Analyzing the Vibrational Signatures of Thiophenol Adsorbed on Small Gold Clusters by DFT Calculations

Using density functional theory, we calculate the IR and Raman signatures of the thiophenol (TP) molecule adsorbed on gold clusters by mimicking the different types of adsorption sites, and we analyze these signatures by using advanced tools implemented into the pyvib2 program. First, we follow the evolution of the vibrational normal modes from the isolated TP molecule to those of TP adsorbed on different clusters to highlight the influence of the site of adsorption on the vibrational motions. The use of the overlap matrix between the modes enables mode permutations, mode mixings, and mode splittings to be highlighted, all of which depend not only on the adsorption but also on the type of cluster and its symmetry. Second, the IR and Raman signatures were analyzed by using group coupling matrices and atomic contribution patterns based on the Hug decomposition scheme. Key results include 1) the fact that Raman spectroscopy is more sensitive than IR spectroscopy with respect to the nature of the coordination site, 2) an IR criterion that distinguishes between on‐top coordination (onefold coordinated) with respect to the bridge (twofold coordinated) and hexagonal close‐packed hollow site coordination (threefold coordinated), and 3) the best agreement to the experimental Raman spectrum with regard to signatures in the 500 to 1200 cm^?1 region is obtained for bridged, twofold coordination.     

Vibrational and quantum-chemical study of nonlinear optical chromophores containing dithienothiophene as the electron relay

A series of nonlinear optical (NLO) donor-acceptor (D-A) chromophores containing a fused terthiophene, namely dithienothiophene (DTT), as the electron relay, the same donor group, and acceptors of various strengths, has been investigated by means of infrared and Raman spectroscopies, both in the solid state as well as in a variety of solvents, to evaluate the effectiveness of the intramolecular charge transfer from the electron-donor to the electron-acceptor end groups. The Raman spectral profiles of these NLO-phores measured from their dilute solutions have been found to be rather similar to those of the corresponding solids, and thus their intramolecular charge transfer (ICT) shows very little dependence on the solvent polarity. The experimental results obtained for the DTT-containing NLO-phore with a 4-(N,N-dibutylamino)styryl end group as the donor and a 2,2-dicyanoethen-1-yl end group as the acceptor differ from those previously obtained for two parent "push-pull" chromophores with the same D-A pair but built-up around either a bis(3,4-ethylenedioxythienyl) (BEDOT) or a bithienyl (BT) electron relay. Vibrational spectroscopy shows that DTT is significantly more efficient as an electron relay than BT (which has the same number of conjugated C=C bonds) or BEDOT (which can be viewed as a rigidified version of BT on account of noncovalent intramolecular interactions between heteroatoms of adjacent rings). Density functional theory (DFT) calculations have also been performed on these NLO-phores to assign their main electronic and vibrational features and to obtain information about their structures. An additional merit of these molecular materials was revealed by the infrared spectra of the DTT-based NLO-phores recorded at different temperatures. Thus, spectra recorded between -170 and 150 degrees C did not show any substantial change, indicating that the materials have a high thermal stability, which is of significance for their use as active components in optoelectronic devices.     

Vibrational spectroscopic study of mimetite-pyromorphite solid solutions

A number of compounds of the mimetite Pb₅(AsO₄)₃Cl-pyromorphite Pb₅(PO₄)₃Cl solid solution series were synthesized at room temperature and analyzed with Raman and infrared spectroscopy. The fundamental antisymmetric stretching (ν₃) and bending (ν₄) vibrations of the mimetite-pyromorphite solid solutions occur in the regions 720-1040 cm⁻¹ and 400-580 cm⁻¹. The band originating from the ν₃ and ν₄ modes shifts to higher wavenumbers between mimetite and pyromorphite because the atomic mass of As is higher than P and As-O bonds are longer than P-O bonds. The position, shape and relative intensity of the bands vary primarily as a function of As/(As + P) in the analyzed solid. The strong correlations between the positions of the vibrational modes and the As/(As + P) ratio can be used to determine the composition of the investigated natural and synthetic samples of the minerals from the mimetite-pyromorphite series.     

Theoretical Simulation of Vibrational Sum‐Frequency Generation Spectra from Density Functional Theory: Application to p‐Nitrothiophenol and 2,4‐Dinitroaniline

The molecular orientation of adsorbed molecules forming self‐assembled monolayers can be determined by combining vibrational sum‐frequency generation (SFG) measurements with quantum chemical calculations. Herein, we present a theoretical methodology used to simulate the SFG spectra for different combinations of polarizations. These simulations are based on calculations of the IR vectors and Raman tensors, which are obtained from density functional theory computations. The dependency of the SFG vibrational signature with respect to the molecular orientation is presented for the molecules p‐nitrothiophenol and 2,4‐dinitroaniline. It is found that a suitable choice of basis set as well as of exchange‐correlation (XC) functional is mandatory to correctly simulate the SFG intensities and consequently provide an accurate estimation of the adsorbed molecule orientation. Comparison with experimental data shows that calculations performed at the B3LYP/6‐311++G(d,p) level of approximation provide good agreement with experimental frequencies, and with IR and Raman intensities. In particular, it is demonstrated that polarization and diffuse functions are compulsory for reproducing the IR and Raman spectra, and consequently vibrational SFG spectra, of systems such as p‐nitrothiophenol. Moreover, the investigated XC functionals reveal their influence on the relative intensities, which show rather systematic variations with the amount of Hartree–Fock exchange. Finally, further aspects of the modeling are revealed by considering the frequency dependence of the Raman tensors.     

Vibrational Sum‐Frequency Generation Activity of a 2,4‐Dinitrophenyl Phospholipid Hybrid Bilayer: Retrieving Orientational Parameters from a DFT Analysis of Experimental Data

The vibrational nonlinear activity of films of 2,4‐dinitrophenyl phospholipid (DNP) at the solid interface is measured by sum‐frequency generation spectroscopy (SFG). Hybrid bilayers are formed by a Langmuir–Schaefer approach in which the lipid layer is physisorbed on top of a self‐assembled monolayer of dodecanethiol on Pt with the polar heads pointing out from the surface. The SFG response is investigated in two vibrational frequency domains, namely, 3050–2750 and 1375–1240 cm^?1. The first region probes the CH stretching modes of DNP films, and the latter explores the vibrational nonlinear activity of the 2,4‐dinitroaniline moiety of the polar head of the lipid. Analysis of the CH stretching vibrations suggests substantial conformational order of the aliphatic chains with only a few gauche defects. To reliably assign the detected SFG signals to specific molecular vibrations, DFT calculations of the IR and Raman activities of molecular models are performed and compared to experimental solid‐state spectra. This allows unambiguous assignment of the observed SFG vibrations to molecular modes localized on the 2,4‐dinitroaniline moiety of the polar head of DNP. Then, SFG spectra of DNP in the 1375–1240 cm^?1 frequency range are simulated and compared with experimental ones, and thus the 1,4‐axis of the 2,4‐dinitrophenyl head is estimated to have tilt and rotation angles of 45±5° and 0±30°, respectively.     

Vibrational and quantum-chemical study of push-pull chromophores for second-order nonlinear optics from rigidified thiophene-based pi-conjugating spacers

Two types of push-pull chromophores built around thiophene-based pi-conjugating spacers rigidified by either covalent bonds or noncovalent intramolecular interactions have been analysed by means of IR and Raman spectroscopical measurements in the solid state as well as in a variety of solvents. Comparison of the Raman features of NLO-phores based on a covalently rigidified dithienylene (DTE) spacer with those of their open chain DTE analogues shows that the bridging of the central double bond of DTE with the nearest beta-positions of the thienyl units through two ethylene bridges significantly improves the intramolecular charge transfer. This also occurs for NLO-phores based on a 2,2'-bi(3,4-ethylenedioxythiophene) (BEDOT) spacer as compared with their corresponding parent compounds based on an unsubstituted bithiophene (BT) spacer. For NLO-phores based on a BEDOT spacer, noncovalent intramolecular interactions between sulfur and oxygen atoms are responsible for the rigidification of the spacer. The Raman spectra of these NLO-phores obtained in the form of solutes in dilute solutions reveal two different behaviours: i) chromophores based on covalently bridged or open chain DTE spacers display Raman spectral profiles in solution quite similar to those of the corresponding solids, with a very little dependence on the polarity of the solvent, while ii) larger spectral changes are noticed for NLO-phores built around BEDOT or BT spacers on going from solids to solutions. In the second case, spectral changes must be ascribed not solely to conformational distortions of the donor and acceptor end groups with respect to the pi-conjugated backbone mean-square-plane (as for the DTE-based NLO-phores) but also to distortions of the thienyl units of the pi-conjugating spacer from coplanarity. The insertion of vinylenic bridges between the thienyl units of the pi-conjugating spacer and between the spacer and the donor and acceptor end groups is a suitable strategy to reach a fairly large intramolecular charge transfer both in polar and nonpolar solvents. Density functional theory (DFT) calculations have been carried out to assign the relevant electronic and vibrational features and to derive useful information about the molecular structure of these NLO-phores.     

Infrared Absorption Spectra of t‐HNOH Radicals Generated on VUV Irradiation of NO in Solid Hydrogen

Photoproduct signature: Irradiation of solid hydrogen near 3 K containing NO with vacuum‐UV light from synchrotron radiation yields new infrared absorption lines at 1241.7, 1063.6 and 726.2 cm^?1 (see figure). These new lines are assigned to vibrational modes of t‐HNOH. This photoproduct is formed from electronically excited NO reacting with neighboring hydrogen in the solid sample.

     

A Tunable,Fullerene-Based Molecular Amplifier for Vibrational Circular Dichroism

Vibrational circular dichroism (VCD) studies are reported on a chiral compound in which a fullerene C₆₀ moiety is used as an electron acceptor and local VCD amplifier for an alanine-based peptide chain. Four redox states are investigated in this study, of which three are reduced species that possess low-lying electronic states as confirmed by UV/Vis spectroelectrochemistry. VCD measurements in combination with (TD)DFT calculations are used to investigate (i) how the low-lying electronic states of the reduced species modulate the amplification of VCD signals, (ii) how this amplification depends on the distance between oscillator and amplifier, and (iii) how the spatial extent of the amplifier influences amplification. These results pave the way for further development of tailored molecular VCD amplifiers.     

Vibrational structure of endohedral fullerene Sc3N@C78 (D3h'): evidence for a strong coupling between the Sc3N cluster and C78 cage.

The vibrational structure of the endohedral cluster fullerene Sc(3)N@C(78) is studied by FTIR spectroscopy, Raman spectroscopy and DFT-based quantum chemical calculations. Remarkably good agreement between experimental and calculated spectra is achieved and a full assignment of the Sc(3)N-based vibrational modes is given. Significant differences in the vibrational structure of the endohedral cluster fullerene Sc(3)N@C(78) and the empty, charged C(78) (6-): 5 (D(3h)') are rationalized by the strong coupling between the Sc(3)N cluster and the fullerene cage. This coupling has its origin in a significant overlap of the Sc(3)N and C(78) molecular orbitals, and causes atomic-charge and bond-length redistributions compared to the neutral C(78) and the C(78) (6-) anion. An ionic model is not sufficient to describe the electronic, geometric and vibrational structure of the Sc(3)N@C(78) nitride cluster fullerene.     

用密度泛函理论研究一种新型有机硅化合物异构体的振动光谱

在B3LYP/6-31＋G(d)的水平上, 对两种含有手性Si原子的新型有机硅单体Si₂(CH₃)₂H₂N₂(C₂H₅)₄和Si₄(CH₃)₄H₄N₂(C₆H₅)₂的几种异构体进行了研究, 在全参量几何构型优化的基础上, 进行了简谐振动频率计算, 同时对所研究的体系进行了热力学性质和低能激发态的含时密度泛函理论(TDDFT)计算. 理论计算表明, 构象异构体之间的红外光谱差异不大, 热力学和低能激发态性质也相似; 顺/反结构相似的异构体之间红外光谱差异不大, 但热力学和低能激发态性质却呈现差异; 旋光异构体或顺/反结构相差较大的异构体之间, 红外光谱和热力学及低能激发态性质有明显的差异. 从理论上解释了实验红外光谱中Si—H振动峰的裂分是由异构体的存在所致, 并找到裂分峰所对应的异构结构. Si—H键振动频率与其键长相关.     

Determination of the Absolute Configuration of Pentacoordinate Chiral Phosphorus Compounds in Solution by Using Vibrational Circular Dichroism Spectroscopy and Density Functional Theory

Vibrational circular dichroism (VCD) spectroscopic measurements and density functional theory (DFT) calculations have been used to obtain the absolute structural information about four sets of diastereomers of pentacoordinate spirophosphoranes derived separately from l‐ (or d‐ ) valine and l‐ (or d‐ ) leucine for the first time. Each compound contains three stereogenic centers: one at the phosphorus center and two at the amino acid ligands. Extensive conformational searches for the compounds have been carried out and their vibrational absorption (VA) and VCD spectra have been simulated at the B3LYP/6‐311++G** level. Although both VA and VCD spectra are highly sensitive to the structural variation of the apical axis, that is, the O? P? O or N? P? O arrangement, the rotamers generated by the aliphatic amino side chains show little effect on both. The dominant experimental VCD features in the 1100–1500 cm^?1 region were found to be controlled by the chirality at the phosphorus center, whereas those at the C?O stretching region are determined by the chirality of the amino acid ligands. The good agreement between the experimental VA and VCD spectra in CDCl₃ solution and the simulated ones allows us to assign the absolute configurations of these pentacoordinate phosphorus compounds with high confidence. This study shows that the VCD spectroscopy complemented with DFT calculations is a powerful and reliable method for determining the absolute configurations and dominating conformers of synthetic phosphorus coordination complexes in solution.     

Vibrational Property of α-Borophene Determined by Tip-Enhanced Raman Spectroscopy

We report a Raman characterization of the α borophene polymorph by scanning tunneling microscopy combined with tip-enhanced Raman spectroscopy. A series of Raman peaks were discovered, which can be well related with the phonon modes calculated based on an asymmetric buckled α structure. The unusual enhancement of high-frequency Raman peaks in TERS spectra of α borophene is found and associated with its unique buckling when landed on the Ag(111) surface. Our paper demonstrates the advantages of TERS, namely high spatial resolution and selective enhancement rule, in studying the local vibrational properties of materials in nanoscale.     

Reinterpretation of Dynamic Vibrational Spectroscopy to Determine the Molecular Structure and Dynamics of Ferrocene

Molecular distortion of dynamic molecules gives a clear signature in the vibrational spectra, which can be modeled to give estimates of the energy barrier and the sensitivity of the frequencies of the vibrational modes to the reaction coordinate. The reaction coordinate method (RCM) utilizes ab initio‐calculated spectra of the molecule in its ground and transition states together with their relative energies to predict the temperature dependence of the vibrational spectra. DFT‐calculated spectra of the eclipsed (D_5h) and staggered (D_5d) forms of ferrocene (Fc), and its deuterated analogue, within RCM explain the IR spectra of Fc in gas (350 K), solution (300 K), solid solution (7–300 K), and solid (7–300 K) states. In each case the D_5h rotamer is lowest in energy but with the barrier to interconversion between rotamers higher for solution‐phase samples (ca. 6 kJ mol^?1) than for the gas‐phase species (1–3 kJ mol^?1). The generality of the approach is demonstrated with application to tricarbonyl(η⁴‐norbornadiene)iron(0), Fe(NBD)(CO)₃. The temperature‐dependent coalescence of the ν(CO) bands of Fe(NBD)(CO)₃ is well explained by the RCM without recourse to NMR‐like rapid exchange. The RCM establishes a clear link between the calculated ground and transition states of dynamic molecules and the temperature‐dependence of their vibrational spectra.     

Self‐Assembly Structures of 1H‐Indazoles in the Solution and Solid Phases: A Vibrational (IR,FIR, Raman,and VCD) Spectroscopy and Computational Study

1H‐indazoles are good candidates for studying the phenomena of molecular association and spontaneous resolution of chiral compounds. Thus, because the 1H‐indazoles can crystallize as dimers, trimers, or catemers, depending on their structure and the phase that they are in, the difficulty in the experimental analysis of the structure of the family of 1H‐indazoles becomes clear. This difficulty leads us to contemplate several questions: How can we determine the presence of different structures of a given molecular species if they change according to the phase? Could these different structures be present in the same phase simultaneously? How can they be determined? To shed light on these questions, we outline a very complete strategy by using various vibrational spectroscopic techniques that are sensitive (VCD) and insensitive (IR, FIR, and Raman) towards the chirality, together with quantum chemical calculations.     

Vibrational Circular Dichroism and Theoretical Study of the Conformational Equilibrium in (−)‐S‐Nicotine

We report an extensive study of the molecular and electronic structure of (?)‐S‐nicotine, to deduce the phenomenon that controls its conformational equilibrium and to solve its solution‐state conformer population. Density functional theory, ab initio, and molecular mechanics calculations were used together with vibrational circular dichroism (VCD) and Fourier transform infrared spectroscopies. Calculations and experiments in solution show that the structure and the conformational energy profile of (?)‐S‐nicotine are not strongly dependent on the medium, thus suggesting that the conformational equilibrium is dominated by hyperconjugative interactions rather than repulsive electronic effects. The analysis of the first recorded VCD spectra of (?)‐S‐nicotine confirmed the presence of two main conformers at room temperature. Our results provide further evidence of the hypersensitivity of vibrational optical activity spectroscopies to the three‐dimensional structure of chiral samples and prove their suitability for the elucidation of solution‐state conformer distribution.     

Computational study of the vibrational spectra of alpha- and beta-Keggin polyoxometalates

The structures and vibrational frequencies of the alpha- and beta-isomers of the phosphomolybdate Keggin anion [PMo(12)O(40)](3-) have been calculated by using density functional theory. Good agreement between the calculated unscaled vibrational frequencies and those determined experimentally and between the calculated and observed IR traces has been obtained allowing the IR and Raman spectra to be assigned. For the alpha-isomer, the agreement with experiment using the current level of theory is superior to that obtained previously. For the beta-isomer, for which no non-empirical study has previously been reported, the agreement with experiment is slightly poorer but still allows the spectrum to be assigned unambiguously. To calculate the structure and vibrational spectra of these large molydate cluster ions requires large basis sets and a good treatment of electron correlation and relativistic effects. For the 53-atom [PMo(12)O(40)](3-) ions, the computational demands are very high, requiring several months computational time. The calculated IR spectral traces for the two isomers are quite similar due to the relative flexibility of the molybdates, where the slight weakening of the bonding of the rotated trimetallic unit to the rest of the cluster in the beta-isomer is compensated by contraction of the bonds within the unit, and the structure of the [MO(6)] and [PO(4)] units in the two isomers is nearly identical. The vibrations characteristic of the bridging Mo-O-Mo bonds involve both the "2-2" junctions between rotated [M(3)O(13)] units and the "1-2" junctions between rotated and unrotated units. The separation of "ligand" and "interligand" vibrations is not clear. The vibrational analyses confirm the high symmetry, namely T(d) and C(3v) for the alpha- and beta-isomers, respectively, assumed by previous workers in this field. The characteristic group frequencies for the Type I polyoxometalates containing both edge- and corner-sharing I octahedra have been identified.