Showing papers by "Dor Ben-Amotz published in 2008"
TL;DR: This Account explains how linear response theory can provide remarkably accurate descriptions of the process of filling aqueous cavities with nonpolar, polar, or charged molecules and explains previously mystifying observations of hydration.
Abstract: Most chemical processes on earth are intimately linked to the unique properties of water, relying on the versatility with which water interacts with molecules of varying sizes and polarities. These interactions determine everything from the structure and activity of proteins and living cells to the geological partitioning of water, oil, and minerals in the Earth’s crust. The role of hydrophobic hydration in the formation of biological membranes and in protein folding, as well as the importance of electrostatic interactions in the hydration of polar and ionic species, are all well known. However, the underlying molecular mechanisms of hydration are often not as well understood. This Account summarizes and extends emerging understandings of these mechanisms to reveal a newly unified view of hydration and explain previously mystifying observations. For example, rare gas atoms (e.g., Ar) and alkali-halide ions (e.g., K+ and Cl–) have nearly identical experimental hydration entropies, despite the significant c...
123 citations
TL;DR: The results reveal vibrational spectra of solvation-shell molecules that are perturbed by each solute, and the perturbed solvent-shell water molecules are found to have different OH stretch bands.
Abstract: Raman spectral features associated with the reorganization of solvent molecules around a solute are obtained using multivariate curve resolution. Spectra collected from solutions of variable concentration are resolved into unperturbed and perturbed components assuming only that the spectra and concentrations of each component are non-negative (with no peak-fitting or constraints on the shapes of either the perturbed or unperturbed spectral features). The capabilities of the method are demonstrated using solutions of acetonitrile, acetone, and pyridine in water as well as acetonitrile and cyclohexane in 1,2-dichloroethane (DCE). The results reveal vibrational spectra of solvation-shell molecules that are perturbed by each solute. The perturbed solvent-shell water molecules are found to have different OH stretch bands (of higher frequency and narrower width than bulk water), and the gauche−trans equilibrium of solvent-shell DCE molecules are perturbed in opposite directions by the polar and nonpolar solutes.
58 citations
TL;DR: Synthesis of isotopomeric Rhodamine dye-linked bioconjugation reagents enabled direct labeling of surface lysines on a variety of proteins using isotope-edited surface enhanced resonance Raman spectroscopy.
Abstract: Accurate quantification of protein content and composition has been achieved using isotope-edited surface enhanced resonance Raman spectroscopy. Synthesis of isotopomeric Rhodamine dye-linked bioconjugation reagents enabled direct labeling of surface lysines on a variety of proteins. When separated in polyacrylamide gels and stained with silver nanoparticles. The spectral signatures reflect the expected statistical distribution of isotopomeric labels on the labeled proteins in the gel matrix format without interference from protein features.
29 citations
TL;DR: Theoretical predictions suggest that UFRD may be used to screen binding events with a dissociation constant cut-off of the order of 10 microM, and perhaps also to quantify dissociation constants in the 100 nM to 100 microM range.
16 citations
TL;DR: Three rhodamine 6G isotopomers have been created and show distinct Raman spectra, demonstrating the principle of the approach for application as a multiplex technique in biomolecular detection/quantification.
Abstract: Quantitative applications of surface-enhanced resonance Raman scattering (SERRS) are often limited by the reproducibility of SERRS intensities, given the difficulty of controlling analyte-substrate interactions and the associated local field enhancement. As demonstrated here, SERRS from dye molecules even within the same structural class that compete with similar substrates display distinct spectral intensities that are not proportional to analyte concentrations, which limits their use as internal standardization probes and/or for multiplex analysis. Recently, we demonstrated that isotopic variants of rhodamine 6G (R6G), namely R6G-d0 and R6G-d4, can be used for internal standards in SERRS experiments with a linear optical response from picomolar to micromolar concentrations (of total analytes). Here we extend these results by describing a straightforward method for obtaining isotopomeric pairs of other Raman active dyes by hydrogen-deuterium exchange conditions for substitution at electron rich aromatic heterocycles. Most of the known SERRS active probes can be converted into the corresponding isotopomeric molecule by this exchange method, which significantly expands the scope of the isotopic edited internal standard (IEIS) approach. The relative quantification using IEIS enables accurate, reproducible (residual standard deviation+/-2.2%) concentration measurements over a range of 200 pM to 2 microM. These studies enable easy access to a variety of isotopically substituted Raman active dyes and establish the generality of the methodology for quantitative SERRS measurements. For the first time, three rhodamine 6G isotopomers have been created and show distinct Raman spectra, demonstrating the principle of the approach for application as a multiplex technique in biomolecular detection/quantification.
15 citations
TL;DR: The results represent a prototype for future applications of isotopic surface-enhanced resonance Raman scatter to quantification of protein distributions, and high quantification accuracies for small differences in protein populations at low nanogram abundance were demonstrated.
10 citations
TL;DR: This water internal standard (WIS) method is demonstrated using quantitative comparisons of commercially available protein standards that were either covalently tagged or passively stained with fluorescent tags to open up the possibility of enhancing intra- and intergel quantitative comparisons.
Abstract: We have developed a method to enhance fluorescence quantification in two-dimensional gel electrophoresis using the inherent Raman scattering of water as an internal standard. We demonstrate this water internal standard (WIS) method using quantitative comparisons of commercially available protein standards that were either covalently tagged or passively stained with fluorescent tags. Thus, WIS opens up the possibility of enhancing intra- and intergel quantitative comparisons.
3 citations
TL;DR: In this article, Clausius' Virial Theorem is invoked to predict the partitioning of kinetic and potential energies in either classical or quantum systems with simple power-law potentials.
Abstract: Clausius’ Virial Theorem is often invoked to predict the partitioning of kinetic and potential energies in either classical or quantum systems with simple power-law potentials. Here, the Virial Theorem, and related statistical mechanical identities, are used to investigate energy partitioning in classical systems with mixed power-law potentials, in either one or three dimensions, with either positive or negative mixed power-law exponents. Such classical systems are found to have temperature-dependent heat capacities reminiscent of quantum behaviour, as well as other unusual properties. Closed form analytical expressions are obtained for energy partitioning in a family of one-dimensional generalised asymmetric oscillators. Unlike the corresponding symmetric oscillators, these systems are predicted to undergo a thermally driven migration of energy between spatially separated regions. Analogous behaviour is obtained for three-dimensional systems with mixed inverse power-law potentials, as exemplified by non-...
2 citations