Isotope effects in liquid water by infrared spectroscopy. V. A sea of OH4 of C2v symmetry

The two water gas OH stretch vibrations that absorb in the infrared (IR) near 3700 cm(-1) are redshifted to near 3300 cm(-1) upon liquefaction. The bathochromic shift is due to the formation of four H-bonds: two are from the labile hydrogen atoms to neighbors and two are received from neighbors by the oxygen free electron pairs. Therefore, the water oxygen atom is surrounded by four hydrogen atoms, two of these make covalent bonds that make H-bonds and two are oxygen H-bonded. However, these permute at rate in the ps range. When the water molecules are isolated in acetonitrile (MeCN) or acetone (Me(2)CO), only the labile hydrogen atoms make H-bonds with the solvent. The bathochromic shift of the OH stretch bands is then almost 130 cm(-1) with, however, the asymmetric (ν(3)) and symmetric (ν(1)) stretch bands maintained. When more water is added to the solutions, the oxygen lone doublets make H-bonds with the available labile hydrogen atoms from neighboring water molecules. With one bond accepted, the bathochromic shift is further displaced by almost 170 cm(-1). When the second oxygen doublet is filled, another bathochromic shift by almost 100 cm(-1) is observed. The total bathochromic shift is near 400 cm(-1) with a full width at half height of near 400 cm(1). This is the case of pure liquid water. Notwithstanding the shift and the band broadness, the ν(3) and ν(1) band individualities are maintained with, however, added satellite companions that come from the far IR (FIR) absorption. These added to the fundamental bands are responsible for the band broadness and almost featureless shape of the massive OH stretch absorption of liquid water. Comparison of light and heavy water mixture spectra indicates that the OH and OD stretch regions show five different configurations: OH(4); OH(3)D; OH(2)D(2); OHD(3); and OD(4) [J. Chem. Phys. 116, 4626 (2002)]. The comparison of the OH bands of OH(4) with that of OHD(3) indicates that the main component in OHD(3) is ν(OH), whereas in OH(4) two main components are present: ν(3) and ν(1). Similar results are obtained for the OD bands of OD(4) and ODH(3). These results indicate that the C(2) (v) symmetry of H(2)O and D(2)O is preserved in the liquid and aqueous solutions whereas C(s) is that of HDO.     

Infrared spectroscopy of acetone-water liquid mixtures. II. Molecular model

In aqueous acetone solutions, the strong bathochromic shifts observed on the OH and CO stretch infrared (IR) bands are due to hydrogen bonds between these groups. These shifts were evaluated by factor analysis (FA) that separated the band components from which five water and five acetone principal factors were retrieved [J. Chem. Phys. 119, 5632 (2003)]. However, these factors were abstract making them difficult to interpret. To render them real an organization model of molecules is here developed whose abundances are compared to the experimental ones. The model considers that the molecules are randomly organized limited by the hydrogen bond network formed between the water hydrogen atoms and the acetone or water oxygen atoms, indifferently. Because the oxygen of water has two covalent hydrogen atoms which are hydrogen-bonded and may receive up to two hydrogen atoms from neighbor molecules hydrogen-bonded to it, three types of water molecules are found: OH2, OH3, and OH4 (covalent and hydrogen bonds). In the OH stretch region these molecules generate three absorption regimes composed of nu3, nu1, and their satellites. The strength of the H-bond given increases with the number of H-bonds accepted by the oxygen atom of the water H-bond donor, producing nine water situations. Since FA cannot separate those species that evolve concomitantly the nine water situations are regrouped into five factors, the abundance of which compared exactly to that retrieved by FA. From the factors' real spectra the OH stretch absorption are simulated to, respectively, give for the nu3 and nu1 components the mean values for OH2, 3608, 3508; OH3, 3473, 3282 and OH4, 3391, 3223 cm(-1). The mean separations from the gas-phase position which are respectively about 150, 330, and 400 cm(-1) are related to the vacancy of the oxygen electron doublets: two, one, and zero, respectively. No acetone hydrate that sequesters water molecules is formed. Similarly, acetone produces ten species, two of which evolve concomitantly. Spectral similarities further reduce these to five principal IR factors, the abundance of which compared adequately to the experimental results obtained from FA. The band assignment of the five-acetone spectra is given.     

Infrared spectroscopy of Si(CO)n+ complexes: evidence for asymmetric coordination

Si(CO)(n)(+) and Si(CO)(n)(+)Ar complexes are produced via laser vaporization with a pulsed nozzle source and cooled in a supersonic beam. The ions are mass selected in a reflectron time-of-flight mass spectrometer and studied with infrared laser photodissociation spectroscopy near the free molecular CO vibration (2143 cm(-1)). Si(CO)(n)(+) complexes larger than n = 2 fragment by the loss of CO, whereas Si(CO)(n)(+)Ar complexes fragment by the loss of argon. All clusters have resonances near the free molecular CO stretch that provide distinctive patterns from which information on their structure and bonding can be obtained. The number of infrared-active bands, their frequency positions, and relative intensities indicate that larger species consist of an asymmetrically coordinated Si(CO)(2)(+) core with additional CO ligands attached via van der Waals interactions. Density functional theory computations are carried out in support of the experimental spectra.     

Intermolecular vibrations of fluorobenzene-Ar up to 130 cm(-1) in the ground electronic state

Sixteen intermolecular vibrational levels of the S(0) state of the fluorobenzene-Ar van der Waals complex have been observed using dispersed fluorescence. The levels range up to ～130 cm(-1) in vibrational energy. The vibrational energies have been modelled using a complete set of harmonic and quartic anharmonic constants and a cubic anharmonic coupling between the stretch and long axis bend overtone that becomes near ubiquitous at higher energies. The constants predict the observed band positions with a root mean square deviation of 0.04 cm(-1). The set of vibrational levels predicted by the constants, which includes unobserved bands, has been compared with the predictions of ab initio calculations, which include all vibrational levels up to 70-75 cm(-1). There are small differences in energy, particularly above 60 cm(-1), however, the main differences are in the assignments and are largely due to the limitations of assigning the ab initio wavefunctions to a simple stretch, bend, or combination when the states are mixed by the cubic anharmonic coupling. The availability of these experimental data presents an opportunity to extend ab initio calculations to higher vibrational energies to provide an assessment of the accuracy of the calculated potential surface away from the minimum. The intermolecular modes of the fluorobenzene-Ar(2) trimer complex have also been investigated by dispersed fluorescence. The dominant structure is a pair of bands with a ～35 cm(-1) displacement from the origin band. Based on the set of vibrational modes calculated from the fluorobenzene-Ar frequencies, they are assigned to a Fermi resonance between the symmetric stretch and symmetric short axis bend overtone. The analysis of this resonance provides a measurement of the coupling strength between the stretch and short axis bend overtone in the dimer, an interaction that is not directly observed. The coupling matrix elements determined for the fluorobenzene-Ar stretch-long axis bend overtone and stretch-short axis bend overtone couplings are remarkably similar (3.8 cm(-1) cf. 3.2 cm(-1)). Several weak features seen in the fluorobenzene-Ar(2) spectrum have also been assigned.     

New infrared bands of nonpolar OCS dimer and experimental frequencies for two intermolecular modes

Spectra of the nonpolar carbonyl sulfide dimer in the region of the OCS ν(1) fundamental band were observed in a slit-jet supersonic expansion. The jet was probed using radiation from a tunable diode laser employed in a rapid-scan signal averaging mode. Six new bands were observed and analyzed, all of which originate from the dimer ground vibrational state. Three were vibrational fundamentals involving the ((18)OCS)(2) and (16)OCS-(18)OCS isotopologues. They enabled an estimate to be made of the frequency of the infrared-forbidden mode corresponding to in-phase vibration of the OCS monomers in the dimer, a value needed to obtain an intermolecular vibrational frequency from one of the observed combination bands. A relatively weak b-type dimer band centered at 2103.105 cm(-1) was assigned to the OCS 4ν(2) (l = 0) bending overtone. Combination bands were observed involving the geared bend and van der Waals stretch intermolecular modes. The resulting experimental frequencies of 37.5(20) cm(-1) for the bend and 42.9727(1) cm(-1) for the stretch are in good agreement with a recent high level theoretical calculation.     

Ab initio rotation-vibration spectra of HCN and HNC

We have calculated an ab initio HCN/HNC linelist for all transitions up to J= 25 and 18000 cm(-1) above the zero point energy. This linelist contains more than 200 million lines each with frequencies and transition dipoles. The linelist has been calculated using our semi-global HCN/HNC VQZANO + PES and dipole moment surface, which were reported in van Mourik et al. (J. Chem. Phys. 115 (2001) 3706). With this linelist we synthesise absorption spectra of HCN and HNC at 298 K and we present the band centre and band transition dipoles for the bands which are major features in these spectra. Several of the HCN bands and many of the HNC bands have not been previously studied. Our line intensities reproduce via fully ab initio methods the unusual intensity structure of the HCN CN stretch fundamental (00(0)1) for the first time and also the forbidden (02(2)0) HCN bending overtone. We also compare the J = 1-->0 pure rotational transition dipole in the HCN/HNC ground and vibrationally excited states with experimental and existing ab initio results.     

Modified UBFF calculations of the alpha-L-fucopyranose molecule in the crystalline state

Normal co-ordinate analysis has been realised in the crystalline state using a modified Urey-Bradley-Shimanouchi force field combined with an intermolecular potential energy function that includes van der Waals interactions, some electrostatic terms and an explicit hydrogen bond function. The vibrational spectra of the alpha-L-fucose molecule have been recorded in the crystalline state, in the 4000-500 cm(-1) spectral region for the mid-IR spectra, in the 500-100 cm(-1) spectral region for the far-IR spectra, and in the 4000-20 cm(-1) spectral range for Raman spectra. These spectra constitute the experimental support for the establishment of a force field for the molecule in the crystalline state through a normal co-ordinate analysis.     

Two-dimensional laser induced fluorescence spectroscopy of van der Waals complexes: fluorobenzene-Ar(n) (n = 1,2)

The technique of two-dimensional laser induced fluorescence (2D-LIF) spectroscopy has been used to observe the van der Waals complexes fluorobenzene-Ar and fluorobenzene-Ar(2) in the region of their S(1)-S(0) electronic origins. The 2D-LIF spectral images reveal a number of features assigned to the van der Waals vibrations in S(0) and S(1). An advantage of 2D-LIF spectroscopy is that the LIF spectrum associated with a particular species may be extracted from an image. This is illustrated for fluorobenzene-Ar. The S(1) van der Waals modes observed in this spectrum are consistent with previous observations using mass resolved resonance enhanced multiphoton ionisation techniques. For S(0), the two bending modes previously observed using a Raman technique were observed along with three new levels. These agree exceptionally well with ab initio calculations. The Fermi resonance between the stretch and bend overtone has been analysed in both the S(0) and S(1) states, revealing that the coupling is stronger in S(0) than in S(1). For fluorobenzene-Ar(2) the 2D-LIF spectral image reveals the S(0) symmetric stretch van der Waals vibration to be 35.0 cm(-1), closely matching the value predicted based on the fluorobenzene-Ar van der Waals stretch frequency. Rotational band contour analysis has been performed on the fluorobenzene-Ar 0(0)(0) transition to yield a set of S(1) rotational constants A' = 0.05871 ± 0.00014 cm(-1), B' = 0.03803 ± 0.00010 cm(-1), and C' = 0.03103 ± 0.00003 cm(-1). The rotational constants imply that in the S(1) 0(0) level the Ar is on average 3.488 ? from the fluorobenzene centre of mass and displaced from it towards the centre of the ring at an angle of ~6° to the normal. The rotational contour for fluorobenzene-Ar(2) was predicted using rotational constants calculated on the basis of the fluorobenzene-Ar geometry and compared with the experimental contour. The comparison is poor which, while due in part to expected saturation effects, suggests the presence of another band lying beneath the contour.     

The intensity change of IR OH bands by H-bonds

The integrated intensity change by H-bonds are measured for CH₃OH solved in different solvents of fundamental, 1. and 2. overtone OH stretching bands. A function A=f(ν) for the strong intensity change by H-bonds of the fundamental band is given, it shows a kink between pure van der Waals solvents and H-bond acceptors. - The contrary behavior of fundamental and 1. overtone bands for the T-dependence of pure CH₃OH and its LiClO₄-solutions could be canceled if the fundamental spectra are intensity corrected by A=f(ν). It is shown that the discussions between species and continuum models of water could become unique taking into account the function f(ν) and its kink, different for fundamental and overtone bands.     

Bound state spectroscopy of NH-He

The NH-He van der Waals complex was characterized via laser excitation of bands associated with the NH A (3)Pi-X (3)Sigma(-) transition. It was demonstrated that the ground state supports a bound level with a rotational constant of B"=0.334(2) cm(-1). These results are in agreement with the predictions of recent high-level theoretical calculations. Spin-orbit predissociation of the excited complex was observed, and the spectra yield insights regarding the NH(A)+He potential energy surfaces.     

Comparison of calorimetric and IR-spectroscopic data for alcohols and alcoholic solutions

The heats of solution of alcohols in hexane can be considered as the energy necessary to break hydrogen bonds (H-bond). The amount of non H-bonded OH groups estimated from caloric data, are in good agreement with IR-spectroscopic data. Comparison of calorimetric and IR-spectroscopically determined H-bond energies permit the separation of intermolecular van der Waals effects from H-bond interactions. This separation shows that van der Waals interactions of alcohols or water should not be underestimated.     

Characteristics and relaxation dynamics of van der Waals complexes between p-difluorobenzene and Ne

Characteristics of the single and double Ne van der Waals complexes of p-difluorobenzene (pDFB) have been explored with ultraviolet fluorescence excitation and dispersed fluorescence spectroscopy. Eight S(1)-S(0) fluorescence excitation bands involving six ring modes of pDFB-Ne and two bands of pDFB-Ne(2) have been identified. Band assignments are confirmed by dispersed fluorescence from the pumped band. Shifts of the complex bands from the analogous monomer bands are generally 4 cm(-1) to the red for pDFB-Ne and 8 cm(-1) for pDFB-Ne(2). None of the observed ring modes is significantly perturbed by complexation in either the S(1) or S(0) states. The pDFB-Ne S(1) van der Waals binding energy D(0')相似文献   

Quantum cascade laser spectroscopy and photoinduced chemistry of Al-(CO)n clusters in helium nanodroplets

Helium nanodroplet isolation and a tunable quantum cascade laser are used to probe the fundamental CO stretch bands of aluminum carbonyl complexes, Al-(CO)(n) (n ≤ 5). The droplets are doped with single aluminum atoms via the resistive heating of an aluminum wetted tantalum wire. The downstream sequential pick-up of CO molecules leads to the rapid formation and cooling of Al-(CO)(n) clusters within the droplets. Near 1900 cm(-1), rotational fine structure is resolved in bands that are assigned to the CO stretch of a linear (2)Π(1/2) Al-CO species and the asymmetric and symmetric CO stretch vibrations of a planar C(2v) Al-(CO)(2) complex in a (2)B(1) electronic state. Bands corresponding to clusters with n ≥ 3 lack resolved rotational fine structure; nevertheless, the small frequency shifts from the n = 2 bands indicate that these clusters consist of an Al-(CO)(2) core with additional CO molecules attached via van der Waals interactions. A second n = 2 band is observed near the CO stretch of Al-CO, indicating a local minimum on the n = 2 potential consisting of an "unreacted" (Al-CO)-CO cluster. The line width of this band is ～0.3 cm(-1), which is about 30 times broader than the transitions within the Al-CO band. The additional broadening is consistent with a homogeneous mechanism corresponding to a rapid vibrational excitation induced reaction within the (Al-CO)-CO cluster to form the covalently bonded Al-(CO)(2) complex. Ab initio CCSD(T) calculations and natural bond orbital (NBO) analyses are carried out to investigate the nature of the bonding in the n = 1, 2 complexes. The NBO calculations show that both π-donation (from the occupied aluminum p orbital into a π* antibonding CO orbital) and σ-donation (from CO into the empty aluminum p orbitals) play a significant role in the bonding, analogous to transition-metal carbonyl complexes. The large red shift observed for the CO stretch vibrations is consistent with this bonding analysis.     

Synthesis and testing of a focused phenothiazine library for binding to HIV-1 TAR RNA

We have synthesized a series of phenothiazine derivatives, which were used to test the structure-activity relationship of binding to HIV-1 TAR RNA. Variations from our initial compound, 2-acetylphenothiazine, focused on two moieties: ring substitutions and n-alkyl substitutions. Binding characteristics were ascertained via NMR, principally by saturation transfer difference spectra of the ligand and imino proton resonance shifts of the RNA. Both ring and alkyl substitutions manifested NMR changes upon binding. In general, the active site, while somewhat flexible, has regions that can be capitalized for increased binding through van der Waals interactions and others that can be optimized for solubility in subsequent stages of development. However, binding can be nontrivially enhanced several-fold through optimization of van der Waals and hydrophilic sites of the scaffold.     

Experimental and theoretical investigation of the first overtone spectrum of 1,3,5-trinitrotoluene

Vibrational overtone spectroscopy is a powerful tool for studying intramolecular and intermolecular interactions. We report on a combined experimental and modeling study of the C-H stretch first overtone of bulk 1,3,5-trinitrotoluene (TNT) and TNT on fumed-silica powder. We recorded the overtone spectra by laser photoacoustic spectroscopy and compared them with those predicted with the harmonically coupled anharmonic oscillator model in the 5600-6600 cm(-1) region. The model systems included single molecules and hybrid quantum and molecular mechanical (QM:MM) clusters to account for the effects of intermolecular interactions on the observed spectra. We performed the hybrid QM:MM calculations at the HF/6-31+G(d,p), B3LYP/6-31+G(d,p), and MP2/6-31+G(d,p) levels of theory and with the universal force field (UFF) to account for van der Waals and electrostatic effects from surrounding molecules. Overtone spectra calculated from the MP2 level of theory, using a HF/3-21+G* calculation to assign molecular charges in the MM layer, and the Merz-Singh-Kollman population analysis for assigning partial charge in the QM layer and determining the transition dipole moment agreed best with the experimental data.     

Intermolecular vibrational coherence in the bacteriochlorophyll proteins B777 and B820 from Rhodospirillum rubrum

The low-frequency vibrational coherence in the bacteriochlorophyll (BChl)-containing subunit proteins B777 and B820 from the LH1 light-harvesting complex isolated from Rhodospirillum rubrum G9 exhibits rapidly damped modulation components arising from intermolecular, formally nonbonding interactions between the BChl macrocycle and polar groups in the surrounding detergent or protein. The vibrational coherence observed in the monomeric B777 system resembles that observed previously with BChl in acetone because it contains a pair of broad overlapping line shapes with a mean frequency of 191 cm(-1), but the 10:1 intensity ratio of the librational and translational components is distinctive of the motions of the polar head groups in the nonionic detergent micelle that solvates the BChl macrocycle. In contrast, the vibrational coherence observed with the dimeric B820 complex is almost 20 times weaker in intensity and exhibits narrower line shapes and lower average frequencies than observed in B777. The structure of the B820 complex sterically protects the pair of BChl macrocycles from the surrounding solvent, so modulation components assigned to intrinsic interactions between the BChl and the protein and between the pair of BChl's are revealed. A relatively well-ordered interaction between the BChl macrocycle and a tryptophan residue in each alpha-helical polypeptide accounts for a 28 cm(-1) component with a narrow line shape, but most of the intensity arises from a broader 46 cm(-1) component that is assigned to the interaction between the paired BChl macrocycles. The breadth of the line shape for this component is a measure of the disorder in the ensemble of B820 subunits. The results support the hypothesis that the excited-state vibrational dynamics and the optical and/or Marcus charge-transfer reorganization energies of BChl in photosynthetic light-harvesting proteins and reaction centers are strongly controlled by van der Waals modes with neighboring molecules, with dominant contributions to the intermolecular potential arising from the London dispersion and dipole-dipole interactions.     

Phosphole modified pentathienoacene: synthesis, electronic properties and self-assembly

A series of new ladder π-conjugated materials, phosphole modified pentathienoacene (PO-PTA), are synthesized and characterized. Single-crystal X-ray results demonstrate that methyl-disubstituted PO-PTA forms a face-to-face dimer structure driven by π-π interactions. The investigations of optical properties showed that the oxidized phosphole moiety in this ladder system can effectively narrow the band gap. PO-PTA is a promising building block in π-conjugated polymers and oligomers for optoelectronic applications. The derivative of PO-PTA, obtained by introducing four long alkyl chains, can self-assemble into one-dimensional (1D) fibers based on intermolecular π-π interactions, dipole-dipole interactions and van der Waals interactions. Interestingly, the uniform and well-ordered monolayers were also obtained for PO-PTA derivative on a HOPG (highly oriented pyrolytic graphite) surface.     

The infrared and Raman spectra of trans- and cis-tetrachloro-tetramethylbicyclopropylidene

The title compounds trans- and cis-2,2,2',2'-tetrachloro-3,3,3',3'-tetramethyl-bicyclopopylidene were synthesized, and their infrared and Raman spectra were recorded. Non-coincidence between the IR and Raman bands of the trans compound suggested C(2h) symmetry and a planar ring system. In the cis compound most of the IR and Raman bands coincided and a C(2v) symmetry seems likely. The exocyclic CC double bond gave rise to a medium/weak Raman band at 1,847 cm(-1) in the trans compound. In the cis derivative IR and Raman bands both at 1,825 cm(-1) were observed. From similarities with related molecules, the ring breathing, the antisymmetric ring stretch, the CCl(2) out-of-phase and in-phase stretch and the out-of-plane ring bending modes have been tentatively assigned for the trans and cis compounds.     

Information from IR fundamental and overtone spetra of diatomics adsorbed in zeolites NaCaA

From fundamental and overtone spectra of CO, NO and D₂ adsorbed in zeolites NaCaA the constants of the internuclear potential can be derived for the adsorbed state. As the interactions with the zeolite surface are dominated by van der Waals forces, they remain less affected by adsorption. In contrast to diatomics adsorbed on transition metal surfaces, no considerable alteration of bond energy can be observed. The frequency shift is essentially due to the change of the harmonic force constant and indicates the interaction potential depending almost linearly on the vibrational state. The heterogeneity of the cation distribution inside the zeolites is reflected in the broadening of the adsorbate bands.