AI Article Synopsis
- The Molecular Vibration Explorer is a free online database that allows users to explore vibrational spectra and light-vibration coupling strengths of thiolated molecules.
- The "Gold" version includes data on 2800 thiol compounds linked to gold, while the "Thiol" version focuses on 1900 unbound thiolated compounds, providing detailed spectroscopic parameters for each.
- Users can customize their searches and visualizations, such as checking for large Raman cross-sections or sum-frequency generation efficiencies, and the tool is demonstrated using examples in surface-enhanced spectroscopy.
Article 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.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9310003 | PMC |
| http://dx.doi.org/10.1021/acs.jpca.2c03700 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
The Melamine-Driven Solvation Effect Promotes Oxygen Reduction on a Platinum Catalyst: Machine Learning-Aided Free Energy Calculations.
J Phys Chem Lett
December 2024
Toyota Central R&D Laboratories, Inc., Nagakute 480-1192, Aichi, Japan.
The modification of Pt surfaces with organic compounds like melamine enhances oxygen reduction reaction activity and catalyst durability. Through first-principles free energy calculations utilizing thermodynamic integration and finite-temperature molecular dynamics, enhanced by machine learning force fields for efficient sampling of nanosecond-scale interfacial water fluctuations and incorporating corrections to accurately reproduce first-principles free energies, we demonstrate that melamine destabilizes OH adsorbates, facilitating their removal and enhancing catalytic activity. Unlike alloys, where OH destabilization is driven by changes in electronic structure and surface strain, melamine disrupts hydrogen bonding between OH and interfacial water.
View Article and Find Full Text PDFOrientational Disorder and Molecular Correlations in Hybrid Organic-Inorganic Perovskites: From Fundamental Insights to Technological Applications.
ACS Appl Mater Interfaces
December 2024
Group of Characterization of Materials, Departament de Física, Universitat Politècnica de Catalunya, Campus Diagonal-Besòs, Av. Eduard Maristany 10-14, Barcelona 08019, Spain.
Hybrid organic-inorganic perovskites (HOIP) have emerged in recent years as highly promising semiconducting materials for a wide range of optoelectronic and energy applications. Nevertheless, the rotational dynamics of the organic components and many-molecule interdependencies, which may strongly impact the functional properties of HOIP, are not yet fully understood. In this study, we quantitatively analyze the orientational disorder and molecular correlations in archetypal perovskite CHNHPbI (MAPI) by performing comprehensive molecular dynamics simulations and entropy calculations.
View Article and Find Full Text PDFDesign, Synthesis, and Evaluation of Novel 2,4-disubstituted Pyrimidine Derivatives as Double Mutant Epidermal Growth Factor Receptor-L858R/T790M Tyrosine Kinase Inhibitors.
J Biochem Mol Toxicol
January 2025
Department of Pharmaceutical Chemistry, Division of Computer-Aided Drug Design, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra, India.
A series of 2,4-disubstituted pyrimidine derivatives bearing 5-substituted-1,3,4 thidiazole were devised and synthesized based on the binding mode of the approved drug Osimertinib with the ATP competitive site of EGFR-L858R/T790M in order to increase selectivity towards double mutant EGFR and potent antitumor activity. Their cellular bioactivity and corresponding enzyme inhibition were studied, and it was revealed that several compounds had significant biological activity and selectivity when compared to the control compounds. One of the most promising compound 8, substantially suppressed the proliferation of H1975 cells and showed significant inhibition of double mutant EGFR-L858R/T790M TK with IC values of 0.
View Article and Find Full Text PDFMolecular Dynamics Simulations on Heat Transport of Nanoconfined Water under Electric Fields: Effect of Nanochannel Size.
J Phys Chem B
December 2024
School of Energy and Power Engineering, Northeast Electric Power University, Jilin 132012, China.
When water is confined in a nanochannel, its thermodynamic and kinetic properties change dramatically compared to the macroscale. To investigate these phenomena, we conducted nonequilibrium molecular dynamics simulations on the heat transfer in copper-water nanochannels with lengths ranging from 12 to 20 nm in the absence and presence of an electric field. The results indicate that in the absence of an electric field ( = 12-20 nm), the binding force between water molecules in the 20 nm nanochannel is the weakest, facilitating thermal motion in the liquid phase.
View Article and Find Full Text PDFPotential Energy Curves of Hydrogen Halides HX(F, Cl, Br) with the -DMFT Method.
J Phys Chem A
December 2024
Institute of atomic and molecular physics, Jilin University, Changchun 130012, China.
The information entropy based on the occupation numbers has been found to play a central role in a description of electron correlation within the density-matrix functional theory [-DMFT, see , 128, 013001]. In this article, the -DMFT method is applied to predict potential energy curves, equilibrium bond lengths, and harmonic vibrational frequencies for the hydrogen halides: HF, HCl, and HBr. The results are compared with other theoretical calculations and experimental spectroscopic data.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!