Clarification of the thermally-induced pretransition of ribonuclease A in solution by principal component analysis and two-dimensional correlation infrared spectroscopy

Thermal denaturation of ribonuclease A (RNase A) in D₂O solution is studied by Fourier transform infrared (FT-IR) spectroscopy. Sample–sample two-dimensional correlation (SS 2D) spectroscopy and principal component analysis (PCA) are applied to these spectral data to reveal the thermal kinetics of RNase A. The second scores plot of PCA constructed from temperature-dependent original IR spectra illustrates a pretransition at 46 °C as well as a clear main transition at 66 °C. The latter is revealed by the SS 2D correlation spectra and the first score of PCA because of their illustration of the main denaturation event of RNase A, while the former cannot. Therefore, the present study demonstrates the great potential of PCA in revealing subtle phase transition of proteins in aqueous solutions.     

The Structure of Water-Swollen Poly(Vinyl Alcohol) and the Swelling Mechanism

The swelling mechanism of poly(vinyl alcohol) (PVA) in a wide range of the equilibrium swelling index, of 7–153% (with H₂O) and of 12-297% (with D₂O), was investigated by IR, Raman, and broad-band NMR spectroscopy. Analysis of the spectral data obtained confirmed the presence of hydration water (bonded with polymer-free hydroxyl groups) and condensation water (not having been bonded with polymer hydroxyl groups) in poly(vinyl alcohol) swollen samples at low (～7%) and high (>23%) equilibrium swelling indexes, respectively. Moreover, it revealed the intra- and inter-molecular hydrogen bonds breaking in the polymer swollen to higher extent (equilibrium swelling index > 85%).     

Application of two-dimensional near-infrared correlation spectroscopy to the discrimination of Chinese herbal medicine of different geographic regions

Fructus Lycii is a traditional Chinese medicinal herb. The objective of this paper was to apply two-dimensional (2D) near-infrared (NIR) correlation spectroscopy to the discrimination of Fructus Lycii of four different geographic regions. Generalized 2D-NIR correlation spectroscopy was able to enhance spectral resolution, simplify the spectrum with overlapped bands, and provide information about temperature-induced spectral intensity variations that was hard to obtain from one-dimensional NIR spectroscopy. The 2D synchronous and asynchronous spectra showed remarkable differences within the range of 4950-5700cm(-1) between samples of different geographic regions. Using NIR instead of IR made the 2D approach more convenient and fast, and it can be applied to more area like process control. This approach can also be applied analogously to the discrimination of other Chinese herbal medicine of different geographic regions.     

Cd3(H2O)3((O3PCH2)2NH-CH2C6H4-COOH)2].11H2O: a layered cadmium phosphonate with reversible dehydration/hydration properties

In a recent systematic study on the influence of the reaction temperature on the structure formation in the system CdCl2/H(HO3PCH2)2NH-CH2C6H4-COOH (H5L) /NaOH, [Cd3(H2O)3((O3PCH2)2NH-CH2C6H4-COOH)2].11H2O was obtained as a microcrystalline compound. We have now been able to elucidate the structure from single-crystal data: triclinic, P; a=5.4503(9), b=12.880(2), and c=16.417(3) A; alpha=67.841(6) degrees, beta=80.633(6) degrees, gamma=87.688(8) degrees, V=1052.9(3) A3; Z=1; R1=0.1143, R2=0.2108 (all data); 0.0705, 0.1823 ((I>2sigmaI)). The structure of [Cd3(H2O)3((O3PCH2)2NH-CH2C6H4-COOH)2].11H2O is built up of cadmium phosphonate layers connected by water-mediated hydrogen bonds between aryl-carboxylic acid groups and water molecules coordinated to Cd2+ ions of adjacent layers (C-OH...H2O...H2O-Cd2+). The title compound was characterized by IR spectroscopy and energy dispersive X-ray, elemental, and thermogravimetric analyses. Furthermore, temperature-dependent X-ray diffraction data are presented. [Cd3(H2O)3((O3PCH2)2NH-CH2C6H4-COOH)2].11H2O can be reversibly dehydrated, and mechanical stress and grinding in the presence of water leads to the intercalation of additional water molecules.     

Synthesis and characterization of a new catalyst for RhB degradation constructed by [SiMo12O40]4- anionic cluster

A Keggin-type polyoxomolybdate[H_2biim]{Ni(biim)_3(SiMO_(12)O_(40))}[biim =1H,1'H-[2,2']biimidazolyl]has been synthesized under hydrothermal condition and characterized by XRD,temperature-dependent IR,TG,temperature-induced and magnetism-induced 2D infrared correlation spectroscopy(2D-IR COS)and UV-vis DRS in order to explore the relationship between structure and properties.Temperatureinduced 2D-IR COS spectroscopy indicates that the terminal Mo-O_(μ/υ) bonds are more sensitive than the bridging Mo=O_t,bands to temperature variation,which is in agreement with the conclusion of temperature-dependent IR.Magnetism-dependent 2D-IR COS spectroscopy reveals the stretching vibration of the Mo=O_t,occurs prior to the stretching vibration of the Mo-O_(μ/υ),which is due to the coordination environment and the valence of the Si atom.The stability of compound 1 is investigated via TG and temperature-dependent IR.In RhB degradation,compound 1 shows good photocatalytic abilities.     

Moving-window two-dimensional correlation infrared spectroscopy study on structural variations of partially hydrolyzed poly(vinyl alcohol)

In the present study, the molecular chain changes and structural transitions of partially hydrolyzed poly(vinyl alcohol) (PVA) having a 12 mol% acetate unit were analyzed by moving-window two-dimensional (MW2D) correlation infrared spectroscopy combined with differential scanning calorimetry and thermogravimetric analysis. The results show the glass-transition temperature (T _g ) of PVA is clearly distinguished by MW2D correlation infrared spectroscopy, and the acetate groups start to be eliminated around the melting temperature, whereas the free water molecules in PVA are eliminated above T _g. The correlation movements of the O–H stretching modes, including the free hydroxyl groups and the hydrogen bonds, are clearly determined using MW2D correlation infrared spectroscopy. The spectral variations in the C=O stretching region caused by the elimination of the acetate unit from polymer chains are also discussed on the basis of the results of the MW2D correlation analysis. Such results cannot be obtained by traditional infrared spectroscopy owing to the complex overlapping peaks.

Intermolecular Hydrogen Bonds Formed Between Amino Acid Molecules in Aqueous Solution Investigated by Temperature-jump NanosecondTime-resolved Transient Mid-IR Spectroscopy

Carboxyl (COO?) vibrational modes of two amino acids histidine and glycine in D2O solution were investigated by temperature-dependent FTIR spectroscopy and temperature-jump nanosecond time-resolved IR di?erence absorbance spectroscopy. The results show that hydrogen bonds are formed between amino acid molecules as well as between the amino acid molecule and the solvent molecules. The asymmetric vibrational frequency of COO? around 1600-1610 cm?1 is blue shifted when raising temperature, indicating that the strength of the hydrogen bonds becomes weaker at higher temperature. Two bleaching peaks at 1604 and 1612 cm?1 were observed for histidine in response to a temperature jump from 10 ±C to 20 ±C. The lower vibrational frequency at 1604 cm?1 is assigned to the chain COO? group which forms the intermolecular hydrogen bond with NH3+ group, while the higher frequency at 1612 cm?1 is assigned to the end COO? group forming hydrogen bonds with the solvent molecules. This is because that the hydrogen bonds in the former are expected to be stronger than the latter. In addition the intensities of these two bleaching peaks are almost the same. In contrast, only the lower frequency at 1604 cm?1 bleaching peak has been observed for glycine. The fact indicates that histidine molecules form a dimer-like intermolecular chain while glycine forms a relatively longer chain in the solution. The rising phase of the IR absorption kinetics in response to the temperature-jump detected at 1604 cm?1 for histidine is about 30§10 ns, within the resolution limit ofour instrument, indicating that breaking or weakening the hydrogen bond is a very fast process.     

Characterization of the thermal behavior of poly(hydroxybutylate) by principal component analysis-based two-dimensional correlation spectroscopy.

Principal component analysis-based two-dimensional (PCA2D) correlation spectroscopy, combined with the eigenvalue manipulating transformation (EMT) of a spectral data set, was applied to the temperature-dependent IR spectra of poly(hydroxybutylate) (PHB). In asynchronous PCA2D correlation spectrum, we clearly captured the existence of two components in the crystalline band of the C=O stretching mode, well-ordered primary crystals observed at lower wavenumber and less ordered secondary crystals observed at higher wavenumber, which is not readily detectable in the 1D spectra. By lowering the power of a set of eigenvalues associated with the original data, subtle differences in the thermal responses of PHB, which are difficult to observe even by conventional 2D correlation analysis, are revealed. When the contributions from minor factors are enhanced by eigenvalue manipulating transformation, intensities of bands assignable to the amorphous component of PHB are accentuated more in the C-O-C stretching region, while the intensities of bands assignable to the crystalline component become most prominent in the CH stretching region. However, the 2D correlation between CH and C=O stretching region reveals that the spectral intensity change of the CH(3) stretching bands at 2975 cm(-1) contains a component due to the amorphous contribution.     

Hydrogen bond lifetimes and energetics for solute/solvent complexes studied with 2D-IR vibrational echo spectroscopy

Weak pi hydrogen-bonded solute/solvent complexes are studied with ultrafast two-dimensional infrared (2D-IR) vibrational echo chemical exchange spectroscopy, temperature-dependent IR absorption spectroscopy, and density functional theory calculations. Eight solute/solvent complexes composed of a number of phenol derivatives and various benzene derivatives are investigated. The complexes are formed between the phenol derivative (solute) in a mixed solvent of the benzene derivative and CCl4. The time dependence of the 2D-IR vibrational echo spectra of the phenol hydroxyl stretch is used to directly determine the dissociation and formation rates of the hydrogen-bonded complexes. The dissociation rates of the weak hydrogen bonds are found to be strongly correlated with their formation enthalpies. The correlation can be described with an equation similar to the Arrhenius equation. The results are discussed in terms of transition state theory.     

Noise perturbation in functional principal component analysis filtering for two-dimensional correlation spectroscopy: its theory and application to infrared spectra of a poly(3-hydroxybutyrate) thin film

A method based on noise perturbation in functional principal component analysis (NPFPCA) is for the first time introduced to overcome the noise interference problem in two-dimensional correlation spectroscopy (2D-COS). By the systematic addition of synthetic noise to the dynamic multivariate spectral data, the functional principal component analysis (FPCA) described in this report is able to accurately determine which eigenvectors are representing significant signals instead of noise in the original data. This feature is especially useful for the data reconstruction and noise filtering. Reconstructed data resulted from the smooth eigenvectors can produce much more reliable 2D correlation spectra by removing the correlation artifacts from noise, which in turn enable more accurate interpretation of the spectral variations. The usefulness of this method is demonstrated with a theoretical framework and applications to the 2D correlation analyses of both simulated data and temperature-dependent reflection-absorption infrared spectra of a poly(3-hydroxybutyrate) (PHB) thin film.     

Effect of temperature and concentration on the structure of N-methylacetamide-water complexes: Near-infrared spectroscopic study

Generalized two-dimensional (2D) FT-NIR correlation spectroscopy and chemometric methods have been used to study temperature-dependent spectral changes in pure N-methylacetamide (NMA) and NMA-water mixtures. We also examined the effect of varying water content on the structure of the mixture. It has been found that the extent of self-association of NMA in CCl4 is very high; the association occurs even at concentration of 0.001 M. In the pure liquid NMA, the population of the monomers is negligible and the structure is dominated by the linear associates. An increase in temperature reduces the number of hydrogen bonds, but in contrast to alcohols their strength remains nearly the same. This reflects a difference in the mechanism of thermal breaking of the associates of NMA and alcohols. The present results reveal that the interaction between NMA and water in the NMA-rich region (X(H2O) < 0.1) does not have a significant effect on the intrinsic structure of NMA. The structure of NMA is dominant, and the molecules of water do not form separate clusters but are dispersed and incorporated into the structure of NMA. We did not observe the presence of the free OH groups in the mixture. This led to the suggestion that each molecule of water forms two hydrogen bonds to two different molecules of NMA. An analysis of the asynchronous spectra reveals that most of the peaks observed in the asynchronous spectra, constructed from the temperature-dependent data, simply result from the frequency shift. This assumption is supported by the simulation studies.     

A two-dimensional infrared correlation spectroscopic study on the thermal degradation of poly(2-hydroxyethyl acrylate)-co-methyl methacrylate/SiO2 nanohybrids

Two-dimensional infrared (2D IR) correlation spectroscopy was applied to study the structural changes occurring in the decomposition of PHEA-co-MMA/SiO₂. Complicated absorption spectral changes were observed in the heating process. 2D IR analysis indicates that during heating, covalent bonds, (Si-O-C), between the polymer and the inorganic moiety were formed, which was the main factor in the improvement in thermal properties of the hybrids such as the decomposition temperatures (T_d). The thermal stability of the hybrids was also studied by solid-state ²⁹Si MAS NMR spectroscopy and TGA tests. Their results complemented each other well.     

A thermal oxidative degradation study of triallyl isocyanurate crosslinking moiety in fluorinated rubber by two-dimensional infrared correlation spectroscopy

Thermal degradation of crosslinking moiety in fluorinated rubbers was studied with a new method using spatial-dependent infrared (IR) microscopy and two-dimensional (2D) IR correlation spectroscopy. Upon heating the fluorinated rubber, initially the amount of crosslinker decreased followed by generating another chemical species with carbonyl substituent with IR absorption at around 1730 cm^–1, implying generation of carboxylic acids forming intermolecular hydrogen bonding. Furthermore, projection 2D IR correlation analysis revealed that another chemical species with IR absorption at around 1755 cm^–1 generates, indicating that further degradation progresses upon heating and intermolecular hydrogen bonding were broken. As a result, the multi-step degradation process of the crosslinker in the fluorinated rubber could be detected by combination of spatial-dependent IR microscopy and projection 2D IR correlation spectroscopy.     

N-乙基丙酰胺的飞秒二维红外光谱

利用飞秒二维红外实验方法, 结合稳态红外光谱实验和计算化学手段, 对β-肽模型分子N-乙基丙酰胺(NEPA)的超快结构动力学进行了研究. 结果表明, 在水溶液中, NEPA具有类α-肽酰胺-I 带的振动特征, 并表现出对分子结构和化学环境的灵敏性. 二维红外光谱动力学结果揭示了一个1 ps 左右的光谱扩散时间, 与酰胺-水之间的氢键结构动力学时间尺度一致.     

Fine Structure of Hydrogen Bonds in Cholic Acid Revealed by 2DIR Spectroscopy

Based on cryogenic FT-IR spectroscopic studies of hydrogen bonds in cholic acid, two-dimensional FT-IR spectroscopy was applied to enhance our understanding of the hydrogen bonds of cholic acid. Fine spectral structures were revealed by asynchronous 2D FT-IR spectra. The co-relationship among various bands was discussed according to the synchronous 2D FT-IR spectrum.     

Fine Structure of Hydrogen Bond in Cholic Acid Revealed by 2DIR Spectroscopy

Based on cryogenic FT-IR spectroscopic studies of hydrogen bonds in cholic acid, two-dimensional FT-IR spectroscopy was applied to enhance our understanding of the hydrogen bonds of cholic acid. Fine spectral structures were revealed by asynchronous 2D FT-IR spectra. The co-relationship among various bands was discussed according to the synchronous 2D FT-IR spectrum.     

Monitoring selected hydrogen bonds in crystal hydrates of amino acid salts: combining variable-temperature single-crystal X-ray diffraction and polarized Raman spectroscopy

Predicting behaviour of hydrogen bonds with varying temperature, in particular-correlating donor-acceptor distances in the O-H···O hydrogen bonds with the frequencies of O-H stretching vibrations is important for understanding dynamics of biomolecules and phase transitions in crystals. A commonly used correlation suggested earlier in the literature is based on statistical analysis of different compounds [A. Novak, Structure and Bonding, 1974, 18, 177; K. Nakamoto, M. Margoshes, R. E. Rundle, J. Am. Chem. Soc., 1955, 77, 6480]. The present study is a rare example when correlations between geometry and energy parameters have been found for selected individual hydrogen bonds in the same crystalline compound at multiple temperatures. The properties of several types of O-H···O hydrogen bonds in bis(DL-serinium) oxalate dihydrate and DL-alaninium semi-oxalate monohydrate have been studied by a combination of variable-temperature single-crystal X-ray diffraction and polarized Raman spectroscopy. The changes in the hydrogen bonds geometry could be compared with the changes of the corresponding spectral modes. The correlation suggested by Novak is roughly followed, better for medium and weak, than for short hydrogen bonds. Fine details of spectral changes differ for individual bonds. The way how H-bonds are affected by cooling depends on their environment in the crystal structure. Short O-H···O hydrogen bonds in bis(DL-serinium) oxalate dihydrate expand or remain almost unchanged on cooling, whereas in DL-alaninium semi-oxalate monohydrate all strong H-bonds are compressed under these conditions. The distortion of individual hydrogen bonds on temperature variations is correlated with the anisotropy of lattice strain.     

X-ray and IR studies on crystal and molecular structure of 4-nitro-2,6-diphenylphenol. Stereochemistry of bifurcated OH⋯π hydrogen bonds

The crystals of the title compound contain both intra- and inter-molecular OH?π hydrogen bonds (the first example of bifurcated OH?π bonds), the stereochemistry of which has been elucidated by an X-ray structure analysis; this bifurcated bond is also supported by the observation based on the IR spectrum of the crystals.     

聚酰胺酸结构及其亚胺化的红外光谱分析

利用变温透射红外光谱方法,通过跟踪聚酰胺酸（PAA）的亚胺化过程,对由均苯四酸二酐和4,4′-二氨基二苯醚合成的聚酰胺酸及经过加热亚胺化后生成的聚酰亚胺(PI)的红外吸收光谱进行分析,对聚酰胺酸和聚酰亚胺的红外谱峰进行合理的归属,发现聚酰胺酸在亚胺化过程中有-COO-和-NH+2存在,-COO-中羰基的对称与反对称伸缩振动分别位于1607和1406 cm-1,NH+2的伸缩振动则有3200、3133、2938、2880、2820和2610 cm-1等多个精细谱带。 并根据对-COO-和-NH+2谱峰的归属,提出聚酰胺酸生成聚酰亚胺的机理为聚酰胺酸中COOH的H+转移到聚酰胺酸中的NH上,形成NH+2,然后脱水环化生成聚酰亚胺。     

Application of dynamic 2D FTIR to cellulose

Cellulose, the dominant polymer in the biosphere, is a homopolysaccharide composed of (1,4)-β-d-glucopyranose. Interactions between and within the cellulose polymer chains are mainly determined by inter- and intramolecular hydrogen bonds, which are therefore mainly responsible for mechanical properties of cellulosic materials. The coupling of dynamic mechanical analysis (DMA) and 2D step-scan Fourier transform infrared (FTIR) spectroscopy, is shown to be a very promising way of investigating these submolecular interactions in cellulosic materials. The broad and unstructured band in the OH-stretching vibration region (3100 and 3700 cm⁻¹) of the cellulose vibrational spectra, which contains information about the intra- and intermolecular hydrogen bonds, can be unraveled by this new technique. In the experiments reported here, cellulose sheets have been stretched sinusoidally at low strains while being irradiated with polarized infrared light. For the obtained dynamic IR signals (the in-phase and the out-of-phase responses of the sample), the dynamic IR cross-correlation was defined. It consists of two terms which are referred to as the synchronous and the asynchronous 2D infrared correlation intensities. In the 2D spectra, obtained by DMA–FTIR, several distinct peaks are observed in the OH-range between 3700 and 3100 cm⁻¹ which may be related to specific interactions.