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Biomedical subjects

Shaul Mukamel

Publications and source records attributed to Shaul Mukamel.

At least 37 records · Page 2Linked to original sources
PubMed2005

Stochastic Liouville equations for hydrogen-bonding fluctuations and their signatures in two-dimensional vibrational spectroscopy of water.

The effects of hydrogen-bond forming and breaking kinetics on the linear and coherent third-order infrared spectra of the OH stretch of HOD in D2O are described by Markovian, not necessarily Gaussian, fluctuations and simulated using the stochastic Liouville equations. Slow (0.5 ps) fluctuations are represented by a collective electrostatic coordinate, whereas fast (<100 fs) frequency fluctuations are described using either a second collective electrostatic coordinate or a four-state jump (FSJ) model for hydrogen-bonding configurations. Parameters for both models were obtained using a 1-ns molecular-dynamics trajectory calculated using the TIP4P force field combined with an electrostatic ab initio map. The asymmetry of the photon-echo spectra (larger linewidth on the blue side than on the red side) predicted by the FSJ is in better agreement with recent experiments.

Algorithms↗
PubMed2005

Dissecting coherent vibrational spectra of small proteins into secondary structural elements by sensitivity analysis.

The response of proteins to sequences of femtosecond infrared pulses provides a multidimensional view into their equilibrium distribution of structures and snapshot pictures of fast-triggered dynamical events. Analyzing these experiments requires advanced computational tools for assigning regions in the resulting multi-dimensional correlation plots to specific secondary-structure elements and their couplings. A differential sensitivity analysis technique based on a perturbation of the local (real space) Hamiltonian is developed to achieve that goal. Application to the amide I region of a small globular protein reveals regions associated with the alpha-helix, beta-sheet, and their coupling. Comparison of signals generated in different directions shows that the double-quantum-coherence signal has a higher sensitivity to the couplings compared with the single-quantum-coherence (photon echo) technique.

Infrared Rays↗
PubMed2005

Dephasing-induced vibronic resonances in difference frequency generation spectroscopy.

The difference frequency generation (DFG) signal from a two electronic level system with vibrational modes coupled to a Brownian oscillator bath is computed. Interference effects between two Liouville space pathways result in pure-dephasing-induced, excited-state resonances provided the two excitation pulses overlap and time ordering is not enforced. Numerical simulations of two-dimensional DFG signals illustrate how the ground and excited electronic state resonances may be distinguished.

Chemistry Techniques, Analytical↗
PubMed2005

Coherent third-order spectroscopic probes of molecular chirality.

The third-order optical response of a system of coupled localized anharmonic vibrations is studied using a Green's function solution of the nonlinear exciton equations for bosonized excitons, which are treated as interacting quasiparticles. The explicit calculation of two-exciton states is avoided and the scattering of quasiparticles provides the mechanism of optical nonlinearities. To first-order in the optical wave vector we find several rotationally invariant tensor components for isotropic ensembles which are induced by chirality. The nonlocal nonlinear susceptibility tensor is calculated for infinitely large periodic structures in momentum space, where the problem size reduces to the exciton interaction radius. Applications are made to alpha and 3(10) helical infinite peptides.

Circular Dichroism↗
PubMed2005

Stacking effect of polyfluorene on the chemical shift and electron transport.

We investigate the structures, NMR chemical shifts, absorption spectra, frontier molecular orbitals, and transition density matrices of pi-stacked polyfluorenes by ab initio calculations. For F1-F4, we consider two different conformations, syn and anti. The simulated 1H NMR chemical shifts are in good agreement with the previous experiment, and the significantly upfielded chemical shifts explain that the fluorene moieties are stacked on each other. It is found that the relative stability for syn and anti conformers is almost equivalent in B3LYP calculations; however, the syn conformer becomes much more stable than the anti conformer in MP2 calculations, which is consistent with the experimental finding that only the syn conformers are relevant. The vertical detachment energy, which is linearly proportional to the ionization potential, shows the same size dependence as the previous experiment. The electron attachment energy decreases exponentially as the size increases, which implies that the electron transport would be possible even for long chains such as F3 and F4. This was evident from the frontier molecular orbitals (HOMO and LUMO). Also, it is found that the syn conformers are very favorable for electron transport through the pi-stacked fluorene moieties.

Biophysics↗
PubMed2005

Collective solvent coordinates for the infrared spectrum of HOD in D2O based on an ab initio electrostatic map.

An ab initio MP2 vibrational Hamiltonian of HOD in an external electrostatic potential parametrized by the electric field and its gradient-tensor is constructed. By combining it with the fluctuating electric field induced by the D(2)O solvent obtained from molecular dynamics simulations, we calculate the infrared absorption of the O-H stretch. The resulting solvent shift and infrared line shape for three force fields (TIP4P, SPC/E, and SW) are in good agreement with the experiment. A collective coordinate response for the solvent effect is constructed by identifying the main electrostatic field and gradient components contributing to the line shape. This allows a realistic stochastic Liouville equation simulation of the line shapes which is not restricted to Gaussian frequency fluctuations.

Computer Simulation↗
PubMed2004

Simulation of x-ray absorption near edge spectra of electronically excited ruthenium tris-2,2'-bipyridine.

The L(3) edge x-ray absorption near edge spectrum (XANES) of the ground electronic state and the metal to ligand charge transfer state of ruthenium tris-2,2(')-bipyridine is calculated. The final valence states and energies in the presence of the photoelectron and core hole, and the corresponding transition intensities are computed using time dependent density functional theory with the Becke three-parameter density functional with the Lee-Yang-Parr correlation functional. Calculations show a valence shift of the primary XANES peak and the appearance of the new XANES transition to the hole created by the optical excitation, in agreement with experiment [M. Saes, C. Bressler, R. Abela, D. Grolimund, S. L. Johnson, P. A. Heimann, and M. Chergui, Phys. Rev. Lett. 90, 047403 (2003)].

Journal Article↗
PubMed2004

Stochastic Liouville equation simulation of multidimensional vibrational line shapes of trialanine.

The line shapes detected in coherent femtosecond vibrational spectroscopies contain direct signatures of peptide conformational fluctuations through their effect on vibrational frequencies and intermode couplings. These effects are simulated in trialanine using a Green's function solution of a stochastic Liouville equation constructed for four collective bath coordinates (two Ramachandran angles affecting the mode couplings and two diagonal energies). We find that fluctuations of the Ramachandran angles which hardly affect the linear absorption can be effectively probed by two-dimensional spectra. The signal generated at k(1)+k(2)-k(3) is particularly sensitive to such fluctuations.

Alanine↗
PubMed2004

Effect of quantum collapse on the distribution of work in driven single molecules.

Two sources of quantum deviations from Jarzynski's celebrated classical relation between the free energy change and the distribution of work are analyzed using an exactly solvable harmonic model: Quantum dynamics retains the Gaussian profile of the distribution and merely gives rise to analytic corrections in variant Planck's over 2pi, whereas quantum measurements (wave function collapse) induce extended power-law tails which fundamentally alter the distribution. These results may be observed in quantum information processing and in experiments involving mechanically or optically driven single quantum objects.

Journal Article↗
PubMed2004

Coherent low-frequency motions of hydrogen bonded acetic acid dimers in the liquid phase.

Ultrafast vibrational dynamics of cyclic hydrogen bonded dimers and the underlying microscopic interactions are studied in temporally and spectrally resolved pump-probe experiments with 100 fs time resolution. Femtosecond excitation of the O-H and/or O-D stretching mode gives rise to pronounced changes of the O-H/O-D stretching absorption displaying both rate-like kinetic and oscillatory components. A lifetime of 200 fs is measured for the v=1 state of the O-H stretching oscillator. The strong oscillatory absorption changes are due to impulsively driven coherent wave packet motions along several low-frequency modes of the dimer between 50 and 170 cm(-1). Such wave packets generated via coherent excitation of the high-frequency O-H/O-D stretching oscillators represent a clear manifestation of the anharmonic coupling of low- and high-frequency modes. The underdamped low-frequency motions dephase on a time scale of 1-2 ps. Calculations of the vibrational potential energy surface based on density functional theory give the frequencies, anharmonic couplings, and microscopic elongations of the low-frequency modes, among them intermolecular hydrogen bond vibrations. Oscillations due to the excitonic coupling between the two O-H or O-D stretching oscillators are absent as is independently confirmed by experiments on mixed dimers with uncoupled O-H and O-D stretching oscillators.

Acetic Acid↗
PubMed2004

All-forward semiclassical simulations of nonlinear response functions.

We propose a quantum trajectory algorithm for computing nonlinear response functions of condensed phase molecular systems based on a time-ordered expansion of the density matrix. The nth-order response function is expressed as a sum of 2(n) impulsive response pathways representing trajectories involving zero, one, and up to n interactions with short external pulses. These are evaluated using a forward propagation algorithm based upon a Liouville space extension of the Bohmian propagation method.

Journal Article↗
PubMed2004

Disentangling multidimensional femtosecond spectra of excitons by pulse shaping with coherent control.

Sequences of carefully timed and shaped optical pulses provide femtosecond snapshots of molecular structure as well as electronic and vibrational dynamical processes, in analogy with multidimensional NMR. We apply a genetic learning algorithm towards the design of pulse sequences which simplify the multidimensional signals by controlling the relative intensities of various peaks. Numerical simulations demonstrate how poorly resolved weak features may be amplified and observed by using optimized optical pulses, specifically shaped to achieve a desired spectroscopic target.

Algorithms↗
PubMed2004

Efficient fluoride-selective fluorescent host: experiment and theory.

A new naphthalene derivative containing a urea group at the 1,8-position of naphthalene was synthesized and showed a unique absorption and fluorescence peak with fluoride ion. Calculations suggested that a new peak was attributed to the increased anionic character of urea nitrogen due to the strongly charged hydrogen bonding between fluoride and amide protons of the urea. The fluoride selectivity among halides (F(-), Cl(-), Br(-)) comes from the fact that the fluoride approaches much closer to the amide protons than other halides and resides in the cavity with fast dynamics. The nature of electronic transitions that were analyzed from the calculations by the collective electronic oscillator method also supports the anionic nature of the complex between host and fluoride.

Journal Article↗
PubMed2004

Many-body effects in molecular photoionization in intense laser fields; time-dependent Hartree-Fock simulations.

The time evolution of the reduced single electron density matrix for eight electrons in a one-dimensional finite box potential driven by an intense laser field is calculated by numerically integrating the time-dependent Hartree-Fock equations. We study the effects of the Coulomb interaction, field intensity, and frequency on the time profile of the ionization process. Our computed saturation ionization intensity (Isat) is in good agreement with experimental results for decatetraene [Ivanov et al. J. Chem. Phys. 117, 1575 (2002)].

Journal Article↗
PubMed2004

The origin of vibrational mode couplings in various secondary structural motifs of polypeptides.

Electrostatic (through-space) and covalent (through-bond) contributions to couplings involving the C[double bond]O and C[bond]N vibrational stretching modes of the amide group in the alpha-helix and the parallel and antiparallel beta-sheet structures of alanine polypeptides are analyzed. Coupling constants computed at the density functional theory level are compared with the transition dipole coupling model and the complete electrostatic interaction between transition densities. We find that the transition densities of C[double bond]O modes are localized, and the electrostatic mechanism then holds. In contrast, the C[bond]N mode transition densities are delocalized, and covalent contributions to the coupling are significant.

Models, Molecular↗
PubMed2003

Resonant enhancement and dissipation in nonequilibrium van der Waals forces.

Dispersion forces between molecules that are in relative motion, coupled to baths at different temperatures, or in excited states, are calculated using a Green function Liouville space expansion that extends the celebrated McLachlan response theory to the nonlinear regime. Our dynamical theory is applicable to systems that may be in any initial nonequilibrium state and that are subject to an arbitrary time-dependent coupling. In contrast to equilibrium forces which are attractive, nonequilibrium forces may be attractive or repulsive, exhibit chemically specific resonances, are far stronger, and may be nonconservative (with either positive or negative dissipation).

Adenosine Triphosphate↗