scholarly journals Methyl groups as widespread Lewis bases in noncovalent interactions

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Oliver Loveday ◽  
Jorge Echeverría

AbstractIt is well known that, under certain conditions, C(sp3) atoms behave, via their σ-hole, as Lewis acids in tetrel bonding. Here, we show that methyl groups, when bound to atoms less electronegative than carbon, can counterintuitively participate in noncovalent interactions as electron density donors. Thousands of experimental structures are found in which methyl groups behave as Lewis bases to establish alkaline, alkaline earth, triel, tetrel, pnictogen, chalcogen and halogen bonds. Theoretical calculations confirm the high directionality and significant strength of the interactions that arise from a common pattern based on the electron density holes model. Moreover, despite the absence of lone pairs, methyl groups are able to transfer charge from σ bonding orbitals into empty orbitals of the electrophile to reinforce the attractive interaction.

Inorganics ◽  
2019 ◽  
Vol 7 (3) ◽  
pp. 35 ◽  
Author(s):  
Ibon Alkorta ◽  
Anthony Legon

Geometries, equilibrium dissociation energies (De), intermolecular stretching, and quadratic force constants (kσ) determined by ab initio calculations conducted at the CCSD(T)/aug-cc-pVTZ level of theory, with De obtained by using the complete basis set (CBS) extrapolation [CCSD(T)/CBS energy], are presented for the B···BeR2 and B···MgR2 complexes, where B is one of the following Lewis bases: CO, H2S, PH3, HCN, H2O or NH3, and R is H, F or CH3. The BeR2 and MgR2 precursor molecules were shown to be linear and non-dipolar. The non-covalent intermolecular bond in the B···BeR2 complexes is shown to result from the interaction of the electrophilic band around the Be atom of BeR2 (as indicated by the molecular electrostatic potential surface) with non-bonding electron pairs of the base, B, and may be described as a beryllium bond by analogy with complexes such as B···CO2, which contain a tetrel bond. The conclusions for the B···MgR2 series are similar and a magnesium bond can be correspondingly invoked. The geometries established for B···BeR2 and B···MgR2 can be rationalized by a simple rule previously enunciated for tetrel-bonded complexes of the type B···CO2. It is also shown that the dissociation energy, De, is directly proportional to the force constant, kσ, in each B···MR2 series, but with a constant of proportionality different from that established for many hydrogen-bonded B···HX complexes and halogen-bonded B···XY complexes. The values of the electrophilicity, EA, determined from the De for B···BeR2 complexes for the individual Lewis acids, A, reveal the order A = BeF2 > BeH2 > Be(CH3)2—a result that is consistent with the −I and +I effects of F and CH3 relative to H. The conclusions for the MgR2 series are similar but, for a given R, they have smaller electrophilicities than those of the BeR2 series. A definition of alkaline-earth non-covalent bonds is presented.


Crystals ◽  
2019 ◽  
Vol 9 (10) ◽  
pp. 506 ◽  
Author(s):  
Irina Yushina ◽  
Natalya Tarasova ◽  
Dmitry Kim ◽  
Vladimir Sharutin ◽  
Ekaterina Bartashevich

The interrelation between noncovalent bonds and physicochemical properties is in the spotlight due to the practical aspects in the field of crystalline material design. Such study requires a number of similar substances in order to reveal the effect of structural features on observed properties. For this reason, we analyzed a series of three substituted thiazolo[2,3-b][1,3]thiazinium triiodides synthesized by an iodocyclization reaction. They have been characterized with the use of X-ray diffraction, Raman spectroscopy, and thermal analysis. Various types of noncovalent interactions have been considered, and an S…I chalcogen bond type has been confirmed using the electronic criterion based on the calculated electron density and electrostatic potential. The involvement of triiodide anions in the I…I halogen and S…I chalcogen bonding is reflected in the Raman spectroscopic properties of the I–I bonds: identical bond lengths demonstrate different wave numbers of symmetric triiodide vibration and different values of electron density at bond critical points. Chalcogen and halogen bonds formed by the terminal iodine atom of triiodide anion and numerous cation…cation pairwise interactions can serve as one of the reasons for increased thermal stability and retention of iodine in the melt under heating.


Inorganics ◽  
2019 ◽  
Vol 7 (3) ◽  
pp. 40 ◽  
Author(s):  
Pradeep Varadwaj ◽  
Arpita Varadwaj ◽  
Helder Marques

In addition to the underlying basic concepts and early recognition of halogen bonding, this paper reviews the conflicting views that consistently appear in the area of noncovalent interactions and the ability of covalently bonded halogen atoms in molecules to participate in noncovalent interactions that contribute to packing in the solid-state. It may be relatively straightforward to identify Type-II halogen bonding between atoms using the conceptual framework of σ-hole theory, especially when the interaction is linear and is formed between the axial positive region (σ-hole) on the halogen in one monomer and a negative site on a second interacting monomer. A σ-hole is an electron density deficient region on the halogen atom X opposite to the R–X covalent bond, where R is the remainder part of the molecule. However, it is not trivial to do so when secondary interactions are involved as the directionality of the interaction is significantly affected. We show, by providing some specific examples, that halogen bonds do not always follow the strict Type-II topology, and the occurrence of Type-I and -III halogen-centered contacts in crystals is very difficult to predict. In many instances, Type-I halogen-centered contacts appear simultaneously with Type-II halogen bonds. We employed the Independent Gradient Model, a recently proposed electron density approach for probing strong and weak interactions in molecular domains, to show that this is a very useful tool in unraveling the chemistry of halogen-assisted noncovalent interactions, especially in the weak bonding regime. Wherever possible, we have attempted to connect some of these results with those reported previously. Though useful for studying interactions of reasonable strength, IUPAC’s proposed “less than the sum of the van der Waals radii” criterion should not always be assumed as a necessary and sufficient feature to reveal weakly bound interactions, since in many crystals the attractive interaction happens to occur between the midpoint of a bond, or the junction region, and a positive or negative site.


2020 ◽  
Vol 18 (1) ◽  
pp. 936-942
Author(s):  
Ardhmeri Alija ◽  
Drinisa Gashi ◽  
Rilinda Plakaj ◽  
Admir Omaj ◽  
Veprim Thaçi ◽  
...  

AbstractThis study is focused on the adsorption of hexavalent chromium ions Cr(vi) using graphene oxide (GO). The GO was prepared by chemical oxidation (Hummers method) of graphite particles. The synthesized GO adsorbent was characterized by Fourier transform infrared spectroscopy and UV-Vis spectroscopy. It was used for the adsorption of Cr(vi) ions. The theoretical calculations based on density functional theory and Monte Carlo calculations were used to explore the preferable adsorption site, interaction type, and adsorption energy of GO toward the Cr(vi) ions. Moreover, the most stable adsorption sites were used to calculate and plot noncovalent interactions. The obtained results are important as they give molecular insights regarding the nature of the interaction between GO surface and the adsorbent Cr(vi) ions. The found adsorption energy of −143.80 kcal/mol is indicative of the high adsorptive tendency of this material. The adsorption capacity value of GO toward these ions is q = 240.361 mg/g.


Author(s):  
Eva Vos ◽  
Inés Corral ◽  
M. Merced Montero-Campillo ◽  
Otilia Mó ◽  
José Elguero ◽  
...  

Be4 clusters are very powerful Lewis acids leading to the total dissociation of all the bonds of the Lewis bases interacting with them. The product of the bond dissociation cascade possesses a hyper-coordinated center. Multireference methods are needed to correctly describe these complexes.


2014 ◽  
Vol 70 (a1) ◽  
pp. C287-C287
Author(s):  
Juan Van der Maelen ◽  
Javier Cabeza

The C-alkyl groups of cationic triruthenium cluster complexes of the type [Ru3(µ-H)(µ-κ2N1,C2-EtnMemPyHk)(CO)10]+ (EtnMemPyHk represents a generic C-alkyl-N-methyl-pyrazium species) have been deprotonated to give kinetic products that contain unprecedented C-alkylidene derivatives and maintain the original edge-bridged decacarbonyl structure. When the starting complexes contain various C-alkyl groups, the selectivity of these deprotonation reactions is related to the atomic charges of the alkyl H atoms, as suggested by DFT/natural-bond orbital (NBO) calculations. Three additional electronic properties of the C-alkyl C-H bonds have also been found to correlate with the experimental regioselectivity since, in all cases, the deprotonated C-H bond has the smallest electron density at the bond critical point (bcp), the greatest Laplacian of the electron density at the bcp, and the greatest total energy density ratio at the bcp (computed by using the quantum theory of atoms in molecules, QTAIM). The kinetic decacarbonyl products evolve, under appropriate reaction conditions that depend upon the position of the C-alkylidene group in the heterocyclic ring, towards face-capped nonacarbonyl derivatives (thermodynamic products). Theoretical calculations support the proposal that the selectivity of these deprotonation reactions is primarily determined by the atomic charge of the alkyl H atoms: the higher the charge the easier the deprotonation when the starting complexes contain various C-alkyl groups. On the other hand, although QTAIM results have been obtained here only from theoretical electron densities for the above clusters, comparisons with local and integral topological parameters derived from both experimental and theoretical electron densities for the related triruthenium complex [Ru3(μ-H)2(μ3-MeImCH)(CO)9] (Me2Im = 1,3-dimethylimidazol-2-ylidene) may easily be made.


2017 ◽  
Vol 203 ◽  
pp. 187-199 ◽  
Author(s):  
Peter C. Ho ◽  
Hilary A. Jenkins ◽  
James F. Britten ◽  
Ignacio Vargas-Baca

The supramolecular macrocycles spontaneously assembled by iso-tellurazole N-oxides are stable towards Lewis bases as strong as N-heterocyclic carbenes (NHC) but readily react with Lewis acids such as BR3 (R = Ph, F). The electron acceptor ability of the tellurium atom is greatly enhanced in the resulting O-bonded adducts, which consequently enables binding to a variety of Lewis bases that includes acetonitrile, 4-dimethylaminopyridine, 4,4′-bipyridine, triphenyl phosphine, a N-heterocyclic carbene and a second molecule of iso-tellurazole N-oxide.


2013 ◽  
Vol 2013 (22-23) ◽  
pp. 4008-4015 ◽  
Author(s):  
Zachary Thammavongsy ◽  
Micah E. LeDoux ◽  
Andrew G. Breuhaus-Alvarez ◽  
Takele Seda ◽  
Lev N. Zakharov ◽  
...  

2021 ◽  
Vol 2 (74) ◽  
pp. 38-41
Author(s):  
A. Al-Khazraji ◽  
I. Dudkin ◽  
E. Ofitserov ◽  
A. Finko ◽  
E. Beloglazkina

Analysis of the valence angles of the Si and carbon atoms of the C-S bond in the obtained complexes of CiVg2 c (5Z, 5'Z)-2,2’-(ethane-1,2-diyldisulfanyldiyl)bis(5-(2-pyridylmethylene)-3-allyl-3,5-dihydro-4Нimidazole-4-one) unambiguously indicates the determinant effect of the non-valent interactions of the electron density centroids of the NEP of bromine atoms and sulfur atoms, leading to a change in the plane structure of Cu(II) towards tetrahedral with a likely change in the magnetochemical properties of the copper atom, and the angle of rotation of the planes is almost 900. This interaction is the opposite of what is commonly called a halogen bond. In this case, it is an "anti-halogen" bond.


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