Sulfoxide stretching mode as a structural reporter via dual-frequency two-dimensional infrared spectroscopy

The S=O stretching mode in sulfoxides, having a frequency in the 950-1150?cm(-1) range, is tested as a structural label via dual-frequency two-dimensional infrared (2DIR) spectroscopy. The properties of this structural reporter are studied in several compounds, including (4,4(')-dimethyl-2,2(')-bipyridyl)(o-methylsulfinylbenzoate) ruthenium II, [Ru(dmb)(2)(BzSO)](+), (RuBzSO), octylsulfinylpropionic acid (OSPA), and o- and p-methylsulfinyl-benzoic acid (oMSBA and pMSBA). The mode assignment in the fingerprint region for these compounds is made using a combination of density functional theory calculations and 2DIR and relaxation-assisted 2DIR (RA 2DIR) spectroscopies. The SO stretching mode frequency and IR intensity demonstrate substantial sensitivity to the molecular structure. Multiple cross peaks of the C=O and S=O stretching modes with modes in the fingerprint region (930-1450?cm(-1)) were recorded. The 2DIR and RA 2DIR spectra focusing at interactions of a high-frequency mode of a ligand with the modes in the fingerprint region provide a spectral fingerprint of a compound and help mode assignment in the often congested fingerprint region. The cross-peak amplitudes in oMSBA, pMSBA, and OSPA were compared with the theoretical predictions based on the computed values for the off-diagonal anharmonicities and a reasonable match is found. The SO stretching mode provides means for assigning other modes in the fingerprint region and constitutes a promising structural reporter for the 2DIR and RA 2DIR spectroscopy measurements.     

Excitonic effects in two-dimensional vibrational spectra of liquid formamide

The linear and two-dimensional infrared (2DIR) responses of the amide I vibrational mode in liquid formamide are investigated experimentally and theoretically using molecular dynamics simulations. The recent method based on the numerical integration of the Schr?dinger equation is employed to calculate the 2DIR spectra. Special attention is devoted to the interplay of the structural dynamics and the excitonic nature of the amide I modes in determining the optical response of the studied system. In particular, combining experimental data, simulated spectra and analysis of the simulated atomic trajectory in terms of a transition dipole coupling model, we provide a convincing explanation of the peculiar features of the 2DIR spectra, which show a substantial increase of the antidiagonal bandwidth with increasing frequency. We point out that, at variance with liquid water, the 2DIR spectral profile of formamide is determined more by the excitonic nature of the vibrational states than by the fast structural dynamics responsible for the frequency fluctuations.     

Fenchone, camphor, 2-methylenefenchone and 2-methylenecamphor: a vibrational circular dichroism study

We report and discuss the infrared (IR) vibrational circular dichroism (VCD) spectra of the enantiomeric pairs of the olefin derivatives of fenchone (1,3,3-trimethyl-2-methylenebicyclo[2.2.1]heptane) and camphor (1,7,7-trimethyl-2-methylenebicyclo[2.2.1]heptane), respectively, together with those of the parent molecules. The VCD spectra were taken in three spectral regions: the mid-IR region, encompassing the fundamental deformation modes, the region of CH-stretching fundamental modes and the NIR-region between 1100 and 1300 nm, which corresponds to the second CH-stretching overtone. The VCD and absorption spectra in the first two regions are analyzed by use of current density functional theory (DFT) calculations. The NIR region is analyzed by a protocol that consists of the use of DFT-based calculations and in assuming local mode behavior: the local mode approach is found appropriate for interpreting the absorption spectra and, for the moment, acceptable for calculating NIR-VCD spectra. The analysis of the first region allows us to track the contribution of the C=O group in the vibrational optical activity of C-C stretching modes; notable differences are indeed found in olefins and ketones. On the contrary, in the other two regions the VCD spectra of olefins and ketones are more similar: in the normal mode region of CH stretching fundamentals the spectra are determined by the mutual orientation of the CH bonds; in the second overtone local mode region olefins and ketones signals show some differences.     

Single crystal vibrational studies of hydrogen bonding in ethylenediammonium chloride

Ethylenediammonium chloride (EDC) single crystal vibrational studies have been performed at room and low temperature as well. The results allowed to get further insight as to the nature of the unusual profile of the NH stretching spectral region. A careful analysis of the infrared spectra in polarized light of the ab and ac crystal faces using the oriented gas model approximation has shown that the absorption profile of the higher frequency region is due mainly to an anharmonic interaction between NH stretching modes and those combination tones which develop parallel transition moments. Single crystal Raman spectra at room and low temperatures (≈10 K) have allowed to localize the peaks of the NH stretching modes. The Raman active lattice mode frequencies were measured at 10 K and 300 K as well. Finally, an almost complete assignment of the internal modes has been reported.     

Ballistic energy transport along PEG chains: distance dependence of the transport efficiency

Dual-frequency relaxation-assisted two-dimensional infrared (RA 2DIR) spectroscopy was used to investigate energy transport in polyethylene glycol (PEG) oligomers of different length, having 0, 4, 8, and 12 repeating units and end-labeled with azido and succinimide ester moieties (azPEGn). The energy transport initiated by excitation of the N≡N stretching mode of the azido group in azPEGn in CCl(4) at ca. 2100 cm(-1) was recorded by probing the C=O stretching modes (reporters) of the succinimide ester moiety. Sensitive to the excess energy delivered to the reporter modes, RA 2DIR permits observation of both the through-bond and through-solvent energy transport contributions. The cross-peak data involving the reporter modes with different thermal sensitivity and the data for mixtures of compounds permitted concluding that through-bond energy transport is the dominant mechanism for most cross peaks in all four azPEGn compounds. The through-bond energy transport time, evaluated as the waiting time at which the cross peak maximum is reached, was found to be linearly dependent on the chain length of up to 60 ?, suggesting a ballistic energy transport regime. The through-bond energy transport speed determined from the chain-length dependence of T(max) in CCl(4) is found to be ca. 450 m s(-1). The cross-peak amplitude at the maximum decays exponentially with the chain length; a characteristic decay distance is found to be 15.7 ± 1 ?. The cross-peak amplitude at zero waiting time, determined by the end-to-end distance distribution, is found to decay with the chain length (L) as ～L(-1.4), which is close to predictions of the free flight chain model. The match indicates that the end-group interaction does not strongly perturb the end-to-end distribution, which is close to the ideal random coil distribution with the Gaussian probability density.     

Spectroscopic characterization of aminoacetonitrile,its ions and protonated aminoacetonitrile using quantum chemical methods

We present theoretical vibrational and absorption spectra of aminoacetonitrile, its cation, anion, cyanoprotonated, and aminoprotonated aminoacetonitrile. We used second‐order Moller–Plesset perturbation method (MP2) with TZVP basis set to obtain ground state geometries and vibrational spectra. Time dependent density functional theory method was used to obtain absorption spectra. Shifts in vibrational modes for aminoacetonitrile upon ionization and protonation are determined. The C≡N stretching mode which is the most important mode in detection of nitriles in space is more intense in aminoacetonitrile ions and its two protonated form and is less IR active for neutral aminoacetonitrile. The nature of electronic transition for these molecules is identified. All the electronic transitions for neutral aminoacetonitrile and its cation are the σ → σ* electronic transitions, whereas its anion and protonated aminoacetonitrile display the σ → σ* as well as π → π* transitions. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

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.     

Vibrationally quantum-state-specific dynamics of the reactions of CN radicals with organic molecules in solution

The dynamics of reactions of CN radicals with cyclohexane, d(12)-cyclohexane, and tetramethylsilane have been studied in solutions of chloroform, dichloromethane, and the deuterated variants of these solvents using ultraviolet photolysis of ICN to initiate a reaction. The H(D)-atom abstraction reactions produce HCN (DCN) that is probed in absorption with sub-picosecond time resolution using ～500 cm(-1) bandwidth infrared (IR) pulses in the spectral regions corresponding to C-H (or C-D) and C≡N stretching mode fundamental and hot bands. Equivalent IR spectra were obtained for the reactions of CN radicals with the pure solvents. In all cases, the reaction products are formed at early times with a strong propensity for vibrational excitation of the C-H (or C-D) stretching (v(3)) and H-C-N (D-C-N) bending (v(2)) modes, and for DCN products there is also evidence of vibrational excitation of the v(1) mode, which involves stretching of the C≡N bond. The vibrationally excited products relax to the ground vibrational level of HCN (DCN) with time constants of ～130-270 ps (depending on molecule and solvent), and the majority of the HCN (DCN) in this ground level is formed by vibrational relaxation, instead of directly from the chemical reaction. The time-dependence of reactive production of HCN (DCN) and vibrational relaxation is analysed using a vibrationally quantum-state specific kinetic model. The experimental outcomes are indicative of dynamics of exothermic reactions over an energy surface with an early transition state. Although the presence of the chlorinated solvent may reduce the extent of vibrational excitation of the nascent products, the early-time chemical reaction dynamics in these liquid solvents are deduced to be very similar to those for isolated collisions in the gas phase. The transient IR spectra show additional spectroscopic absorption features centered at 2037 cm(-1) and 2065 cm(-1) (in CHCl(3)) that are assigned, respectively, to CN-solvent complexes and recombination of I atoms with CN radicals to form INC molecules. These products build up rapidly, with respective time constants of 8-26 and 11-22 ps. A further, slower rise in the INC absorption signal (with time constant >500 ps) is attributed to diffusive recombination after escape from the initial solvent cage and accounts for more than 2/3 of the observed INC.     

Decongestion of methylene spectra in biological and non-biological systems using picosecond 2DIR spectroscopy measuring electron-vibration–vibration coupling

Methylene is found in the repeat units of many polymers including proteins. In some cases it appears to be a useful reporter of variation in local environment whilst in other contexts average behaviour seems to dominate. In this paper we apply a particular 2DIR technique to a range of systems containing methylene groups, showing that mode frequencies, linewidths and splittings can be easily extracted even when the infrared absorption bands are too congested to allow reliable analysis. 2DIR spectra of polyethylene and several liquid alkanes are compared and it is shown for the case of l-arginine that the methylene scissor modes are split and that this can be resolved by tracking the 2DIR spectrum as a function of time. Calculations from first principles reveal that for most of the methylene modes studied, electrical anharmonicity is the dominant contributor to the 2DIR cross-peak intensity, with the mechanical anharmonicity making only a small contribution.     

Infrared detection of a phenylboronic acid terminated alkane thiol monolayer on gold surfaces

Polarization modulation infrared reflectance absorption spectroscopy (PM-IRRAS) and infrared reflectance absorption spectroscopy (IRRAS) have been used to characterize the formation of a self-assembled monolayer of N-(3-dihydroxyborylphenyl)-11-mercaptoundecanamide) (abbreviated PBA) on a gold surface and the subsequent binding of various sugars to the PBA adlayer through the phenylboronic acid moiety to form a phenylboronate ester. Vibrationally resonant sum frequency generation (VR-SFG) spectroscopy confirmed the ordering of the substituted phenyl groups of the PBA adlayer on the gold surface. Solution FTIR spectra and density functional theory were used to confirm the identity of the observed vibrational modes on the gold surface of PBA with and without bound sugar. The detection of the binding of glucose on the gold surface was confirmed in part by the presence of a C-O stretching mode of glucose and the observed O-H stretching mode of glucose that is shifted in position relative to the O-H stretching mode of boronic acid. An IR marker mode was also observed at 1734 cm(-1) upon the binding of glucose. Additionally, changes in the peak profile of the B-O stretching band were observed upon binding, confirming formation of a phenylboronate ester on the gold surface. The binding of mannose and lactose were also detected primarily through the IR marker mode at approximately 1736 to 1742 cm(-1) depending on the identity of the bound sugar.     

Gas‐Phase Infrared Spectroscopy of Substituted Cyanobutadiynes: Roles of the Bromine Atom and Methyl Group as Substituents

The IR spectra of 5‐bromo‐2,4‐pentadiynenitrile (Br?C≡C?C≡C?CN) and 2,4‐hexadiynenitrile (CH₃?C≡C?C≡C?CN), a compound of interstellar interest, have been recorded within the 4000–500 cm^?1 spectral region and calculated by means of high‐level ab initio and density functional calculations. Although the calculated structures of both compounds are rather similar, there are very subtle differences, mainly in the strength of the C≡C bond not directly bound to the substituent. These subtle bonding differences are reflected in small, but not negligible, differences in the electron density at the corresponding bond critical points, and, more importantly, are reflected in the IR spectra. Indeed, the IR spectrum for the bromine derivative presents two well‐differentiated strong bands around 2250 cm^?1, whereas for the methyl derivative both absorptions coalesce in a single band. These bands correspond in both cases to the coupling between C≡C and C≡N stretching displacements. A third, very weak, band also associated with C≡C and C≡N coupled stretches is observed for the bromine derivative, but not for the methyl one, owing to its extremely low intensity.     

Fourier-transform Raman and infrared spectroscopic analysis of dipyrrinones and mesobilirubins

The Fourier-transform Raman (FT-Raman), infrared (FT-IR), and UV-visible absorption spectra of four dipyrrinones and two mesobilirubins have been investigated in the solid state and in CH2Cl2 solutions. A detailed spectral analysis, assignment and discussion of these spectra are presented. The bands at 1735-1738, 1691-1707 and 1359-1377 cm(-1) which were assigned to the stretching vibrations of the C-O-C and C-O-H and symmetric deformation of C-H bonds, respectively, can act as a marker to distinguish the compounds of this class. The striking differences between the spectra of the compounds suggest that mesobilirubin XIIIalpha is tending to adopt as ridge-tile conformation, rather than linear conformation.     

Collective oscillations and the linear and two-dimensional infrared spectra of inhomogeneous beta-sheets

We numerically calculate the collective amide I oscillations and the associated linear and two-dimensional infrared (2DIR) spectra for model antiparallel beta-sheets and study the effect of inhomogeneity. To visualize the collective vibrational exciton states, a new method is introduced, which proves very useful in classifying the optically dominant states with respect to their symmetry properties and phase relations, even in the absence of exact symmetries. We find that energy (diagonal) and interaction (off-diagonal) disorder may have profoundly different effects on the main peaks in the linear spectrum. We also show that in the 2DIR spectra energy disorder leads to diagonal stretching of the diagonal peaks, while the cross-peaks are typically stretched more horizontally. This offers an explanation for the recently observed overall Z-shape in experimental spectra. Finally, we find that the anharmonic splitting between associated positive and negative features in the 2DIR spectra scales inversely proportionally with the exciton delocalization size imposed by the disorder, thus offering a spectroscopic ruler for this size.     

Temperature effect on the surface phase transitions of monolayer films of C12E1 at air/water interface

The temperature-dependent conformational states of a monolayer film of ethylene glycol monododecyl ether (C₁₂E₁) at the air/water interface have been investigated using ellipsometry, surface tension, external reflection–absorption FTIR spectroscopy and two-dimensional infrared (2DIR) correlation analysis. The ellipticity coefficients and the entropy associated with C₁₂E₁ adsorption changed almost discontinuously at certain temperatures, which manifested the interfacial phase transitions. The phase transition and coexistence of two phases were further clarified using 2DIR correlation analysis with temperature perturbation. The asynchronous correlation maps revealed that both bands of asymmetric and symmetric C–H stretching vibration in one-dimensional IR were split into two components, which confirmed the coexistence of two phases at the interface.     

EPR, optical, infrared and Raman spectral studies of Actinolite mineral

Electron paramagnetic resonance (EPR), optical, infrared and Raman spectral studies have been performed on a natural Actinolite mineral. The room temperature EPR spectrum reveals the presence of Mn(2+) and Fe(3+) ions giving rise to two resonance signals at g = 2.0 and 4.3, respectively. The resonance signal at g = 2.0 exhibits a six line hyperfine structure characteristic of Mn(2+) ions. EPR spectra have been studied at different temperatures from 123 to 433 K. The number of spins (N) participating in the resonance at g = 2.0 has been calculated at different temperatures. A linear relationship is observed between log N and 1/T in accordance with Boltzmann law and the activation energy was calculated. The paramagnetic susceptibility (chi) has been calculated at different temperatures and is found to be increasing with decreasing temperature as expected from Curie's law. From the graph of 1/chi versus T, the Curie constant and Curie temperature have been evaluated. The optical absorption spectrum exhibits bands characteristic of Fe(2+) and Fe(3+) ions. The crystal field parameter Dq and the Racah parameters B and C have been evaluated from the optical absorption spectrum. The infrared spectral studies reveal the formation of Fe(3+)--OH complexes due to the presence of higher amount of iron in this mineral. The Raman spectrum exhibits bands characteristic of Si--O--Si stretching and Mg?OH translation modes.     

Hplc Method for Kinetic Study of Mutarotation of Sugars

Abstract

A high-performance liquid chromatographic (HPLC) method was established for kinetic studies of the interconversion (mutarotation) between pyranose sugar anomers in solution. At very low temperature, HPLC chromatograms of each sugar indicated the concentrations of each anomer in the state prior to the HPLC analysis. Thus, when one of the pyranose anomers obtained by recrystallization was dissolved into water and was analyzed by HPLC repeatedly, gradual changes in the chromatogrphic patterns were observed. The equilibrium concentrations of each sugar anomer in different solvents were found to vary, which was also investigated by HPLC.     

Vibrational and Structural Dynamics of Mn(CO)5Br and Re(CO)5Br Examined Using Nonlinear Infrared Spectroscopy

Vibrational and structural dynamics of two transition metal carbonyl complexes, Mn(CO)₅Br and Re(CO)₅Br were examined in DMSO, using ultrafast infrared pump-probe spectroscopy, steady-state linear infrared spectroscopy and quantum chemistry computations. Two carbonyl stretching vibrational modes (a low-frequency A₁ mode and two high-frequency degenerate E modes) were used as vibrational probes. Central metal effect on the CO bond order and force constant was responsible for a larger E-A₁ frequency separation and a generally more red-shifted E and A₁ peaks in the Re complex than in the Mn complex. A generally broader spectral width for the A₁ mode than the E mode is believed to be partially due to vibrational lifetime effect. Vibrational mode-dependent diagonal anharmonicity was observed in transient infrared spectra, with a generally smaller anharmonicity found for the E mode in both the Mn and Re complexes.     

Comparative Raman study of two laterally fluorinated LC compounds having different terminal chains

In this article, we present the Raman study of two laterally fluorinated liquid crystal compounds, namely, C3PP(23F)P-NCS and C3PP(23F)PC3. The two compounds have different terminal groups, one with NCS which is more polar than the other which has an alkyl group. The Raman bands were deconvoluted with Lorentzian profiles to get the values of spectral parameters. The main feature of the work is the temperature-dependent behaviour of the spectra profiles of the C–H bending mode, C–F stretching modes and aromatic C–C stretching mode in the vicinity of the phase transitions. The effect on the charge distribution over different bonds of the molecule and the vibrational energy of the bonds due to the presence of the more polar group on the terminal chain is well observed. The contrasting behaviours of the spectral profiles at the Cr–N and N–I transitions were also observed which we have ascribed to some pre-transitional effect associated with the breaking of the orientational order near the N–I transition. Density functional theory using B3LYP exchange correlation with the 6-31G (d,p) basis set was also used to generate a theoretical spectra which were found to be matching with the experimental spectra.     

Infrared spectra of the water-nitrogen complexes (H2O)2-(N2)n(n = 1-4) in argon matrices

The infrared spectra of the water-nitrogen complexes trapped in argon matrices have been studied with Fourier transform infrared absorption spectroscopy. The absorption lines of the H20-N2 1:1, 1:2, 1:n, and 2:1 complexes have been confirmed on the basis of the concentration effects. In addition, we have observed a few lines and propose the assignments for the 2:2, 2:3, and 2:4 complexes in the nu1 symmetric stretching and nu2 bending regions of the proton-acceptor molecule, and in the bonded OH stretching region of the proton-donor molecule. The redshifts in the bonded OH stretching mode and blueshifts in the OH bending mode suggest that the hydrogen bonds in the (H2O)2-(N2)n complexes with n = 1-4 are strengthened by the cooperative effects compared to the pure H2O dimer. Two absorption bands due to the 3:n complexes are also observed near the bonded OH stretching region of the H2O trimer.     

Study on the molecular orientation of an anti-ferroelectric liquid crystal by two-dimensional correlation polarized infrared spectroscopy

Polarization-dependent infrared spectra of an antiferroelectric liquid crystal in the phase were measured at 60°C, for investigation of the relative orientation of the terminal alkyl chain and mesogen. The polarization angle-dependent infrared spectra obtained were analysed by two-dimensional (2D) correlation spectroscopy. The orientation of the mesogen segment and the alkyl chains in the phase is similar to that in the SmC* phase. Four new CH₃ and CH₂ stretching modes were observed from the 2D correlation spectra. From these we can clearly separate the vibrational mode for two hydrocarbon chains and conclude that the orientations of the two chains are different. The C=O group adjacent to the chiral segment is also separated by 2D correlation spectra into two bands, which may arise from either the C=O group hydrogen-bonded with the phenyl ring, or from another rotational conformation of the molecule.