Interplays of electron and nuclear motions along CO dissociation trajectory in myoglobin revealed by ultrafast X-rays and quantum dynamics calculations.

Ultrafast structural dynamics with different spatial and temporal scales were investigated during photodissociation of carbon monoxide (CO) from iron(II)-heme in bovine myoglobin during the first 3 ps following laser excitation. We used simultaneous X-ray transient absorption (XTA) spectroscopy and X-ray transient solution scattering (XSS) at an X-ray free electron laser source with a time resolution of 80 fs. Kinetic traces at different characteristic X-ray energies were collected to give a global picture of the multistep pathway in the photodissociation of CO from heme. In order to extract the reaction coordinates along different directions of the CO departure, XTA data were collected with parallel and perpendicular relative polarizations of the laser pump and X-ray probe pulse to isolate the contributions of electronic spin state transition, bond breaking, and heme macrocycle nuclear relaxation. The time evolution of the iron K-edge X-ray absorption near edge structure (XANES) features along the two major photochemical reaction coordinates, i.e., the iron(II)-CO bond elongation and the heme macrocycle doming relaxation were modeled by time-dependent density functional theory calculations. Combined results from the experiments and computations reveal insight into interplays between the nuclear and electronic structural dynamics along the CO photodissociation trajectory. Time-resolved small-angle X-ray scattering data during the same process are also simultaneously collected, which show that the local CO dissociation causes a protein quake propagating on different spatial and temporal scales. These studies are important for understanding gas transport and protein deligation processes and shed light on the interplay of active site conformational changes and large-scale protein reorganization.

Time-Dependent, Optically Controlled Dielectric Function.

We suggest optical modulation of the dielectric function of a molecular monolayer adsorbed on a metal surface as a potential means of controlling plasmon resonance phenomena. The dielectric function is altered using a laser pulse of moderate intensity and linear polarization to align the constituent molecules. After the pulse, the monolayer returns to its initial state. Time-dependent, optically controlled dielectric function is illustrated by molecular dynamics calculations.

Axis-dependence of molecular high harmonic emission in three dimensions.

High-order harmonic generation in an atomic or molecular gas is a promising source of sub-femtosecond vacuum ultraviolet coherent radiation for transient scattering, absorption, metrology and imaging applications. High harmonic spectra are sensitive to Ångstrom-scale structure and motion of laser-driven molecules, but interference from radiation produced by random molecular orientations obscures this in all but the simplest cases, such as linear molecules. Here we show how to extract full body-frame high harmonic generation information for molecules with more complicated geometries by utilizing the methods of coherent transient rotational spectroscopy. To demonstrate this approach, we obtain the relative strength of harmonic emission along the three principal axes in the asymmetric-top sulphur dioxide. This greatly simplifies the analysis task of high harmonic spectroscopy and extends its usefulness to more complex molecules.

Predicted ordered assembly of ethylene molecules induced by polarized off-resonance laser pulses.

We illustrate a new phenomenon in the dynamics of molecular ensembles subjected to moderately intense, far-off-resonance laser fields, namely, field-driven formation of perfectly ordered, defect-free assembly. Interestingly, both the arrangement of the constituting molecules within the individual assembly and the long-range order of the assembly with respect to one another are subject to control through choice of the field polarization. Relying on strong induced dipole-induced dipole interactions that are established in dense molecular media, the effect is expected to be general.

Molecular focusing and alignment with plasmon fields.

We show the possibility of simultaneously aligning molecules and focusing their center-of-mass motion near a metal nanoparticle in the field intensity gradient created by the surface plasmon enhancement of incident light. The rotational motion is described quantum mechanically while the translation is treated classically. The effects of the nanoparticle shape on the alignment and focusing are explored. Our results carry interesting implications to the field of molecular nanoplasmonics and suggest several potential applications in nanochemistry.

Quantum optimal control of isomerization dynamics of a one-dimensional reaction-path model dominated by a competing dissociation channel.

Quantum wave packet optimal control simulations with intense laser pulses have been carried out for studying molecular isomerization dynamics of a one-dimensional (1D) reaction-path model involving a dominant competing dissociation channel. The 1D intrinsic reaction coordinate model mimics the ozone open --> cyclic ring isomerization along the minimum energy path that successively connects the ozone cyclic ring minimum, the transition state (TS), the open (global) minimum, and the dissociative O(2) + O asymptote on the O(3) ground-state (1)A(') potential energy surface. Energetically, the cyclic ring isomer, the TS barrier, and the O(2) + O dissociation channel lie at approximately 0.05, approximately 0.086, and approximately 0.037 hartree above the open isomer, respectively. The molecular orientation of the modeled ozone is held constant with respect to the laser-field polarization and several optimal fields are found that all produce nearly perfect isomerization. The optimal control fields are characterized by distinctive high temporal peaks as well as low frequency components, thereby enabling abrupt transfer of the time-dependent wave packet over the TS from the open minimum to the targeted ring minimum. The quick transition of the ozone wave packet avoids detrimental leakage into the competing O(2) + O channel. It is possible to obtain weaker optimal laser fields, resulting in slower transfer of the wave packets over the TS, when a reduced level of isomerization is satisfactory.

Theory of three-dimensional alignment by intense laser pulses.

We introduce a theoretical framework for study of three-dimensional alignment by moderately intense laser pulses and discuss it at an elementary level. Several features of formal interest are noted and clarified. Our approach is nonperturbative, treating the laser field within classical and the material system within quantum mechanics. The theory is implemented numerically using a basis set of rotational eigenstates, transforming the time-dependent Schrodinger equation to a set of coupled differential equations where all matrix elements are analytically soluble. The approach was applied over the past few years to explore different adiabatic and nonadiabatic three-dimensional alignment approaches in conjunction with experiments, but its formal details and numerical implementation were not reported in previous studies. Although we provide simple numerical examples to illustrate the content of the equations, our main goal is to complement previous reports through an introductory discussion of the underlying theory.

Design of infrared laser pulses for the deexcitation of highly excited homonuclear diatomic molecules.

We explore the possibility of using shaped infrared laser pulses to deexcite a homonuclear diatomic molecule from its highest vibrational state down to its ground vibrational state. The motivation for this study arises from the need to deexcite alkali metal dimers in a similar way so as to stabilize molecular Bose-Einstein condensates. We demonstrate that for the case of the H(2) molecule, where it is possible to evaluate all the necessary high accuracy ab initio data on the interaction of the molecule with an electric field, we are able to successfully design a sequence of infrared laser pulses to accomplish the desired deexcitation process in a highly efficient manner.

Quantum optimal control of molecular isomerization in the presence of a competing dissociation channel.

The quantum optimal control of isomerization in the presence of a competing dissociation channel is simulated on a two-dimensional model. The control of isomerization of a hydrogen atom is achieved through vibrational transitions on the ground-state surface as well as with the aid of an excited-state surface. The effects of different competing dissociation channel configurations on the isomerization control are explored. Suppression of the competing dissociation dynamics during the isomerization control on the ground-state surface becomes easier with an increase in the spatial separation between the isomerization and dissociation regions and with a decrease in the dissociation channel width. Isomerization control first involving transfer of amplitude to an excited-state surface is less influenced by the dissociation channel configuration on the ground-state surface, even in cases where the excited-state surface allows for a moderate spreading of the excited wave packet.

Quantum control of molecular vibrational and rotational excitations in a homonuclear diatomic molecule: a full three-dimensional treatment with polarization forces.

The optimal control of the vibrational excitation of the hydrogen molecule [Balint-Kurti et al., J. Chem. Phys. 122, 084110 (2005)] utilizing polarization forces is extended to three dimensions. The polarizability of the molecule, to first and higher orders, is accounted for using explicit ab initio calculations of the molecular electronic energy in the presence of an electric field. Optimal control theory is then used to design infrared laser pulses that selectively excite the molecule to preselected vibrational-rotational states. The amplitude of the electric field of the optimized pulses is restricted so that there is no significant ionization during the process, and a new frequency sifting method is used to simplify the frequency spectrum of the pulse. The frequency spectra of the optimized laser pulses for processes involving rotational excitation are more complex than those relating to processes involving only vibrational excitation.

Quantum control of molecular motion including electronic polarization effects with a two-stage toolkit.

A method for incorporating strong electric field polarization effects into optimal control calculations is presented. A Born-Oppenheimer-type separation, referred to as the electric-nuclear Born-Oppenheimer (ENBO) approximation, is introduced in which variations of both the nuclear geometry and the external electric field are assumed to be slow compared with the speed at which the electronic degrees of freedom respond to these changes. This assumption permits the generation of a potential energy surface that depends not only on the relative geometry of the nuclei but also on the electric field strength and on the orientation of the molecule with respect to the electric field. The range of validity of the ENBO approximation is discussed in the paper. A two-stage toolkit implementation is presented to incorporate the polarization effects and reduce the cost of the optimal control dynamics calculations. As an illustration of the method, it is applied to optimal control of vibrational excitation in a hydrogen molecule aligned along the field direction. Ab initio configuration interaction calculations with a large orbital basis set are used to compute the H-H interaction potential in the presence of the electric field. The significant computational cost reduction afforded by the toolkit implementation is demonstrated.

High-dimensional model representations generated from low order terms--lp-RS-HDMR.

High-dimensional model representation (HDMR) is a general set of quantitative model assessment and analysis tools for improving the efficiency of deducing high dimensional input-output system behavior. RS-HDMR is a particular form of HDMR based on random sampling (RS) of the input variables. The component functions in an HDMR expansion are optimal choices tailored to the n-variate function f(x) being represented over the desired domain of the n-dimensional vector x. The high-order terms (usually larger than second order, or equivalently beyond cooperativity between pairs of variables) in the expansion are often negligible. When it is necessary to go beyond the first and the second order RS-HDMR, this article introduces a modified low-order term product (lp)-RS-HDMR method to approximately represent the high-order RS-HDMR component functions as products of low-order functions. Using this method the high-order truncated RS-HDMR expansions may be constructed without directly computing the original high-order terms. The mathematical foundations of lp-RS-HDMR are presented along with an illustration of its utility in an atmospheric chemical kinetics model.