Studies of intermolecular interactions by matrix isolation vibrational spectroscopy and normal coordinate analysis: Self-association of hydrogen cyanide

A detailed study of the infrared spectra of hydrogen and deuterium cyanide in noble gas, nitrogen and carbon monoxide matrices at 4 K and 20 K has enabled the bands observed to be assigned to monomer, dimer, trimer, tetramer and higher multimer species. Force constants calculated for the linear dimer are used to predict the spectrum of the trimer. The nature of the trapping sites occupied by the monomer and linear dimer, and the structure and trapping site of a second type of dimer observed only in argon matrices, are discussed.     

Vibrational spectra of glyoxylic acid monomers

Infrared spectra of glyoxylic acid monomers, including the hydroxyl deuterated and general O-18 isotopomers, are reported for argon and nitrogen matrix-isolated samples in the range 400–4000 cm^?1. Values for all 15 fundamental vibrations of the intramolecular H-bonded monomer are listed. Bands attributed to the trans-carbonyl conformer with a free car?yl group are also observed and about half of its fundamental frequencies are listed. Some modes of the intramolecular H-bonded glyoxylic acid monomer are strongly matrix dependent, and differences between Ar and N₂ matrix spectra are exploited in sorting out the spectral information.     

Water pair and three-body potential of spectroscopic quality from Ab initio calculations

We present the first pair plus three-body potential of water from ab initio calculations that quantitatively reproduces the experimental far-infrared spectra of the water dimer and trimer. The dimer spectrum was obtained from the pair potential through rigorous six-dimensional quantum calculations of the vibration-rotation-tunneling levels. The three-body interactions, together with the pair potential, produce an accurate representation of the hydrogen bond torsional levels of the water trimer.     

Raman spectroscopy of acetic acid monomer and dimers isolated in solid argon

Acetic acid (AA) monomer and its dimers were studied by means of Raman spectroscopy combined with the matrix isolation technique. All fundamental bands of CH₃COOH monomer were identified, including the CH₃ torsional mode. Additionally, three overtone or combination modes were observed as a result of their enhanced intensities by Fermi resonance (FR). Twenty bands of the cyclic dimer (C_2h) were identified and assigned, among which appear all intermolecular modes. Bands due to two different higher energy forms of the dimer were also identified. The experimental assignments are supported by ab initio calculations. Copyright © 2011 John Wiley & Sons, Ltd.     

The effect of resonance interactions on the absorption spectra of (SF6)2 dimers in low-temperature matrices: Calculations and experiment

The IR absorption spectra of (SF₆)₂ dimers in Ar and N₂ matrices are investigated at 11 K. As a result of the resonance dipole-dipole interaction, the band of the triply degenerate vibration v ₃ is split into two components v _{X, Y} and v _Z. In comparison with the gaseous state, the splitting Δv = v _{X, Y} ? v _Z in the argon matrix decreases to 18.45 cm^?1, whereas, in the nitrogen matrix, the band v _{X, Y} is split into components v _X and v _Y, with the splitting being equal to δ ≈ 0.9 cm^?1. A model that takes into account the influence of the matrix on the spectra of dimers is developed. The model makes it possible to successively (i) calculate the resonance spectrum of an isolated dimer in terms of the model of local modes taking into account resonance interactions, (ii) determine with the help of the Monte Carlo method the structure of a matrix consisting of 512–1440 Ar (or N₂) atoms and a rigid (SF₆)₂ dimer, and (iii) take into account interactions of local dipole moments of a dimer with particles of the matrix in the approximation of dipole-induced dipole interactions. The model developed satisfactorily describes the experimental results. The calculated frequencies v _Z, v _X, and v _Y of a dimer in the matrix are shifted toward smaller frequencies as compared to the gaseous state, while the resonance splitting decreases virtually by 2 cm^?1. It is shown that, in an argon matrix with a symmetric arrangement of argon atoms nearest to a dimer, the splitting of v _{X, Y} proves to be smaller than 0.05 cm^?1. In a nitrogen matrix, this splitting increases virtually to 0.4 cm^?1.     

Localization and Environment of Tryptophans in Different Structural States of Concanavalin A

We have investigated the localization and environment of tryptophan residues in different quaternary and conformational states (tetrameric, dimeric, monomeric and unfolded) of metallized and demetallized concanavalin A (ConA) by selective chemical modification, fluorescence, and phosphorescence. ConA has four tryptophan residues (Trp 40, Trp 88, Trp 109 and Trp 182) per subunit. The pattern of oxidation by N-bromosuccinimide (NBS) shows that NBS modifies, in dimer, only Trp 182 which remains inaccessible in tetramer, two (Trp 88 along with Trp 182) in monomer, all four in unfolded form in presence of EDTA, and three (possibly Trp 40 along with Trp 88 and Trp 182) in unfolded form from native or remetallized ConA. Utilizing wavelength-selective fluorescence approach, we have observed a red edge excitation shift (REES) of 6–8 nm for tetramer and dimer. A more pronounced REES (11 nm) is observed for oxidized monomer compared to REES (3 nm) for unoxidized species. Acrylamide quenching shows the Stern-Volmer constant (K_SV) for dimer, monomer, unfolded ConA and unfolded apo-ConA being 3.8, 5.2, 12.8, 14.0 M⁻¹, respectively. Phosphorescence studies at 77 K give more structured spectra, with two (0,0) bands at 406.2 (weak) and 413.2 nm for tetramer. However, a single (0,0) band appears at 413.2 for dimer and 412.6 nm for monomer, while the (0,0) band of the oxidized monomer is red shifted to 414.4 nm. These results may provide important insight into subtlety of organization and environment of tryptophans in the context of folding and structural studies of oligomeric proteins including lectins.     

Resonance Raman and fluorescence spectra of chlorine dioxide in argon,krypton, xenon,and nitrogen matrices at 16 K

Laser excitation studies of matrix-isolated ClO₂ at 16 K using the 4579, 4765, 4880, and 5145 Å argon ion lines and argon, krypton, xenon, and nitrogen matrices were conducted. Quenching of fluorescence by the matrix was evidenced by the observation of displaced bands in the Ar, Kr, and N₂ work and increased background in the Xe studies. An intense progression in ν₁ of ClO₂ with regularly decreasing intensities out to 6ν₁ observed in solid Ar with 4579 Å excitation was attributed to the resonance Raman effect. Shorter resonance Raman progressions were observed in Xe and N₂ matrices.     

Near-infrared spectra of hydrogen-bonded cyclic dimers of some carboxylic acids

Near-infrared spectra in the 3900–11000 cm⁻¹ region were measured for formic and acetic acids and also for their deutero analogs in the gaseous state at various temperatures. Observed monomer and dimer bands were assigned to overtone and summation bands of various vibrational modes. Special attention was paid to the first overtone bands of the OH and OD stretching modes of the hydrogen-bonded cyclic dimers, which were observed at ∼5930 cm⁻¹ and ∼5870 cm⁻¹ for formic-d acid and acetic-d₃ acid, respectively, and also at ∼4370 cm⁻¹ for acetic acid-d. On the basis of these data the anharmonicity constants were calculated for the OH and OD stretching modes and were found to increase by hydrogen-bond formation in the gaseous state. Hydrogen-bonded overtone bands are broad and have submaxima with intervals nearly half of those of the OH and OD fundamental bands. The results concerning the band breadths of the OH and OD stretching vibrations of the dimers were interpreted on the line of the idea that they strongly couple with the O?O stretching vibration.     

Infrared observation of OC-C2H2, OC-(C2H2)2 and their isotopologues

ABSTRACT

The fundamental band for the OC-C₂H₂ dimer and two combination bands involving the intermolecular bending modes ν₉ and ν₈ in the carbon monoxide CO stretch region are re-examined. Spectra are obtained using a pulsed supersonic slit jet expansion probed with a mode-hop free tuneable infrared quantum cascade laser. Analogous bands for OC-C₂D₂ and the fundamental for OC–DCCH as an impurity are also observed and analysed. A much weaker band in the same spectral region is assigned to a new mixed trimer, CO-(C₂H₂)₂. The trimer band is composed uniquely of a-type transitions, establishing that the CO monomer is nearly aligned with the a-inertial axis. The observed rotational constants agree well with ab initio calculations and a small inertial defect value indicates that the trimer is planar. The structure is a compromise between the T-shaped structure of free acetylene dimer and the linear geometry of free OC-C₂H_2. A similar band for the fully deuterated isotopologue CO-(C₂D₂)₂ confirms our assignment.     

Possibilities of the observation of the discrete spectrum of the water dimer at equilibrium in millimeter-wave band

Attempts of experimental observations of the water dimer spectrum at equilibrium conditions have lasted for more than 40 years since the dimeric hypothesis for extra absorption, but have not yielded any positive confirmed result. In the present paper a new approach is considered: using a high-resolution millimeter-wave spectrum of the water dimer at equilibrium, calculated by a rigorous fully quantum method, we show the potential existence of discernible spectral series of discrete features of the water dimer, which correspond to J+1←J, K lines of E₁ symmetry, already observed in cold molecular beam experiments and having, therefore, well-defined positions. The intensity of spectral series and contrast to the remaining continuum-like spectrum of the dimer are calculated and compared with the monomer absorption. The suitability of two types of microwave spectrometers for observing these series is considered. The collisional line-width of millimeter lines of the dimer at equilibrium is estimated and the width of IR dimer bands is discussed. It is pointed out that the large width of IR dimer bands may pose difficulties for their reliable observation and conclusive separation from the rest of absorption in water vapor. This situation contrasts with the suggested approach of dimer detection in millimeter-waves.     

Complexes d'autoassociation du cyclohexanol. I - modele thermodynamique des solutions diluees.

Activity coefficients for cyclohexanol in diluted isooctane solutions at 25°C and 45°C are obtained from vapour pressure measurements, x_u = 10^?3 to 5.10^?2 (x_u mole fraction of cyclohexanol) ; enthalpies of mixing for the same composition range are obtained at 25°C. The results are interpreted in terms of the model of ideal association where open dimer and trimer, open and cyclic other i-mers are considered in a six parameters model : two standard enthalpies for formation of the H-bonds (Δ$\text{H}$_2o for the dimer and h for the stepwise formation for other bonds), four equilibrium constants (K_2o and K_3o for the dimer and trimer formation from the monomer, K_c for the cyclisation of an open i-mer and k for the stepwise formation of an open, or cyclic, i-mer higher than the trimer). The cyclic form of the tetramer is shown to be the predominent one.     

Pd diffusion on MgO(1 0 0): The role of defects and small cluster mobility

Density functional theory is used to explore the energy landscape of Pd atoms adsorbed on the terrace of MgO(1 0 0) and at oxygen vacancy sites. Saddle point finding methods reveal that small Pd clusters diffuse on the terrace in interesting ways. The monomer and dimer diffuse via single atom hops between oxygen sites with barriers of 0.34 eV and 0.43 eV respectively. The trimer and tetramer, however, form 3D clusters by overcoming a 2D-3D transition barrier of less than 60 meV. The trimer diffuses along the surface either by a walking or flipping motion, with comparable barriers of ca. 0.5 eV. The tetramer rolls along the terrace with a lower barrier of 0.42 eV. Soft rotational modes at the saddle point lead to an anomalously high prefactor of 1.3 × 10¹⁴ s⁻¹ for tetramer diffusion. This prefactor is two order of magnitude higher than for monomer diffusion, making the tetramer the fastest diffusing species on the terrace at all temperatures for which diffusion is active (above 200 K). Neutral oxygen vacancy sites are found to bind Pd monomers with a 2.63 eV stronger binding energy than the terrace. A second Pd atom, however, binds to this trapped monomer with a smaller energy of 0.56 eV, so that dimers at defects dissociate on a time scale of milliseconds at room temperature. Larger clusters bind more strongly at defects. Trimers and tetramers dissociate from monomer-bound-defects at elevated temperatures of ca. 600 K. These species are also mobile on the terrace, suggesting they are important for the ripening observed at ?600 K during Pd vapor deposition on MgO(1 0 0) by Haas et al. [G. Haas, A. Menck, H. Brune, J.V. Barth, J.A. Venables, K. Kern, Phys. Rev. B 61 (2000) 11105].     

具有电子推拉结构的多支化分子的光物理特性的研究

利用稳态光谱和飞秒时间分辨荧光亏蚀的技术,研究了不同溶剂中一系列有分子内电荷转移特性的分子的结构与光物理性质的关系,研究体系为三苯胺作为电子给体,2,1,3-苯并噻二唑作为受体的单支分子及其对应的两支和三支分子. 并结合TD-DFT计算进一步解释了实验中所观察到的现象. 三个分子相似的吸收和荧光光谱以及强的溶剂依赖光谱特性表明两支与三支分子激发态与单支分子相似,表明激发态都定域在其中一支上. 激发时多支分子内发生多维电荷转移,然后快速地定域到某一支上发射. 另一方面多支分子相对于单支分子吸收和发射光谱的红     

Electronic and vibrational absorption spectra in otwayite,a new nickel mineral

The optical absorption spectrum of Ni²⁺ ion in otwayite crystal has been studied at room and liquid nitrogen temperatures. From the nature and positions of the observed bands a successful interpretation of all the bands could be made assuming octahedral symmetry for the Ni²⁺ ion in the crystal. The splittings observed for the ³T_1g(F) band at liquid nitrogen temperature have been interpreted due to spin-orbit interaction. The observed band positions in the crystal have been fitted with four parameters B, CDq and ξ. NIR and IR spectra of the otwayite sample are presented. The fundamental vibrational modes of H₂O and CO^2-₃ ion are identified in the IR region. The bands observed in NIR spectrum are due to overtones and combination tones of water and carbonate ion.     

Water dimer vibration-rotation tunnelling levels from vibrationally averaged monomer wavefunctions

The vibration-rotation tunnelling (VRT) spectra for the water dimer obtained by vibrationally averaging the dimer potential over accurate water monomer wavefunctions is reported. The vibrational averaging requires evaluation of the 12D dimer potential energy surface at more than 10¹² distinct geometries. The resulting vibrational spectra of the low-lying dimer states are presented and compared with both less computationally expensive methods based on fixed nuclei approximations and the recent (6+6)d adiabatic calculations of Leforestier et al. [38] (2009). The procedure gives some modest improvement in the agreement with experimental values for the vibration-rotation tunnelling (VRT) states of (H₂O)₂ and (D₂O)₂. This approach can be extended to treat dimer states involving monomer overtone excitations, which is important in obtaining water dimer spectra at infrared and visible wavelengths at atmospheric temperatures, and in characterizing the dimer contribution to the so-called water continuum absorption at these wavelengths.     

The infrared spectrum of C2F5Cl in cryogenic matrices

We have measured the infrared spectrum of pentafluoroethyl chloride in cryogenic matrices of argon, nitrogen, krypton, and xenon from 880 to 1360 cm^?1. Numerous combination bands were observed; assignments and symmetries are reported for most. Appreciably more structure was observed in argon than in other matrices. The observed splitting of the fundamental bands in an argon matrix into two or more components may be due to multiple trapping sites.     

IR absorption spectrum (4200–3100 cm) of H2O and (H2O)2 in CCl4. Estimates of the equilibrium constant and evidence that the atmospheric water absorption continuum is due to the water dimer

IR absorption spectra, 4200–3100 cm⁻¹, of water in CCl₄ solutions are presented. It is shown that for saturated solutions significant amounts of water are present as dimer (ca. 2%). The IR spectra of the monomer and dimer are retrieved. The integrated absorption coefficients of the monomer absorption are significantly enhanced relative to the gas phase values. The dimer spectrum consists of 5 bands, of which 4 were expected from data from cold beams and cold matrices. The origin of the “extra” band is discussed. In addition it is argued that the dimer absorption bands intensities must be enhanced relative to the gas phase values. Based on recent calculations of band strengths, and observed frequency shifts relative to the gas phase, the intensity enhancement factors are estimated as well as the monomer/dimer equilibrium constant in CCl₄ solution at T=296 K (K_c=1.29 mol⁻¹ L). It is noted that the observed dimer spectrum has a striking resemblance with the water vapour continuum determined by Burch in 1985 which was recently remeasured by Paynter et al. and it is concluded that the atmospheric water absorption continuum in the investigated spectral region must be due to water dimer. Based on the newly published spectral data a revised value of the gas phase equilibrium constant is suggested (K_p=0.035 atm⁻¹ at T=296 K) as well as a value for the standard enthalpy of formation, ΔH⁰=15.4 kJ mol⁻¹.     

LIF excitation spectra for S0 → S1 transition of anthranilic acid: Detailed studies

Laser-induced fluorescence (LIF) excitation spectra of jet-cooled molecules of anthranilic acid were investigated. In order to distinguish bands belonging to the monomer from those belonging to the dimer species three different spectra were recorded under conditions which differed in the value of partial pressure of vapours of anthranilic acid. Narrow bandwidth of rotational profiles in the acquired spectra made it possible to resolve new interesting spectral features and to analyse the rather small anharmonicity in progressions of several low-frequency vibrations. Eleven fundamental bands up to ca. 1400 cm⁻¹ and five overtones of out-of-plane vibrations were assigned. Simulation based on approximate relations of the experimental band intensities of overtones and combination bands with respect to fundamental bands was carried out. This simulation was found a simple and practical tool in analysis of the spectra and an aid to verify the proposed assignment.Harmonic and anharmonic frequencies of vibrational modes were calculated using the HF/6-31G∗∗ and CIS/6-31G∗∗ methods for the S₀ and S₁ state, respectively. Modelling of band intensities using displacement parameters derived from the results of the ab initio calculations was performed. This modelling significantly underestimates the displacement parameters. The Dushinsky matrix derived from the results of the ab initio calculations was used to check the validity of the models and to find modes which undergo large frequency changes and mode mixing upon electronic excitation.     

Electron Spin Polarization of Photo-Excited Copper Coproporphyrin I: From Monomers to Dimers

The results of the electron paramagnetic resonance (EPR) and transient EPR (TREPR) of copper complexes of coproporphyrin I in different solvents before and after the laser pulse photo-excitation have been presented. Continuous-wave EPR spectra of the CuCPP-1 complex in o-terphenyl indicate the presence of only monomer fragments, while in the solution of the chloroform and isopropanol mixture, the complexes dimerize and the amount of dimers is five times larger than that of monomer complexes. Parameters describing EPR spectra of monomer and dimer CuCPP-1 complexes have been determined. It was established that the fine structure tensor of the dimer complex is rotated with respect to the g-tensor, which coincides with the tensor of monomer complexes. TREPR spectra of CuCPP-1 complexes in o-terphenyl and in the chloroform and isopropanol mixture after the laser photo-excitation are mainly due to spin-polarized ground states of monomer and dimer complexes, respectively. The TREPR spectra of the monomer CuCPP-1 show the emissive spin-polarized signal of the ground state. For dimer fragments, the net polarization is observed in the form of absorption and there is a small contribution from the multiplet polarization, which decays fast in time. The time dependence of TREPR of CuCPP-1 complexes in the chloroform and isopropanol mixture is described with allowance for these contributions from the ground state of the dimer and the contribution from the ground state of the monomer, which is manifested at larger times. Differences in the spin polarization of ground states and their possible origin are discussed.     

An electron spin resonance study of dimeric,trimeric, and tetrameric paramagnetic silver atom clusters

The low temperature γ-irradiation of frozen benzene solutions containing AgClO₄ leads directly to the formation of the paramagnetic species Ag₂ ⁺, no Ag⁰ centre being detected. When benzene or toluene solutions containing AgBF₄ were similarly treated and the matrix carefully annealed, well-resolved E.S.R. spectra attributed to paramagnetic clusters containing three and four equivalent silver atoms were detected. The lack of resolved anisotropy in the spectrum of the trimer and tetramer are thought to argue in favour of a triangular and tetrahedral geometry respectively rather than linear chains.