Molecular Vibration Explorer: an Online Database and Toolbox for Surface-Enhanced Frequency Conversion and Infrared and Raman Spectroscopy

Abstract

We present Molecular Vibration Explorer, a freely accessible online database and interactive tool for exploring vibrational spectra and tensorial light-vibration coupling strengths of a large collection of thiolated molecules. The “Gold” version of the database gathers the results from density functional theory calculations on 2800 commercially available thiol compounds linked to a gold atom, with the main motivation to screen the best molecules for THz and mid-infrared to visible upconversion. Additionally, the “Thiol” version of the database contains results for 1900 unbound thiolated compounds. They both provide access to a comprehensive set of computed spectroscopic parameters for all vibrational modes of all molecules in the database. The user can simultaneously investigate infrared absorption, Raman scattering, and vibrational sum- and difference-frequency generation cross sections. Molecules can be screened for various parameters in custom frequency ranges, such as a large Raman cross-section under a specific molecular orientation, or a large orientation-averaged sum-frequency generation (SFG) efficiency. The user can select polarization vectors for the electromagnetic fields, set the orientation of the molecule, and customize parameters for plotting the corresponding IR, Raman, and sum-frequency spectra. We illustrate the capabilities of this tool with selected applications in the field of surface-enhanced spectroscopy.

Molecular optomechanics in the anharmonic regime: from nonclassical mechanical states to mechanical lasing

“…Here we approximate the Raman dipole as linear in displacement x-higher order terms can in principle yield two-phonon signatures in the Raman spectrum. For a more careful consideration of the Raman tensor and polarizability, we direct the reader to [9,44,45]. The explicit connection to the molecular vibrations is made by representing x in the basis of the eigenstates |ϕ k ⟩ of equation ( 2):…”

Synthesis and Raman Detection of 5-Amino-2-mercaptobenzimidazole Self-Assembled Monolayers in Nanoparticle-on-a-Mirror Plasmonic Cavity Driven by Dielectric Waveguides

“…Figure 1 shows a sketch of the 5-A-2MBI molecule. 18 The IR, Raman, and upconversion response of 5-A-2MBI molecule extracted from the online platform Molecular Vibration Explorer 19 are shown in Figure 1b. With this tool, we were able to simultaneously theoretically investigate IR absorption, Raman scattering, and vibrational sum and difference frequency generation cross sections.…”

“…Therefore, upconversion-based detection of other infrared (IR) or even terahertz (THz) frequencies depends on our capacity to functionalize Au surfaces with a wide variety of molecular monolayers that should provide a large Raman scattering cross-section and a high IR absorption. Amongst the different molecules providing both requirements (to be Raman and IR active), 5-amino-2-mercaptobenzimidazole (5-A-2MBI) exhibits this property in the THz range (15–60 THz) …”

“…Representative Raman peaks and assignment to vibrational modes are summarized in Table (based on the calculated vibrational frequencies from ref and experimental results of our work in Figures and ). The C–S stretching vibration gives a band in Raman in the region 750–570 cm –l (peak 1) .…”

“…Amongst the different molecules providing both requirements (to be Raman and IR active), 5-amino-2-mercaptobenzimidazole (5-A-2MBI) 18 exhibits this property in the THz range (15−60 THz). 19 In this work, we present a new strategy for effective functionalization of Au surfaces with 5-A-2MBI SAMs. 20,21 We investigate the synthesis and characterization of the 5-A2MBI SAM and its homogeneity, stability, and surface coverage.…”