Intermolecular interactions in hydrates of 4-methylpiperidine and 4-chloropiperidine – a structural and computational study

CrystEngComm ◽  
2021 ◽  
Author(s):  
Pawel Socha ◽  
Bernadeta Prus ◽  
Lukasz Dobrzycki ◽  
Roland Boese ◽  
Michal Ksawery Cyranski
Keyword(s):  
Quantum Chemistry ◽  
Intermolecular Interactions ◽  
Computational Study ◽  
Piperidine Ring ◽  
X Ray ◽  
X Ray Crystallography

The structures and interactions in four new hydrates of substituted piperidines have been studied using X¬ray crystallography and quantum chemistry. The piperidine ring substitution leads to a significant reduction in...

scholarly journals Synthesis, X-Ray Crystallography, Thermal Analysis, and DFT Studies of Ni(II) Complex with 1-Vinylimidazole Ligand

2014 ◽  
Vol 2014 ◽  
pp. 1-9 ◽  
Author(s):  
Fatih Şen ◽  
Ramazan Şahin ◽  
Muharrem Dinçer ◽  
Ömer Andaç ◽  
Murat Taş
Keyword(s):  
Density Functional ◽  
Computational Study ◽  
Basis Sets ◽  
Mulliken Charge ◽  
Monoclinic Space Group ◽  
X Ray Diffraction ◽  
Dft Methods ◽  
X Ray ◽  
X Ray Crystallography ◽  
The Density Functional Theory

The paper presents a combined experimental and computational study of hexa(1-vinylimidazole)Ni(II) perchlorate complex. The complex was prepared in the laboratory and crystallized in the monoclinic space group P21/n with a=8.442(5), b=13.686(8), c=16.041(9) Å, α=γ=90, β=96.638(5), and Z=1. The complex has been characterized structurally (by single-crystal X-Ray diffraction) and its molecular structure in the ground state has been calculated using the density functional theory (DFT) methods with 6-31G(d) and LanL2DZ basis sets. Thermal behaviour and stability of the complex were studied by TGA/DTA analyses. Besides, the nonlinear optical effects (NLO), molecular electrostatic potential (MEP), frontier molecular orbitals (FMO), and the Mulliken charge distribution were investigated theoretically.

scholarly journals A Raman Spectroscopic and Computational Study of New Aromatic Pyrimidine-Based Halogen Bond Acceptors

Inorganics ◽  
2019 ◽  
Vol 7 (10) ◽  
pp. 119 ◽  
Author(s):  
Hardin ◽  
Ellington ◽  
Nguyen ◽  
Rheingold ◽  
Tschumper ◽  
...  
Keyword(s):  
Self Assembly ◽  
Density Functional ◽  
Computational Study ◽  
Halogen Bond ◽  
Normal Modes ◽  
Halogen Bonding ◽  
Building Blocks ◽  
Molecular Assembly ◽  
X Ray ◽  
X Ray Crystallography

Two new aromatic pyrimidine-based derivatives designed specifically for halogen bond directed self-assembly are investigated through a combination of high-resolution Raman spectroscopy, X-ray crystallography, and computational quantum chemistry. The vibrational frequencies of these new molecular building blocks, pyrimidine capped with furan (PrmF) and thiophene (PrmT), are compared to those previously assigned for pyrimidine (Prm). The modifications affect only a select few of the normal modes of Prm, most noticeably its signature ring breathing mode, ν1. Structural analyses afforded by X-ray crystallography, and computed interaction energies from density functional theory computations indicate that, although weak hydrogen bonding (C–H···O or C–H···N interactions) is present in these pyrimidine-based solid-state co-crystals, halogen bonding and π-stacking interactions play more dominant roles in driving their molecular-assembly.

Synthesis and Crystal Structure of Lead(II) Thenoyltrifluoroacetonate Complexes with Substituted 2,2' -Bipyridines: Interplay of Intermolecular Interactions in Crystals

2010 ◽  
Vol 65 (2) ◽  
pp. 128-134 ◽  
Author(s):  
Farzin Marandi ◽  
Zahra Nikpey ◽  
Jia Hao Goh ◽  
Hoong-Kun Fun
Keyword(s):  
Crystal Structure ◽  
Thermal Analysis ◽  
Nmr Spectroscopy ◽  
Intermolecular Interactions ◽  
Synthesis And Crystal Structure ◽  
X Ray ◽  
X Ray Crystallography ◽  
C Nmr

Three substituted 2,2'-bipyridine adducts of lead(II) thenoyltrifluoroacetonate, [Pb(4,4'-dm-2,2’- bpy)(ttfa)2]2, 1, [Pb(5,5' -dm-2,2’-bpy)(ttfa)2]2, 2, and [Pb(4,4'-dmo-2,2’-bpy)(ttfa)2], 3, (4,4’ -dm- 2,2’-bpy, 5,5’-dm-2,2’-bpy, 4,4’-dmo-2,2’-bpy and ttfa are the abbreviations for 4,4’-dimethyl-, 5,5’-dimethyl-, and 4,4’-dimethoxy-2,2’-bipyridine, and thenoyltrifluoroacetonate, respectively) have been synthesized, characterized by elemental and thermal analysis, IR and 1H- and 13C-NMR spectroscopy, and studied by X-ray crystallography. The supramolecular features in these complexes are guided/controlled by weak directional intermolecular interactions.

Merging Structural Information from X-ray Crystallography, Quantum Chemistry, and EXAFS Spectra: The Oxygen-Evolving Complex in PSII

2016 ◽  
Vol 120 (42) ◽  
pp. 10899-10922 ◽  
Author(s):  
Petko Chernev ◽  
Ivelina Zaharieva ◽  
Emanuele Rossini ◽  
Artur Galstyan ◽  
Holger Dau ◽  
...  
Keyword(s):  
Quantum Chemistry ◽  
Structural Information ◽  
Oxygen Evolving Complex ◽  
X Ray ◽  
X Ray Crystallography ◽  
Oxygen Evolving ◽  
Exafs Spectra

scholarly journals Solid-state structure of cyclic dipeptides: an X-ray and computational study of cis- and trans-diketopiperazines of N-methyl-phenylalanine with the thia-pipecolic acids and thia-prolines

2017 ◽  
Vol 73 (6) ◽  
pp. 1179-1193 ◽  
Author(s):  
Milos Budesinsky ◽  
Ivana Cisarova ◽  
Frans Borremans ◽  
Jose C. Martins ◽  
Ewald Pauwels
Keyword(s):  
Density Functional ◽  
Computational Study ◽  
Density Functional Theory Calculations ◽  
Amide Bond ◽  
Functional Theory ◽  
Torsion Angles ◽  
Molecular Conformations ◽  
X Ray ◽  
X Ray Crystallography ◽  
Cis And Trans

Ten new crystal structures of cis and trans bicyclic diketopiperazines (DKPs) of thia-pipecolic acid (with sulfur in the β, γ or δ position) or thia-proline (with sulfur in the β or γ position) and N-methyl phenylalanine [(NMe)Phe]: cyclo[(β-S)Pip-(NMe)Phe], cyclo[(γ-S)Pip-(NMe)Phe], cyclo[(δ-S)Pip-(NMe)Phe], cyclo[(β-S)Pro-(NMe)Phe] and cyclo[(γ-S)Pro-(NMe)Phe] were determined with X-ray crystallography. Density functional theory calculations of these molecules in the gas phase succeed in reproducing the observed molecular conformations in the crystal remarkably well. This illustrates the weak to moderate impact of intermolecular packing forces in the absence of classical N—H...O hydrogen bonds. The effect of sulfur on the geometry of the DKP ring and details of amide bond non-planarity are discussed. Molecular flexibility of the DKP ring, as estimated from the calculated deformation energies of its endocyclic ring torsion angles, is not in general the decisive factor for the occurrence of multiple symmetry independent molecules in the unit cell (Z′ > 1), though in some cases a correlation is observed.

The Structural Chemistry of Metallocorroles: Combined X-ray Crystallography and Quantum Chemistry Studies Afford Unique Insights

2012 ◽  
Vol 45 (8) ◽  
pp. 1203-1214 ◽  
Author(s):  
Kolle E. Thomas ◽  
Abraham B. Alemayehu ◽  
Jeanet Conradie ◽  
Christine M. Beavers ◽  
Abhik Ghosh
Keyword(s):  
Quantum Chemistry ◽  
Structural Chemistry ◽  
X Ray ◽  
X Ray Crystallography

Synthesis and structural study of five new phosphoric triamides: interplay between classical and non-classical intermolecular interactions

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Bahar Bakhshipour ◽  
Atekeh Tarahhomi ◽  
Arie van der Lee
Keyword(s):  
Hydrogen Bonds ◽  
Intermolecular Interactions ◽  
Crystal Packing ◽  
Asymmetric Unit ◽  
X Ray Diffraction ◽  
X Ray ◽  
X Ray Crystallography ◽  
Phosphoric Triamide ◽  
Ft Ir ◽  
Phosphoric Triamides

Abstract Phosphoric triamides are attractive to investigate because of their extensive applications in various fields, especially in medicine. Five new phosphoric triamides with the main parts [N]P(O)[NH]2 and [C(O)NH]P(O)[N]2 have been structurally analyzed by single crystal MoKα/synchrotron-based X-ray diffraction and characterized by spectroscopic methods (FT-IR and 1H, 13C, 31P NMR). Compounds crystallize in orthorhombic (1 with space group Pnma) and monoclinic (2 (P21/a), 3 (C2/c), 4 (P21/n) and 5 (P21/c)) crystal systems. The asymmetric unit of all structures consists of one phosphoric triamide molecule, except for 1 with one half of molecule. X-ray crystallography data reveal that the molecular architectures constructed by classical N—H … O hydrogen bonds are as 1D linear (building the R 2 1 ( 6 ) ${R}\_{2}^{1}(6)$ , C(4) and R 2 2 ( 10 ) / R 2 1 ( 6 ) ${R}\_{2}^{2}(10)/{R}\_{2}^{1}(6)$ motifs, respectively, for 1–3) or dimeric (the R 2 2 ( 8 ) ${R}\_{2}^{2}(8)$ ring motif for 4 and 5). A detailed investigation of the intermolecular interactions using Hirshfeld surface (HS) analysis illustrates that the H … H, O … H/H … O and C … H/H … C contacts for all compounds, and Cl … H/H … Cl and F … H/H … F contacts for 3–5, are the most significant contributors to the crystal packing. Moreover, based on the calculated enrichment ratios (E), the O … H/H … O contacts including the classical N—H … O hydrogen bonds for all structures are considered as favoured contacts.

scholarly journals 2-N-Benzyl-2,6-dideoxy-2,6-imino-3,4-O-isopropylidene-D-allononitrile

2013 ◽  
Vol 69 (12) ◽  
pp. o1772-o1772 ◽  
Author(s):  
Benjamin J. Ayers ◽  
Sarah F. Jenkinson ◽  
George W. J. Fleet ◽  
Amber L. Thompson
Keyword(s):  
Absolute Configuration ◽  
Title Compound ◽  
Starting Material ◽  
Piperidine Ring ◽  
Boat Conformation ◽  
X Ray ◽  
X Ray Crystallography ◽  
Compound C ◽  
Relative Stereochemistry ◽  
Twisted Boat

X-ray crystallography firmly established the relative stereochemistry of the title compound, C16H20N2O3. The acetonide ring adopts an envelope conformation with one of the O atoms as the flap and the piperidine ring adopts a slightly twisted boat conformation. The absolute configuration was determined by use of D-ribose as the starting material. The compound exists as O—H...O hydrogen-bonded chains of molecules running parallel to thebaxis.

Difference Fourier Analysis of Glucose Embedded and Frozen Hydrated Purple Membrane

1982 ◽  
Vol 40 ◽  
pp. 74-75
Author(s):  
Jules S. Jaffe ◽  
Robert M. Glaeser
Keyword(s):  
Purple Membrane ◽  
Data Set ◽  
High Resolution Data ◽  
X Ray ◽  
X Ray Crystallography ◽  
Fourier Techniques ◽  
Versus Protein ◽  
The Difference ◽  
Difference Fourier ◽  
Ideal Method

Although difference Fourier techniques are standard in X-ray crystallography it has only been very recently that electron crystallographers have been able to take advantage of this method. We have combined a high resolution data set for frozen glucose embedded Purple Membrane (PM) with a data set collected from PM prepared in the frozen hydrated state in order to visualize any differences in structure due to the different methods of preparation. The increased contrast between protein-ice versus protein-glucose may prove to be an advantage of the frozen hydrated technique for visualizing those parts of bacteriorhodopsin that are embedded in glucose. In addition, surface groups of the protein may be disordered in glucose and ordered in the frozen state. The sensitivity of the difference Fourier technique to small changes in structure provides an ideal method for testing this hypothesis.

3-D reconstruction of molecular shape from microcrystal thin sections

1983 ◽  
Vol 41 ◽  
pp. 748-749
Author(s):  
S. Cusack ◽  
J.-C. Jésior
Keyword(s):  
Three Dimensional ◽  
Molecular Shape ◽  
Biological Molecules ◽  
Fourier Space ◽  
Single Particles ◽  
Thin Sections ◽  
Standard Methods ◽  
X Ray ◽  
X Ray Crystallography ◽  
Dimensional Reconstruction

Three-dimensional reconstruction techniques using electron microscopy have been principally developed for application to 2-D arrays (i.e. monolayers) of biological molecules and symmetrical single particles (e.g. helical viruses). However many biological molecules that crystallise form multilayered microcrystals which are unsuitable for study by either the standard methods of 3-D reconstruction or, because of their size, by X-ray crystallography. The grid sectioning technique enables a number of different projections of such microcrystals to be obtained in well defined directions (e.g. parallel to crystal axes) and poses the problem of how best these projections can be used to reconstruct the packing and shape of the molecules forming the microcrystal.Given sufficient projections there may be enough information to do a crystallographic reconstruction in Fourier space. We however have considered the situation where only a limited number of projections are available, as for example in the case of catalase platelets where three orthogonal and two diagonal projections have been obtained (Fig. 1).

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