Recent progress in theoretical analysis of vibrational sum frequency generation spectroscopy

This article summarizes the computational analysis of the vibrational sum frequency generation (SFG) spectroscopy with molecular dynamics simulation. The analysis allows direct comparison of experimental SFG spectra and microscopic interface structure obtained by molecular simulation, and thereby obviates empirical fitting procedures of the observed spectra. In the theoretical formulation, the frequency-dependent nonlinear susceptibility of an interface is calculated in two ways, based on the energy representation and time-dependent representation. The application to aqueous interfaces revealed a number of new insights into the local structure of electrolyte interfaces and the interpretation of SFG spectroscopy.     

The absorption and fluorescence properties of pyrene crystal: a theoretical approach. III. Relaxation from highly excited vibrational levels

It is shown that the model based on vibrational relaxation to the bath, while invalid for highly excited vibrational levels at low temperatures, is valid at high temperature. Thus relaxation time of ～10^?13 s previously estimated is acceptable. Using this time, known radiative lifetimes, and a reasonable value for relaxation times of the vibrations of the isolated molecules, a modified model for excimer absorption and emission is proposed.     

Frequency-frequency correlation functions and apodization in two-dimensional infrared vibrational echo spectroscopy: a new approach

Ultrafast two-dimensional infrared (2D-IR) vibrational echo spectroscopy can probe structural dynamics under thermal equilibrium conditions on time scales ranging from femtoseconds to approximately 100 ps and longer. One of the important uses of 2D-IR spectroscopy is to monitor the dynamical evolution of a molecular system by reporting the time dependent frequency fluctuations of an ensemble of vibrational probes. The vibrational frequency-frequency correlation function (FFCF) is the connection between the experimental observables and the microscopic molecular dynamics and is thus the central object of interest in studying dynamics with 2D-IR vibrational echo spectroscopy. A new observable is presented that greatly simplifies the extraction of the FFCF from experimental data. The observable is the inverse of the center line slope (CLS) of the 2D spectrum. The CLS is the inverse of the slope of the line that connects the maxima of the peaks of a series of cuts through the 2D spectrum that are parallel to the frequency axis associated with the first electric field-matter interaction. The CLS varies from a maximum of 1 to 0 as spectral diffusion proceeds. It is shown analytically to second order in time that the CLS is the T(w) (time between pulses 2 and 3) dependent part of the FFCF. The procedure to extract the FFCF from the CLS is described, and it is shown that the T(w) independent homogeneous contribution to the FFCF can also be recovered to yield the full FFCF. The method is demonstrated by extracting FFCFs from families of calculated 2D-IR spectra and the linear absorption spectra produced from known FFCFs. Sources and magnitudes of errors in the procedure are quantified, and it is shown that in most circumstances, they are negligible. It is also demonstrated that the CLS is essentially unaffected by Fourier filtering methods (apodization), which can significantly increase the efficiency of data acquisition and spectral resolution, when the apodization is applied along the axis used for obtaining the CLS and is symmetrical about tau=0. The CLS is also unchanged by finite pulse durations that broaden 2D spectra.     

Rozen's epoxidation reagent, CH3CN.HOF: a theoretical study of its structure, vibrational spectroscopy, and reaction mechanism

Rozen's epoxidation reagent, CH(3)CN.HOF, and a prototype epoxidation reaction employing it, have been subjected to an extensive ab initio and density functional study. Its anharmonic force field reveals a very strong red shift for the OH stretch and a strong blue shift for the HOF bend, in semiquantitative agreement with experiment. The very strong hydrogen bond (8.20 kcal/mol at the W1 level) not only serves to stabilize the reactant but also considerably lowers the barrier height for epoxidation of ethylene. Moreover, the reaction byproduct HF is found to act autocatalytically. The OH moiety acquires HO(+) character in the transition state. Our W1 benchmark data for the reaction profile allow the performance of various DFT functionals to be assessed. In general, "kinetics" functionals overestimate barrier heights, the BMK functional less so than the others. The B1B95 and TPSS33B95 meta-GGA functionals both perform very well, whereas general-purpose hybrid GGAs underestimate barrier heights. The simple PBE0 functional does reasonably well.     

Use of vibrational spectroscopy to study protein and DNA structure,hydration, and binding of biomolecules: A combined theoretical and experimental approach

We report on our work with vibrational absorption, vibrational circular dichroism, Raman scattering, Raman optical activity, and surface‐enhanced Raman spectroscopy to study protein and DNA structure, hydration, and the binding of ligands, drugs, pesticides, or herbicides via a combined theoretical and experimental approach. The systems we have studied systematically are the amino acids (L ‐alanine, L ‐tryptophan, and L ‐histidine), peptides (N‐4271 acetyl L ‐alanine N′‐methyl amide, N‐acetyl L ‐tryptophan N′‐methyl amide, N‐acetyl L ‐histidine N′‐methyl amide, L ‐alanyl L ‐alanine, tri‐L ‐serine, N‐acetyl L ‐alanine L ‐proline L ‐tyrosine N′‐methyl amide, Leu‐enkephalin, cyclo‐(gly‐L ‐pro)₃, N‐acetyl (L ‐alanine)_n N′‐methyl amide), 3‐methyl indole, and a variety of small molecules (dichlobenil and 2,6‐dochlorobenzamide) of relevance to the protein systems under study. We have used molecular mechanics, the SCC‐DFTB, SCC‐DFTB+disp, RHF, MP2, and DFT methodologies for the modeling studies with the goal of interpreting the experimentally measured vibrational spectra for these molecules to the greatest extent possible and to use this combined approach to understand the structure, function, and electronic properties of these molecules in their various environments. The application of these spectroscopies to biophysical and environmental assays is expanding, and therefore a thorough understanding of the phenomenon from a rigorous theoretical basis is required. In addition, we give some exciting and new preliminary results which allow us to extend our methods to even larger and more complex systems. The work presented here is the current state of the art to this ever and fast changing field of theoretical spectroscopic interpretation and use of VA, VCD, Raman, ROA, EA, and ECD spectroscopies. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

The factor group splitting phenomenon: a vibrational spectroscopy approach to assess polymer crystallinity and crystalline density

This paper gathers a number of relevant recent findings where Raman spectroscopy has been successfully applied by the author and coworkers to gain a unique structural picture about the crystalline phase present in isotropic and cold-drawn polyethylenes and in a range of aliphatic polyketone materials. In these semicrystalline polymers a relatively well-known spectroscopic phenomenon called factor group splitting (or correlation field splitting) is thought to occur. By careful analysis of the behaviour of this splitting phenomenon, chiefly in the -CH₂- bending range of the spectrum and in terms of alterations in band intensity and position, a valid approach to asses crystallinity content and morphology, crystalline polymorphism, and crystalline density is displayed. The potential of this spectroscopic phenomenon to yield information about the crystalline phase present in these polymers can therefore be regarded as analogous to that gained by wide-angle X-ray scattering.     

Time-resolved vibrational spectroscopy of a molecular shuttle

Time-resolved vibrational spectroscopy is used to investigate the inter-component motion of an ultraviolet-triggered two-station molecular shuttle. The operation cycle of this molecular shuttle involves several intermediate species, which are observable in the amide I and amide II regions of the mid-IR spectrum. Using ab initio calculations on specific parts of the rotaxane, and by comparing the transient spectra of the normal rotaxane with that of the N-deuterated version, we can assign the observed vibrational modes of each species occurring during the shuttling cycle in an unambiguous way. The complete time- and frequency-dependent data set is analyzed using singular value decomposition (SVD). Using a kinetic model to describe the time-dependent concentrations of the transient species, we derive the absorption spectra associated with each stage in the operation cycle of the molecular shuttle, including the recombination of the charged species.     

Broadband vibrational sum frequency generation spectroscopy of a liquid surface.

An important advance in surface science has been the evolution of sum frequency generation to the application of studying surface structure and chemistry of liquid surfaces at the molecular-level by probing the vibrational signatures of surface molecules. Recently, broad-bandwidth sum frequency generation (BBSFG) spectroscopy has become an important tool for investigating gas-solid interfaces. BBSFG spectroscopy allows, theoretically, a surface sum frequency spectrum to be acquired within one pulse of the laser. In this paper, the viability of BBSFG to study inherently small nonlinear response interfaces and the time-resolving capability of this surface-selective technology are demonstrated. Presented here are the first published accounts of spectra from a liquid surface utilizing the broad-bandwidth sum frequency technology with acquisition times as low as 500 milliseconds.     

Signatures of beta-peptide unfolding in two-dimensional vibrational echo spectroscopy: a simulation study.

An ensemble of exciton Hamiltonians for the amide-I band of the folded and unfolded states of a helical beta-heptapeptide is generated using a molecular dynamics (MD) simulation. The correlated fluctuations of its parameters and their signatures in two-dimensional (2D) vibrational echo spectroscopy are computed. This technique uses infrared pulse sequences to provide ultrafast snapshots of molecular structural fluctuations, in analogy with multidimensional NMR. The present study demonstrates that, by combining a method of calculating the vibrational Hamiltonian from MD snapshots and the nonlinear exciton equations (NEE), it may be possible to simulate realistic multidimensional IR spectra of chemically and biologically interesting systems.     

Whole-molecule approach for determining orientation at isotropic surfaces by nonlinear vibrational spectroscopy

Nonlinear vibrational spectroscopies such as visible-infrared sum-frequency spectroscopy may serve as powerful probes of interfacial structure. Obtaining quantitative orientation information, however, has been limited by the required knowledge of the corresponding molecular-level nonlinear optical properties. We provide a general scheme for calculating the vibrational hyperpolarizability of any infrared- and Raman-active mode, regardless of the molecular symmetry or complexity of the structure. Our method involves all atoms and therefore does not rely on making any local mode approximations. We show how this information is used together with experimental data to arrive at the tilt and twist angles of a surfactant headgroup at the air/water interface. Since our approach is completely general, it may be used for the analysis of any adsorbate at an isotropic interface.     

Towards numerical vibrational spectroscopy

From the mathematical standpoint, it is possible to reduce a spectral study to the solution of the so-called inverse spectral problems. In practice, the inverse problem is solved through consistent comparison of the spectrum of the model with the experimental spectrum, the degree of closeness between theoretical and experimental spectra providing a quality criterion for the solution. The model may be characterized by different levels of complexity. This paper discusses the course of recent developments in theoretical spectroscopy, the present state-of-the-art, and forecasts future union of experimental and theoretical methods.     

An approach to compatible multiple nonlinear vibrational spectroscopy measurements using a commercial sum frequency generation system

In this paper, we designed a compatible multiple nonlinear vibrational spectroscopy system that can be used for recording infrared-visible sum frequency generation vibrational spectra (SFG) and infrared-infrared-visible three-pump-field four-wave-mixing (IIV-TPF-FWM) spectra using a commercial EKSPLA SFG system. This is the first time IIV-TPF-FWM signals were obtained using picosecond laser pulses. We have applied this compatible system to study the surface and vibrational structures of riboflavin molecules (also known as vitamin B2). The SFG spectra of eight polarization combinations have non-vanishing signals. The signals with incoming s-polarized IR are relatively weaker than the signals with incoming p-polarized IR. Under the double resonant conditions, the SFG signals of the conjugated tricyclic ring are greatly enhanced. For the IIV-TPF-FWM spectra with incoming p-polarized IR, only the sspp and pppp polarization combinations have non-vanishing signals. The IIV-TPF-FWM spectra show a very strong peak at 1585 cm(-1) that is mainly dominated by the N(5)-C(4a) stretch. The method developed in this study will be helpful for researchers, either using a home-built or commercial (EKSPLA) SFG system, to obtain independent and complementary measurements for SFG spectroscopy and more detailed structural information of interfacial molecules.     

Arsenic in prebiotic species: a theoretical approach

A recent controversy about the presence of arsenic in biological systems prompted us to investigate the possible replacement of phosphorus by arsenic in prebiotic species small enough to be potentially identified in space. Systematic computational experiments were carried out on simple systems able to form a peptide or analogous bond. Density Functional Theory (DFT) within the B3LYP formalism, MP2 and CCSD(T) methods were used to determine the most stable isomers that can possibly form from the [C,H,O,As] and [C,3H,O,As] sets of atoms. It was found that HAsCO, like HPCO and HNCO was the most stable isomer. With three hydrogen atoms, the peptide-like bond (AsH(2)-CH=O) is not the most stable structure, contrary to NH(2)-CH=O. It is ～9 kcal mol(-1) higher than the most stable structure, CH(2)[double bond, length as m-dash]As-OH. To assess the plausibility of the As to P substitution, a comparative study of the dimethylphosphate (DMP) and dimethylarsenate (DMA) anions was then carried out. It was found that the gauche-gauche arrangement that mimics the helix structure is the most stable one in both model molecules, showing that there is no structural evidence to discard the hypothesis of the possible inclusion of As in place of P in the DNA architecture. The topological analysis of the ELF function showed a weakening by 50% of two As-O covalent bonds in all the DMA conformers. It means that if As replaces P, the structure of the DNA helix could be weakened. Rotational constants and IR frequencies of the low-lying isomers are given to encourage laboratory experiments on these prototype molecules.     

High-pressure effects in pyrene crystals: vibrational spectroscopy

The response of pyrene crystals to high pressure was examined using Raman and FTIR spectroscopies. Raman spectra of external and internal modes were measured up to 11 GPa. Changes in the external modes were observed at approximately 0.3 GPa, indicating the onset of a phase transition. We demonstrated that at this pressure pyrene I (P2(1)/a, 4 mol/unit cell) transforms to pyrene III (P2(1)/a, 2 mol/unit cell). Further increase of pressure produced a gradual broadening of the internal modes and an increase of fluorescence background, indicating the formation of another phase above 2.0 GPa. Irreversible chemical changes were observed upon gradual compression to 40 GPa. FTIR spectroscopy of the recovered product indicated a transformation of pyrene into an amorphous hydrogenated carbon (a-C:H) structure.     

The vibrational spectroscopy of indigo: A reassessment

We report the neutron vibrational spectra of indigo and its model compounds thioindigo and isatin. The neutron data extend the low energy range of the vibrational spectra of these molecules. The assignments, made with the help of ab-initio calculations, give convincing fits between the observed and scaled calculated results, and correct errors in the published literature. The indigo eigenvectors are described in terms of those of its model compound isatin. Finally, candidate modes, that could be used to study indigoids in matices (e.g. ‘Maya Blue’), are selected.     

DNA vibrational coupling revealed with two-dimensional infrared spectroscopy: insight into why vibrational spectroscopy is sensitive to DNA structure

Two-dimensional infrared (2D IR) spectroscopy was used to study the carbonyl vibrational modes of guanine and cytosine bases in A- and B-form DNA. Located between 1600 and 1700 cm(-1), these modes are often used to monitor DNA secondary structure with traditional infrared spectroscopies such as FTIR, but traditional spectroscopies lack the necessary observables to unravel the coupling mechanisms that make these modes sensitive to secondary structure. By using 2D IR spectroscopy and electronic structure calculations on d(G(5)C(5)) and d(GC)(8) model nucleic acids, we find that hydrogen-bonded guanine/cytosine base pairs are primarily electrostatically coupled and that the coupling between these modes can be modeled with a transition dipole density approach. In comparison, electrostatics is insufficient to model stacked bases because of cooperative charge-sharing effects, but the coupling can be accurately calculated using a finite difference method. We find that the coupling is very strong for both hydrogen-bonded and stacked base geometries, creating vibrational modes that extend both across the base pairs and along the lengths of the helices. Our results provide a physical basis for understanding how strong coupling gives rise to the empirically established relationship between infrared spectroscopy and DNA/RNA secondary structure.     

Rovibrational interactions in linear triatomic molecules: a theoretical study in curvilinear vibrational coordinates

Variational solution of the rovibrational problem in curvilinear vibrational coordinates has been implemented and used to investigate the nuclear motions in several linear triatomic molecules, like HCN, OCS, and HCP. The dependence of the rovibrational energy levels on the rotational quantum numbers and the l-doubling has been studied. Two approximations to the rovibrational Hamiltonian have been examined, depending on the level of truncation of the potential energy operator. It turns out that the truncation after the fifth order in the potential is sufficient to produce vibrational energies of high accuracy. An interesting feature of the present formulation of the problem in terms of the curvilinear vibrational coordinates is the explanation of the l-doubling of the rovibrational levels, which in this picture is interpreted as the result of the inequivalency of the average rotational constants in mutually perpendicular planes, rather than as the effect of the Coriolis-type interactions between the vibrational and rotational motions. The present theoretical results are compared with the available experimental data from high-resolution spectroscopy, as well as with other ab initio calculations.     

Polymers and supercritical fluids: opportunities for vibrational spectroscopy

Supercritical fluids are used for enhanced processing of polymeric materials. Therefore, there is a need to understand how supercritical fluids interact with polymeric materials and how they may modify many facets of process operations. In situ spectroscopy provides a route for understanding and optimising polymer processing with supercritical fluids. In situ spectroscopy probes interactions between supercritical CO₂ and polymers at a molecular level and provides a fundamental understanding of the origin of the plasticising effect of supercritical carbon dioxide on glassy polymers. The changes in polymers subjected to supercritical fluids have been elucidated via in situ ATR(Attenuated Total Reflectance)-IR spectroscopy. The key feature of our new approach is the use of a modified diamond ATR accessory to measure spectra of polymers subjected to high-pressure gas, supercritical fluids or near-critical water. A variety of novel applications for the use of in situ ATR-IR spectroscopy to polymers are described.