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.

scholarly journals Prediction of solvation properties of low transition temperature mixtures (LTTMs) using COSMO-RS and NMR approach

2021 ◽  
Vol 1195 (1) ◽  
pp. 012006
Author(s):  
N R Yusuf ◽  
S Yusup ◽  
C L Yiin ◽  
P J Ratri ◽  
A A Halim ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Transition Temperature ◽  
Environmental Science ◽  
Choline Chloride ◽  
Monosodium Glutamate ◽  
Experimental Studies ◽  
Green Solvent ◽  
Hydrogen Bond Donor ◽  
Hydrogen Bond Acceptor

Abstract The concept of sustainable and green solvent has always highlighted in the field of energy and environmental science. The synthesis and application of natural-based Low Transition Temperature Mixture (LTTM) as a novel and green solvent for the lignocellulose biomass pre-treatment such as delignification of Oil-Palm Empty Fruit Bunch (EFB) have been greatly emphasized. In this present work, the investigation of LTTM efficiency as green solvent in delignification process was conducted using both theoretical and experimental studies. Initially, screening of solvation properties of different types of hydrogen bond acceptor (HBA) and predicted hydrogen bond donor (HBD) for synthesis of LTTMs was conducted using conductor-like screening model (COSMO-RS) software and formation of hydrogen bonding was evidenced using NMR spectroscopy analysis. Three types of HBA namely sucrose, choline chloride and monosodium glutamate were mixed with malic acids as HBD and their charge density distribution on the surface was determined through sigma profile (σ). The COSMO-RS results determined the σ profile of pure component malic acid to be 11.42, sucrose to be 25.37 and the total value of σ profile for mixtures is 14.19 as the best combination of LTTM composition compared to LTTM from choline chloride and monosodium glutamate (MSG). The reliability of the COSMO-RS predictions data was correlated with Nuclear Magnetic Resonance (NMR) analysis through determination of peaks with chemical shifts hydrogen bonding that suggested existence of potential interaction between malic acids and sucrose has occurred.

42 salt forms of tyramine: structural comparison and the occurrence of hydrate formation

2012 ◽  
Vol 68 (4) ◽  
pp. 453-464 ◽  
Author(s):  
Naomi E. B. Briggs ◽  
Alan R. Kennedy ◽  
Catriona A. Morrison
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Single Crystal ◽  
Hydrate Formation ◽  
Structural Comparison ◽  
Hydrogen Bond Donor ◽  
Single Crystal Diffraction ◽  
Hydrogen Bond Acceptor ◽  
First Time ◽  
Salt Forms

The single-crystal diffraction structures of 38 salt forms of the base tyramine (4-hydroxyphenethylamine) are reported for the first time. Together with literature examples, these structures are discussed with respect to cation conformation, cation packing, hydrogen bonding and hydrate formation. It is found that isostructural cation packing can occur even with structurally different anions, with different hydration states and with different hydrogen bonding. Hydrate formation is found to be more likely both (i) when there is an increase in the total number of potential hydrogen bond acceptor and donor atoms; and (ii) when the ratio of potential hydrogen bond donor to acceptor atoms is low.

Hydrogen-bonding properties of galanthamine: an investigation through crystallographic database observations and computational chemistry

2008 ◽  
Vol 64 (3) ◽  
pp. 338-347 ◽  
Author(s):  
Soleymane Koné ◽  
Nicolas Galland ◽  
El-Hadji Sawaliho Bamba ◽  
Jean-Yves Le Questel
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Density Functional ◽  
Data Bank ◽  
Spatial Proximity ◽  
Hydrogen Bond Donor ◽  
Hydrogen Bond Acceptor ◽  
Oh Groups ◽  
Interaction Sites ◽  
Bonding Properties

The hydrogen-bonding properties of galanthamine have been investigated experimentally from a thorough analysis of crystallographic data retrieved from the Protein Data Bank and Cambridge Structural Database databases and theoretically through ab initio [MP2/6-311++G(2d,p)] and density functional theory [MPWB1K/6-31++G(d,p)] calculations. The main hydrogen-bond acceptor (HBA) interaction sites of the molecule are the O atoms and their spatial proximity allows multi-centered hydrogen-bond (HB) motifs. The hydrogen-bond donor (HBD) sites of the molecule are the NH+ and OH groups as well as several CH donors. Among them, the preferred ones are those directly linked to the ammonium nitrogen, followed by aromatic CH and finally the methyl group of the methoxy substituent. All these observations are in fairly good agreement with the computed positions of the molecular electrostatic potential (MEP) minima and maxima of various galanthamine species. The galanthamine HBD and HBA properties, investigated through the MEP analysis, appear sensitive to the degree of neutralization of the ammonium NH+ positive charge.

Defining the hydrogen bond: An account (IUPAC Technical Report)

2011 ◽  
Vol 83 (8) ◽  
pp. 1619-1636 ◽  
Author(s):  
Elangannan Arunan ◽  
Gautam R. Desiraju ◽  
Roger A. Klein ◽  
Joanna Sadlej ◽  
Steve Scheiner ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Bond Formation ◽  
Blue Shift ◽  
Hydrogen Bond Donor ◽  
Hydrogen Bond Acceptor ◽  
Hydrogen Bond Formation ◽  
Technical Report ◽  
Definition Of ◽  
Covalent Nature

The term “hydrogen bond” has been used in the literature for nearly a century now. While its importance has been realized by physicists, chemists, biologists, and material scientists, there has been a continual debate about what this term means. This debate has intensified following some important experimental results, especially in the last decade, which questioned the basis of the traditional view on hydrogen bonding. Most important among them are the direct experimental evidence for a partial covalent nature and the observation of a blue-shift in stretching frequency following X–H···Y hydrogen bond formation (XH being the hydrogen bond donor and Y being the hydrogen bond acceptor). Considering the recent experimental and theoretical advances, we have proposed a new definition of the hydrogen bond, which emphasizes the need for evidence. A list of criteria has been provided, and these can be used as evidence for the hydrogen bond formation. This list is followed by some characteristics that are observed in typical hydrogen-bonding environments.

scholarly journals Diversifying molecular and topological space via a supramolecular solid-state synthesis: a purely organic mok net sustained by hydrogen bonds

IUCrJ ◽  
2019 ◽  
Vol 6 (6) ◽  
pp. 1032-1039 ◽  
Author(s):  
Shalisa M. Oburn ◽  
Michael A. Sinnwell ◽  
Devin P. Ericson ◽  
Eric W. Reinheimer ◽  
Davide M. Proserpio ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Solid State ◽  
Topological Space ◽  
Organic Molecule ◽  
Three Dimensional ◽  
Protecting Group ◽  
Hydrogen Bond Donor ◽  
Hydrogen Bond Acceptor ◽  
Structural Requirements ◽  
Donor And Acceptor

A three-dimensional hydrogen-bonded network based on a rare mok topology has been constructed using an organic molecule synthesized in the solid state. The molecule is obtained using a supramolecular protecting-group strategy that is applied to a solid-state [2+2] photodimerization. The photodimerization affords a novel head-to-head cyclobutane product. The cyclobutane possesses tetrahedrally disposed cis-hydrogen-bond donor (phenolic) and cis-hydrogen-bond acceptor (pyridyl) groups. The product self-assembles in the solid state to form a mok network that exhibits twofold interpenetration. The cyclobutane adopts different conformations to provide combinations of hydrogen-bond donor and acceptor sites to conform to the structural requirements of the mok net.

New supramolecular architectures using hydrogen bonding

1993 ◽  
Vol 345 (1674) ◽  
pp. 49-56 ◽  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bond Donor ◽  
Binding Strength ◽  
Supramolecular Architectures ◽  
Self Assembling ◽  
Donor And Acceptor ◽  
The Stability ◽  
Bonded Complexes ◽  
Hydrogen Bonded

Several new multiply hydrogen bonded complexes have been studied to determine their strength and the specificity with which they form. While many factors contribute to the stability of multiply hydrogen bonded complexes, it appears that the arrangement of the hydrogen bond donor and acceptor groups is a particularly good predictor of binding strength. The results are consistent with W. L. Jorgensen’s secondary electrostatic hypothesis. The heterocyclic recognition units that have been synthesized may serve as the basis for constructing new synthetic hosts or new self-assembling systems.

6,9-Dibromo-2a,10b-diphenyl-2a,5,10,10b-tetrahydro-2H,3H-2,3,4a,10a-tetraazabenzo[g]cyclopenta[cd]azulene-1,4-dione monohydrate

2006 ◽  
Vol 62 (5) ◽  
pp. o1754-o1755
Author(s):  
Neng-Fang She ◽  
Sheng-Li Hu ◽  
Hui-Zhen Guo ◽  
An-Xin Wu
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Water Molecule ◽  
Title Compound ◽  
Supramolecular Structure ◽  
Hydrogen Bond Donor ◽  
Hydrogen Bond Acceptor ◽  
Compound C ◽  
Bifurcated Hydrogen Bond

The title compound, C24H18Br2N4O2·H2O, forms a supramolecular structure via N—H...O, O—H...O and C—H...O hydrogen bonds. In the crystal structure, the water molecule serves as a bifurcated hydrogen-bond acceptor and as a hydrogen-bond donor.

The hydrogen bond donor and acceptor ability of thioformic acid

2011 ◽  
Vol 22 (5) ◽  
pp. 1015-1030 ◽  
Author(s):  
Damanjit Kaur ◽  
Ritika Sharma ◽  
Darpandeep Aulakh
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bond Donor ◽  
Donor And Acceptor

Selective encapsulation and extraction of hydrogenphosphate by a hydrogen bond donor tripodal receptor

CrystEngComm ◽  
2020 ◽  
Vol 22 (37) ◽  
pp. 6152-6160
Author(s):  
Sandeep Kumar Dey ◽  
Archana ◽  
Sybil Pereira ◽  
Sarvesh S. Harmalkar ◽  
Shashank N. Mhaldar ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Hydrogen Bond Donor ◽  
Tripodal Receptor ◽  
Multiple Hydrogen Bonds

Intramolecular N–H⋯OC hydrogen bonding between the inner amide groups dictates the receptor–anion complementarity in a tripodal receptor towards selective encapsulation of hydrogenphosphate in the outer urea cavity by multiple hydrogen bonds.

Polysulfonylamine, CXXVI [1] Wasserstoffbrücken in kristallinen Onium-dimesylamiden: Ein robustes Achtring-Synthon in Koexistenz mit einem dritten Wasserstoffbrückenmotiv - Cyclodimere, Ketten, supramolekulare Bindungsisomere und ein fünffach verwobenes dreidimensionales (C-H ∙∙∙ O - Netzwerk / Polysulfonylamines, CXXVI [1] Hydrogen Bonding in Crystalline Onium Dimesylamides: A Robust Eight- Membered Ring Synthon in Coexistence with a Third Hydrogen Bonding Motif - Cyclodimers, Chains, Supramolecular Linkage Isomers, and a Quintuply Interwoven Three-Dimensional C - H ∙∙∙ O Network

2000 ◽  
Vol 55 (8) ◽  
pp. 738-752 ◽  
Author(s):  
Oliver Moers ◽  
Karna Wijaya ◽  
Ilona Lange ◽  
Armand Blaschette ◽  
Peter G. Jones
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Crystal Engineering ◽  
Ion Pairs ◽  
Three Dimensional ◽  
Membered Ring ◽  
Monoclinic Space Group ◽  
Hydrogen Bond Donor ◽  
Linkage Isomers ◽  
Ionic Solids

As an exercise in crystal engineering, low-temperature X-ray structures were determined for six rationally designed ionic solids of general formula BH+(MeSO2)2N−, where BH+ is 2-aminopyridinium (2, monoclinic, space group P21/c, Z = 4), 2-aminopyrimidinium (3, orthorhombic, Pbca, Z = 8), 2-aminothiazolium (4, orthorhombic, Pbcn, Z = 8), 2-amino-6-methylpyridinium (5, solvated with 0.5 H20, monoclinic, C2/c, Z = 8), 2-amino-1,3,4-thiadiazolium (6, triclinic, P1̄, Z = 2), or 2-amino-4,6-dimethylpyrimidinium (7, orthorhombic. Fdd2, Z = 16). The onium cations in question exhibit a trifunctional hydrogen-bond donor sequence H − N (H*)-C (sp2) − N − H , which is complementary to an O − S (sp3)−N fragment of the anion and simultaneously expected to form a third hydrogen bond via the exocyclic N − H* donor. Consequently, all the crystal packings contain cation-anion pairs assembled by an N − H ∙∙∙ N and an N −H ∙∙∙ O hydrogen bond, these substructures being mutually associated through an N − H* ∙∙∙ O bond. For the robust eight-membered ring synthon within the ion pairs [graph set N2 = R22(8), antidromic], two supramolecular isomers were observed: In 2 and 3, N − H ∙∙∙ N originates from the ring NH donor and N − H ∙∙∙ O from the exocyclic amino group, whereas in 4-7 these connectivities are reversed. The third hydrogen bond, N − H*∙∙∙ O , leads either to chains of ion pairs (generated by a 21 transformation in 2-4 or by a glide plane in 5) or to cyclic dimers of ion pairs (Ci symmetric in 6, C2-symmetric in 7). The overall variety of motifs observed in a small number of structures reflects the limits imposed on the prediction of hydrogen bonding patterns. Owing to the excess of potential acceptors over traditional hydrogen-bond donors, several of the structures display prominent non-classical secondary bonding. Thus, the cyclodimeric units of 6 are associated into strands through short antiparallel O ∙∙∙ S(cation) interactions. In the hemihydrate 5, two independent C-H(cation) ∙∙∙ O bonds generate a second antidromic R22(8) pattern, leading to sheets composed of N − H ∙∙∙ N/O connected catemers; the water molecules are alternately sandwiched between and O - H ∙∙∙ O bonded to the sheets to form bilayers, which are cross-linked by a third C − H (cation ) ∙∙∙ O contact. The roof-shaped cyclodimers occurring in 7 occupy the polar C2 axes parallel to z and build up hollow Car− H ∙∙∙ O bonded tetrahedral lattices; in order to fill their large empty cavities, five translationally equivalent lattices mutually interpenetrate.

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