Molecular dynamics simulations and instantaneous normal-mode analysis of the vibrational relaxation of the C-H stretching modes of N-methylacetamide-d in liquid deuterated water

Nonequilibrium molecular dynamics (MD) simulations and instantaneous normal mode (INMs) analyses are used to study the vibrational relaxation of the C-H stretching modes (ν(s)(CH?)) of deuterated N-methylacetamide (NMAD) in aqueous (D2O) solution. The INMs are identified unequivocally in terms of the equilibrium normal modes (ENMs), or groups of them, using a restricted version of the recently proposed Min-Cost assignment method. After excitation of the parent ν(s)(CH?) modes with one vibrational quantum, the vibrational energy is shown to dissipate through both intramolecular vibrational redistribution (IVR) and intermolecular vibrational energy transfer (VET). The decay of the vibrational energy of the ν(s)(CH?) modes is well fitted to a triple exponential function, with each characterizing a well-defined stage of the entire relaxation process. The first, and major, relaxation stage corresponds to a coherent ultrashort (τ(rel) = 0.07 ps) energy transfer from the parent ν(s)(CH?) modes to the methyl bending modes δ(CH?), so that the initially excited state rapidly evolves into a mixed stretch-bend state. In the second stage, characterized by a time of 0.92 ps, the vibrational energy flows through IVR to a number of mid-range-energy vibrations of the solute. In the third stage, the vibrational energy accumulated in the excited modes dissipates into the bath through an indirect VET process mediated by lower-energy modes, on a time scale of 10.6 ps. All the specific relaxation channels participating in the whole relaxation process are properly identified. The results from the simulations are finally compared with the recent experimental measurements of the ν(s)(CH?) vibrational energy relaxation in NMAD/D?O(l) reported by Dlott et al. (J. Phys. Chem. A 2009, 113, 75.) using ultrafast infrared-Raman spectroscopy.     

Time scales and pathways of vibrational energy relaxation in liquid CHBr3 and CDBr3

Molecular dynamics simulations are used in conjunction with Landau-Teller, fluctuating Landau-Teller, and time-dependent perturbation theories to investigate energy flow out of various vibrational states of liquid CHBr3 and CDBr3. The CH stretch overtone is found to relax with a time scale of about 1 ps compared to the 50 ps rate for the fundamental. The relaxation pathways and rates for the CD stretch decay in CDBr3 are computed in order to understand the changes arising from deuteration. While the computed relaxation rate agrees well with experiments, the pathway is found to be more complex than anticipated. In addition to the above channels for CH(D) stretch relaxation that involve only the hindered translations and rotations of the solvent, routes involving off-resonant and resonant excitations of solvent vibrational modes are also examined. Finally, the decay of energy from low frequency states to near-lying solute states and solvent vibrations are studied.     

Conformational transitions of glycine induced by vibrational excitation of the O-H stretch

Vibrational energy flow and conformational transitions following excitation of the OH stretching mode of the most stable conformer of glycine are studied by classical trajectories. "On the fly" simulations with the PM3 semiempirical electronic structure method for the potential surface are used. Initial conditions are selected to correspond to the ν=1 excitation of the OH stretch. The main findings are: (1) An an equilibrium-like ratio is established between the populations of the 3 lowest-lying conformers after about 10 picoseconds. (2) There is a high probability throughout the 150 ps of the simulations for finding the molecule in geometries far from the equilibrium structures of the lowest-energy conformers. (3) Energy from the initial excited OH (ν=1) stretch flows preferentially to 5 other vibrational modes, including the bending motion of the H atom. (4) RRK theory yields conformational transition rates that deviate substantially from the classical trajectory results. Possible implication of these results for vibrational energy flow and conformational transitions in small biological molecules are discussed.     

Solvation-driven excited-state dynamics of [Re(4-Et-Pyridine)(CO)3(2,2'-bipyridine)]+ in imidazolium ionic liquids. A time-resolved infrared and phosphorescence study

Excited-state dynamics of [Re(Etpy)(CO)3(bpy)]+ was studied in three imidazolium ionic liquids by time-resolved IR and emission spectroscopy on the picosecond to nanosecond time scale. Low-lying excited states were characterized by TD-DFT calculations, which also provided molecular dipole moment vectors in the relevant electronic states. TRIR spectra in ionic liquids show initial populations of two excited states: predominantly bpy-localized 3IL and 3MLCT, characterized by nu(CO) bands shifted to lower and higher frequencies, respectively, relative to the ground state. Internal conversion of 3IL to the lowest triplet 3MLCT occurred on a time scale commensurate with solvent relaxation. The nu(CO) IR bands of the 3MLCT state undergo a dynamic shift to higher wavenumbers during relaxation. Its three-exponential kinetics were determined and attributed to vibrational cooling (units of picoseconds), energy dissipation to the bulk solvent (tens of picoseconds), and solvent relaxation, the lifetime of which increases with increasing viscosity: [EMIM]BF4 (330 ps) < [BMIM]BF4 (470 ps) < [BMIM]PF6 (1570 ps). Time-resolved phosphorescence spectra in [BMIM]PF6 show a approximately 2 ns drop in intensity due to the 3IL --> 3MLCT conversion and a dynamic Stokes shift to lower energies with a lifetime decreasing from 1.8 ns at 21 degrees C to 1.1 ns at 37 degrees C, due to decreasing viscosity of the ionic liquid. It is proposed that solvent relaxation predominantly involves collective translational motions of ions. It drives the 3IL --> 3MLCT conversion, increases charge reorganization in the lowest excited-state 3MLCT, and affects vibrational anharmonic coupling, which together cause the dynamic shift of excited-state IR bands. TRIR spectroscopy of carbonyl-diimine complexes emerges as a new way to investigate various aspects of solvation dynamics, while the use of slowly relaxing ionic liquids offers new insight into the photophysics of Re(I) carbonyl polypyridyls.     

Hydrogen bond breaking dynamics of the water trimer in the translational and librational band region of liquid water.

The effect of exciting each of the three classes of intermolecular vibrations on the hydrogen bond lifetime (tau(H)) of the isolated water trimer is investigated by far-infrared laser spectroscopy. Single excitation of a librational vibration decreases tau(H) by 3 orders of magnitude to tau(H) = 1-6 ps, comparable to the time scale of a number of important bulk water dynamical relaxation processes. In contrast, excitation of translational or torsional vibrations has no significant effect (tau(H) = 1-2 ns). Although such a dependence of tau(H) on intermolecular motions has also been proposed for liquid water via computer simulations, these are the first experiments that provide a detailed molecular picture of the respective motions without extensive interpretation.     

Energy transfer in single hydrogen-bonded water molecules.

We study the structure and dynamics of hydrogen-bonded complexes of H2O/HDO and acetone dissolved in carbon tetrachloride by probing the response of the O-H stretching vibrations with linear mid-infrared spectroscopy and femtosecond mid-infrared pump-probe spectroscopy. We find that the hydrogen bonds in these complexes break and reform with a characteristic time scale of approximately 1 ps. These hydrogen-bond dynamics are observed to play an important role in the equilibration of vibrational energy over the two O-H groups of the H2O molecule. For both H2O and HDO, the O-H stretching vibrational excitation relaxes with a time constant of 6.3+/-0.3 ps, and the molecular reorientation has a time constant of 6+/-1 ps.     

Vibrational relaxation of CH3I in the gas phase and in solution

Transient electronic absorption measurements reveal the vibrational relaxation dynamics of CH(3)I following excitation of the C-H stretch overtone in the gas phase and in liquid solutions. The isolated molecule relaxes through two stages of intramolecular vibrational relaxation (IVR), a fast component that occurs in a few picoseconds and a slow component that takes place in about 400 ps. In contrast, a single 5-7 ps component of IVR precedes intermolecular energy transfer (IET) to the solvent, which dissipates energy from the molecule in 50 ps, 44 ps, and 16 ps for 1 M solutions of CH(3)I in CCl(4), CDCl(3), and (CD(3))(2)CO, respectively. The vibrational state structure suggests a model for the relaxation dynamics in which a fast component of IVR populates the states that are most strongly coupled to the initially excited C-H stretch overtone, regardless of the environment, and the remaining, weakly coupled states result in a secondary relaxation only in the absence of IET.     

Population lifetime of CH-stretching modes in medium-size molecules

Vibrational modes are excited by ultrashort tunable IR pulses and the time dependence of the excitation is measured by a second (visible) pulse. Spectra taken at a time delay of several picoseconds give evidence for the population lifetimes of CH-stretching modes of aromatic hydrogen, CH₂ and CH₃ vibrations. Relaxation times between 6 and 8 ps were found. Results are presented for two coumarins in different solvents.     

Molecular dynamics simulations of shock waves in oriented nitromethane single crystals

The structural relaxation of crystalline nitromethane initially at T = 200 K subjected to moderate (~15 GPa) supported shocks on the (100), (010), and (001) crystal planes has been studied using microcanonical molecular dynamics with the nonreactive Sorescu-Rice-Thompson force field [D. C. Sorescu, B. M. Rice, and D. L. Thompson, J. Phys. Chem. B 104, 8406 (2000)]. The responses to the shocks were determined by monitoring the mass density, the intermolecular, intramolecular, and total temperatures (average kinetic energies), the partitioning of total kinetic energy among Cartesian directions, the radial distribution functions for directions perpendicular to those of shock propagation, the mean-square displacements in directions perpendicular to those of shock propagation, and the time dependence of molecular rotational relaxation as a function of time. The results show that the mechanical response of crystalline nitromethane strongly depends on the orientation of the shock wave. Shocks propagating along [100] and [001] result in translational disordering in some crystal planes but not in others, a phenomenon that we refer to as plane-specific disordering; whereas for [010] the shock-induced stresses are relieved by a complicated structural rearrangement that leads to a paracrystalline structure. The plane-specific translational disordering is more complete by the end of the simulations (~6 ps) for shock propagation along [001] than along [100]. Transient excitation of the intermolecular degrees of freedom occurs in the immediate vicinity of the shock front for all three orientations; the effect is most pronounced for the [010] shock. In all three cases excitation of molecular vibrations occurs more slowly than the intermolecular excitation. The intermolecular and intramolecular temperatures are nearly equal by the end of the simulations, with 400-500 K of net shock heating. Results for two-dimensional mean-square molecular center-of-mass displacements, calculated as a function of time since shock wave passage in planes perpendicular to the direction of shock propagation, show that the molecular translational mobility in the picoseconds following shock wave passage is greatest for [001] and least for the [010] case. In all cases the root-mean-square center-of-mass displacement is small compared to the molecular diameter of nitromethane on the time scale of the simulations. The calculated time scales for the approach to thermal equilibrium are generally consistent with the predictions of a recent theoretical analysis due to Hooper [J. Chem. Phys. 132, 014507 (2010)].     

Solvent-dependent photophysics of 1-cyclohexyluracil: ultrafast branching in the initial bright state leads nonradiatively to the electronic ground state and a long-lived 1npi* state

The modified nucleic acid base, 1-cyclohexyluracil, was studied by femtosecond transient absorption spectroscopy in protic and aprotic solvents of varying polarity. UV excitation at 267 nm populates the lowest-energy bright state, a (1)pipi* state, which has a lifetime of 120-270 fs, depending on the solvent. In all solvents, this initial bright state population bifurcates with approximately 60% undergoing subpicosecond nonradiative decay to the electronic ground state and the remaining population branching to a singlet dark state. The latter absorbs between 340 and 450 nm. The latter state is assigned to the lowest-energy (1)npi* state. It decays to the electronic ground state with a lifetime that varies from 26 ps in water to at least several nanoseconds in aprotic solvents. The results suggest that the two nonradiative decay pathways identified for photoexcited uracil in recent quantum chemical calculations (Matsika, S. J. Phys. Chem. A. 2004, 108, 7584) are simultaneously operative in a wide variety of solvent environments. The lowest-energy triplet state was also detected by transient absorption. The triplet population appears in a few picoseconds and is not formed from the thermalized (1)npi* state. It is suggested that high spin-orbit coupling is found only along initial segments of the nonradiative decay pathways. Efficient intersystem crossing prior to vibrational cooling offers a possible explanation for the wavelength-dependent triplet yields seen in single DNA bases.     

Vibrational energy transfer in cyclopropane (C3H6)

Infrared laser-induced fluorescence measurements of vibrational relaxation in cyclopropane are presented. Following laser excitation of the CH-stretch vibrations υ₆ and υ₈ time-dependent fluorescence signals from υ₁₀ and υ₇/υ₁₁ were recorded. Activation and deactivation rate constants for C₃H₆C₃H₆ collisions were found for υ₁₀ and υ₇/υ₁₁. A simplified model for the vibrational relaxation of cyclopropane is discussed.     

Femtosecond absorption spectroscopy of cytochrome <Emphasis Type="Italic">c</Emphasis> oxidase: Excited electronic states and relaxation processes in heme <Emphasis Type="Italic">a</Emphasis> and heme <Emphasis Type="Italic">a</Emphasis><Subscript>3</Subscript> centers

Cytochrome c oxidase, the key bioenergetic protein, was studied by femtosecond absorption spectroscopy. Time-resolved spectral characteristics of the difference spectra recorded in the timescale from 80 fs to 20 ps were analyzed. Electronic relaxation of the excitation energy in heme a occurs in three successive steps. After completion of these steps, heme a is in the excited vibrational state of the ground state. Vibrational relaxation, cooling of the heme, occurs for several picoseconds.     

Vibrational coherence transfer characterized with Fourier-transform 2D IR spectroscopy

Two-dimensional infrared (2D IR) spectroscopy of the symmetric and asymmetric C[Triple Bond]O stretching vibrations of Rh(CO)(2)acac in hexane has been used to investigate vibrational coherence transfer, dephasing, and population relaxation in a multilevel vibrational system. The transfer of coherence between close-lying vibrational frequencies results in extra relaxation-induced peaks in the 2D IR spectrum, whose amplitude depends on the coherence transfer rate. Coherence transfer arises from the mutual interaction of the bright CO stretches with dark states, which in this case reflects the mutual d-pi(*) back bonding of the Rh center to both the terminal carbonyls and the acetylacenonate ligand. For 2D IR relaxation experiments with variable waiting times, coherent dynamics lead to the modulation of peak amplitudes, while incoherent population relaxation and exchange results in the growth of the relaxation-induced peaks. We have modeled the data by propagating the density matrix with the Redfield equation, incorporating all vibrational relaxation processes during all three experimental time periods and including excitation reorientation effects arising from relaxation. Coherence and population transfer time scales from the symmetric to the asymmetric stretch were found to be 350 fs and 3 ps, respectively. We also discuss a diagrammatic approach to incorporating all vibrational relaxation processes into the nonlinear response function, and show how coherence transfer influences the analysis of structural variables from 2D IR spectroscopy.     

Comprehensive investigation of vibrational relaxation of non-hydrogen-bonded water molecules in liquids

The vibrational dynamics of isolated water molecules dissolved in the nonpolar organic liquids 1,2-dichloroethane (C(2)H(4)Cl(2)) and d-chloroform (CDCl(3)) have been studied using an IR pump-probe experiment with approximately 2 ps time resolution. Analyzing transient, time, and spectrally resolved data in both the OH bending and the OH stretching region, the anharmonic constants of the bending overtone (v=2) and the bend-stretch combination modes were obtained. Based on this knowledge, the relaxation pathways of single water molecules were disentangled comprehensively, proving that the vibrational energy of H(2)O molecules is relaxing following the scheme OH stretch-->OH bend overtone-->OH bend-->ground state. A lifetime of 4.8+/-0.4 ps is determined for the OH bending mode of H(2)O in 1,2-dichloroethane. For H(2)O in CDCl(3) a numerical analysis based on rate equations suggests a bending overtone lifetime of tau(020)=13+/-5 ps. The work also shows that full 2-dimensional (pump-probe) spectral resolution with access to all vibrational modes of a molecule is required for the comprehensive analysis of vibrational energy relaxation in liquids.     

Femtosecond photolysis of aqueous formamide

In this work, we investigate the primary photodynamics of aqueous formamide. The formamide was photolyzed using 200 nm femtosecond pulses, and formation of products and their relaxation was followed with approximately 300 fs time resolution using probe pulses covering the range from 193 to 700 nm. Following excitation, the majority of formamide molecules (approximately 80%) converts the electronic excitation energy to vibrational excitation, which effectively is dissipated to the solvent through vibrational relaxation in just a few picoseconds. The vibrational relaxation is observed as a distinct modulation of the electronic absorption spectrum of formamide. The relaxation process is modeled by a simple one-dimensional wavepacket calculation. A smaller fraction of the excited formamide molecules dissociates to the CHO and NH2 radical pairs, of which 50% escape recombination. In addition to the electronic excitation of formamide, we also observe a small contribution from one-photon ionization of formamide and two-photon ionization and dissociation of the water solvent.     

Vibrational coupled cluster response theory: a general implementation

The calculation of vibrational contributions to molecular properties using vibrational coupled cluster (VCC) response theory is discussed. General expressions are given for expectation values, linear response functions, and transition moments. It is shown how these expressions can be evaluated for arbitrary levels of excitation in the wave function parameterization as well as for arbitrary coupling levels in the potential and property surfaces. The convergence of the method is assessed by benchmark calculations on formaldehyde. Furthermore, excitation energies and infrared intensities are calculated for the fundamental vibrations of furan using VCC limited to up to two-mode and up to three-mode excitations, VCC[2] and VCC[3], as well as VCC with full two-mode and approximate three-mode couplings, VCC[2pt3].     

Vibrational relaxation pathways of amide I and amide II modes in N-methylacetamide

We studied the vibrational energy relaxation mechanisms of the amide I and amide II modes of N-methylacetamide (NMA) monomers dissolved in bromoform using polarization-resolved femtosecond two-color vibrational spectroscopy. The results show that the excited amide I vibration transfers its excitation energy to the amide II vibration with a time constant of 8.3 ± 1 ps. In addition to this energy exchange process, we observe that the excited amide I and amide II vibrations both relax to a final thermal state. For the amide I mode this latter process dominates the vibrational relaxation of this mode. We find that the vibrational relaxation of the amide I mode depends on frequency which can be well explained from the presence of two subbands with different vibrational lifetimes (~1.1 ps on the low frequency side and ~2.7 ps on the high frequency side) in the amide I absorption spectrum.     

Dynamics of liquid benzene: a cage analysis

Dynamics of single molecules in liquids, inspected in the picosecond time scale by means of spectroscopic measurements or molecular-dynamics (MD) simulations, reveals a complex behavior which can be addressed as due to local confinement (cage). This work is devoted to the analysis of cage structures in liquid benzene, obtained from MD simulations. According to a paradigm proposed for previous analysis of atomic and molecular liquids [see, for example, A. Polimeno, G. J. Moro, and J. H. Freed, J. Chem. Phys. 102, 8094 (1995)], the istantaneous cage structure is specified by the frame of axes which identifies the molecular configuration at the closest minimum on the potential-energy landscape. In addition, the modeling of the interaction potential between probe molecule and molecular environment, based on symmetry considerations, and its parametrization from the MD trajectories, allows the estimation of the structural parameters which quantify the strength of molecular confinement. Roto-translational dynamics of probe and related cage with respect to a laboratory frame, dynamics of the probe within the cage (vibrations, librations, re-orientational motions), and the restructuring processes of the cage itself are analyzed in terms of selected time self-correlation functions. A time-scale separation between the processes is established. Moreover, by exploiting the evidence of fast vibrational motions of the probe with respect to the cage center, an orientational effective potential is derived to describe the caging in the time scale longer than approximately 0.2 ps.     

Hydrogen-bond disruption by vibrational excitations in water

An excitation of the OH-stretch nu(OH) of water has unique disruptive effects on the local hydrogen bonding. The disruption is not an immediate vibrational predissociation, which is frequently the case with hydrogen-bonded clusters, but instead is a delayed disruption caused by a burst of energy from a vibrationally excited water molecule. The disruptive effects are the result of a fragile hydrogen-bonding network subjected to a large amount of vibrational energy released in a short time by the relaxation of nu(OH) stretching and delta(H2O) bending excitations. The energy of a single nu(OH) vibration distributed over one, two, or three (classical) water molecules would be enough to raise the local temperature to 1100, 700, or 570 K, respectively. Our understanding of the properties of the metastable water state having this excess energy in nearby hydrogen bonds, termed H2O*, has emerged as a result of experiments where a femtosecond IR pulse is used to pump nu(OH), which is probed by either Raman or IR spectroscopy. These experiments show that the H2O* spectrum is blue-shifted and narrowed, and the spectrum looks very much like supercritical water at approximately 600 K, which is consistent with the temperature estimates above. The H2O* is created within approximately 400 fs after nu(OH) excitation, and it relaxes with an 0.8 ps lifetime by re-formation of the disrupted hydrogen-bond network. Vibrationally excited H2O* with one quantum of excitation in the stretching mode has the same 0.8 ps lifetime, suggesting it also relaxes by hydrogen-bond re-formation.