Glucose,not cellobiose,is the repeating unit of cellulose and why that is important

Despite nomenclature conventions of the International Union of Pure and Applied Chemistry and the International Union of Biochemistry and Molecular Biology, the repeating unit of cellulose is often said to be cellobiose instead of glucose. This review covers arguments regarding the repeating unit in cellulose molecules and crystals based on biosynthesis, shape, crystallographic symmetry, and linkage position. It is concluded that there is no good reason to disagree with the official nomenclature. Statements that cellobiose is the repeating unit add confusion and limit thinking on the range of possible shapes of cellulose. Other frequent flaws in drawings with cellobiose as the repeating unit include incorporation of O-1 as the linkage oxygen atom instead of O-4 (the O-1 hydroxyl is the leaving group in glycoside synthesis). Also, n often erroneously represents the number of cellobiose units when n should denote the degree of polymerization i.e., the number of glucose residues in the polysaccharide.     

In defense of adiabatic ϕ/ψ mapping for cellobiose and other disaccharides

Thorough conformational study of cellobiose requires consideration of numerous arrangements of the exocyclic groups. Therefore, it is customary to prepare a number of structures with different arrangements of hydroxyl and hydroxymethyl groups. These “starting geometries” are then given different values of the glycosidic linkage torsion angles ϕ and ψ. At each increment of ϕ and ψ, the energy is calculated. Usually, the final product is an “adiabatic” contour plot of the lowest energy at each ϕ/ψ point after considering all of the starting geometries. The present paper advocates for adiabatic maps despite the statement by Schnupf and Momany (preceding paper) that adiabatic maps are not of interest because they contain sparse details about the structures at each minimum. Similar information is computed by their method and adiabatic mapping, and comparable details can be provided from adiabatic studies. Although Schnupf and Momany presented maps from calculations in vacuum and in water that considered all of their calculated energies, they favored the presentation of two to four maps for each of 36 individual minima, each with its own zero of relative energy. However, previous work showed that more structures are needed to provide the lowest energies at each point in ϕ/ψ space. Following their preferred strategy would result in even more maps when the added structures are considered. The need to map individual minima can be avoided by starting calculations with the same exocyclic orientations at each ϕ/ψ point instead of using the preceding optimized structure to start the next energy minimization. Using the same orientations at each point allows periodic maps that depict barriers between minima.     

Terahertz spectroscopy of enantiopure and racemic polycrystalline valine

Experimental and computational THz (or far-infrared) spectra of polycrystalline valine samples are reported. The experimental spectra have been measured using THz time-domain spectroscopy. Spectra of the pure enantiomers, both D and L, as well as the dl racemate have been taken at room temperature and low temperature (78 K). The spectra of the pure D and L enantiomers are essentially identical, and they are markedly different from the DL racemate. In addition, a temperature-dependent study of L-valine was undertaken in which the absorption maxima were found to red shift as a function of increasing temperature. The vibrational absorption spectra (frequencies and intensities) were calculated using the harmonic approximation with the Perdew-Burke-Ernzerhof (PBE) functional, localized atomic orbital basis sets, and periodic boundary conditions. The calculated and experimental spectra are in good qualitative agreement. A general method of quantifying the degree to which a calculated mode is intermolecular versus intramolecular is demonstrated, with the intermolecular motions further separated into translational versus rotational/librational motion. This allows straightforward comparison of spectra calculated using different basis sets or other constraints.     

Synthesis,structural analysis,and self-assembly of phenylene ethynylene oligomers and their ?F, ?CF3, and ?CH3 substituted derivatives

Oligomers consisting of aromatic building blocks separated by alkynyl units were synthesized by Sonogashira cross-coupling of aryl halides with terminal acetylenes. Strong electron acceptors such as  F and  CF₃ and weak electron donors like  CH₃ were placed as substituents on one of the benzene rings. Acetyl-protected sulfhydryl groups were attached to one end of these molecules to promote their self-organization on gold surfaces. The electron-transport properties of such self-assembled monolayers (SAMs) are highly sensitive to the local order of the molecules in the solid state. Single crystals were analyzed by X-ray diffraction experiments that revealed structural details that could lead to a better understanding of the electron-transport properties. The unsymmetrical substitution of the aromatic rings by electron-active groups in the ortho-, meta-, or para positions resulted in changes of such molecular parameters as bonding and torsion angles and planarity. These parameters, in turn, can affect the angle of the molecular attachment to a gold substrate and the density of the resulting SAMs. Patterned SAMs of some of these molecules and comparison alkane thiols were obtained on gold by microcontact printing or flooding. The SAM thickness was determined by spectroscopic ellipsometry. Surface potential differences between adjacent SAMs or between SAMs and the gold substrate were measured by scanning surface potential microscopy under ambient conditions. © 2003 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 541–550, 2004     

Wavelength-Resolved 3-Dimensional Fluorescence Lifetime Imaging

We have developed a compact system for wide-field fluorescence imaging, resolved in three spatial dimensions, lifetime and wavelength, that is based on a gated optical intensifier and an all-solid-state diode pumped Cr:LiSAF oscillator-amplifier system. Exploiting spectral separation, the system has been applied to human teeth, obtaining good lifetime contrast between enamel, dentin and caries. Exploiting spectral separation combined with depth resolution, the study of fluorescent microspheres led to an enhancement in both lifetime contrast and lateral resolution.