The First Silver-Based Plasmonic Nanomaterial for Shell-Isolated Nanoparticle-Enhanced Raman Spectroscopy with Magnetic Properties.

Nanostructures made of magnetic cores (from Fe3O4) with attached silver plasmonic nanostructures were covered with a very thin layer of silica. The (Fe3O4@Ag)@SiO2 magnetic-plasmonic nanomaterial can be manipulated using a magnetic field. For example, one can easily form homogeneous layers from this nanomaterial using a very simple procedure: deposition of a layer of a sol of such a nanostructure and evaporation of the solvent after placing the sample in a strong magnetic field. Due to the rapid magnetic immobilization of the magnetic-plasmonic nanomaterial on the investigated surface, no coffee-ring effect occurs during the evaporation of the solvent. In this contribution, we report the first example of a magnetic, silver-based plasmonic nanomaterial for shell-isolated nanoparticle-enhanced Raman spectroscopy (SHINERS). Nanoresonators based on silver plasmonic nanostructures locally enhance the intensity of the exciting electromagnetic radiation in a significantly broader frequency range than the previously used magnetic SHINERS nanoresonators with gold plasmonic nanostructures. Example applications where the resulting nanomaterial was used for the SHINERS investigation of a monolayer of mercaptobenzoic acid chemisorbed on platinum, and for a standard SERS determination of dopamine, are also presented.

Attachment of Single-Stranded DNA to Certain SERS-Active Gold and Silver Substrates: Selected Practical Tips.

Layers formed from single-stranded DNA on nanostructured plasmonic metals can be applied as "working elements" in surface-enhanced Raman scattering (SERS) sensors used to sensitively and accurately identify specific DNA fragments in various biological samples (for example, in samples of blood). Therefore, the proper formation of the desired DNA layers on SERS substrates is of great practical importance, and many research groups are working to improve the process in forming such structures. In this work, we propose two modifications of a standard method used for depositing DNA with an attached linking thiol moiety on certain SERS-active structures; the modifications yield DNA layers that generate a stronger SERS signal. We propose: (i) freezing the sample when forming DNA layers on the nanoparticles, and (ii) when forming DNA layers on SERS-active macroscopic silver substrates, using ω-substituted alkanethiols with very short alkane chains (such as cysteamine or mercaptopropionic acid) to backfill the empty spaces on the metal surface unoccupied by DNA. When 6-mercapto-1-hexanol is used to fill the unoccupied places on a silver surface (as in experiments on standard gold substrates), a quick detachment of chemisorbed DNA from the silver surface is observed. Whereas, using ω-substituted alkanethiols with a shorter alkane chain makes it possible to easily form mixed DNA/backfilling thiol monolayers. Probably, the significantly lower desorption rate of the thiolated DNA induced by alkanethiols with shorter chains is due to the lower stabilization energy in monolayers formed from such compounds.

SERS Studies of Adsorption on Gold Surfaces of Mononucleotides with Attached Hexanethiol Moiety: Comparison with Selected Single-Stranded Thiolated DNA Fragments.

The attachment of DNA strands to gold surfaces is performed in many devices, such as various DNA sensors. One of the standard methods used to immobilize DNA on gold surfaces involves two steps: the attachment of a thiol linker group (usually in the form of alkanethiol moiety) to the DNA strand, and the chemical reaction between the thiol-terminated DNA and the gold surface. Since thiols react chemically with the surface of gold substrates, forming very stable Au-S bonds, it is often assumed that the chemisorption on the gold surface of nucleotides with an attached thiol linker group leads to the formation of an order layer with the linking moieties relatively densely packed on the gold surface. In this contribution we show that chemisorption of thiolated mononucleotides does not occur according to this model. For example, the thiolated mononucleotide containing adenine strongly interacts with the gold surface via the adenine moiety. Moreover, bonding of the mononucleotide containing adenine to the gold surface is relatively similar to the bonding of adenine, and the main difference is that the adenine interacts with the gold surface mainly through the pyrimidine ring, while for adenine mononucleotide interaction via the imidazole ring also significantly contributes to the total bonding. A similar effect was observed for the mononucleotide containing cytosine, and the main difference between the interaction with the gold surface of cytosine and cytosine mononucleotide is that mononucleotide containing cytosine interacts with the gold surface to a significantly larger extend via the carboxylic group of the base. We also show that the structure of the layer formed on the gold surface by the thiolated mononucleotides may be significantly different than the structure of the layer formed by thiolated single-stranded DNA containing even as few as two bases.

Surface Enhanced Raman Spectroscopy for DNA Biosensors-How Far Are We?

A sensitive and accurate identification of specific DNA fragments (usually containing a mutation) can influence clinical decisions. Standard methods routinely used for this type of detection are PCR (Polymerase Chain Reaction, and its modifications), and, less commonly, NGS (Next Generation Sequencing). However, these methods are quite complicated, requiring time-consuming, multi-stage sample preparation, and specially trained staff. Usually, it takes weeks for patients to obtain their results. Therefore, different DNA sensors are being intensively developed by many groups. One technique often used to obtain an analytical signal from DNA sensors is Raman spectroscopy. Its modification, surface-enhanced Raman spectroscopy (SERS), is especially useful for practical analytical applications due to its extra low limit of detection. SERS takes advantage of the strong increase in the efficiency of Raman signal generation caused by a local electric field enhancement near plasmonic (typically gold and silver) nanostructures. In this condensed review, we describe the most important types of SERS-based nanosensors for genetic studies and comment on their potential for becoming diagnostic tools.

Raman, surface-enhanced Raman, and density functional theory characterization of (diphenylphosphoryl)(pyridin-2-, -3-, and -4-yl)methanol.

This work presents near-infrared Raman spectroscopy (FT-RS) and surface-enhanced Raman scattering (SERS) studies of three pyridine-α-hydroxymethyl biphenyl phosphine oxide isomers: (diphenylphosphoryl)(pyridin-2-yl)methanol (α-Py), (diphenylphosphoryl)(pyridin-3-yl)methanol (ß-Py), and (diphenylphosphoryl)(pyridin-4-yl)methanol (γ-Py) adsorbed onto colloidal and roughened in oxidation-reduction cycles silver surfaces. The molecular geometries in the equilibrium state and vibrational frequencies were calculated by density functional theory (DFT) at the B3LYP 6-311G(df,p) level of theory. The results imply that the most stable structure of the investigated molecules is a dimer created by two intermolecular hydrogen bonds between the H atom of the α-hydroxyl group (in up (HOU) or down (HOD) stereo bonds position) and the O atom of tertiary phosphine oxide (═O) of the two monomers. Comparison the FT-RS spectra with the respective SERS spectra allowed us to predict the orientation of the hydroxyphosphonate derivatives of pyridine that depends upon both the position of the substituent relative to the ring N atom (in α-, ß-, and γ-position, respectively) and the type of silver substrate.

Plasmonic substrates for biochemical applications of surface-enhanced Raman spectroscopy.

Due to its great practical importance, the detection and determination of many biomolecules in body fluids and other samples is carried out in a large number of laboratories around the world. One of the most promising analytical techniques now being widely introduced into medical analysis is surface-enhanced Raman scattering (SERS) spectroscopy. SERS is one of the most sensitive analytical methods, and in some cases, a good quality SERS spectrum dominated by the contribution of even a single molecule can be obtained. Highly sensitive SERS measurements can only be carried out on substrates generating a very high SERS enhancement factor and a low Raman spectral background, and so using of right nanomaterials is a key element in the success of SERS biochemical analysis. In this review article, we present progress that has been made in the preparation of nanomaterials used in SERS spectroscopy for detecting various kinds of biomolecules. We describe four groups of nanomaterials used in such measurements: nanoparticles of plasmonic metals and deposits of plasmonic nanoparticles on macroscopic substrates, nanocomposites containing plasmonic and non-plasmonic parts, nanostructured macroscopic plasmonic metals, and nanostructured macroscopic non-plasmonic materials covered by plasmonic films. We also describe selected SERS biochemical analyses that utilize the nanomaterials presented. We hope that this review will be useful for researchers starting work in this fascinating field of ​​science and technology.

Why Does One Measure Resonance Raman Optical Activity? A Unique Case of Measurements under Strong Resonance versus Far-from-Resonance Conditions.

Raman optical activity (ROA) spectroscopy exhibits significant potential in the study of (bio)molecules as it encodes information on their molecular structure, chirality, and conformations. Furthermore, the method reveals details on excited electronic states when applied under resonance conditions. Here, we present a combined study of the far from resonance (FFR)-ROA and resonance ROA (RROA) of a single relatively small molecular system. Notably, this study is the first to employ the density functional theory (DFT) analysis of both FFR-ROA and RROA spectra. This is illustrated for cobalamin derivatives using near-infrared and visible light excitation. Although the commonly observed monosignate RROA spectra lose additional information visible in bisignate nonresonance ROA spectra, the RROA technique acts as a complement to nonresonance ROA spectroscopy. In particular, the combination of these methods integrated with DFT calculations can reveal a complete spectral picture of the structural and conformational differences between tested compounds.

Vibrational and theoretical studies of the structure and adsorption mode of m-nitrophenyl α-guanidinomethylphosphonic acid analogues on silver surfaces.

This work presents Fourier transform Raman (FT-Raman), Fourier transform absorption infrared (FT-IR), and surface-enhanced Raman scattering (SERS) spectroscopic investigations of three m-nitrophenyl α-guanidinomethylphonic acids, including m-NO2PhG(cHex)P, m-NO2PhG(Morf)P, and m-NO2PhG(An)P, adsorbed onto colloidal and roughened silver surfaces. The SERS spectra were deconvoluted to determine the overlapped bands from which the specific molecular orientation can be deducted. The vibrational wavenumbers are calculated through density functional theory (DFT) at the B3LYP/6-31++G** level with the Gaussian 03, Raint, GaussSum 0.8, and GAR2PED software packages. The experimental and calculated vibrational bands are compared to those from SERS for the investigated compounds adsorbed on colloidal and roughened silver surfaces. The geometry of these molecules on the SERS-active silver surfaces is deduced from the observed changes in both the intensity and width of the Raman bands in the spectra of the bound species relative to the free species.

Nanomaterials for Surface Enhanced Raman Spectroscopy.

For many decades, Raman spectroscopy has been disregarded as an ineffective analytical tool because of the very low efficiency of "normal" Raman scattering (the typical cross-section for Raman scattering is about 11 and 8 orders of magnitude smaller than the typical cross-sections for absorption in ultraviolet and infrared wavelengths, respectively [...].

Influence of sandwich-type DNA construction strategy and plasmonic metal on signal generated by SERS DNA sensors.

The DNA biosensors are powerful tools in the gene mutation or pathogens detection. That is why there are a lot of DNA detection strategies and methods. Here we present the insight on a slightly overlooked DNA detection technique, surface-enhanced Raman scattering (SERS). The present work is a summary of the influence of the plasmonic metal of the SERS substrate and strategy of the sandwich-type biosensor construction, simply the placement of the Raman reporter and mismatches, on the SERS signal enhancement. We found that, although in general there is an increase in the intensity of the SERS signal when the distance between the Raman scatterer and the SERS-active surface decreases, for this type of DNA SERS sensor a greater intensity of the measured Raman signal is usually observed when the Raman reporter is farther away from the plasmonic substrate. This is probably caused by a significant change in the hybridisation efficiency for the different structures of the sensor analysed due to some steric hindrances.

New, fast and cheap prediction tests for BRCA1 gene mutations identification in clinical samples.

Despite significant progress in cancer therapy, cancer is still the second cause of mortality in the world. The necessity to make quick therapeutic decisions forces the development of procedures allowing to obtain a reliable result in a quick and unambiguous manner. Currently, detecting predictive mutations, including BRCA1, is the basis for effectively treating advanced breast cancer. Here, we present new insight on gene mutation detection. We propose a cheap BRCA1 mutation detection tests based on the surface plasmon resonance (SPR) or quartz crystal microbalance with energy dissipation (QCM-D) response changes recorded during a hybridization process of an oligonucleotide molecular probe with DNA fragments, with and without the BRCA1 mutation. The changes in the morphology of the formed DNA layer caused by the presence of the mutation were confirmed by atomic force microscopy. The unique property of the developed SPR and QCM tests is really short time of analysis: ca. 6 min for SPR and ca. 25 min for QCM. The proposed tests have been verified on 22 different DNA extracted from blood leukocytes collected from cancer patients: 17 samples from patients with various BRCA1 gene mutation variants including deletion, insertion and missense single-nucleotide and 5 samples from patients without any BRCA1 mutation. Our test is a response to the need of medical diagnostics for a quick, unambiguous test to identify mutations of the BRCA1 gene, including missense single-nucleotide (SNPs).

Fourier transform infrared and Raman and surface-enhanced Raman spectroscopy studies of a novel group of boron analogues of aminophosphonic acids.

Five analogues of a novel group of boron derivatives of aminophosphonic acids-N-benzylamino-(3-boronphenyl)-S-methylphosphonic acid (m-PhS), N-benzylamino-(4-boronphenyl)-S-methylphosphonic acid (p-PhS), N-benzylamino-(2-boronphenyl)-R-methylphosphonic acid (o-PhR), N-benzylamino-(3-boronphenyl)-R-methylphosphonic acid (m-PhR), and N-benzylamino-(4-boronphenyl)-R-methylphosphonic acid (p-PhR)-were studied using Fourier transform infrared (FT IR), Fourier transform Raman (FT RS), and surface-enhanced Raman (SERS) spectroscopies. Analysis of obtained FT IR and FT RS spectra show that all investigated compounds in the solid state exist as dimeric species formed by an H-bonding interaction between -B(OH)(2) moieties of each monomer. In addition, comparison of the wavenumbers, intensities, and broadness of bands from the FT Raman and SERS spectra allowed information to be obtained regarding the adsorption geometry of the investigated compounds immobilized onto an electrochemically roughened silver substrate.

Magnetic iron oxide cores with attached gold nanostructures coated with a layer of silica: An easily, homogeneously deposited new nanomaterial for surface-enhanced Raman scattering measurements.

Nanostructures made of magnetic cores (Fe3O4) with many smaller plasmonic (Au) nanostructures attached were covered with a very thin layer of silica. The first example of the application of this type of material for surface-enhanced Raman scattering (SERS) measurements is presented. (Fe3O4@Au)@SiO2 nanoparticles turned out to be very efficient substrates for SERS measurements. Moreover, due to the nanomaterial's strong magnetic properties, it can be easily manipulated using a magnetic field, and it is therefore possible to form homogeneous layers (with no significant 'coffee-ring' effect) of (Fe3O4@Au)@SiO2 nanoparticles using a very simple procedure: depositing a drop of a sol of such nanoparticles and evaporating the solvent after placing the sample in a strong magnetic field. Synthesised (Fe3O4@Au)@SiO2 nanostructures have been used for the SERS detection of penicillin G in milk. Good quality SERS spectra of penicillin G were obtained even at a concentration of penicillin G in milk of 1 nmol/l - this means that the SERS detection of penicillin G in milk is possible at a concentration lower than the maximum residue limit of penicillin G in milk established by the European Commission. .

Influence of the Co-Adsorbed Ions on the Surface-Enhanced Raman Scattering Spectra of Dopamine Adsorbed on Nanostructured Silver.

The abnormal metabolism or imbalance of dopamine may lead to some neurological disorders. Therefore, the facile and fast detection of this neurotransmitter is essential in the early diagnosis of some diseases. One of the methods that can be used for the detection and determination of dopamine is the surface-enhanced Raman scattering (SERS). In this contribution, we report a very strong influence of some salts (we used salts containing Na+ cations and the following anions: SO42-, F-, Cl-, Br-, and I-) on the spectral patterns and intensity of the SERS spectra of dopamine adsorbed on a nanostructured macroscopic silver substrate. The analysis of the recorded SERS spectra based on the assignments of Raman bands from the density-functional theory (DFT) calculations and based on the SERS surface selection rules reveals that when molecules of dopamine are adsorbed from an aqueous solution to which no electrolytes have been added, they adopt a flat orientation versus the silver surface; whereas, the molecules of dopamine co-adsorbed with various ions interact with the silver surface, mainly via phenolic groups, and they adopt a perpendicular orientation versus the metal surface. An addition of electrolytes also significantly influences the intensity of the recorded SERS spectrum; for example, an addition of Na2SO4 to a final concentration of 1 M induces an increase in the intensity of the measured SERS spectrum by a factor of ca. 40. This means that the addition of electrolytes to the analyzed solution can reduce the limit of detection of dopamine by SERS spectroscopy. The abovementioned findings may facilitate the construction of dopamine SERS sensors.

Ordered zirconium dioxide nanotubes covered with an evaporated gold layer as reversible, chemically inert and very efficient substrates for surface-enhanced Raman scattering (SERS) measurement.

The deposition of a layer of plasmonic metal on a surface of highly ordered nanostructured oxide is one of the important methods of preparation of substrates for surface-enhanced Raman scattering (SERS) measurements. In this contribution we describe formation of SERS substrates by the deposition of a gold layer on ordered ZrO2 nanotubes. The influence of various experimental parameters on the structure of formed composites and the achievable SERS enhancement factor has been analysed. Like commonly used SERS substrates formed by the deposition of plasmonic metals on TiO2 nanotubes, gold-covered ZrO2 nanotubes also could be used as reversible SERS platform after water rinsing: there is no any significant decrease in the SERS activity of the substrate even after 20 radiation-induced cleaning cycles. Moreover, SERS substrates formed on ZrO2 nanotubes are significantly more stable in strongly acidic media than the previously developed SERS substrates based on ordered TiO2 nanotubes.

Nanofunctionalization of Additively Manufactured Titanium Substrates for Surface-Enhanced Raman Spectroscopy Measurements.

Powder bed fusion using a laser beam (PBF-LB) is a commonly used additive manufacturing (3D printing) process for the fabrication of various parts from pure metals and their alloys. This work shows for the first time the possibility of using PBF-LB technology for the production of 3D titanium substrates (Ti 3D) for surface-enhanced Raman scattering (SERS) measurements. Thanks to the specific development of the 3D titanium surface and its nanoscale modification by the formation of TiO2 nanotubes with a diameter of ~80 nm by the anodic oxidation process, very efficient SERS substrates were obtained after deposition of silver nanoparticles (0.02 mg/cm2, magnetron sputtering). The average SERS enhancement factor equal to 1.26 × 106 was determined for pyridine (0.05 M + 0.1 M KCl), as a model adsorbate. The estimated enhancement factor is comparable with the data in the literature, and the substrate produced in this way is characterized by the high stability and repeatability of SERS measurements. The combination of the use of a printed metal substrate with nanofunctionalization opens a new path in the design of SERS substrates for applications in analytical chemistry. Methods such as SEM scanning microscopy, photoelectron spectroscopy (XPS) and X-ray diffraction analysis (XRD) were used to determine the morphology, structure and chemical composition of the fabricated materials.

Thermally Stable Magneto-Plasmonic Nanoparticles for SERS with Tunable Plasmon Resonance.

Bifunctional magneto-plasmonic nanoparticles that exhibit synergistically magnetic and plasmonic properties are advanced substrates for surface-enhanced Raman spectroscopy (SERS) because of their excellent controllability and improved detection potentiality. In this study, composite magneto-plasmonic nanoparticles (Fe3O4@AgNPs) were formed by mixing colloid solutions of 50 nm-sized magnetite nanoparticles with 13 nm-sized silver nanoparticles. After drying of the layer of composite Fe3O4@AgNPs under a strong magnetic field, they outperformed the conventional silver nanoparticles during SERS measurements in terms of signal intensity, spot-to-spot, and sample-to-sample reproducibility. The SERS enhancement factor of Fe3O4@AgNP-adsorbed 4-mercaptobenzoic acid (4-MBA) was estimated to be 3.1 × 107 for a 633 nm excitation. In addition, we show that simply by changing the initial volumes of the colloid solutions, it is possible to control the average density of the silver nanoparticles, which are attached to a single magnetite nanoparticle. UV-Vis and SERS data revealed a possibility to tune the plasmonic resonance frequency of Fe3O4@AgNPs. In this research, the plasmon resonance maximum varied from 470 to 800 nm, suggesting the possibility to choose the most suitable nanoparticle composition for the particular SERS experiment design. We emphasize the increased thermal stability of composite nanoparticles under 532 and 442 nm laser light irradiation compared to that of bare Fe3O4 nanoparticles. The Fe3O4@AgNPs were further characterized by XRD, TEM, and magnetization measurements.

Surface-enhanced Raman scattering used to study the structure of layers formed on metal surfaces from single-stranded DNA and 6-mercaptohexan-1-ol: influence of hybridization with the complementary DNA and influence of the metal substrate.

Capture single-stranded DNA with an attached alkanethiol linking moiety (capture HS-ssDNA) and 6-mercaptohexan-1-ol were chemisorbed on nanostructured GaN covered with sputtered layers of plasmonic metals (like silver and gold). The structure of the formed layer was determined by surface-enhanced Raman scattering (SERS) measurements. Hybridization with the target ssDNA, complementary to the chains of immobilized capture HS-ssDNA, induced changes in the conformation of the chains of chemisorbed ω-substituted alkanetiols (6-mercaptohexan-1-ol and the alkanethiol linking moiety of HS-ssDNA). Such changes are significantly larger in the case of experiments on silver than on gold and gold/silver SERS substrates. This means that silver substrates are significantly more promising for the SERS observation of such hybridization-induced rearrangements than the gold substrates previously used. Although the sputtered metal films have a nanograin structure, the nanostructuring of the GaN substrates plays an important role in the SERS-activity of this nanomaterial.

Applications of Surface-Enhanced Raman Scattering in Biochemical and Medical Analysis.

In this mini-review, we briefly describe certain recently developed applications of the surface-enhanced Raman spectroscopy (SERS) for determining various biochemically (especially medically) important species from ones as simple as hydrogen cations to those as complex as specific DNA fragments. We present a SERS analysis of species whose characterization is important to our understanding of various mechanisms in the human body and to show its potential as an alternative for methods routinely used in diagnostics and clinics. Furthermore, we explain how such SERS-based sensors operate and point out future prospects in this field.

Intracellular pH - Advantages and pitfalls of surface-enhanced Raman scattering and fluorescence microscopy - A review.

The value of pH in various parts of protoplasm can affect nearly all aspects of cell functions. Therefore, the determination of intracellular acid-base features is required in many areas of biological and biochemical studies. Because of a significant scientific importance of in vivo intracellular pH measurements, various groups carried out such experiments. In this review article we describe intracellular pH measurements using two the most sensitive optical spectroscopies: surface-enhanced Raman scattering (SERS) and fluorescence. It is reasonable to present these two techniques in one review article because the experimental approach in Raman and fluorescence experiments is relatively similar. The basic theoretical background explaining the mechanism of operation of fluorescence and SERS sensors are discussed and the motivations to carry out intracellular pH measurements are briefly described. Future perspectives in this field are also discussed.