CH Stretching Region: Computational Modeling of Vibrational Optical Activity

An electron density clustering based adaptive segmentation method for protein Raman spectrum calculation

Raman spectroscopy is a powerful technique for protein detection, but the calculation of Raman spectrum is a longstanding challenging problem due to the large sizes and complex structures of protein molecules. Dividing proteins into fragments can greatly accelerate the calculation, but this usually introduces large errors originating from ignored interactions between fragments into obtained spectra. In this paper, we proposed a new adaptive segmentation method based on the strength of interactions and molecular shapes and structures, i.e., electron density clustering, to divide proteins. It can reduce errors of obtained Raman spectra by about 20% compared to the uniform segmentation method without a significant increase in computational cost. This method can facilitate the validation and analysis of detected Raman spectra of proteins and promote the application of Raman spectroscopy in biological detection.

Quantification of Surface Relation Between Experimental Polylactic Acid Dental Matrix and Type II Glass Ionomers Using Peel Adhesion Test and Fourier Transform Infrared Spectroscopy

AIM

Type II glass ionomer cement (GIC) is a posterior restorative material that is generally not recommended for interaction with stainless steel due to chemical ion exchange. The purpose of this study is to quantify the surface relation of experimental three-dimensional (3D)-printed polylactic acid (PLA) and type II GIC using the peel adhesion test and Fourier transform infrared spectroscopy (FT-IR).

MATERIALS AND METHODS

Experimental PLA dental matrix specimens were 3D printed in the form of an open circumferential dental matrix (75x6x0.0055 mm) using a fused deposition modeling (FDM) machine. The peel resistance test (ASTM D1876) was applied to determine the relative peel resistance of the adhesive bonds between the PLA dental matrix, traditional circumferential stainless steel (SS) matrix, and GIC. The PLA bands were characterized using an FT-IR spectrophotometer (Spectrum 100, PerkinElmer Inc., Waltham, MA, USA) for the simultaneous determination of the chemical relationships of the surfaces before and after the GIC was set in a simulated class II cavity model.

RESULTS

The mean peel strengths (P/b) ± standard deviations of the PLA and SS dental matrix bands were 0.0017 ± 0.0003 N/mm and 0.3122 ± 0.0042 N/mm, respectively. The -C H stretching was observed at 3383 cm^-1 after adhesion, which corresponded to vibrational movements on the surface.

CONCLUSION

 It required ~184 times less force to separate the GIC from the PLA surface compared to the traditional SS matrix. Additionally, there was no evidence of a new chemical bond or strong chemical interaction occurring between the GIC and the experimental PLA dental matrix.

Binary Effects of Gynostemma Gold Nanoparticles on Obesity and Inflammation via Downregulation of PPARγ/CEPBα and TNF-α Gene Expression

Nanoscience is a multidisciplinary skill with elucidated nanoscale particles and their advantages in applications to various fields. Owing to their economical synthesis, biocompatible nature, and widespread biomedical and environmental applications, the green synthesis of metal nanoparticles using medicinal plants has become a potential research area in biomedical research and functional food formulations. Gynostemma pentaphyllum (GP) has been extensively used in traditional Chinese medicine to cure several diseases, including diabetes mellitus (DM). This is the first study in which we examined the efficacy of G. pentaphyllum gold nanoparticles (GP-AuNPs) against obesity and related inflammation. GP extract was used as a capping agent to reduce Au²⁺ to Au⁰ to form stable gold nanoparticles. The nanoparticles were characterized by using UV–VIS spectroscopy, and TEM images were used to analyze morphology. In contrast, the existence of the functional group was measured using FTIR, and size and shape were examined using XRD analysis. In vitro analysis on GP-AuNPs was nontoxic to RAW 264.7 cells and 3T3-L1 cells up to a specific concentration. It significantly decreased lipid accumulation in 3T3-L1 obese and reduced NO production in Raw 264.7 macrophage cells. The significant adipogenic genes PPARγ and CEPBα and a major pro-inflammatory cytokine TNF-α expression were quantified using RT-PCR. The GP-AuNPs decreased the face of these genes remarkably, revealing the antiadipogenic and anti-inflammatory activity of our synthesized GP-AuNPs. This study represents thorough research on the antiobesity effect of Gynostemma pentaphyllum gold nanoparticles synthesized using a green approach and the efficacy instead of related inflammatory responses.

Low-frequency Raman Optical Activity Provides Insight into Structure of Chiral Liquids

Vibrational frequencies of modes involving intermolecular motions in liquids are relatively small, in the Raman scattering close to the excitation frequency, and the bands may merge into a diverging uninterpretable...

Two-dimensional Infrared Spectroscopy Reveals Better Insights of Structure and Dynamics of Protein

Proteins play an important role in biological and biochemical processes taking place in the living system. To uncover these fundamental processes of the living system, it is an absolutely necessary task to understand the structure and dynamics of the protein. Vibrational spectroscopy is an established tool to explore protein structure and dynamics. In particular, two-dimensional infrared (2DIR) spectroscopy has already proven its versatility to explore the protein structure and its ultrafast dynamics, and it has essentially unprecedented time resolutions to observe the vibrational dynamics of the protein. Providing several examples from our theoretical and experimental efforts, it is established here that two-dimensional vibrational spectroscopy provides exceptionally more information than one-dimensional vibrational spectroscopy. The structural information of the protein is encoded in the position, shape, and strength of the peak in 2DIR spectra. The time evolution of the 2DIR spectra allows for the visualisation of molecular motions.

Origins of Optical Activity in an Oxo-Helicene: Experimental and Computational Studies

Helicenes are known to provide extremely strong optical activity. Prediction of the properties of helicenes may facilitate their design and synthesis for analytical or materials sciences. On a model 7,12,17-trioxa[11]helicene molecule, experimental results from multiple spectroscopic techniques are analyzed on the basis of density functional theory (DFT) simulations to test computational methodology and analyze the origins of chirality. Infrared (IR), vibrational circular dichroism (VCD), electronic circular dichroism (ECD), magnetic circular dichroism (MCD), and Raman optical activity (ROA, computations only) spectra are compared. Large dissymmetry factors are predicted both for vibrational (ROA/Raman ∼ VCD/IR ∼ 10^-3) and electronic (ECD/Abs ∼10^-2) optical activity, which could be verified experimentally except for ROA. Largest VCD signals come from a strong vibrational coupling of the C-H in-plane and out-of-plane bending modes in stacked helicene rings. The sum-over-states (SOS) approach appeared convenient for simulation of MCD spectra. Our results demonstrated that selected computational methods can be successfully used for reliable modeling of spectral and chiroptical properties of large helicenes. In particular, they can be used for guiding rational design of strongly chiral chromophores.

Theory and algorithms for chiroptical properties and spectroscopies of aqueous systems

Chiroptical properties and spectroscopies are valuable tools to study chiral molecules and assign absolute configurations. The spectra that result from chiroptical measurements may be very rich and complex, and hide much of their information content. For this reason, the interplay between experiments and calculations is especially useful, provided that all relevant physico-chemical interactions that are present in the experimental sample are accurately modelled. The inherent difficulty associated to the calculation of chiral signals of systems in aqueous solutions requires the development of specific tools, able to account for the peculiarities of water-solute interactions, and especially its ability to form hydrogen bonds. In this perspective we discuss a multiscale approach, which we have developed and challenged to model the most used chiroptical techniques.

Europium (III) as a Circularly Polarized Luminescence Probe of DNA Structure

We report as a proof-of-concept the first application of circularly polarized luminescence (CPL) measured with a Raman optical activity (ROA) spectrometer to differentiate several DNA structures without need of sensitizing complexes. The ROA/CPL approach provides sufficiently high CPL intensity to use hydrated Eu³⁺ ions, thus avoiding DNA structural changes associated with binding of sensitizers and overcoming the sensitizer quenching issue. We showed that deoxyguanosine monophosphate (dGMP), single- and double-stranded DNA provide different CPL spectra, which could be used for their discrimination. Our results demonstrate that ROA/CPL method is a promising approach to measure CPL spectra of complex biomolecules when the use of sensitizers is not possible. The method can be extended to other biomolecules, such as proteins, lipids, sugars, etc.

A vibrational circular dichroism (VCD) methodology for the measurement of enantiomeric excess in chiral compounds in the solid phase and for the complementary use of NMR and VCD techniques in solution: the camphor case

For the first time, the success of a methodology for the determination of enantiomeric excess (% ee) in chiral solid samples by vibrational circular dichroism (VCD) spectroscopy is reported. We have used camphor to determine the % ee in a blind sample constituted by a mixture of its two enantiomers as a test for the validity of our approach. IR and VCD spectra of different enantiomeric mixtures of R/S-camphor in Nujol mulls were recorded and linear regressions of VCD intensities (ΔAbs.) vs. % ee for selected bands were found. Finally, the VCD intensities of a blind sample were interpolated in these linear regressions, obtaining its % ee with a rms of 2.4. These results in the solid phase were complemented with the determination of % ee in the liquid phase by VCD and NMR techniques, which are proved to be complementary techniques to carry out this kind of analysis. In the same way as in the VCD solid phase, linear regressions of ΔAbs. vs. % ee for selected bands were established, obtaining a rms of 1.1 in the % ee determination of a blind sample. ¹H NMR experiments at 600 MHz using the chiral solvating agent, (S,S)-ABTE, allow the determination of the proportions of enantiomers in CD₂Cl₂ solution with great accuracy. ¹³C CPMAS NMR spectra prove that this technique cannot be used for conglomerates and/or solid solutions.

Establishing the link between fibril formation and Raman optical activity spectra of insulin

Molecular dynamics and density functional simulations are used to explain changes in Raman optical activity accompanying the formation of insulin fibrils.

Anharmonic Theoretical Vibrational Spectroscopy of Polypeptides

Because of the size of polypeptides and proteins, the quantum-chemical prediction of their vibrational spectra presents an exceptionally challenging task. Here, we address one of these challenges, namely, the inclusion of anharmonicities. By performing the expansion of the potential energy surface in localized-mode coordinates instead of the normal-mode coordinates, it becomes possible to calculate anharmonic vibrational spectra of polypeptides efficiently and reliably. We apply this approach to calculate the infrared, Raman, and Raman optical activity spectra of helical alanine polypeptides consisting of up to 20 amino acids. We find that while anharmonicities do not alter the band shapes, simple scaling procedures cannot account for the different shifts found for the individual bands. This closes an important gap in theoretical vibrational spectroscopy by making it possible to quantify the anharmonic contributions and opens the door to a first-principles calculation of multidimensional vibrational spectra.

Vibrational spectroscopy of Methyl benzoate

Methyl benzoate is studied as a model compound for the development of new IR pulse schemes with possible applicability to biomolecules.