Bond angles and bond lengths in monosubstituted benzene and ethene derivatives: a comparison of computational and crystallographic results

2002 ◽  
Vol 58 (5) ◽  
pp. 877-883 ◽  
Author(s):  
Otto Exner ◽  
Stanislav Böhm
Keyword(s):  
Substitution Effect ◽  
Benzene Derivatives ◽  
Monosubstituted Benzene ◽  
Bond Angles ◽  
Bond Lengths ◽  
Bond Alternation ◽  
Structural Database ◽  
Azo Derivatives ◽  
Strong Deformation ◽  
Small Deformations

Bond angles and bond lengths in 29 monosubstituted benzene derivatives and in the same number of ethene derivatives were calculated at the B3LYP/6-311+G(d,p) level. Angle deformations in benzene derivatives agree reasonably with those derived statistically from the crystallographic data; in the case of small deformations, the calculated parameters are even more reliable. There is little correlation between geometry and reactivity parameters (σ-constants) in spite of some previous claims. Nevertheless, three components of the substitution effect can be distinguished: (a) strong deformation of the adjoining angles and bonds can be ascribed to changes of hybridization; (b) a weaker effect in the meta and para positions is only partially related to resonance; (c) in the case of unsymmetrical substituents, the symmetry of the benzene ring is also broken – the angular group-induced bond alternation (AGIBA) effect. The latter effect was also confirmed by searches in the Cambridge Structural Database for alkoxy, alkylthio, acyl and azo derivatives.

Structural characteristics of dibromoborylated benzene derivatives

2012 ◽  
Vol 68 (6) ◽  
pp. o226-o230 ◽  
Author(s):  
Sebastian Popp ◽  
Kai Ruth ◽  
Hans-Wolfram Lerner ◽  
Michael Bolte
Keyword(s):  
Crystal Structures ◽  
Aromatic Ring ◽  
Structural Characteristics ◽  
Geometric Parameters ◽  
Mirror Plane ◽  
Methyl Groups ◽  
Benzene Derivatives ◽  
Asymmetric Unit ◽  
Bond Lengths ◽  
Structural Database

The crystal structures of five dibromobenzene derivatives, namely dibromoborylbenzene, C6H5BBr2, (I), 1-dibromoboryl-4-(trimethylsilyl)benzene, C9H13BBr2Si, (II), 4-bromo-1-(dibromoboryl)benzene, C6H4BBr3, (III), dibromo(dimethylamino)(phenyl)borane, C8H12BBr2N, (IV), and dibromo(dimethylsulfanyl)[4-(trimethylsilyl)phenyl]borane, C11H19BBr2SSi, (V), have been determined. Compounds (I)–(IV) crystallize with one molecule in the asymmetric unit, but the molecule of (V) is located on a crystallographic mirror plane, implying twofold disorder of the central aromatic ring, the S atom and one of the methyl groups bonded to the S atom. In (I), (II) and (III), the B atom is three-coordinated, and in (IV) and (V) it is four-coordinated. The geometric parameters of the –BBr2group in these five structures agree well with those of comparable structures retrieved from the Cambridge Structural Database. The C—B and B—Br bond lengths in the molecules with a three-coordinated B atom are significantly shorter than those in the molecules with a four-coordinated B atom. In the compounds with a three-coordinated B atom, the –BBr2group tends to be coplanar with the aromatic ring to which it is attached.

Synthesis and Crystal Structures of Three Carboxylate- Bridged Tetranuclear Copper(II) - Lanthanide(III) Complexes of Ph3P+CH2CH2CO2−

1999 ◽  
Vol 52 (10) ◽  
pp. 983 ◽  
Author(s):  
Yang-Yi Yang ◽  
Seik Weng Ng ◽  
Xiao-Ming Chen
Keyword(s):  
Oxygen Atom ◽  
Crystal Structures ◽  
Triclinic Space Group ◽  
Coordination Environment ◽  
Space Group ◽  
Bond Angles ◽  
Bond Lengths ◽  
Metal Atoms ◽  
Apical Site

Three tetranuclear copper(II)–lanthanide(III) complexes of triphenylphosphoniopropionate (Ph3P+CH2CH2CO2−,tppp), namely [Cu2Ln2(tppp)8(H2O)8](ClO4)10·2H 2 O [Ln = EuIII, NdIII or CeIII], were synthesized and characterized by crystallography. The EuIII complex crystallizes in the triclinic space group P1 – with a 16.249(7), b 17.185(11), c 17.807(11) Å, α 69.750(10), β 89.230(10), γ 84.070(10)˚, V 4639(5) Å3, Z 1. In the crystal structures, four tppp ligands bridge a pair of CuII and tetraaquo-EuIII atoms (Cu···Eu 3.527(2) Å) through their µ2-carboxylato ends to form a dinuclear subunit; two of these subunits are additionally linked by one of the CuII -bonded carboxylato oxygen ends, across a centre of inversion, to furnish a dimeric tetranuclear [Cu(tppp)4 Eu(H2O)4]2 species (Cu···Cu 3.323(2) Å). This CuII -bonded oxygen atom occupies the apical site of the square-pyramidal coordination environment of the CuII atom. The EuIII atom is eight-coordinated in a square-antiprismatic geometry. The NdIII and CeIII complexes are isomorphous to the EuIII complex, and only minor differences in bond lengths and bond angles involving the metal atoms are noted.

Three new phosphoric triamides with a [C(O)NH]P(O)[N(C)(C)]2skeleton: a database analysis of C—N—C and P—N—C bond angles

2014 ◽  
Vol 70 (10) ◽  
pp. 998-1002 ◽  
Author(s):  
Mehrdad Pourayoubi ◽  
Atekeh Tarahhomi ◽  
Arnold L. Rheingold ◽  
James A. Golen
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Structures ◽  
The Other ◽  
Database Analysis ◽  
Acta Cryst ◽  
Bond Angles ◽  
Cyclic Amide ◽  
Phosphoric Triamide ◽  
Structural Database ◽  
Phosphoric Triamides

InN,N,N′,N′-tetraethyl-N′′-(4-fluorobenzoyl)phosphoric triamide, C15H25FN3O2P, (I), andN-(2,6-difluorobenzoyl)-N′,N′′-bis(4-methylpiperidin-1-yl)phosphoric triamide, C19H28F2N3O2P, (II), the C—N—C angle at each tertiary N atom is significantly smaller than the two P—N—C angles. For the other new structure,N,N′-dicyclohexyl-N′′-(2-fluorobenzoyl)-N,N′-dimethylphosphoric triamide, C21H33FN3O2P, (III), one C—N—C angle [117.08 (12)°] has a greater value than the related P—N—C angle [115.59 (9)°] at the same N atom. Furthermore, for most of the analogous structures with a [C(=O)NH]P(=O)[N(C)(C)]2skeleton deposited in the Cambridge Structural Database [CSD; Allen (2002).Acta Cryst.B58, 380–388], the C—N—C angle is significantly smaller than the two P—N—C angles; exceptions were found for four structures with theN-methylcyclohexylamide substituent, similar to (III), one structure with the seven-membered cyclic amide azepan-1-yl substituent and one structure with anN-methylbenzylamide substituent. The asymmetric units of (I), (II) and (III) contain one molecule, and in the crystal structures, adjacent molecules are linkedviapairs of N—H...O=P hydrogen bonds to form dimers.

scholarly journals Structural Modeling of Glutathiones Containing Selenium and Tellurium

2016 ◽  
Vol 8 (1) ◽  
pp. 102
Author(s):  
Valter A. Nascimento ◽  
Petr Melnikov ◽  
André V. D. Lanoa ◽  
Anderson F. Silva ◽  
Lourdes Z. Z. Consolo
Keyword(s):  
Molecular Mechanics ◽  
Structural Characteristics ◽  
Structural Modeling ◽  
Structural Description ◽  
Ionic Radii ◽  
X Ray ◽  
Bond Angles ◽  
Bond Lengths ◽  
Available Information ◽  
Related Compounds

<p>The comparative structural modeling of reduced and oxidized glutathiones, as well as their derivatives containing selenium and tellurium in chalcogen sites (Ch = Se, Te) has provided detailed information about the bond lengths and bond angles, filling the gap in the structural characteristics of these tri-peptides. The investigation using the molecular mechanics technique with good approximation confirmed the available information on X-ray refinements for the related compounds. It was shown that Ch-H and Ch-C bond lengths grow in parallel with the increasing chalcogen ionic radii. Although the distances C-C, C-O, and C-N are very similar, the geometry of GChChG glutathiones is rich in conformers owing to the possibility of rotation about the bridge Ch-Ch. It is confirmed that the distances Ch-Ch are essentially independent of substituents in most of chalcogen compounds from elemental chalcogens to oxydized glutathiones. The standard program Hyperchem 7.5 has proved to be an appropriate tool for the structural description of less-common bioactive compositions when direct X-ray data are missing.</p>

scholarly journals What’s in an Atom? a Comparison of Carbon and Silicon-Centered Amidinium···carboxylate Frameworks

2020 ◽  
Author(s):  
Stephanie Boer ◽  
Li-Juan Yu ◽  
Tobias Genet ◽  
Kaycee Low ◽  
Duncan Cullen ◽  
...  
Keyword(s):  
Quantum Chemical Calculations ◽  
Quantum Chemical ◽  
Building Blocks ◽  
Cambridge Structural Database ◽  
Bond Angles ◽  
Framework Materials ◽  
Carboxylate Anions ◽  
Tetrahedral Bond ◽  
Structural Database ◽  
Apparent Similarity

<div><div><div><p>Despite their apparent similarity, framework materials based on tetraphenylmethane and tetraphenylsilane building blocks often have quite different structures and topologies. Herein, we describe a new silicon tetraamidinium compound and use it to prepare crystalline hydrogen bonded frameworks with carboxylate anions in water. The silicon-containing frameworks are compared with those prepared from the analogous carbon tetraamidinium: when biphenyldicarboxylate or tetrakis(4-carboxyphenyl)methane anions were used similar channel-containing networks are observed for both the silicon and carbon tetraamidinium. When terephthalate or bicarbonate anions were used, different products form. Insights into possible reasons for the different products are provided by a survey of the Cambridge Structural Database and quantum chemical calculations, both of which indicate that, contrary to expectations, tetraphenylsilane derivatives have less geometrical flexibility than tetraphenylmethane derivatives, i.e. they are less able to distort away from ideal tetrahedral bond angles.</p></div></div></div>

scholarly journals DFT STUDIES OF STRUCTURAL PARAMETERS, VIBRATIONAL FREQUENCIES AND NMR SPECTRA OF 3-(1H-BENZO[D]IMIDAZOL-1-YL)-N'-(TOSYLOXY)PROPANIMIDAMIDE

2021 ◽  
pp. 15-25
Author(s):  
E.M. Yergaliyeva ◽  
◽  
L.A. Kayukova ◽  
A.V. Vologzhanina ◽  
G.P. Baitursynova ◽  
...  
Keyword(s):  
Nmr Spectra ◽  
Chemical Shifts ◽  
Structural Parameters ◽  
Correlation Coefficients ◽  
Biological Properties ◽  
Vibrational Frequencies ◽  
Substitution Product ◽  
Bond Angles ◽  
Bond Lengths ◽  
B3lyp Level

Amidoxime derivatives have practically valuable biological properties. We have previously obtained new spiropyrazolinium compounds by arylsulfo-chlorination of β-aminopropioamidoximes, but in case of β-(benzimidazol-1-yl)pro-pioamidoxime we have obtained O-substitution product – 3-(1H-benzo[d]imidazol-1-yl)-N'-(tosyloxy)pro-panimidamide. The aim of the work is predicting of structural parameters (bond lengths, bond angles), vibrational frequencies and NMR spectra of 3-(1H-benzo-[d]imidazol-1-yl)-N'-(tosyloxy)propanimidamide. The calculations were performed using Gaussian 09 package. Structural parameters and vibrational frequencies was calculated using DFT (B3LYP/B3PW91/WB97XD)/6-31G(d,p). 1H and 13C NMR was predicted using DFT B3LYP/6-31G(d,p)-GIAO in DMSO. All calculated values are in good agreement with experimental data. The calculated bond lengths and bond angles were compared with results of X-ray structural analysis. The best correlation coefficient was 0.981 (calcu-lations with B3LYP level). For bond angles, the best result was obtained with B3LYP level (0.990). For vibrational frequencies correlation coefficients between the calculated and experimental values were 0.997 (B3LYP), 0.996 (B3PW91) and 0.995 (WB97XD). The most accurate method was used for predic-ting NMR spectrum. The correlation coefficients between the experimental and calculated 1H and 13C chemical shifts were 0.949 and 0.999 respectively.

Accuracy of the final model

2002 ◽  
Author(s):  
David Blow
Keyword(s):  
Data Bank ◽  
The Other ◽  
Protein Crystal ◽  
Major Error ◽  
Final Model ◽  
Bond Angles ◽  
Bond Lengths ◽  
R Factor ◽  
Insight Into

The result of all the work described in the previous chapters will be a set of coordinates and other data suitable for deposit in the Protein Data Bank. You or I may use these coordinates, and we need to have some insight into their accuracy and reliability. In the previous chapters, indicators have been described, which may suggest aspects of the data or interpretation procedures that might lead to problems. But as the determination of protein crystal structures becomes more routine, many of these indicators are omitted from publications. Fortunately, crystallographic procedures are self-checking to a large extent. It is rare for a major error of interpretation to lead right through to a published refined structure. A high Rfree factor is a warning, especially if coupled with departures from the requirements of correct bond lengths, angles, and acceptable dihedral angles. On the other hand, there will always be a desire to squeeze more results from the data. All interpretations are subject to error; nearly all protein crystals have regions that are less ordered, where accurate interpretation is less feasible; and the structure may be overrefined, using too many variables for the data. If the majority of the molecule is correctly interpreted, a reasonable R factor may be obtained even though some small regions are completely wrong. During refinement it is usual to restrain the bond lengths and bond angles to be near their theoretical values, as described in Chapter 12. The extent to which bond lengths and bond angles depart from these values is often quoted as an indicator of accuracy. These departures are, however, difficult to interpret because they depend on how tightly the restraints have been applied. The same applies to the restraint of certain coordinates to lie in a plane. This difficulty illustrates a general problem. Designers of refinement procedures are understandably anxious to improve their procedures to lead directly to a well-refined structure. Every aspect of structure that can be recognized as having a regularity could, in principle, be expressed as a restraint which enforces it during refinement.

Notizen: Schwingungsspektren der Gold(I)-halogenide AuX (X = Cl, Br und I); Strukturprognosen für AuCl und AuBr / Vibrational Spectra of the Aurous Halides AuX (X= Cl, Br and I); Structural Prognoses for AuCl and AuBr

1974 ◽  
Vol 29 (11-12) ◽  
pp. 806-807 ◽  
Author(s):  
Dietrich Breitinger ◽  
Heiko Leuchtenstern
Keyword(s):  
Vibrational Spectra ◽  
Chain Structure ◽  
Force Constants ◽  
Bond Angles ◽  
Bond Lengths

Chain structure, Force constantsFrom vibrational spectra chain structures are predicted for AuCl and AuBr; bond angles, bond lengths and force constants have been estimated for these aurous halides.

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