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1.
Chemphyschem ; 22(20): 2099-2106, 2021 10 14.
Article in English | MEDLINE | ID: mdl-34318574

ABSTRACT

Supramolecular adducts between dimethyl-2,2,3,3-tetracyanocyclopropane (Me2 TCCP) with 21 small (polar) molecules and 10 anions were computed with DFT (B3LYP-D3/def2-TZVP). Their optimized geometries were used to obtain interaction energies, and perform energy decomposition and 'atoms-in-molecules' analyses. A set of 38 other adducts were also evaluated for comparison purposes. Selected examples were further scrutinized by inspection of the molecular electrostatic potential maps, Noncovalent Interaction index plots, the Laplacian, the orbital interactions, and by estimating the Gibbs free energy of complexation in hexane solution. These calculations divulge the thermodynamic feasibility of Me2 TCCP adducts and show that complexation is typically driven by dispersion with less polarized partners, but by orbital interactions when more polarized or anionic guests are deployed. Most Me2 TCCP adducts are more stable than simple hydrogen bonding with water, but less stable than traditional Lewis adducts involving Me3 B, or a strong halogen bond such as with Br2 . Several bonding analyses showed that the locus of interaction is found near the electron poor sp3 -hydridized (NC)2 C-C(CN)2 carbon atoms. An empty hybrid σ*/π* orbital on Me2 TCCP was identified that can be held responsible for the stability of the most stable adducts due to donor-acceptor interactions.

2.
J Chem Educ ; 98(2): 540-545, 2021 Feb 09.
Article in English | MEDLINE | ID: mdl-33583952

ABSTRACT

Mixing the liquids hexafluorobenzene (1) and 1,3,5-trimethylbenzene (mesitylene, 2) results in a crystalline solid with a melting point of 34 °C. The solid consists of alternating π-π stacked pillars of both aromatics. This simple experiment can be used to visually demonstrate the existence and the effect of noncovalent intermolecular π-π stacking interactions. Both benzene derivatives are relatively benign and widely available, and the experiment can be performed within minutes for less than $15 when done on a 22 mL scale (total volume). The demonstration is very robust, as 1:2 mixtures in volume ratios between 2/3 and 3/2 all give a visually similar result (molar ratios of 1.8-0.8). Substituting 2 with the liquid aromatics o-xylene, p-xylene, and aniline also resulted in the formation of a crystalline solid, while using many other liquid aromatics did not.

4.
Chemphyschem ; 22(2): 141-153, 2021 01 18.
Article in English | MEDLINE | ID: mdl-33241585

ABSTRACT

The interpretation of 36 charge neutral 'contact pairs' from the IsoStar database was supported by DFT calculations of model molecules 1-12, and bimolecular adducts thereof. The 'central groups' are σ-hole donors (H2 O and aromatic C-I), π-hole donors (R-C(O)Me, R-NO2 and R-C6 F5 ) and for comparison R-C6 H5 (R=any group or atom). The 'contact groups' are hydrogen bond donors X-H (X=N, O, S, or R2 C, or R3 C) and lone-pair containing fragments (R3 C-F, R-C≡N and R2 C=O). Nearly all the IsoStar distributions follow expectations based on the electrostatic potential of the 'central-' and 'contact group'. Interaction energies (ΔEBSSE ) are dominated by electrostatics (particularly between two polarized molecules) or dispersion (especially in case of large contact area). Orbital interactions never dominate, but could be significant (∼30 %) and of the n/π→σ*/π* kind. The largest degree of directionality in the IsoStar plots was typically observed for adducts more stable than ΔEBSSE ≈-4 kcal⋅mol-1 , which can be seen as a benchmark-value for the utility of an interaction in crystal engineering. This benchmark could be met with all the σ- and π-hole donors studied.

5.
Chemistry ; 26(44): 10126-10132, 2020 Aug 06.
Article in English | MEDLINE | ID: mdl-32557861

ABSTRACT

1,1,2,2-Tetracyanocyclopropane derivatives 1 and 2 were designed and synthesized to probe the utility of sp3 -C centred tetrel bonding interactions in crystal engineering. The crystal packing of 1 and 2 and their 1,4-dioxane cocrystals is dominated by sp3 -C(CN)2 ⋅⋅⋅O interactions, has significant C⋅⋅⋅O van der Waals overlap (≤0.266 Å) and DFT calculations indicate interaction energies of up to -11.0 kcal mol-1 . A cocrystal of 2 with 1,4-thioxane reveals that the cyclopropane synthon prefers interacting with O over S. Computational analyses revealed that the electropositive C2 (CN)4 pocket in 1 and 2 can be seen as a strongly directional 'tetrel-bond donor', similar to halogen bond or hydrogen bond donors. This disclosure is expected to have implications for the utility of such 'tetrel bond donors' in molecular disciplines such as crystal engineering, supramolecular chemistry, molecular recognition and medicinal chemistry.

6.
Chemistry ; 25(58): 13436-13443, 2019 Oct 17.
Article in English | MEDLINE | ID: mdl-31453653

ABSTRACT

Studying noncanonical intermolecular interactions between a ligand and a protein constitutes an emerging research field. Identifying synthetically accessible molecular fragments that can engage in intermolecular interactions is a key objective in this area. Here, it is shown that so-called "π-hole interactions" are present between the nitro moiety in nitro aromatic ligands and lone pairs within protein structures (water and protein carbonyls and sulfurs). Ample structural evidence was found in a PDB analysis and computations reveal interaction energies of about -5 kcal mol-1 for ligand-protein π-hole interactions. Several examples are highlighted for which a π-hole interaction is implicated in the superior binding affinity or inhibition of a nitro aromatic ligand versus a similar non-nitro analogue. The discovery that π-hole interactions with nitro aromatics are significant within protein structures parallels the finding that halogen bonds are biologically relevant. This has implications for the interpretation of ligand-protein complexation phenomena, for example, involving the more than 50 approved drugs that contain a nitro aromatic moiety.


Subject(s)
Computer Simulation , Models, Molecular , Nitro Compounds/chemistry , Proteins/chemistry , Amino Acid Sequence , Databases, Protein , Hydrogen Bonding , Hydrophobic and Hydrophilic Interactions , Ligands , Molecular Structure , Protein Binding , Structure-Activity Relationship , Thermodynamics , Water
7.
Chem Commun (Camb) ; 54(85): 12049-12052, 2018 Oct 23.
Article in English | MEDLINE | ID: mdl-30294741

ABSTRACT

A thorough analysis of the Cambridge Structure Database reveals that intermolecular π-hole/n→π* interactions with carbon monoxide ligands are abundant in the solid state and somewhat directional, particularly with fac-like M(CO)3 fragments (P < 4.0). High level DFT calculations suggest interacting energies up to about -10 kcal mol-1 for adducts of charge neutral complexes.

8.
Chem Commun (Camb) ; 54(76): 10742-10745, 2018 Sep 20.
Article in English | MEDLINE | ID: mdl-30191212

ABSTRACT

A thorough analysis of the Cambridge Structure Database shows that π-hole/n→π* interactions with acetonitrile are abundant in the solid state, particularly when acetonitrile is coordinated to a metal. The interaction is weakly directional (P ≤ 1.5) and high level computations suggest a complexation energy of about -5 kcal mol-1.

9.
Dalton Trans ; 39(28): 6483-7, 2010 Jul 28.
Article in English | MEDLINE | ID: mdl-20549005

ABSTRACT

Three compounds with the general formulae [H(2)N(Me)(2)](3)[Ln(2,6-dpa)(3)] were prepared from cheap and readily available reactants. Microcrystalline compounds could be isolated in high yields (>80%) by a simple filtration, after only one hour reaction time in refluxing DMF. The Eu and Tb compounds have been structurally characterized by single crystal X-ray diffraction. The compounds have unusual high-absorption coefficients (>95%) and quantum efficiencies (approximately 70%). Furthermore, they are thermally stable up to 250 degrees C and appear to be UV and water tolerant. The emission colour of the final compound can be easily fine-tuned, by varying the Eu:Tb ratio during the preparation.

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