Vibrational spectral diffusion of CN− in water

Force Fields for Deep Eutectic Mixtures: Application to Structure, Thermodynamics and 2D-Infrared Spectroscopy

Parametrizing energy functions for ionic systems can be challenging. Here, the total energy function for an eutectic system consisting of water, SCN-, K+ and acetamide is improved vis-a-vis experimentally measured properties. Given the importance of electrostatic interactions, two different types of models are considered: the first (model M0) uses atom-centered multipole whereas the other two (models M1 and M2) are based on fluctuating minimal distributed charges (fMDCM) that respond to geometrical changes of SCN-. The Lennard-Jones parameters of the anion are adjusted to best reproduce experimentally known hydration free energies and densities, which are matched to within a few percent for the final models irrespective of the electrostatic model. Molecular dynamics simulations of the eutectic mixtures with varying water content (between 0 and 100%) yield radial distribution functions and frequency correlation functions for the CN-stretch vibration. Comparison with experiments indicates that models based on fMDCM are considerably more consistent than those using multipoles. Computed viscosities from models M1 and M2 are within 30% of measured values and their change with increasing water content is consistent with experiments. This is not the case for model M0.

Ultrafast Vibrational Energy Transfer through the Covalent Bond and Intra- and Intermolecular Hydrogen Bonds in a Supramolecular Dimer by Two-Dimensional Infrared Spectroscopy

In this work, the structural fluctuations and vibrational energy transfer dynamics in a supramolecular homodimer model, which is composed of 2-(9-anthracene)ureido-6-(1-undecyl)-4[1H]-pyrimidinone (UPAn) with quadruple intermolecular and single intramolecular hydrogen bonds (HBs), have been examined using ultrafast two-dimensional infrared (2D IR) and steady-state IR spectroscopies. A less structurally fluctuating intermolecular HB is found between the pyrimidinone C═O and ureido N-H groups. However, a larger structurally fluctuating intramolecular HB is suggested by the equilibrium and dynamical line-shape measurements of the ureido C═O stretch. Further, dynamical time-dependent 2D IR diagonal and off-diagonal signals show that intra- and intermolecular vibrational energy transfer processes occur on the picosecond timescale, where the latter is more efficient due to intermolecular hydrogen bonding interaction and through-space interaction.

Measuring Ultrafast Spectral Diffusion and Correlation Dynamics by Two-Dimensional Electronic Spectroscopy

The frequency fluctuation correlation function (FFCF) measures the spectral diffusion of a state's transition while the frequency fluctuation cross-correlation function (FXCF) measures the correlation dynamics between the transitions of two separate states. These quantities contain a wealth of information on how the chromophores or excitonic states interact and couple with its environment and with each other. We summarize the experimental implementations and theoretical considerations of using two-dimensional electronic spectroscopy to characterize FFCFs and FXCFs. Applications can be found in systems such as the chlorophyll pigment molecules in light-harvesting complexes and CdSe nanomaterials.

Vibrational Spectroscopy of N3- in the Gas and Condensed Phase

Azido-derivatized amino acids are potentially useful, positionally resolved spectroscopic probes for studying the structural dynamics of proteins and macromolecules in solution. To this end, a computational model for the vibrational modes of N₃^- based on accurate electronic structure calculations and a reproducing kernel Hilbert space representation of the potential energy surface for the internal degrees of freedom is developed. Fully dimensional quantum bound state calculations yield the antisymmetric stretch vibration at 1974 cm^-1 compared with 1986 cm^-1 from experiment. This mode shifts by 64 cm^-1 (from the frequency distribution) and 74 cm^-1 (from the IR line shape) to the blue, respectively, compared with 61 cm^-1 from experiment for N₃^- in water. The decay time of the frequency fluctuation correlation function is 1.1 ps, which is in good agreement with experiment (1.2-1.3 ps) and the full width at half maximum of the asymmetric stretch in solution is 18.5 cm^-1 compared with 25.2 cm^-1 from experiment. A computationally more efficient analysis based on instantaneous normal modes is shown to provide comparable, albeit somewhat less quantitative results compared to solving the three-dimensional Schrödinger equation for the fundamental vibrations.

Unmasking Rare, Large-Amplitude Motions in D2-Tagged I-·(H2O)2 Isotopomers with Two-Color, Infrared-Infrared Vibrational Predissociation Spectroscopy

We describe a two-color, isotopomer-selective infrared-infrared population-labeling method that can monitor very slow spectral diffusion of OH oscillators in H-bonded networks and apply it to the I^-·(HDO)·(D₂O) and I^-·(H₂O)·(D₂O) systems, which are cryogenically cooled and D₂-tagged at an ion trap temperature of 15 K. These measurements reveal very large (>400 cm^-1), spontaneous spectral shifts despite the fact that the predissociation spectra in the OH stretching region of both isotopologues are sharp and readily assigned to four fundamentals of largely decoupled OH oscillators held in a cyclic H-bonded network. This spectral diffusion is not observed in the untagged isotopologues of the dihydrate clusters that are generated under the same source conditions but does become apparent at about 75 K. These results are discussed in the context of the large-amplitude "jump" mechanism for H-bond relaxation dynamics advanced by Laage and Hynes in an experimental scenario where rare events can be captured by following the migration of OH groups among the four available positions in the quasi-rigid equilibrium structure.

Ultrafast dynamics induced by the interaction of molecules with electromagnetic fields: Several quantum, semiclassical, and classical approaches

Several strategies for simulating the ultrafast dynamics of molecules induced by interactions with electromagnetic fields are presented. After a brief overview of the theory of molecule-field interaction, we present several representative examples of quantum, semiclassical, and classical approaches to describe the ultrafast molecular dynamics, including the multiconfiguration time-dependent Hartree method, Bohmian dynamics, local control theory, semiclassical thawed Gaussian approximation, phase averaging, dephasing representation, molecular mechanics with proton transfer, and multipolar force fields. In addition to the general overview, some focus is given to the description of nuclear quantum effects and to the direct dynamics, in which the ab initio energies and forces acting on the nuclei are evaluated on the fly. Several practical applications, performed within the framework of the Swiss National Center of Competence in Research "Molecular Ultrafast Science and Technology," are presented: These include Bohmian dynamics description of the collision of H with H2, local control theory applied to the photoinduced ultrafast intramolecular proton transfer, semiclassical evaluation of vibrationally resolved electronic absorption, emission, photoelectron, and time-resolved stimulated emission spectra, infrared spectroscopy of H-bonding systems, and multipolar force fields applications in the condensed phase.

Probing the dynamics of N-methylacetamide in methanol via ab initio molecular dynamics

Two-dimensional infrared (2D IR) spectroscopy of amide 1 vibrational bands provides a valuable probe of proteins as well as molecules such as N-methylacetamide (NMA), which present peptide-like H-bonding possibilities to a solvent.

Hydration and vibrational dynamics of betaine (N,N,N-trimethylglycine)

Zwitterions are naturally occurring molecules that have a positive and a negative charge group in its structure and are of great importance in many areas of science. Here, the vibrational and hydration dynamics of the zwitterionic system betaine (N,N,N-trimethylglycine) is reported. The linear infrared spectrum of aqueous betaine exhibits an asymmetric band in the 1550-1700 cm(-1) region of the spectrum. This band is attributed to the carboxylate asymmetric stretch of betaine. The potential of mean force computed from ab initio molecular dynamic simulations confirms that the two observed transitions of the linear spectrum are related to two different betaine conformers present in solution. A model of the experimental data using non-linear response theory agrees very well with a vibrational model comprising of two vibrational transitions. In addition, our modeling shows that spectral parameters such as the slope of the zeroth contour plot and central line slope are both sensitive to the presence of overlapping transitions. The vibrational dynamics of the system reveals an ultrafast decay of the vibrational population relaxation as well as the correlation of frequency-frequency correlation function (FFCF). A decay of ∼0.5 ps is observed for the FFCF correlation time and is attributed to the frequency fluctuations caused by the motions of water molecules in the solvation shell. The comparison of the experimental observations with simulations of the FFCF from ab initio molecular dynamics and a density functional theory frequency map shows a very good agreement corroborating the correct characterization and assignment of the derived parameters.

Femtosecond 2DIR spectroscopy of the nitrile stretching vibration of thiocyanate anions in liquid-to-supercritical heavy water. Spectral diffusion and libration-induced hydrogen-bond dynamics

Femtosecond two-dimensional infrared (2DIR) spectroscopy was carried out to study the dynamics of vibrational spectral diffusion of the nitrile stretching vibration of thiocyanate.

Vibrational Energy Relaxation of Thiocyanate Ions in Liquid-to-Supercritical Light and Heavy Water. A Fermi's Golden Rule Analysis

The vibrational relaxation dynamics following an ultrafast nitrile stretching (ν3) excitation of thiocyanate anions dissolved in light and heavy water have been studied over a wide temperature and density range corresponding to the aqueous liquid up to the supercritical phase. In both solvents, the relaxation of the ν3 = 1 state of the anion leads to a direct recovery of the vibrational ground state and involves the resonant transfer of the excess vibrational energy onto the solvent. In light water, the energy-accepting states are provided by the bending-librational combination band (νb + νL), while in heavy water, the relaxation is thermally assisted by virtual acceptor states derived from the stretching-librational/restricted translational hot band (νS - νL,T). The relaxation rate is found to strictly obey Fermi's Golden Rule when the density of resonant solvent states is estimated from the linear infrared spectra of the solute and the pure solvents.

2D IR spectra of cyanide in water investigated by molecular dynamics simulations

Using classical molecular dynamics simulations, the 2D infrared (IR) spectroscopy of CN(-) solvated in D2O is investigated. Depending on the force field parametrizations, most of which are based on multipolar interactions for the CN(-) molecule, the frequency-frequency correlation function and observables computed from it differ. Most notably, models based on multipoles for CN(-) and TIP3P for water yield quantitatively correct results when compared with experiments. Furthermore, the recent finding that T1 times are sensitive to the van der Waals ranges on the CN(-) is confirmed in the present study. For the linear IR spectrum, the best model reproduces the full widths at half maximum almost quantitatively (13.0 cm(-1) vs. 14.9 cm(-1)) if the rotational contribution to the linewidth is included. Without the rotational contribution, the lines are too narrow by about a factor of two, which agrees with Raman and IR experiments. The computed and experimental tilt angles (or nodal slopes) α as a function of the 2D IR waiting time compare favorably with the measured ones and the frequency fluctuation correlation function is invariably found to contain three time scales: a sub-ps, 1 ps, and one on the 10-ps time scale. These time scales are discussed in terms of the structural dynamics of the surrounding solvent and it is found that the longest time scale (≈10 ps) most likely corresponds to solvent exchange between the first and second solvation shell, in agreement with interpretations from nuclear magnetic resonance measurements.

Vibrational dynamics and solvatochromism of the label SCN in various solvents and hemoglobin by time dependent IR and 2D-IR spectroscopy

The vibrational label SCN is used to report on local structural dynamics in a protein revealing spectral diffusion on a picosecond scale. The SCN spectra are compared to the response of methylthiocyanate in solvents with different polarity and hydrogen-bonding capabilities.

Differential hydration of tricyanomethanide observed by time resolved vibrational spectroscopy

The degenerate transition corresponding to asymmetric stretches of the D(3h) tricyanomethanide anion, C(CN)(3)(-), in aqueous solution was investigated by linear FTIR spectroscopy, femtosecond pump–probe spectroscopy, and 2D IR spectroscopy. Time resolved vibrational spectroscopy shows that water induces vibrational energy transfer between the degenerate asymmetric stretch modes of tricyanomethanide. The frequency–frequency correlation function and the vibrational energy transfer show two significantly different ultrafast time scales. The system is modeled with molecular dynamics simulations and ab initio calculations. A new model for theoretically describing the vibrational dynamics of a degenerate transition is presented. Microscopic models, where water interacts axially and radially with the ion, are suggested for the transition dipole reorientation mechanism.

Fluctuations and Relaxation Dynamics of Liquid Water Revealed by Linear and Nonlinear Spectroscopy

Many efforts have been devoted to elucidating the intra- and intermolecular dynamics of liquid water because of their important roles in many fields of science and engineering. Nonlinear spectroscopy is a powerful tool to investigate the dynamics. Because nonlinear response functions are described by more than one time variable, it is possible to analyze static and dynamic mode couplings. Here we review the intra- and intermolecular dynamics of liquid water revealed by recent linear and nonlinear spectroscopic experiments and computer simulations. In particular, we discuss the population relaxation, anisotropy decay, and spectral diffusion of the intra- and intermolecular motions of water and their temperature dependence, which play important roles in ultrafast dynamics and relaxations in water.

Ligand binding studied by 2D IR spectroscopy using the azidohomoalanine label

We explore the capability of the azidohomoalanine (Aha) as a vibrational label for 2D IR spectroscopy to study the binding of the target peptide to the PDZ2 domain. The Aha label responds sensitively to its local environment and its peak extinction coefficient of 350-400 M(-1) cm(-1) is high enough to routinely measure it in the low millimolar concentration regime. The central frequency, inhomogeneous width and spectral diffusion times deduced from the 2D IR line shapes of the Aha label at various positions in the peptide sequence is discussed in relationship to the known X-ray structure of the peptide bound to the PDZ2 domain. The results suggest that the Aha label introduces only a small perturbation to the overall structure of the peptide in the binding pocket. Finally, Aha is a methionine analog that can be incorporated also into larger proteins at essentially any position using protein expression. Altogether, Aha thus fulfills the requirements a versatile label should have for studies of protein structure and dynamics by 2D IR spectroscopy.

On the role of nonbonded interactions in vibrational energy relaxation of cyanide in water

The vibrationally excited cyanide ion (CN(-)) in H2O or D2O relaxes back to the ground state within several tens of picoseconds. Pump-probe infrared spectroscopy has determined relaxation times of T1 = 28 ± 7 and 71 ± 3 ps in H2O and D2O, respectively. Atomistic simulations of this process using nonequilibrium molecular dynamics simulations allow determination of whether it is possible at all to describe such a process, what level of accuracy in the force fields is required, and whether the information can be used to understand the molecular mechanisms underlying vibrational relaxation. It is found that, by using the best electrostatic models investigated, absolute relaxation times can be described rather more qualitatively (T1(H2O) = 19 ps and T1(D2O) = 34 ps) whereas the relative change in going from water to deuterated water is more quantitatively captured (factor of 2 vs 2.5 from experiment). However, moderate adjustment of the van der Waals ranges by less than 20% (for NVT) and 7.5% (for NVE), respectively, leads to almost quantitative agreement with experiment. Analysis of the energy redistribution establishes that the major pathway for CN(-) relaxation in H2O or D2O proceeds through coupling to the water-bending plus libration mode.

2D-IR study of a photoswitchable isotope-labeled alpha-helix

A series of photoswitchable, alpha-helical peptides were studied using two-dimensional infrared spectroscopy (2D-IR). Single-isotope labeling with (13)C(18)O at various positions in the sequence was employed to spectrally isolate particular backbone positions. We show that a single (13)C(18)O label can give rise to two bands along the diagonal of the 2D-IR spectrum, one of which is from an amide group that is hydrogen-bonded internally, or to a solvent molecule, and the other from a non-hydrogen-bonded amide group. The photoswitch enabled examination of both the folded and unfolded state of the helix. For most sites, unfolding of the peptide caused a shift of intensity from the hydrogen-bonded peak to the non-hydrogen-bonded peak. The relative intensity of the two diagonal peaks gives an indication of the fraction of molecules hydrogen-bonded at a certain location along the sequence. As this fraction varies quite substantially along the helix, we conclude that the helix is not uniformly folded. Furthermore, the shift in hydrogen bonding is much smaller than the change of helicity measured by CD spectroscopy, indicating that non-native hydrogen-bonded or mis-folded loops are formed in the unfolded ensemble.

Dynamical transition in a small helical peptide and its implication for vibrational energy transport

The two-dimensional infrared spectrum of an octameric helical peptide in chloroform was measured as a function of temperature. Isotope labeling of the carbonyl group of one of the amino acids was used to obtain information for an isolated vibration. The antidiagonal width of the 2D-IR signal, which is a measure of the homogeneous dephasing time T(2), is constant from 220 to 260 K (within experimental error), and increases steeply above. The homogeneous dephasing time of the carbonyl vibration is attributed to the flexibility of the system and/or its immediate surrounding. The system undergoes a dynamical transition at about 270 K, with similarities to the protein dynamical transition. Furthermore, the temperature dependence of the antidiagonal width strongly resembles that of the efficiency of vibrational energy transport along the helix, which has been studied in a recent paper (J. Phys. Chem. B 2008, 112, 15487). The connection between the two processes, structural flexibility and energy transport mechanism, is discussed.

Carbon-deuterium vibrational probes of peptide conformation: alanine dipeptide and glycine dipeptide

The utility of alpha-carbon deuterium-labeled bonds (C(alpha)-D) as infrared reporters of local peptide conformation was investigated for two model dipeptide compounds: C(alpha)-D labeled alanine dipeptide (Adp-d(1)) and C(alpha)-D(2) labeled glycine dipeptide (Gdp-d(2)). These model compounds adopt structures that are analogous to the motifs found in larger peptides and proteins. For both Adp-d(1) and Gdp-d(2), we systematically mapped the entire conformational landscape in the gas phase by optimizing the geometry of the molecule with the values of phi and psi, the two dihedral angles that are typically used to characterize the backbone structure of peptides and proteins, held fixed on a uniform grid with 7.5 degrees spacing. Since the conformations were not generally stationary states in the gas phase, we then calculated anharmonic C(alpha)-D and C(alpha)-D(2) stretch transition frequencies for each structure. For Adp-d(1) the C(alpha)-D stretch frequency exhibited a maximum variability of 39.4 cm(-1) between the six stable structures identified in the gas phase. The C(alpha)-D(2) frequencies of Gdp-d(2) show an even more substantial difference between its three stable conformations: there is a 40.7 cm(-1) maximum difference in the symmetric C(alpha)-D(2) stretch frequencies and an 81.3 cm(-1) maximum difference in the asymmetric C(alpha)-D(2) stretch frequencies. Moreover, the splitting between the symmetric and asymmetric C(alpha)-D(2) stretch frequencies of Gdp-d(2) is remarkably sensitive to its conformation.

Coherent multidimensional vibrational spectroscopy of biomolecules: concepts, simulations, and challenges

The response of complex molecules to sequences of femtosecond infrared pulses provides a unique window into their structure, dynamics, and fluctuating environments. Herein we survey the basic principles of modern two-dimensional infrared (2DIR) spectroscopy, which analogous to those of multidimensional NMR spectroscopy. The perturbative approach for computing the nonlinear optical response of coupled localized chromophores is introduced and applied to the amide backbone transitions of proteins, liquid water, membrane lipids, and amyloid fibrils. The signals are analyzed using classical molecular dynamics simulations combined with an effective fluctuating Hamiltonian for coupled localized anharmonic vibrations whose dependence on the local electrostatic environment is parameterized by an ab initio map. Several simulation methods, (cumulant expansion of Gaussian fluctuation, quasiparticle scattering, the stochastic Liouville equations, direct numerical propagation) are surveyed. Chirality-induced techniques which dramatically enhance the resolution are demonstrated. Signatures of conformational and hydrogen-bonding fluctuations, protein folding, and chemical-exchange processes are discussed.