Frequency-Resolved Nanoscale Chemical Imaging of 4,4′-Dimercaptostilbene on Silver

El‐Khoury, Patrick Z.; Ueltschi, Tyler W.; Mifflin, Amanda L.; Hu, Dehong; Hess, Wayne P.

doi:10.1021/jp509082c

Cited by 9 publications

(30 citation statements)

References 28 publications

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“…The relative size and weight of the nucleotides as compared with nucleobases reduce rotational motion inside the pore [ 46 , 47 , 48 , 49 ] that is further controlled by translocation velocity. For the given graphene-nucleotide setup, evaluation of the vibrational spectral maps of the DNA nucleotides, cytosine, thymine, adenine, and guanine, has been initially carried out in reactive coordinates by accumulating spectra of individual atom of bonds obtained by autocorrelation functions of Equation (1).…”

Section: Model and Methodsmentioning

confidence: 99%

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

2021

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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.

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Section: Model and Methodsmentioning

confidence: 99%

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

2021

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“…The graphene-molecule C-X (X = H, O, N, C) potential is considered as a VdW one to avoid bond creation and nucleotide attachment to the pore. The relative size and weight of the nucleotides as compared with nucleobases reduce rotational motion inside the pore [37][38][39][40] that is further controlled by translocation velocity. For the given graphene-nucleotide setup, evaluation of the vibrational spectral maps of the DNA nucleotides cytosine, thymine, adenine, and guanine has been initially done in reactive coordinates by accumulating spectra of individual atom of bonds obtained by autocorrelation functions of Equation (1).…”

Section: Model and Methodsmentioning

confidence: 99%

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

Zolotoukhina

Yamada

Iwakura

2020

The 1st International Electronic Conference on Biosensors

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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.

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“…in which ω s is the scattered frequency in cm −1 , ω n is the frequency of the nth vibrational mode in cm −1 , and the calculated S i is typically in A 4 amu −1 , governed by Equations (1)-(3). In the realm of single molecules, orientational averaging according to Equations (1)-(3) is no longer appropriate [22,24,25,30]. In this case, the scattering tensor that governs Raman activity may be expressed as where E L i,s are the enhanced incident and scattered local electric fields, ′ n is the molecular polarizability derivative tensor of the nth vibrational Eigenstate, and Ω = , , are the Euler angles which determine molecular orientation relative to the local electric fields.…”

Section: Theoretical Frameworkmentioning

confidence: 99%

“…from finite-difference time domain (FDTD) simulations, (ii) the expansion of molecular polarizability and the inclusion of higher order terms, e.g. at plasmonic nanojunctions where electric field gradients are operative and may lead to optical activity [22], and (iii) the use of molecular polarizabilities of a molecule chemisorbed/physisorbed onto silver nanoclusters/slabs, and simulated using the electronic structure method of choice [24,25,30]. That said, there are limitations to this formalism.…”

Section: Theoretical Frameworkmentioning

confidence: 99%

See 1 more Smart Citation

The information content in single-molecule Raman nanoscopy

El‐Khoury

Abellán²,

Chantry³

et al. 2016

Advances in Physics: X

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It is now possible to establish the chemical identity of a substance at the ultimate detection limit of a single molecule, i.e. the sensitivity required to probe 1.66 yoctomoles (1/NA), using surface-enhanced Raman scattering (SERS). It is also possible to image within an individual molecule, all while retaining chemical selectivity, using tip-enhanced Raman scattering (TERS). The potential applications of ultrasensitive SERS and TERS in chemical and biological detection and imaging are evident, and have attracted significant attention over the past decade. Rather than focusing on conventional single/few-molecule SERS and TERS experiments, where the objective is ultrasensitive spectroscopy and nanoscale chemical imaging, herein we consider greatly informative, yet significantly underrated, signatures of single molecules. Namely, we review recent efforts ultimately aimed at probing different aspects of a molecule's local environment through a detailed analysis of its SERS and TERS spectra and images. Particular attention is devoted to local electric field imaging using TERS; we describe how the vector components and absolute magnitude of the local electric field may be inferred from molecular Raman signatures. We also propose experiments that can potentially be used to cross-check the insights gained from the described SERS and TERS measurements. The ultimate goal of this review is to demonstrate that there is much more to single-molecule Raman scattering than mere ultrasensitive chemical analysis.

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Frequency-Resolved Nanoscale Chemical Imaging of 4,4′-Dimercaptostilbene on Silver

Cited by 9 publications

References 28 publications

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

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

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

The information content in single-molecule Raman nanoscopy

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