Nonadiabatic vibronic dynamics as a tool. From surface nanochemistry to coherently driven molecular machines

Resonances are ubiquitous in molecular heterojunctions and in scanning tunneling microscopy (STM) experiments. In the former environment, resonance tunneling is essential for favorable wire-length-dependence of the conductance and is often the mechanism underlying conductance enhancement through application of a gate voltage. In the latter environment, resonance tunneling has served to develop a powerful vibrational spectroscopy. Resonance conductance is often strongly nonadiabatic; in the course of the tunneling event, electron energy is channelled into vibrational modes and triggers molecular dynamics. The qualitative physics underlying current-driven, resonance-mediated dynamics in molecular electronics is very simple, and is familiar from related phenomena such as gas phase electron-molecule scattering and photochemistry on conducting surfaces. Equilibrium displacement between the initial and resonant states translates into vibronic coupling in the language of the Marcus theory of electron transfer; it produces a nonstationary superposition in the nuclear subspace that evolves during the resonance lifetime. Upon relaxation the system is internally excited and interesting dynamics is likely to ensue. While the underlying physics is very general, the single-molecule STM and molecular heterojunction environments open unique and exciting opportunities. The former introduces the possibility of determining resonance lifetimes through fit of experimental voltage dependencies to a quantum mechanical theory. The latter introduces the possibility of developing coherently driven molecular machines, a new form of nanolithography, and a new means of manipulating the conductivity of molecular-scale devices. We briefly review the theory of current-driven dynamics in molecular-scale devices, discuss the results of ongoing research on surface nanochemistry and molecular machines, and sketch a variety of potential applications.     

The Role of Charge Localization in Current-Driven Dynamics

We explore the role of charge localization in current-triggered, resonance-mediated, dynamical events in molecular junctions. To that end we use a simple model for a molecular rattle, a Li⁺C₉H⁻₉ zwitterion attached between two metal clusters. By varying the size of the metal clusters we systematically vary the degree of delocalization of the electronic orbitals underlying the resonant current, and thus can draw general conclusions regarding the effect of delocalization on dynamical processes induced by resonance inelastic current in molecular electronics. In the small cluster limit, we find interesting quantum dynamics in the nuclear subspace, corresponding to coherent tunneling of the wave packet through the barrier of an asymmetric double-well potential. These dynamics are rapidly damped with increasing charge delocalization in extended systems.     

A Methionine Chemical Shift Based Order Parameter Characterizing Global Protein Dynamics

Coupling of side chain dynamics over long distances is an important component of allostery. Methionine side chains show the largest intrinsic flexibility among methyl-containing residues but the actual degree of conformational averaging depends on the proximity and mobility of neighboring residues. The ¹³C NMR chemical shifts of the methyl groups of methionine residues located at long distances in the same protein show a similar scaling with respect to the values predicted from the static X-ray structure by quantum methods. This results in a good linear correlation between calculated and observed chemical shifts. The slope is protein dependent and ranges from zero for the highly flexible calmodulin to 0.7 for the much more rigid calcineurin catalytic domain. The linear correlation is indicative of a similar level of side-chain conformational averaging over long distances, and the slope of the correlation line can be interpreted as an order parameter of the global side-chain flexibility.     

On the generalized Hartman effect presumption in semiconductors and photonic structures

We analyze different examples to show that the so-called generalized Hartman effect is an erroneous presumption. The results obtained for electron tunneling and transmission of electromagnetic waves through superlattices and Bragg gratings show clearly the resonant character of the phase time behavior so that a generalized Hartman effect is not expected to occur. A reinterpretation of the experimental results in double Bragg gratings is proposed.     

Effect of self-assembled InAs islands on the interfacial roughness of optical-switched resonant tunneling diode

ABSTRACT: Embedding a quantum dot [QD] layer between the double barriers of resonant tunneling diode [RTD] is proved to be an effective method to increase the sensitivity of QD-RTD single-photon detector. However, the interfacial flatness of this device would be worsened due to the introduction of quantum dots. In this paper, we demonstrate that the interfacial quality of this device can be optimized through increasing the growth temperature of AlAs up barrier. The glancing incidence X-ray reflectivity and the high-resolution transmission electron microscopy measurements show that the interfacial smoothness has been greatly improved, and the photo-luminescence test indicated that the InAs QDs were maintained at the same time. The smoother interface was attributed to the evaporation of segregated indium atoms at InGaAs surface layer. PACS: 73.40.GK, 73.23._b, 73.21.La, 74.62.Dh.     

Tunneling Quantum Dynamics in Ammonia

Ammonia is a well-known example of a two-state system and must be described in quantum-mechanical terms. In this article, we will explain the tunneling phenomenon that occurs in ammonia molecules from the perspective of trajectory-based quantum dynamics, rather than the usual quantum probability perspective. The tunneling of the nitrogen atom through the potential barrier in ammonia is not merely a probability problem; there are underlying reasons and mechanisms explaining why and how the tunneling in ammonia can happen. Under the framework of quantum Hamilton mechanics, the tunneling motion of the nitrogen atom in ammonia can be described deterministically in terms of the quantum trajectories of the nitrogen atom and the quantum forces applied. The vibrations of the nitrogen atom about its two equilibrium positions are analyzed in terms of its quantum trajectories, which are solved from the Hamilton equations of motion. The vibration periods are then computed by the quantum trajectories and compared with the experimental measurements.     

Dependence of the electrical and optical properties on growth interruption in AlAs/In0.53Ga0.47As/InAs resonant tunneling diodes

ABSTRACT: The dependence of interface roughness of pseudomorphic AlAs/In0.53Ga0.47As/InAs resonant tunneling diodes [RTDs] grown by molecular beam epitaxy on interruption time was studied by current-voltage [I-V] characteristics, photoluminescence [PL] spectroscopy, and transmission electron microscopy [TEM]. We have observed that a splitting in the quantum-well PL due to island formation in the quantum well is sensitive to growth interruption at the AlAs/In0.53Ga0.47As interfaces. TEM images also show flatter interfaces with a few islands which only occur by applying an optimum value of interruption time. The symmetry of I-V characteristics of RTDs with PL and TEM results is consistent because tunneling current is highly dependent on barrier thickness and interface roughness.     

Mode-selective stereomutation tunneling as compared to parity violation in hydrogen diselenide isotopomers 1,2,3H280Se2

We present quantitative calculations of the mode-selective stereomutation tunneling in the chiral hydrogen diselenide isotopomers X₂Se₂ with X = H, D, and T. The torsional tunneling stereomutation dynamics were investigated with a quasi-adiabatic channel quasi-harmonic reaction path Hamiltonian approach, which treats the torsional motion anharmonically in detail and all remaining coordinates as harmonic (but anharmonically coupled to the reaction coordinate). We also investigated the influence of the excitation of fundamental modes on the stereomutation dynamics and predict which modes should be promoting or inhibiting. Our stereomutation dynamics results and the influence of parity violation on these are discussed in relation to our recent investigations for the analogous molecules H₂O₂, HSOH, H₂S₂, and Cl₂S₂. The electronic potential energy barrier heights for the torsional motion of hydrogen diselenide are similar to those of HSOH, whereas the torsional tunneling splittings are similar to the corresponding values of HSSH. The ground-state torsional tunneling splittings calculated here for D₂Se₂ are of the same order as the parity-violating energy difference reported by Laerdahl and Schwerdtfeger (Phys. Rev. A 1999, 60, 4439), whereas for T₂Se₂ the corresponding tunneling splitting is about three orders of magnitude smaller.     

Temperature effects during practical operation of microfluidic chips

The temperature dependent fluorescence of Rhodamine B was used to investigate the temperature effect of several system parameters in a microfluidic chip. This was combined with computational fluid dynamics calculations. Limited air movement over the chip had no significant effect on the temperature of the fluid running through the chip. Also, fluid flow through the channels at had no effect on the chip temperature or heating and cooling dynamics. The temperature varied greatly over the length of the chip. During transient operation of the chip, the heat up and cool down rates varied over the chip, and were dependent on the distance to the heater. The thermal time constant for heat up was four to five times lower than for cool down. The results can be used as tools for operating a temperature controlled microfluidic chip.     

Molecular Dynamics Study of the Mechanism of Ion Diffusion in an Na2O–ZnO–P2O5 Melt

The specific features of the dynamics of structure-forming ions in an Na₂O · ZnO · P₂O₅ melt are studied by the molecular dynamics method in the ion approximation of the interparticle interaction potential. It is shown that the oxygen diffusion mechanism in the pyrophosphate system is generally similar to that investigated previously for silicate systems. The main difference of the former mechanism is the absence of overcoordinated defect phosphorus–oxygen complexes. Owing to the use of long phase trajectories, the oxygen diffusion scenarios involving four tetrahedra are detected for the first time. It is demonstrated that the dominant movements of the zinc ion are long (no shorter than 0.25 nm) jumps, which makes it possible to retain a strong correlation of the relative positions of these ions over long (about 0.6 nm) distances.     

Temperature dependence of time-resolved photoluminescence in closely packed alignment of Si nanodisks with SiC barriers

We study the temperature dependence of time-resolved photoluminescence (PL) in closely packed alignment of Si nanodisks (NDs) with SiC barriers, fabricated by neutral beam etching using bio-nano-templates. The PL time profile indicates three decaying components with different decay times. The PL intensities in the two slower decaying components depend strongly on temperature. These temperature dependences of the PL intensity can be quantitatively explained by a three-level model with thermal activation energies of 410 and 490 meV, depending on the PL components. The activation energies explain PL quenching due to thermal escape of electrons from individual NDs. This thermal escape affects the PL decay times above 250 K. Dark states of photo-excited carriers originating from the separate localization of electron and hole into different NDs are elucidated with the localization energies of 70 and 90 meV. In contrast, the dynamics of the fastest PL decaying component is dominated by electron tunneling among NDs, where the PL intensity and decay time are constant for temperature.     

Thermal stability enhancement of Cr2AlC coatings on Zr by utilizing a double layer diffusion barrier

Decomposition of Cr₂AlC deposited onto a Zr substrate and vacuum-annealed is observed at 800 °C as Al diffuses from the MAX phase into the Zr substrate. A double layer of ZrN and AlN has been predicted by CALPHAD calculations to act as diffusion barrier between the Zr substrate and Cr₂AlC. Experimental thermal stability investigations corroborate this prediction by confirming that the proposed double layer diffusion barrier coatings suppress the decomposition of Cr₂AlC for one hour at temperatures of up to 1000 °C.     

A theoretical investigation on the transport properties of overlapped graphene nanoribbons

The transport characteristics of overlapped junctions of Zigzag Graphene NanoRibbons (ZGNRs) are simulated and analyzed using Non-Equilibrium Green’s function combined with the Density Functional Theory. It is found that the carriers pass through an overlapped junction via several different energy states by tunneling process. In general, the current passing across the junction is mainly due to tunneling of carriers between many quasi-bound states. Meanwhile, few transmissions are observed between individual states. The latter behaviors cannot be explained by quasi-bound states; however, they are interpreted as the states which show long range resonance phenomenon. A combination of these states results in complex variations of transmission characteristics. These variations introduce several negative differential resistances by increasing the voltage across the junction of ZGNRs. In other words, misalignment in the states along the junction leads to periodic changes in the coupling of the quasi-bound states and long range resonant states. This makes an oscillation in the current voltage characteristics of the overlapped junction in ZGNRs. Consequently, the overlapped junction in ZGNR has a lower electrical transport comparing to that of an ideal (non-overlapped) ZGNR.     

Dynamical resonances in the fluorine atom reaction with the hydrogen molecule

[Reaction: see text]. The concept of transition state has played a crucial role in the field of chemical kinetics and reaction dynamics. Resonances in the transition state region are important in many chemical reactions at reaction energies near the thresholds. Detecting and characterizing isolated reaction resonances, however, have been a major challenge in both experiment and theory. In this Account, we review the most recent developments in the study of reaction resonances in the benchmark F + H 2 --> HF + H reaction. Crossed molecular beam scattering experiments on the F + H 2 reaction have been carried out recently using the high-resolution, highly sensitive H-atom Rydberg tagging technique with HF rovibrational states almost fully resolved. Pronounced forward scattering for the HF (nu' = 2) product has been observed at the collision energy of 0.52 kcal/mol in the F + H 2 (j = 0) reaction. Quantum dynamical calculations based on two new potential energy surfaces, the Xu-Xie-Zhang (XXZ) surface and the Fu-Xu-Zhang (FXZ) surface, show that the observed forward scattering of HF (nu' = 2) in the F + H 2 reaction is caused by two Feshbach resonances (the ground resonance and first excited resonance). More interestingly, the pronounced forward scattering of HF (nu' = 2) at 0.52 kcal/mol is enhanced considerably by the constructive interference between the two resonances. In order to probe the resonance potential more accurately, the isotope substituted F + HD --> HF + D reaction has been studied using the D-atom Rydberg tagging technique. A remarkable and fast changing dynamical picture has been mapped out in the collision energy range of 0.3-1.2 kcal/mol for this reaction. Quantum dynamical calculations based on the XXZ surface suggest that the ground resonance on this potential is too high in comparison with the experimental results of the F + HD reaction. However, quantum scattering calculations on the FXZ surface can reproduce nearly quantitatively the resonance picture of the F + HD reaction observed in the experiment. It is clear that the dynamics of the F + HD reaction below the threshold was dominated by the ground resonance state. Furthermore, the forward scattering HF (nu' = 3) channel from the F + H 2 ( j = 0) reaction was investigated and was attributed mainly to a slow-down mechanism over the centrifugal exit barrier, with small contributions from a shape resonance mechanism in a narrow collision energy range. A striking effect of the reagent rotational excitation on resonance was also observed in F + H 2 ( j = 1), in comparison with F + H 2 ( j = 0). From these concerted experimental and theoretical studies, a clear physical picture of the reaction resonances in this benchmark reaction has emerged, providing a textbook example of dynamical resonances in elementary chemical reactions.     

Molecular dynamics simulation of cis-1,4-polybutadiene. 1. Comparison with experimental data for static and dynamic properties

Molecular dynamics (MD) calculations of cis-1,4-polybutadiene in bulk amorphous phase were performed under constant pressure and constant temperature conditions. The static and dynamic properties were evaluated from the results of MD calculations. The obtained density and coefficient of thermal expansion are in good agreement with experimental data. The feature of the calculated static structure factor is similar to the observed one. Molecular motion is examined with mean square displacements and intermediate scattering functions. An onset of a new motion, which corresponds to so-called fast process, was clearly observed in the temperature dependence of the mean square displacement above 100 K. The dynamic structure factors obtained by the Fourier transformation of the intermediate scattering functions are compared with those obtained from quasielastic neutron scattering measurements. The peaks corresponding to the elastic scattering and the low energy excitation at around 2 meV are reproduced in the dynamic structure factors. The excessive intensity observed in the dynamic structure factor, which corresponds to the fast process, is also reproduced above 140 K in our simulation.     

Impact of deposit aging and surface roughness on thermal fouling: Distributed model

A kinetic model was recently proposed to describe the effect of aging on deposit thermal conductivity and the thermal performance of a shell‐and‐tube heat exchanger undergoing crude oil fouling. The model is adapted for implementation within a dynamic, distributed system with spatial and temporal distributions, relaxing several of the previous assumptions. The evolution of surface roughness is also considered, using conjectural linear and asymptotic functions. Simulations are performed for a single tube representative of a refinery exchanger. The results demonstrate the substantial effects over time of aging and roughness on heat transfer and pressure drop. Roughness effects yield apparently negative initial fouling resistances, as reported in some experimental tests. The importance of accounting for roughness dynamics in short time scale pilot plant scale tests and aging over longer time scales in industrial applications is highlighted. © 2010 American Institute of Chemical Engineers AIChE J, 2010     

Spatially resolved electronic inhomogeneities of graphene due to subsurface charges

We probe the local inhomogeneities in the electronic properties of exfoliated graphene due to the presence of charged impurities in the SiO₂ substrate using a combined scanning tunneling and electrostatic force microscope. Contact potential difference measurements using electrostatic force microscopy permit us to obtain the average charge density but it does not provide enough resolution to identify individual charges. We find that the tunneling current decay constant, which is related to the local tunneling barrier height, enables one to probe the electronic properties of graphene distorted at the nanometer scale by individual charged impurities. We observe that such inhomogeneities do not show long-range ordering and their surface density obtained by direct counting is consistent with the value obtained by macroscopic charge density measurements. These microscopic perturbations of the carrier density significantly alter the electronic properties of graphene, and their characterization is essential for improving the performance of graphene based devices.