that the spectral region from 1500 cm-1 to 1800 cm-1 is particularly useful for distinguishing different types of GAs. In addition, its dehydrogenated derivative ganoderenic acid A (GOA) was also studied, which could be identified due to its spectral feature of strong IR and Raman bands around 1620 cm-1. This work therefore may facilitate the application of IR and Raman spectroscopies in the inspection and quality control of Ganoderma lucidum.

Femtosecond laser-induced transformations in ultra-low expansion glass: Microstructure and local density variations by vibrational spectroscopy

We report X-ray diffraction, resonance Raman, and infrared (IR) results on pristine ultra-low expansion (ULE) glass, a binary titanosilicate glass with 5.67 mol. % TiO2. ULE processing by femtosecond (fs) laser radiation leads to nanograting writing and photo-darkening for imaging and data storage. We investigate here the vibrational/structural changes induced by fs laser irradiation of ULE at 515 nm. Optical imaging revealed the formation of micro-cavities, and Raman mapping showed molecular oxygen trapped in such cavities of laser-irradiated ULE glass. While titanium in the pristine glass was found predominantly in tetrahedral Ti4+ sites highly dispersed in the silicate matrix, Raman and IR reflectance spectroscopy on laser-irradiated ULE indicated the formation of Ti3+ sites; Ti3+ octahedral sites are formed in the shells of cavities and aggregate in amorphous Ti2O3-type clusters, while the glass around and below cavities contains Ti3+ tetrahedral sites dispersed in the silicate network. Laser-processed ULE glass was found to also exhibit local restructuring of the silicate matrix. Shifts of the strong IR band at about 1080–1100 cm−1 were translated into changes of the average Si-O-Si bond angle in the laser-transformed areas and found to reflect local density variations; the average local density increases relative to silica glass up to about 8% in the shells of micro-cavities and decreases by about 0.5% in the surrounding material. Chemical processes were proposed to account for photo-darkening and the local structural transformation effect in the probed areas of the fs laser-processed ULE glasses.

THE INFRARED AND UV-VISIBLE SPECTRA OF POLYCYCLIC AROMATIC HYDROCARBONS CONTAINING (5, 7)-MEMBER RING DEFECTS: A THEORETICAL STUDY

We report a theoretical investigation of the infrared (IR) spectra of polycyclic aromatic hydrocarbons (PAHs) containing (5, 7)-member ring defects based on a C48H18 model. Calculations are mostly performed using the hybrid B3LYP density functional theory (DFT) with a 6-31G(d) or 4-31G basis set. The results show that the Stone-Wales defect in PAHs can yield a strong IR band at 1448 cm–1 and a weak band at 611 cm–1, which may contribute to the UIR (unidentified infrared) bands at 6.9 μm and 16.4 μm observed in the interstellar medium. The charge effect on the IR spectra is discussed. The stability of the ring defected PAHs is also addressed by exploring the minimum energy pathway on the potential energy surface and through their UV-visible spectra, which are computed using a TDDFT method.

Infrared and visible absolute and difference spectra of bacteriorhodopsin photocycle intermediates.

We have used new kinetic fitting procedures to obtain infrared (IR) absolute spectra for intermediates of the main bacteriorhodopsin (bR) photocycle(s). The linear-algebra-based procedures of Hendler et al. (J. Phys. Chem. B, 105, 3319-3228 (2001)) for obtaining clean absolute visible spectra of bR photocycle intermediates were adapted for use with IR data. This led to isolation, for the first time, of corresponding clean absolute IR spectra, including the separation of the M intermediate into its M(F) and M(S) components from parallel photocycles. This in turn permitted the computation of clean IR difference spectra between pairs of successive intermediates, allowing for the most rigorous analysis to date of changes occurring at each step of the photocycle. The statistical accuracy of the spectral calculation methods allows us to identify, with great confidence, new spectral features. One of these is a very strong differential IR band at 1650 cm(-1) for the L intermediate at room temperature that is not present in analogous L spectra measured at cryogenic temperatures. This band, in one of the noisiest spectral regions, has not been identified in any previous time-resolved IR papers, although retrospectively it is apparent as one of the strongest L absorbance changes in their raw data, considered collectively. Additionally, our results are most consistent with Arg82 as the primary proton-release group (PRG), rather than a protonated water cluster or H-bonded grouping of carboxylic residues. Notably, the Arg82 deprotonation occurs exclusively in the M(F) pathway of the parallel cycles model of the photocycle.

Infrared and infrared emission spectroscopy of nesquehonite Mg(OH)(HCO 3)·2H 2O–implications for the formula of nesquehonite

The mineral nesquehonite Mg(OH)(HCO 3)·2H 2O has been analysed by a combination of infrared (IR) and infrared emission spectroscopy (IES). Both techniques show OH vibrations, both stretching and deformation modes. IES proves the OH units are stable up to 450 °C. The strong IR band at 934 cm −1 is evidence for MgOH deformation modes supporting the concept of HCO 3 − units in the molecular structure. Infrared bands at 1027, 1052 and 1098 cm −1 are attributed to the symmetric stretching modes of HCO 3 − and CO 3 2− units. Infrared bands at 1419, 1439, 1511, and 1528 cm −1 are assigned to the antisymmetric stretching modes of CO 3 2− and HCO 3 − units. IES supported by thermoanalytical results defines the thermal stability of nesquehonite. IES defines the changes in the molecular structure of nesquehonite with temperature. The results of IR and IES supports the concept that the formula of nesquehonite is better defined as Mg(OH)(HCO 3)·2H 2O.

Vibrational Spectroscopic and Theoretical Studies of Urea Derivatives with Biochemical Interest: N,N′-Dimethylurea, N,N,N′,N′-Tetramethylurea, and N,N′-Dimethylpropyleneurea

Mid-infrared, far-infrared, and Raman vibrational spectroscopic studies were combined with density functional theory (DFT) calculations and normal coordinate force field analyses for N,N′-dimethylurea (DMU), N,N,N′,N′-tetramethylurea (TMU), and N,N′-dimethylpropyleneurea (DMPU: IUPAC name 1,3-dimethyltetrahydropyrimidin-2(1H)-one). The equilibrium molecular geometry of DMU (all three conformers), TMU, and DMPU and the frequencies, intensities, and depolarization ratios of their fundamental infrared (IR) and Raman vibrational transitions were obtained by DFT calculations. The vibrational spectra were fully analyzed by normal coordinate methods as well. A starting force field for DMPU was obtained by adapting corresponding force constants for DMU and TMU, resulting after refinements in the stretching force constants C=O (7.69, 7.30, 7.68 N·cm−1), C–N (5.16, 5.55, 5.05 N·cm−1), and C-Me (5.93, 4.00, 4.22 N·cm−1) for DMU, TMU, and DMPU, respectively. The dominating conformer of liquid DMU was identified as trans-trans, strong intermolecular hydrogen bonding was verified in solid DMU, and weak dipole–dipole association was found in liquid TMU and in DMPU. Special attention was paid to analyzing the methyl group frequencies, which revealed deviations from local C3v symmetry. A linear correlation was found between the CH stretching force constants and the inverse of the CH bond lengths (1/r 2). The averaged NH stretching frequencies of gaseous, dissolved, and solid urea and of DMU, with variations for hydrogen bonding of different strength, are linearly correlated to the NH stretching force constants. Characteristic skeletal vibrations were assigned for a broad variety of urea derivatives and also for pyrimidine derivatives, which all contain the N2C=O entity. The very strong IR bands of C=O stretching (1,676 ± 40 cm−1) and asymmetric CN2 stretching (1,478 ± 60 cm−1), and the very intense Raman feature of symmetric CN2 stretching or ring breathing (757 ± 80 cm−1), can be recognized as fingerprint bands also for the pyrimidine derivatives cytosine, thymine, and uracil, which all are nucleobases in DNA and RNA nucleotides.

FTIR and raman spectra compared with ab initio calculated frequency modes for 5-aminouracil.

Infrared (IR) and Raman spectra of 5-aminouracil were recorded in the region 200-4,000 cm(-1). Assuming under the C(s) point group that the distribution of the normal mode of vibrations between the two species are planar (a') and non-planar (a''), given by 25a' + 11a'' of which 30 modes (21a' + 9a'') correspond to the uracil moiety and six modes (4a' + 2a'') correspond to the NH(2) group, with a comparison of theoretically ab initio calculated frequencies, the results are in reasonably good agreement with the experimental IR and Raman spectra. Consistent assignments have been made for the internal modes of the NH(2) group, especially for the anti-symmetric NH(2) stretching and bending modes. The non-equivalence of the two NH bonds of the NH(2) group suggests a difference in the strength of the two hydrogen bonds on the pyrimidine ring. Symmetry and anti-symmetry NH stretching modes of the NH(2) group show the invalidity of the empirical relationship. These two NH(2) stretching frequencies are distinctly separated from the CH/NH ring stretching frequencies. A strong and sharp IR band that acts at 3,380 cm(-1) could be identified as the anti-symmetric NH(2) mode whereas the band at 3,290 cm(-1) smaller density could be identified as the symmetric NH(2) stretching mode.

Ultrafast IR spectroscopy of the short-lived transients formed by UV excitation of cytosine derivatives

A strong infrared band at 1574 cm(-1) is observed following 267 nm excitation of 2'-deoxycytidine (tau = 37 +/- 4 ps) or 2'-deoxycytidine 5'-monophosphate (tau = 33 +/- 4 ps); this band is provisionally attributed to an 1n(N)pi* state and is absent for cytosine.

Infrared spectroscopy on size-controlled synthesized Pt-based nano-catalysts

Pt, Ru and Pt/Ru nano-particles, synthesized in ethylene glycol solutions, are studied using infrared (IR) spectroscopy and high resolution transmission electron microscopy (HRTEM). The synthesis method allows the control of the mono- and bi-metallic catalyst particle sizes between 1 and 5.5 nm. The IR spectra of CO adsorbed (CO ads) on the Pt, Ru and bi-metallic Pt/Ru colloids are recorded as a function of the particle size. The stretching frequency of CO ads depends on the particle size and composition. Strong IR bands due to the stretching vibration of CO ads are observed between 2010 and 2050 cm −1 for the Pt nano-particles, while two IR bands between 2030 and 2060 cm −1 for linear bonded CO ads, and at lower wavenumbers between 1950 and 1980 cm −1 for bridged bonded CO ads, are found for the Ru particles. The IR spectra for the Pt/Ru nano-sized catalyst particles show complex behaviour. For the larger particles (>2 ± 0.5 nm), two IR bands representative of CO ads on Ru and Pt–Ru alloy phases, are observed in the range of 1970–2050 cm −1. A decrease in the particle size results in the appearance of a third band at ∼2020 cm −1, indicative of CO ads on Pt. The relative intensity of the band for CO ads on the Pt–Ru alloy vs. the Pt phase decreases with decreasing particle size. These results suggest that Ru is partially dissolved in the Pt lattice for the larger Pt/Ru nano-particles and that a separate Ru phase is also present. A Pt–Ru alloy and Ru phase is observed for all Pt/Ru particles prepared in this work. However, a decrease in particle size results in a decrease of the number of Pt and Ru atoms in the Pt–Ru alloy phase, as they are increasingly present as single Pt and Ru phases.

Vibrational spectra and electron–vibration interactions of the naphthalene radical anion — Experimental and theoretical study

Vibrational analysis is carried out for the radical anions of naphthalene-h8 and -d8. Their infrared (IR) spectra are observed in tetrahydrofuran by using a cell designed for IR measurements of unstable species. The vibrational force field and the IR intensities are calculated by the ab initio molecular orbital and density functional methods at various theoretical levels. As found in the cases of the radical cations of many polycyclic aromatic hydrocarbons (PAHs), a few strong IR bands with intensities of the order of 102 km mol–1 are observed in the 1700–900 cm–1 region. These observed spectral features are well reproduced by the calculations at the CASSCF (complete active space self-consistent field) and B3LYP (Becke's three-parameter hybrid method using the Lee–Yang–Parr correlation functional) levels. The calculation at the B3LYP level gives a better fit between the observed and calculated absolute IR intensities. Normal modes and the origin of the strong IR intensities characteristic of the radical anions are discussed in terms of molecular symmetry coordinates and the dipole derivatives based on these coordinates. It is found that the IR intensities of the b2u modes below 2000 cm–1 are dominated by the contribution from one molecular symmetry coordinate, in which the C—C bonds in one ring stretch while those in the other ring shrink. The mechanism that gives rise to the strong IR intensity for this vibration is discussed by examining the changes in the electronic structure induced by this vibration.Key words: vibrational spectra, electron–vibration interaction, naphthalene, radical anion.

An investigation on a broad infrared band with the maximum at ∼1300 cm −1 in magnesia cement, phase 3

In magnesia cement, phase 3, a broad and strong infrared band was observed with the maximum at ∼1300 and 1050 cm −1 in the H and D systems, respectively. To clarify the origin of the 1300 cm −1 band the temperature dependency of the infrared spectra of the H system was observed and the spectra analyzed on the basis of a strong vibrational coupling of the OH stretching with lattice modes. The fitting was quite well, giving rise to the origin of the 1300 cm −1 band of the OH stretching.

Raman and infrared spectroscopic study of the vivianite-group phosphates vivianite, baricite and bobierrite

AbstractThe molecular structure of the three vivianite-structure, compositionally related phosphate minerals vivianite, baricite and bobierrite of formula M32+(PO4)2.8H2O where M is Fe or Mg, has been assessed using a combination of Raman and infrared (IR) spectroscopy. The Raman spectra of the hydroxyl-stretching region are complex with overlapping broad bands. Hydroxyl stretching vibrations are identified at 3460, 3281, 3104 and 3012 cm−1 for vivianite. The high wavenumber band is attributed to the presence of FeOH groups. This complexity is reflected in the water HOH-bending modes where a strong IR band centred around 1660 cm−1 is found. Such a band reflects the strong hydrogen bonding of the water molecules to the phosphate anions in adjacent layers. Spectra show three distinct OH-bending bands fromstrongly hydrogen-bonded, weakly hydrogen bonded water and non-hydrogen bonded water. The Raman phosphate PO-stretching region shows strong similarity between the three minerals. In the IR spectra, complexity exists with multiple antisymmetric stretching vibrations observed, due to the reduced tetrahedral symmetry. This loss of degeneracy is also reflected in the bending modes. Strong IR bands around 800 cm−1 are attributed to water librational modes. The spectra of the three minerals display similarities due to their compositions and crystal structures, but sufficient subtle differences exist for the spectra to be useful in distinguishing the species.

Vibrational Spectra and Structures of Long-Chain Streptocyanine Dyes: Effects of Electron−Vibration Interactions and Vibrational Polarizabilities

The structural and vibrational properties of streptocyanine dyes, expressed as [(CH3)2N(CH)xN(CH3)2]+ClO4- (called SCx in this paper) with x = 2n + 1 (n = 0−10), are examined by measuring the infrared (IR) and Raman spectra in solution and in the polycrystalline state (for x = 1, 3, 7, 9) and by carrying out density functional calculations at the BHandHLYP/6-31G* level. It is shown that the strong IR bands observed and calculated in the 1800−800 cm-1 region arise from the normal modes containing large contributions from the vibrations along the bond-alternation coordinate of the conjugated chains. As the conjugated chain becomes longer, the strongest IR band shifts toward the lower-wavenumber side, inducing noticeable changes in the spectral pattern, and the total IR intensity increases significantly. The shifts to lower wavenumbers and the changes in the spectral pattern are explained by the decrease in the intrinsic wavenumber of the bond-alternation mode. A two-state model Hamiltonian, which involves e...

Ab initio molecular orbital study of the amide I vibrational interactions between the peptide groups in di- and tripeptides and considerations on the conformation of the extended helix

Interrelationships among the coupling between the amide I vibrations of peptide groups, the A–E1 wavenumber difference of the amide I mode and the conformation of helical polypeptide chains were examined theoretically. Ab initio molecular orbital (MO) calculations were performed for a glycine dipeptide and a glycine tripeptide with various ϕ and ψ angles to obtain the coupling constants between the amide I vibrations of the nearest peptide groups and between those of the second nearest peptide groups. It was found that the coupling constants between the second nearest peptide groups were reasonably well explained by the transition dipole coupling mechanism, whereas the coupling constants between the nearest peptide groups contained other factors that mainly depended on ψ. The wavenumbers of the A and E1 components of the amide I mode were calculated for various helices on the basis of these coupling constants. The A component is strong in the infrared (IR) spectrum when the transition dipole of the amide I vibration is nearly parallel to the helix axis, whereas the E1 component has a strong IR intensity when they are nearly perpendicular to each other. The A component has a strong Raman intensity in both cases. Therefore, the Raman–infrared wavenumber difference of 10–20 cm-1 observed for the amide I bands of poly(L-glutamate) and poly(L-lysine) with charged side chains indicates that these polypeptides, in that so-called ‘extended helix’ state, have conformations giving rise to strong IR bands of the E1 component which are lower in wavenumber than the Raman bands of the A component by 10–20 cm-1. The ranges of the ϕ and ψ angles that are consistent with such spectral features are discussed on the basis of the calculated structures and amide I wavenumbers. © 1998 John Wiley & Sons, Ltd.

Ab initio molecular orbital study of the amide I vibrational interactions between the peptide groups in di- and tripeptides and considerations on the conformation of the extended helix

Interrelationships among the coupling between the amide I vibrations of peptide groups, the A–E1 wavenumber difference of the amide I mode and the conformation of helical polypeptide chains were examined theoretically. Ab initio molecular orbital (MO) calculations were performed for a glycine dipeptide and a glycine tripeptide with various ϕ and ψ angles to obtain the coupling constants between the amide I vibrations of the nearest peptide groups and between those of the second nearest peptide groups. It was found that the coupling constants between the second nearest peptide groups were reasonably well explained by the transition dipole coupling mechanism, whereas the coupling constants between the nearest peptide groups contained other factors that mainly depended on ψ. The wavenumbers of the A and E1 components of the amide I mode were calculated for various helices on the basis of these coupling constants. The A component is strong in the infrared (IR) spectrum when the transition dipole of the amide I vibration is nearly parallel to the helix axis, whereas the E1 component has a strong IR intensity when they are nearly perpendicular to each other. The A component has a strong Raman intensity in both cases. Therefore, the Raman–infrared wavenumber difference of 10–20 cm-1 observed for the amide I bands of poly(L-glutamate) and poly(L-lysine) with charged side chains indicates that these polypeptides, in that so-called ‘extended helix’ state, have conformations giving rise to strong IR bands of the E1 component which are lower in wavenumber than the Raman bands of the A component by 10–20 cm-1. The ranges of the ϕ and ψ angles that are consistent with such spectral features are discussed on the basis of the calculated structures and amide I wavenumbers. © 1998 John Wiley & Sons, Ltd.

Spectroscopic studies of thiatri-, penta- and heptamethine cyanine dyes II. Infrared and resonance Raman spectra of thiatri-, penta- and heptamethine cyanine dyes

Infrared (IR) and resonance Raman (RR) spectra of thiatri-, penta- and heptamethine cyanine dyes in the solid state and in solution have been measured. Most of the intense bands observed in the 1600-1100 cm −1 region of the RR spectra may be assigned to totally symmetric stretching modes of the central conjugated system of the cyanines, while most of the strong IR bands in the 1600-1300 cm −1 region are probably due to antisymmetric stretching modes. The intense RR bands do not have their counterparts in the IR spectra and vice versa. A pseudo-mutual exclusion rule seems to be operative for the cyanine vibrational spectra in the 1600-1300 cm −1 region, indicating that the central conjugated systems of the cyanines have nearly symmetrical structure, i.e. the extended all-trans forms of the methine chains and the bond orders of 1.5 of the CC and CN bonds in both the solution and solid states. The IR spectra of 3-ethyl-2-[3-(3-ethyl-2-benzothiazolinylidene)-1-propenyl]benzothiazolium iodide (NK-76) and 3-ethyl-2-[7-(3-ethyl-2-benzothiazolinylidene)-1,3,5-heptatrienyl]benzothiazolium iodide (NK-126) change little between the solid and solution states while those of 3-octadecyl-2-[3-(3-octadecyl-2-benzothiazolinylidene)-1-propenyl]benzothiazolium iodide (NK-2560) and 3-octadecyl-2-[7-(3-octadecyl-2-benzothiazolinylidene)-1,3,5-heptatrienyl]benzothiazolium perchlorate (NK-2861) alter significantly between the two states in the frequencies of bands due to the stretching modes of their central conjugated systems. The results suggest that the electronic states of the central conjugated systems of NK-2560 and NK-2861 undergo appreciable changes on going from the solid to the solution states.