Role of Nanocavity Plasmons in Tunneling Electron Induced Light Emission on and near a Molecule

By using a microscopic quantum model, we study theoretically different roles of nanocavity plasmons in scanning tunneling microscope (STM) induced light emission upon selective initial excitation of molecules or plasmons. The time evolution and spectroscopic properties of the emission from the coupled plasmon-molecule system in each case are studied using time-dependent quantum mater equations. When the STM tip is placed on the molecule to ensure direct carrier injection induced molecular excitation, the major role of the plasmons is to enhance the molecular emission via increasing its radiative decay rate, resulting in sharp molecule-specific emission peaks. On the other hand, when the STM tip is located in close proximity to the edge of the molecule but without direct carrier injection into the molecule, the role of the plasmon-molecule coupling is to cause destructive interferences between the two quantum objects, leading to the occurrence of Fano dips around the energy of the molecular exciton in the plasmonic emission spectra.     

Two-dimensional optical three-pulse photon echo spectroscopy. I. Nonperturbative approach to the calculation of spectra

The nonperturbative approach to the calculation of nonlinear optical spectra of Seidner et al. [J. Chem. Phys. 103, 3998 (1995)] is extended to describe four-wave mixing experiments. The system-field interaction is treated nonperturbatively in the semiclassical dipole approximation, enabling a calculation of third order nonlinear spectroscopic signals directly from molecular dynamics and an efficient modeling of multilevel systems exhibiting relaxation and transfer phenomena. The method, coupled with the treatment of dynamics within the Bloch model, is illustrated by calculations of the two-dimensional three-pulse photon echo spectra of a simple model system-a two-electronic-level molecule. The nonperturbative calculations reproduce well-known results obtained by perturbative methods. Technical limitations of the nonperturbative approach in dealing with a dynamic inhomogeneity are discussed, and possible solutions are suggested. An application of the approach to an excitonically coupled dimer system with emphasis on the manifestation of complex exciton dynamics in two-dimensional optical spectra is presented in paper II Pisliakov et al. [J. Chem. Phys. 124, 234505 (2006), following paper].     

Molecular dynamics integration and molecular vibrational theory. I. New symplectic integrators

New symplectic integrators have been developed by combining molecular dynamics integration with the standard theory of molecular vibrations to solve the Hamiltonian equations of motion. The presented integrators analytically resolve the internal high-frequency molecular vibrations by introducing a translating and rotating internal coordinate system of a molecule and calculating normal modes of an isolated molecule only. The translation and rotation of a molecule are treated as vibrational motions with the vibrational frequency zero. All types of motion are thus described in terms of the normal coordinates. The method's time reversibility requirement was used to determine the equations of motion for internal coordinate system of a molecule. The calculation of long-range forces is performed numerically within the generalized second-order leap-frog scheme, in the same way as in standard second-order symplectic methods. The new methods for integrating classical equations of motion using normal mode analysis allow us to use a long integration step and are applicable to any system of molecules with one equilibrium configuration.     

Chemical-to-mechanical energy conversion in biomacromolecular machines: a plasmon and optimum control theory for directional work. 1. General considerations

To rationalize coherence and mechanochemical aspects of proteins acting as molecular machines, a plasmon concept for dealing with protein nonequilibrium dynamics is introduced and tested with respect to thermodynamic consistency. A stochastic optimum-control theory for protein conformational diffusion is developed and the corresponding stochastic Newton's second law derived for optimum-controlled conformational diffusion in proteins. The plasmon concept is shown to be consistent with this theory, in that optical plasmons can pump entropy out of (or into) the protein, decreasing (or increasing) its conformational diffusion and, at the same time, help decrease intra- and intermolecular friction, as well as (potentially) break the symmetry of the latter. Instead, acoustic plasmons may break the spatial symmetry of a protein's "potential of mean force", thus converting it into an effective Brownian ratchet potential by applying quasistatic deformational corrections to the former. These concepts seem to be of rather general applicability and might also be useful when studying, for example, intercalation of cationic dyes into DNA duplexes, positively charged oligopeptide transduction through cell membranes, or even DNA translocation through nanopores.     

Absorption,fluorescence and stimulated fluorescence by polaritons in thin anthracene crystals. A re-interpretation of spectroscopic properties of anthracene

The transmission, absorption (excitation spectra) and fluorescence spectra of thin (? 47 nm) free mounted anthracene flakes have been measured. True absorption in b polarization in the region of the lowest exciton state occurs as a result of scattering by phonons. It has a minimum near the transverse exciton frequency and a maximum near the longitudinal exciton frequency, in agreement with expected polariton behaviour. Thickness dependent polariton states have finite absorption and fluorescence transition probabilities (due to crystal inhomogeneities) and are observed below the transverse exciton frequency. These polariton states represent the energy reservoir for excitation energy in the bulk of the crystal. A surface-induced exciton state is the origin of the sharp line fluorescence from pure crystals and accounts for the high efficiency of stimulated fluorescence at low temperatures. Stimulated fluorescence can also be observed from the polariton modes when excitation occurs in these modes. Resonance interactions between polariton modes and impurity levels represent an important pathway for fluorescence quenching in crystalline anthracene.     

Fluctuating charge normal modes: An algorithm for implementing molecular dynamics simulations with polarizable potentials

A new method for performing molecular dynamics simulations with fluctuating charge polarizable potentials is introduced. In fluctuating charge models, polarizability is treated by allowing the partial charges to be variables, with values that are coupled to charges on the same molecule as well as those on other molecules. The charges can be efficiently propagated in a molecular dynamics simulation using extended Lagrangian dynamics. By making a coordinate change from the charge variables to a set of normal mode charge coordinates for each molecule, a new method is constructed in which the normal mode charge variables uncouple from those on the same molecule. The method is applied to the TIP4P-FQ model of water and compared to other methods for implementing the dynamics. The methods are compared using different molecular dynamics time steps.     

A spherical electron cloud hopping model for studying product branching ratios of dissociative recombination

A spherical electron cloud hopping (SECH) model is proposed to study the product branching ratios of dissociative recombination (DR) of polyatomic systems. In this model, the fast electron-captured process is treated as an instantaneous hopping of a cloud of uniform spherical fractional point charges onto a target M+q ion (or molecule). The sum of point charges (-1) simulates the incident electron. The sphere radius is determined by a critical distance (Rc eM) between the incoming electron (e-) and the target, at which the potential energy of the e(-)-M+q system is equal to that of the electron-captured molecule M+q(-1) in a symmetry-allowed electronic state with the same structure as M(+q). During the hopping procedure, the excess energies of electron association reaction are dispersed in the kinetic energies of M+q(-1) atoms to conserve total energy. The kinetic energies are adjusted by linearly adding atomic momenta in the direction of driving forces induced by the scattering electron. The nuclear dynamics of the resultant M+q(-1) molecule are studied by using a direct ab initio dynamics method on the adiabatic potential energy surface of M+q(-1), or together with extra adiabatic surface(s) of M+q(-1). For the latter case, the "fewest switches" surface hopping algorithm of Tully was adapted to deal with the nonadiabaticity in trajectory propagations. The SECH model has been applied to study the DR of both CH+ and H3O+(H2O)2. The theoretical results are consistent with the experiment. It was found that water molecules play an important role in determining the product branching ratios of the molecular cluster ion.     

Biomolecules under mechanical stress: a simple mechanism of complex behavior

The unfolding of a biomolecule by stretching force is commonly treated theoretically as one-dimensional dynamics along the reaction coordinate coincident with the direction of pulling. Here we explore a situation, particularly relevant to complex biomolecules, when the pulling direction alone is not an adequate reaction coordinate for the unfolding or rupture process. We show that in this case the system can respond to pulling force in unusual ways. Our theory points out a remarkably simple, but largely overlooked, mechanism of the complex responses of biomolecules to force. The mechanism originates from the basic property of the transition state to change its structure under applied force. A relationship is established between a key experimental observable--force-dependent lifetime--and the microscopic properties of the biomolecule in the form of an analytical solution to the problem of a force-induced molecular transition in two dimensions. The theory is applicable to biological contexts ranging from protein folding to ligand-receptor interactions.     

Molecular dynamics simulations of liquid crystal molecules on a polyimide monolayer

Preliminary results are presented on the molecular dynamics simulations of alignment of the liquid crystal molecule, 4-n-octyl-4'-cyanobiphenyl (8CB), on a polyimide (pyromelltic dianhydride-p-phenylene diamine) oligomer monolayer. We actually simulated a three-layer system, i.e., liquid crystal molecule/polyimide oligomer/a basal plane of graphite. First, simulations of the oligomers adsorbed on graphite were done in order to obtain reasonable adsorption structures, as the pre-stage simulation of the three-layer system. Then, by placing a liquid crystal layer on top, the three-layer system was simulated. The stable liquid crystal alignment direction on the polyimide monolayer was found roughly to be the polyimide chain direction with zero pretilt in this combination of liquid crystal and polymer materials. The calculated adsorption energy of an 8CB molecule to the polyimide monolayer was 128 kJ mol^-1 and the carbonyl group of the polyimide was the main adsorption site.     

Markov processes in single molecule fluorescence

This article examines the current status of Markov processes in single molecule fluorescence. For molecular dynamics to be described by a Markov process, the Markov process must include all states involved in the dynamics and the first-passage time (FPT) distributions out of those states must be describable by a simple exponential law. The observation of non-exponential FPT distributions or other evidence of non-Markovian dynamics is common in single molecule studies and offers an opportunity to expand the Markov model to include new dynamics or states that improve understanding of the system.     

Finite element interpolation for combined classical/quantum mechanical molecular dynamics simulations

A method is presented to interpolate the potential energy function for a part of a system consisting of a few degrees of freedom, such as a molecule in solution. The method is based on a modified finite element (FE) interpolation scheme. The aim is to save computer time when expensive methods such as quantum-chemical calculations are used to determine the potential energy function. The expensive calculations are only carried out if the molecule explores new unknown regions of the conformation space. If the molecule resides in regions previously explored, a cheap interpolation is performed instead of an expensive calculation, using known neighboring points. We report the interpolation techniques for the energies and the forces of the molecule, the handling of the FE mesh, and an application to a simple test example in molecular dynamics (MD) simulations. Good performance of the method was obtained (especially for MD simulations with a preceding Monte Carlo mesh generation) without losing accuracy. © 1997 John Wiley & Sons, Inc. J Comput Chem 18 : 1484–1495, 1997     

Modeling molecular effects on plasmon transport: silver nanoparticles with tartrazine

Modulation of plasmon transport between silver nanoparticles by a yellow fluorophore, tartrazine, is studied theoretically. The system is studied by combining a finite-difference time-domain Maxwell treatment of the electric field and the plasmons with a time-dependent parameterized method number 3 simulation of the tartrazine, resulting in an effective Maxwell∕Schro?dinger (i.e., classical∕quantum) method. The modeled system has three linearly arranged small silver nanoparticles with a radius of 2 nm and a center-to-center separation of 4 nm; the molecule is centered between the second and third nanoparticles. We initiate an x-polarized current on the first nanoparticle and monitor the transmission through the system. The molecule rotates much of the x-polarized current into the y-direction and greatly reduces the overall transmission of x-polarized current.     

Proton transfer in nanoconfined polar solvents. II. Adiabatic proton transfer dynamics

The reaction dynamics for a model phenol-amine proton transfer system in a confined methyl chloride solvent have been simulated by mixed quantum-classical molecular dynamics. In this approach, the proton vibration is treated quantum mechanically (and adiabatically), while the rest of the system is described classically. Nonequilibrium trajectories are used to determine the proton transfer reaction rate constant. The reaction complex and methyl chloride solvent are confined in a smooth, hydrophobic spherical cavity, and radii of 10, 12, and 15 A have been considered. The effects of the cavity radius and the heavy atom (hydrogen bond) distance on the reaction dynamics are considered, and the mechanism of the proton transfer is examined in detail by analysis of the trajectories.     

Anchoring and electro-optical dynamics of thin liquid crystalline films in a polyimide cell: experiment and theory

The surface-dependent anchoring and electro-optical (EO) dynamics of thin liquid crystalline films have been examined using Fourier transform infrared spectroscopy. A simple nematic liquid crystal, 4-n-pentyl-4'-cyanobiphenyl (5CB), is confined as 40, 50, and 390 nm thick films in nanocavities defined by gold interdigitated electrode arrays (IDEAs) patterned on polyimide-coated zinc selenide (ZnSe) substrates [Noble et al., J. Am. Chem. Soc. 124, 15020 (2002)]. New strategies for controlling the anchoring interactions and EO dynamics are explored based on coating a ZnSe surface with an organic polyimide layer in order to both planarize the substrate and induce a planar alignment of the liquid crystalline film. The polyimide layer can be further treated so as to induce a strong alignment of the nematic director along a direction parallel to the electrode digits of the IDEA. Step-scan time-resolved spectroscopy measurements were made to determine the rate constants for the electric-field-induced orientation and thermal relaxation of the 5CB films. In an alternate set of experiments, uncoated ZnSe substrates were polished unidirectionally to produce a grooved surface presenting nanometer-scale corrugations. The dynamical rate constants measured for several nanoscale film thicknesses and equilibrium organizations of the director in these planar alignments show marked sensitivities. The orientation rates are found to vary strongly with both the magnitude of the applied potential and the initial anisotropy of the alignment of the director within the IDEA. The relaxation rates do not vary in this same way. The marked variations seen in EO dynamics can be accounted for by a simple coarse-grained dynamical model.     

On the mechanism of reorientational and structural relaxation in supercooled liquids: the role of border dynamics and cooperativity

Molecular dynamics simulation and analysis based upon the many-body potential energy landscape (PEL) are employed to characterize single molecule reorientation and structural relaxation, and their interrelation, in deeply supercooled liquid CS(2). The rotational mechanism changes from small-step Debye diffusion to sudden large angle reorientation (SLAR) as the temperature falls below the mode-coupling temperature T(c). The onset of SLAR is explained in terms of the PEL; it is an essential feature of low-T rotational dynamics, along with the related phenomena of dynamic heterogeneity and the bifurcation of slow and fast relaxation processes. A long trajectory in which the system is initially trapped in a low energy local minimum, and eventually escapes, is followed in detail, both on the PEL and in real space. During the trapped period, "return" dynamics occurs, always leading back to the trap. Structural relaxation is identified with irreversible escape to a new trap. These processes lead to weak and strong SLAR, respectively; strong SLAR is a clear signal of structural relaxation. Return dynamics involves small groups of two to four molecules, while a string-like structure composed of all the active groups participates in the escape. It is proposed that, rather than simple, nearly instantaneous, one-dimensional barrier crossings, relaxation involves activation of the system to the complex, multidimensional region on the borders of the basins of attraction of the minima for an extended period.     

Ab initio ground and excited state potential energy surfaces for NO-Kr complex and dynamics of Kr solids with NO impurity

The intermolecular potentials for the NO(X 2Pi)-Kr and NO(A 2Sigma+)-Kr systems have been calculated using highly accurate ab initio calculations. The spin-restricted coupled cluster method for the ground 1 2A' state [NO(X 2Pi)-Kr] and the multireference singles and doubles configuration interaction method for the excited 2 2A' state [NO(A 2Sigma+)-Kr], respectively, were used. The potential energy surfaces (PESs) show two linear wells and one that is almost in the perpendicular position. An analytical representation of the PESs has been constructed for the triatomic systems and used to carry out molecular dynamics (MD) simulations of the NO-doped krypton matrix response after excitation of NO. MD results are shown comparatively for three sets of potentials: (1) anisotropic ab initio potentials [NO molecule direction fixed during the dynamics and considered as a point (its center of mass)], (2) isotropic ab initio potentials (isotropic part in a Legendre polynomial expansion of the PESs), and (3) fitted Kr-NO potentials to the spectroscopic data. An important finding of this work is that the anisotropic and isotropic ab initio potentials calculated for the Kr-NO triatomic system are not suitable for describing the dynamics of structural relaxation upon Rydberg excitation of a NO impurity in the crystal. However, the isotropic ab initio potential in the ground state almost overlaps the published experimental potential, being almost independent of the angle asymmetry. This fact is also manifested in the radial distribution function around NO. However, in the case of the excited state the isotropic ab initio potential differs from the fitted potentials, which indicates that the Kr-NO interaction in the matrix is quite different because of the presence of the surrounding Kr atoms acting on the NO molecule. MD simulations for isotropic potentials reasonably reproduce the experimental observables for the femtosecond response and the bubble size but do not match spectroscopic results. A general overall view of the results suggests that, when the Kr-NO interaction takes place inside the matrix, potentials are rather symmetric and less repulsive than those for the triatomic system.     

NIR-plasmon-enhanced Systems for Energy Conversion and Environmental Remediation

The introduction of plasmons is an important method to solve the insufficient utilization of the full spectrum of solar energy by semiconductor catalysts. However, semiconductor catalysts combined with traditional noble metal plasmons(Au, Ag) can only extend the absorption spectrum to partially visible light. In order to further improve the photoenergy absorption efficiency of catalysts, they need to be able to effectively utilize near-infrared light, which has become a new research direction. Recent studies have shown that traditional noble metal plasmons can absorb a part of NIR through special morphology, size control and material composite. At the same time, gratifying achievements have been made in the application of plasmonic semiconductors with broad spectrum absorption in catalysis. This article reviews the principles of generating and regulating plasmonic effects in different catalytic systems. The applications of plasmon absorption of near-infrared light in energy conversion and environmental remediation have also been presented.     

Stereoisomerism of molecular multipropellers. 2. Dynamic stereochemistry of bis- and tris-triaryl systems

The dynamic stereochemistry of bis- and tris-triaryl systems, the most simple "molecular multipropellers", is discussed on the basis of an extension of a systematic stereochemical analysis based on a symmetry-adapted symbolic notation developed specifically for these molecules. A suitable theoretical basis for our study is provided by the classical hypotheses concerning the dynamics of simple triaryl systems as formulated by Mislow and co-workers (J. Am. Chem. Soc. 1973, 95, 1535-1547), which, once applied to molecular multipropellers, show the existence of two modes of rearrangement for each propeller. Interconversion graphs for all molecules under study, covering a wide span of structural complexity, are presented. A complete NMR study of a two- and a three-propeller molecule indicates that all experimentally observable exchange pathways are indeed predicted by theoretical analysis. Moreover, quantitative analysis of 2D-EXSY experiments affords the activation energy of the subset of pathways that give rise to observable interconversions on the NMR time scale. Assuming that two-ring flips are the threshold mechanism for individual propeller interconversion, the experimental evidence indicates a preference for the flip of the central ring and one of the outer rings over the flip of two outer rings.