Vibronic line shapes of PTCDA oligomers in helium nanodroplets

Oligomers of the organic semiconductor 3,4,9,10-perylene-tetracarboxylic-dianhydride, C(24)H(8)O(6) (PTCDA) are studied by means of helium nanodroplet isolation spectroscopy. In contrast to the monomer absorption spectrum, which exhibits clearly separated, very sharp absorption lines, it is found that the oligomer spectrum consists of three main peaks having an apparent width orders of magnitude larger than the width of the monomer lines. Using a simple theoretical model for the oligomer, in which a Frenkel exciton couples to internal vibrational modes of the monomers, these experimental findings are nicely reproduced. The three peaks present in the oligomer spectrum can already be obtained taking only one effective vibrational mode of the PTCDA molecule into account. The inclusion of more vibrational modes leads to quasicontinuous spectra, resembling the broad oligomer spectra.     

Temporal fluctuations in the SERRS spectra of single iron–protoporphyrin IX molecule

Surface enhanced resonance Raman spectra of Fe–protoporphyrin IX, adsorbed on silver colloidal nanoparticles immobilized onto a polymer-coated glass slide have been investigated at very low concentrations. The spectra exhibit drastic temporal fluctuations on a time scale of seconds in both line frequency and intensity; such a trend suggesting that the single molecule limit is approached. Sequences of spectra have been analyzed in terms of an underlying continuum and of Raman peaks superimposed on this continuum. A statistical analysis of the spectrum intensity has allowed us to put into evidence that main contribution to the intensity fluctuations arises from the continuum. In addition, a high correlation between the total integrated intensity and the intensity detected at different Raman peaks has been revealed. Furthermore, the ratio between the intensity detected in correspondence of different FePP vibrational modes shows a temporal variability likely reflecting the intrinsic dynamics of the molecule. All these findings have been ascribed to a desorption–adsorption mechanism of the molecules at the silver surface.     

Phenol-benzene complexation dynamics: quantum chemistry calculation, molecular dynamics simulations, and two dimensional IR spectroscopy

Molecular dynamics (MD) simulations and quantum mechanical electronic structure calculations are used to investigate the nature and dynamics of the phenol-benzene complex in the mixed solvent, benzene/CCl4. Under thermal equilibrium conditions, the complexes are continuously dissociating and forming. The MD simulations are used to calculate the experimental observables related to the phenol hydroxyl stretching mode, i.e., the two dimensional infrared vibrational echo spectrum as a function of time, which directly displays the formation and dissociation of the complex through the growth of off-diagonal peaks, and the linear absorption spectrum, which displays two hydroxyl stretch peaks, one for the complex and one for the free phenol. The results of the simulations are compared to previously reported experimental data and are found to be in quite reasonable agreement. The electronic structure calculations show that the complex is T shaped. The classical potential used for the phenol-benzene interaction in the MD simulations is in good accord with the highest level of the electronic structure calculations. A variety of other features is extracted from the simulations including the relationship between the structure and the projection of the electric field on the hydroxyl group. The fluctuating electric field is used to determine the hydroxyl stretch frequency-frequency correlation function (FFCF). The simulations are also used to examine the number distribution of benzene and CCl4 molecules in the first solvent shell around the phenol. It is found that the distribution is not that of the solvent mole fraction of benzene. There are substantial probabilities of finding a phenol in either a pure benzene environment or a pure CCl4 environment. A conjecture is made that relates the FFCF to the local number of benzene molecules in phenol's first solvent shell.     

Second-derivative method: Application to vibrational spectroscopy in excited electronic states

The second-derivative method, which has been known to be useful for finding peaks overlapped in a broad band, is applied to u.v. and visible absorption bands to derive vibrational frequencies in excited electronic states of molecules in solution. By using this method, much better estimates of vibrational frequencies are possible for Franck—Condon active modes than can be made from the absorption spectrum itself. Computational procedure and the results obtained for trans-1,3,5-hexatriene, azulene, pyrazine and anthracene are described with remarks about the effectiveness and limitations of the second-derivative method.     

Theoretical analysis of correlation between ionization threshold fluence in IR‐MALDI and IR absorption spectrum of matrix molecules

To investigate the correlation between the wavelength dependence of ionization threshold fluence of target molecule in matrix‐assisted laser desorption/ionization by infrared (IR) laser and the IR absorption spectrum of matrix molecule, we have analyzed the IR absorption spectra of four matrix molecules using density functional theory and correlated ab initio molecular orbital method. The calculated IR absorption spectra of the isolated molecules showed more qualitative correlation with the wavelength dependence of ionization threshold fluence than those of the solid state structures. We can consider that a portion of matrix molecules lost the ordered crystal structure and that the transition to the diluted or isolated state occurred at the early process of IR laser irradiation. © 2012 Wiley Periodicals, Inc.     

Chlorofluoroiodomethane as a potential candidate for parity violation measurements

CHFClI is among the more favorable molecules for parity violation (PV) measurements in molecules. Despite the fact that calculated PV effects are two orders of magnitude smaller than in some organometallic compounds, CHFClI displays interesting features which could make possible a new experimental PV test on this molecule. Indeed, ultrahigh resolution spectroscopy using an ultrastable CO(2) laser is favored by several intrinsic properties of this molecule. For example, the high vapor pressure of CHFClI allows investigation by supersonic beam spectroscopy. Indeed, the spectroscopic constants have been accurately determined by microwave and millimetre wave spectroscopy. This is important for the subsequent selection of an appropriate absorption band of CHFClI that could be brought to co?ncide with the absorption of CO(2). Partially resolved (+)- and (-)-CHFClI enantiomers with respectively 63.3 and 20.5% ee's have been recently prepared and analyzed by molecular recognition using chiral hosts called cryptophanes. Finally, the S-(+)/R-(-) absolute configuration was ascertained by vibrational circular dichro?sm (VCD) in the gas phase.     

Nonperturbative vibrational energy relaxation effects on vibrational line shapes

A general formulation of nonperturbative quantum dynamics of solutes in a condensed phase is proposed to calculate linear and nonlinear vibrational line shapes. In the weak solute-solvent interaction limit, the temporal absorption profile can be approximately factorized into the population relaxation profile from the off-diagonal coupling and the pure-dephasing profile from the diagonal coupling. The strength of dissipation and the anharmonicity-induced dephasing rate are derived in Appendix A. The vibrational energy relaxation (VER) rate is negligible for slow solvent fluctuations, yet it does not justify the Markovian treatment of off-diagonal contributions to vibrational line shapes. Non-Markovian VER effects are manifested as asymmetric envelops in the temporal absorption profile, or equivalently as side bands in the frequency domain absorption spectrum. The side bands are solvent-induced multiple-photon effects which are absent in the Markovian VER treatment. Exact path integral calculations yield non-Lorentzian central peaks in absorption spectrum resulting from couplings between population relaxations of different vibrational states. These predictions cannot be reproduced by the perturbative or the Markovian approximations. For anharmonic potentials, the absorption spectrum shows asymmetric central peaks and the asymmetry increases with anharmonicity. At large anharmonicities, all the approximation schemes break down and a full nonperturbative path integral calculation that explicitly accounts for the exact VER effects is needed. A numerical analysis of the O-H stretch of HOD in D(2)O solvent reveals that the non-Markovian VER effects generate a small recurrence of the echo peak shift around 200 fs, which cannot be reproduced with a Markovian VER rate. In general, the nonperturbative and non-Markovian VER contributions have a stronger effect on nonlinear vibrational line shapes than on linear absorption.     

Hydrogen bond and the structures of 2-, 3-and 4-biphenylmethanols

Density functional theory (B3LYP/6-31G*) is applied to calculate structures, energy, dipole moment, polarizability, frequencies of normal vibrations in the harmonic approximation and intensities in vibrational spectra of 2-, 3-, and 4-biphenylmethanol molecules and their H-complexes that can form in crystalline, amorphous, and liquid phases. Based on the analysis of simulation results, the effect of the position of a methanol group in the molecule on its vibrational spectrum is discussed. The structure forming role of a hydrogen bonds in biphenylmethanols and the possibility of realization of two polymorphic modifications in 2-biphenylmethanol are stated. These modifications are: metastable monoclinic, in which each of four molecules of the unit cell is a link of a chain H-associate; and stable triclinic, in which four molecules of the unit cell organize an H-complex in the form of a cyclic tetramer. It is found that crystalline samples of 3-and 4-biphenylmethanols consist of chain H-associates. A glass-like sample of 2BPhM being a mixture of H-complexes consisting of cyclic tetramers and chain associates contains crystalline nuclei of triclinic and monoclinic polymorphous modifications in the supercooled state. In a liquid sample of 2BPhm, chain H-associates and free molecules are realized.     

Intermolecular Hydrogen Bonds Formed Between Amino Acid Molecules in Aqueous Solution Investigated by Temperature-jump NanosecondTime-resolved Transient Mid-IR Spectroscopy

Carboxyl (COO?) vibrational modes of two amino acids histidine and glycine in D2O solution were investigated by temperature-dependent FTIR spectroscopy and temperature-jump nanosecond time-resolved IR di?erence absorbance spectroscopy. The results show that hydrogen bonds are formed between amino acid molecules as well as between the amino acid molecule and the solvent molecules. The asymmetric vibrational frequency of COO? around 1600-1610 cm?1 is blue shifted when raising temperature, indicating that the strength of the hydrogen bonds becomes weaker at higher temperature. Two bleaching peaks at 1604 and 1612 cm?1 were observed for histidine in response to a temperature jump from 10 ±C to 20 ±C. The lower vibrational frequency at 1604 cm?1 is assigned to the chain COO? group which forms the intermolecular hydrogen bond with NH3+ group, while the higher frequency at 1612 cm?1 is assigned to the end COO? group forming hydrogen bonds with the solvent molecules. This is because that the hydrogen bonds in the former are expected to be stronger than the latter. In addition the intensities of these two bleaching peaks are almost the same. In contrast, only the lower frequency at 1604 cm?1 bleaching peak has been observed for glycine. The fact indicates that histidine molecules form a dimer-like intermolecular chain while glycine forms a relatively longer chain in the solution. The rising phase of the IR absorption kinetics in response to the temperature-jump detected at 1604 cm?1 for histidine is about 30§10 ns, within the resolution limit ofour instrument, indicating that breaking or weakening the hydrogen bond is a very fast process.     

Efficient electron dynamics with the planewave-based real-time time-dependent density functional theory: absorption spectra, vibronic electronic spectra, and coupled electron-nucleus dynamics

The electron dynamics with complex third-order Suzuki-Trotter propagator (ST(3)) has been implemented into a planewave (PW) based density functional theory program, and several applications including linear absorption spectra and coupled electron-nucleus dynamics have been calculated. Since the ST(3) reduces the number of Fourier transforms to less than half compared to the fourth-order Suzuki-Trotter propagator (ST(4)), more than twice faster calculations are possible by exploiting the ST(3). We analyzed numerical errors of both the ST(3) and the ST(4) in the presence∕absence of an external field for several molecules such as Al(2), N(2), and C(2)H(4). We obtained that the ST(3) gives the same order of numerical errors (10(-5) Ry after 100 fs) as the ST(4). Also, the time evolution of dipole moments, hence the absorption spectrum, is equivalent for both ST(3) and ST(4). As applications, the linear absorption spectrum for an ethylene molecule was studied. From the density difference analysis, we showed that the absorption peaks at 6.10 eV and 7.65 eV correspond to the π → 4a(g) and π → π* excitation bands, respectively. We also investigated the molecular vibrational effect to the absorption spectra of an ethylene molecule and the dynamics of a hydrogen molecule after the σ → σ* transition by formulating coupled electron-nucleus dynamics within the Ehrenfest regime. The trajectory of nuclei follows the excited state potential energy curve exactly.     

Taking apart the two-dimensional infrared vibrational echo spectra: more information and elimination of distortions

Ultrafast two-dimensional infrared (2D-IR) vibrational echo spectroscopy can probe the fast structural evolution of molecular systems under thermal equilibrium conditions. Structural dynamics are tracked by observing the time evolution of the 2D-IR spectrum, which is caused by frequency fluctuations of vibrational mode(s) excited during the experiment. However, there are a variety of effects that can produce line shape distortions and prevent the correct determination of the frequency-frequency correlation function (FFCF), which describes the frequency fluctuations and connects the experimental observables to a molecular level depiction of dynamics. In addition, it can be useful to analyze different parts of the 2D spectrum to determine if dynamics are different for subensembles of molecules that have different initial absorption frequencies in the inhomogeneously broadened absorption line. Here, an important extension to a theoretical method for extraction of the FFCF from 2D-IR spectra is described. The experimental observable is the center line slope (CLSomega(m)) of the 2D-IR spectrum. The CLSomega(m) is obtained by taking slices through the 2D spectrum parallel to the detection frequency axis (omega(m)). Each slice is a spectrum. The slope of the line connecting the frequencies of the maxima of the sliced spectra is the CLSomega(m). The change in slope of the CLSomega(m) as a function of time is directly related to the FFCF and can be used to obtain the complete FFCF. CLSomega(m) is immune to line shape distortions caused by destructive interference between bands arising from vibrational echo emission, from the 0-1 vibrational transition (positive), and from the 1-2 vibrational transition (negative) in the 2D-IR spectrum. The immunity to the destructive interference enables the CLSomega(m) method to compare different parts of the bands as well as comparing the 0-1 and 1-2 bands. Also, line shape distortions caused by solvent background absorption and finite pulse durations do not affect the determination of the FFCF with the CLSomega(m) method. The CLSomega(m) can also provide information on the cross correlation between frequency fluctuations of the 0-1 and 1-2 vibrational transitions.     

Ultrafast dynamics of the azobenzene-coumarin complex: investigation of cooling dynamics measured by an integrated molecular thermometer

The energy dissipation mechanism from photoexcited azobenzene (Az) was studied by femtosecond time-resolved UV absorption spectroscopy using 7-amino-4-trifluoromethylcoumarin (ATC) as a probe. The distance between the probe molecule and Az was fixed by covalently linking them together through a rigid proline spacer. Picosecond dynamics in THF solutions were studied upon excitation into the S1 state by a 100 fs laser pulse at 480 nm. Transient absorption spectra obtained for Az-Pro-ATC combined the S1 state absorption and vibrationally excited ground-state absorption of ATC. Correction of the transient spectrum of Az-Pro-ATC for the S1 absorption provided the time-resolved absorption spectrum of the ATC hot band. Three major components were observed in the transient kinetics of Az-Pro-ATC vibrational cooling. It is proposed that in ca. 0.25 ps after the excitation, the S1 state of azobenzene decays to form an initial vibrationally excited nonthermalized ground state of Az-Pro-ATC that involves vibrational modes of both azobenzene and coumarin. This hot ground state decays in ca. 0.32 ps to the next, vibrationally equilibrated, transient state by redistributing the energy within the molecule. Subsequently, the latter state cools by transferring its energy to the closest solvent molecules in ca. 5 ps; then, the energy diffuses to the bulk solvent in 13 ps.     

Simple evaluation of the adsorption states of benzene molecule on the hydroxyl,H+ and Na+ sites of Y-zeolite surfaces by using UV absorption spectroscopy

Chemical properties of benzene molecules adsorbed on the hydroxyl, H⁺ and Na⁺ sites of Y-zeolite surfaces were investigated by using UV absorption and FT-IR spectroscopies. The analyses on the IR peaks assigned to a C–H out-of-plane vibration mode revealed two different adsorption states of benzene: (1) a benzene molecule located a little distance from the hydroxyl groups of zeolite inner walls, and (2) a benzene molecule positioned a short distance from the H⁺ or Na⁺ sites of zeolite walls. Furthermore, the electronic properties of benzene molecules adsorbed on these Y-zeolites were investigated by UV absorption measurements. The vibrational splitting in UV absorption spectra of benzene provided the information about IR-inactive skeletal vibrations of the benzene ring, such as C–C–C in-plane bending and breathing modes. The benzene molecules strongly interacting with H⁺ or Na⁺ sites of Y-zeolites showed smaller breathing vibration energy as compared to benzene in gas or liquid phases, clearly indicating the stabilization of the benzene ring. In contrast, the benzene molecules weakly interacting with hydroxyl groups of siliceous USY zeolite were barely stabilized.     

Mono,di, tri and tetraethylene glycol: Spectroscopic characterization using density functional method and experiment

We report infrared and electronic absorption spectra of mono, di, tri and tetra ethylene glycol (EG) in gas phase, their cation and anion and in water solvent using density functional theory calculations at B3LYP/TZVP level. Structural paramaters, rotational and centrifugal distortional constants and dipole moments are also reported. A siginificant shifts in vibrational frequencies and peaks in electronic absorption spectra have been observed upon ionization of mono, di, tri and tetra ethylene glycols. We have also obtained experimental vibrational spectrum of monoethylene glycol. Vibrational frequencies of mono ethylene glycol from theory and experiment are compared. We have used integral equation formalism polarizable continuum model (IEFPCM) model to study the influence of water solvent on vibrational frequencies of neutral mono, di, tri and tetra ethylene glycol. Electronic absorption spectra for these molecules have been obtained using Time dependent density functional theory (TDDFT).     

Solvent effect on the absorption spectra of coumarin 120 in water: A combined quantum mechanical and molecular mechanical study

The solvent effect on the absorption spectra of coumarin 120 (C120) in water was studied utilizing the combined quantum mechanical∕molecular mechanical (QM∕MM) method. In molecular dynamics (MD) simulation, a new sampling scheme was introduced to provide enough samples for both solute and solvent molecules to obtain the average physical properties of the molecules in solution. We sampled the structure of the solute and solvent molecules separately. First, we executed a QM∕MM MD simulation, where we sampled the solute molecule in solution. Next, we chose random solute structures from this simulation and performed classical MD simulation for each chosen solute structure with its geometry fixed. This new scheme allowed us to sample the solute molecule quantum mechanically and sample many solvent structures classically. Excitation energy calculations using the selected samples were carried out by the generalized multiconfigurational perturbation theory. We succeeded in constructing the absorption spectra and realizing the red shift of the absorption spectra found in polar solvents. To understand the motion of C120 in water, we carried out principal component analysis and found that the motion of the methyl group made the largest contribution and the motion of the amino group the second largest. The solvent effect on the absorption spectrum was studied by decomposing it in two components: the effect from the distortion of the solute molecule and the field effect from the solvent molecules. The solvent effect from the solvent molecules shows large contribution to the solvent shift of the peak of the absorption spectrum, while the solvent effect from the solute molecule shows no contribution. The solvent effect from the solute molecule mainly contributes to the broadening of the absorption spectrum. In the solvent effect, the variation in C-C bond length has the largest contribution on the absorption spectrum from the solute molecule. For the solvent effect on the absorption spectrum from the solvent molecules, the solvent structure around the amino group of C120 plays the key role.     

溶剂效应和取代基效应对2-(2-氨基苯基)苯并噻唑光谱性质及激发态分子内质子转移的影响

合成了多种2-(2-氨基苯基)苯并噻唑(APBT)氨基氢原子被供电子及吸电子基团取代的衍生物, 并用紫外光谱﹑荧光光谱等方法和密度泛函理论(DFT)计算研究了溶剂效应和取代基效应对衍生物的光谱性质及激发态分子内质子转移(ESIPT)的影响规律. 结果表明, 相比于非极性溶剂环己烷, 随溶剂极性的增加及APBT-溶剂分子间氢键的形成, APBT的紫外-可见最大吸收峰和荧光最大发射峰均发生了一定程度的红移, 并对APBT的ESIPT产生了影响. 在APBT分子的氨基氮原子上引入不同的吸电子或斥电子取代基, 对氮原子的电荷性质有较大的影响. 在环己烷溶剂中, 甲基取代后的APBT仅有单重荧光发射峰, 体系未发生ESIPT过程; 而COCH₂Cl等吸电子基团能促进APBT的ESIPT, 其荧光发射光谱出现了明显的双重峰, 表明体系发生了激发态分子内质子转移反应. 量子化学的理论计算较好地验证了光谱实验结果.     

Correlating the vibrational spectra of structurally related molecules: A spectroscopic measure of similarity

Using catastrophe theory and the concept of a mutation path, an algorithm is developed that leads to the direct correlation of the normal vibrational modes of two structurally related molecules. The mutation path is defined by weighted incremental changes in mass and geometry of the molecules in question, which are successively applied to mutate a molecule into a structurally related molecule and thus continuously converting their normal vibrational spectra from one into the other. Correlation diagrams are generated that accurately relate the normal vibrational modes to each other by utilizing mode‐mode overlap criteria and resolving allowed and avoided crossings of vibrational eigenstates. The limitations of normal mode correlation, however, foster the correlation of local vibrational modes, which offer a novel vibrational measure of similarity. It will be shown how this will open new avenues for chemical studies. © 2017 Wiley Periodicals, Inc.     

FTIR and Ab initio investigations of the MTBE-water complex

The infrared spectrum of methyl tert-butyl ether (MTBE) in liquid water has been studied using both FTIR absorption and FTIR-ATR spectroscopy in conjunction with ab initio calculations. Compared to the liquid MTBE IR spectrum, the C-O and C-C stretching vibrational frequencies of MTBE in water are found to shift to the red and blue by up to 26 and 9 cm (-1), respectively. Ab initio calculations suggest that these shifts are caused by complexation of the MTBE molecule with water molecules through hydrogen bonding. Our observation of the vibrational frequency shifts in the IR spectrum of MTBE in water provides the IR spectroscopic evidence of organics-water complexes in the diluted aqueous solution. The implication of the effect of the hydrogen bond in organics-water complexation on solvation and reactivity of the organic compound in aqueous chemical processes is discussed.     

Excitation transfer induced spectral diffusion and the influence of structural spectral diffusion

The theory of vibrational excitation transfer, which causes spectral diffusion and is also influenced by structural spectral diffusion, is developed and applied to systems consisting of vibrational chromophores. Excitation transfer induced spectral diffusion is the time-dependent change in vibrational frequency induced by an excitation on an initially excited molecule jumping to other molecules that have different vibrational frequencies within the inhomogeneously broadened vibrational absorption line. The excitation transfer process is modeled as Fo?rster resonant transfer, which depends on the overlap of the homogeneous spectra of the donating and accepting vibrational chromophores. Because the absorption line is inhomogeneously broadened, two molecules in close proximity can have overlaps of their homogeneous lines that range from substantial to very little. In the absence of structural dynamics, the overlap of the homogeneous lines of the donating and accepting vibrational chromophores would be fixed. However, dynamics of the medium that contains the vibrational chromophores, e.g., a liquid solvent or a surrounding protein, produce spectral diffusion. Spectral diffusion causes the position of a molecule's homogeneous line within the inhomogeneous spectrum to change with time. Therefore, the overlap of donating and accepting molecules' homogeneous lines is time dependent, which must be taken into account in the excitation transfer theory. The excitation transfer problem is solved for inhomogeneous lines with fluctuating homogeneous line frequencies. The method allows the simultaneous treatment of both excitation transfer induced spectral diffusion and structural fluctuation induced spectral diffusion. It is found that the excitation transfer process is enhanced by the stochastic fluctuations in frequencies. It is shown how a measurement of spectral diffusion can be separated into the two types of spectral diffusion, which permits the structural spectral diffusion to be determined in the presence of excitation transfer spectral diffusion. Various approximations and computational methodologies are explored.     

Spectral investigations on 1,4-dimethylamino anthraquinone under laser excitation

Surface enhanced Raman spectrum of 1,4-dimethylamino anthraquinone (1,4-DMAAQ) adsorbed on silver particles has been analyzed to understand the interaction between the molecule and silver surface. By studying the band intensities, the orientation of the molecule is determined. The high intensity and frequency downshifted peak due to carbonyl stretching vibration plays a major role, which shows that the molecules are chemisorbed through coordinating sites. The new peaks observed due to C-N and N-H stretching vibrations also provide the evidence for adsorption through co-ordinating sites. Optical absorption and laser induced fluorescence spectra of this molecule have also been studied in different solvents to understand the effect of environment. Polarization and anisotropy measurements provide the change in orientation induced by solvent molecules between absorption and emission transition dipoles.