Study Of Intramolecular Dynamics Research Articles

Time-resolved photoelectron spectroscopy: from wavepackets to observables

Time-resolved photoelectron spectroscopy (TRPES) is a powerful tool for the study of intramolecular dynamics, particularly excited state non-adiabatic dynamics in polyatomic molecules. Depending on the problem at hand, different levels of TRPES measurements can be performed: time-resolved photoelectron yield; time- and energy-resolved photoelectron yield; time-, energy-, and angle-resolved photoelectron yield. In this pedagogical overview, a conceptual framework for time-resolved photoionization measurements is presented, together with discussion of relevant theory for the different aspects of TRPES. Simple models are used to illustrate the theory, and key concepts are further amplified by experimental examples. These examples are chosen to show the application of TRPES to the investigation of a range of problems in the excited state dynamics of molecules: from the simplest vibrational wavepacket on a single potential energy surface; to disentangling intrinsically coupled electronic and nuclear motions; to identifying the electronic character of the intermediate states involved in non-adiabatic dynamics by angle-resolved measurements in the molecular frame, the most complete measurement.

High-Resolution Spectroscopic Studies and Theory of Parity Violation in Chiral Molecules

We review the high-resolution spectroscopic approach toward the study of intramolecular dynamics, emphasizing molecular parity violation. Theoretical work in the past decade has shown that parity-violating potentials in chiral molecules are much larger (typically one to two orders of magnitude) than anticipated on the basis of older theories. This makes experimental approaches toward small molecular parity-violating effects promising. The concepts and results of intramolecular dynamics derived from spectroscopy are analyzed as a sequence of symmetry breakings. We summarize the concepts of symmetry breakings (de facto and de lege) in view of parity violation in chiral molecules. The experimental schemes and the current status of spectroscopic experiments on molecular parity violation are established. We discuss the promises of detecting and accurately measuring parity-violating energy differences Delta(pv) E on the order of 10(11) J mol(1) (approximately 100 aeV) in enantiomers of chiral molecules with regard to their contribution to fundamental physics in the framework of the standard model of particle physics and more speculative future fundamental symmetry tests such as for the combined charge conjugation, parity, and time-reversal (CPT) symmetry violation.

Intramolecular dynamics from frequency domain spectroscopy

Vibrationally mediated photodissociation is emerging as a useful tool for studies of intramolecular dynamics in polyatomic molecules since it is a sensitive indicator of both the vibrational and electronic dynamics. The method involves energy deposition in skeletal motions of molecules, their subsequent promotion to excited electronic states and dissociation. Jet-cooled action spectra, reflecting the yield of the ensuing atomic fragments as a function of vibrational excitation, are compared to simultaneously measured room temperature photoacoustic spectra and simulated spectra. The narrowed action spectra expose resonance splitting and enable estimating the homogeneous broadening and thus time scales for intramolecular vibrational energy redistribution to close resonating states and to bath states. Overtone spectra of the acetylenic and alkyl C H stretches of the acetylene homologues, propyne and 1-butyne, demonstrate how the nature of rovibrationally excited states is highlighted by photolysis of pre-excited molecules.

Structure, dipole moment and large amplitude motions of 1-benzofuran

The rotational spectrum of 1-benzofuran has been investigated by three different rotational spectroscopy techniques: (i) millimeterwave absorption free jet spectroscopy, useful for a fast assignment of the spectrum; (ii) molecular beam Fourier transform microwave spectroscopy, sensitive to detect less abundant isotopic species in natural abundance; (iii) waveguide conventional microwave spectroscopy, useful for the study of intramolecular dynamics, through the rotational spectra of the vibrational satellites of low energy modes. Besides the rotational spectrum of the ground state of the normal species, the spectra of 9 singly substituted 13C and 18O isotopomers in natural abundance, and of 6 vibrational satellites, have been measured. Precise structural parameters for the molecule, as well as information on the potential energy surface of the low energy vibrations, have been obtained. The dipole moment components have been determined to be micro(a)= 0.216 (2) and micro(b)= 0.720 (3) D, respectively.

EPR study of intramolecular dynamics in o-semiquinonic nickel complexes with PCP-pincer ligand in solution.

A number of square pyramidal o-semiquinonic nickel complexes with 2,6-bis(diphenylphosphinomethyl)phenyl were investigated by EPR spectroscopy in solution. The complexes have flexible coordination spheres and can exist in solution as two isomers rapidly (on the EPR timescale) interconverting one to another at room temperature. The equilibrium is entropy driven and does not significantly depend on the substituents in the semiquinone ring. The spin density distribution depends on mesomeric properties and bulkiness of substituents in ortho-position to oxygen atoms.

Reevaluation of the use of photoelectron angular distributions as a probe of dynamical processes: strong dependence of such distributions from s1 paradifluorobenzene on photoelectron kinetic energy.

Photoelectron angular distributions (PADs) have been measured following the excitation of the S1 origin band in paradifluorobenzene using a range of ionizing wavelengths and for resolved ion vibrational states. The PADs show a dramatic sensitivity to the photoelectron kinetic energy over an energy range of at least 1 eV from threshold, and almost no sensitivity to any prepared intermediate state alignment. This has important consequences for those studies of intramolecular dynamics that use PADs. We suggest that the observed behavior is caused by a shape resonance in the continuum.

Reply to comment on “Checking the influence of numerically induced chaos in the computational study of intramolecular dynamics using trajectory equivalence”

Time evolutions of mode energies averaged over equivalent trajectories are presented for an uncoupled two-dimensional harmonic oscillator. The mode energies hardly show any significant damping. Hence, our previous interpretation that the excessive damping observed for HOD was due to the onset of numerically induced chaos caused by the coupling terms in the Hamiltonian is upheld.

Comment on `Checking the influence of numerically induced chaos in the computational study of intramolecular dynamics using trajectory equivalence'

The interpretation of a recent molecular dynamics study of equivalent trajectories is questioned. It is shown by a simple counter-example that the observed sudden damping of modes can be explained by a simple dephasing effect due to round-off error, rather than numerical chaos due to coupling terms in the Hamiltonian. The effect can be eliminated by a simple change to the averaging procedure.

PHOSPHORESCENCE OF TRYPTOPHAN RESIDUES OF PROTEINS AT ROOM TEMPERATURE

A brief overview of the results of our works concerned with the study of intramolecular dynamics of proteins by the method of tryptophan phosphorescence at room temperature is given. The mechanisms of quenching tryptophan phosphorescence at room temperature are considered. The lifetimes and quantum yields of tryptophan phosphorescence of proteins at room temperature in different states of aggregation are given. The functional importance of the changes recorded by the phosphorescence method in the intramolecular dynamics of fermented proteins is shown.

Checking the influence of numerically induced chaos in the computational study of intramolecular dynamics using trajectory equivalence

Influence of the numerical chaos induced by the numerical round-off errors in the classical trajectory study of intramolecular dynamics has been investigated using HOD as an example. Calculation of the trajectory equivalence based on the scaling theorem for classical dynamics has been found useful to check the onset of the numerically induced chaos. It has also been found that the use of higher precision arithmetic is not very effective to delay this onset.

Time-dependent Hartree approaches for the study of intramolecular dynamics in dimer systems

We apply and the time-dependent Hartree (TDH) method to the study of intramolecular dynamics in dimer systems. The HCl dimer is chosen as test case. Model calculations are performed on reduced dimensional representation of this system namely two-, three-, and four-dimensional ones. We assess the validity of different implementations of the TDH method including the account of direct correlations between coordinate pairs, and mixed quantum-classical and quantum-Gaussian wave packets treatments. The latter yields very good results compared to the fully quantal treatment.

The semiclassical regime of intramolecular vibrational dynamics

We report on a study of intramolecular dynamics after an ultrashort excitation. We show that a semiclassical regime of the vibrational dynamics exists on an intermediate time scale between the initial dephasing on the ultrashort time of the excitation pulse and the Heisenberg time scale associated with the mean level spacing. In this semiclassical regime, intramolecular dynamics presents time recurrences at the periods of the classical orbits. The amplitudes of these semiclassical time recurrences are evaluated for classically integrable and chaotic systems using Gutzwiller and the Berry–Tabor trace formulas.

State‐to‐state studies of intramolecular dynamics and unimolecular reactions

AbstractDouble‐resonance vibrational overtone excitation spectra of small molecules, in combination with laser‐induced fluorescence product detection, provide information on both their energetics and intramolecular energy redistribution dynamics. Application of this approach to measure OH stretch overtone spectra of HOOH and NH2OH near their dissociation threshold provides estimates of the O‐O and N‐O bond energies of 17051.8±4 cm−1 and 21620±20 cm−1 respectively.In symmetrical molecules, such as HOOH, the double‐resonance excitation technique allows us to prepare molecules in either pure OH stretch overtone levels or combination levels in which the excitation energy is divided between two identical OH stretch oscillators. Comparison of the resulting vibrational overtone linewidths indicates no clear difference between the pure OH stretch and the local‐local combination levels. However, comparison of the energy transfer rates from pure OH stretch vibrations and those in which one quantum of energy is put in a low frequency mode reveals faster rates from the latter. This observation clearly indicates that coupling strengths depend markedly on the vibrational character of the coupling partner and not simply on the total energy.Comparison of the OH stretch overtone spectra of the structurally similar molecules HOOH, NH2OH, and CH3OH reveal similar rates of vibrational energy redistribution, despite the difference in the density of states in these molecules. This observation reinforces the notion that energy flow between the OH stretch and dark background states is not statistical but rather is controlled by coupling to a small subset of background states.

ChemInform Abstract: The Study of Intramolecular Dynamics by Nuclear Magnetic Resonance.

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Spin-lattice relaxation and intramolecular motions in transferrin on the Mössbauer spectroscopy data

A new approach for the investigation of intramolecular motions in proteins, based on the study of spin-lattice relaxation of the iron atom of the protein active centres, has been developed. The gamma-resonance spectra have been obtained for the globules of transferrin enriched with57Fe. They possessed a paramagnetic hyperfine structure up to room temperature. This afforded the opportunity to experimentally investigate high temperature conformational motions in proteins and to study their influence on the spin-lattice relaxation. A theoretical model of relaxational spectra calculations has been developed, which enabled us to extract the frequency distribution of the spin-lattice relaxation from the shape of the spectra. The approach developed for the study of intramolecular dynamics of proteins based on the examination of spin-lattice relaxation in gamma-resonance spectra increases the frequency scale by at least one order in comparison with conventional methods.

Mössbauer study of spin-lattice relaxation and intramolecular motions in transferrin

A new approach for the investigation of intramolecular motions in proteins, based on the study of spin-lattice relaxation of ferric iron in the protein active centres, has been developed. The Mössbauer spectra of dry and hydrated transferrin enriched with 57Fe isotope have been obtained. They revealed a paramagnetic hyperfine structure with the magnetic splitting of lines up to room temperature. This allowed one to investigate experimentally high temperature conformational motions in the protein and to study their influence on spin-lattice relaxation. A theoretical model for the fitting of the relaxation spectra has been developed that made it possible to restore the frequency distribution of spin-lattice relaxation rates from experimental data. Two peaks in these distributions at 10 8 s −1 and 10 10 s −1 have been discovered in the temperature interval 78–300 K. It proves that there is a difference in the dynamic states of two iron atoms in the active centres of the transferrin molecule for N- and C-lobes. The approach developed for the study of intramolecular dynamics of proteins based on the analysis of spin-lattice relaxation increases the frequency range of the molecular motions under investigation at least one order in comparison with the traditional methods, based on the study of the Mössbauer effect probabilities and mean-square displacements of atoms.

The study of intramolecular dynamics by nuclear magnetic resonance

Abstract

Intramolecular dynamics of chain molecules monitored by fluctuations in efficiency of excitation energy transfer. A theoretical study

The fluorescence quantum yield of a polymer molecule to which an energy donor chromophore and an energy acceptor chromophore are attached depends on the distance between the donor and acceptor chromophores. If this distance fluctuates with time, the fluorescence intensity is expected to fluctuate as well, and the time course of the intensity fluctuations will be correlated with the time course of the changes in the interchromophore distance. The intensity fluctuations are experimentally measurable if the number of illuminated molecules is small. A theoretical treatment of such fluorescence intensity fluctuations is presented in terms of a parameter that describes the polymer chain dynamics. Computer simulations were performed to illustrate the dependence of the autocorrelation function of the intensity fluctuations on the polymer chain conformation, the interchromophore energy transfer properties, and the macromolecular dynamics. These simulations demonstrate that the intensity fluctuations due to nonradiative energy transfer between chromophores attached to polymer chains can be large enough to be experimentally useful in the study of intramolecular dynamics of macromolecules.

Time-dependent self-consistent field approximation for intramolecular energy transfer. I. Formulation and application to dissociation of van der Waals molecules

The time-dependent self-consistent field method (TDSCF) is formulated and applied to the study of intramolecular dynamics and unimolecular decomposition processes. The method is illustrated by calculations on vibrational predissociation in van der Waals molecules, such as I2(v)Ne→I2(v′)+Ne. The TDSCF has the advantage of achieving formal separability of the modes by associating a time-dependent Hamiltonian with each mode, while permitting (possibly extensive) energy transfer among the modes via the time-dependent mean potential which acts on each mode. We present quantal, semiclassical, and classical versions of the method; a proper classical limit of the quantum TDSCF replaces the averages over wave functions by averages over self-consistently obtained bundles of trajectories. In all three versions, considerable computational economy is retained in comparison with full dynamics calculation. A detailed study is made of those properties which can be correctly obtained in such a time-dependent mean field theory. Attention is drawn to problems such as the occurrence of spurious states in the asymptotic region, and a simple method for avoiding them is suggested. We find for the I2(v)Ne vibrational predissociation that the TDSCF compares well with corresponding full dynamics calculations for average single mode properties such as dissociation lifetimes and the translational energy release. Moreover, comparison with classical trajectory calculations shows that the TDSCF method reproduces the essential dynamical mechanism of the dissociation (in-phase impulsive I⋅⋅⋅Ne collision following several ineffective vibrations). The self-consistent bundle trajectories and the time-dependent mean fields are analyzed, and provide insight into the process dynamics. It is concluded that the TDSCF approach in both quantal and quasiclassical versions is a potentially powerful tool in the study of intramolecular energy transfer and unimolecular dissociation.