Born–Oppenheimer energy surfaces of similar molecules: Interrelations between bond lengths, bond angles, and frequencies of normal vibrations in alkanes

1982 ◽  
Vol 77 (9) ◽  
pp. 4542-4550 ◽  
Author(s):  
Shneior Lifson ◽  
Peter S. Stern
Keyword(s):  
Normal Vibrations ◽  
Bond Angles ◽  
Bond Lengths ◽  
Frequencies Of Normal Vibrations ◽  
Energy Surfaces

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.

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 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.

Distortion isomers of PtM, Pt2M, PtM2 and PtMM′ (M = non-transition metals) derivatives-structural aspects

2018 ◽  
Vol 0 (0) ◽  
Author(s):  
Milan Melník ◽  
Peter Mikuš
Keyword(s):  
Transition Metals ◽  
Structural Parameters ◽  
Bond Angles ◽  
Bond Lengths ◽  
Metal Atoms ◽  
Independent Molecules ◽  
Structural Aspects

Abstract An analysis of the structural parameters of PtM, Pt2M, PtM2 and PtMM′ (M = non-transition metals) derivatives shows that each complex contains two crystallographically independent molecules within the same crystal. The respective molecules differ by the degrees of distortion and exemplify the distortion isomerism. These are discussed in terms of the coordination with the platinum and the M atoms and the correlations are drawn among the metal atoms, donor atoms, bond lengths and bond angles. A wide variety of non-transition metals (Sn, Ga, In, Tl, Zn, Cd, Hg, Sb) exist, among which the most prevalent is Sn.

Electron Diffraction Investigation of the Molecular Structure of Trifluoromethanesulphonic acid (triflic acid)

1981 ◽  
Vol 36 (8) ◽  
pp. 917-918 ◽  
Author(s):  
György Schultz ◽  
Istvan Hargittai ◽  
Ragnhild Seip
Keyword(s):  
Molecular Structure ◽  
Electron Diffraction ◽  
Diffraction Study ◽  
Heavy Atom ◽  
Electron Diffraction Study ◽  
Molecular Geometry ◽  
Triflic Acid ◽  
Electron Diffraction Investigation ◽  
Bond Angles ◽  
Bond Lengths

Abstract The molecular geometry of triflic acid is characterized by the following bond lengths (rg) and bond angles from an electron diffraction study: S-C 183.3±0.5, F-C 133.2 ±0.2, S=O 141.8±0.2, S-O 155.8±0.3 pm, S-C-F 110.3 ±0.3, F-C-F 108.6 ±0.3, C-S=O 105.4±1.1, C-S-O 102.3 ±2.3, O-S= O 109.9±0.7, and O=S=O 122.0 ±1.3°. The heavy-atom-skeleton is staggered with respect to the rotation about the S-C bond with an estimated barrier of rotation of 15 kJ mol-1.

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