Observations of tetrel bonding between sp3-carbon and THF.
Ontology highlight
ABSTRACT:
SUBMITTER: Heywood VL
PROVIDER: S-EPMC8159407 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description: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.
| S-EPMC7496358 | biostudies-literature
Project description:A transition metal free coupling reaction of benzylboronic esters and alkyl halides has been developed. Both alkyl bromides and alkyl iodides were found to be competent substrates with the nucleophilic boronate intermediate generated from the combination of benzylboronic ester and an alkyllithium. Good chemoselectivity was observed in substrates with a second electrophile. Both secondary and tertiary benzylboronic esters were effective nucleophiles in the reaction with primary alkyl halides. Mechanistic observations are consistent with a radical mechanism.
| S-EPMC8966628 | biostudies-literature
Project description:The structural stability of the extensively studied organic-inorganic hybrid methylammonium tetrel halide perovskite semiconductors, MATtX3 (MA = CH3NH3+; Tt = Ge, Sn, Pb; X = Cl, Br, I), arises as a result of non-covalent interactions between an organic cation (CH3NH3+) and an inorganic anion (TtX3-). However, the basic understanding of the underlying chemical bonding interactions in these systems that link the ionic moieties together in complex configurations is still limited. In this study, ion pair models constituting the organic and inorganic ions were regarded as the repeating units of periodic crystal systems and density functional theory simulations were performed to elucidate the nature of the non-covalent interactions between them. It is demonstrated that not only the charge-assisted N-H···X and C-H···X hydrogen bonds but also the C-N···X pnictogen bonds interact to stabilize the ion pairs and to define their geometries in the gas phase. Similar interactions are also responsible for the formation of crystalline MATtX3 in the low-temperature phase, some of which have been delineated in previous studies. In contrast, the Tt···X tetrel bonding interactions, which are hidden as coordinate bonds in the crystals, play a vital role in holding the inorganic anionic moieties (TtX3-) together. We have demonstrated that each Tt in each [CH3NH3+•TtX3-] ion pair has the capacity to donate three tetrel (σ-hole) bonds to the halides of three nearest neighbor TtX3- units, thus causing the emergence of an infinite array of 3D TtX64- octahedra in the crystalline phase. The TtX44- octahedra are corner-shared to form cage-like inorganic frameworks that host the organic cation, leading to the formation of functional tetrel halide perovskite materials that have outstanding optoelectronic properties in the solid state. We harnessed the results using the quantum theory of atoms in molecules, natural bond orbital, molecular electrostatic surface potential and independent gradient models to validate these conclusions.
| S-EPMC10341982 | biostudies-literature
Project description:A set of 35 representative neutral and charged tetrel complexes was investigated with the objective of finding the factors that influence the strength of tetrel bonding involving single bonded C, Si, and Ge donors and double bonded C or Si donors. For the first time, we introduced an intrinsic bond strength measure for tetrel bonding, derived from calculated vibrational spectroscopy data obtained at the CCSD(T)/aug-cc-pVTZ level of theory and used this measure to rationalize and order the tetrel bonds. Our study revealed that the strength of tetrel bonds is affected by several factors, such as the magnitude of the σ-hole in the tetrel atom, the negative electrostatic potential at the lone pair of the tetrel-acceptor, the positive charge at the peripheral hydrogen of the tetrel-donor, the exchange-repulsion between the lone pair orbitals of the peripheral atoms of the tetrel-donor and the heteroatom of the tetrel-acceptor, and the stabilization brought about by electron delocalization. Thus, focusing on just one or two of these factors, in particular, the σ-hole description can only lead to an incomplete picture. Tetrel bonding covers a range of -1.4 to -26 kcal/mol, which can be strengthened by substituting the peripheral ligands with electron-withdrawing substituents and by positively charged tetrel-donors or negatively charged tetrel-acceptors.
| S-EPMC6278569 | biostudies-literature
Project description:A dual photoredox and gold-catalysed cross-coupling reaction of alkynyltrimethylsilanes and aryldiazonium tetrafluoroborates is described. The reaction proceeds through visible-light mediated oxidative addition of aryldiazoniums, transmetalation of alkynyltrimethylsilanes and aryl-alkynyl reductive elimination. Exclusive selectivity for silyl-substituted alkynes is observed, with no reactivity observed for terminal alkynes.
| S-EPMC5947751 | biostudies-literature
Project description:The co-crystallization of the lead(II) complex [Pb(S2CNEt2)2] with tetraiodoethylene (C2I4) gave the co-crystal, [Pb(S2CNEt2)2]∙½C2I4, whose X-ray structure exhibits only a small change of the crystal parameters than those in the parent [Pb(S2CNEt2)2]. The supramolecular organization of the co-crystal is largely determined by an interplay between Pb⋯S tetrel bonding (TeB) and I⋯S halogen bonding (HaB) with comparable contributions from these non-covalent contacts; the TeBs observed in the parent complex, [Pb(S2CNEt2)2], remain unchanged in the co-crystal. An analysis of the theoretical calculation data, performed for the crystal and cluster models of [Pb(S2CNEt2)2]∙½C2I4, revealed the non-covalent nature of the Pb⋯S TeB (-5.41 and -7.78 kcal/mol) and I⋯S HaB (-7.26 and -11.37 kcal/mol) interactions and indicate that in the co-crystal these non-covalent forces are similar in energy.
| S-EPMC9569466 | biostudies-literature
Project description:Metal-catalyzed cross-couplings provide powerful, concise, and accurate methods to construct carbon-carbon bonds from organohalides and organometallic reagents. Recent developments extended cross-couplings to reactions where one of the two partners connects with an aryl or alkyl carbon-hydrogen bond. From an economic and environmental point of view, oxidative couplings between two carbon-hydrogen bonds would be ideal. Oxidative coupling between phenyl and "inert" alkyl carbon-hydrogen bonds still awaits realization. It is very difficult to develop successful strategies for oxidative coupling of two carbon-hydrogen bonds owning different chemical properties. This article provides a solution to this challenge in a convenient preparation of dihydrobenzofurans from substituted phenyl alkyl ethers. For the phenyl carbon-hydrogen bond activation, our choice falls on the carboxylic acid fragment to form the palladacycle as a key intermediate. Through careful manipulation of an additional ligand, the second "inert" alkyl carbon-hydrogen bond activation takes place to facilitate the formation of structurally diversified dihydrobenzofurans.Cross-dehydrogenative coupling is finding increasing application in synthesis, but coupling two chemically distinct sites remains a challenge. Here, the authors report an oxidative coupling between sp 2 and sp 3 carbons by sequentially activating the more active aryl site followed by the alkyl position.
| S-EPMC5552783 | biostudies-literature
Project description:Tetrel bonds represent a category of non-bonding interaction wherein an electronegative atom donates a lone pair of electrons into the sigma antibonding orbital of an atom in the carbon group of the periodic table. Prior computational studies have implicated tetrel bonding in the stabilization of a preliminary state that precedes the transition state in SN2 reactions, including methyl transfer. Notably, the angles between the tetrel bond donor and acceptor atoms coincide with the prerequisite geometry for the SN2 reaction. Prompted by these findings, we surveyed crystal structures of methyltransferases in the Protein Data Bank and discovered multiple instances of carbon tetrel bonding between the methyl group of the substrate S-adenosylmethionine (AdoMet) and electronegative atoms of small molecule inhibitors, ions, and solvent molecules. The majority of these interactions involve oxygen atoms as the Lewis base, with the exception of one structure in which a chlorine atom of an inhibitor functions as the electron donor. Quantum mechanical analyses of a representative subset of the methyltransferase structures from the survey revealed that the calculated interaction energies and spectral properties are consistent with the values for bona fide carbon tetrel bonds. The discovery of methyl tetrel bonding offers new insights into the mechanism underlying the SN2 reaction catalyzed by AdoMet-dependent methyltransferases. These findings highlight the potential of exploiting these interactions in developing new methyltransferase inhibitors.
| S-EPMC6278250 | biostudies-literature
Project description:Three novel isostructural equiatomic gold tetrel pnictides, AuSiAs, AuGeP, and AuGeAs, were synthesized and characterized. These phases crystallize in the noncentrosymmetric (NCS) monoclinic space group Cc (no. 9), featuring square-planar Au within cis-[AuTt2 Pn2 ] units (Tt=tetrel, Si, Ge; Pn=pnictogen, P, As). This is in drastic contrast to the structure of previously reported AuSiP, which exhibits typical linear coordination of Au with Si and P. Chemical bonding analysis through the electron localization function suggests covalent two-center two-electron Tt-Pn bonds, and three-center Au-Tt-Au and Au-Pn-Au bonds with 1.6 e- per bond. X-ray photoelectron spectroscopy studies support the covalent and nonionic nature of Au-Pn and Au-Tt bonds. The title materials were found to be n-type narrow-gap semiconductors or semimetals, with nearly temperature-independent electrical resistivities and low thermal conductivities. A combination of the semimetallic properties with tunable NCS structure provides opportunities for the development of materials based on gold tetrel pnictides.
| S-EPMC8251799 | biostudies-literature
Project description:Although abundant in organic molecules, carbon-hydrogen (C-H) bonds are typically considered unreactive and unavailable for chemical manipulation. Recent advances in C-H functionalization technology have begun to transform this logic, while emphasizing the importance of and challenges associated with selective alkylation at a sp3 carbon1,2. Here we describe iron-based catalysts for the enantio-, regio- and chemoselective intermolecular alkylation of sp3 C-H bonds through carbene C-H insertion. The catalysts, derived from a cytochrome P450 enzyme in which the native cysteine axial ligand has been substituted for serine (cytochrome P411), are fully genetically encoded and produced in bacteria, where they can be tuned by directed evolution for activity and selectivity. That these proteins activate iron, the most abundant transition metal, to perform this chemistry provides a desirable alternative to noble-metal catalysts, which have dominated the field of C-H functionalization1,2. The laboratory-evolved enzymes functionalize diverse substrates containing benzylic, allylic or α-amino C-H bonds with high turnover and excellent selectivity. Furthermore, they have enabled the development of concise routes to several natural products. The use of the native iron-haem cofactor of these enzymes to mediate sp3 C-H alkylation suggests that diverse haem proteins could serve as potential catalysts for this abiological transformation, and will facilitate the development of new enzymatic C-H functionalization reactions for applications in chemistry and synthetic biology.
| S-EPMC6440214 | biostudies-literature