Solvation of copper ions by imidazole: Structures and sequential binding energies of Cu+(imidazole)x, x = 1–4. Competition between ion solvation and hydrogen bonding

2005 ◽  
Vol 7 (5) ◽  
pp. 1014-1025 ◽  
Author(s):  
N. S. Rannulu ◽  
M. T. Rodgers
Keyword(s):  
Hydrogen Bonding ◽  
Copper Ions ◽  
Binding Energies ◽  
Ion Solvation ◽  
Sequential Binding

CAN SEMIEMPIRICAL QUANTUM MODELS CALCULATE THE BINDING ENERGY OF HYDROGEN BONDING FOR BIOLOGICAL SYSTEMS?

2009 ◽  
Vol 08 (04) ◽  
pp. 691-711 ◽  
Author(s):  
FENG FENG ◽  
HUAN WANG ◽  
WEI-HAI FANG ◽  
JIAN-GUO YU
Keyword(s):  
Hydrogen Bonding ◽  
Amino Acid ◽  
Amino Acid Residue ◽  
Density Functional ◽  
Biological Systems ◽  
Binding Energies ◽  
Semiempirical Model ◽  
Hydrogen Bonded Systems ◽  
High Level ◽  
Hydrogen Bonded

A modified semiempirical model named RM1BH, which is based on RM1 parameterizations, is proposed to simulate varied biological hydrogen-bonded systems. The RM1BH is formulated by adding Gaussian functions to the core–core repulsion items in original RM1 formula to reproduce the binding energies of hydrogen bonding of experimental and high-level computational results. In the parameterizations of our new model, 35 base-pair dimers, 18 amino acid residue dimers, 14 dimers between a base and an amino acid residue, and 20 other multimers were included. The results performed with RM1BH were compared with experimental values and the benchmark density-functional (B3LYP/6-31G**/BSSE) and Möller–Plesset perturbation (MP2/6-31G**/BSSE) calculations on various biological hydrogen-bonded systems. It was demonstrated that RM1BH model outperforms the PM3 and RM1 models in the calculations of the binding energies of biological hydrogen-bonded systems by very close agreement with the values of both high-level calculations and experiments. These results provide insight into the ideas, methods, and views of semiempirical modifications to investigate the weak interactions of biological systems.

scholarly journals Probing the origins of human acetylcholinesterase inhibition via QSAR modeling and molecular docking

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2322 ◽  
Author(s):  
Saw Simeon ◽  
Nuttapat Anuwongcharoen ◽  
Watshara Shoombuatong ◽  
Aijaz Ahmad Malik ◽  
Virapong Prachayasittikul ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Molecular Docking ◽  
Binding Pocket ◽  
Binding Energies ◽  
Acetylcholinesterase Inhibition ◽  
Qsar Modeling ◽  
Qsar Study ◽  
Data Set ◽  
Ache Inhibitors ◽  
Redundant Data

Alzheimer’s disease (AD) is a chronic neurodegenerative disease which leads to the gradual loss of neuronal cells. Several hypotheses for AD exists (e.g., cholinergic, amyloid, tau hypotheses, etc.). As per the cholinergic hypothesis, the deficiency of choline is responsible for AD; therefore, the inhibition of AChE is a lucrative therapeutic strategy for the treatment of AD. Acetylcholinesterase (AChE) is an enzyme that catalyzes the breakdown of the neurotransmitter acetylcholine that is essential for cognition and memory. A large non-redundant data set of 2,570 compounds with reported IC50values against AChE was obtained from ChEMBL and employed in quantitative structure-activity relationship (QSAR) study so as to gain insights on their origin of bioactivity. AChE inhibitors were described by a set of 12 fingerprint descriptors and predictive models were constructed from 100 different data splits using random forest. Generated models affordedR2, ${Q}_{\mathrm{CV }}^{2}$ and ${Q}_{\mathrm{Ext}}^{2}$ values in ranges of 0.66–0.93, 0.55–0.79 and 0.56–0.81 for the training set, 10-fold cross-validated set and external set, respectively. The best model built using the substructure count was selected according to the OECD guidelines and it affordedR2, ${Q}_{\mathrm{CV }}^{2}$ and ${Q}_{\mathrm{Ext}}^{2}$ values of 0.92 ± 0.01, 0.78 ± 0.06 and 0.78 ± 0.05, respectively. Furthermore, Y-scrambling was applied to evaluate the possibility of chance correlation of the predictive model. Subsequently, a thorough analysis of the substructure fingerprint count was conducted to provide informative insights on the inhibitory activity of AChE inhibitors. Moreover, Kennard–Stone sampling of the actives were applied to select 30 diverse compounds for further molecular docking studies in order to gain structural insights on the origin of AChE inhibition. Site-moiety mapping of compounds from the diversity set revealed three binding anchors encompassing both hydrogen bonding and van der Waals interaction. Molecular docking revealed that compounds13,5and28exhibited the lowest binding energies of −12.2, −12.0 and −12.0 kcal/mol, respectively, against human AChE, which is modulated by hydrogen bonding,π–πstacking and hydrophobic interaction inside the binding pocket. These information may be used as guidelines for the design of novel and robust AChE inhibitors.

Probing Intramolecular Interaction of Stereoisomers Using Computational Spectroscopy

2020 ◽  
Vol 73 (8) ◽  
pp. 813
Author(s):  
Feng Wang ◽  
Shawkat Islam ◽  
Frederick Backler
Keyword(s):  
Hydrogen Bonding ◽  
Binding Energy ◽  
Gas Phase ◽  
Intramolecular Interaction ◽  
Dipole Moments ◽  
Energy Difference ◽  
Binding Energies ◽  
Intramolecular Interactions ◽  
Computational Spectroscopy ◽  
Ionic States

Several model stereoisomers such as ferrocene (Fc), methoxyphenol, and furfural conformers are discussed. It was discovered that the Fc IR spectroscopic band(s) below 500cm−1 serve as fingerprints for eclipsed (splitting 17 (471–488)cm−1) and staggered Fc (splitting is ~2 (459–461)cm−1) in the gas phase. It is revealed that in the gas phase the dominance of the eclipsed Fc (D5h) at very low temperatures changes to a mixture of both eclipsed and staggered Fc when the temperature increases. However, in solvents such as CCl4, eclipsed Fc dominates at room temperature (300K) due to the additional solvation energy. Intramolecular interactions of organic model compounds such as methoxyphenols (guaiacol (GUA) and mequinol (MEQ)) and furfural, ionization energies such as the carbon 1s (core C1s), as well as valence binding energy spectra serve this purpose well. Hydrogen bonding alters the C1s binding energies of the methoxy carbon (C(7)) of anti-syn and anti-gauche conformers of GUA to 292.65 and 291.91eV, respectively. The trans and cis MEQ conformers, on the other hand, are nearly energy degenerate, whereas their dipole moments are significantly different: 2.66 Debye for cis and 0.63 Debye for trans-MEQ. Moreover, it is found that rotation around the Cring–OH and the Cring–OCH3 bonds differ in energy barrier height by ~0.50 kcal⋅mol−1. The Dyson orbital momentum profiles of the most different ionic states, 25a′ (0.35eV) and 3a′ (−0.33eV), between cis and trans-MEQ in outer valence space (which is measurable using electron momentum spectroscopy (EMS)), exhibit quantitative differences. Finally, the molecular switch from trans and cis-furfural engages with a small energy difference of 0.74 kcal mol−1, however, at the calculated C(3)(–H⋅⋅⋅O=C) site the C1s binding energy difference is 0.105eV (2.42 kcal mol−1) and the NMR chemical shift of the same carbon site is also significant; 7.58ppm from cis-furfural without hydrogen bonding.

Binding affinities and spectra of complexes formed by dehydrotetrapyrido[20]annulene and small molecules

2007 ◽  
Vol 61 (4) ◽  
Author(s):  
Z. Wang ◽  
S. Wu
Keyword(s):  
Hydrogen Bonding ◽  
Chemical Shifts ◽  
Binding Energies ◽  
Binding Affinities ◽  
Dft Methods ◽  
Guest Molecules ◽  
Aromatic Molecules ◽  
Ir Frequencies ◽  
Π Stacking Interaction ◽  
Static Effect

AbstractTheoretical study on the binding affinities of dehydrotetrapyrido[20] annulene to the alkene and aromatic molecules was performed using the AM1 and DFT methods. It indicated that the host possesses the ability to bind the above molecules since the binding energies of the complexes were negative. The complexes were stabilized via the hydrogen bonding, static effect, and π — π stacking interaction between the host and guest molecules. Based on the B3LYP/3-21G optimized geometries, the electronic, IR, and NMR spectra were calculated using the INDO/CIS, AM1, and B3LYP/3-21G methods, respectively. Due to the hydrogen bonding, the first absorption maxima in the electronic spectra of studied complexes were blue-shifted, whereas the main IR frequencies for some of the complexes were red-shifted. At the same time, the chemical shifts of carbon atoms forming the bonds in the complexes were lower, compared to those of the host.

scholarly journals A Double-Deletion Method to Quantifying Incremental Binding Energies in Proteins from Experiment: Example of a Destabilizing Hydrogen Bonding Pair

2005 ◽  
Vol 88 (2) ◽  
pp. 1311-1321 ◽  
Author(s):  
Luis A. Campos ◽  
Santiago Cuesta-López ◽  
Jon López-Llano ◽  
Fernando Falo ◽  
Javier Sancho
Keyword(s):  
Hydrogen Bonding ◽  
Binding Energies ◽  
Double Deletion
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