Hydrogen-bond directionality at the donor H atom—analysis of interaction energies and database statistics

CrystEngComm ◽  
2009 ◽  
Vol 11 (8) ◽  
pp. 1563 ◽  
Author(s):  
Peter A. Wood ◽  
Frank H. Allen ◽  
Elna Pidcock
Keyword(s):  
Hydrogen Bond ◽  
Interaction Energies

Rapid evaluation of the interaction energies for carbohydrate-containing hydrogen-bonded complexes via the polarizable dipole–dipole interaction model combined with NBO or AM1 charge

RSC Advances ◽  
2015 ◽  
Vol 5 (9) ◽  
pp. 6452-6461 ◽  
Author(s):  
Jiao-Jiao Hao ◽  
Chang-Sheng Wang
Keyword(s):  
Hydrogen Bond ◽  
Interaction Model ◽  
Dipole Interaction ◽  
Rapid Evaluation ◽  
Interaction Energies ◽  
Bonded Complexes ◽  
Hydrogen Bonded

The polarizable dipole–dipole interaction model has been developed to rapidly and accurately estimate the hydrogen bond distances and interaction energies for carbohydrate-containing hydrogen-bonded complexes.

scholarly journals Charting Hydrogen Bond Anisotropy

2019 ◽  
Author(s):  
Diogo Santos-Martins ◽  
Stefano Forli
Keyword(s):  
Hydrogen Bond ◽  
Chemical Biology ◽  
Solid Phase ◽  
Electronic Configuration ◽  
Interaction Energies ◽  
X Ray ◽  
X Ray Crystallography ◽  
Chemical Groups ◽  
High Degree ◽  
Context Free

<div>Hydrogen bond (HB) is an essential interaction in countless phenomena, and regulates the chemistry of life. HBs are characterized by two main features, strength and directionality, with a high degree of heterogeneity across different chemical groups. These characteristics are dependent on the electronic configuration of the atoms involved in the interaction, which, in turn, is influenced strongly by the molecular environment where they are found. Studies based on the analysis of HB in solid phase, such as X-ray crystallography, suffer from significant biases due to the packing forces. These will tend to better describe strong HBs at the expenses of weak ones, which are either distorted or under represented. Using quantum mechanics (QM), we calculated interaction energies for about a hundred acceptor and donors, in a rigorously defined set of geometries. We performed about 180,000 independent QM calculations, covering all relevant angular components, and mapping strength and directionality in a context free from external biases, with both single-site and cooperative HBs. We show that by quantifying directionality, there is not correlation with strength, and therefore these two components need to be addressed separately. Results demonstrate that there are very strong HB acceptors (e.g.,DMSO) with nearly isotropic interactions, and weak ones (e.g.,thioacetone) with a sharp directional profile. Similarly, groups can have comparable directional propensity, but be very distant in the strength spectrum (e.g., thioacetone and pyridine). These findings have implications for biophysics and molecular recognition, providing new insight for chemical biology, protein engineering, and drug design. The results require rethinking the way directionality is described, with implications for the thermodynamics of HB.</div>

scholarly journals Theoretical Evaluation on The Interaction Between Triglycerides and Methylxanthines Using Density Functional Theory B3LYP/6-31G(d,p) and Molecular Electrostatic Potential

2020 ◽  
Vol 33 (1) ◽  
pp. 171-178
Author(s):  
N.F.M. Azmi ◽  
R. Ali ◽  
A.A. Azmi ◽  
M.Z.H. Rozaini ◽  
K.H.K. Bulat ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Hydrogen Bond ◽  
Electrostatic Potential ◽  
Density Functional ◽  
Molecular Electrostatic Potential ◽  
Basis Set ◽  
Individual Species ◽  
Interaction Energies ◽  
Binding Interaction ◽  
Functional Theory

The binding, interaction and distortion energies between the main triglycerides, palmitic-oleic-stearic (POS) in cocoa butter versus palmitic-oleic-palmitic (POP) in refined, bleached and deodorized (RBD) palm oil with cocoa′s methylxanthines (caffeine, theobromine, and theophylline) during the production of chocolate were theoretically studied and reported. The quantum mechanical software package of Gaussian09 at the theoretical level of density functional theory B3LYP/6-31G(d,p) was employed for all calculations, optimization, and basis set superposition errors (BSSE). Geometry optimizations were carried out to the minimum potential energy of individual species and binary complexes formed between the triglycerides, methylxanthines and polyphenols. The interaction energies for the optimized complexes were then corrected for the BSSE using the counterpoise method of Boys and Bernardi. The results revealed that the binding energy and interaction energy between methylxanthine components in cocoa powder with triglycerides were almost of the same magnitude (13.6-14.5 and 3.4-3.7 kJ/mol, respectively), except for the binary complex of POS-caffeine (25.1 and 10.7 kJ/mol, respectively). Based on the molecular geometry results, the hydrogen bond length and angle correlated well with the interaction energies. Meanwhile, the POS-caffeine complex with two higher and almost linear bond angles showed higher binding and interaction energies as compared to the other methylxanthines. Therefore, a donor-acceptor analysis showed that the hydrogen bond strength was proven using the molecular electrostatic potential (MEP), which resulted in parallel outcomes. The research results were believed to be one of the factors that contributed to the rheological behaviour and sensory perception of cocoa products, especially chocolate.

Theoretical investigation on the interplay of hydrogen bond and halogen bond in HX⋯(BrCl)n (X = F, Cl, Br and n = 1, 2) complexes

2014 ◽  
Vol 13 (01) ◽  
pp. 1450001 ◽  
Author(s):  
Hexiu Liu ◽  
Ruilin Man ◽  
Zhaoxu Wang ◽  
Pinggui Yi ◽  
Jingjing Liu
Keyword(s):  
Hydrogen Bond ◽  
Molecular Electrostatic Potential ◽  
Halogen Bond ◽  
Atomic Charge ◽  
Molecular Complexes ◽  
Basis Set ◽  
Formation Mechanisms ◽  
Interaction Energies ◽  
Aim Analysis ◽  
Topological Characteristics

Quantum chemical calculations at the MP2 level with the aug-cc-pVTZ basis set were used to investigate the HX ⋯( BrCl )n ( X = F , Cl , Br and n = 1, 2) complexes. They are connected via hydrogen bond or halogen bond in dimers and together in trimers. Molecular geometries, interaction energies, cooperative energies and atomic charge of dyads and triads have been studied at the Mp2/aug-cc-pVTZ computational level. All studied trimers show cooperativity with the simultaneous presence of a hydrogen and one or two halogen bond. The molecular electrostatic potential has been employed to explore the formation mechanisms of these molecular complexes. The AIM analysis has been performed at the Mp2/aug-cc-pVTZ level to examine the topological characteristics, confirming the coexistence of hydrogen bonds and one or two halogen bond for each complex.

scholarly journals Theoretical insight to intermolecular hydrogen bond interactions between methyl N-(2-pyridyl) carbamate and acetic acid: substituent effects, cooperativity and energy decomposition analysis

2019 ◽  
Vol 51 (2) ◽  
pp. 224-233
Author(s):  
S. M. Chalanchi ◽  
A. Ebrahimi ◽  
A. Nowroozi
Keyword(s):  
Hydrogen Bond ◽  
Acetic Acid ◽  
Active Sites ◽  
Intermolecular Hydrogen Bond ◽  
Substituent Effects ◽  
Proton Acceptor ◽  
Orbital Energy ◽  
Energy Decomposition Analysis ◽  
Interaction Energies ◽  
Energy Decomposition

In the present work, the hydrogen bond (HB) interactions between substituted syn and anti rotamers of methyl N-(2-pyridyl) carbamate and acetic acid were investigated using quantum mechanical (QM) calculations. The rotamers have two typical active sites to form hydrogen bonds with acetic acid, such that four stable complexes are found on the potential energy surface. The complexes in which the oxygen atom of carbamate acts as proton acceptor are stabilized by EWSs and are destabilized by EDSs. The trend in the effects of substituents is reversed in the other two complexes, in which the nitrogen atom of ring is involved in the interaction. According to energy data, the substituent effects on the interaction energy can be expressed by Hammett constants. The natural resonance theory (NRT) model was used to investigate the charge distribution on the carbamate group and to discuss the interaction energies. The individual HB energies were estimated to evaluate their cooperative contributions on the interaction energies of the complexes. In addition, the localized molecular orbital energy decomposition analyses (LMO-EDA) demonstrate that the electrostatic interactions are the most important stabilizing components of interactions.

scholarly journals A Theoretical Study of Hydrogen-Bonded Complexes of Ethylene Glycol, Thioglycol and Dithioglycol with Water

2021 ◽  
Vol 34 (1) ◽  
pp. 169-182
Author(s):  
Ruchi Kohli ◽  
Rupinder Preet Kaur
Keyword(s):  
Hydrogen Bond ◽  
Charge Transfer ◽  
Hydrogen Bonds ◽  
Ethylene Glycol ◽  
Structural Parameters ◽  
Intermolecular Hydrogen Bond ◽  
Basis Set ◽  
Interaction Energies ◽  
Orbital Theory ◽  
Hydrogen Bond Formation

In the present study, a theoretical analysis of hydrogen bond formation of ethylene glycol, thioglycol, dithioglycol with single water molecule has been performed based on structural parameters of optimized geometries, interaction energies, deformation energies, orbital analysis and charge transfer. ab initio molecular orbital theory (MP2) method in conjunction with 6-31+G* basis set has been employed. Twelve aggregates of the selected molecules with water have been optimized at MP2/6-31+G* level and analyzed for intramolecular and intermolecular hydrogen bond interactions. The evaluated interaction energies suggest aggregates have hydrogen bonds of weak to moderate strength. Although the aggregates are primarily stabilized by conventional hydrogen bond donors and acceptors, yet C-H···O, S-H···O, O-H···S, etc. untraditional hydrogen bonds also contribute to stabilize many aggregates. The hydrogen bonding involving sulfur in the aggregates of thioglycol and dithioglycol is disfavoured electrostatically but favoured by charge transfer. Natural bond orbital (NBO) analysis has been employed to understand the role of electron delocalizations, bond polarizations, charge transfer, etc. as contributors to stabilization energy.

scholarly journals New methods for computational drug design

2015 ◽  
Author(s):  
Jimmy Charnley Kromann
Keyword(s):  
Hydrogen Bond ◽  
Vibrational Analysis ◽  
Attractive Alternative ◽  
Interaction Energies ◽  
Free Energies ◽  
Order Of Accuracy ◽  
Computational Drug Design ◽  
New Methods ◽  
Small Proteins ◽  
The University

This thesis describes the work that has been carried out in connection with my Masters at the University of Copenhagen. This work has led to new dispersion and hydrogen bond corrections to the PM6 method, PM6-D3H+, and its implementation in the GAMESS program. The method combines the DFT-D3 dispersion correction by Grimme et al. with a modified version of the H+ hydrogen bond correction by Korth. This work also included the implementation of the new HF-3c method in GAMESS and its interface with the fragmentation method FMO. Overall, the interaction energy of PM6-D3H+ is very similar to PM6-DH2 and PM6-DH+, with RMSD and MAD values within 0.02 kcal/mol of one another. HF-3c also shows interaction energies within the same order of accuracy as the PM6 based methods. The main difference is that the geometry optimizations of 88 complexes result in 82, 6, 0, and 0 geometries with 0, 1, 2, and 3 or more imaginary frequencies using PM6-D3H+ implemented in GAMESS, while the corresponding numbers for PM6-DH+ implemented in MOPAC are 54, 17, 15, and 2. PM6-D3H+ and FMO2-HF- 3c in GAMESS was used to optimize two small proteins which resulted in a much more reliable structure compared to the reference structures, than PM6-DH+ in MOPAC, most likely due to the different optimization algorithms associated with the programs. The PM6-D3H+ method as implemented in GAMESS offers an attractive alternative to PM6-DH+ in MOPAC in cases where the LBFGS optimizer must be used and a vibrational analysis is needed, e.g., when computing vibrational free energies. While the GAMESS implementation is up to 10 times slower for geometry optimizations of proteins in bulk solvent compared to MOPAC, it is sufficiently fast to make geometry optimizations of small proteins practically feasible.

Interaction geometries and energies of hydrogen bonds to C=O and C=S acceptors: a comparative study

2008 ◽  
Vol 64 (4) ◽  
pp. 491-496 ◽  
Author(s):  
Peter A. Wood ◽  
Elna Pidcock ◽  
Frank H. Allen
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Electron Delocalization ◽  
Interaction Energies ◽  
Thiourea Derivatives ◽  
Medium Strength ◽  
Geometrical Data ◽  
Structural Database ◽  
Intermolecular Perturbation Theory ◽  
Good Agreement

The occurrence, geometries and energies of hydrogen bonds from N—H and O—H donors to the S acceptors of thiourea derivatives, thioamides and thiones are compared with data for their O analogues – ureas, amides and ketones. Geometrical data derived from the Cambridge Structural Database indicate that hydrogen bonds to the C=S acceptors are much weaker than those to their C=O counterparts: van der Waals normalized hydrogen bonds to O are shorter than those to S by ∼ 0.25 Å. Further, the directionality of the approach of the hydrogen bond with respect to S, defined by the C=S...H angle, is in the range 102–109°, much lower than the analogous C=O...H angle which lies in the range 127–140°. Ab initio calculations using intermolecular perturbation theory show good agreement with the experimental results: the differences in hydrogen-bond directionality are closely reproduced, and the interaction energies of hydrogen bonds to S are consistently weaker than those to O, by ∼ 12 kJ mol−1, for each of the three compound classes. There are no CSD examples of hydrogen bonds to aliphatic thiones, (Csp 3)2C=S, consistent with the near-equality of the electronegativities of C and S. Thioureas and thioamides have electron-rich N substituents replacing the Csp 3 atoms. Electron delocalization involving C=S and the N lone pairs then induces a significant >Cδ+=Sδ− dipole, which enables the formation of the medium-strength C=S...H bonds observed in thioureas and thioamides.

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