Showing papers by "Bart Kahr published in 2008"

Hirshfeld surfaces identify inadequacies in computations of intermolecular interactions in crystals: pentamorphic 1,8-dihydroxyanthraquinone

Abstract: Fingerprint plots of Hirshfeld surfaces were used to locate and analyze the deficiencies in various methodologies employed in the determination of the relative energies of five polymorphs of 1,8-dihydroxyanthraquinone. Nine crystallographically independent molecules were characterized by X-ray crystallography and Hirshfeld surfaces were derived from the X-ray structures. The space groups and number of independent molecules (Z′) for each of the polymorphs (1−5) is as follows: (1) P41 (or P43),Z′ = 1; (2) Pca21, Z′ = 2; (3) P1, Z′ = 4; (4) P21/n, Z′ = 1; (5) P41212 (or P43212), Z′ = 0.5. Form 1 is the most thermodynamically stable among the reproducible structures, as established by competitive solubility tests, followed by 2 and then 4. The unrestrained structures of the five polymorphs were computed using the CVFF and COMPASS force fields as well as with the density functional code, SIESTA.

Optical rotation of achiral compounds.

Abstract: Oriented achiral molecules and crystals with D(2d) symmetry or one of its non-enantiomorphous subgroups, S(4), C(2v), or C(s), can rotate the plane of transmitted polarized light incident in a general direction. This well-established fact of crystal optics is contrary to the teaching of optical activity to students of organic chemistry. This Minireview gives an overview of the measurement and calculation of the chiroptical properties of some achiral compounds and crystals. Methane derivatives with four identical ligands related by reflection symmetry are quintessential optically inactive compounds according to the logic of van't Hoff. Analysis of the optical activity of simple achiral compounds such as H(2)O and NH(3) provides general aspects of chiroptics that are not readily broached when considering chiral compounds exclusively. We show here, through the use of group theoretical arguments, the transformation properties of tensors, and diagrams, why some achiral, acentric compounds are optically active while others are not.

Memory and Spectral Diffusion in Single-Molecule Emission

Abstract: The blinking dynamics of single violamine R (VR) molecules embedded in crystals of potassium acid phthalate (KAP) are analyzed using threshold and change-point detection (CPD) methods (Watkins, L. P.; Yang, H. J. Phys. Chem. B 2005, 109, 617). Analysis employing thresholding resulted in power-law distributions of on and off times corresponding to a power-law exponent of ∼2, consistent with a distributed kinetics model for population and depopulation of the nonemissive state. When the same emission time traces were analyzed using the CPD method, a power-law exponent of ∼1.5 is obtained. In addition, multiple emission states are observed using CPD, inconsistent with a simple two-state blinking model, and indicative of spectral diffusion. The role of spectral diffusion in the distributed blinking kinetics of KAP/VR is investigated by spectrally decomposing the emission using a dichroic mirror. Combining the CPD method with this experiment yielded the emission energy, intensity, and temporal duration of blink...

Applications of single-molecule microscopy to problems in dyed composite materials

Abstract: Recent progress in single-molecule spectroscopy of dyed composite materials is reviewed. In particular, single-molecule studies of dyed polymer films and dye inclusion crystals are described that seek to understand local guest–host interactions and environmental heterogeneity. Single-molecule orientational studies of chromophores in polymer films and mixed crystals are discussed with particular relevance to materials and device applications. Studies of single-molecular reorientational dynamics in polymers in the presence of an electric field designed to establish alignment are described. Static orientational measurements in mixed crystals, wherein alignment is a consequence of crystal growth, reveal a surprisingly wide distribution of molecular orientations. Moreover, the complex photophysics of single molecule in anisomorphous mixed crystals are explored and described in the context of environmental heterogeneity and distributed kinetics. The emerging literature regarding dispersed kinetics observed for ...

Orientational dependence of linear dichroism exemplified by dyed spherulites.

Abstract: D-sorbitol forms so-called spherulites from under-cooled melts. These polycrystalline formations have optically uniaxial radii. Melts pressed between glasses crystallize as plane sections of spheres. Dyes that are soluble in molten sorbitol become oriented as the crystallization front passes through the melt so as to form disks with large linear dichroism in the absorption bands of the dyes. The dyeing of spherulites is thus a general method of solute alignment. The linear optical properties of sorbitol spherulites containing the azo dye amaranth were analyzed in detail so as to correct a persistent confusion in the literature regarding the orientational dependence of linear dichroism. In cases involving thin film dichroism of multilayered samples requiring many corrections of intensity data in non-normal incidence, some authors have taken transmittance and others absorbance as having a cosine-squared angular dependence on the plane of the electric vector of linearly polarized light. Plane sections of doped spherulites present all orientations of an electric dipole oscillator in spatially localized region in normal incidence. As such, the samples described herein are ideally suited to resolving this confusion. Images of transmittance of dyed spherulites in polarized light were recorded with a CCD camera and simulated under the assumption that both absorbance and transmittance show a cosine-squared angular dependence but with respect to different angles. Transmittance with a cosine-squared dependence follows azimuthal rotations of the spherulite radii around the wave vector, while absorbance with a cosine-squared dependence follows rotations about axes perpendicular to the wave vector, natural consequences of the properties of the optical indicatrix that are often overlooked. Spherulites obviate the substantial experimental complexities that are engendered in non-normal incidence by sample reorientation. Thus, the principles of anisotropic absorption are given in a complete and intuitive fashion.

Die optische Aktivität achiraler Substanzen

Abstract: Ausgerichtete achirale Molekule und Kristalle mit D2d-Symmetrie oder einer der nichtenantiomorphen Untergruppen S4, C2v oder Cs konnen beim Durchstrahlen in einer beliebigen Richtung eine Drehung der Schwingungsebene von linear polarisiertem Licht bewirken. Dies ist in der Kristalloptik eine unangefochtene Tatsache, der Unterricht fur Studenten der organischen Chemie vermittelt hingegen eine widerspruchliche Ansicht. Der vorliegende Kurzaufsatz verschafft einen Uberblick uber Messungen und Rechnungen zu den chiroptischen Eigenschaften einiger achiraler Substanzen und Kristalle. Prototypisch fur Verbindungen, die nach van't Hoff optisch inaktiv sein sollten, sind Methanderivate mit vier identischen Liganden, die durch Spiegelebenen in Beziehung stehen. Die Untersuchung der optischen Aktivitat einfacher achiraler Verbindungen wie H2O und NH3 vermittelt weitreichende chiroptische Gesetzmasigkeiten, die oft im Zusammenhang mit chiralen Stoffen ubersehen werden. Hier wird anhand gruppentheoretischen Uberlegungen, des Transformationsverhaltens von Tensoren und intuitiver Skizzen gezeigt, warum einige achirale azentrische Verbindungen optisch aktiv sind, andere hingegen nicht.

Optical Rotation of Achiral Compounds

Abstract: Oriented achiral molecules and crystals with D(2d) symmetry or one of its non-enantiomorphous subgroups, S(4), C(2v), or C(s), can rotate the plane of transmitted polarized light incident in a general direction. This well-established fact of crystal optics is contrary to the teaching of optical activity to students of organic chemistry. This Minireview gives an overview of the measurement and calculation of the chiroptical properties of some achiral compounds and crystals. Methane derivatives with four identical ligands related by reflection symmetry are quintessential optically inactive compounds according to the logic of van't Hoff. Analysis of the optical activity of simple achiral compounds such as H(2)O and NH(3) provides general aspects of chiroptics that are not readily broached when considering chiral compounds exclusively. We show here, through the use of group theoretical arguments, the transformation properties of tensors, and diagrams, why some achiral, acentric compounds are optically active while others are not.