Time-dependent fifth-order bands in nominally third-order 2D IR vibrational echo spectra

Progress in the field of 2D IR vibrational spectroscopy has been bolstered by the production of intense mid-IR laser pulses. As higher-energy pulses are employed, a concomitant increase occurs in the likelihood of fifth-order contributions to the 2D IR spectra. We report the appearance of fifth-order signals in 2D IR spectra of CO bound to the active site of the enzyme cytochrome P450(cam) with the substrate norcamphor. Two bands with novel time dependences, one on the diagonal and one off-diagonal, are not accounted for by normal third-order interactions. These bands are associated with a ν = 1-2 vibrational transition frequency. Both bands decay to 0 and then grow back in with opposite sign. The diagonal band is positive at short time, decays to 0, reappears with negative sign, before eventually decaying to 0. The off-diagonal band is negative at short time, decays to 0, reappears positive, and then decays to 0. The appearance and time dependence of these bands are characterized. Understanding these fifth-order bands is useful because they may be misidentified with time-dependent bands that arise from other processes, such as chemical exchange, vibrational coupling, or energy transfer. The presence and unusual time dependences of the fifth-order bands are reproduced with model calculations that account for the fact that vibrational relaxation from the ν = 2 to 1 level is approximately a factor of 2 faster than that from the ν = 1 to 0 level.     

Effect of cation exchange in T-type zeolite on the IR spectra of sorbed methanol

Sorption of methanol on unexchanged zeolite T and zeolite with 43% and 66% of exchanged cations has been studied at room temperature by means of interferometric spectroscopy. Interaction between methanol and the hydroxy groups of zeolite is revealed. The methoxylation of the zeolite surface has been confirmed.

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, 43 66%, . . .

     

Isotope exchange of heterocyclic compounds with D2O in the presence of transition metals

During a study of deuterium-hydrogen exchange of two-ring condensed heterocycles in the presence of a Pt catalyst it was observed that the degree of deuteration decreases in the order benzofuran naphthalene > benzothiophene. It was found that the degree of deuteration of 2-acetylbenzofuran is 80%, whereas for 2-propylbenzofuran it is only 8%. The degree of deuteration of hydrogenated derivatives decreases in the order coumarin > chromene > dihydrocoumarin; the formation of polydeuterated derivatives is observed for coumarin, whereas products of replacement of one hydrogen atom by deuterium predominate for chromene and dihydrocoumarin.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 4, pp. 451–453, April, 1981.     

Synthesis and IR spectra of some 2-aminobenzoxazole derivatives

A large number of 5-nitro-, 6-nitro-, 5-chloro-, and 6-bromo-2-aminobenzoxazoles were synthesized by the reaction of benzoxazoline-2-thiones with various amines. It was shown by IR spectroscopy that all of the compounds exist in the amino form in solution, whereas the 5-substituted compounds exist in the imino form in the solid state, and the 6-substituted compounds exist simultaneously in the two forms.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 5, pp. 604–607, May, 1981.The authors thank T. Dukhova, P. Braikov, I. Nachev, and T. Georgieva for their assistance in carrying out several of the experiments.     

IR spectra and structure of 2-aryl-3-hydroxypyridines

The IR spectra of methyl, chloro, and phenyl derivatives of 3-hydroxypyridines in CCl₄ solutions and in the crystalline state were studied. A comparison of the frequencies, half widths, and integral intensities of the bands of the stretching vibrations of the hydroxyl groups in the spectra of solutions of the 3-hydroxypyridine derivatives in CCl₄ with the characteristic OH bands in the spectra of phenols demonstrates that 3-hydroxypyridines exist practically completely in the hydroxy form in dilute CCl₄ solutions. The shift in the OH bands in the spectra of 2-phenyl-3-hydroxypyridine derivatives indicates that the OH group forms a -hydrogen bond with the phenyl ring. The presence also of a band of a free OH group is evidence for the existence of s-cis and s-trans conformers relative to the C-O bond.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 2, pp. 187–190, February, 1972.     

IR absorption and Raman spectra of silicon dioxide nanoparticles in the presence of water: Computer experiment

Interactions of (SiO₂)₅₀ clusters with 10, 20, 30, or 40 water molecules are studied by molecular dynamics method. Flat SiO₂ nanoparticle covered with a water layer is formed after the inclusion of water molecules into the cluster. As a rule, the integral intensity of IR and Raman spectra lowers after the absorption of H₂O molecules by the cluster. The power of IR radiation emitted by the cluster increases nonmonotonically with the addition of water molecules to the cluster. The absorption of water molecules by the cluster leads to a significant increase in the absorption coefficient and only a slight increase in the refractive index. The number of electrons participating in the interaction with electromagnetic radiation increases with the addition of water molecules to the cluster.     

Effect of the internal field on the IR absorption spectra of small particles in the case of 3D, 2D, and 1D size confinement

The spectral properties of composite materials based on small particles under 1D, 2D, and 3D size confinement are described using a combination of dispersive internal field and effective media theory approaches. Calculations performed for a number of crystalline materials have shown that the peak position and intensity of the vibrational band of the material under conditions of 1D, 2D, and 3D size confinement are changed, whereas the bandwidth of the band remains the same. In the case of 3D confinement, the peak position of the spectrum of isolated "mesoparticles" (epsilon(meso)(2)) appears to be very close to the intrinsic frequency of the lattice vibrations, calculated from the elastic constants of this crystal, as well as to the Fr?hlich's frequency. The largest shift (Deltanu) of the peak frequency, nu(max), from the bulk value is obtained in the case of 1D confinement when the peak position is practically coincident with the frequency of the longitudinal optical phonon (nu(LO)). These shifts are the result of intermolecular interactions, including both resonant and induced resonant dipole-dipole interactions.     

IR spectra and structure of 2- imino-1,3-dimethylbenzimidazolines

The fine structure of some N-substituted 2-imino-1,3-dimethyl-benzimidazolines is examined with the aid of IR spectroscopy. It is shown that the introduction of an alkyl or phenyl group into the imino group does not affect the C=N group or the imidazoline ring structure. In salts of 2-imino-1,3-dimethylbenzimidazoline and its N-substituted derivatives, the heterocyclic system has the benzimidazolium structure. The structure of 2-imino-1,3-dimethylbenzimidazolines in which the exocyclic nitrogen atom has electrophilic substituents which are conjugated with the heterocycle is characterized by a considerable contribution from dipolar forms, with the imidazole ring bearing a positive charge.Translated from Khimiya Geterotskilicheskikh Soedinenii, Vol. 6, No. 5, pp. 674–678, May 1970.     

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.     

Reversible temperature effects in the matrix IR spectra of halogenated 2-propanols

The reversible temperature effects in the IR spectra of CCl₃CHOHCCl₃ and of a few other halogenated 2-propanols in N₂, CO and mixed N₂-Ar matrices have been studied. Alcohol-nitrogen complexes are formed reversibly and irreversibly in matrices containing nitrogen.     

Vibrational dynamics of DNA. II. Deuterium exchange effects and simulated IR absorption spectra

In Paper I, we studied vibrational properties of normal bases, base derivatives, Watson-Crick base pairs, and multiple layer base pair stacks in the frequency range of 1400-1800 cm(-1). However, typical IR absorption spectra of single- and double-stranded DNA have been measured in D(2)O solution. Consequently, the more relevant bases and base pairs are those with deuterium atoms in replacement with labile amino hydrogen atoms. Thus, we have carried out density functional theory vibrational analyses of properly deuterated bases, base pairs, and stacked base pair systems. In the frequency range of interest, both aromatic ring deformation modes and carbonyl stretching modes appear to be strongly IR active. Basis mode frequencies and vibrational coupling constants are newly determined and used to numerically simulate IR absorption spectra. It turns out that the hydration effects on vibrational spectra are important. The numerically simulated vibrational spectra are directly compared with experiments. Also, the (18)O-isotope exchange effect on the poly(dG):poly(dC) spectrum is quantitatively described. The present calculation results will be used to further simulate two-dimensional IR photon echo spectra of DNA oligomers in the companion Paper III.     

Polarized IR spectra of the hydrogen bond in 2-thiopheneacetic acid and 2-thiopheneacrylic acid crystals: H/D isotopic and temperature effects

Polarized IR spectra of 2-thiopheneacetic acid and of 2-thiopheneacrylic acid crystals were measured at 293 and 77 K in the υ(O-H) and υ(O-D) band frequency ranges. The corresponding spectra of the two individual systems strongly differ, one from the other, by the corresponding band shapes as well as by the temperature effect characterizing the bands. The crystal spectral properties remain in close relation with the electronic structure of the two different molecular systems. We show that a vibronic coupling mechanism involving the hydrogen bond protons and the electrons on the π- electronic systems in the molecules determines the way in which the vibrational exciton coupling between the hydrogen bonds in the carboxylic acid dimers occurs. Strong coupling in 2-thiopheneacrylic acid dimers prefers a "tail-to-head"-type Davydov coupling widespread by the π- electrons. A weak through-space coupling in 2-thiopheneacetic acid dimers, of a van der Waals type, is responsible for a "side-to-side"-type coupling. The relative contribution of each exciton coupling mechanism in the dimer spectra generation is temperature and the molecular electronic structure dependent. This explains the observed difference in the temperature- induced evolution of the compared spectra.     

Synthesis and IR spectra of 2-phenylbenzimidazole and its amino derivatives

2-Phenylbenzimidazole and its mono and diamino derivatives were synthesized in yields up to 85% by cyclodehydration of o-aminobenzanilides in hydrochloric or sulfuric acid. The IR spectra of the compounds obtained were studied, the principal bands of the stretching and deformation vibrations of the NH and NH₂ groups were assigned, and the presence of associates with a hydrogen bond was established.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 1, pp. 115–116, January, 1973.     

Two-dimensional infrared (2D IR) spectroscopy. A new tool for interpreting infrared spectra

Two-dimensional infrared (2D IR) spectroscopy is used to study atactic polystyrene. 2D IR is a technique based on time-resolved detection of IR signals in response to an external perturbation, such as mechanical strain. Since different chemical functional groups respond to the applied perturbation at unique and often different rates, characteristic time-dependent variations of the IR-band intensities are observed. Correlation analysis of the dynamic variation of the IR signals yields a new spectrum defined by two independent wave numbers. Peaks located on a 2D IR spectral plane imply interactions and connectivities among chemical functional groups. By spreading convoluted IR bands over two dimensions, the spectral resolution is also greatly enhanced.     

Liquid crystalline properties and IR spectra of 2'-hydroxy-4'-octyloxyazobenzenes

New azobenzene derivatives, namely 3,5-dichloro, 2,6-dimethyl and 3-chloro-4-methyl derivatives of 2'-hydroxy-4'-octyloxyazobenzene were synthesized and their properties were compared with those of 4-chloro, 4-methyl and 4-nitroderivatives. Special attention was paid to the characteristics of intramolecular O-H...N hydrogen bond reflected in IR spectra of CCl(4) solutions and neat crystalline samples. The spectra were analyzed based on DFT calculations. In all cases of solutions very strong hydrogen bonds are manifested in broad bands centered at about 2700-2800 cm(-1) of low intensity typical of resonance assisted H-bonds. On the other hand, in cases of neat crystalline samples, a broad, intensified absorption is extended down to approximately 600 cm(-1) forming a continuum resembling a Hadzi's trio. However, neither broad maxima nor minima can be assigned to delta(OH) or gamma(OH) overtones. The studies of the H/D isotope effect on the continuum seem to indicate on the role of resonance couplings between nu(OH) vibrators of neighboring molecules as well as hot bands arising from the coupling between high and low frequency modes. These couplings modify the dynamic pattern of the potential for the proton motion leading to a decrease of the barrier for the proton transfer.     

Comparison between IR absorption and raman scattering spectra of liquid and supercritical 1-butanol

Raman spectra of 1-butanol have been obtained at a constant pressure of 500 bar up to 350 degrees C and along isotherms 250, 300, and 350 degrees C up to 600 bar. The purpose of the experiment was to compare responses of Raman and IR absorption spectroscopy to the forming of O-H...O bonds in alcohols. As a result, some important inferences were drawn from the experiment. In particular, it has been estimated quantitatively how the intensity of Raman scattering in the region of the OH band depends on the extent of hydrogen bonding. As might be expected, the dependence is much weaker than in the case of the IR absorption. As was shown, the ratio of integrated intensities of bonded molecules in the absorption and scattering spectra is a constant and does not depend on temperature and density. The effect of cooperativity of hydrogen bonds is confirmed. It was also found that even at high pressures, a noticeable amount of nonbonded molecules exists at room temperature.     

Amide bands in the IR spectra of urethanes

The objective of this article is investigation of the normal modes of vibrations of molecules containing amide or urethane groups. Comparison between methyl-N-methylcarbamate (MMC) and N-methylacetamide (NMA) has been discussed. Density functional (DFT) calculations at B3LYP/6-31G(d) level have been employed to investigate the normal modes of MMC and several simple urethanes. This level was used as a compromise between accuracy and applicability to larger systems. The obtained results are in good agreement with experimental spectra. Finally, we have confirmed that the use of “amide terminology” is correct when addressing urethane molecules.     

Comparison of new and existing algorithms for the analysis of 2D radioxenon beta gamma spectra

The aim of this paper is to compare radioxenon beta–gamma analysis algorithms using simulated spectra with experimentally measured background, where the ground truth of the signal is known. We believe that this is among the largest efforts to date in terms of the number of synthetic spectra generated and number of algorithms compared using identical spectra. We generate an estimate for the minimum detectable counts for each isotope using each algorithm. The paper also points out a conceptual model to put the various algorithms into a continuum. Our results show that existing algorithms can be improved and some newer algorithms can be better than the ones currently used.