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Kenneth D M Harris - One of the best experts on this subject based on the ideXlab platform.
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a rare case of polymorphism in a three component co crystal system with each polymorph having ten independent molecules in the Asymmetric Unit
2013Co-Authors: Yuncheng Yan, Colan E Hughes, Benson M Kariuki, Kenneth D M HarrisAbstract:We report polymorphism in a co-crystal system comprising trimesic acid (benzene-1,3,5-tricarboxylic acid, TMA), tert-butylamine (TBA), and methanol with stoichiometry (TMA)2(TBA)5(methanol)3. The crystal structure of each polymorph (determined from single-crystal X-ray diffraction) is shown to have 10 independent molecules in the Asymmetric Unit. In each polymorph, all five TBA molecules in the Asymmetric Unit exist as protonated cations, whereas, of the two TMA molecules in the Asymmetric Unit, one exists as the doubly deprotonated anion and the other exists as the triply deprotonated anion. In each case, the structure is based on an extensively hydrogen-bonded two-dimensional network involving the −N+H3 groups of TBA cations, the −CO2– and −CO2H groups of TMA anions, and the OH groups of methanol molecules. Although the two polymorphs share some structural features in common, there are nevertheless significant differences in several aspects, including differences in some of the hydrogen-bonding motifs. ...
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challenges in direct space structure determination from powder diffraction data a molecular material with four independent molecules in the Asymmetric Unit
2004Co-Authors: David Albesajove, Benson M Kariuki, Simon J Kitchin, Leanne Grice, Eugene Y Cheung, Kenneth D M HarrisAbstract:Complex structure from powder diffraction: The direct-space strategy for carrying out structure solution directly from powder X-ray diffraction data has been applied successfully in the challenging case of a molecular cocrystal (see graphic) containing four independent molecules in the Asymmetric Unit.
Ueli Aebi - One of the best experts on this subject based on the ideXlab platform.
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Formation of Asymmetric Unit membrane during urothelial differentiation
1996Co-Authors: Haiping Zhao, Ueli Aebi, John Provet, Xue-ru WuAbstract:Mammalian urothelium undergoes unique membrane specialization during terminal differentiation making numerous rigid-looking membrane plaques (0.3–0.5 μm diameter) that cover the apical cell surface. The outer leaflet of these membrane plaques is almost twice as thick as the inner leaflet hence the name Asymmetric Unit membrane (AUM). Ultrastructural studies established that the outer leaflet of AUM is composed of 16 nm particles forming two dimensional crystals, and that each particle forms a ‘twisted ribbon’ structure. We showed recently that highly purified bovine AUMs contain four major integral membrane proteins: uroplakins Ia (27 kD), Ib (28 kD), II (15 kD) and III (47 kD). Studies of the protease sensitivity of the different subdomains of uroplakins and other considerations suggest that UPIa and UPIb have 4 transmembrane domains, while UPII and UPIII have only one transmembrane domain. Chemical Crosslinking studies showed that UPIa and UPIb, which share 39% amino acid sequence, are topologically adjacent to UPII and UPIII, respectively, thus raising the possibility that there exist two biochemically distinct AUM particles, i.e., those containing UPIa/UPII vs. UPIb/UPIII. Bovine urothelial cells grown in the presence of 3T3 feeder cells undergo clonal growth forming stratified colonies capable of synthesizing and processing all known uroplakins. Transgenic mouse studies showed that a 3.6 kb 5′-flanking sequence of mouse uroplakin II gene can drive the expression of bacterial LacZ gene to express in the urothelium. Further studies on the biosynthesis, assembly and targeting of uroplakins will offer unique opportUnities for better understanding the structure and function of AUM as well as the biology of mammalian urothelium.
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towards the molecular architecture of the Asymmetric Unit membrane of the mammalian urinary bladder epithelium a closed twisted ribbon structure
1995Co-Authors: Thomas Walz, Xue-ru Wu, Markus Häner, Christian Henn, Ueli Aebi, Andreas EngelAbstract:The Asymmetric Unit membrane (AUM) forms numerous plaques covering the apical surface of mammalian urinary bladder epithelium. These plaques contain four major integral membrane proteins called uroplakins Ia, Ib, II and III, which form particles arranged in a well-ordered hexagonal lattice with p6 symmetry and a lattice constant of 16.5 nm. Bovine AUM plaques negatively stained with anionic sodium silicotungstate revealed structural detail to 3.1 nm resolution. Correlation averaging resolved each particle into 12 stain-excluding domains arranged in two concentric rings (inner ring radius (rm) = 3.7 nm, outer ring radius (rout) = 6.6 nm), each with six domains which were rotated by roughly 30 degrees relative to each other. Negative staining with cationic uranyl formate increased the resolution to 2.2 nm and unveiled distinct connections between adjacent AUM particles. These connections may provide a molecular basis for the observed insolubility of the plaques in many detergents. Examination of the luminal face of freeze-dried/unidirectionally metal-shadowed AUM plaques established a left-handed vorticity of the 16 nm protein particles, whereas the cytoplasmic face exhibited no significant surface corrugations. Three-dimensional reconstruction from sodium silicotungstate-stained specimens revealed the AUM particles to be built of six "V-shaped" subUnits anchored upright in the membrane. The mass density distribution within uranyl formate-stained AUM particles was similar except that the inner tip of each V was bridged to the outer tip of an adjacent V, so that the 16 nm AUM particle appeared as a continuous, "twisted ribbon" embracing a central cavity. Finally, mass measurements of unstained/freeze-dried plaques by scanning transmission electron microscopy yielded a total mass of 1,120 kDa per membrane-bound AUM particle. By imposing constraints on the possible uroplakin stoichiometries within AUM plaques, these data provide a first glimpse of the molecular architecture of the 16 nm particles constituting the plaques.
Don T Tilley - One of the best experts on this subject based on the ideXlab platform.
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tris tert butoxy siloxy derivatives of boron including the boronous acid hob osi o t bu 3 2 and the metal siloxy boryloxide complex cp 2 zr me ob osi o t bu 3 2 a remarkable crystal structure with 18 independent molecules in its Asymmetric Unit
2003Co-Authors: Kyle L Fujdala, Allen G Oliver, Frederick J Hollander, Don T TilleyAbstract:Silanolysis of B(O(t)Bu)(3) with 2 and 3 equiv of HOSi(O(t)Bu)(3) led to the formation of (t)BuOB[OSi(O(t)Bu)(3)](2) (1) and B[OSi(O(t)Bu)(3)](3) (2), respectively. Compounds 1 and 2 are efficient single-source molecular precursors to B/Si/O materials via thermolytic routes in nonpolar media, as demonstrated by the generation of BO(1.5).2SiO(2) (BOSi2(xg)) and BO(1.5).3SiO(2) (BOSi3(xg)) xerogels, respectively. Use of a block copolymer template provided B/Si/O materials (BOSi2(epe) and BOSi3(epe)) with a broad distribution of mesopores (by N(2) porosimetry) and smaller, more uniform particle sizes (by TEM) as compared to the nontemplated materials. Hydrolyses of 1 and 2 with excess H(2)O resulted in formation of the expected amounts of (t)BuOH and HOSi(O(t)Bu)(3); however, reaction of 1 with 1 equiv of H(2)O led to isolation of the new boronous acid HOB[OSi(O(t)Bu)(3)](2) (3). This ligand precursor is well suited for the synthesis of new metal (siloxy)boryloxide complexes via proton-transfer reactions involving the BOH group. The reaction of 3 with Cp(2)ZrMe(2) resulted in formation of Cp(2)Zr(Me)OB[OSi(O(t)Bu)(3)](2) (4) in high yield. This rare example of a transition metal boryloxide complex crystallizes in the triclinic space group Ponemacr; and exhibits a crystal structure with an unprecedented number of independent molecules in its Asymmetric Unit (i.e., Z' = 18 and Z = 36). This unusual crystal structure presented an opportUnity to perform statistical analyses of the metric parameters for the 18 crystallographically independent molecules. Complex 4 readily converts to Cp(2)Zr[OSi(O(t)Bu)(3)](2) (5) upon thermolysis or upon dissolution in Et(2)O at room temperature.
Xue-ru Wu - One of the best experts on this subject based on the ideXlab platform.
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Formation of Asymmetric Unit membrane during urothelial differentiation
1996Co-Authors: Haiping Zhao, Ueli Aebi, John Provet, Xue-ru WuAbstract:Mammalian urothelium undergoes unique membrane specialization during terminal differentiation making numerous rigid-looking membrane plaques (0.3–0.5 μm diameter) that cover the apical cell surface. The outer leaflet of these membrane plaques is almost twice as thick as the inner leaflet hence the name Asymmetric Unit membrane (AUM). Ultrastructural studies established that the outer leaflet of AUM is composed of 16 nm particles forming two dimensional crystals, and that each particle forms a ‘twisted ribbon’ structure. We showed recently that highly purified bovine AUMs contain four major integral membrane proteins: uroplakins Ia (27 kD), Ib (28 kD), II (15 kD) and III (47 kD). Studies of the protease sensitivity of the different subdomains of uroplakins and other considerations suggest that UPIa and UPIb have 4 transmembrane domains, while UPII and UPIII have only one transmembrane domain. Chemical Crosslinking studies showed that UPIa and UPIb, which share 39% amino acid sequence, are topologically adjacent to UPII and UPIII, respectively, thus raising the possibility that there exist two biochemically distinct AUM particles, i.e., those containing UPIa/UPII vs. UPIb/UPIII. Bovine urothelial cells grown in the presence of 3T3 feeder cells undergo clonal growth forming stratified colonies capable of synthesizing and processing all known uroplakins. Transgenic mouse studies showed that a 3.6 kb 5′-flanking sequence of mouse uroplakin II gene can drive the expression of bacterial LacZ gene to express in the urothelium. Further studies on the biosynthesis, assembly and targeting of uroplakins will offer unique opportUnities for better understanding the structure and function of AUM as well as the biology of mammalian urothelium.
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towards the molecular architecture of the Asymmetric Unit membrane of the mammalian urinary bladder epithelium a closed twisted ribbon structure
1995Co-Authors: Thomas Walz, Xue-ru Wu, Markus Häner, Christian Henn, Ueli Aebi, Andreas EngelAbstract:The Asymmetric Unit membrane (AUM) forms numerous plaques covering the apical surface of mammalian urinary bladder epithelium. These plaques contain four major integral membrane proteins called uroplakins Ia, Ib, II and III, which form particles arranged in a well-ordered hexagonal lattice with p6 symmetry and a lattice constant of 16.5 nm. Bovine AUM plaques negatively stained with anionic sodium silicotungstate revealed structural detail to 3.1 nm resolution. Correlation averaging resolved each particle into 12 stain-excluding domains arranged in two concentric rings (inner ring radius (rm) = 3.7 nm, outer ring radius (rout) = 6.6 nm), each with six domains which were rotated by roughly 30 degrees relative to each other. Negative staining with cationic uranyl formate increased the resolution to 2.2 nm and unveiled distinct connections between adjacent AUM particles. These connections may provide a molecular basis for the observed insolubility of the plaques in many detergents. Examination of the luminal face of freeze-dried/unidirectionally metal-shadowed AUM plaques established a left-handed vorticity of the 16 nm protein particles, whereas the cytoplasmic face exhibited no significant surface corrugations. Three-dimensional reconstruction from sodium silicotungstate-stained specimens revealed the AUM particles to be built of six "V-shaped" subUnits anchored upright in the membrane. The mass density distribution within uranyl formate-stained AUM particles was similar except that the inner tip of each V was bridged to the outer tip of an adjacent V, so that the 16 nm AUM particle appeared as a continuous, "twisted ribbon" embracing a central cavity. Finally, mass measurements of unstained/freeze-dried plaques by scanning transmission electron microscopy yielded a total mass of 1,120 kDa per membrane-bound AUM particle. By imposing constraints on the possible uroplakin stoichiometries within AUM plaques, these data provide a first glimpse of the molecular architecture of the 16 nm particles constituting the plaques.
Gautam R Desiraju - One of the best experts on this subject based on the ideXlab platform.
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on the presence of multiple molecules in the crystal Asymmetric Unit z 1
2007Co-Authors: Gautam R DesirajuAbstract:The presence of multiple molecules in the Asymmetric Unit (Z9) has been noted from the earliest days of crystallography, when such an occurrence might even have prevented structure solution and refinement, till today when the phenomenon is being commented upon regularly and, as some claim, can even be engineered. In the end, however, the fact that some crystals take more than one symmetry independent molecule is still something of an enigma. Is it a matter of no consequence whatsoever, which occurs randomly, or is there a deeper underlying reason why Z9 . 1? Perhaps high Z9 structures appear mysterious simply because there is still not a critical mass of relevant literature on their phenomenological analysis. However, a few authors have attempted to study this difficult problem. Brock has surveyed alcohols and phenols extensively and has given an elegant explanation as to why these compounds have a higher proportion of Z9 . 1 crystal structures when compared with the global sampling of organic molecular crystals. According to her, the tendency of these hydroxy compounds (ROH) to form cooperative hydrogen bonded chains of the O–H...O–H type is countered by the steric demands of the R-groups, and high Z9 is one of the outcomes (the other is crystallisation in a high symmetry system). In general, there seems to be a consensus that when packing problems make it difficult to achieve a structure with Z9 = 1, a higher Z9 is a good alternative option. The idea of interaction frustration has also echoes in the work of Nangia, Steed and Clegg among others. These authors have also elaborated other interesting themes: that structures with high Z9 have a loose packing but good interactions; that crystals which are grown from the melt or by sublimation have a significantly higher proportion of Z9 . 1 structures; that high Z9 structures can be described as modulations; that high Z9 is obtained when the molecule has a large number of equi-energetic conformations, these conformations co-existing in the crystal. Pseudosymmetry is certainly implicated in some cases and the pseudo-elements of symmetry may be either global or local. In the latter category, we noted a very unusual subset more than 15 years ago of P1 crystals which have Z9 = 2, the two symmetry independent molecules being related by a local pseudo-centre of inversion. Why does the crystal take this pseudo-centre, an ‘‘extra’’, almost ‘‘wasted’’ symmetry element? All these observations are undoubtedly interesting, and possibly important, but what struck me as the most unusual fact about high Z9 structures, an observation that seemed almost counter-intuitive, is that the proportion of Z9 . 1 structures relative to all crystal structures has remained practically invariant over the decades. I must admit that I had always felt (and I daresay that this might be true of others, too) that with the advent of CCD diffractometers and high throughput crystallography, the proportion of high Z9 structures should be steadily increasing. Reality is different. During the period 1970–2006, during which time the CSD has become nearly 43 times larger, the proportion of Z9 = 1, Z9 , 1 and Z9 . 1 organic structures has remained virtually constant (i1%) at 73, 16 and 11%. Does this constancy of numbers say anything about the origin of this phenomenon? Is there a basic, universal reason why high Z9 structures are obtained? I would like to suggest that the secrets of high Z9 structures will be most easily revealed through a study of polymorphic systems, wherein a high Z9 structure may be most easily compared with a lower Z9 structure (ideally one with Z9 = 1) of the same chemical substance. We noted that at least in two cases, pentafluorophenol and trans-1,4-bis(phenylethynyl)cyclohexane-1,4-diol, there are two structures with different Z9 values. The structure with the lower Z9 is the more stable structure; the one with the higher Z9 value is obtained under what essentially amount to kinetic conditions: cryo-crystallography for the phenol and melt cooling for the diol. These observations are suggestive. Steed put forth the idea a few years ago that a high Z9 structure is a ‘‘fossil relic’’ of a more stable form. In this way, it is not difficult to associate the higher Z9 polymorphs of these two compounds with kinetic modifications. Indeed, we showed that the discrete O–H...O–H...O–H trimer synthon in the high Z9 polymorph of pentafluorophenol is an ‘‘incomplete’’ version of the infinite O–H...O–H chain in the low Z9 polymorph. Similarly, the high Z9 polymorph of the diol contains a large number of molecular conformations that are essentially ‘‘frozen’’ into the crystal, and these anneal out in the lower Z9 high temperature modification. It is worthwhile to reflect that all the reasons which have been put forward in the past for the adoption of high Z9 structures (packing difficulties and inconsistencies, modulation, pseudosymmetry, equi-energetic conformations, better interactions) are simply different ways of saying the same thing. A high Z9 structure is a crystal ‘‘on the way’’. Many of Brock’s observations on alcohols and phenols follow from the idea that molecules which form stable clusters in solution because of strong hydrogen bonding have a higher tendency to form Z9 . 1 crystals because these clusters are carried forward more or less unaltered into the crystal. Possibly, O–H...O hydrogen bonding in alcohols and phenols is so strong and directional that it becomes difficult to observe a better packed, School of Chemistry, University of Hyderabad, Hyderabad, 500 046, India LETTER www.rsc.org/crystengcomm | CrystEngComm
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multiple molecules in the crystallographic Asymmetric Unit self host guest and doubly interpenetrated hydrogen bond networks in a pair of keto bisphenols
2003Co-Authors: Srinivasulu Aitipamula, Gautam R Desiraju, Mariusz Jaskolski, Ashwini Nangia, Ram ThaimattamAbstract:The presence of two molecules in the crystallographic Asymmetric Unit in a pair of closely related keto-bisphenols that differ by a methyl substituent only, leads to open frameworks that fill space through self-inclusion in one case, and through interpenetration in the other.
