Academic literature on the topic 'TETREL BONDING'

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.

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.

In recent years, noncovalent interactions involving group-14 elements of the periodic table acting as a Lewis acid center (or tetrel-bonding interactions) have attracted considerable attention due to their potential applications in supramolecular chemistry, material science and so on. The aim of the present study is to characterize the geometry, strength and bonding properties of strong tetrel-bond interactions in some charge-assisted tetrel-bonded complexes. Ab initio calculations are performed, and the results are supported by the quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) approaches. The interaction energies of the anionic tetrel-bonded complexes formed between XF3M molecule (X=F, CN; M=Si, Ge and Sn) and A− anions (A−=F−, Cl−, Br−, CN−, NC− and N3−) vary between −16.35 and −96.30 kcal/mol. The M atom in these complexes is generally characterized by pentavalency, i.e., is hypervalent. Moreover, the QTAIM analysis confirms that the anionic tetrel-bonding interaction in these systems could be classified as a strong interaction with some covalent character. On the other hand, it is found that the tetrel-bond interactions in cationic tetrel-bonded [p-NH3(C6H4)MH3]+···Z and [p-NH3(C6F4)MH3]+···Z complexes (M=Si, Ge, Sn and Z=NH3, NH2CH3, NH2OH and NH2NH2) are characterized by a strong orbital interaction between the filled lone-pair orbital of the Lewis base and empty BD*M-C orbital of the Lewis base. The substitution of the F atoms in the benzene ring provides a strong orbital interaction, and hence improved tetrel-bond interaction. For all charge-assisted tetrel-bonded complexes, it is seen that the formation of tetrel-bond interaction is accompanied bysignificant electron density redistribution over the interacting subunits. Finally, we provide some experimental evidence for the existence of such charge-assisted tetrel-bond interactions in crystalline phase.

Carbon bonding is a weak interaction, particularly when a neutral molecule acts as an electron donor. Thus, there is an interesting question of how to enhance carbon bonding. In this paper, we found that the –OCH3 group at the exocyclic carbon of fulvene can form a moderate carbon bond with NH3 with an interaction energy of about −10 kJ/mol. The –OSiH3 group engages in a stronger tetrel bond than does the –OGeH3 group, while a reverse result is found for both –OSiF3 and –OGeF3 groups. The abnormal order in the former is mainly due to the stronger orbital interaction in the –OSiH3 complex, which has a larger deformation energy. The cyano groups adjoined to the fulvene ring not only cause a change in the interaction type, from vdW interactions in the unsubstituted system of –OCF3 to carbon bonding, but also greatly strengthen tetrel bonding. The formation of tetrel bonding has an enhancing effect on the aromaticity of the fulvene ring.

We report for the first time the concurrent agostic and tetrel bonding interactions involving the heaviest tetrel atom (Pb) in N′-(phenyl(pyridin-2-yl)methylene)isonicotinohydrazide–PbX complexes (X = Cl, I, NCS, NO₂).

The role of the closing lecture in a Faraday Discussion is to summarise the contributions made to the Discussion over the course of the meeting and in so doing capture the main themes that have arisen. This article is based upon my Closing Remarks Lecture at the 203^rdFaraday Discussion meeting on Halogen Bonding in Supramolecular and Solid State Chemistry, held in Ottawa, Canada, on 10–12^thJuly, 2017. The Discussion included papers on fundamentals and applications of halogen bonding in the solid state and solution phase. Analogous interactions involving main group elements outside group 17 were also examined. In the closing lecture and in this article these contributions have been grouped into the four themes: (a) fundamentals, (b) beyond the halogen bond, (c) characterisation, and (d) applications. The lecture and paper also include a short reflection on past work that has a bearing on the Discussion.

Thesis (Ph. D.)--University of Nevada, Reno, 2007.
"December, 2007." Includes bibliographical references (leaves 125-129). Library also has microfilm. Ann Arbor, Mich. : ProQuest Information and Learning Company, [2008]. 1 microfilm reel ; 35 mm. Online version available on the World Wide Web.

The importance of non-covalent interactions cannot be undermined, as it permeates nearly every sphere of chemistry. The hydrogen bond is the most well-known and ubiquitous non-covalent interaction. In recent times similar interactions involving other elements, that include nearly half the periodic table, have been proposed and studied. The tetrel bond (Group 14 elements) is one such interaction which is analogous to the hydrogen bond1,2. The ‘carbon bond’ is an important subset of these interactions1. Our objective is to understand these non-covalent interactions by studying the structures of weakly bound complexes. Rotational spectroscopy is an extremely accurate technique to obtain the geometrical parameters of molecules in the gas phase. We have used a home-built pulsed nozzle Fourier transform microwave (PNFTMW) spectrometer to record the spectra3. Weakly bound complexes are formed via a supersonic expansion of the gases into a vacuum chamber. These complexes interact with the microwave radiation to give a rotational spectrum. Structural information is then extracted from the rotational spectrum. The rotational spectroscopic studies are supplemented by computational studies such as the Atoms in Molecules theory. There is a paucity of experimental data involving tetrel bonded interactions. This Thesis focusses on hydrogen and tetrel bonded complexes. Chapter 1 of this thesis gives a brief introduction to non-covalent interactions and expounds on the hydrogen and tetrel bonding interactions. This chapter also provides pertinent details about rotational spectroscopy. Chapter 2 details the functioning of the microwave spectrometer and other computational methods used in the Thesis. Chapter 3 discusses the rotational spectra of the propargyl alcohol (PA)∙∙∙water complex. PA is multifunctional molecule having a hydroxyl group and an acetylenic moiety. The hydroxyl group present in both alcohol and water can act as either an H-bond donor or as an H-bond acceptor. This offers different binding options leading to a number of different possible hydrogen bonded structures for the PA∙∙∙H2O complex. The two lowest energy structures calculated for the complex differ only in the position of the non-bonded hydrogen atom. The spectrum obtained indicates the presence of the global minimum structure, G-PW-1a. In this structure, PA donates an O-H∙∙∙O H-bond to H2O and accepts an O-H∙∙∙π H-bond from H2O. The spectra for the isotopologues help to determine the position of the non-bonded hydrogen atom of water. This helps to differentiate between the two lowest energy structures. The matrix isolation IR spectroscopic study on the PA∙∙∙H2O complex cannot differentiate between these two structures. The rotational spectrum shows a doubling of the lines caused by the internal rotation of the H2O moiety about its C2 axis. We were also able to generalize the H-bond donor/acceptor capabilities of the hydroxyl groups in an alcohol∙∙∙water complex based on the electron donating/withdrawing abilities of the groups present in the alcohol. The rotational spectra for the acetonitrile∙∙∙carbon dioxide are discussed in Chapter 4. The ab initio calculations for the CH3CN∙∙∙CO2 complex optimized four tetrel bonded structures. Therefore, investigating this complex provides an opportunity to study tetrel bonded structures in the gas phase. We have observed the rotational spectra corresponding to the two lowest energy structures, the π-stacked and the T-shaped. The spectra for the isotopologues were also recorded. The spectra show hyperfine splitting due to the nuclear quadrupole coupling of the N-14 nucleus. The π-stacked structure has CO2 and CH3CN stacked in a parallel manner with the oxygen end of CO2 interacting with the positively charged C atom of the cyano group in CH3CN. The Atoms in Molecules analysis finds that the methyl C-H forms a hydrogen bond with the same oxygen atom leading to a closed network of non-covalent interactions. In the T-shaped structure the nitrogen end of CH3CN donates electron density to the central positively charged C atom of CO2. The spin-less indistinguishable oxygen nuclei in the C2v symmetry of the T-shaped structure dictates that odd |K-m| levels will be missing. We find no K=1 lines for the m=0 state confirming that T-shaped structure has been observed. The structure of CH5+ has been highly debated upon. Chapter 5 discusses the structure of CH5+ using Atom in Molecules (AIM), natural bond orbital (NBO), and normal coordinate analyses. Contrary to the popular perception, we find that the structure of CH5+ cannot be considered as the complex between CH3+ and H2. It has a pentacoordinate carbon center having five C-H bonds4. The congeners of CH5+, SiH5+ and GeH5+ were also explored to see if they form similar structures as CH5+ or not. We find that the structures are different from CH5+. The structures of SiH5+ and GeH5+ form a complex between the TH3+ and H2. The identity of the H2 moiety is retained in these complexes. The H2 moiety donates electron density to the positively charged T atom forming a tetrel bonded complex. This work led us to classify the 3c-2e bonds based on the connectivity patterns of the three nuclei involved in the 3c-2e. We were able to classify them into V, L, Δ, T, and I (linear) types5. Chapter 6 explores the structures and rotational spectra of the weakly bound complexes of methyl fluoride with water, argon, and itself. We intended to observe a tetrel bonded structure for the CH3F∙∙∙H2O complex. However only the global minimum hydrogen bonded structure having a bent O-H∙∙∙F bond was observed. Three structures are possible for the CH3F∙∙∙Ar complex, the T-shaped, tetrel bonded, and linear structures. These three structures are very close in energy. We have evidence for the formation of the T-shaped structure, where the Ar atom is positioned perpendicular to the C-F bond. The large number of unassigned lines could belong to the other two structures. The global minimum structure for the CH3F∙∙∙CH3F dimer is an antiparallel structure where the two CH3F units are bound by two symmetrical C-H∙∙∙F hydrogen bonds. However, it is not possible to observe this structure because it has a net zero electric dipole moment. So the lines observed could possibly belong to the tetrel bonded structures, linear or skewed linear. In both these structures the electron rich F atom donates electron density to the σ-hole formed over the methyl face of CH3F. Chapter 7 summarizes the results and conclusions for the molecular structures investigated in this Thesis.

Ascidians belonging to Phylum Chordata are the most largest and diverse of the Sub-phylum Tunicata (Urochordata). Marine ascidians are one of the richest sources of bioactive peptides. These bioactive peptides from marine ascidians are confined to various types of structures such as cyclic peptides, acyclic peptides (depsipeptides), linear helical peptides with abundance of one amino acid (proline, trytophane, histidine), peptides forming hairpin like beta sheets or α-helical/β-sheet mixed structures stabilized by intra molecular disulfide bonding. Cyanobactins are fabricated through the proteolytic cleavage and cyclization of precursor peptides coupled with further posttranslational modifications such as hydroxylation, glycosylation, heterocyclization, oxidation, or prenylation of amino acids. Ascidians are known to be a rich source of bioactive alkaloids. β-carbolines form a large group of tryptophan derived antibiotics. Pyridoacridines from ascidians are tetra- or penta- cyclic aromatic alkaloids with broad range of bioactivities. Didemnidines derived from ascidian symbiotic microbes are inhibitors of phospholipase A2 and induce cell apoptosis. Meridianins are indulged in inhibiting various protein kinases such as, cyclindependent kinases, glycogen synthase kinase-3, cyclic nucleotide dependent kinases, casein kinase, and also implicate their activity of interfering with topoisomerase, altering the mitochondrial membrane potential and binding to the DNA minor groove to inhibit transcriptional activation. Most of these bioactive compounds from ascidians are already in different phases of the clinical and pre-clinical trials. They can be used for their nutraceutical values because of their antineoplastic, antihypertensive, antioxidant, antimicrobial, cytotoxic, antibacterial, antifungal, insecticidal, anti-HIV and anti-parasitic, anti-malarial, anti-trypanosomal, anti-cancer etc. This chapter mostly deals with antibacterial compounds from ascidian and their associate symbiotic cyanobacteria.

Flip-chip bonding is important to integrate MEMS devices with other components or to make novel devices. The use of tethers when flip-chip bonding is valuable because it enables the release of the MEMS based device prior to bonding. Releasing the device prior to bonding allows the possibility to bond to a substrate that includes materials that are incompatible with the release process, increase yield since any devices lost during release are not bonded, and avoid damage to the bond. This paper presents a set of design rules for devices created with the MUMPs process that can be implemented to allow the device to be tether flip-chip bonded. The rules outline the design of tethers, mechanical stops, and locking bumps, which work as a system to keep the device from slipping or twisting during bonding, but break free from the donor substrate after bonding. Examples of success, reasons for past failures and the solutions are presented.

Abstract The frictional properties of a hybrid lubricant film composited from perfluoropolyether (PFPE) lubricant (Moresco DDOH) with single end group and PFPE film deposited from HT170 (Solvay) via photoelectron-assisted chemical vapor deposition (PACVD) were evaluated using a pin-on-disk tester and compared with that of a Z-tetraol dip-coated film. The frictional coefficient of only the HT170 film deposited via PACVD was considerably high; however, the hybrid lubricant film without the mobile fraction showed a friction coefficient equivalent to that of the Z-tetraol film with a mobile fraction of 40%.

The technical potential of a new plasmonic sensor, which can acquire surface-enhanced Raman spectra with high sensitivity by controlling surface plasmons is demonstrated for the chemical analysis of diamond-like carbon (DLC) films, lubricant films, and the DLC/lubricant interface on magnetic disks of sub-nanometer scale. The Raman spectra of thin DLC films and lubricated DLC carbon can be acquired with a high S/N ratio. Raman spectra of lubricated DLC carbon can also be acquired with the high S/N ratio. The wavenumber shift and intensity change of the Raman peaks of the phenyl and hydroxyl groups in the mixed lubricants (ADOH and Z-tetraol) show that the chemical interaction with the DLC surfaces of the phenyl group in the lubricant molecule decreases with increasing nitrogen content, whereas that of the hydroxyl group with the nitrogenated carbon increases. Raman spectra of nitrogenated DLC films are also acquired, the peaks show good agreement with density functional theory calculations. The calculated bonding energy indicates that the hydroxyl groups interact with the nitrogenated carbon.

In the developing heat-assisted magnetic recording (HAMR) technology, a laser heats up the magnetic media to the Curie temperature of a few hundred degrees Celsius for a short time of the order of a few nanoseconds. Accordingly, the thin-film lubricant coating on the disk experiences effects such as thermo-capillary shear stress, evaporation, viscosity drop, and eventually, lubricant depletion [1, 2]. Our previous work [3] studied these effects on the lubricant depletion for various lubricants and a prescribed Gaussian temperature distribution with a peak temperature of 350°C and a Full-Width Half Maximum (FWHM) of Ls = 20nm, close to the target laser spot size for HAMR. In order to maintain a reliable head-disk interaction, the lubricant needs to recover to the initial uniform profile. A previous work by Dahl and Bogy [4] studied the recovery process after HAMR writing for Z-dol 2000 using lubrication theory. In this paper, we focus on the effect of the lubricant functional end-groups on the recovery process, using the same method. Z-dol, Z-tetraol, and ZTMD lubricant families have the same polymer backbone but different numbers of hydroxyl end-groups [5]. This difference modifies two key parameters, both affecting the recovery time significantly. First, it changes the bonding ratio and the disjoining pressure properties of the lubricant. Figure 1 shows the disjoining pressure derivative, including both the polar and dispersive components, as a function of film thickness for Z-dol2000, Z-tetraol2200, and ZTMD2200 based on experiments [1, 6, 7]. Second, a major increase in lubricant viscosity occurs as the number of hydroxyl end-groups increases from two (Z-dol) to four (Z-tetraol) to eight (ZTMD) [3]. Fig. 2 shows the viscosity μ(h) as a function of the local lubricant thickness for all three different families of lubricants at the room temperature.