6.2.2. Definition of Effective Properties 3064 6.3. Response Properties to Magnetic Fields 3066 6.3.1. Nuclear Shielding 3066 6.3.2. Indirect Spin−Spin Coupling 3067 6.3.3. EPR Parameters 3068 6.4. Properties of Chiral Systems 3069 6.4.1. Electronic Circular Dichroism (ECD) 3069 6.4.2. Optical Rotation (OR) 3069 6.4.3. VCD and VROA 3070 7. Continuum and Discrete Models 3071 7.1. Continuum Methods within MD and MC Simulations 3072

/pdf/quantum-mechanical-continuum-solvation-models-3edv963g14.pdf

Quantum mechanical continuum solvation models.

Detection of chemical and biological agents plays a fundamental role in biomedical, forensic and environmental sciences1–4 as well as in anti bioterrorism applications.5–7 The development of highly sensitive, cost effective, miniature sensors is therefore in high demand which requires advanced technology coupled with fundamental knowledge in chemistry, biology and material sciences.8–13

In general, sensors feature two functional components: a recognition element to provide selective/specific binding with the target analytes and a transducer component for signaling the binding event. An efficient sensor relies heavily on these two essential components for the recognition process in terms of response time, signal to noise (S/N) ratio, selectivity and limits of detection (LOD).14,15 Therefore, designing sensors with higher efficacy depends on the development of novel materials to improve both the recognition and transduction processes. Nanomaterials feature unique physicochemical properties that can be of great utility in creating new recognition and transduction processes for chemical and biological sensors15–27 as well as improving the S/N ratio by miniaturization of the sensor elements.28

Gold nanoparticles (AuNPs) possess distinct physical and chemical attributes that make them excellent scaffolds for the fabrication of novel chemical and biological sensors (Figure 1).29–36 First, AuNPs can be synthesized in a straightforward manner and can be made highly stable. Second, they possess unique optoelectronic properties. Third, they provide high surface-to-volume ratio with excellent biocompatibility using appropriate ligands.30 Fourth, these properties of AuNPs can be readily tuned varying their size, shape and the surrounding chemical environment. For example, the binding event between recognition element and the analyte can alter physicochemical properties of transducer AuNPs, such as plasmon resonance absorption, conductivity, redox behavior, etc. that in turn can generate a detectable response signal. Finally, AuNPs offer a suitable platform for multi-functionalization with a wide range of organic or biological ligands for the selective binding and detection of small molecules and biological targets.30–32,36 Each of these attributes of AuNPs has allowed researchers to develop novel sensing strategies with improved sensitivity, stability and selectivity. In the last decade of research, the advent of AuNP as a sensory element provided us a broad spectrum of innovative approaches for the detection of metal ions, small molecules, proteins, nucleic acids, malignant cells, etc. in a rapid and efficient manner.37



Figure 1

Physical properties of AuNPs and schematic illustration of an AuNP-based detection system.



In this current review, we have highlighted the several synthetic routes and properties of AuNPs that make them excellent probes for different sensing strategies. Furthermore, we will discuss various sensing strategies and major advances in the last two decades of research utilizing AuNPs in the detection of variety of target analytes including metal ions, organic molecules, proteins, nucleic acids, and microorganisms.

/pdf/gold-nanoparticles-in-chemical-and-biological-sensing-5e2qojkdzn.pdf

Gold nanoparticles in chemical and biological sensing.

The ability to control the size, shape, and material of a surface has reinvigorated the field of surface-enhanced Raman spectroscopy (SERS). Because excitation of the localized surface plasmon resonance of a nanostructured surface or nanoparticle lies at the heart of SERS, the ability to reliably control the surface characteristics has taken SERS from an interesting surface phenomenon to a rapidly developing analytical tool. This article first explains many fundamental features of SERS and then describes the use of nanosphere lithography for the fabrication of highly reproducible and robust SERS substrates. In particular, we review metal film over nanosphere surfaces as excellent candidates for several experiments that were once impossible with more primitive SERS substrates (e.g., metal island films). The article also describes progress in applying SERS to the detection of chemical warfare agents and several biological molecules.

Surface-Enhanced Raman Spectroscopy

Multiplexed detection of oligonucleotide targets has been performed with gold nanoparticle probes labeled with oligonucleotides and Raman-active dyes. The gold nanoparticles facilitate the formation of a silver coating that acts as a surface-enhanced Raman scattering promoter for the dye-labeled particles that have been captured by target molecules and an underlying chip in microarray format. The strategy provides the high-sensitivity and high-selectivity attributes of gray-scale scanometric detection but adds multiplexing and ratioing capabilities because a very large number of probes can be designed based on the concept of using a Raman tag as a narrow-band spectroscopic fingerprint. Six dissimilar DNA targets with six Raman-labeled nanoparticle probes were distinguished, as well as two RNA targets with single nucleotide polymorphisms. The current unoptimized detection limit of this method is 20 femtomolar.

https://science.sciencemag.org/content/sci/297/5586/1536.full.pdf

Nanoparticles with Raman Spectroscopic Fingerprints for DNA and RNA Detection

Surface-enhanced Raman scattering (SERS) is a powerful spectroscopy technique that can provide non-destructive and ultra-sensitive characterization down to single molecular level, comparable to single-molecule fluorescence spectroscopy. However, generally substrates based on metals such as Ag, Au and Cu, either with roughened surfaces or in the form of nanoparticles, are required to realise a substantial SERS effect, and this has severely limited the breadth of practical applications of SERS. A number of approaches have extended the technique to non-traditional substrates, most notably tip-enhanced Raman spectroscopy (TERS) where the probed substance (molecule or material surface) can be on a generic substrate and where a nanoscale gold tip above the substrate acts as the Raman signal amplifier. The drawback is that the total Raman scattering signal from the tip area is rather weak, thus limiting TERS studies to molecules with large Raman cross-sections. Here, we report an approach, which we name shell-isolated nanoparticle-enhanced Raman spectroscopy, in which the Raman signal amplification is provided by gold nanoparticles with an ultrathin silica or alumina shell. A monolayer of such nanoparticles is spread as 'smart dust' over the surface that is to be probed. The ultrathin coating keeps the nanoparticles from agglomerating, separates them from direct contact with the probed material and allows the nanoparticles to conform to different contours of substrates. High-quality Raman spectra were obtained on various molecules adsorbed at Pt and Au single-crystal surfaces and from Si surfaces with hydrogen monolayers. These measurements and our studies on yeast cells and citrus fruits with pesticide residues illustrate that our method significantly expands the flexibility of SERS for useful applications in the materials and life sciences, as well as for the inspection of food safety, drugs, explosives and environment pollutants.

http://www.dstuns.iitm.ac.in/grouppresentations/2010/Shell-isolated%20nanoparticle%20-%20enhanced%20Raman%20spectroscopy.pdf

Shell-isolated nanoparticle-enhanced Raman spectroscopy

In the Raman effect, incident light is inelastically scattered from a sample and shifted in frequency by the energy of its characteristic molecular vibrations. Since its discovery in 1927, the effect has attracted attention from a basic research point of view as well as a powerful spectroscopic technique with many practical applications. The advent of laser light sources with monochromatic photons at high flux densities was a milestone in the history of Raman spectroscopy and resulted in dramatically improved scattering signals (for a general overview of modern Raman spectroscopy, see refs 1-5). In addition to this so-called spontaneous or incoherent Raman scattering, the development of lasers also opened the field of stimulated or coherent Raman spectroscopies, in which molecular vibrations are coherently excited. Whereas the intensity of spontaneous Raman scattering depends linearly on the number of probed molecules, the coherent Raman signal is proportional to the square of this number (for an overview, see refs 6 and 7). Coherent Raman techniques can provide interesting new opportunities such as vibrational imaging of biological samples,8 but they have not yet advanced the field of ultrasensitive trace detection. Therefore, in the following article, we shall focus on the spontaneous Raman effect, in the following simply called Raman scattering. Today, laser photons over a wide range of frequencies from the near-ultraviolet to the near-infrared region are used in Raman scattering studies, allowing selection of optimum excitation conditions for each sample. By choosing wavelengths which excite appropriate electronic transitions, resonance Raman studies of selected components of a sample or parts of a molecule can be performed.9 In the past few years, the range of excitation wavelengths has been extended to the near-infrared (NIR) region, in which background fluorescence is reduced and photoinduced degradation from the sample is diminished. High-intensity NIR diode lasers are easily available, making this region attractive for compact, low cost Raman instrumentation. Further, the development of low noise, high quantum efficiency multichannel detectors (chargecoupled device (CCD) arrays), combined with highthroughput single-stage spectrographs used in combination with holographic laser rejection filters, has led to high-sensitivity Raman spectrometers (for an overview on state-of-the-art NIR Raman systems, see ref 10). As we shall show in section 2, the nearinfrared region also has special importance for ultrasensitive Raman spectroscopy at the singlemolecule level. As with optical spectroscopy, the Raman effect can be applied noninvasively under ambient conditions in almost every environment. Measuring a Raman spectrum does not require special sample preparation techniques, in contrast with infrared absorption spectroscopy. Optical fiber probes for bringing excitation laser light to the sample and transporting scattered light to the spectrograph enable remote detection of Raman signals. Furthermore, the spatial and temporal resolution of Raman scattering are determined by the spot size and pulse length, respectively, of the excitation laser. By using a confocal microscope, Raman signals from femtoliter volumes (∼1 μm3) can by observed, enabling spatially resolved measurements in chromosomes and cells.11 Techniques such as multichannel Hadamard transform Raman microscopy12,13 or confocal scanning Fourier transform Raman microscopy14 allow generation of high-resolution Raman images of a sample. Recently, Raman spectroscopy was performed using near-field optical microscopy.15-17 Such techniques overcome the diffraction limit and allow volumes significantly smaller than the cube of the wavelength to be investigated. In the time domain, Raman spectra can be measured on the picosecond time scale, providing information on short-lived species such as excited 2957 Chem. Rev. 1999, 99, 2957−2975

Ultrasensitive Chemical Analysis by Raman Spectroscopy

Surface-Enhanced Raman Scattering 103

Surface-enhanced spectroscopy, such as surface-enhanced Raman spectroscopy employs aggregates that are of a size that allows easy handling. The aggregates are generally at least about 500 nm in dimension. The aggregates can be made of metal particles of size less than 100 nm, allowing enhanced spectroscopic techniques that operate at high sensitivity. This allows the use of larger, easily-handleable aggregates. Signals are determined that are caused by single analytes adsorbed to single aggregates, or single analytes adsorbed on a surface. The single analytes can be DNA or RNA fragments comprising at least one base.

Single molecule detection with surface-enhanced Raman scattering and applications in DNA or RNA sequencing

Enkephalin, an endogeneous substance in the human brain showing morphine-like biological functions, has been detected at the single molecule level based on the surface-enhanced Raman signal of the ring breathing mode of phenylalanine, which is one building block of the molecule. For enhancing the Raman signal the enkephalin molecules have been attached to silver colloidal cluster structures. The experiments demonstrate that the SERS signal of the strongly enhanced ring breathing vibration of phenylalanine at 1000 cm −1 can be used as "intrinsic marker" for detecting a single enkephalin molecule without using a specific label molecule. The reported result suggests the use of the phenylalanine 1000 cm −1 SERS line as spectroscopic signature for monitoring single proteins containing this amino acid as a building block.

/pdf/single-molecule-raman-detection-of-enkephalin-on-silver-1pr26p8v7y.pdf

Katrin Kneipp

Papers

Ultrasensitive Chemical Analysis by Raman Spectroscopy

Surface-Enhanced Raman Scattering 103

Ultrasensitive Chemical Analysis by Raman Spectroscopy

Single molecule detection with surface-enhanced Raman scattering and applications in DNA or RNA sequencing

Single molecule Raman detection of enkephalin on silver colloidal particles