scholarly journals Ability of Lewis Acids with Shallow σ-Holes to Engage in Chalcogen Bonds in Different Environments

Molecules ◽  
2021 ◽  
Vol 26 (21) ◽  
pp. 6394
Author(s):  
Rafał Wysokiński ◽  
Wiktor Zierkiewicz ◽  
Mariusz Michalczyk ◽  
Steve Scheiner
Keyword(s):  
Gas Phase ◽  
Electrostatic Interaction ◽  
Lewis Acids ◽  
Lone Pair ◽  
Electrostatic Energy ◽  
Chalcogen Bond ◽  
Polarization Energy ◽  
Polarization Term

Molecules of the type XYT = Ch (T = C, Si, Ge; Ch = S, Se; X,Y = H, CH3, Cl, Br, I) contain a σ-hole along the T = Ch bond extension. This hole can engage with the N lone pair of NCH and NCCH3 so as to form a chalcogen bond. In the case of T = C, these bonds are rather weak, less than 3 kcal/mol, and are slightly weakened in acetone or water. They owe their stability to attractive electrostatic energy, supplemented by dispersion, and a much smaller polarization term. Immersion in solvent reverses the electrostatic interaction to repulsive, while amplifying the polarization energy. The σ-holes are smaller for T = Si and Ge, even negative in many cases. These Lewis acids can nonetheless engage in a weak chalcogen bond. This bond owes its stability to dispersion in the gas phase, but it is polarization that dominates in solution.

scholarly journals Theoretical Study of Sigmatropic Rearrangement of Cycloprop-2-en-1-ol and its Fluorine Derivatives: Pericyclic or Pseudopericyclic Character from NICS and LLPE

2019 ◽  
Vol 31 (3) ◽  
pp. 597-601
Author(s):  
A. Sangeetha ◽  
A. Thaminum Ansari ◽  
Jebakumar Jeevanandam ◽  
S. Jayaprakash
Keyword(s):  
Oxygen Atom ◽  
Gas Phase ◽  
Energy Barrier ◽  
Fluorine Atom ◽  
Theoretical Study ◽  
Lone Pair ◽  
Sigmatropic Rearrangement ◽  
Nucleus Independent Chemical Shift ◽  
Lone Pair Electron ◽  
Rearrangement Reaction

Sigmatropic rearrangement reaction of cycloprop-2-en-1-ol and its fluorine derivatives has been studied theoretically in gas phase and its energy barrier has been calculated. Nucleus-independent chemical shift (NICS) shows sigmatropic rearrangement of cycloprop-2-en-1-ol is pericyclic in nature whereas fluorine derivatives show pseudopericyclic and pericyclic nature. Substitution of fluorine atom at ring is found to increase the energy barrier for –OH migration, while substitution at oxygen atom reduces the barrier. To know the involvement of lone pair of electrons during the reaction, lone pair electron present on oxygen atom is locked by hydrogen bonding. CR-CCSD(T)/6-311+G** levels are used to study the reactions more accurately.

Quantum-Chemical Investigations on the Structural Variability of Anion–π Interactions

2014 ◽  
Vol 69 (7) ◽  
pp. 339-348 ◽  
Author(s):  
Verena Moha ◽  
Michael Giese ◽  
Richard Moha ◽  
Markus Albrecht ◽  
Gerhard Raabe
Keyword(s):  
Gas Phase ◽  
Aromatic Ring ◽  
Energy Surface ◽  
Electrostatic Energy ◽  
Dispersion Energy ◽  
Substitution Pattern ◽  
Energy Of Interaction ◽  
Electron Withdrawing Group ◽  
Energy Surfaces ◽  
Structural Versatility

The structural versatility of anion-p interactions was investigated computationally. Employing quantum-chemically optimized structures of a series of C6H6-nFn/Br- complexes and the Coulomb law together with the London formula to calculate the electrostatic and the dispersion energy of the interaction between the anion and the π-system led to the result that up to the number of n = 2 due to a significantly repulsive electrostatic energy of interaction the dispersion energy is not sufficient to stabilize such structures in the gas phase where the anion is located above the plane defined by the aromatic ring. The energy surfaces resulting from the interaction of bromide anions with isolated arenes bearing varying numbers of fluorine atoms in different positions of the aromatic ring also show a pronounced dependency on the subsitution pattern of the aromatic system. Depending on the nature of the electron withdrawing group and its position, the energy surface can have a sharply defined energetically low minimum, in which the anion is ‘fixed’. Other substitution patterns result in very flat energy surfaces, and even a surface with more than two local minima within the scanned area was found. Thus, our study reveals the reason for the experimentally observed structural versatility depending on the substitution pattern in the solid state.

Configurations and conformations of glycosyl sulfoxides

2010 ◽  
Vol 88 (11) ◽  
pp. 1154-1174 ◽  
Author(s):  
Hong Liang ◽  
Micheline MacKay ◽  
T. Bruce Grindley ◽  
Katherine N. Robertson ◽  
T. Stanley Cameron
Keyword(s):  
Solid State ◽  
Dft Calculations ◽  
Gas Phase ◽  
Density Functional ◽  
Lone Pair ◽  
Azido Group ◽  
X Ray Diffraction ◽  
X Ray ◽  
Comparison Of The Results ◽  
P Type

X-ray crystallographic studies of two axial glycosyl sulfoxides having RS configurations (derivatives of phenyl 2-azido-2-deoxy-1-thio-α-d-galactopyranoside S-oxide) show that they adopt anti conformations in the solid state, in contrast to previous observations and assumptions. Density functional theory (DFT) calculations at the B3lYP6–311G+(d,p)/6–31G(d) level confirm that anti conformations of both phenyl and methyl RS glycosyl sulfoxides of 2-azido-2-deoxy-α-d-pyranosides are more stable than exo-anomeric conformations in the gas phase. 1D NOE measurements indicate that the more polar exo-anomeric conformers are only populated to a slight extent in solution. The anti conformations are distorted so that the glycosyl substituents are closer to being eclipsed with H1. This distortion allows S n → σ* overlap if the sulfur lone pair is a p-type lone pair. Evidence for this overlap comes from short C1–S bond distances, as short as the comparable bond distances in the X-ray crystal structure and in the results from DFT calculations for the SS glycoside, which does adopt the expected exo-anomeric conformation, both in the solid state and in solution, and has normal n → σ* overlap. For 2-deoxy derivatives not bearing a 2-azido group, gas-phase DFT calculations at the same level indicate that the anti- and exo-anomeric conformers have comparable stabilities. Comparison of the results of the two series shows that electronegative substituents in equatorial orientations at C2 destabilize conformations with parallel S–O arrangements, the conformation favored by having an endocyclic C–O dipole antiparallel to the S–O dipole, by about 2.5 kcal mol–1 (1 cal = 4.184 J). An equatorial glycosyl sulfoxide, (SS) phenyl 3,4,6-tri-O-acetyl-2-deoxy-2-phthalimido-1-thio-β-d-glucopyranoside S-oxide, also adopts an anti conformation in the solid state as shown by X-ray diffraction. It also adopts this conformation in solution, in contrast to studies of other equatorial glycosyl sulfoxides.

scholarly journals A rush to explore protein–ligand electrostatic interaction energy with Charger

2021 ◽  
Vol 77 (10) ◽  
pp. 1292-1304 ◽  
Author(s):  
Vedran Vuković ◽  
Theo Leduc ◽  
Zoe Jelić-Matošević ◽  
Claude Didierjean ◽  
Frédérique Favier ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Interaction Energy ◽  
Electrostatic Interaction ◽  
Glutathione Transferase ◽  
Multipole Moment ◽  
Point Of View ◽  
Electrostatic Energy ◽  
Electron Densities ◽  
Acta Cryst ◽  
Ligand Interaction

The mutual penetration of electron densities between two interacting molecules complicates the computation of an accurate electrostatic interaction energy based on a pseudo-atom representation of electron densities. The numerical exact potential and multipole moment (nEP/MM) method is time-consuming since it performs a 3D integration to obtain the electrostatic energy at short interaction distances. Nguyen et al. [(2018), Acta Cryst. A74, 524–536] recently reported a fully analytical computation of the electrostatic interaction energy (aEP/MM). This method performs much faster than nEP/MM (up to two orders of magnitude) and remains highly accurate. A new program library, Charger, contains an implementation of the aEP/MM method. Charger has been incorporated into the MoProViewer software. Benchmark tests on a series of small molecules containing only C, H, N and O atoms show the efficiency of Charger in terms of execution time and accuracy. Charger is also powerful in a study of electrostatic symbiosis between a protein and a ligand. It determines reliable protein–ligand interaction energies even when both contain S atoms. It easily estimates the individual contribution of every residue to the total protein–ligand electrostatic binding energy. Glutathione transferase (GST) in complex with a benzophenone ligand was studied due to the availability of both structural and thermodynamic data. The resulting analysis highlights not only the residues that stabilize the ligand but also those that hinder ligand binding from an electrostatic point of view. This offers new perspectives in the search for mutations to improve the interaction between the two partners. A proposed mutation would improve ligand binding to GST by removing an electrostatic obstacle, rather than by the traditional increase in the number of favourable contacts.

Photoelectron Spectroscopy of Heterocycles. Polypyridines

1978 ◽  
Vol 33 (2) ◽  
pp. 247-248 ◽  
Author(s):  
I. Novak ◽  
L. Klasinc
Keyword(s):  
Gas Phase ◽  
Photoelectron Spectroscopy ◽  
Lone Pair ◽  
Mo Calculations ◽  
Factors Influencing ◽  
Nitrogen Lone Pair ◽  
Lcao Mo

The photoelectron (PE) spectra of 2,2′-bipyridine 1, 2,2′:6′,2″-terpyridine 2, and 2,2′,2″,2‴-tetrapyridine 3 have been measured using He I radiation. For 1-3 standard SCF LCAO MO calculations wer also performed. Comparison of PE spectra and these calculations allowed the assignment of π-ionizations and indirectly also the nitrogen lone pair ionizations in 1-3. Factors influencing the conformations of 1-3 in the gas phase are also mentioned.

KINETICS OF RAPID GAS PHASE REACTIONS. THE ADDITION OF LEWIS ACIDS TO BASES

1963 ◽  
Author(s):  
S.H. Bauer ◽  
J. V. Martinez ◽  
Dennis Price ◽  
Walter D. Jones ◽  
Nicholas Rol ◽  
...  
Keyword(s):  
Gas Phase ◽  
Lewis Acids ◽  
Gas Phase Reactions ◽  
Kinetics Of

The bond dissociation energies of SO3—X– (X = F, Cl, Br, and I)

2005 ◽  
Vol 83 (11) ◽  
pp. 2013-2019 ◽  
Author(s):  
Changtong Hao ◽  
Thomas M Gilbert ◽  
Lee S Sunderlin
Keyword(s):  
Gas Phase ◽  
Lewis Acids ◽  
Basis Sets ◽  
Collision Induced Dissociation ◽  
Bond Dissociation Energies ◽  
Flowing Afterglow ◽  
Bond Dissociation ◽  
Dissociation Energies ◽  
Upper Limit ◽  
Bond Strengths

The gas-phase strengths of the SO3—X- bonds (X = Cl, Br, and I) have been determined to be 222 ± 13, 179 ± 11, and 161 ± 9 kJ/mol, respectively, by measuring thresholds for collision-induced dissociation in a flowing afterglow-tandem mass spectrometer. An upper limit of D(SO3—F–) ≤ 488 ± 19 kJ/mol was also determined. The periodic trends in the halide affinities of SO3 closely parallel those for SO2 and other Lewis acids. Bond strengths computed using the B3LYP, MP2, QCISD(T), and other models with several basis sets are generally lower than experiment.Key words: bond dissociation energies, computational chemistry, Lewis acids, superacids, halide affinities.

scholarly journals An Example of Lone Pair Orbital and Their Interaction——Gas Phase Ultravlolet Photoelctron Spectroscople Study of some Nitrogen Heterocyclle Compounds

1992 ◽  
Vol 8 (06) ◽  
pp. 809-813
Author(s):  
Wang Dian-Xun ◽  
◽  
Wang Dong ◽  
Zhao Heng-Qi ◽  
Tang Qing ◽  
...  
Keyword(s):  
Gas Phase ◽  
Lone Pair ◽  
Lone Pair Orbital

Unique cation–cyclohexane interactions in tri- and hexa-fluorocyclohexane multidecker complexes in the gas phase: a DFT study

RSC Advances ◽  
2016 ◽  
Vol 6 (113) ◽  
pp. 111856-111864 ◽  
Author(s):  
Dipshikha Sarma ◽  
Bapan Saha ◽  
Bhabesh Chandra Deka ◽  
Pradip Kr. Bhattacharyya
Keyword(s):  
Density Functional Theory ◽  
Gas Phase ◽  
Electrostatic Interaction ◽  
Density Functional ◽  
Dft Study ◽  
Functional Theory

The formation of stable sandwich and multidecker complexes through electrostatic interaction in tri- and hexa-fluorocyclohexane has been analyzed in the light of density functional theory.

Sign in / Sign up

Export Citation Format

Share Document