Theoretical and computational methods for tip- and surface-enhanced Raman scattering.

Raman spectroscopy is a versatile tool for acquiring molecular structure information. The incorporation of plasmonic fields has significantly enhanced the sensitivity and resolution of surface-enhanced Raman scattering (SERS) and tip-enhanced Raman spectroscopy (TERS). The strong spatial confinement effect of plasmonic fields has challenged the conventional Raman theory, in which a plane wave approximation for the light has been adopted. In this review, we comprehensively survey the progress of a generalized theory for SERS and TERS in the framework of effective field Hamiltonian (EFH). With this approach, all characteristics of localized plasmonic fields can be well taken into account. By employing EFH, quantitative simulations at the first-principles level for state-of-the-art experimental observations have been achieved, revealing the underlying intrinsic physics in the measurements. The predictive power of EFH is demonstrated by several new phenomena generated from the intrinsic spatial, momentum, time, and energy structures of the localized plasmonic field. The corresponding experimental verifications are also carried out briefly. A comprehensive computational package for modeling of SERS and TERS at the first-principles level is introduced. Finally, we provide an outlook on the future developments of theory and experiments for SERS and TERS.

Enhancing the thermopower of single-molecule junctions by edge substitution effects.

Heteroatom substitution and anchoring groups have an important impact on the thermoelectric properties of single-molecule junctions. Herein, thermoelectric properties of several anthracene derivative based single-molecule junctions are studied by means of first-principles calculations. In particular, we pay great attention to the edge substitution effects and find that edge substitution with nitrogen can induce a transmission peak near the Fermi energy, leading to large transmission coefficients and electrical conductance at the Fermi energy. Additionally, the steep shape of the transmission function gives rise to a high Seebeck coefficient. Therefore, an enhanced power factor can be expected. The robustness of this edge substitution effect has been examined by altering the electrode distance and introducing heteroatoms at different positions. The enhancement of the power factor due to edge substitution makes the studied single-molecule junction a promising candidate for efficient thermoelectric devices.

Regulation of π-π interactions between single aromatic molecules by bias voltage.

π-stacking interaction, as a fundamental type of intermolecular interaction, plays a crucial role in generating new functional molecules, altering the optoelectronic properties of materials, and maintaining protein structural stability. However, regulating intermolecular π-π interactions at the single-molecule level without altering the molecular conformation as well as the chemical properties remains a significant challenge. To this end, via conductance measurement with thousands of single molecular junctions employing a series of aromatic molecules, we demonstrate that the π-π coupling between neighboring aromatic molecules with rigid structures in a circuit can be greatly enhanced by increasing the bias voltage. We further reveal that this universal regulating effect of bias voltage without molecular conformational variation originates from the increases of the molecular dipole upon an applied electric field. These findings not only supply a non-destructive method to regulate the intermolecular interactions offering an approach to modulate the electron transport through a single molecular junction, but also deepen the understanding of the mechanism of π-π interactions.

Adsorption properties of a paracyclophane molecule on NaCl/Au surfaces: a first-principles study.

Ultrathin insulating layers are commonly applied in scanning tunneling microscope (STM) measurements on molecular systems to preserve the intrinsic properties of a sample. We examine in the present work the adsorption properties of a double-decker 3,3-paracyclophane (PCP) molecule supported on Au surfaces with thin NaCl monolayers (MLs) as the decoupling spacer by using first-principles calculations. The interactions between the adsorbed molecule and the substrate were analyzed in terms of the adsorption energy, dispersion interactions, charge transfer, and molecular structure changes. The simulation results show that the presence of NaCl can significantly reduce the adsorption energy as well as the charge transfer between the molecule and the substrate. Detailed analysis of the differential charge density and partial charge density of states indicates that three MLs of NaCl are sufficient to decouple the molecule from the Au substrate with no significant changes in the adsorption properties of the PCP with the further increase of the thickness of the NaCl spacer. These results could be helpful for the application of the interesting double-decker molecules as functional single-molecule devices where the intrinsic molecular properties need to be preserved.

Vibrationally-Resolved X-ray Photoelectron Spectra of Six Polycyclic Aromatic Hydrocarbons from First-Principles Simulations.

Vibrationally resolved C 1s X-ray photoelectron spectra (XPS) of a series of six polycyclic aromatic hydrocarbons (PAHs; phenanthrene, coronene, naphthalene, anthracene, tetracene, and pentacene) were computed by combining the full core hole density functional theory and the Franck-Condon simulations with the inclusion of the Duschinsky rotation effect. Simulated spectra of phenanthrene, coronene, and naphthalene agree well with experiments both in core binding energies (BEs) and profiles, which validate the accuracy of our predictions for the rest molecules with no high-resolution experiments. We found that three types of carbons i (inner C), p (peripheral C bonded to three C atoms), and h (peripheral C bonded to an H atom) show decreasing BEs. In linear PAHs (the latter four), h-type carbons further split into h1 or h2 (on inner or edge benzene ring) subtypes with chemical shifts of ca. 0.2-0.4 eV. All major Franck-Condon-active modes are characterized to be in-plane vibrations: low-frequency (<800 cm-1) C-C ring deformation modes play an essential role in determining the peak asymmetries; and for each h-type carbon a high-frequency (ca. 3600 cm-1) C*-H stretching mode is responsible for the high-energy tail. We found that core ionization leads to reduction of all C*-C and C*-H bond lengths and ring deformation with a definite direction. Based on theoretical spectra of four linear PAHs, we found asymptotic relations and anticipated possible spectral features for even larger linear PAHs. Our calculations provide accurate reference spectra for XPS characterizations of PAHs, which are useful in understanding the vibronic coupling effects in this family.

Ultrafast stimulated resonance Raman signatures of lithium polysulfides for shuttling effect characterization: An ab initio study.

The shuttling effect is a crucial obstacle to the practical deployment of lithium sulfur batteries (LSBs). This can be ascribed to the generation of lithium polysulfide (LiPS) redox intermediates that are soluble in the electrolyte. The detailed mechanism of the shuttling, including the chemical structures responsible for the loss of effective mass and the dynamics/kinetics of the redox reactions, are not clear so far. To obtain this microscopic information, characterization techniques with high spatial and temporal resolutions are required. Here, we propose that resonance Raman spectroscopy combined with ultrafast broadband pulses is a powerful tool to reveal the mechanism of the shuttling effect. By combining the chemical bond level spatial resolution of resonance Raman and the femtosecond scale temporal resolution of the ultrafast pulses, this novel technique holds the potential of capturing the spectroscopic fingerprints of the LiPS intermediates during the working stages of LSBs. Using ab initio simulations, we show that, in addition to the excitation energy selective enhancement, resonance Raman signals of different LiPS intermediates are also characteristic and distinguishable. These results will facilitate the real-time in situ monitoring of LiPS species and reveal the underlying mechanism of the shuttling effect.

Combined experimental and theoretical study on photoionization cross sections of benzonitrile and o/m/p-cyanotoluene.

Photoionization cross sections (PICSs) for the products of the reaction from CN with toluene, including benzonitrile and o/m/p-cyanotoluene, were obtained at photon energies ranging from ionization thresholds to 14 eV by tunable synchrotron vacuum ultraviolet photoionization mass spectrometry (SVUV-PIMS). Theoretical calculations based on the frozen-core Hartree-Fock approximation and Franck-Condon simulations were carried out to cross-verify the measured PICS. The results show that the photoionization cross sections of benzonitrile and cyanotoluene isomers are similar. The generalized charge decomposition analysis was used to investigate the components of the highest occupied molecular orbital (HOMO) and HOMO-1. It was found that the HOMO and HOMO-1 of benzonitrile and cyanotoluene isomers are dominated by the features of the benzene ring, indicating that the substitution of CN and methyl has a minor influence on the PICS of the studied molecules. The reported PICS on benzonitrile and cyanotoluene isomers in the present work could contribute to the near-threshold PIMS experiments and determine the ionization and dissociation rates in interstellar space for these crucial species. The theoretical analysis on characteristics of molecular orbitals provides clues to estimating the PICS of similar substituted aromatic compounds.

Theoretical assessment of vibrationally resolved C1s X-ray photoelectron spectra of simple cyclic molecules.

An interface between our in-house DynaVib package and quantum chemistry software Gamess-US is implemented for computing vibrationally-resolved K-edge X-ray photoelectron spectra (XPS) of molecules at the density functional theory level with both the full (FCH) and equivalent (ECH, or Z+1) core-hole approximations. To assess the influence of theoretical parameters (core-hole methods, vibronic coupling models, and basis sets), vibrationally-resolved C1s XPS of six simple cyclic molecules [furan, pyrrole, thiophene; benzene (C6H6 and C6D6); pyridine] were evaluated in the gas phase by both core-hole methods in combination with two time-independent vibronic coupling models, the Duschinsky rotation (DR) method and the linear coupling model (LCM). We achieved excellent/acceptable performance for FCH/Z+1 simulations in comparison with experiments. The most accurate method FCH-DR correctly reproduced all experimental features and gave an accuracy of ca. 0.2 eV in absolute binding energies (BEs). The choice of the vibronic model is less sensitive to that of electronic structure method. Results indicate that Z+1 overestimates the core-hole effect on the geometry of the ionization state.

Harvesting of surface plasmon polaritons: Role of the confinement factor.

Surface plasmon polaritons (SPPs) are propagating waves generated at the interface of a metal (metamaterial) and a dielectric. The intensity of SPPs often exponentially decays away from the surface, while their wavelengths can be tuned by the confinement effect. We present here a computational method based on quantum-mechanical theory to fully describe the interaction between confined SPPs and adsorbed molecules at the interface. Special attention has been paid to the roles of the confinement factor. Taking a prototype dye sensitized solar cell as an example, calculated results reveal that with the increase in the confinement factor in metal/dielectric interfaces, the breakdown of the conventional dipole approximation emerges, which allows efficient harvesting of SPPs with low excitation energies and, thus, increases the efficiency of the solar energy conversion by dye molecules. Furthermore, at the metamaterial/dielectric interface, SPPs with large confinement factors could directly excite the dye molecule from its ground singlet state to the triplet state, opening an entirely new channel with long-living carriers for the photovoltaic conversion. Our results not only provide a rigorous theory for the SPP-molecule interaction but also highlight the important role played by the momentum of the light in plasmon related studies.

Estimation for Runway Friction Coefficient Based on Multi-Sensor Information Fusion and Model Correlation.

Friction is a crucial factor affecting air accident occurrence on landing or taking off. Tire-runway friction directly contributes to aircraft stability on land. Therefore, an accurate friction estimation is a rising issue for all stakeholders. This paper summarizes the existing measurement methods, and a multi-sensor information fusion scheme is proposed to estimate the friction coefficient between the tire and the runway. Acoustic sensors, optical sensors, tread sensors, and other physical sensors form a sensor system that is used to measure friction-related parameters and fuse them through a neural network. So far, many attempts have been made to link the ground friction coefficient with the aircraft braking friction coefficient. The models that have been developed include the International Runway Friction Index (IRFI), Canada Runway Friction Index (CRFI), and other fitting models. Additionally, this paper attempts to correlate the output of the neural network (estimated friction coefficient) with the correlation model to predict the friction coefficient between the tire and the runway when the aircraft brakes. The sensor system proposed in this paper can be regarded as a mobile weather-runway-tire system, which can estimate the friction coefficient by integrating the runway surface conditions and the tire conditions, and fully consider their common effects. The role of the correlation model is to convert the ground friction coefficient to the grade of the aircraft braking friction coefficient and the information is finally reported to the pilots so that they can make better decisions.

Optomagnetic Effect Induced by Magnetized Nanocavity Plasmon.

We propose a new type of optomagnetic effect induced by a highly confined plasmonic field in a nanocavity. It is shown that a very large dynamic magnetic field can be generated as the result of the inhomogeneity of nanocavity plasmons, which can directly activate spin-forbidden transitions in molecules. The dynamic optomagnetic effects on optical transitions between states of different spin multiplicities are illustrated by first-principles calculations for C60. Remarkably, the intensity of spin forbidden singlet-to-triplet transitions can even be stronger than that of singlet-to-singlet transitions when the spatial distribution of plasmon is comparable with the molecular size. This approach not only offers a powerful optomagnetic means to rationally fabricate molecular excited states with different multiplicities but also provides a groundbreaking concept of the light-matter interaction that could lead to the observation of new physical phenomena and the development of new techniques.

Chiral Nanostructured Composite Films via Solvent-Tuned Self-Assembly and Their Enantioselective Performances.

Chiral nanostructures exhibited distinctive functions and attractive applications in complex biological systems, which demonstrated the subject of many outstanding research studies. In this work, various hierarchical composite film nanostructures were designed via supramolecular self-assembly using chiral amphiphilic glutamate derivatives and achiral porphyrin derivatives and their macroscopic enantioselective recognition properties were investigated. We have found that intermolecular hydrogen-bonding interactions between water (donor and acceptor) and N, N-dimethylformamide (DMF) as well as chloroform (CHCl3) (acceptor only) and DMF could subtly alter the molecular packing and significantly affected the supramolecular self-assembled nanostructures and triggered circular dichroism (CD) signal reversal. Present research work exemplified a feasible method to fabricate chiral flower-like and brick-like nanostructure films in different mixed solvents and large-scale chiral transfer from the molecular level to complex structures, which also provided a facile approach to identify certain l-/d-amino acids by means of contact angle detection using present obtained self-assembled composted films.

Histological improvement in chronic hepatitis B patients treated with bicyclol: real world experience.

BACKGROUND: Bicyclol, the most commonly-used liver hepatoprotective drug in China, is often selected to control disease progression in CHB patients who refuse anti-viral treatment. However, data on histological changes after bicyclol treatment in these patients are scarce. Therefore, this study has been conducted to find out whether bicyclol has good benefits of histological improvement in CHB patients who refuse anti-viral agents. METHODS: The demographic, clinical and pathological data were collected from CHB patients who received bicyclol from January 2010 to June 2016. Improvement in liver inflammation or fibrosis is defined as at least one-grade or one-stage decrease as measured by the Scheuer scoring system. Thirty patients treated with ETV for 48 weeks were chosen as a control group to compare the histological improvement between bicyclol and entecavir (ETV) after 48-week treatment. RESULTS: A total of 123 patients with CHB treated with bicyclol were included in this study. Paired liver biopsies were performed in 70 patients. Inter-biopsy interval was 17.44 ± 8.90 months (12-60 months). As shown by facts, 41.4% patients achieved liver inflammation improvement, while only 10.0% patients showed liver inflammation progression after bicyclol treatment. In regarding to liver fibrosis, as shown by facts, 28.6% patients achieved fibrosis improvement. More importantly, It was found that the proportions of patients with liver inflammation and fibrosis improvement were both not significantly lower than those in ETV group (53.3% vs 63.3 and 36.7% vs 43.4%). Most of patients (82.4%) with elevated baseline ALT became normal after bicyclol treatment. More importantly, as shown by the multi-variate analysis, the treatment course of bicyclol was an independent factor for liver inflammation improvement. With the HBeAg status adjusted, ALT and HBV-DNA quantity, the odds ratio (95% confidence interval) of patients with ≥48-week treatment was 5.756 (1.893,17.500) when compared with patients via < 48-week treatment. CONCLUSION: Bicyclol can improve liver inflammation and the ALT normalization rate of CHB patients, especially when the treatment course is prolonged. This has confirmed that bicyclol could control hepatitis activity, which might be a good choice for CHB patients who refuse anti-viral treatments.

On the spectral profile change in the Q band absorption spectra of metalloporphyrins (Mg, Zn, and Pd): A first-principles study.

We performed a systematic study of the vibrationally resolved absorption spectra in the Q band of three metalloporphyrins (Mg, Zn, and Pd) to understand the spectral changes in this series, including both the Franck-Condon (FC) and Herzberg-Teller (HT) contributions. The ground (S0) and the lowest singlet excited (S1) states were, respectively, simulated by the static and time-dependent density functional theory, with which the Duschinsky rotation effect was considered. Different functionals and basis sets were tested and compared with experiment. Results show that the long-range corrected functional CAM-B3LYP can nicely describe the spectral fingerprints of these metalloporphyrins, while the B3LYP functional significantly underestimates the FC contributions. We found that the absorption fine structures of these molecules are mainly caused by the HT vibronic couplings. The experimentally observed enhancements to the on-site 0-0 absorption peak in the series of Mg, Zn, and Pd are nicely reproduced. Enhanced absorption intensity is caused by larger FC contributions of molecules with heavier metal ions. The structure-spectroscopy relationship was analyzed, and it was found that the smaller cavity size of the porphyrin ring can significantly enhance the oscillator strength of the S0 → S1 transition.

Franck-Condon Blockade and Aggregation-Modulated Conductance in Molecular Devices Using Aggregation-Induced Emission-Active Molecules.

We report an effective modulation of the quantum transport in molecular junctions consisting of aggregation-induced-emission(AIE)-active molecules. Theoretical simulations based on combined density functional theory and rate-equation method calculations show that the low-bias conductance of the junction with a single tetraphenylethylene (TPE) molecule can be completely suppressed by strong electron-vibration couplings, that is, the Franck-Condon blockade effect. It is mainly associated with the low-energy vibration modes, which is also the origin of the fluorescence quenching of the AIE molecule in solution. We further found that the conductance of the junction can be lifted by restraining the internal motion of the TPE molecule by either methyl substitution on the phenyl group or by aggregation, a mechanism similar to the AIE process. The present work demonstrates the correlation between optical processes of molecules and quantum transport in their junction, and thus opens up a new avenue for the application of AIE-type molecules in molecular electronics and functional devices.

Thermally Activated Delayed Fluorescence in an Organic Cocrystal: Narrowing the Singlet-Triplet Energy Gap via Charge Transfer.

Harvesting non-emissive spin-triplet charge-transfer (CT) excitons of organic semiconductors is fundamentally important for increasing the operation efficiency of future devices. Here we observe thermally activated delayed fluorescence (TADF) in a 1:2 CT cocrystal of trans-1,2-diphenylethylene (TSB) and 1,2,4,5-tetracyanobenzene (TCNB). This cocrystal system is characterized by absorption spectroscopy, variable-temperature steady-state and time-resolved photoluminescence spectroscopy, single-crystal X-ray diffraction, and first-principles calculations. These data reveal that intermolecular CT in cocrystal narrows the singlet-triplet energy gap and therefore facilitates reverse intersystem crossing (RISC) for TADF. These findings open up a new way for the future design and development of novel TADF materials.

Cluster-model DFT simulations of the infrared spectra of triazine-based molecular crystals.

Understanding the intermolecular interactions in the context of crystal packing is of fundamental significance in molecular materials science. Infrared (IR) spectroscopy can provide complementary structural information; however, it still remains a great challenge to accurately predict the molecular IR vibrations in the crystalline phase. Here we report a cluster-model approach to simulate the IR spectra of triazine-based molecular crystals via density functional theory (DFT) calculations. In the properly designed cluster models, the molecular IR vibrations are expressed by a representative unit, while the nearest-neighbouring molecules are treated as a "frozen shell" to mimic the surrounding crystallographic environments. Much smaller clusters can be built by considering the crystallographic equivalence in the unit cell, which are able to perform DFT calculations on more complicated crystal structures with endurable computational costs. The simulated spectra show excellent consistencies with the experimental ones, particularly providing an in-depth understanding of the vibrational modes closely related to hydrogen bonding. Most importantly, the selectively built clusters based on the crystallographically independent molecules in the unit cell allow us to perform specific IR-spectral simulations, by which their distinct hydrogen-bonding environments have been clearly revealed for the first time.

First-principles study on vibrationally resolved fluorescence of fused 5,15-(diphenyl)-10,20-(dibromo)porphyrin molecule.

The vibrationally resolved fluorescence spectrum of a narrow-line single-molecule transducer, fused 5,15-(diphenyl)-10,20-(dibromo)porphyrin (fused-H2P) molecule, has been calculated by time-dependent density functional theory with the inclusion of both Franck-Condon and Herzberg-Teller contributions. Analytical transition dipole derivatives are used for the calculations of Herzberg-Teller terms to eliminate the possible errors caused by numerical differentials. The performance of different exchange-correlation functionals including B3LYP, ωB97X-D, and M06-2X has been examined. The comparison with the high-resolution experimental emission spectrum indicates that all three functionals can satisfactorily describe the fluorescence spectral profile, while ωB97X-D and M06-2X give slightly better excitation energy than B3LYP. Detailed analysis shows that the fluorescence spectrum is dominated by the Franck-Condon contribution, while the Herzberg-Teller term contributes mostly to its low energy tail. It is found that the size of the basis set has limited influence on the fluorescence spectrum, and a standard 6-31G(d, p) basis set is adequate for the purpose. The substitution of terthiophene side chains is found to have minor effects on the fluorescence spectrum. Our study provides unambitious assignments for all the vibronic structures in the experimental spectrum.

Gauge invariant theory for super high resolution Raman images.

The use of a highly localized plasmonic field has enabled us to achieve sub-nanometer resolution of Raman images for single molecules. The inhomogeneous spatial distribution of plasmonic field has become an important factor that controls the interaction between the light and the molecule. We present here a gauge invariant interaction Hamiltonian (GIIH) to take into account the non-uniformity of the electromagnetic field distribution in the non-relativistic regime. The theory has been implemented for both resonant and nonresonant Raman processes within the sum-over-state framework. It removes the gauge origin dependence in the phenomenologically modified interaction Hamiltonian (PMIH) employed in previous studies. Our calculations show that, in most resonant cases, the Raman images from GIIH are similar to those from PMIH when the origin is set to the nuclear charge center of the molecule. In the case of nonresonant Raman images, distinct differences can be found from two different approaches, while GIIH calculations provide more details and phase information of the images. Furthermore, the results from GIIH calculations are more stable with respect to the computational parameters. Our results not only help to correctly simulate the resonant and nonresonant Raman images of single molecules but also lay the foundation for developing gauge invariant theory for other linear and nonlinear optical processes under the excitation of non-uniform electromagnetic field.

Nonempirical Simulations of Inhomogeneous Broadening of Electronic Transitions in Solution: Predicting Band Shapes in One- and Two-Photon Absorption Spectra of Chalcones.

We have examined several approaches relying on the Polarizable Embedding (PE) scheme to predict optical band shapes for two chalcone molecules in methanol solution. The PE-TDDFT and PERI-CC2 methods were combined with molecular dynamics simulations, where the solute geometry was kept either as rigid, flexible or partly-flexible (restrained) body. The first approach, termed RBMD-PE-TDDFT, was employed to estimate the inhomogeneous broadening for subsequent convolution with the vibrationally-resolved spectra of the molecule in solution determined quantum-mechanically (QM). As demonstrated, the RBMD-PE-TDDFT/QM-PCM approach delivers accurate band widths, also reproducing their correct asymmetric shapes. Further refinement can be obtained by the estimation of the inhomogeneous broadening using the RBMD-PERI-CC2 method. On the other hand, the remaining two approaches (FBMD-PE-TDDFT and ResBMD-PE-TDDFT), which lack quantum-mechanical treatment of molecular vibrations, lead to underestimated band widths. In this study, we also proposed a simple strategy regarding the rapid selection of the exchange-correlation functional for the simulations of vibrationally-resolved one- and two-photon absorption spectra based on two easy-to-compute metrics.