Nature ofE2X2σ(4c–6e) of theX---E—E---Xtype at naphthalene 1,8-positions and model, elucidated by X-ray crystallographic analysis and QC calculations with the QTAIM approach

2017 ◽  
Vol 73 (2) ◽  
pp. 265-275 ◽  
Author(s):  
Yutaka Tsubomoto ◽  
Satoko Hayashi ◽  
Waro Nakanishi ◽  
Takahiro Sasamori ◽  
Norihiro Tokitoh
Keyword(s):  
Closed Shell ◽  
Crystallographic Analysis ◽  
Dynamic Nature ◽  
Total Electron ◽  
X Ray ◽  
Dual Functional ◽  
Total Electron Energy ◽  
Polar Coordinate ◽  
Static Nature

The nature ofE2X2σ(4c–6e) of theX-*-E-*-E-*-Xtype is elucidated for 1-(8-XC10H6)E–E(C10H6X-8′)-1′ [(1)E,X= S, Cl; (2) S, Br; (3) Se, Cl; (4) Se, Br] after structural determination of (1), (3) and (4), together with modelA[MeX---E(H)—E(H)---XMe (E= S and Se;X= Cl and Br)]. The quantum theory of atoms-in-molecules dual functional analysis (QTAIM-DFA) is applied. The total electron energy densitiesHb(rc) are plottedversus Hb(rc) –Vb(rc)/2 for the interactions at the bond critical points (BCPs; *), whereVb(rc) show the potential energy densities at the BCPs. Data for the perturbed structures around the fully optimized structures are employed for the plots, in addition to those of the fully optimized structures. The plots were analysed using the polar coordinate (R, θ) representation of the data of the fully optimized structures. Data containing the perturbed structures were analysed by (θp, κp), where θpcorresponds to the tangent line of the plot and κpis the curvature. Whereas (R, θ) shows the static nature, (θp, κp) represents the dynamic nature of interactions.E-*-Eare all classified as shared shell (S) interactions for (1)–(4) and as weak covalent (Cov-w) in nature (S/Cov-w). The nature ofpureCS (closed shell)/typical-HB (hydrogen bond) with no covalency is predicted forE-*-Xin (1) and (3),regularCS/typical-HB nature with covalency is predicted for (4), and an intermediate nature is predicted for (2). The NBO energies evaluated forE-*-Xin (1)–(4) are substantially larger than those in modelAdue the shortened length at the naphthalene 1,8-positions. The nature ofE2X2of σ(4c–6e) is well elucidatedviaQTAIM-DFA.

scholarly journals Dynamic and Static Nature of Br4σ(4c–6e) and Se2Br5σ(7c–10e) in the Selenanthrene System and Related Species Elucidated by QTAIM Dual Functional Analysis with QC Calculations

2020 ◽  
Vol 2020 ◽  
pp. 1-14
Author(s):  
Satoko Hayashi ◽  
Taro Nishide ◽  
Waro Nakanishi
Keyword(s):  
Functional Analysis ◽  
Hydrogen Bond ◽  
Charge Transfer ◽  
Related Species ◽  
Adduct Formation ◽  
Dynamic Nature ◽  
Dual Functional ◽  
Trigonal Bipyramidal ◽  
Treatment Data ◽  
Static Nature

The nature of Br4σ(4c–6e) of the BBr-∗-ABr-∗-ABr-∗-BBr form is elucidated for SeC12H8(Br)SeBr---Br-Br---BrSe(Br)C12H8Se, the selenanthrene system, and the models with QTAIM dual functional analysis (QTAIM-DFA). Asterisks (∗) are employed to emphasize the existence of bond critical points on the interactions in question. Data from the fully optimized structure correspond to the static nature of interactions. In our treatment, data from the perturbed structures, around the fully optimized structure, are employed for the analysis, in addition to those from the fully optimized one, which represent the dynamic nature of interactions. The ABr-∗-ABr and ABr-∗-BBr interactions are predicted to have the CT-TBP (trigonal bipyramidal adduct formation through charge transfer) nature and the typical hydrogen bond nature, respectively. The nature of Se2Br5σ(7c–10e) is also clarified typically, employing an anionic model of [Br-Se(C4H4Se)-Br---Br---Br-Se(C4H4Se)-Br]−, the 1,4-diselenin system, rather than (BrSeC12H8)Br---Se---Br-Br---Br-Se(C12H8Se)-Br, the selenanthrene system.

Structure Determination of Triplet Diphenylcarbenes by in Situ X-ray Crystallographic Analysis

2007 ◽  
Vol 129 (8) ◽  
pp. 2383-2391 ◽  
Author(s):  
Masaki Kawano ◽  
Katsuyuki Hirai ◽  
Hideo Tomioka ◽  
Yuji Ohashi
Keyword(s):  
Structure Determination ◽  
Crystallographic Analysis ◽  
X Ray

scholarly journals Intrinsic Dynamic and Static Nature of Halogen Bonding in Neutral Polybromine Clusters, with the Structural Feature Elucidated by QTAIM Dual-Functional Analysis and MO Calculations

Molecules ◽  
2021 ◽  
Vol 26 (10) ◽  
pp. 2936
Author(s):  
Satoko Hayashi ◽  
Taro Nishide ◽  
Eiichiro Tanaka ◽  
Waro Nakanishi
Keyword(s):  
Functional Analysis ◽  
Noncovalent Interactions ◽  
Halogen Bonding ◽  
Bond Critical Point ◽  
Strongly Correlated ◽  
Dynamic Nature ◽  
Dual Functional ◽  
Compliance Constants ◽  
Intrinsic Dynamic ◽  
Static Nature

The intrinsic dynamic and static nature of noncovalent Br-∗-Br interactions in neutral polybromine clusters is elucidated for Br4–Br12, applying QTAIM dual-functional analysis (QTAIM-DFA). The asterisk (∗) emphasizes the existence of the bond critical point (BCP) on the interaction in question. Data from the fully optimized structures correspond to the static nature of the interactions. The intrinsic dynamic nature originates from those of the perturbed structures generated using the coordinates derived from the compliance constants for the interactions and the fully optimized structures. The noncovalent Br-∗-Br interactions in the L-shaped clusters of the Cs symmetry are predicted to have the typical hydrogen bond nature without covalency, although the first ones in the sequences have the vdW nature. The L-shaped clusters are stabilized by the n(Br)→σ*(Br–Br) interactions. The compliance constants for the corresponding noncovalent interactions are strongly correlated to the E(2) values based on NBO. Indeed, the MO energies seem not to contribute to stabilizing Br4 (C2h) and Br4 (D2d), but the core potentials stabilize them, relative to the case of 2Br2; this is possibly due to the reduced nuclear–electron distances, on average, for the dimers.

Relative and Absolute Structure Assignments of Alkenes Using Crystalline Osmate Derivatives for X-Ray Analysis

2019 ◽  
Author(s):  
Alexander S. Burns ◽  
Charles dooley ◽  
Paul R. Carlson ◽  
Joseph W. Ziller ◽  
Scott Rychnovsky
Keyword(s):  
Absolute Configuration ◽  
Osmium Tetroxide ◽  
Heavy Atom ◽  
Crystallographic Analysis ◽  
Enol Ethers ◽  
X Ray ◽  
Silyl Enol Ethers ◽  
Absolute Structure ◽  
Structure Of Liquid

<div><div><p>Osmium tetroxide and TMEDA form stable crystalline adducts with alkenes. The structure of liquid alkenes can be determined through X-ray analysis of these derivatives. Osmium, a heavy atom, facilitates the crystallographic analysis and the determination of the absolute configuration using common Mo X-ray sources. The utility of this method for assigning structures and absolute configurations was demonstrated on a number of unsaturated substrates that include simple alkenes, enones, enol ethers, and silyl enol ethers.</p></div></div>

scholarly journals Preliminary X-ray crystallographic analysis of an engineered glutamyl-tRNA synthetase fromEscherichia coli

2014 ◽  
Vol 70 (7) ◽  
pp. 922-927 ◽  
Author(s):  
Nipa Chongdar ◽  
Saumya Dasgupta ◽  
Ajit Bikram Datta ◽  
Gautam Basu
Keyword(s):  
Structure Function ◽  
Thermus Thermophilus ◽  
Trna Synthetase ◽  
Crystallographic Analysis ◽  
X Ray ◽  
E Coli ◽  
Crystal Contacts ◽  
Function Correlation ◽  
Trna Substrate

The nature of interaction between glutamyl-tRNA synthetase (GluRS) and its tRNA substrate is unique in bacteria in that many bacterial GluRS are capable of recognizing two tRNA substrates: tRNAGluand tRNAGln. To properly understand this distinctive GluRS–tRNA interaction it is important to pursue detailed structure–function studies; however, because of the fact that tRNA–GluRS interaction in bacteria is also associated with phylum-specific idiosyncrasies, the structure–function correlation studies must also be phylum-specific. GluRS fromThermus thermophilusandEscherichia coli, which belong to evolutionarily distant phyla, are the biochemically best characterized. Of these, only the structure ofT. thermophilusGluRS is available. To fully unravel the subtleties of tRNAGlu–GluRS interaction inE. coli, a model bacterium that can also be pathogenic, determination of theE. coliGluRS structure is essential. However, previous attempts have failed to crystallizeE. coliGluRS. By mapping crystal contacts of a homologous GluRS onto theE. coliGluRS sequence, two surface residues were identified that might have been hindering crystallization attempts. Accordingly, these two residues were mutated and crystallization of the double mutant was attempted. Here, the design, expression, purification and crystallization of an engineeredE. coliGluRS in which two surface residues were mutated to optimize crystal contacts are reported.

Synthesis and Structure Determination of 2,3-Diphenyl-2H-1,4-Benzoxazin-2-ol

2007 ◽  
Vol 2007 (9) ◽  
pp. 548-551 ◽  
Author(s):  
Katayoun Marjani ◽  
Jafar Asgarian ◽  
Mohsen Mousavi
Keyword(s):  
Elemental Analysis ◽  
Structure Determination ◽  
Main Product ◽  
Crystallographic Analysis ◽  
Spectroscopic Methods ◽  
X Ray

A stable hemiacetal, 2,3-diphenyl-2H-1,4-benzoxazin-2-ol, was isolated as the main product from the reaction of benzil and o-aminophenol in THF. The structure of the product is confirmed by elemental analysis, common spectroscopic methods, and X-ray crystallographic analysis.

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