scholarly journals The advanced treatment of hydrogen bonding in quantum crystallography

2021 ◽  
Vol 54 (3) ◽  
Author(s):  
Lorraine A. Malaspina ◽  
Alessandro Genoni ◽  
Dylan Jayatilaka ◽  
Michael J. Turner ◽  
Kunihisa Sugimoto ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Advanced Treatment ◽  
Test Cases ◽  
X Ray Diffraction ◽  
Intermolecular Hydrogen Bonds ◽  
New Developments ◽  
X Ray ◽  
Localized Molecular Orbitals ◽  
Quantum Crystallography

Although hydrogen bonding is one of the most important motifs in chemistry and biology, H-atom parameters are especially problematic to refine against X-ray diffraction data. New developments in quantum crystallography offer a remedy. This article reports how hydrogen bonds are treated in three different quantum-crystallographic methods: Hirshfeld atom refinement (HAR), HAR coupled to extremely localized molecular orbitals and X-ray wavefunction refinement. Three different compound classes that form strong intra- or intermolecular hydrogen bonds are used as test cases: hydrogen maleates, the tripeptide L-alanyl-glycyl-L-alanine co-crystallized with water, and xylitol. The differences in the quantum-mechanical electron densities underlying all the used methods are analysed, as well as how these differences impact on the refinement results.

Hydrogen Bonding in Acid Li-, Ni-, Tetrabutylammonium, and Ammonium Salts of Benzene-1,2,4,5-tetracarboxylic Acid (Pyromellitic Acid)

1992 ◽  
Vol 47 (8) ◽  
pp. 1141-1153 ◽  
Author(s):  
Sven M. Jessen ◽  
Horst Küppers ◽  
Dean C. Luehrs
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Ammonium Salts ◽  
Tetracarboxylic Acid ◽  
X Ray Diffraction ◽  
Intermolecular Hydrogen Bonds ◽  
Pyromellitic Acid ◽  
X Ray ◽  
Carboxylic Groups ◽  
Intramolecular Hydrogen

Four acid salts of pyromellitic acid (benzene-1,2,4,5-tetracarboxylic acid) have been synthesized and studied by X-ray diffraction and IR spectroscopy. (1) Dilithium dihydrogen pyromellitate pentahydrate, Li2[C6H2(COO)4H2]· 5H2O; monoclinic, P21/m, a = 6.214(2), b = 19.647(7), c = 6.592(2)Å, β = 115.90(2)°, Ζ = 2, R = 0.068, Rw = 0.067. (2) Hexaaquanickel dihydrogen pyromellitate, [Ni(H2O)6][C6H2(COO)4H2]; monoclinic, P2/m, a = 6.528(1), b = 9.927(2), c = 6.472(1)Å, β = 115.57(1)°, Z = 1, R = 0.044, Rw = 0.039. (3) Tetrabutylammonium trihydrogen pyromellitate, [(C4H9)4N][C6H2(COO)4H3]; monoclinic, P21/c, a = 9.719(4), b = 18.823(8), c = 15.795(5)Å, β = 107.42(3)°, Z = 4, R = 0.059, Rw = 0.039. (4) Diammonium dihydrogen pyromellitate, [NH4]2[C6H2(COO)4H2]; monoclinic, P21/c, a = 4.7665(6), b = 11.681(3), c = 10.149(2)Å, ß = 102.19(2)°, Z = 2, R = 0.045, Rw = 0.039. Compounds 1, 2, and 3 show very short intramolecular hydrogen bonds between adjacent carboxylic groups (O ••• O distances 2.384(6), 2.386(5), 2.387(3)Å, respectively). Compound 4 forms intermolecular hydrogen bonds (O ··· O distance 2.642(2) A). The different hydrogen bonding modes are also evident in the IR spectra.

scholarly journals ISOLATION AND STRUCTURAL ELUCIDATION OF A NEW DEPSIDE OF LICHEN Everniopsis trulla

2021 ◽  
Vol 87 (2) ◽  
pp. 97-106
Author(s):  
Olivio Nino Castro ◽  
Jesús López Rodilla ◽  
Sofia Pombal ◽  
Francisca Sanz González ◽  
Julio Santiago Contreras
Keyword(s):  
Mass Spectrometry ◽  
Melting Point ◽  
Hydrogen Bonds ◽  
Single Crystal ◽  
Spectroscopic Data ◽  
Intermolecular Forces ◽  
X Ray Diffraction ◽  
Intermolecular Hydrogen Bonds ◽  
X Ray ◽  
Uv Visible

In this research, a new depside of the lichen Everniopsis trulla has been isolated. The extraction was carried out to 400 g of dry sample and ground with ethanol for 3 repetitions, then, it was fractionated by applying column chromatography with the CHCl3-MeOH system and purified by recrystallization with MeOH-Acetone (1: 1); Finally, white crystals in the form of needles (solid C) with a melting point of 198 ° C were obtained, whose structure was elucidated based on spectroscopic data (UV-Visible, IR, NMR-H1, NMR-C13, mass spectrometry and single crystal X-ray diffraction). According to the Science Finder databases, it is a new depside, called trullarin, and it is observed that molecular packing is influenced by both intramolecular and intermolecular forces. Intermolecular hydrogen bonds of O - H -O type binds neighboring molecules forming dimers.

Structure and hydrogen bonding in 2,4-dihydroxybenzoic acid at 90, 100, 110 and 150 K; a theoretical and single-crystal X-ray diffraction study

2007 ◽  
Vol 63 (2) ◽  
pp. 303-308 ◽  
Author(s):  
Andrew Parkin ◽  
Martin Adam ◽  
Richard I. Cooper ◽  
Derek S. Middlemiss ◽  
Chick C. Wilson
Keyword(s):  
Hydrogen Bonding ◽  
Solid State ◽  
Hydrogen Bonds ◽  
X Ray Diffraction ◽  
Dihydroxybenzoic Acid ◽  
X Ray ◽  
Hydrogen Bond System ◽  
Proton Disorder ◽  
Intramolecular Hydrogen ◽  
Carboxylic Acid Dimer

A new polymorph of 2,4-dihydroxybenzoic acid is reported. The structure was characterized by multiple-temperature X-ray diffraction and solid-state DFT computations. The material shows a geometric pattern of hydrogen bonding consistent with cooperativity between the intermolecular carboxylic acid dimer and intramolecular hydrogen bonds. The presence of proton disorder within this hydrogen-bond system, which would support such a cooperative model, was not fully ruled out by the initial X-ray studies. However, solid-state calculations on the three possible end-point tautomers indicate that the dominant crystallographically observed configuration is substantially lower in energy than the other tautomers (by at least 9 kJ mol−1), indicating that no disorder should be expected. It is therefore concluded that no disorder is observed either in the intra- or intermolecular hydrogen bonds of the title compound and that the cooperativity between the hydrogen bonds is not present within the temperature range studied.

Unusual hydrogen bonding inL-cysteine hydrogen fluoride

2015 ◽  
Vol 71 (8) ◽  
pp. 733-741
Author(s):  
V. S. Minkov ◽  
V. V. Ghazaryan ◽  
E. V. Boldyreva ◽  
A. M. Petrosyan
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Hydrogen Fluoride ◽  
Fluoride Ion ◽  
X Ray Diffraction ◽  
Monoclinic System ◽  
X Ray ◽  
Short Hydrogen Bond ◽  
Doubly Charged

L-Cysteine hydrogen fluoride, or bis(L-cysteinium) difluoride–L-cysteine–hydrogen fluoride (1/1/1), 2C3H8NO2S+·2F−·C3H7NO2S·HF or L-Cys+(L-Cys...L-Cys+)F−(F−...H—F), provides the first example of a structure with cations of the `triglycine sulfate' type,i.e.A+(A...A+) (whereAandA+are the zwitterionic and cationic states of an amino acid, respectively), without a doubly charged counter-ion. The salt crystallizes in the monoclinic system with the space groupP21. The dimeric (L-Cys...L-Cys+) cation and the dimeric (F−...H—F) anion are formedviastrong O—H...O or F—H...F hydrogen bonds, respectively, with very short O...O [2.4438 (19) Å] and F...F distances [2.2676 (17) Å]. The F...F distance is significantly shorter than in solid hydrogen fluoride. Additionally, there is another very short hydrogen bond, of O—H...F type, formed by a L-cysteinium cation and a fluoride ion. The corresponding O...F distance of 2.3412 (19) Å seems to be the shortest among O—H...F and F—H...O hydrogen bonds known to date. The single-crystal X-ray diffraction study was complemented by IR spectroscopy. Of special interest was the spectral region of vibrations related to the above-mentioned hydrogen bonds.

scholarly journals Synthese und Umsetzungen von 4-Acyl/Carbamoyl-N-aryl-3-chloropyrrol-2,5-dionen: Kristallstruktur eines auf Wasserstoffbrückenbindungen basierenden supramolekularen Bandes [1] / Synthesis and Reactions of 4-Acyl/Carbamoyl-N-aryl-3-chloro-pyrrol-2,5-diones: Crystal Structure of a Supramolecular Ribbon Based on Hydrogen Bonds [ 1]

1996 ◽  
Vol 51 (8) ◽  
pp. 1084-1098 ◽  
Author(s):  
Rolf W. Saalfrank ◽  
Bernd Hörner ◽  
Stephan Reck ◽  
Jochen Nachtrab ◽  
Eva-Maria Peters ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Diffraction Analysis ◽  
Thionyl Chloride ◽  
Oxalyl Chloride ◽  
X Ray Diffraction ◽  
Intermolecular Hydrogen Bonds ◽  
X Ray

Reaction of malondiamides 1 with oxalyl chloride (2) leads to the formation of 2,3-dioxo-2,3- dihydrofuran hydrochlorides 3 and 2,3-dioxo-2,3-dihydro-furanes 4, respectively. The structure of 3a was established by X-ray diffraction. The β-oxo-dibenzylamides 5 react with 2 regiospecifically to give the 2,3-dioxo-2,3-dihydrofuranes 6. Addition of water in 1,4-position to 6a yields hydroxy-enol 7, which forms bimolecular aggregates via intermolecular hydrogen bonds as shown by X-ray analysis. Intramolecular C,N-bisacylation of β-oxoamides 8 and malondiamides 11 with 2 leads to the pyrrol-2,5-diones 9 and 12. Reaction of the enols 9 and 12 with thionyl chloride leads to 3-chloro-pyrrol-2,5-diones 13. 3-Amino-pyrrol-2,5-diones 15 are obtained from 13 and amines 14, while 1, ω-diamines 16 yield the bispyrrol systems 17. X-ray diffraction analysis of 17g reveals a supramolecular ribbon based on intermolecular hydrogen bonds between two different conformeres of 17g and in addition establishes unequivocally the imid-structures of 9 and 12. Intermolecular cyclisation of 13 with amino-tetrazol 18 gives the azido-pyrrolo-pyrimidine-diones 20, which reacts with triphenylphosphane to give phosphinimines 22. The structure of 22a was established by X-ray diffraction.

Structures and phase transitions of (BrCH2CH2NH3)2CdBr4 and (BrCH2CH2CH2NH3)2CdBr4 as investigated by 81Br NQR, DTA, and single-crystal X-ray diffraction

2020 ◽  
Vol 75 (3) ◽  
pp. 295-302
Author(s):  
Hideta Ishihara ◽  
Asuka Koga ◽  
Koh-ichi Suzuki ◽  
Hiromitsu Terao
Keyword(s):  
Thermal Analysis ◽  
Hydrogen Bonding ◽  
Differential Thermal Analysis ◽  
Phase Transitions ◽  
Hydrogen Bonds ◽  
Layered Perovskite ◽  
X Ray Diffraction ◽  
X Ray ◽  
81Br Nqr ◽  
Successive Phase

AbstractThe crystal structures of (BrCH2CH2NH3)2CdBr4 (1) and (BrCH2CH2CH2NH3)2CdBr4 (2) have been determined at T = 113 K: orthorhombic, Pbcn, a = 843.8(4), b = 775.4(4), c = 2339.6(11) pm, Z = 4 for 1; orthorhombic, Pbcn, a = 858.7(3), b = 783.6(2), c = 2519.4(7) pm, Z = 4 for 2. Both crystals are isomorphic, showing distinctive layered perovskite-related structures, in which the cations orient their aliphatic parts toward each other in their cation layers and connect to the infinite anion layers with their ammonium parts through N–H · · · Br hydrogen bonds. 81Br NQR and differential thermal analysis measurements for both compounds revealed the existence of successive phase transitions as seen in n-(CH3CH2CH2NH3)2CdBr4 (3). These phase transitions appear to be induced by the activated motions of the cations. The changes in the hydrogen bonding schemes resulting from the motions of the cations lead to the different phases of the respective crystals.

scholarly journals Molecular and Crystal Structure of a Chitosan−Zinc Chloride Complex

Nanomaterials ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1407
Author(s):  
Toshifumi Yui ◽  
Takuya Uto ◽  
Kozo Ogawa
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Theoretical Calculations ◽  
Chloride Complex ◽  
Fiber Axis ◽  
X Ray Diffraction ◽  
Intermolecular Hydrogen Bonds ◽  
Chain Packing ◽  
X Ray ◽  
Packing Structure

We determined the molecular and packing structure of a chitosan–ZnCl2 complex by X-ray diffraction and linked-atom least-squares. Eight D-glucosamine residues—composed of four chitosan chains with two-fold helical symmetry, and four ZnCl2 molecules—were packed in a rectangular unit cell with dimensions a = 1.1677 nm, b = 1.7991 nm, and c = 1.0307 nm (where c is the fiber axis). We performed exhaustive structure searches by examining all of the possible chain packing modes. We also comprehensively searched the positions and spatial orientations of the ZnCl2 molecules. Chitosan chains of antiparallel polarity formed zigzag-shaped chain sheets, where N2···O6, N2···N2, and O6···O6 intermolecular hydrogen bonds connected the neighboring chains. We further refined the packing positions of the ZnCl2 molecules by theoretical calculations of the crystal models, which suggested a possible coordination scheme of Zn(II) with an O6 atom.

scholarly journals (3-Ammonio-2,2-dimethyl-propyl)carbamate Dihydrate

Molbank ◽  
10.3390/m1015 ◽  
2018 ◽  
Vol 2018 (3) ◽  
pp. M1015
Author(s):  
Jaqueline Heimgert ◽  
Dennis Neumann ◽  
Guido Reiss
Keyword(s):  
Hydrogen Bond ◽  
Raman Spectroscopy ◽  
Acetic Acid ◽  
Hydrogen Bonds ◽  
Chain Structure ◽  
X Ray Diffraction ◽  
Intermolecular Hydrogen Bonds ◽  
X Ray ◽  
Title Molecule ◽  
Intramolecular Hydrogen

(3-Ammonio-2,2-dimethylpropyl)carbamate dihydrate was synthesised. The title compound was characterised by single crystal X-ray diffraction and IR-/Raman-spectroscopy. It has been demonstrated that a mixture of dilute acetic acid and 2,2-dimethyl-1,3-diaminopropane is able to capture CO2 spontaneously from the atmosphere. An intramolecular hydrogen bond stabilises the conformation of the ylide-type title molecule. Intermolecular hydrogen bonds between all moieties connect them to a strand-type chain structure.

Structure in “Amorphous Regions”, Accessible Segments of Fibrils, of the Cotton Fiber

1988 ◽  
Vol 58 (2) ◽  
pp. 96-101 ◽  
Author(s):  
Stanley P. Rowland ◽  
Phyllis S. Howley
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Cotton Fiber ◽  
Cotton Fibers ◽  
X Ray Diffraction ◽  
X Ray ◽  
Chemical Studies

The extent of hydrogen bonding of O(3)H and O(6)H in “amorphous” regions, more specifically in accessible segments of fibrils, of the cotton fiber varied from near perfection to almost complete disorder in samples under examination. Perfection of hydrogen bonding in various samples and segments of cotton fibers decreased with decreasing crystallinity of the cellulose within the fibrils. For the most part, extents of O(3)H hydrogen bonding and O(6)H hydrogen bonding followed similar patterns with substantial differences in degrees of perfection, the O(3)H ranging from about 95% hydrogen bonding down to 8% and the O(6)H) from 92% down to 41%. Details of hydrogen bonds assessed in these chemical studies are discussed relative to crystallinities and assignments of hydrogen bond structures from x-ray diffraction studies.

Study on Novel Structure of Nitric Acid Phenanthroline Vanadium Monohydrate: [ V(C12H8N2) ·O2·(H2O)]·NO3·H2O

2012 ◽  
Vol 554-556 ◽  
pp. 852-855
Author(s):  
Hai Xing Liu ◽  
Jing Zhong Xiao ◽  
Lan Xu ◽  
Vitor Hugo Nunes Rodrigues ◽  
Manuela Ramos Marques da Silva ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Nitric Acid ◽  
Hydrogen Bonds ◽  
Single Crystal ◽  
Vanadium Complex ◽  
X Ray Diffraction ◽  
Intermolecular Hydrogen Bonds ◽  
X Ray ◽  
Simple Reaction ◽  
Novel Structure

A new vanadium complex [ V(C12H8N2) ·O2·(H2O)]·NO3·H2O h as been synthesized from a simple reaction and the crystal structure has been determined by means of single-crystal X-ray diffraction. Monoclinic, P2(1)/c. a = 9.5137(2) Å b = 19.3181(4) Å c = 7.51800(10) Å α=γ=90 β= 93.6830. V= 1378.85(4) Å3. Z=2. Rgt(F) = 0.0255, wRref(F2) = 0.0809. T= 273(2) K. The compound consisted of a [ V(C12H8N2) ·O2·(H2O)]+ cation, one NO3-anion and one water molecular. Molecule structure is stabilized by OHN , OHO intramolecular and intermolecular hydrogen bonds.

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