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.

Resonance-Induced Hydrogen Bonding at Sulfur Acceptors in R 1 R 2C=S and R 1CS2 − Systems

1997 ◽  
Vol 53 (4) ◽  
pp. 680-695 ◽  
Author(s):  
F. H. Allen ◽  
C. M. Bird ◽  
R. S. Rowland ◽  
P. R. Raithby
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Bond Formation ◽  
Lone Pair ◽  
Molecular Orbital Calculations ◽  
Hydrogen Bond Acceptor ◽  
Hydrogen Bond Formation ◽  
Coordination Numbers ◽  
Wide Range

The hydrogen-bond acceptor ability of sulfur in C=S systems has been investigated using crystallographic data retrieved from the Cambridge Structural Database and via ab initio molecular orbital calculations. The R1R2C=S bond lengths span a wide range, from 1.58 Å in pure thiones (R 1 = R 2 = Csp 3) to 1.75 Å in thioureido species (R 1 = R 2 = N) and in dithioates —CS^{-}_2. The frequency of hydrogen-bond formation at =S increases from 4.8% for C=S > 1.63 Å to more than 70% for C=S > 1.70 Å in uncharged species. The effective electronegativity of S is increased by conjugative interactions between C=S and the lone pairs of one or more N substituents (R 1 R 2): a clear example of resonance-induced hydrogen bonding. More than 80% of S in —CS^{-}_2 accept hydrogen bonds. C=S...H—N,O bonds are shown to be significantly weaker than their C=O...H—N,O analogues by (a) comparing mean S...H and O...H distances (taking account of the differing non-bonded sizes of S and O and using neutron-normalized H positions) and (b) comparing frequencies of hydrogen-bond formation in `competitive' environments, i.e. in structures containing both C=S and C=O acceptors. The directional properties and hydrogen-bond coordination numbers of C=S and C=O acceptors have also been compared. There is evidence for lone-pair directionality in both systems, but =S is more likely (17% of cases) than =O (4%) to accept more than two hydrogen bonds. Ab initio calculations of residual atomic charges and electrostatic potentials reinforce the crystallographic observations.

Theoretical analysis of the (HNO)2, (HNO···HNS), and (HNS)2 dimers — A case of red and blue shifts of N–H stretching frequency

2010 ◽  
Vol 88 (8) ◽  
pp. 849-857 ◽  
Author(s):  
Nguyen Tien Trung ◽  
Tran Thanh Hue ◽  
Minh Tho Nguyen
Keyword(s):  
Hydrogen Bond ◽  
Quantum Chemical ◽  
Bond Formation ◽  
Blue Shift ◽  
Proton Donor ◽  
Basis Sets ◽  
Coupled Cluster ◽  
Hydrogen Bond Formation ◽  
Length Contraction ◽  
Moller Plesset

The hydrogen-bonded interactions in the simple (HNZ)2 dimers, with Z = O and S, were investigated using quantum chemical calculations with the second-order Møller–Plesset perturbation (MP2), coupled-cluster with single, double (CCSD), and triple excitations (CCSD(T)) methods in conjunction with the 6-311++G(2d,2p), aug-cc-pVDZ, and aug-cc-pVTZ basis sets. Six-membered cyclic structures were found to be stable complexes for the dimers (HNO)2, (HNS)2, and (HNO–HNS). The pair (HNS)2 has the largest complexation energy (–11 kJ/mol), and (HNO)2 the smallest one (–9 kJ/mol). A bond length contraction and a frequency blue shift of the N–H bond simultaneously occur upon hydrogen bond formation of the N–H···S type, which has rarely been observed before. The stronger the intramolecular hyperconjugation and the lower the polarization of the X–H bond involved as proton donor in the hydrogen bond, the more predominant is the formation of a blue-shifting hydrogen bond.

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 Salicylaldehyde Hydrazones: Buttressing of Outer-Sphere Hydrogen-Bonding and Copper Extraction Properties

2017 ◽  
Vol 70 (5) ◽  
pp. 556 ◽  
Author(s):  
Benjamin D. Roach ◽  
Tai Lin ◽  
Heiko Bauer ◽  
Ross S. Forgan ◽  
Simon Parsons ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Outer Sphere ◽  
Copper Extraction ◽  
Hydrogen Bond Acceptor ◽  
Hydrogen Bond Formation ◽  
Oxime Derivatives ◽  
Intramolecular Hydrogen

Salicylaldehyde hydrazones are weaker copper extractants than their oxime derivatives, which are used in hydrometallurgical processes to recover ~20 % of the world’s copper. Their strength, based on the extraction equilibrium constant Ke, can be increased by nearly three orders of magnitude by incorporating electron-withdrawing or hydrogen-bond acceptor groups (X) ortho to the phenolic OH group of the salicylaldehyde unit. Density functional theory calculations suggest that the effects of the 3-X substituents arise from a combination of their influence on the acidity of the phenol in the pH-dependent equilibrium, Cu2+ + 2Lorg ⇌ [Cu(L–H)2]org + 2H+, and on their ability to ‘buttress’ interligand hydrogen bonding by interacting with the hydrazone N–H donor group. X-ray crystal structure determination and computed structures indicate that in both the solid state and the gas phase, coordinated hydrazone groups are less planar than coordinated oximes and this has an adverse effect on intramolecular hydrogen-bond formation to the neighbouring phenolate oxygen atoms.

Enthalpies of hydrogen bond formation of 1-octanol with aprotic organic solvents. A comparison of the solvation enthalpy, pure base, and non-hydrogen-bonding baseline methods

1985 ◽  
Vol 63 (2) ◽  
pp. 342-348 ◽  
Author(s):  
W. Kirk Stephenson ◽  
Richard Fuchs
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Bond Formation ◽  
Enthalpies Of Solution ◽  
Dispersion Interactions ◽  
Butyl Ether ◽  
Hydrogen Bond Formation ◽  
Solvation Enthalpy ◽  
Benzene Toluene ◽  
Good Agreement

Enthalpies of solution (ΔHs) of 1-octanol and five model compounds (di-n-butyl ether, n-heptyl methyl ether, 1-fluoro-octane, 1-chlorooctane, and n-octane) have been determined in 13 solvents (heptane, cyclohexane, CCl4, 1,1,1-trichloro-ethane, 1,2-dichloroethane, triethylamine, butyl ether, ethyl acetate, DMF, DMSO, benzene, toluene, mesitylene), and combined with heats of vaporization to give enthalpies of transfer from vapor to solvent (ΔH(v → S)). These values have been used to calculate the enthalpy of hydrogen bond formation (ΔHh) of 1-octanol with each solvent, using the pure base (PB), solvation enthalpy (SE), and non-hydrogen-bonding baseline (NHBB) methods. Evidence is presented suggesting that (a) the SE method is susceptible to mismatches of the 1-octanol vs. model polar and dispersion interactions, (b) the PB method is sensitive to polar interaction mismatches, whereas (c) the NHBB method compensates for both polar and dispersion interactions mismatches. The (apparent) ΔHh values determined by the SE and PB methods may be as much as several kcal/mol (nearly 50%) too large, because of the inclusion of other polar and dispersion interactions. The NHBB method is therefore preferred for determining enthalpies of H-bond formation from calorimetric data. However, apparent ΔHh values from the SE and PB methods can be incorporated into total solvatochromic equations using Taft–Kamiet π*, β, and ξ parameters, to provide enthalpies of H-bond formation in good agreement with ΔHh (NHBB).

Anharmonicity, solvent effects, and hydrogen bonding: NH stretching vibrations

1970 ◽  
Vol 48 (14) ◽  
pp. 2197-2203 ◽  
Author(s):  
A. Foldes ◽  
C. Sandorfy
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Solvent Effects ◽  
Bond Formation ◽  
Hydrogen Bond Formation ◽  
Stretching Vibration ◽  
Solvent Shifts ◽  
Stretching Vibrations ◽  
Secondary Amides ◽  
Influence Of Solvent

The influence of solvent effects and hydrogen bond formation on the anharmonicity of the NH stretching vibration of simple secondary amides, lactams, anilides, indole, pyrrole, and imidazole have been studied; and the frequencies of the first and second overtones, their half widths and solvent shifts measured. The validity of Buckingham's theory is established in the case of inert solvents; whereas the second order perturbation treatments are shown to be inapplicable to the case of hydrogen bonding solvents. All NH stretching modes seem to exhibit the same anharmonic behavior which is very different from that of OH vibrations.

Dynamics of the chemical bond: inter- and intra-molecular hydrogen bond

2015 ◽  
Vol 177 ◽  
pp. 51-64 ◽  
Author(s):  
Elangannan Arunan ◽  
Devendra Mani
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Molecular Hydrogen ◽  
Theoretical Calculations ◽  
Bond Formation ◽  
Chem Phys ◽  
Equilibrium Structure ◽  
Molecular Hydrogen Bond ◽  
Mode Vibration ◽  
Definition Of

In this discussion, we show that a static definition of a ‘bond’ is not viable by looking at a few examples for both inter- and intra-molecular hydrogen bonding. This follows from our earlier work (Goswami and Arunan,Phys. Chem. Chem. Phys.2009,11, 8974) which showed a practical way to differentiate ‘hydrogen bonding’ from ‘van der Waals interaction’. We report results fromab initioand atoms in molecules theoretical calculations for a series of Rg⋯HX complexes (Rg = He/Ne/Ar and X = F/Cl/Br) and ethane-1,2-diol. Results for the Rg⋯HX/DX complexes show that Rg⋯DX could have a ‘deuterium bond’ even when Rg⋯HX is not ‘hydrogen bonded’, according to the practical criterion given by Goswami and Arunan. Results for ethane-1,2-diol show that an ‘intra-molecular hydrogen bond’ can appear during a normal mode vibration which is dominated by the O⋯O stretching, though a ‘bond’ is not found in the equilibrium structure. This dynamical ‘bond’ formation may nevertheless be important in ensuring the continuity of electron density across a molecule. In the former case, a vibration ‘breaks’ an existing bond and in the later case, a vibration leads to ‘bond’ formation. In both cases, the molecule/complex stays bound irrespective of what happens to this ‘hydrogen bond’. Both these cases push the borders on the recent IUPAC recommendation on hydrogen bonding (Arunanet al. Pure. Appl. Chem.2011,831637) and justify the inclusive nature of the definition.

Hydrogen bonding of n-alcohols of different chain lengths

1985 ◽  
Vol 63 (1) ◽  
pp. 40-45 ◽  
Author(s):  
Lucie Wilson ◽  
R. Bicca de Alencastro ◽  
C. Sandorfy
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Chain Length ◽  
Bond Formation ◽  
Hydrocarbon Chain ◽  
Hydrogen Bond Formation ◽  
Degree Of Association ◽  
Chain Lengths ◽  
Anesthetic Potency

The anesthetic potency of n-alcohols exhibits a somewhat irregular dependence on the length of the hydrocarbon chain. An attempt has therefore been made to ascertain if this is related to the relative tendency for hydrogen bond formation by these alcohols. No such relationship was found. The result was rather that the degree of association by hydrogen bond formation of dissolved alcohols appears to be independent of the chain length, that is of the extent of other interactions that exist in these solutions.

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