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.

Alignment Thresholds of Molecules.

Molecules have long been known to align in moderately intense, far off-resonance laser fields with a large variety of applications in physics and optics. We illustrate and describe the physical origin of a previously unexplored phenomenon in the adiabatic alignment dynamics of molecules, which is fundamentally interesting and also has an important practical implication. Specifically, the intensity dependence of the degree of adiabatic alignment exhibits a threshold behavior, below which molecules are isotropically distributed rotationally and above which the alignment rapidly reaches a plateau. Furthermore, we show that both the intensity and the temperature dependencies of the alignment of all linear molecules exhibit universal curves and derive analytical forms to describe these dependencies. Finally, we illustrate that the alignment threshold occurs very generally at a lower intensity than the off-resonance ionization threshold, a numerical observation that is readily illustrated analytically. The threshold behavior is attributed to a tunneling mechanism that rapidly switches off at the threshold intensity, where tunneling between the potential wells corresponding to the two orientations of the aligned molecules becomes impossible. The universal threshold behavior of molecular alignment is a simple phenomenon, but one that was not realized before and can be readily tested experimentally.

Light-Triggered Switching of Quantum Dot Photoluminescence through Excited-State Electron Transfer to Surface-Bound Photochromic Molecules.

This paper describes reversible "on-off" switching of the photoluminescence (PL) intensity of CdSe quantum dots (QDs), mediated by photochromic furylfulgide carboxylate (FFC) molecules chemisorbed to the surfaces of the QDs. Repeated cycles of UV and visible illumination switch the FFC between "closed" and "open" isomers. Reversible switching of the QDs' PL intensity by >80% is enabled by different rates and yields of PL-quenching photoinduced electron transfer (PET) from the QDs to the respective isomers. This difference is consistent with cyclic voltammetry measurements and density functional calculations of the isomers' frontier orbital energies. This work demonstrates fatigue-resistant modulation of the PL of a QD-molecule complex through remote control of PET. Such control potentially enables applications, such as all-optical memory, sensing, and imaging, that benefit from a fast, tunable, and reversible response to light stimuli.

Photoisomerization-coupled electron transfer.

Photochromic molecular structures constitute a unique platform for constructing molecular switches, sensors, and memory devices. One of their most promising applications is as light-switchable electron acceptor or donor units. Here, we investigate a previously unexplored process that we postulate may occur in such systems: an ultrafast electron transfer triggered by a simultaneous photoisomerization of the donor or the acceptor moiety. We propose a theoretical model for this phenomenon and, with the aid of density functional theory calculations, apply it to the case of a dihydropyrene-type photochromic molecular donor. By considering the wavepacket dynamics and the photoisomerization yield, we show that the two processes involved, electron transfer and photoisomerization, are in general inseparable and need to be treated in a unified manner. We finish by discussing how the efficiency of photoisomerization-coupled electron transfer can be controlled experimentally.

Beyond Marcus theory and the Landauer-Büttiker approach in molecular junctions. II. A self-consistent Born approach.

Marcus and Landauer-Büttiker approaches to charge transport through molecular junctions describe two contrasting mechanisms of electronic conduction. In previous work, we have shown how these charge transport theories can be unified in the single-level case by incorporating lifetime broadening into the second-order quantum master equation. Here, we extend our previous treatment by incorporating lifetime broadening in the spirit of the self-consistent Born approximation. By comparing both theories to numerically converged hierarchical-equations-of-motion results, we demonstrate that our novel self-consistent approach rectifies shortcomings of our earlier framework, which are present especially in the case of relatively strong electron-vibrational coupling. We also discuss circumstances under which the theory developed here simplifies to the generalized theory developed in our earlier work. Finally, by considering the high-temperature limit of our new self-consistent treatment, we show how lifetime broadening can also be self-consistently incorporated into Marcus theory. Overall, we demonstrate that the self-consistent approach constitutes a more accurate description of molecular conduction while retaining most of the conceptual simplicity of our earlier framework.

Ultrahigh-Vacuum Tip-Enhanced Raman Spectroscopy.

Molecule-surface interactions and processes are at the heart of many technologies, including heterogeneous catalysis, organic photovoltaics, and nanoelectronics, yet they are rarely well understood at the molecular level. Given the inhomogeneous nature of surfaces, molecular properties often vary among individual surface sites, information that is lost in ensemble-averaged techniques. In order to access such site-resolved behavior, a technique must possess lateral resolution comparable to the size of surface sites under study, analytical power capable of examining chemical properties, and single-molecule sensitivity. Tip-enhanced Raman spectroscopy (TERS), wherein light is confined and amplified at the apex of a nanoscale plasmonic probe, meets these criteria. In ultrahigh vacuum (UHV), TERS can be performed in pristine environments, allowing for molecular-resolution imaging, low-temperature operation, minimized tip and molecular degradation, and improved stability in the presence of ultrafast irradiation. The aim of this review is to give an overview of TERS experiments performed in UHV environments and to discuss how recent reports will guide future endeavors. The advances made in the field thus far demonstrate the utility of TERS as an approach to interrogate single-molecule properties, reactions, and dynamics with spatial resolution below 1 nm.

Modeling optical coupling of plasmons and inhomogeneously broadened emitters.

Optically coupling quantum emitters to nanoparticles provides the foundation for many plasmonic applications. Including quantum mechanical effects within the calculations can be crucial for designing new devices, but classical approximations are sometimes sufficient. Comprehending how the classical and quantum mechanical descriptions of quantum emitters alter their calculated optical response will lead to a better understanding of how to design devices. Here, we describe how the semiclassical Maxwell-Liouville method can be used to calculate the optical response from inhomogeneously broadened states. After describing the Maxwell-Liouville algorithm, we use the method to study the photon echoes from quantum dots and compare the results against analytical models. We then modify the quantum dot's state distribution to match a PbS 850 nm quantum dot's absorption spectra to see how the complete quasi-band structure affects their coupling to gold nanoislands. Finally, we compare the results with previously published work to demonstrate where the complete quantum dot description is necessary.

Probing Molecular-Scale Catalytic Interactions between Oxygen and Cobalt Phthalocyanine Using Tip-Enhanced Raman Spectroscopy.

Ultrahigh vacuum tip-enhanced Raman spectroscopy (UHV-TERS) is used to investigate adsorption of molecular oxygen (O2) on cobalt(II) phthalocyanine (CoPc) supported on Ag(111) single crystal surfaces, which is the initial step for the oxygen reduction reaction (ORR) using metal Pc catalysts. Two adsorption configurations are primarily observed, assigned as O2/CoPc/Ag(111) and O/CoPc/Ag(111) based on scanning tunneling microscopy (STM) imaging, TERS, isotopologue substitution, and density functional theory (DFT) calculations. Distinct vibrational features are observed for different adsorption configurations such as the 18O-18O stretching frequency at 1151 cm-1 for O2/CoPc/Ag(111), and Co-16O and Co-18O vibrational frequencies at 661 and 623 cm-1, respectively, for O/CoPc/Ag(111). DFT calculations show vibrational mode coupling of O-O and Co-O vibrations to the Pc ring, resulting in different symmetries of oxygen-related normal modes. This study establishes UHV-TERS as a chemically sensitive tool for probing catalytic systems at the molecular scale.

Photoinduced Plasmon-Driven Chemistry in trans-1,2-Bis(4-pyridyl)ethylene Gold Nanosphere Oligomers.

Continuous wave (CW) pump-probe surface-enhanced Raman spectroscopy (SERS) is used to examine a range of plasmon-driven chemical behavior in the molecular SERS signal of trans-1,2-bis(4-pyridyl)ethylene (BPE) adsorbed on individual Au nanosphere oligomers (viz., dimers, trimers, tetramers, etc.). Well-defined new transient modes are caused by high fluence CW pumping at 532 nm and are monitored on the seconds time scale using a low intensity CW probe field at 785 nm. Comparison of time-dependent density functional theory (TD-DFT) calculations with the experimental data leads to the conclusion that three independent chemical processes are operative: (1) plasmon-driven electron transfer to form the BPE anion radical; (2) BPE hopping between two adsorption sites; and (3) trans-to- cis-BPE isomerization. Resonance Raman and electron paramagnetic resonance (EPR) spectroscopy measurements provide further substantiation for the observation of an anion radical species formed via a plasmon-driven electron transfer reaction. Applications of these findings will greatly impact the design of novel plasmonic devices with the future ability to harness new and efficient energetic pathways for both chemical transformation and photocatalysis at the nanoscale level.

Nonconservative Forces via Quantum Reservoir Engineering.

A systematic approach is given for engineering dissipative environments that steer quantum wave packets along desired trajectories. The methodology is demonstrated with several illustrative examples: environment-assisted tunneling, trapping, effective mass assignment, and pseudorelativistic behavior. Nonconservative stochastic forces do not inevitably lead to decoherence-we show that purity can be well preserved. These findings highlight the flexibility offered by nonequilibrium open quantum dynamics.

Unified theory of plasmon-induced resonance energy transfer and hot electron injection processes for enhanced photocurrent efficiency.

Plasmons in metal nanoparticles (MNPs) promise to enhance solar energy conversion in semiconductors. Two essential mechanisms of enhancement in the near-field regime are hot electron injection (HEI) and plasmon-induced resonance energy transfer (PIRET). Individual studies of both mechanisms indicate that the PIRET efficiency is limited by the short lifetime of the plasmon, whereas the hot electrons result from the plasmon decay. The development of a unified theory of the coupled HEI and PIRET processes is fundamentally interesting and necessary for making reliable predictions but is complicated by the multiple interactions between various components that participate in the enhancement process. In this paper, we use the model-Hamiltonian approach to develop a combined theoretical framework including both PIRET and HEI. The coupled dynamics as well as the time evolution of hot electron energy distribution are studied. The theory further predicts an interference-induced asymmetry in the spectral dependence of PIRET, which can be used to distinguish it from HEI. As the relative contributions of PIRET and HEI strongly depend on the size of the MNPs, this presents itself as a simple route to control the strength of their contributions. The results presented here can further guide future applications of plasmonic solar energy harvesting.

Emergence of Landauer transport from quantum dynamics: A model Hamiltonian approach.

The Landauer expression for computing current-voltage characteristics in nanoscale devices is efficient but not suited to transient phenomena and a time-dependent current because it is applicable only when the charge carriers transition into a steady flux after an external perturbation. In this article, we construct a very general expression for time-dependent current in an electrode-molecule-electrode arrangement. Utilizing a model Hamiltonian (consisting of the subsystem energy levels and their electronic coupling terms), we propagate the Schrödinger wave function equation to numerically compute the time-dependent population in the individual subsystems. The current in each electrode (defined in terms of the rate of change of the corresponding population) has two components, one due to the charges originating from the same electrode and the other due to the charges initially residing at the other electrode. We derive an analytical expression for the first component and illustrate that it agrees reasonably with its numerical counterpart at early times. Exploiting the unitary evolution of a wavefunction, we construct a more general Landauer style formula and illustrate the emergence of Landauer transport from our simulations without the assumption of time-independent charge flow. Our generalized Landauer formula is valid at all times for models beyond the wide-band limit, non-uniform electrode density of states and for time and energy-dependent electronic coupling between the subsystems. Subsequently, we investigate the ingredients in our model that regulate the onset time scale of this steady state. We compare the performance of our general current expression with the Landauer current for time-dependent electronic coupling. Finally, we comment on the applicability of the Landauer formula to compute hot-electron current arising upon plasmon decoherence.

Observation of Single Molecule Plasmon-Driven Electron Transfer in Isotopically Edited 4,4'-Bipyridine Gold Nanosphere Oligomers.

We clarify mechanistic questions regarding plasmon-driven chemistry and nanoscale photocatalysis within optically confined near-field plasmonic systems. Using surface-enhanced Raman scattering (SERS), we directly monitor the photoinduced reaction dynamics of 4,4'-bipyridine molecules, localized in plasmonic hot spots within individual gold nanosphere oligomers. Our experiment generates surface electrons from the gold nanoparticle using an intense off-molecular resonance continuous wave pump field, and detects radical anion products via SERS. This is done by adopting a dual-wavelength spectroscopic approach. Empirical evidence of plasmon-driven electron transfer is provided for the first time by direct detection of the 4,4'-bipyridine radical anion species localized in the plasmonic hot spots of individual gold nanosphere oligomers, corroborated by open-shell density functional theory calculations. An isotopologue approach using both protonated and deuterated 4,4'-bipyridine molecules demonstrates the single molecule response of plasmon-driven electron transfer occurring in single nanosphere oligomer systems with a 3% yield, a phenomenon unobserved in ensemble measurements under analogous experimental conditions. This mechanism has broad applicability to using nanoscale chemical reactors for surface redox reactions on the subnanometer scale.

Probing Intermolecular Vibrational Symmetry Breaking in Self-Assembled Monolayers with Ultrahigh Vacuum Tip-Enhanced Raman Spectroscopy.

Ultrahigh vacuum tip-enhanced Raman spectroscopy (UHV-TERS) combines the atomic-scale imaging capability of scanning probe microscopy with the single-molecule chemical sensitivity and structural specificity of surface-enhanced Raman spectroscopy. Here, we use these techniques in combination with theory to reveal insights into the influence of intermolecular interactions on the vibrational spectra of a N-N'-bis(2,6-diisopropylphenyl)-perylene-3,4:9,10-bis(dicarboximide) (PDI) self-assembled monolayer adsorbed on single-crystal Ag substrates at room temperature. In particular, we have revealed the lifting of a vibrational degeneracy of a mode of PDI on Ag(111) and Ag(100) surfaces, with the most strongly perturbed mode being that associated with the largest vibrational amplitude on the periphery of the molecule. This work demonstrates that UHV-TERS enables direct measurement of molecule-molecule interaction at nanoscale. We anticipate that this information will advance the fundamental understanding of the most important effect of intermolecular interactions on the vibrational modes of surface-bound molecules.

Laser-Controlled Torsions: Four-Dimensional Theory and the Validity of Reduced Dimensionality Models.

A multitude of possible applications along with unique coherence, chirality, and symmetry properties makes the control of molecular torsion with moderately strong, nonresonant laser pulses a fascinating subject. A description of combined rotation and torsion requires at least four angular degrees of freedom, which is challenging for the majority of systems. Lower-dimensional models have been proposed but also questioned. Here, we develop a four-dimensional model for the coupled rotational-torsional motions of molecules consisting of two identical moieties. By comparing four-dimensional calculations with a two-dimensional model, we define conditions under which the lower-dimensional model is valid. In particular, we point to the crucial role of coordinate dependence of the polarizability tensor. Our results do not agree with those of previous four-dimensional calculations but support the conclusions of recent experiments.

No Thermalization without Correlations.

The proof of the long-standing conjecture is presented that Markovian quantum master equations are at odds with quantum thermodynamics under conventional assumptions of fluctuation-dissipation theorems (implying a translation invariant dissipation). Specifically, except for identified systems, persistent system-bath correlations of at least one kind, spatial or temporal, are obligatory for thermalization. A systematic procedure is proposed to construct translation invariant bath models producing steady states that well approximate thermal states. A quantum optical scheme for the laboratory assessment of the developed procedure is outlined.

Development and application of a 2-electron reduced density matrix approach to electron transport via molecular junctions.

Can an electronic device be constructed using only a single molecule? Since this question was first asked by Aviram and Ratner in the 1970s [Chem. Phys. Lett. 29, 277 (1974)], the field of molecular electronics has exploded with significant experimental advancements in the understanding of the charge transport properties of single molecule devices. Efforts to explain the results of these experiments and identify promising new candidate molecules for molecular devices have led to the development of numerous new theoretical methods including the current standard theoretical approach for studying single molecule charge transport, i.e., the non-equilibrium Green's function formalism (NEGF). By pairing this formalism with density functional theory (DFT), a wide variety of transport problems in molecular junctions have been successfully treated. For some systems though, the conductance and current-voltage curves predicted by common DFT functionals can be several orders of magnitude above experimental results. In addition, since density functional theory relies on approximations to the exact exchange-correlation functional, the predicted transport properties can show significant variation depending on the functional chosen. As a first step to addressing this issue, the authors have replaced density functional theory in the NEGF formalism with a 2-electron reduced density matrix (2-RDM) method, creating a new approach known as the NEGF-RDM method. 2-RDM methods provide a more accurate description of electron correlation compared to density functional theory, and they have lower computational scaling compared to wavefunction based methods of similar accuracy. Additionally, 2-RDM methods are capable of capturing static electron correlation which is untreatable by existing NEGF-DFT methods. When studying dithiol alkane chains and dithiol benzene in model junctions, the authors found that the NEGF-RDM predicts conductances and currents that are 1-2 orders of magnitude below those of B3LYP and M06 DFT functionals. This suggests that the NEGF-RDM method could be a viable alternative to NEGF-DFT for molecular junction calculations.

Nanoscale Chemical Imaging of a Dynamic Molecular Phase Boundary with Ultrahigh Vacuum Tip-Enhanced Raman Spectroscopy.

Nanoscale chemical imaging of a dynamic molecular phase boundary has broad implications for a range of problems in catalysis, surface science, and molecular electronics. While scanning probe microscopy (SPM) is commonly used to study molecular phase boundaries, its information content can be severely compromised by surface diffusion, irregular packing, or three-dimensional adsorbate geometry. Here, we demonstrate the simultaneous chemical and structural analysis of N-N'-bis(2,6-diisopropylphenyl)-1,7-(4'-t-butylphenoxy)perylene-3,4:9,10-bis(dicarboximide) (PPDI) molecules by UHV tip-enhanced Raman spectroscopy. Both condensed and diffusing domains of PPDI coexist on Ag(100) at room temperature. Through comparison with time-dependent density functional theory simulations, we unravel the orientation of PPDI molecules at the dynamic molecular domain boundary with unprecedented ∼4 nm spatial resolution.

Conformational Contrast of Surface-Mediated Molecular Switches Yields Ångstrom-Scale Spatial Resolution in Ultrahigh Vacuum Tip-Enhanced Raman Spectroscopy.

Tip-enhanced Raman spectroscopy (TERS) combines the ability of scanning probe microscopy (SPM) to resolve atomic-scale surface features with the single-molecule chemical sensitivity of surface-enhanced Raman spectroscopy (SERS). Here, we report additional insights into the nature of the conformational dynamics of a free-base porphyrin at room temperature adsorbed on a metal surface. We have interrogated the conformational switch between two metastable surface-mediated isomers of meso-tetrakis(3,5-ditertiarybutylphenyl)-porphyrin (H2TBPP) on a Cu(111) surface. At room temperature, the barrier between the porphyrin ring buckled up/down conformations of the H2TBPP-Cu(111) system is easily overcome, and a 2.6 Å lateral resolution by simultaneous TERS and STM analysis is achieved under ultrahigh vacuum (UHV) conditions. This work demonstrates the first UHV-TERS on Cu(111) and shows TERS can unambiguously distinguish the conformational differences between neighboring molecules with Ångstrom-scale spatial resolution, thereby establishing it as a leading method for the study of metal-adsorbate interactions.

Unraveling near-field and far-field relationships for 3D SERS substrates--a combined experimental and theoretical analysis.

Simplicity and low cost has positioned inkjet paper- and fabric-based 3D substrates as two of the most commonly used surface-enhanced Raman spectroscopy (SERS) platforms for the detection and the identification of chemical and biological analytes down to the nanogram and femtogram levels. The relationship between far-field and near-field properties of these 3D SERS platforms remains poorly understood and warrants more detailed characterization. Here, we investigate the extremely weak optical scattering observed from commercial and home-fabricated paper-, as well as fabric-based 3D SERS substrates. Using wavelength scanned surface-enhanced Raman excitation spectroscopy (WS-SERES) and finite-difference time-domain (FDTD) calculations we were able to determine their near-field SERS properties and correlate them with morphological and far-field properties. It was found that nanoparticle dimers, trimers, and higher order nanoparticle clusters primarily determine the near-field properties of these substrates. At the same time, the far-field response of 3D SERS substrates either originates primarily from the monomers or cannot be clearly defined. Using FDTD we demonstrate that LSPR bands of nanoparticle aggregates near perfectly overlap with the maxima of the near-field surface-enhanced Raman scattering responses of the 3D SERS substrates. This behaviour of far-field spectroscopic properties and near-field surface-enhanced Raman scattering has not been previously observed for 2D SERS substrates, known as nanorod arrays. The combination of these analytical approaches provides a full spectroscopic characterization of 3D SERS substrates, while FDTD simulation can be used to design new 3D SERS substrates with tailored spectral characteristics.