Dual-frequency 2D IR on interaction of weak and strong IR modes

Dual-frequency 2D IR heterodyne photon-echo spectroscopy of C[triple bond]N and C=O stretching vibrational modes in 2-cyanocoumarin is reported. We have shown that the interaction among these modes provides convenient and useful structural constraints for molecules. Implementation of two pulse sequences, 4, 4, and 6 microm and 6, 6, and 4 microm, allowed the clear determination of contributions caused by vibrational relaxation. Positive correlation between C[triple bond]N and C=O frequency distributions was observed in 2-cyanocoumarin. Because C[triple bond]N modes are highly localized and have frequencies in a spectral region with minimal water absorption, the C[triple bond]N/C=O interactions have a strong potential for use as structural reporters in proteins. In addition to CN/CO peaks, the cross-peaks responsible for the C[triple bond]N/C=C interaction are also observed in the 2D IR spectra, where C=C is a coumarin ring stretching mode. We have demonstrated that 2D IR spectroscopy can utilize interactions of strong IR modes with weak local modes as structural reporters.     

Anharmonic vibrational modes of nucleic acid bases revealed by 2D IR spectroscopy

Polarization-dependent two-dimensional infrared (2D IR) spectra of the purine and pyrimadine base vibrations of five nucleotide monophosphates (NMPs) were acquired in D(2)O at neutral pH in the frequency range 1500-1700 cm(-1). The distinctive cross-peaks between the ring deformations and carbonyl stretches of NMPs indicate that these vibrational modes are highly coupled, in contrast with the traditional peak assignment, which is based on a simple local mode picture such as C═O, C═N, and C═C double bond stretches. A model of multiple anharmonically coupled oscillators was employed to characterize the transition energies, vibrational anharmonicities and couplings, and transition dipole strengths and orientations. No simple or intuitive structural correlations are found to readily assign the spectral features, except in the case of guanine and cytosine, which contain a single local CO stretching mode. To help interpret the nature of these vibrational modes, we performed density functional theory (DFT) calculations and found that multiple ring vibrations are coupled and delocalized over the purine and pyrimidine rings. Generally, there is close correspondence between the experimental and computational results, provided that the DFT calculations include explicit waters solvating hydrogen-bonding sites. These results provide direct experimental evidence of the delocalized nature of the nucleotide base vibrations via a nonperturbative fashion and will serve as building blocks for constructing a structure-based model of DNA and RNA vibrational spectroscopy.     

Simulation studies of amide I IR absorption and two-dimensional IR spectra of beta hairpins in liquid water

Amide I IR absorption and two-dimensional (2D) IR photon echo spectra of a model beta hairpin in aqueous solution are theoretically studied and simulated by combining semiempirical quantum chemistry calculations and molecular dynamics simulation methods. The instantaneous normal-mode analysis of the beta hairpin in solution is performed to obtain the density of states and the inverse participation ratios of the one-exciton states. The motional and exchange narrowing processes are taken into account by employing the time-correlation function theory for the linear and nonlinear response functions. Numerically simulated IR absorption and 2D spectra are then found to be determined largely by the amide I normal modes delocalized on the peptides in the two strands. The site-specific isotope-labeling effects on the IR and 2D IR spectra are discussed. The simulation results for the ideal (A17) beta hairpin are directly compared with those of the realistic 16-residue (GB1) beta hairpin from an immunoglobulin G-binding protein. It was found that the characteristic features in IR and 2D spectra of both the ideal (A17) beta hairpin and the GB1 beta hairpin are the same. The simulated IR spectrum of the GB1 beta hairpin is found to be in good agreement with experiment, which demonstrates that the present computational method is quantitatively reliable.     

Vibrational relaxation pathways of amide I and amide II modes in N-methylacetamide

We studied the vibrational energy relaxation mechanisms of the amide I and amide II modes of N-methylacetamide (NMA) monomers dissolved in bromoform using polarization-resolved femtosecond two-color vibrational spectroscopy. The results show that the excited amide I vibration transfers its excitation energy to the amide II vibration with a time constant of 8.3 ± 1 ps. In addition to this energy exchange process, we observe that the excited amide I and amide II vibrations both relax to a final thermal state. For the amide I mode this latter process dominates the vibrational relaxation of this mode. We find that the vibrational relaxation of the amide I mode depends on frequency which can be well explained from the presence of two subbands with different vibrational lifetimes (~1.1 ps on the low frequency side and ~2.7 ps on the high frequency side) in the amide I absorption spectrum.     

Ultrafast 2D IR anisotropy of water reveals reorientation during hydrogen-bond switching

Rearrangements of the hydrogen bond network of liquid water are believed to involve rapid and concerted hydrogen bond switching events, during which a hydrogen bond donor molecule undergoes large angle molecular reorientation as it exchanges hydrogen bonding partners. To test this picture of hydrogen bond dynamics, we have performed ultrafast 2D IR spectral anisotropy measurements on the OH stretching vibration of HOD in D(2)O to directly track the reorientation of water molecules as they change hydrogen bonding environments. Interpretation of the experimental data is assisted by modeling drawn from molecular dynamics simulations, and we quantify the degree of molecular rotation on changing local hydrogen bonding environment using restricted rotation models. From the inertial 2D anisotropy decay, we find that water molecules initiating from a strained configuration and relaxing to a stable configuration are characterized by a distribution of angles, with an average reorientation half-angle of 10°, implying an average reorientation for a full switch of ≥20°. These results provide evidence that water hydrogen bond network connectivity switches through concerted motions involving large angle molecular reorientation.     

Novel carbonyl allylation mediated by SnCl2/TiCl3 in water

[reaction: see text] Under the Lewis acid catalysis offered by TiCl(3), SnCl(2) can efficiently mediate the aqueous Barbier reactions between aldehydes and allyl chloride or bromide.     

HPLC-NMR-IR法对脂肪酰胺聚氧乙烯型非离子表面活性剂的分离与鉴定

采用HPLC法,选择最佳分离条件,对分子量分布较宽,分散性大的高碳脂肪酸胺聚氧乙烯非离子表面活性剂的全组分,进行了分离;在无标准样时,制备主要馏分,以核磁波谱及红外光谱鉴定,对该类型样品获得了较理想结果。本方法适用于复杂组分的分析,且快速、高效、定性简单。     

Simulation of vibrational energy transfer in two-dimensional infrared spectroscopy of amide I and amide II modes in solution

Population transfer between vibrational eigenstates is important for many phenomena in chemistry. In solution, this transfer is induced by fluctuations in molecular conformation as well as in the surrounding solvent. We develop a joint electrostatic density functional theory map that allows us to connect the mixing of and thereby the relaxation between the amide I and amide II modes of the peptide building block N-methyl acetamide. This map enables us to extract a fluctuating vibrational Hamiltonian from molecular dynamics trajectories. The linear absorption spectrum, population transfer, and two-dimensional infrared spectra are then obtained from this Hamiltonian by numerical integration of the Schrodinger equation. We show that the amide I/amide II cross peaks in two-dimensional infrared spectra in principle allow one to follow the vibrational population transfer between these two modes. Our simulations of N-methyl acetamide in heavy water predict an efficient relaxation between the two modes with a time scale of 790 fs. This accounts for most of the relaxation of the amide I band in peptides, which has been observed to take place on a time scale of 450 fs in N-methyl acetamide. We therefore conclude that in polypeptides, energy transfer to the amide II mode offers the main relaxation channel for the amide I vibration.     

Characterization of fungal degraded lime wood by FT-IR and 2D IR correlation spectroscopy

The action of soft-rot fungus Chaetomium globosum has been studied. The decayed lime wood samples were observed for different periods of exposure. The degree of decay was determined by weight loss which was of 50.4% after 133 days. The samples were analyzed by FT-IR and 2D IR correlation spectroscopy.The intensity bands assigned to different vibrations from cellulose and hemicelluloses show a decrease, while the intensities of the bands assigned to C–O vibrations due to the formation of oxidized structures increase. At the same time, the intensity of the band assigned to C–O in metoxyl groups from lignin shows a decrease with increasing exposure time. The differences between reference and decayed wood spectra were examined in detail using 2D correlation spectroscopy and the second derivative analysis for two exposure time periods — of 0–70 days and 70–133 days. The formation of reactive species due to oxidation reactions induced by enzymes and the demethoxylation of the lignin structure was evidenced.     

Bridgehead enolates: substitution and asymmetric desymmetrization of small bridged carbonyl compounds by lithium amide bases

[reaction: see text] Contrary to expectations, a number of bridged carbonyl compounds undergo facile bridgehead metalation with lithium amide bases. Diketone, lactone, lactam, and imide functions are all demonstrated to participate in this type of "bridgehead enolate" chemistry, leading to a range of substituted products. Meso compounds can also be desymmetrized in very high ee by asymmetric bridgehead metalation.     

Dynamic structures of aqueous oxalate and the effects of counterions seen by 2D IR

Two dimensional vibrational echo spectra of oxalate in the carboxylate asymmetric stretch region in D(2)O show two transitions having anomalously slow spectral diffusion and a third transition having relaxation properties typical of the free carboxylate ion. Quantitative analysis of the frequency shifts of the carboxylate asymmetric stretch modes caused by a singly charged cation in the oxalate hydration shell supports that ion pairs can be responsible for these new transitions. Experimental evidence and DFT calculations are consistent with oxalate forming a mixture of "side-on" and "end on" contact ion pairs wherein the carboxylate groups are protected from mobile heavy water molecules.     

Ultrafast Vibrational Population Transfer Dynamics in 2‐Acetylcyclopentanone Studied by 2D IR Spectroscopy

2‐Acetylcyclopentanone (2‐ACP), which is a β‐dicarbonyl compound, undergoes keto–enol isomerization, and its enol tautomers are stabilized by a cyclic intramolecular hydrogen bond. 2‐ACP (keto form) has symmetric and asymmetric vibrational modes of the two carbonyl groups at 1748 and 1715 cm^?1, respectively, which are well separated from the carbonyl modes of its enol tautomers in the FTIR spectrum. We have investigated 2‐ACP dissolved in carbon tetrachloride by 2D IR spectroscopy and IR pump–probe spectroscopy. Vibrational population transfer dynamics between the two carbonyl modes were observed by 2D IR spectroscopy. To extract the population exchange dynamics (i.e., the down‐ and uphill population transfer rate constants), we used the normalized volumes of the cross‐peaks with respect to the diagonal peaks at the same emission frequency and the survival and conditional probability functions. As expected, the downhill population transfer time constant (3.2 ps) was measured to be smaller than the uphill population transfer time constant (3.8 ps). In addition, the vibrational population relaxation dynamics of the two carbonyl modes were observed to be the same within the experimental error and were found to be much slower than vibrational population transfer between two carbonyl modes.     

The selective reaction of primary amines with carbonyl imidazole containing compounds: selective amide and carbamate synthesis

A new highly selective synthesis of amides and carbamates is described. In both cases the syntheses involve the formation of carbonyl imidazole intermediates which subsequently undergo previously unreported selective reactions with primary amines. Acid imidazolides with sufficient chain length will exclusively react with primary amines even in the presence of secondary and tertiary functionality. The imidazole carboxylic esters of secondary or tertiary alcohols also react selectively with primary amines, forming controlled carbamate structures.     

The anharmonic vibrational potential and relaxation pathways of the amide I and II modes of N-methylacetamide

We investigate the influence of isotopic substitution and solvation of N-methylacetamide (NMA) on anharmonic vibrational coupling and vibrational relaxation of the amide I and amide II modes. Differences in the anharmonic potential of isotopic derivatives of NMA in D2O and DMSO-d6 are quantified by extraction of the anharmonic parameters and the transition dipole moment angles from cross-peaks in the two-dimensional infrared (2D-IR) spectra. To interpret the effects of isotopic substitution and solvent interaction on the anharmonic potential, density functional theory and potential energy distribution calculations are performed. It is shown that the origin of anharmonic variation arises from differing local mode contributions to the normal modes of the NMA isotopologues, particularly in amide II. The time domain manifestation of the coupling is the coherent exchange of excitation between amide modes seen as the quantum beats in femtosecond pump-probes. The biphasic behavior of population relaxation of the pump-probe and 2D-IR experiments can be understood by the rapid exchange of strongly coupled modes within the peptide backbone, followed by picosecond dissipation into weakly coupled modes of the bath.     

The IR spectra of carbonyl oxide and dioxirane: a theoretical investigation at a correlated level

Harmonic frequencies, IR intensities and ¹⁸O isotopic shifts for carbonyl oxide and dioxirane have been calculated at the MP2/6-31G level of theory. The results are discussed with respect to an experimental distinction between the two peroxide isomers by low-temperature IR spectroscopy.     

Identification of carbonyl species of weathered LDPE films by curve fitting and derivative analysis of IR spectra

We describe the examination of the weathering degradation of LDPE (low density polyethylene - locally produced B24/2 and imported LDPE 2100T), supplied by two different manufacturers and processed into films for greenhouse coverings, over several months in a sub-Saharan region of Algeria. The three IR regions most affected by weathering degradation are 800–1100 cm⁻¹, 1680–1800 cm⁻¹ and 3300–3600 cm⁻¹. The IR spectral region most affected by the aging process is the carbonyl region. Curve fitting combined with derivative spectroscopy revealed that the composite carbonyl band encompasses more than 10 different oxidation products. The most significant among these in terms of absorbance are carboxylic acids, ketones, aldehydes and esters. The oxidation kinetics with respect to the type of LDPE film shows that B24/2 LDPE undergoes less oxidization than LDPE 2100 T. Calculating the concentrations of different carbonyl species compared to their respective absorbances indicates that the aldehydes are the predominant component of the final compound, rather than the carboxylic acids.     

Benign and highly efficient synthesis of quinolines from 2-aminoarylketone or 2-aminoarylaldehyde and carbonyl compounds mediated by hydrochloric acid in water

An environmentally friendly and highly efficient procedure for the preparation of substituted quinoline derivatives was developed by a simple Friedländer reaction of 2-aminoarylketone or 2-aminoarylaldehyde with carbonyl compounds in the presence of hydrochloric acid utilizing water as the solvent.