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.

Association of thyroid autoantibodies with aggressive characteristics of papillary thyroid cancer: a case-control study.

PURPOSE: Although the potential association between autoimmune thyroiditis and papillary thyroid cancer (PTC) has been acknowledged, whether the clinicopathological features of PTC will be affected by thyroid autoantibodies remains unknown. PATIENTS AND METHODS: We conducted a case-control study to investigate the association of thyroid autoantibodies with clinicopathological characteristics of PTC in 15,305 patients (including 11,465 females and 3,840 males) from 3 medical centers in the central province of China. Logistic regression and restricted cubic spline models were performed to analyze the association of thyroid autoantibodies with clinicopathological features of PTC. RESULTS: In total, out of the 15,305 patients enrolled in this study, 10,087 (65.9%) had negative thyroid autoantibodies, while 5,218(34.1%) tested positive thyroid autoantibodies. Among these individuals, 1,530(10.0%) showed positivity for TPOAb only, 1,247(8.2%) for TGAb only and a further 2,441(15.9%) exhibited dual positivity for both TPOAb and TGAb combined. Thyroid autoantibodies level demonstrated significant correlations with certain aggressive features in PTC. Specifically, TGAb level displayed a direct correlation to an increased likelihood of multifocality, bilateral tumor, extrathyroidal extension, lymph node metastasis, as well as more than five affected lymph nodes. However, TPOAb level exhibited an inverse association with the risk associated with extrathyroidal extension, lymph node metastasis, and more than five affected lymph nodes. CONCLUSION: Elevated level of TGAb were positively correlated with the risk of aggressive features in PTC, while high level of TPOAb were inversely associated with the risk of extrathyroidal extension and lymph node metastasis.

Pyridinic Nitrogen Modification for Selective Acetylenic Homocoupling on Au(111).

On-surface acetylenic homocoupling has been proposed to construct carbon nanostructures featuring sp hybridization. However, the efficiency of linear acetylenic coupling is far from satisfactory, often resulting in undesired enyne products or cyclotrimerization products due to the lack of strategies to enhance chemical selectivity. Herein, we inspect the acetylenic homocoupling reaction of polarized terminal alkynes (TAs) on Au(111) with bond-resolved scanning probe microscopy. The replacement of benzene with pyridine moieties significantly prohibits the cyclotrimerization pathway and facilitates the linear coupling to produce well-aligned N-doped graphdiyne nanowires. Combined with density functional theory calculations, we reveal that the pyridinic nitrogen modification substantially differentiates the coupling motifs at the initial C-C coupling stage (head-to-head vs head-to-tail), which is decisive for the preference of linear coupling over cyclotrimerization.

The potential role of reprogrammed glucose metabolism: an emerging actionable codependent target in thyroid cancer.

Although the incidence of thyroid cancer is increasing year by year, most patients, especially those with differentiated thyroid cancer, can usually be cured with surgery, radioactive iodine, and thyroid-stimulating hormone suppression. However, treatment options for patients with poorly differentiated thyroid cancers or radioiodine-refractory thyroid cancer have historically been limited. Altered energy metabolism is one of the hallmarks of cancer and a well-documented feature in thyroid cancer. In a hypoxic environment with extreme nutrient deficiencies resulting from uncontrolled growth, thyroid cancer cells utilize "metabolic reprogramming" to satisfy their energy demand and support malignant behaviors such as metastasis. This review summarizes past and recent advances in our understanding of the reprogramming of glucose metabolism in thyroid cancer cells, which we expect will yield new therapeutic approaches for patients with special pathological types of thyroid cancer by targeting reprogrammed glucose metabolism.

Core-Shell Nanostructure-Enhanced Raman Spectroscopy for Surface Catalysis.

ConspectusThe rational design of highly efficient catalysts relies on understanding their structure-activity relationships and reaction mechanisms at a molecular level. Such an understanding can be obtained by in situ monitoring of dynamic reaction processes using surface-sensitive techniques. Surface-enhanced Raman spectroscopy (SERS) can provide rich structural information with ultrahigh surface sensitivity, even down to the single-molecule level, which makes it a promising tool for the in situ study of catalysis. However, only a few metals (like Au, Ag, and Cu) with particular nanostructures can generate strong SERS effects. Thus, it is almost impossible to employ SERS to study transition metals (like Pt, Pd, Ru, etc.) and other nonmetal materials that are usually used in catalysis (material limitation). Furthermore, SERS is also unable to study model single crystals with atomically flat surface structures or practical nanocatalysts (morphology limitation). These limitations have significantly hindered the applications of SERS in catalysis over the past four decades since its discovery, preventing SERS from becoming a widely used technique in catalysis. In this Account, we summarize the extensive efforts done by our group since the 1980s, particularly in the past decade, to overcome the material and morphology limitations in SERS. Particular attention has been paid to the work using core-shell nanostructures as SERS substrates, because they provide high Raman enhancement and are highly versatile for application on different catalytic materials. Different SERS methodologies for catalysis developed by our group, including the "borrowing" strategy, shell-isolated nanoparticle-enhanced Raman spectroscopy (SHINERS), and SHINERS-satellite strategy, are discussed in this account, with an emphasis on their principles and applications. These methodologies have successfully overcome the long-standing limitations of traditional SERS, enabling in situ tracking of catalysis at model single-crystal surfaces and practical nanocatalysts that can hardly be studied by SERS. Using these methodologies, we systematically studied a series of fundamentally important reactions, such as oxygen reduction reaction, hydrogen evolution reaction, electrooxidation, CO oxidation, and selective hydrogenation. As such, direct spectroscopic evidence of key intermediates that can hardly be detected by other traditional techniques was obtained. Combined with density functional theory and other in situ techniques, the reaction mechanisms and structure-activity relationships of these catalytic reactions were revealed at a molecular level. Furthermore, the future of SERS in catalysis has also been proposed in this work, which we believe should be focused on the in situ dynamic studies at the single-molecule, or even single-atom, level using techniques with ultrahigh sensitivity or spatial resolution, for example, single-molecule SERS or tip-enhanced Raman spectroscopy. In summary, core-shell nanostructure-enhanced Raman spectroscopies are shown to greatly boost the application of SERS in catalysis, from model systems like single-crystal surfaces to practical nanocatalysts, liquid-solid interfaces to gas-solid interfaces, and electrocatalysis to heterogeneous catalysis to photocatalysis. Thus, we believe this Account would attract increasing attention to SERS in catalysis and opens new avenues for catalytic studies.

Identification of Water Hexamer on Cu(111) Surfaces.

While being considered as the building block of ice on a hydrophobic metal surface, the global minimum of the water hexamer is still elusive, which has impeded our understanding of water/metal interfaces. Herein, we comprehensively investigate water hexamer on Cu(111) theoretically and propose the boat configuration as the new in situ adsorption configuration from the scanning tunneling microscope experiments. All existing experimental measurements can therefore be well reproduced. Calculations in high-level theories reveal that the boat configuration is indeed the global minimum under experimental conditions, solving a long-standing discrepancy.

Microphotoelectrochemical Surface-Enhanced Raman Spectroscopy: Toward Bridging Hot-Electron Transfer with a Molecular Reaction.

The rational design and applications of plasmon-mediated chemical reactions (PMCRs) are fundamentally determined by an understanding of photon-electron-molecule interactions. However, the current understanding of the PMCR of plasmon-decayed hot electron-mediated reactions remains implicit, since there has not been a single measurement of both hot-electron transfer and molecular transformation following photon excitation. Therefore, we invented a method called microphotoelectrochemical surface-enhanced Raman spectroscopy (µPEC-SERS) that uses an ultramicroelectrode (UME) whose dimensions match those of the focused laser spot. This system can simultaneously record the photocurrent (∼picoamps) of hot-electron transfer with a high signal-to-noise ratio and the SERS spectra of a molecular reaction in the same electrode area. The responses of the photocurrent and SERS spectra to laser illumination can correlate the surface reaction activated by hot electrons with the SERS spectral changes. A typical PMCR of p-aminothiophenol (PATP) on a Ag UME was used to illustrate that the correlation of the photocurrent with the spectral changes is capable of revealing the reaction mechanism in terms of the formation of activated oxygenated species. The laser power-, laser wavelength-, and surface roughness-dependent photocurrents link the formation of activated oxygenated species to the hot-electron transfer. Further comparisons of the photocurrent with the conventional electrochemical current of the oxygen reduction reaction indicate that the activated oxygenated species are oxidative in transforming PATP to p,p'-dimercaptoazobenzene, which is supported by a density functional theory (DFT) calculation. Therefore, µPEC-SERS could be a powerful tool for investigating PMCRs and other systems involving photon-electron-molecule interactions.

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.

Selective Catalytic Dehydrogenative Oxidation of Bio-Polyols to Lactic Acid.

The global demand for lactic acid (LA) is increasing due to its successful application as monomer for the manufacture of bioplastics. Although N-heterocyclic carbene (NHC) iridium complexes are promising molecular catalysts for LA synthesis, their instabilities have hindered their utilization especially in commercial applications. Here, we report that a porous self-supported NHC-iridium coordination polymer can efficiently prevent the clusterization of corresponding NHC-Ir molecules and can function as a solid molecular recyclable catalyst for dehydrogenation of bio-polyols to form LA with excellent activity (97 %) and selectivity (>99 %). A turnover number of up to 5700 could be achieved in a single batch, due to the synergistic participation of the Ba2+ and hydroxide ions, as well as the blockage of unwanted pathways by adding methanol. Our findings demonstrate a potential route for the industrial production of LA from cheap and abundant bio-polyols, including sorbitol.

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.

Identifying the structure of 4-chlorophenyl isocyanide adsorbed on Au(111) and Pt(111) surfaces by first-principles simulations of Raman spectra.

Surface Raman spectroscopy has become one of the most powerful analytical tools for interfacial structures. However, theoretical modeling for the Raman spectra of molecular adsorbate on metallic surfaces is a long-standing challenge because accurate descriptions of the electronic structure for both the metallic substrates and adsorbates are required. Here we present a quasi-analytical method for high-precision surface Raman spectra at the first principle level. Using this method, we correlate both geometrical and electronic structures of a single 4-chlorophenyl isocyanide (CPI) molecule adsorbed on a Au(111) or Pt(111) surface with its Raman spectra. The "finger-print" frequency shift of the CN stretching mode reveals the in situ configuration of CPI is vertical adsorption on the top site of the Au(111) surface, but a bent configuration when it adsorbs on the hollow site of the Pt(111) surface. Electronic structure calculations reveal that a π-back donation mechanism often causes a red shift to the Raman response of CN stretching mode. In contrast, σ donation as well as a wall effect introduces a blue shift to the CN stretching mode. A clear relationship for the dependence of Raman spectra on the surface electronic and geometrical information is built up, which largely benefits the understanding of chemical and physical changes during the adsorption. Our results highlight that high-precision theoretical simulations are essential for identifying in situ geometrical and electronic surface structures.

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.

Optical Excitation in Donor-Pt-Acceptor Complexes: Role of the Structure.

The optical properties of the Pt complexes in the form of donor-metal-acceptor (D-M-A) were studied at the first-principles level. Calculated results show that for the frontier molecular orbitals (MOs) of a D-M-A structure the energies of unoccupied frontier MO can be mainly determined by the interaction between M and A, whereas the M-A and M-D interactions both determine the energies of occupied frontier MO. By developing a straightforward transition dipole decomposition method, we found that not only the local excitations in D but also those in A can significantly contribute to the charge-transfer (CT) excitation. Furthermore, the calculations also demonstrate that by tuning the dihedral angle between D and A the transition probability can be precisely controlled so as to broaden the spectrum region of photoabsorption. For the D-M-A molecule with a delocalized π system in A, the CT excitation barely affects the electronic structures of metal, suggesting that the oxidation state of the metal can be kept during the excitation. These understandings for the optical properties of the D-M-A molecule would be useful for the design of dye-sensitized solar cells, photocatalysis, and luminescence systems.

Visualization of Vibrational Modes in Real Space by Tip-Enhanced Non-Resonant Raman Spectroscopy.

We present a general theory to model the spatially resolved non-resonant Raman images of molecules. It is predicted that the vibrational motions of different Raman modes can be fully visualized in real space by tip-enhanced non-resonant Raman scattering. As an example, the non-resonant Raman images of water clusters were simulated by combining the new theory and first-principles calculations. Each individual normal mode gives rise its own distinct Raman image, which resembles the expected vibrational motions of the atoms very well. The characteristics of intermolecular vibrations in supermolecules could also be identified. The effects of the spatial distribution of the plasmon as well as nonlinear scattering processes were also addressed. Our study not only suggests a feasible approach to spatially visualize vibrational modes, but also provides new insights in the field of nonlinear plasmonic spectroscopy.

Theoretical Modeling of Plasmon-Enhanced Raman Images of a Single Molecule with Subnanometer Resolution.

Under local plasmonic excitation, Raman images of single molecules can now surprisingly reach subnanometer resolution. However, its physical origin has not been fully understood. Here we report a quantum-mechanical description of the interaction between a molecule and a highly confined plasmonic field. We show that when the spatial distribution of the plasmonic field is comparable to the size of the molecule, the optical transition matrix of the molecule becomes dependent on the position and distribution of the plasmonic field, resulting in a spatially resolved high-resolution Raman image of the molecule. The resonant Raman image reflects the electronic transition density of the molecule. In combination with first-principles calculations, the simulated Raman image of a porphyrin derivative adsorbed on a silver surface nicely reproduces its experimental counterpart. The present theory provides the basic framework for describing linear and nonlinear responses of molecules under highly confined plasmonic fields.

The effect of Duschinsky rotation on charge transport properties of molecular junctions in the sequential tunneling regime.

We present here a systematic theoretical study on the effect of Duschinsky rotation on charge transport properties of molecular junctions in the sequential tunneling regime. In the simulations we assume that only two electronic charging states each coupled to a two dimensional vibrational potential energy surface (PES) are involved in the transport process. The Duschinsky rotation effect is accounted by varying the rotational angle between the two sets of displaced PESs. Both harmonic potential and anharmonic Morse potential have been considered for the cases of the intermediate to strong electron-vibration couplings. Our calculations show that the inclusion of the Duschinsky rotation effect can significantly change the charge transport properties of a molecular junction. Such an effect makes the otherwise symmetric Coulomb diamond become asymmetric in harmonic potentials. Depending on the angle of the rotation, the low bias current could be significantly suppressed or enhanced. This effect is particularly prominent in the Franck-Condon (FC) blockade regime where the electron-vibration coupling is strong. These changes are caused by the variation of the FC factors which are closely related to the rotational angle between the two sets of PESs involved in the charge transport process. For a molecular junction with Morse potentials, the changes caused by Duschinsky rotation are much more complicated. Both the amplitude and shape of the Coulomb diamond are closely dependent on the rotational angle in the whole range from 0 to 2π. One interesting result is that with a rotation angle of π (and also π/2 for certain cases) symmetric Coulomb diamonds can even be formed from the intrinsically asymmetric Morse potential. These results could be important for the interpretation of experimental observations.

Infrared spectra of small anionic water clusters from density functional theory and wavefunction theory calculations.

We performed systematic theoretical studies on small anionic water/deuterated water clusters W/D(-)(N=2-6) at both density functional theory (B3LYP) and wavefunction theory (MP2) levels. The focus of the study is to examine the convergence of calculated infrared (IR) spectra with respect to the increasing number of diffuse functions. It is found that at the MP2 level for larger clusters (n = 4-6), only one extra diffuse function is needed to obtain the converged relative IR intensities, while two or three more sets of extra diffuse functions are needed for smaller clusters. Such behaviour is strongly associated with the convergence of the electronic structure of corresponding clusters at the MP2 level. It is striking to observe that at the B3LYP level, the calculated relative IR intensities for all the clusters under investigations are diverse and show no trend of convergence upon increasing the number of diffuse functions. Moreover, the increasing contribution from the extra diffuse functions to the dynamic IR dipole moment indicates that the B3LYP electronic structure also fails to converge. These results manifest that MP2 is a preferential theoretical method, as compared to the widely used B3LYP, for the IR intensity of dipole bounded electron systems.

Aggregation-induced chiral symmetry breaking of a naphthalimide-cyanostilbene dyad.

Spontaneously emerged supramolecular chirality and chiral symmetry breaking from achiral/racemic constituents remain poorly understood. We here report that supramolecular chirality may emerge from the structural flexibility of achiral aryl nitrogen centres which provide instantaneous chirality. Employing a naphthalimide-cyanostilbene dyad as a model, we explored the underlying mechanism of aggregation-induced chiral symmetry breaking and found that the conformations of the N-naphthylpiperazine and the N,N-dimethylaniline units facilitate the formation of ordered supramolecular structures and offer opposite handedness. Furthermore, chiral symmetry breaking of the monomers was amplified by the formation of dimers. The microscopic and the macroscopic observations from the theoretical simulations and experimental measurements are thus rationalized by connecting the population of the dihedral angles of the aryl nitrogen centres, the morphology of the self-assemblies, and the observed circular dichroism spectra.

Predicting central cervical lymph node metastasis in papillary thyroid microcarcinoma using deep learning.

Background: The aim of this study is to design a deep learning (DL) model to preoperatively predict the occurrence of central lymph node metastasis (CLNM) in patients with papillary thyroid microcarcinoma (PTMC). Methods: This research collected preoperative ultrasound (US) images and clinical factors of 611 PTMC patients. The clinical factors were analyzed using multivariate regression. Then, a DL model based on US images and clinical factors was developed to preoperatively predict CLNM. The model's efficacy was evaluated using the receiver operating characteristic (ROC) curve, along with accuracy, sensitivity, specificity, and the F1 score. Results: The multivariate analysis indicated an independent correlation factors including age ≥55 (OR = 0.309, p < 0.001), tumor diameter (OR = 2.551, p = 0.010), macrocalcifications (OR = 1.832, p = 0.002), and capsular invasion (OR = 1.977, p = 0.005). The suggested DL model utilized US images achieved an average area under the curve (AUC) of 0.65, slightly outperforming the model that employed traditional clinical factors (AUC = 0.64). Nevertheless, the model that incorporated both of them did not enhance prediction accuracy (AUC = 0.63). Conclusions: The suggested approach offers a reference for the treatment and supervision of PTMC. Among three models used in this study, the deep model relied generally more on image modalities than the data modality of clinic records when making the predictions.

Research insights into the chemokine-like factor (CKLF)-like MARVEL transmembrane domain-containing family (CMTM): their roles in various tumors.

The chemokine-like factor (CKLF)-like MARVEL transmembrane domain-containing (CMTM) family includes CMTM1-8 and CKLF, and they play key roles in the hematopoietic, immune, cardiovascular, and male reproductive systems, participating in the physiological functions, cancer, and other diseases associated with these systems. CMTM family members activate and chemoattract immune cells to affect the proliferation and invasion of tumor cells through a similar mechanism, the structural characteristics typical of chemokines and transmembrane 4 superfamily (TM4SF). In this review, we discuss each CMTM family member's chromosomal location, involved signaling pathways, expression patterns, and potential roles, and mechanisms of action in pancreatic, breast, gastric and liver cancers. Furthermore, we discuss several clinically applied tumor therapies targeted at the CMTM family, indicating that CMTM family members could be novel immune checkpoints and potential targets effective in tumor treatment.