scholarly journals Different intra- and intermolecular hydrogen-bonding patterns in (3S,4aS,8aS)-2-[(2R,3S)-3-(2,5-X2-benzamido)-2-(2,5-X2-benzoyloxy)-4-phenylbutyl]-N-tert-butyldecahydroisoquinoline-3-carboxamides (X= H or Cl): compounds with moderate aspartyl protease inhibition activity

2017 ◽  
Vol 73 (6) ◽  
pp. 913-917
Author(s):  
Wilson Cunico ◽  
Maria de Lourdes G. Ferreira ◽  
James L. Wardell ◽  
William T. A. Harrison
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Solid State ◽  
Hydrogen Bonds ◽  
Aspartyl Protease ◽  
Intermolecular Hydrogen Bonding ◽  
Inhibition Activity ◽  
Chemical Similarity ◽  
Protease Inhibition ◽  
Donor And Acceptor

The crystal structures of (3S,4aS,8aS)-2-[(2R,3S)-3-benzamido-2-benzoyloxy-4-phenylbutyl]-N-tert-butyldecahydroisoquinoline-3-carboxamide, C38H47N3O4, (I), and (3S,4aS,8aS)-2-[(2R,3S)-3-(2,5-dichlorobenzamido)-2-(2,5-dichlorobenzoyloxy)-4-phenylbutyl]-N-tert-butyldecahydroisoquinoline-3-carboxamide, C38H43Cl4N3O4, (II), are described. Despite their chemical similarity, they adopt different conformations in the solid state: (I) features a bifurcated intramolecular N—H...(N,O) hydrogen bond from thetert-butylamide NH group to the piperidine N atom and the benzoate O atom, whereas (II) has an intramolecular N—H...O link from the benzamide NH group to thetert-butylamide O atom. In the crystal of (I), molecules are linked byC(4) amide N—H...O hydrogen bonds into chains propagating in the [010] direction, with both donor and acceptor parts of the benzamide group. In the extended structure of (II),C(11) N—H...O chains propagating in the [010] direction arise, with the donor being thetert-butylamide NH group and the acceptor being the O atom of the benzamide group.

scholarly journals Structure Elucidation of N-aryl-2-chloro-3-oxobutanamides with respect to intra- and intermolecular hydrogen bonding

2002 ◽  
Vol 2002 (1) ◽  
pp. 13-14 ◽  
Author(s):  
Petra Frohberg ◽  
Guntram Drutkowski ◽  
Christoph Wagner ◽  
Olaf Lichtenberger
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Solid State ◽  
Structure Elucidation ◽  
Intermolecular Hydrogen Bond ◽  
Carbonyl Oxygen ◽  
Intermolecular Hydrogen Bonding ◽  
Intramolecular Association

In general, N-aryl-2-chloro-3-oxobutanamides form in solid state an intermolecular hydrogen bond between the anilide hydrogen and the anilide carbonyl oxygen of a neighbouring molecule, which is disrupted in solution. An intramolecular association could not be detected.

A Neutral Donor-Acceptor p-Stack: Solid-State Structures of 1 : 1 Pyromellitic Diimide-Dialkoxynaphthalene Cocrystals

1997 ◽  
Vol 50 (5) ◽  
pp. 439 ◽  
Author(s):  
Darren G. Hamilton ◽  
Daniel E. Lynch ◽  
Karl A. Byriel ◽  
Colin H. L. Kennard
Keyword(s):  
Hydrogen Bonding ◽  
Solid State ◽  
Hydrogen Bonds ◽  
Neutral Donor ◽  
Hydrogen Bonding Interactions ◽  
Donor And Acceptor ◽  
Structural Preferences ◽  
Donor Acceptor ◽  
Covalently Linked ◽  
Solid State Structures

Pyromellitic diimide forms orange-coloured cocrystals of 1 : 1 stoichiometry with dialkoxynaphthalene derivatives. The solid-state structures of two examples are presented. The cocrystal formed with 2,6-dimethoxynaphthalene presents vertical stacks of alternating π-rich and π-deficient subunits with the long axes of the respective components approximately parallel. Investigation of the packing in the cocrystal also reveals a stabilizing array of hydrogen bonds between the components of adjacent stacks. Cocrystallization with 1,5-[2-(2-hydroxyethoxy)ethoxy]naphthalene, a derivative bearing hydroxy terminated ethyleneoxy chains, gives rise to an altered structural arrangement. Alternating donor- acceptor stacks once again dominate the structure but adopt a geometry where the long axes of the constituents are essentially perpendicular. Hydrogen-bonding interactions result in the formation of continuous non-covalently linked columns of donor and acceptor subunits by linking the terminal hydroxy functions of the naphthalene component to the imide protons. The structural preferences revealed by these solid-state analyses indicate that these complexes are useful prototypes of more complex neutral supramolecular assemblies.

scholarly journals On hydrogen bonding in 1,6-anhydro-β-D-glucopyranose (levoglucosan): X-ray and neutron diffraction and DFT study

2006 ◽  
Vol 62 (5) ◽  
pp. 912-918 ◽  
Author(s):  
Ľubomír Smrčok ◽  
Mariana Sládkovičová ◽  
Vratislav Langer ◽  
Chick C. Wilson ◽  
Miroslav Koóš
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Solid State ◽  
Hydrogen Bonds ◽  
Neutron Diffraction ◽  
Dft Calculations ◽  
Diffraction Data ◽  
Neutron Diffraction Study ◽  
Single Crystal Diffraction ◽  
X Ray

The geometry of hydrogen bonds in 1,6-anhydro-β-D-glucopyranose (levoglucosan) is accurately determined by refinement of time-of-flight neutron single-crystal diffraction data. Molecules of levoglucosan are held together by a hydrogen-bond array formed by a combination of strong O—H...O and supporting weaker C—H...O bonds. These are fully and accurately detailed by the neutron diffraction study. The strong hydrogen bonds link molecules in finite chains, with hydroxyl O atoms acting as both donors and acceptors of hydroxyl H atoms. A comparison of molecular and solid-state DFT calculations predicts red shifts of O—H and associated blue shifts of C—H stretching frequencies due to the formation of hydrogen bonds in this system.

A New Hydrogen-Bonding Motif with Constituents Bearing Donor and Acceptor Sites 7 Å Apart

2005 ◽  
Vol 60 (7) ◽  
pp. 758-762 ◽  
Author(s):  
Katja Heinze ◽  
Anja Reinhart
Keyword(s):  
Hydrogen Bonding ◽  
Solid State ◽  
Nitrogen Atom ◽  
Hydrogen Bonds ◽  
Hydrogen Donor ◽  
Para Position ◽  
Hydrogen Acceptor ◽  
Aryl Ring ◽  
Donor And Acceptor ◽  
Pyrrole Nitrogen

Aryl substituted dipyrromethanes [di(pyrrol-2-yl)-phenyl-methanes] with hydrogen acceptor substituents R in para position of the aryl ring [R = CO2Me, CO2H, CONH(iPr) and NH2] located 7 Å apart from the hydrogen donor pyrrole nitrogen atom are shown to self-assemble in the solid state via hydrogen bonds to form rings or chains.

Rage Against Conformity: Ruthenium(ɪɪ) Bisterpyridine Complexes Respond to Crystal Engineering Instructions with Whelming Results

2017 ◽  
Vol 70 (5) ◽  
pp. 529 ◽  
Author(s):  
Hasti Iranmanesh ◽  
Kasun S. A. Arachchige ◽  
William A. Donald ◽  
Niamh Kyriacou ◽  
Chao Shen ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Solid State ◽  
Single Crystal ◽  
Crystal Engineering ◽  
Intermolecular Hydrogen Bonding ◽  
Hydrogen Bond Donor ◽  
One Dimensional ◽  
X Ray ◽  
Hydrogen Bonded

Four heteroleptic ruthenium(ii) complexes of 4′-functionalised 2,2′:6′,2′′-terpyridine are reported, along with their solid-state single-crystal X-ray structures. The complexes feature complementary hydrogen-bond donor (phenol) and acceptor (pyridyl) groups designed to assemble into one-dimensional polymers. In one example, the system obeys the programmed instructions to form a one-dimensional, self-complementary hydrogen-bonded polymer. In one other example, a water-bridged hydrogen-bonded polymer is formed. In the remaining two structures, aryl–aryl interactions dominate the intermolecular interactions, and outweigh the contribution of intermolecular hydrogen bonding.

Analysis of structures with saturated hydrogen bonding

2007 ◽  
Vol 63 (1) ◽  
pp. 132-141 ◽  
Author(s):  
James H. Loehlin ◽  
Elizabeth L. N. Okasako
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Self Assembled Monolayers ◽  
Donor And Acceptor ◽  
Assembled Monolayers ◽  
Graph Set ◽  
Hydrogen Bond Patterns ◽  
Self Assembled ◽  
Acceptor Numbers

All simple structures with saturated hydrogen bonding (SHB) are classified into eight categories on the basis of the donor and acceptor numbers on the atoms at each end of the hydrogen bonds. Examples from the literature are included where known, along with seven structures investigated as part of this study (five have SHB). Graph-set descriptions of the hydrogen-bond patterns are given for each of these structures and for some selected literature examples. The structures presented are: piperazine (I), morpholinium chloride (II) and iodide (III) [(II) and (III) are not SHB], three 1:1 cocrystals of diols with 1,4-phenylenediamine (PDA) – PDA·1,8-octane diol (IV), PDA·1,10-decane diol (V), and PDA·1,12-dodecane diol (VI) and 6-amino-1-hexanol (VII). This study discusses some structures that show limitations of the graph-set model, along with possible suggestions to cover these limitations. The cocrystalline PDA·aliphatic diol structures may provide details applicable to the structure of self-assembled monolayers of aliphatic thiol molecules on Au(111) surfaces.

scholarly journals The role of hydrogen bonds in condensed monolayers

1942 ◽  
Vol 179 (979) ◽  
pp. 470-485 ◽  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Protein Molecule ◽  
Energy Difference ◽  
Detailed Examination ◽  
Intermolecular Hydrogen Bonding ◽  
Head Groups ◽  
Potential Methods

From the behaviour of monolayers of compounds containing the —CO.NH— linkage it is concluded that intermolecular hydrogen bonding can play a major role in determining the properties of condensed monolayers. Such effects, which are well marked in the ureas, amides, acetanilides, unsubstituted and α -amino acids, tend to bring about condensation and solidification, and a marked increase in the half-expansion temperature. A detailed examination of the acetamides has been made in both the expanded and condensed regions by combined force area and surface potential methods. Comparison of the condensed films with those of the analogous acetates, where no such intermolecular hydrogen bonding is possible, shows several striking differences. With the acetamides and ureas the hydrogen bonding has been shown to be quite sensitive to the pH of the substrate, very acid substrates leading to complete liquefaction. The hydrogen bond distances can be calculated and the values so obtained are found to agree quite well with those in the crystal for the same or similar head groups. The free energy difference between the —CO.NH— group when forming hydrogen bonds to water (as in the expanded films), and when cross-linked (as in the low temperature form), is calculated for the acetamides to be about 840 cal./g.mol. Values of the same order can be calculated for the other systems discussed. The importance of such measurements in determining the part played by the hydrogen bond in the protein molecule is pointed out.

Investigation of Hydrogen Bonding Interaction between Bolaform Schiff Bases with Barbituric Acid by HPLC

2011 ◽  
Vol 356-360 ◽  
pp. 48-51
Author(s):  
Qi Tong ◽  
Ti Feng Jiao
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Liquid Chromatography ◽  
Schiff Bases ◽  
Barbituric Acid ◽  
Flexible Structure ◽  
Intermolecular Hydrogen Bonding ◽  
Acid Molecule ◽  
Hydrogen Bonding Interaction ◽  
Bonding Interaction

In order to investigate the intermolecular hydrogen bonding of special amphiphiles, two bolaform amphiphilic Schiff bases (GN1 and GN2) with different hydrophilic spacers were designed, and their interaction with barbituric acid were tested by liquid chromatography. The chromatographic properties showed that both the Schiff bases showed hydrogen bonding interaction with barbituric acid. In addition, the influence of various detectors was also studied on both cases. Experimental results show that the test with FLD showed better determination than other detectors. It is proposed that due to the directionality and strong matching of hydrogen bond, one barbituric acid molecule can be encapsulated into the intramolecular area of GN1, while two barbituric acid molecules were trapped into the GN2 molecule through intermolecular H-bonds for GN2 due to the long spacer and flexible structure. A rational complex mode was proposed.

(Acetylacetonato-κ2O,O′)[1-(4-bromophenyl-κC2)-3-methylimidazol-2-ylidene-κC2]platinum(II)

2012 ◽  
Vol 68 (8) ◽  
pp. m203-m205 ◽  
Author(s):  
Mario Tenne ◽  
Yvonne Unger ◽  
Thomas Strassner
Keyword(s):  
Hydrogen Bonding ◽  
Solid State ◽  
Intermolecular Hydrogen Bonding ◽  
Coordination Environment ◽  
Π Interactions ◽  
New Class ◽  
Square Planar ◽  
Parallel Fashion

The title platinum(II) complex, [Pt(C10H8BrN2)(C5H7O2)], has a bidentate cyclometallated phenylimidazolylidene ligand and an acetylacetonate spectator ligand, which form a distorted square-planar coordination environment around the PtIIcentre. In the solid state, the molecules are oriented in a parallel fashion by intermolecular hydrogen bonding and π–π and C—H...π interactions, while close Pt...Pt contacts are not observed. The structure is only the second example for this new class of compounds.

scholarly journals Machine learning models for hydrogen bond donor and acceptor strengths using large and diverse training data generated by first-principles interaction free energies

2019 ◽  
Vol 11 (1) ◽  
Author(s):  
Christoph A. Bauer ◽  
Gisbert Schneider ◽  
Andreas H. Göller
Keyword(s):  
Machine Learning ◽  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Training Data ◽  
Free Energies ◽  
Hydrogen Bond Donor ◽  
Chemical Application ◽  
Hydrogen Bond Acceptor ◽  
Donor And Acceptor ◽  
Target Values

Abstract We present machine learning (ML) models for hydrogen bond acceptor (HBA) and hydrogen bond donor (HBD) strengths. Quantum chemical (QC) free energies in solution for 1:1 hydrogen-bonded complex formation to the reference molecules 4-fluorophenol and acetone serve as our target values. Our acceptor and donor databases are the largest on record with 4426 and 1036 data points, respectively. After scanning over radial atomic descriptors and ML methods, our final trained HBA and HBD ML models achieve RMSEs of 3.8 kJ mol−1 (acceptors), and 2.3 kJ mol−1 (donors) on experimental test sets, respectively. This performance is comparable with previous models that are trained on experimental hydrogen bonding free energies, indicating that molecular QC data can serve as substitute for experiment. The potential ramifications thereof could lead to a full replacement of wetlab chemistry for HBA/HBD strength determination by QC. As a possible chemical application of our ML models, we highlight our predicted HBA and HBD strengths as possible descriptors in two case studies on trends in intramolecular hydrogen bonding.

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