scholarly journals Vibrational Spectra of Nucleotides in the Presence of the Au Cluster Enhancer in MD Simulation of a SERS Sensor

Biosensors ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 37
Author(s):  
Tatiana Zolotoukhina ◽  
Momoko Yamada ◽  
Shingo Iwakura
Keyword(s):  
Vibrational Spectra ◽  
Density Functional ◽  
Protein Identification ◽  
Generalized Gradient ◽  
Reaction Coordinates ◽  
Conformational Variations ◽  
Surface Enhanced Raman ◽  
Spectral Libraries ◽  
Eam Potential

Surface-enhanced Raman scattering (SERS) nanoprobes have shown tremendous potential in in vivo imaging. The development of single oligomer resolution in the SERS promotes experiments on DNA and protein identification using SERS as a nanobiosensor. As Raman scanners rely on a multiple spectrum acquisition, faster imaging in real-time is required. SERS weak signal requires averaging of the acquired spectra that erases information on conformation and interaction. To build spectral libraries, the simulation of measurement conditions and conformational variations for the nucleotides relative to enhancer nanostructures would be desirable. In the molecular dynamic (MD) model of a sensing system, we simulate vibrational spectra of the cytosine nucleotide in FF2/FF3 potential in the dynamic interaction with the Au20 nanoparticles (NP) (EAM potential). Fourier transfer of the density of states (DOS) was performed to obtain the spectra of bonds in reaction coordinates for nucleotides at a resolution of 20 to 40 cm−1. The Au20 was optimized by ab initio density functional theory with generalized gradient approximation (DFT GGA) and relaxed by MD. The optimal localization of nucleotide vs. NP was defined and the spectral modes of both components vs. interaction studied. Bond-dependent spectral maps of nucleotide and NP have shown response to interaction. The marker frequencies of the Au20—nucleotide interaction have been evaluated.

scholarly journals Influence of the Au Cluster Enhancer on Vibrational Spectra of Nucleotides in MD Simulation of a SERS Sensor

Proceedings ◽  
2020 ◽  
Vol 60 (1) ◽  
pp. 25
Author(s):  
Tatiana Zolotoukhina ◽  
Momoko Yamada ◽  
Shingo Iwakura
Keyword(s):  
Vibrational Spectra ◽  
Protein Identification ◽  
Reaction Coordinates ◽  
Surface Enhanced ◽  
Conformational Variations ◽  
Surface Enhanced Raman ◽  
Enhanced Raman Scattering ◽  
Spectral Libraries ◽  
Eam Potential

Surface-enhanced Raman scattering (SERS) nanoprobes have shown tremendous potential in in vivo imaging. The development of single oligomer resolution in the SERS promotes experiments on DNA and protein identification using SERS as a nanobiosensor. As Raman scanners rely on a multiple spectrum acquisition, the faster imaging in real-time is required. SERS weak signal requires averaging of the acquired spectra that erases information on conformation and interaction. To build spectral libraries, the simulation of measurement conditions and conformational variations for the nucleotides relative to enhancer nanostructures would be desirable. In the molecular dynamic (MD) model of a sensing system, we simulate vibrational spectra of the cytosine nucleotide in FF2/FF3 potential in the dynamic interaction with the Au20 nanoparticles (NP) (EAM potential). Fourier transfer of the density of states (DOS) was performed to obtain the spectra of bonds in reaction coordinates for nucleotides at a resolution 20 to 40 cm−1. The Au20 was optimized by ab initio DFT GGA and relaxed by MD. The optimal localization of nucleotide vs. NP was defined and spectral modes of both components vs. interaction studied. Bond-dependent spectral maps of nucleotide and NP have shown response to interaction. The marker frequencies of the Au20—nucleotide interaction have been evaluated.

Chemical adsorption of salicylate on silver - A systematic approach to the interpretation of surface-enhanced vibrational spectra

2004 ◽  
Vol 82 (6) ◽  
pp. 987-997 ◽  
Author(s):  
P J.G Goulet ◽  
R F Aroca
Keyword(s):  
Salicylic Acid ◽  
Raman Spectra ◽  
Vibrational Spectra ◽  
Density Functional ◽  
Ir And Raman Spectra ◽  
Chemical Adsorption ◽  
Surface Enhanced ◽  
Surface Enhanced Raman ◽  
Enhanced Raman Scattering ◽  
Ir And Raman

In this work, surface-enhanced vibrational spectroscopy and normal vibrational spectroscopy as well as density functional theory (DFT) computational methods have been employed to investigate the nature of the chemical adsorption and orientation of the surface species generated from salicylic acid at silver surfaces. The structure of salicylic acid and its IR and Raman spectra are determined at the B3LYP/6-311+G(d,p) level of theory. These results are used in the assignment of the vibrational spectra. Surface-enhanced Raman scattering (SERS) spectra obtained from silver island films thinly coated with salicylic acid confirm chemical adsorption on the Ag nanostructures. To probe the nature of this surface complex, the optimized geometries and IR and Raman spectra of two model salicylate-silver complexes (Ag1 and Ag2) were calculated at the B3LYP/Lanl2DZ level of theory. It was found that good agreement exists between experimentally observed SERS spectra and the simulated SERS spectra of a complex with the salicylate monoanion bound to a Ag+ ion through its carboxylate group (Ag1). The carboxylate silver salt of salicylic acid (essentially the Ag1 complex) was also prepared, and its IR and Raman spectra were recorded for comparison with the surface-enhanced vibrational spectra. These results, along with the application of surface selection rules, suggest that salicylic acid is deprotonated at silver surfaces, interacting through its carboxylate group alone, and is preferentially in a tilted head-on orientation.Key words: chemisorption, salicylic acid, silver, density functional theory, surface-enhanced Raman scattering, reflection-absorption IR spectroscopy, surface-enhanced IR absorption.

Vibrational and Surface-Enhanced Raman Spectra of 1,6-Diphenyl-1,3,5-hexatriene

2007 ◽  
Vol 61 (9) ◽  
pp. 1001-1006 ◽  
Author(s):  
Igor O. Osorio-Roman ◽  
Victor C. Vargas ◽  
Ricardo F. Aroca
Keyword(s):  
Raman Spectra ◽  
Vibrational Spectra ◽  
Density Functional ◽  
Geometry Optimization ◽  
Functional Theory ◽  
Cis And Trans Isomers ◽  
Surface Enhanced ◽  
Surface Enhanced Raman ◽  
Enhanced Raman Scattering ◽  
Cis And Trans

The vibrational spectra and surface-enhanced Raman scattering (SERS) of 1,6-diphenyl-1,3,5-hexatriene (DPH) are discussed. The fundamental vibrational frequencies, overtones, and combinations observed in the infrared and Raman spectra of DPH are reported. The interpretation of the observed vibrational spectra was supported by a complete geometry optimization, followed by vibrational frequency and intensity computations for the cis- and trans- isomers of the DPH using density functional theory at the B3LYP/6-31G(d,p) level of theory. Because the molecule is photo-chemically active on Ag metal surfaces, the best SERS results for silver islands were obtained at low temperature and low energy density of the exciting laser line. DPH SERS on Au films was obtained at room temperature.

scholarly journals Size variation of infrared vibrational spectra from molecules to hydrogenated diamond nanocrystals: a density functional theory study

2013 ◽  
Vol 4 ◽  
pp. 262-268 ◽  
Author(s):  
Mudar A Abdulsattar
Keyword(s):  
Density Functional Theory ◽  
Vibrational Spectra ◽  
Density Functional ◽  
Size Variation ◽  
Blue Shift ◽  
Radial Breathing Mode ◽  
Generalized Gradient ◽  
Functional Theory ◽  
Optical Branch ◽  
Bulk Diamond

Infrared spectra of hydrogenated diamond nanocrystals of one nanometer length are calculated by ab initio methods. Positions of atoms are optimized via density functional theory at the level of the generalized gradient approximation of Perdew, Burke and Ernzerhof (PBE) using 3-21G basis states. The frequencies in the vibrational spectrum are analyzed against reduced masses, force constants and intensities of vibration. The spectrum can be divided into two regions depending on the properties of the vibrations or the gap separating them. In the first region, results show good matching to several experimentally obtained lines. The 500 cm−1 broad-peak acoustical branch region is characterized by pure C–C vibrations. The optical branch is centered at 1185 cm−1. Calculations show that several C–C vibrations are mixed with some C–H vibrations in the first region. In the second region the matching also extends to C–H vibration frequencies that include different modes such as symmetric, asymmetric, wagging, scissor, rocking and twisting modes. In order to complete the picture of the size dependence of the vibrational spectra, we analyzed the spectra of ethane and adamantane. The present analysis shows that acoustical and optical branches in diamond nanocrystals approach each other and collapse at 963 cm−1 in ethane. Variation of the highest reduced-mass-mode C–C vibrations from 1332 cm−1 of bulk diamond to 963 cm−1 for ethane (red shift) is shown. The analysis also shows the variation of the radial breathing mode from 0 cm−1 of bulk diamond to 963 cm−1 for ethane (blue shift). These variations compare well with experiment. Experimentally, the above-mentioned modes appear shifted from their exact positions due to overlap with neighboring modes.

Lattice dynamics, phonon vibrational spectra, and thermal properties of tetragonal SrPt3P: a first-principles study

RSC Advances ◽  
2016 ◽  
Vol 6 (32) ◽  
pp. 27060-27067 ◽  
Author(s):  
Xiu-Qing Zhang ◽  
Zhao-Yi Zeng ◽  
Yan Cheng ◽  
Guang-Fu Ji
Keyword(s):  
Density Functional Theory ◽  
Thermal Properties ◽  
Vibrational Spectra ◽  
First Principles ◽  
Lattice Dynamics ◽  
Density Functional ◽  
Generalized Gradient ◽  
Functional Theory ◽  
Generalized Gradient Approximation ◽  
First Principles Study

The phonon vibrational spectra and thermal properties of the platinum-based superconductor SrPt3P are investigated by the generalized gradient approximation (GGA) in the framework of density functional theory (DFT).

Ab initio calculation on the Optical Properties of AA- Stacked two dimensional Graphene, Silicene, Germanene, and Stanene

2018 ◽  
Vol 1 (1) ◽  
pp. 46-50
Author(s):  
Rita John ◽  
Benita Merlin
Keyword(s):  
Optical Properties ◽  
Band Structure ◽  
Density Functional ◽  
Electronic Band Structure ◽  
Complex Refractive Index ◽  
Single Layer ◽  
Generalized Gradient ◽  
Electronic Band ◽  
Wide Range ◽  
Optical Region

In this study, we have analyzed the electronic band structure and optical properties of AA-stacked bilayer graphene and its 2D analogues and compared the results with single layers. The calculations have been done using Density Functional Theory with Generalized Gradient Approximation as exchange correlation potential as in CASTEP. The study on electronic band structure shows the splitting of valence and conduction bands. A band gap of 0.342eV in graphene and an infinitesimally small gap in other 2D materials are generated. Similar to a single layer, AA-stacked bilayer materials also exhibit excellent optical properties throughout the optical region from infrared to ultraviolet. Optical properties are studied along both parallel (||) and perpendicular ( ) polarization directions. The complex dielectric function (ε) and the complex refractive index (N) are calculated. The calculated values of ε and N enable us to analyze optical absorption, reflectivity, conductivity, and the electron loss function. Inferences from the study of optical properties are presented. In general the optical properties are found to be enhanced compared to its corresponding single layer. The further study brings out greater inferences towards their direct application in the optical industry through a wide range of the optical spectrum.

scholarly journals Biochemical, Ameliorative and Cytotoxic Effects of Newly Synthesized Curcumin Microemulsions: Evidence from In Vitro and In Vivo Studies

Nanomaterials ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 817
Author(s):  
Abbas Rahdar ◽  
Mohammad Reza Hajinezhad ◽  
Saman Sargazi ◽  
Maryam Zaboli ◽  
Mahmood Barani ◽  
...  
Keyword(s):  
Hepg2 Cells ◽  
Density Functional ◽  
Liver Enzymes ◽  
Elevated Serum ◽  
Ethyl Butyrate ◽  
Polymeric Chain ◽  
Prolonged Release ◽  
Advanced Therapies

Curcumin is known to exhibit antioxidant and tissue-healing properties and has recently attracted the attention of the biomedical community for potential use in advanced therapies. This work reports the formulation and characterization of oil-in-water F127 microemulsions to enhance the bioavailability of curcumin Microemulsions showed a high encapsulation efficiency and prolonged release. To investigate the interactions of curcumin with one unit of the polymeric chain of surfactant F127, ethyl butyrate, and sodium octanoate, as well as the interaction between ethyl butyrate and one unit of the F127 polymer chain, the Density Functional Theory (DFT) calculations at the M06-2X level of theory, were performed in water solution. The MTT assay was used to assess the cytotoxicity of free and encapsulated curcumin on non-malignant and malignant cell lines. Combination effects were calculated according to Chou-Talalay’s principles. Results of in vitro studies indicated that MCF7 and HepG2 cells were more sensitive to curcumin microemulsions. Moreover, a synergistic relationship was observed between curcumin microemulsions and cisplatin in all affected fractions of MCF7 and HepG2 cells (CI < 0.9). For in vivo investigation, thioacetamide-intoxicated rats received thioacetamide (100 mg/kg Sc) followed by curcumin microemulsions (30 mg/kg Ip). Thioacetamide-intoxicated rats showed elevated serum liver enzymes, blood urea nitrogen (BUN), and creatinine levels, and a significant reduction in liver superoxide dismutase (SOD) and catalase (CAT) activities (p < 0.05). Curcumin microemulsions reduced liver enzymes and serum creatinine and increased the activity of antioxidant enzymes in thioacetamide-treated rats in comparison to the untreated thioacetamide-intoxicated group. Histopathological investigations confirmed the biochemical findings. Overall, the current results showed the desirable hepatoprotective, nephroprotective, and anti-cancer effects of curcumin microemulsions.

scholarly journals Performance of SCAN Meta-GGA Functionals on Nonlinear Mechanics of Graphene-Like g-SiC

Crystals ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 120
Author(s):  
Qing Peng
Keyword(s):  
Mechanical Properties ◽  
Density Functional ◽  
Large Strains ◽  
Two Dimensional ◽  
Nonlinear Mechanics ◽  
Generalized Gradient ◽  
Mechanics Of Materials ◽  
Nonlinear Mechanical ◽  
Direct Band ◽  
Simulations And Modeling

Although meta-generalized-gradient approximations (meta-GGAs) are believed potentially the most accurate among the efficient first-principles calculations, the performance has not been accessed on the nonlinear mechanical properties of two-dimensional nanomaterials. Graphene, like two-dimensional silicon carbide g-SiC, has a wide direct band-gap with applications in high-power electronics and solar energy. Taken g-SiC as a paradigm, we have investigated the performance of meta-GGA functionals on the nonlinear mechanical properties under large strains, both compressive and tensile, along three deformation modes using Strongly Constrained and Appropriately Normed Semilocal Density Functional (SCAN) as an example. A close comparison suggests that the nonlinear mechanics predicted from SCAN are very similar to that of Perdew-Burke-Ernzerhof (PBE) formulated functional, a standard Density Functional Theory (DFT) functional. The improvement from SCAN calculation over PBE calculation is minor, despite the considerable increase of computing demand. This study could be helpful in selection of density functionals in simulations and modeling of mechanics of materials.

scholarly journals A Biochemical and Pharmacological Characterization of Phospholipase A2 and Metalloproteinase Fractions from Eastern Russell’s Viper (Daboia siamensis) Venom: Two Major Components Associated with Acute Kidney Injury

Toxins ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 521
Author(s):  
Janeyuth Chaisakul ◽  
Orawan Khow ◽  
Kulachet Wiwatwarayos ◽  
Muhamad Rusdi Ahmad Rusmili ◽  
Watcharamon Prasert ◽  
...  
Keyword(s):  
Acute Kidney Injury ◽  
Phospholipase A2 ◽  
Protein Identification ◽  
Clinical Manifestations ◽  
Kidney Injury ◽  
Factor X ◽  
Pharmacological Characterization ◽  
Russell’S Viper

Acute kidney injury (AKI) following Eastern Russell’s viper (Daboia siamensis) envenoming is a significant symptom in systemically envenomed victims. A number of venom components have been identified as causing the nephrotoxicity which leads to AKI. However, the precise mechanism of nephrotoxicity caused by these toxins is still unclear. In the present study, we purified two proteins from D. siamensis venom, namely RvPLA2 and RvMP. Protein identification using LCMS/MS confirmed the identity of RvPLA2 to be snake venom phospholipase A2 (SVPLA2) from Thai D. siamensis venom, whereas RvMP exhibited the presence of a factor X activator with two subunits. In vitro and in vivo pharmacological studies demonstrated myotoxicity and histopathological changes of kidney, heart, and spleen. RvPLA2 (3–10 µg/mL) caused inhibition of direct twitches of the chick biventer cervicis muscle preparation. After administration of RvPLA2 or RvMP (300 µg/kg, i.p.) for 24 h, diffuse glomerular congestion and tubular injury with minor loss of brush border were detected in envenomed mice. RvPLA2 and RvMP (300 µg/kg; i.p.) also induced congestion and tissue inflammation of heart muscle as well as diffuse congestion of mouse spleen. This study showed the significant roles of PLA2 and SVMP in snake bite envenoming caused by Thai D. siamensis and their similarities with observed clinical manifestations in envenomed victims. This study also indicated that there is a need to reevaluate the current treatment strategies for Thai D. siamensis envenoming, given the potential for irreversible nephrotoxicity.

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