Hydrogen bonding and steric effects on rotamerization in 3,4-alkylenedioxy-, 3-alkoxy- and 3,4-dialkoxy-2-thienyldi(tert-butyl)methanols: an NMR, IR and X-ray crystallographic studyElectronic supplementary information (ESI) available: NMR data; activation parameters for rotation; MMFF94 steric energies and alkoxy group geometries; thermodynamic data; quantum mechanical calculations of geometries; bond lengths, bond angles and torsion angles of 8A-Et; NMR and IR data on new compounds. See http://www.rsc.org/suppdata/p2/b1/b109612p/

2002 ◽  
pp. 216-224 ◽  
Author(s):  
John S. Lomas ◽  
Alain Adenier ◽  
Kun Gao ◽  
François Maurel ◽  
Jacqueline Vaissermann
Keyword(s):  
Activation Parameters ◽  
Alkoxy Group ◽  
Supplementary Information ◽  
Steric Effects ◽  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
Torsion Angles ◽  
X Ray ◽  
Nmr Data ◽  
New Compounds

Crystal Forms of Semisynthetic Ergot Alkaloid Terguride

2002 ◽  
Vol 67 (4) ◽  
pp. 479-489 ◽  
Author(s):  
Michal Hušák ◽  
Bohumil Kratochvíl ◽  
Ivana Císařová ◽  
Ladislav Cvak ◽  
Alexandr Jegorov ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Ergot Alkaloid ◽  
Simplified Model ◽  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
X Ray Diffraction ◽  
Torsion Angles ◽  
Crystal Forms ◽  
X Ray ◽  
Independent Molecules

Two new structures of semisynthetic ergot alkaloid terguride created by unusual number of symmetry-independent molecules were determined by X-ray diffraction methods at 150 K. Form A (monoclinic, P212121, Z = 12) contains three symmetry-independent terguride molecules and two molecules of water in the asymmetric part of the unit cell. The form CA (monoclinic, P21, Z = 8) is an anhydrate remarkable by the presence of four symmetry-independent molecules in the crystal structure. Conformations of twelve symmetry-independent molecules that were found in four already described terguride structures are compared with torsion angles obtained by ab initio quantum-mechanical calculations for the simplified model of N-cyclohexyl-N'-diethylurea.

scholarly journals Interpreting Disordered PXRD Structures using Molecular Dynamics

2014 ◽  
Vol 70 (a1) ◽  
pp. C1569-C1569
Author(s):  
Kristoffer Johansson ◽  
Xiaozhou Li ◽  
Andrew Bond ◽  
Jacco van de Streek
Keyword(s):  
Molecular Dynamics ◽  
Structural Information ◽  
Supplementary Information ◽  
Rational Approach ◽  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
X Ray Diffraction ◽  
X Ray ◽  
Crystal Properties ◽  
Solid Form

A central topic in the formulation of solid medicinal products is the identification of a suitable solid form of an active compound to obtain optimal physicochemical properties. To this end, disorder may be important for relevant crystal properties like stability. For example, disorder may account for more than 10% of the crystal volume. A rational approach to solid-form selection is typically based on structural information at atomic resolution. In practice, pharmaceutical compounds are not always well-behaved and especially in the study of polymorphs or compounds with flexible groups it can be challenging to obtain crystals suitable for single-crystal X-ray diffraction. Powder X-ray diffraction (PXRD) is a popular alternative, but it generally requires supplementary information like molecular connectivity in simple cases or computational models to solve larger structures. Computational modeling has come a long way and accurate and reliable structures of pharmaceutically relevant compounds can indeed be obtained using laboratory PXRD measurements and quantum-mechanical calculations [1]. The major limitation of quantum mechanical calculations, however, is that they do not consider time nor temperature but only static structures at zero temperature. Thus, these methods cannot model phenomena related to disorder. The molecular dynamics (MD) method can add temperature as well as time and spatial resolution to a model and has in recent years developed to be a scalable, reliable and increasingly available technique. As more and more groups from academia as well as industry employ MD in their work, the development will increase to gain momentum in the coming years. We use MD in a high-performance setting to study crystal properties that are relevant for pharmaceutical research. Using a combination of models from first principles and MD we are able to study highly disordered structures and polymorphs on the basis of PXRD data.

Conformational Study of 2,4-Diaryl-3-azabicyclo[3.3.1]nonan-9-ones and Their 3-Methyl Derivatives by Quantum Mechanical Calculations, NMR, and X-ray Crystallography

1994 ◽  
Vol 59 (9) ◽  
pp. 2565-2569 ◽  
Author(s):  
Maria-Selma Arias ◽  
Yves G. Smeyers ◽  
Maria-Jose Fernandez ◽  
Nadine J. Smeyers ◽  
Enrique Galvez ◽  
...  
Keyword(s):  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
Conformational Study ◽  
X Ray ◽  
X Ray Crystallography ◽  
Methyl Derivatives

Molecular X-ray Spectra of Sulfur and Chlorine Bearing Substances

1970 ◽  
Vol 14 ◽  
pp. 453-486 ◽  
Author(s):  
G. Andermann ◽  
H. C. Whitehead
Keyword(s):  
Theoretical Models ◽  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
Molecular Models ◽  
X Ray ◽  
Starting Point ◽  
State Models ◽  
Basic Features ◽  
Photon Spectra ◽  
Molecular Bonding

AbstractThe interpretation and use of x-ray photon spectra of substances containing second row elements has utilized a number of theoretical models. These models may be divided into three basic categories, namely, the isolated atom model, various molecular models, and a number of solid state models, it is the purpose of this paper to examine critically the validity and limitations of molecular models for interpreting published x-ray photon spectra and spectra obtained by this group on chlorine and sulfur bearing substances.Chlorine and sulfur bearing substances were chosen for at least three important reasons. First, a great deal of published experimental data already exists on the Kα, Kβ, and L2, 3 transitions of these substances. Second, motivated in part by the long standing controversy concerning possible 3d orbital participation in the bonding of second row elements, there are extensive quantum mechanical calculations for ions containing sulfur and chlorine via simple molecular orbital concepts. Thirdj the availability of accurate photoelectron spectroscopic data on these substances now permits a detailed quantitative comparison of x-ray photon transitions with quantum mechanical calculations.Detailed evaluation along these lines indicates that for many substances the theoretically calculated energy values are frequently within a few electron volts (or less) of the experimentally observed energies. This study, therefore, tends to substantiate a viewpoint suggested by some recently; namely, that for many substances the starting point in interpreting most of the basic features of soft x-ray spectra should be based upon molecular bonding approaches.

scholarly journals Determination of the electron density in methyl (±)-(1S,2S,3R)-2-methyl-1,3-diphenylcyclopropanecarboxylate using refinements with X-ray scattering factors from wavefunction calculations of the whole molecule

2013 ◽  
Vol 69 (8) ◽  
pp. 910-914 ◽  
Author(s):  
John Bacsa ◽  
John Briones
Keyword(s):  
Electron Density ◽  
Title Compound ◽  
Cyclopropane Ring ◽  
Topological Analysis ◽  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
X Ray ◽  
Compound C ◽  
X Ray Scattering

The molecule of the title compound, C18H18O2, is a substituted cyclopropane ring. The electron density in this molecule has been determined by refining single-crystal X-ray data using scattering factors derived from quantum mechanical calculations. Topological analysis of the electron densities in the three cyclopropane C—C bonds was carried out. The results show the effects of this substitution on these C—C bonds.

Crystal Structure and Tautomerism of 1-[N-(4-Iodophenyl)]aminomethylidene-2(1H)naphthalenone

2001 ◽  
Vol 56 (10) ◽  
pp. 1003-1008 ◽  
Author(s):  
H. Ünver ◽  
M. Kabak ◽  
D. M. Zengin ◽  
T. N. Durlu
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Quantum Mechanical ◽  
Monoclinic Space Group ◽  
Quantum Mechanical Calculations ◽  
X Ray ◽  
H Nmr ◽  
Mechanical Methods ◽  
Intramolecular Hydrogen ◽  
Semi Empirical

1-[N-(4-Iodophenyl)]aminomethylidene-2(1H)naphthalenone (1) (C17H12NOI) has been studied by X-ray analysis, IR, 1H NMR, UV and AM1 semi-empirical quantum mechanical methods. It crystallises in the monoclinic space group P21/n with a = 4.844(3), b = 21.428(2), c = 13.726(2) Å, ß = 93.07(2)° (R1 =0.032 for 4132 reflections [I > 2σ(I)]). The title compound is not planar and an intramolecular hydrogen bond connects O1 and N1 [2.530(4) Å]. Complementary IR, 1H NMR and UV measurements out. Tautomerism and conformations of the title semi-empirical quantum mechanical calculations and the results are compared with the X-ray data.

scholarly journals Influence of per-O-sulfation upon the conformational behaviour of common furanosides

2019 ◽  
Vol 15 ◽  
pp. 685-694 ◽  
Author(s):  
Alexey G Gerbst ◽  
Vadim B Krylov ◽  
Dmitry A Argunov ◽  
Maksim I Petruk ◽  
Arsenii S Solovev ◽  
...  
Keyword(s):  
Ab Initio Calculations ◽  
Quantum Chemical ◽  
Low Energy ◽  
Coupling Constants ◽  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
Ring Conformation ◽  
Nmr Data ◽  
Conformational Investigation ◽  
Conformational Distribution

The studies on the recently discovered pyranoside-into-furanoside rearrangement have led us to conformational investigations of furanosides upon their total sulfation. Experimental NMR data showed that in some cases drastic changes of the ring conformation occurred while sometimes only the conformation of the exocyclic C4–C5 linkage changed. Herein we describe a combined quantum chemical and NMR conformational investigation of three common monosaccharide furanosides as their propyl glycosides: α-mannose, β-glucose and β-galactose. Full exploration of the furanoside ring by means of ab initio calculations was performed and coupling constants were calculated for each of the low-energy conformers. The results demonstrated preferred trans-orientation of H4–H5 protons in the non-sulfated molecules which changed to gauche-orientation upon sulfation. The effect is less pronounced in the galactosides. For all the studied structures changes in the conformational distribution were revealed by quantum mechanical calculations, that explained the observed changes in intraring coupling constants occurring upon introduction of sulfates.

scholarly journals Quantum Mechanical Study of Protonation of Oxygen Ligands in the Laccase Active Site Based on X-Ray Structures of Subatomic Resolution

2022 ◽  
Author(s):  
Sergei Gavryushov ◽  
Nikolay Kuzmich ◽  
Konstantin Polyakov
Keyword(s):  
Oxygen Reduction ◽  
Molecular Oxygen ◽  
High Precision ◽  
Active Site ◽  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
Stable States ◽  
Hydrogen Atoms ◽  
X Ray ◽  
Wide Range

Laccases are enzymes catalyzing oxidation of a wide range of organic and inorganic substrates accompanied by molecular oxygen reduction to water. Previously studies of oxygen reduction by laccases have recently been reported. They were based on single-crystal serial X-ray crystallography with increasing absorption doses at subatomic resolution, As a result, coordinates of all non-hydrogen atoms of the active site have been determined with high precision for both oxidized and reduced states of the enzyme. Those data can be used to clarify the mechanism of molecular oxygen reduction by laccases. However, the X-ray data lack information about protonation states of the oxygen ligands involved. Applying quantum mechanical calculations, in the present work protonation of oxygen ligands in the active site of laccase was determined for both reduced and oxidized states of the enzyme (the stable states observed in experiments at reduction of molecular oxygen in laccase). The high precision of X-ray-determined atom coordinates allowed us to simplify preliminary calculations of molecular mechanics for models used in the quantum mechanical calculations.

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