scholarly journals The Nature of the Chemical Bond in Linear Three-Body Systems: From I3–to Mixed Chalcogen/Halogen and Trichalcogen Moieties

2007 ◽  
Vol 2007 ◽  
pp. 1-46 ◽  
Author(s):  
M. Carla Aragoni ◽  
Massimiliano Arca ◽  
Francesco A. Devillanova ◽  
Alessandra Garau ◽  
Francesco Isaia ◽  
...  
Keyword(s):  
Chemical Bond ◽  
Energy Surface ◽  
Structural Data ◽  
Closed Shell ◽  
Structural Features ◽  
Donor Acceptor ◽  
Structural Database ◽  
Three Body ◽  
Van Der Waals Radii ◽  
Symmetric Systems

The 3 centre-4 electrons (3c-4e) and the donor/acceptor or charge-transfer models for the description of the chemical bond in linear three-body systems, such as I3–and related electron-rich (22 shell electrons) systems, are comparatively discussed on the grounds of structural data from a search of the Cambridge Structural Database (CSD). Both models account for a total bond order of 1 in these systems, and while the former fits better symmetric systems, the latter describes better strongly asymmetric situations. The 3c-4e MO scheme shows that any linear system formed by three aligned closed-shell species (24 shell electrons overall) has reason to exist provided that two electrons are removed from it to afford a 22 shell electrons three-body system: all combinations of three closed-shell halides and/or chalcogenides are considered here. A survey of the literature shows that most of these three-body systems exist. With some exceptions, their structural features vary continuously from the symmetric situation showing two equal bonds to very asymmetric situations in which one bond approaches to the value corresponding to a single bond and the second one to the sum of the van der Waals radii of the involved atoms. This indicates that the potential energy surface of these three-body systems is fairly flat, and that the chemical surrounding of the chalcogen/halogen atoms can play an important role in freezing different structural situations; this is well documented for the I3–anion. The existence of correlations between the two bond distances and more importantly the linearity observed for all these systems, independently on the degree of their asymmetry, support the state of hypervalency of the central atom.

scholarly journals Three-Dimensional Structures of Carbohydrates and Where to Find Them

2020 ◽  
Vol 21 (20) ◽  
pp. 7702 ◽  
Author(s):  
Sofya I. Scherbinina ◽  
Philip V. Toukach
Keyword(s):  
Experimental Data ◽  
Molecular Modeling ◽  
Computational Methods ◽  
Three Dimensional ◽  
Structural Diversity ◽  
Structural Data ◽  
Structural Features ◽  
Data Validation ◽  
Data Generation ◽  
Efficient Treatment

Analysis and systematization of accumulated data on carbohydrate structural diversity is a subject of great interest for structural glycobiology. Despite being a challenging task, development of computational methods for efficient treatment and management of spatial (3D) structural features of carbohydrates breaks new ground in modern glycoscience. This review is dedicated to approaches of chemo- and glyco-informatics towards 3D structural data generation, deposition and processing in regard to carbohydrates and their derivatives. Databases, molecular modeling and experimental data validation services, and structure visualization facilities developed for last five years are reviewed.

scholarly journals Frequency Response Evaluation of Guitar Bodies with Different Bracing Systems

Symmetry ◽  
2020 ◽  
Vol 12 (5) ◽  
pp. 795
Author(s):  
Mircea Mihălcică ◽  
Mariana D. Stanciu ◽  
Sorin Vlase
Keyword(s):  
Structural Features ◽  
Dynamic Force ◽  
Classical Guitar ◽  
Elastic Symmetry ◽  
Frequency Responses ◽  
Points Of View ◽  
Coupled Plates ◽  
Natural Composite ◽  
Theoretical Results ◽  
Symmetric Systems

Wood is a natural composite, having a porous structure, with a complex elastic symmetry specific to orthotropic solid, influenced by three mutually perpendicular planes of elastic symmetry. The classical guitar is obtained from different wooden species, each of them having their own elastic properties and, as a whole, forming a lignocellulosic composite structure. Generally, some constructive parts of the classical guitar body are based on symmetry, starting from the structural features of wooden plates, which are symmetrically cut, and some patterns of the stiffening bars. The other elements, such as the strings system, are not symmetric. This study aims to evaluate the frequency responses of the guitar body as a symmetrical mechanical system from constructive points of view. Because theoretical results (analytic and numeric) regarding the symmetrical systems cannot be applied to quasi-symmetric systems, the dynamic response was analyzed from experiments performed on four types of classical guitar body (without neck), different from each other by the pattern of stiffening bars placed inside of the top plate. The experiments were performed using a Brüel&Kjær mini-shaker to excite the structure, and the signal was captured with accelerometers. The symmetric behavior of coupled plates from the guitar body was noticed in the case of an applied dynamic force of 110 Hz and 440 Hz, but in the case of 146 Hz, 588 Hz, 720 Hz, quasi skew symmetrical modes were recorded.

Applications of the Cambridge Structural Database to molecular inorganic chemistry

2002 ◽  
Vol 58 (3) ◽  
pp. 398-406 ◽  
Author(s):  
A. Guy Orpen
Keyword(s):  
Inorganic Chemistry ◽  
Structural Data ◽  
Cambridge Structural Database ◽  
High Quality ◽  
Computational Data ◽  
Inorganic Complexes ◽  
Fundamental Research ◽  
Structural Database ◽  
Structure Correlation ◽  
Molecular Dimensions

Applications of the data in the Cambridge Structural Database (CSD) to knowledge acquisition and fundamental research in molecular inorganic chemistry are reviewed. Various classes of application are identified, including the derivation of typical molecular dimensions and their variability and transferability, the derivation and testing of theories of molecular structure and bonding, the identification of reaction paths and related conformational analyses based on the structure correlation hypothesis, and the identification of common and presumably energetically favourable intermolecular interactions. In many of these areas, the availability of plentiful structural data from the CSD is set against the emergence of high-quality computational data on the geometry and energy of inorganic complexes.

Ultrastructure of the osphradium of the Tertiary relict snail, Campanile symbolicum Iredale (Mollusca, Streptoneura)

1992 ◽  
Vol 337 (1282) ◽  
pp. 457-469 ◽  
Keyword(s):  
Smooth Endoplasmic Reticulum ◽  
Sense Organ ◽  
Central Zone ◽  
Structural Data ◽  
Structural Features ◽  
Sensory Epithelium ◽  
Sensory Cells ◽  
Cell Type ◽  
Sensory Cilia ◽  
A Cell

The osphradium of Campanile symbolicum Iredale, 1917 is a gill-like, bipectinate sense organ, which is located at the left side of the mantle roof. The mass of the deeply clefted sensory epithelium of the leaflets is built up by sensory cells, which are provided with deeply invaginated aberrant cilia and large cytosomes containing pigment formations. In addition, many free nerve processes are present, bearing a single or few sensory cilia with accessory centrioles. Polyciliary cells are interspersed. A cell type with netlike or concentrically arranged smooth endoplasmic reticulum is commonly found near the central axis of the osphradium . The central zone of each leaflet includes nervous tissue and a complicated muscular grid, with pore cells and fibroblasts also present. Based on the fine-structural data the functional and ecological significance of the osphradium of Campanile symbolicum is discussed. The com bination of herbivory and a lamellar osphradium is rare among the Gastropoda, suggesting that the osphradium of Campanile might also be involved in reproductive biology. Many fine-structural features of the osphradium of Campanile symbolicum are unique among the gastropods and reflect the phylogenetic isolation of this relict snail. The net-like cell type, however, is probably homologous with the so-called Si4 cell in the rem aining caenogastropods, for which a largely different osphradial fine-structure is diagnostic. The affinities of Campanile symbolicum are probably closer to the Caenogastropoda than to the Allogastropoda and Euthyneura. With present knowledge it might be best classified near the base or even as the first clade within the Caenogastropoda.

scholarly journals Structure and Dynamics of Zr4+ in Aqueous Solution: An Ab Initio QM/MM Molecular Dynamics Study

2015 ◽  
Vol 15 (2) ◽  
pp. 155-162 ◽  
Author(s):  
Suwardi Suwardi ◽  
Harno Dwi Pranowo ◽  
Ria Armunanto
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Distribution Function ◽  
Pair Potential ◽  
Structural Data ◽  
Angular Distribution Function ◽  
Dilute Aqueous Solution ◽  
Dynamical Properties ◽  
Experimental Values ◽  
Three Body

A QM/MM molecular dynamics (MD) simulation has been carried out using three-body corrected pair potential to investigate the structural and dynamical properties of Zr4+ in dilute aqueous solution. Structural data in the form of radial distribution function, coordination number distribution, and angular distribution function were obtained. The results indicate eight water molecules coordinate to zirconium ion and have two angles of O-Zr4+-O, i.e. 72.0° and 140.0° with a Zr4+-O distance of 2.34 Å. According to these results, the hydration structure of Zr4+ ion in water was more or less well-defined square antiprismatic geometry. The dynamical properties have been characterized by the ligand’s mean residence time (MRT) and Zr4+-O stretching frequencies. The inclusion of the three-body correction was important for the description of the hydrated Zr4+ ion, and the results indicated in good agreement with experimental values.

Wechselwirkungen in Molekülkristallen, 166 [1, 2]. Polyiod-Moleküle I2C=CI2, (IC)4S, (IC)4NH, (IC)4N-CH3 und HCI3: Strukturbestimmung nach Kristallzüchtung oder durch Dichtefunktionaltheorie-Berechnung / Interaction in Molecular Crystals, 166 [1, 2], Polyiodo Molecules I2C=CI2, (IC)4S, (IC)4 NH, (IC)4N-CH and HCI3: Structure Determination Following Crystallization or by Density Functional Theory Calculation

2001 ◽  
Vol 56 (1) ◽  
pp. 13-24 ◽  
Author(s):  
Hans Bock ◽  
Sven Holl ◽  
Volker Krenzel
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Crystal Packing ◽  
Density Functional Theory Calculation ◽  
Density Functional Theory Calculations ◽  
Structural Data ◽  
Basis Sets ◽  
Functional Theory ◽  
Donor Acceptor ◽  
Density Functional Theory Optimization

Abstract The structures of tri-and tetraiodo-substituted carbon compounds are determined either expe­rimentally by X-Ray Structure Analysis or, because crystallization of tetraiodothiophene could not be achieved, approximated by Density Functional Theory optimization of structural data from a donor/acceptor complex. The structures show noteworthy details such as a second po­lymorph of tetraiodoethene crystallized by sublimation or herringbone crystal packing patterns of tetraiodopyrrole derivatives. All molecular geometries are discussed and compared based on relativistic density functional theory calculations with 6 -31G* basis sets including iodine pseudopotentials. They reproduce even finer structural details due to van der Waals repulsion of the bulky iodo substituents. Natural Bond Orbital (NBO) charge distributions suggest positive partial charges at all iodine centers with the strongest polarization Cδ㊀ → Iδ㊉ in HCI3, which contains well over 97% iodine.

scholarly journals Understanding Structural Features of Microbial Lipases–-An Overview

2008 ◽  
Vol 3 ◽  
pp. ACI.S551 ◽  
Author(s):  
John Geraldine Sandana Mala ◽  
Satoru Takeuchi
Keyword(s):  
Structural Analysis ◽  
Candida Rugosa ◽  
Structural Data ◽  
Data Bank ◽  
Candida Rugosa Lipase ◽  
Structural Features ◽  
X Ray Crystallography ◽  
Versatile Tool ◽  
Microbial Lipases

The structural elucidations of microbial lipases have been of prime interest since the 1980s. Knowledge of structural features plays an important role in designing and engineering lipases for specific purposes. Significant structural data have been presented for few microbial lipases, while, there is still a structure-deficit, that is, most lipase structures are yet to be resolved. A search for ‘lipase structure’ in the RCSB Protein Data Bank ( http://www.rcsb.org/pdb/ ) returns only 93 hits (as of September 2007) and, the NCBI database ( http://www.ncbi.nlm.nih.gov ) reports 89 lipase structures as compared to 14719 core nucleotide records. It is therefore worthwhile to consider investigations on the structural analysis of microbial lipases. This review is intended to provide a collection of resources on the instrumental, chemical and bioinformatics approaches for structure analyses. X-ray crystallography is a versatile tool for the structural biochemists and is been exploited till today. The chemical methods of recent interests include molecular modeling and combinatorial designs. Bioinformatics has surged striking interests in protein structural analysis with the advent of innumerable tools. Furthermore, a literature platform of the structural elucidations so far investigated has been presented with detailed descriptions as applicable to microbial lipases. A case study of Candida rugosa lipase (CRL) has also been discussed which highlights important structural features also common to most lipases. A general profile of lipase has been vividly described with an overview of lipase research reviewed in the past.

scholarly journals Membrane Protein Complex ExbB4-ExbD1-TonB1from Escherichia coli Demonstrates Conformational Plasticity

2015 ◽  
Vol 197 (11) ◽  
pp. 1873-1885 ◽  
Author(s):  
Aleksandr Sverzhinsky ◽  
Jacqueline W. Chung ◽  
Justin C. Deme ◽  
Lucien Fabre ◽  
Kristian T. Levey ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Iron Acquisition ◽  
Proton Translocation ◽  
Three Dimensional ◽  
Structural Data ◽  
Structural Features ◽  
Gram Negative Bacteria ◽  
Gram Negative ◽  
Content Type

ABSTRACTIron acquisition at the outer membrane (OM) of Gram-negative bacteria is powered by the proton motive force (PMF) of the cytoplasmic membrane (CM), harnessed by the CM-embedded complex of ExbB, ExbD, and TonB. Its stoichiometry, ensemble structural features, and mechanism of action are unknown. By panning combinatorial phage libraries, periplasmic regions of dimerization between ExbD and TonB were predicted. Using overexpression of full-length His6-taggedexbB-exbDand S-taggedtonB, we purified detergent-solubilized complexes of ExbB-ExbD-TonB fromEscherichia coli. Protein-detergent complexes of ∼230 kDa with a hydrodynamic radius of ∼6.0 nm were similar to previously purified ExbB4-ExbD2complexes. Significantly, they differed in electronegativity by native agarose gel electrophoresis. The stoichiometry was determined to be ExbB4-ExbD1-TonB1. Single-particle electron microscopy agrees with this stoichiometry. Two-dimensional averaging supported the phage display predictions, showing two forms of ExbD-TonB periplasmic heterodimerization: extensive and distal. Three-dimensional (3D) particle classification showed three representative conformations of ExbB4-ExbD1-TonB1. Based on our structural data, we propose a model in which ExbD shuttles a proton across the CM via an ExbB interprotein rearrangement. Proton translocation would be coupled to ExbD-mediated collapse of extended TonB in complex with ligand-loaded receptors in the OM, followed by repositioning of TonB through extensive dimerization with ExbD. Here we present the first report for purification of the ExbB-ExbD-TonB complex, molar ratios within the complex (4:1:1), and structural biology that provides insights into 3D organization.IMPORTANCEReceptors in the OM of Gram-negative bacteria allow entry of iron-bound siderophores that are necessary for pathogenicity. Numerous iron-acquisition strategies rely upon a ubiquitous and unique protein for energization: TonB. Complexed with ExbB and ExbD, the Ton system links the PMF to OM transport. Blocking iron uptake by targeting a vital nanomachine holds promise in therapeutics. Despite much research, the stoichiometry, structural arrangement, and molecular mechanism of the CM-embedded ExbB-ExbD-TonB complex remain unreported. Here we demonstratein vitroevidence of ExbB4-ExbD1-TonB1complexes. Using 3D EM, we reconstructed the complex in three conformational states that show variable ExbD-TonB heterodimerization. Our structural observations form the basis of a model for TonB-mediated iron acquisition.

Conformational behaviour of bridging diphenylphosphido ligands

1999 ◽  
Vol 55 (2) ◽  
pp. 203-208 ◽  
Author(s):  
John J. Barker ◽  
A. Guy Orpen
Keyword(s):  
Phenyl Ring ◽  
Global Minimum ◽  
Energy Surface ◽  
Low Energy ◽  
Block Element ◽  
Torsion Angles ◽  
Representative Species ◽  
Universal Force Field ◽  
Structural Database ◽  
Good Agreement

Data retrieved from the Cambridge Structural Database for crystal structures containing (μ-diphenylphosphido) metal complexes, [M 2{μ-PPh2}] (where M is a d-block element), have been analysed to evaluate the conformational behaviour of these species. The observed distribution of torsion angles about the P—C bonds has been compared with the potential energy surface (PES) for phenyl rotations in a representative species [(AuBr)2{μ-PPh2}]− computed using the universal force field. Good agreement was obtained between the low-energy (<8 kJ mol−1 above the global minimum) regions of the PES and the occupied regions of the two-dimensional P—Ph rotor conformation space. Phenyl ring rotations occur by coupled, geared disrotatory and uncoupled conrotatory motions of the phenyl groups in this and other classes of PPh2 rotors.

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