Wavelet Transform for Spectroscopic Analysis: Application to Diols in Water

Blueshift of the CN stretching vibration of acetonitrile in solution: computational and experimental study

Acetonitrile, a polar molecule that cannot form hydrogen bonds on its own, interacts with solvent molecules mainly through the lone pair of its nitrogen atom and the π electrons of its CN triple bond [Correction added on 17 July 2024, after first online publication: Acetole has been changed to Acetonitrile in the preceeding sentence.]. Interestingly, acetonitrile exhibits an unexpected strengthening of the triple bond's force constant in an aqueous environment, leading to an upshift (blueshift) in the corresponding stretching vibration: this effect contrasts with the usual consequence of hydrogen bonding on the vibrational frequencies of the acceptor groups, that is, frequency redshift. This investigation elucidates this phenomenon using Raman spectroscopy to examine the behavior of acetonitrile in organic solvent, water, and silver ion aqueous solutions, where an even more pronounced upshift is observed. Raman spectroscopy is particularly well suited for analyzing aqueous solutions due to the minimal scattering effect of water molecules across most of the vibrational spectrum. Computational approaches, both static and dynamical, based on Density Functional Theory and hybrid functionals, are employed here to interpret these findings, and accurately reproduce the vibrational frequencies of acetonitrile in different environments. Our calculations also allow an explanation for this unique behavior in terms of electric charge displacements. On the other hand, the study of the interaction of acetonitrile with water molecules and metal ions is relevant for the use of this molecule as a solvent in both chemical and pharmaceutical applications.

Homogeneous Dephasing in Photosynthetic Bacterial Reaction Centers: Time Correlation Function Approach

A new tractable linear electronic transition dipole moment time correlation function (ETDMTCF) that accurately accounts for electronic dephasing, asymmetry, and width of 1-phonon profile, which the zero-phonon line (ZPL) contributes to it, in Rhodopseudomonas viridis bacterial reaction center is derived. This time correlation function proves to be superior to other frequency-domain expressions in case of strong electron-phonon coupling (which is often the case in bacterial RCs and pigment-protein complexes), many vibrational modes involved, and high temperature, whereby more vibronic and electronic (sequence) transitions would arise. The Fourier transform of this ETDMTCF leads to asymmetric multiphonon profiles composed of Lorentzian distribution and Gaussian distribution on the high- and low-energy sides, respectively, whereby the overtone widths fold themselves with that of the one-phonon profile. This ETDMTCF also features expedient computation in large systems using asymmetric phonon profiles to account correctly for dephasing and pigment-protein interaction (electron-phonon coupling). The derived ETDMTCF allows computing all nonlinear optical signals in both time and frequency domains, through the nonlinear dipole moment time correlation functions (as guided by nonlinear optical response theory) in line with the eight Liouville space pathways. The linear transition dipole moment time correlation function is of a central value as the nonlinear transition dipole moment time correlation function is expressed in terms of the linear transition dipole moment time correlation function, derived herein. One of the great advantages of presenting this ETDMTCF is its applicability to nonlinear transition dipole moment time correlation functions in line with the eight Liouville space pathways needed in computing nonlinear signals. As such, there is more to the utility and applicability of the presented ETDMTCF besides computational expediency and efficiency. Results show good agreement with the reported literature. The intimate connection between a one-phonon profile and the corresponding bath spectral density in photosynthetic complexes is discussed.

DFT and TD-DFT Study of the Chemical Effect in the SERS Spectra of Piperidine Adsorbed on Silver Colloidal Nanoparticles

The surface-enhanced Raman scattering (SERS) spectra of piperidine adsorbed on silver/chloride colloids were studied by a combined density functional theory (DFT)/time dependent DFT (TD-DFT) approach. The mechanism of chemical enhancement on the Raman signals is due to at least two contributions: the first comes from the changes in the molecular force constants and the dynamic polarizabilities of the normal modes, when the molecule is chemisorbed. DFT calculations satisfactorily reproduce the SERS spectra of piperidine adsorbed on silver, showing that the species formed on the silver particle is a complex formed by a deprotonated piperidine linked to a silver cation. A second contribution to the SERS chemical enhancement is due to a resonance Raman effect occurring when the wavelength of the Raman excitation falls within the electronic excitation band of the molecule/metal complex. Actually, the SERS spectra of piperidine show a significant dependence on the wavelength of the laser excitation, with a marked enhancement in the green-light region. TD-DFT calculations on the most-probable complex explain this behavior, because a strong excitation band of the complex is calculated in the green spectral region. This pinpoints that a resonance between the exciting radiation and the absorption band of this complex is responsible for this enhancement effect.

Water-Mediated Excited State Proton Transfer of Pyranine-Acetate in Aqueous Solution: Vibrational Fingerprints from Ab Initio Molecular Dynamics

In this work, we simulate the excited state proton transfer (ESPT) reaction involving the pyranine photoacid and an acetate molecule as proton acceptor, connected by a bridge water molecule. We employ ab initio molecular dynamics combined with an hybrid quantum/molecular mechanics (QM/MM) framework. Furthermore, a time-resolved vibrational analysis based on the wavelet-transform allows one to identify two low frequency vibrational modes that are fingerprints of the ESPT event: a ring wagging and ring breathing. Their composition suggests their key role in optimizing the structure of the proton donor–acceptor couple and promoting the ESPT event. We find that the choice of the QM/MM partition dramatically affects the photoinduced reactivity of the system. The QM subspace was gradually extended including the water molecules directly interacting with the pyranine–water–acetate system. Indeed, the ESPT reaction takes place when the hydrogen bond network around the reactive system is taken into account at full QM level.

Effect of the Hydration Shell on the Carbonyl Vibration in the Ala-Leu-Ala-Leu Peptide

The vibrational spectrum of the Ala-Leu-Ala-Leu peptide in solution, computed from first-principles simulations, shows a prominent band in the amide I region that is assigned to stretching of carbonyl groups. Close inspection reveals combined but slightly different contributions by the three carbonyl groups of the peptide. The shift in their exact vibrational signature is in agreement with the different probabilities of these groups to form hydrogen bonds with the solvent. The central carbonyl group has a hydrogen bond probability intermediate to the other two groups due to interchanges between different hydrogen-bonded states. Analysis of the interaction energies of individual water molecules with that group shows that shifts in its frequency are directly related to the interactions with the water molecules in the first hydration shell. The interaction strength is well correlated with the hydrogen bond distance and hydrogen bond angle, though there is no perfect match, allowing geometrical criteria for hydrogen bonds to be used as long as the sampling is sufficient to consider averages. The hydrogen bond state of a carbonyl group can therefore serve as an indicator of the solvent's effect on the vibrational frequency.

Time-Resolved Vibrational Analysis of Excited State Ab Initio Molecular Dynamics to Understand Photorelaxation: The Case of the Pyranine Photoacid in Aqueous Solution

We present a novel time-resolved vibrational analysis for studying photoinduced nuclear relaxation. Generalized modes velocities are defined from ab initio molecular dynamics and wavelet transformed, providing the time localization of vibrational signals in the electronic excited state. The photoexcited pyranine in aqueous solution is presented as a case study. The transient and sequential activation of the simulated vibrational signals is in good agreement with vibrational dynamics obtained from femtosecond stimulated Raman spectroscopy data.

Unveiling anharmonic coupling by means of excited state ab initio dynamics: application to diarylethene photoreactivity

In this work, excited state ab initio molecular dynamics together with a time resolved vibrational analysis is employed to shed light on the vibrational photoinduced dynamics of a well-known diarylethene molecule experiencing a ring opening reaction upon electronic excitation. The photoreactivity of diarylethenes is recognized to be controlled by a non-adiabatic intersection point between the ground and the first excited state surfaces. The computation of an energy scan, along a suitable reaction coordinate, allows us to identify the region of potential energy surfaces in which the ground (S0) and the first excited (S1) state are well separated. The adiabatic sampling of that region in S1 shows that in the first 3 picoseconds, the central CC bond, which is subject to break, oscillates in an antiphase with respect to the energy gap ΔE(S1 - S0). A multiresolution analysis based on the wavelet transform was then applied to the structural parameters extracted from the excited state dynamics. The wavelet maps show characteristic oscillations of the frequencies, mainly CC stretching and CCC bending localized on the central 4-ring moiety. Moreover, we have identified the main frequency (methyl wagging motion) involved in the modulation of these oscillations. The anharmonic coupling within a group of vibrational modes was therefore highlighted, in good agreement with experimental evidence. For the first time, a quantitative analysis of time resolved signals from a wavelet transform/ab initio molecular dynamics approach was performed.

The viscous consequence of different trends in clustering of 1,2-diol and 1,n-diol molecules

This paper presents the molecular basis for the quite different behavior of the viscosity of 1,2- and 1,n-diols in dependence of the length of the alkyl part of the molecules of these compounds. The experimental data on the dipolar orientational effects revealed a decidedly different role of that part of the molecules in creating a microstructure of both the hydrogen-bonded liquids. In the case of 1,n-diols, an increase in the alkyl radical length, i.e. an increasing of the distance between the OH groups within the molecule, highly stimulates molecular self-assembly in form of gradually longer and wider ribbon-like clusters. This effect yields a quite important increase in the viscosity of 1,n-diols as n increases. In the case of 1,2-diols, due to gradual separation of the hydrophilic and hydrophobic parts of the molecules, the situation is quite different. Two OH groups situated on one of the ends of the hydrocarbon radical form the clusters of a micelle-like shape, however, the dipole moment is not compensated. Along with an increase in the hydrocarbon part in 1,2-diol molecules, one only observes an increase in the intermolecular consolidation within the micelle-like entities. This manifests as a gradual decrease in the polarity of these clusters. So, actually, there are no relevant reasons for essential differences of viscosities in the series of 1,2-diols.

Using Wavelet Analysis To Assist in Identification of Significant Events in Molecular Dynamics Simulations

Long time scale molecular dynamics (MD) simulations of biological systems are becoming increasingly commonplace due to the availability of both large-scale computational resources and significant advances in the underlying simulation methodologies. Therefore, it is useful to investigate and develop data mining and analysis techniques to quickly and efficiently extract the biologically relevant information from the incredible amount of generated data. Wavelet analysis (WA) is a technique that can quickly reveal significant motions during an MD simulation. Here, the application of WA on well-converged long time scale (tens of μs) simulations of a DNA helix is described. We show how WA combined with a simple clustering method can be used to identify both the physical and temporal locations of events with significant motion in MD trajectories. We also show that WA can not only distinguish and quantify the locations and time scales of significant motions, but by changing the maximum time scale of WA a more complete characterization of these motions can be obtained. This allows motions of different time scales to be identified or ignored as desired.

Identification of Di(oxymethylene)glycol in the Raman Spectrum of Formaldehyde Aqueous Solutions by ab Initio Molecular Dynamics Simulations and Quantum Chemistry Calculations

Di(oxymethylene)glycol forms in formaldehyde aqueous solutions by polymerization of methanediol. The structure and hydrogen bond interactions of di(oxymethylene)glycol with water were characterized by performing Car-Parrinello molecular dynamics simulations. The anharmonic vibrational frequencies of di(oxymethylene)glycol in solution were determined with ab initio calculations considering explicitly the hydrogen-bonded water molecules, while other interactions with solvent were described within a polarizable continuum model approach. The calculations allow for a detailed interpretation of the experimental Raman spectrum of formaldehyde aqueous solutions, leading to the assignment of the band at 920 cm(-1) to the symmetric CO stretching mode of di(oxymethylene)glycol.

On the opto-electronic properties of phosphine and thiolate-protected undecagold nanoclusters

A schematic description of the UV-vis spectrum of Au₁₁(PPh₃)₇Cl₃ nanoclusters. Metal → metal transitions are ubiquitous, metal → ligand transitions appear above the visible threshold, while ligand → metal and ligand → ligand transitions are much rarer in the investigated range of energies.