Hydrogen and Lithium Bonds-Lewis Acid Units Possessing Multi-Center Covalent Bonds.
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ABSTRACT:
SUBMITTER: Aarabi M
PROVIDER: S-EPMC8624437 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:It is shown that the dissociation energy D e for the process B⋯A = B + A for 250 complexes B⋯A composed of 11 Lewis bases B (N₂, CO, HC≡CH, CH₂=CH₂, C₃H₆, PH₃, H₂S, HCN, H₂O, H₂CO and NH₃) and 23 Lewis acids (HF, HCl, HBr, HC≡CH, HCN, H₂O, F₂, Cl₂, Br₂, ClF, BrCl, H₃SiF, H₃GeF, F₂CO, CO₂, N₂O, NO₂F, PH₂F, AsH₂F, SO₂, SeO₂, SF₂, and SeF₂) can be represented to good approximation by means of the equation D e = c ' N B E A , in which N B is a numerical nucleophilicity assigned to B, E A is a numerical electrophilicity assigned to A, and c ' is a constant, conveniently chosen to have the value 1.00 kJ mol-1 here. The 250 complexes were chosen to cover a wide range of non-covalent interaction types, namely: (1) the hydrogen bond; (2) the halogen bond; (3) the tetrel bond; (4) the pnictogen bond; and (5) the chalcogen bond. Since there is no evidence that one group of non-covalent interaction was fitted any better than the others, it appears the equation is equally valid for all the interactions considered and that the values of N B and E A so determined define properties of the individual molecules. The values of N B and E A can be used to predict the dissociation energies of a wide range of binary complexes B⋯A with reasonable accuracy.
| S-EPMC6151704 | biostudies-literature
Project description:An analysis of the effects induced by F, Cl, and Br-substituents at the α-position of both, the hydroxyl or the amino group for a series of amino-alcohols, HOCH2(CH2)nCH2NH2 (n = 0-5) on the strength and characteristics of their OH···N or NH···O intramolecular hydrogen bonds (IMHBs) was carried out through the use of high-level G4 ab initio calculations. For the parent unsubstituted amino-alcohols, it is found that the strength of the OH···N IMHB goes through a maximum for n = 2, as revealed by the use of appropriate isodesmic reactions, natural bond orbital (NBO) analysis and atoms in molecules (AIM), and non-covalent interaction (NCI) procedures. The corresponding infrared (IR) spectra also reflect the same trends. When the α-position to the hydroxyl group is substituted by halogen atoms, the OH···N IMHB significantly reinforces following the trend H < F < Cl < Br. Conversely, when the substitution takes place at the α-position with respect to the amino group, the result is a weakening of the OH···N IMHB. A totally different scenario is found when the amino-alcohols HOCH2(CH2)nCH2NH2 (n = 0-3) interact with BeF2. Although the presence of the beryllium derivative dramatically increases the strength of the IMHBs, the possibility for the beryllium atom to interact simultaneously with the O and the N atoms of the amino-alcohol leads to the global minimum of the potential energy surface, with the result that the IMHBs are replaced by two beryllium bonds.
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Project description:Acetylenedicarboxylic acid dihydrate (ADAD) represents a complex with strong hydrogen bonding between the carboxylic OH and the water molecule. An X-ray re-examination of the ADAD crystal structure confirms the O…O distance of the short hydrogen bonds, and clearly shows different bond lengths between the two oxygen atoms with respect to the carbon atom in the carboxyl group, indicating a neutral structure for the complex. The neutral structure was also confirmed by vibrational spectroscopy, as no proton transfer was observed. The diffraction studies also revealed two polymorph modifications: room temperature (α) and low temperature (β), with a phase transition at approximately 4.9 °C. The calculated vibrational spectra are in satisfactory agreement with the experimental spectra. A comparison of the structure and the vibrational spectra between the ADAD and the oxalic acid dihydrate reveals some interesting details. The crystal structures of both crystal hydrates are almost identical; only the O…O distances of the strongest hydrogen bonds differ by 0.08 Å. Although it was expected that a larger O…O spacing in the ADAD crystal may significantly change the infrared and Raman spectra, especially for the frequency and the shape of the acidic OH stretching vibration, both the shape and frequency are almost identical, with all subpeaks topped on the broad OH stretching vibration. The O…O distance dependent are only in- and out-of-plane OH deformations modes. The presence of polarons due to the ionized defects was not observed in the vibrational spectra of ADAD. Therefore, the origin of the broad OH band shape was explained in a similar way to the acid dimers. The anharmonicity of a potential enhances the coupling of the OH stretching with the low-frequency hydrogen bond stretching, which, in addition to the Fermi resonance, structures the band shape of the OH stretching. The fine structure found as a superposition of a broad OH stretching is attributed to Davydov coupling.
| S-EPMC9181247 | biostudies-literature
Project description:Over the last decade there has been an explosion in the reactivity and applications of frustrated Lewis pair (FLP) chemistry. Despite this, the Lewis acids (LAs) in these transformations are often boranes, with heavier p-block elements receiving surprisingly little attention. The novel LA Bn3SnOTf (1) has been synthesized from simple, inexpensive starting materials and has been spectroscopically and structurally characterized. Subtle modulation of the electronics at the tin centre has led to an increase in its Lewis acidity in comparison with previously reported R3SnOTf LAs, and has facilitated low temperature hydrogen activation and imine hydrogenation. Deactivation pathways of the R3Sn+ LA core have also been investigated.This article is part of the themed issue 'Frustrated Lewis pair chemistry'.
| S-EPMC5540841 | biostudies-literature
Project description:Small-molecule dual hydrogen-bond (H-bond) donors such as ureas, thioureas, squaramides, and guanidinium ions enjoy widespread use as effective catalysts for promoting a variety of enantioselective reactions. However, these catalysts are only weakly acidic and therefore require highly reactive electrophilic substrates to be effective. We introduce here a mode of catalytic activity with chiral H-bond donors that enables enantioselective reactions of relatively unreactive electrophiles. Squaramides are shown to interact with silyl triflates by binding the triflate counterion to form a stable, yet highly Lewis acidic, complex. The silyl triflate-chiral squaramide combination promotes the generation of oxocarbenium intermediates from acetal substrates at low temperatures. Enantioselectivity in nucleophile additions to the cationic intermediates is then controlled through a network of noncovalent interactions between the squaramide catalyst and the oxocarbenium triflate.
| S-EPMC5728151 | biostudies-literature
Project description:Reduced graphene oxide-azobenzene (RGO-AZO) hybrids were prepared via covalent functionalization for long-term solar thermal storage. Thermal barrier (ΔEa) of cis to tran reversion and thermal storage (ΔH) were improved by molecular hydrogen bonds (H-bonds) through ortho- or para-substitution of AZO. Intramolecular H-bonds thermally stabilized cis-ortho-AZO on RGO with a long-term half-life of 5400 h (ΔEa = 1.2 eV), which was much longer than that of RGO-para-AZO (116 h). RGO-para-AZO with one intermolecular H-bond showed a high density of thermal storage up to 269.8 kJ kg(-1) compared with RGO-ortho-AZO (149.6 kJ kg(-1)) with multiple intra- and intermolecular H-bonds of AZO according to relaxed stable structures. Thermal storage in experiment was the same order magnitude to theoretical data based on ΔH calculated by density functional theory and packing density. Photoactive RGO-AZO hybrid can be developed for high-performance solar thermal storage by optimizing molecular H-bonds.
| S-EPMC3832871 | biostudies-literature
Project description:We report a computational study on homo- and heteronuclear e+[X-Y-] compounds formed by two halide anions (X-, Y- = F-, Cl-, Br-) and one positron. Our results indicate the formation of energetically stable positronic molecules in all cases. Analysis of the electron and positron densities points out that the formation of positron covalent bonds underlies the stabilization of the otherwise repelling dihalides, revealing that positronic bonding can reach far beyond the previously addressed e+[H-H-] molecule [J. Charry, M. T. do N. Varella and A. Reyes, Angew. Chem. Int. Ed., 2018, 57, 8859-8864.]. To a significant extent, the properties of the positron dihalides are similar to those of the purely electronic analogs, e-[A+B+], molecular cations with isoelectronic atomic cores (A+, B+ = Na+, K+, Rb+) bound by one electron. The positron bonds in the e+[X-Y-] complexes are however stronger than those in the isoelectronic e-[A+B+] counterparts, as the former have shorter bond lengths and higher bond energies. While an energy decomposition analysis points out that both electronic and positronic bonds essentially arise from electrostatic interactions, the more stable positron bonds are partly due to the higher polarizabilities of the dihalide anions, and partly to more significant contributions from correlation and relaxation effects.
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Project description:Short hydrogen bonds (H-bonds) have been proposed to play key functional roles in several proteins. The location of the proton in short H-bonds is of central importance, as proton delocalization is a defining feature of low-barrier hydrogen bonds (LBHBs). Experimentally determining proton location in H-bonds is challenging. Here, bond length analysis of atomic (1.15-0.98 Å) resolution X-ray crystal structures of the human protein DJ-1 and its bacterial homologue, YajL, was used to determine the protonation states of H-bonded carboxylic acids. DJ-1 contains a buried, dimer-spanning 2.49 Å H-bond between Glu15 and Asp24 that satisfies standard donor-acceptor distance criteria for a LBHB. Bond length analysis indicates that the proton is localized on Asp24, excluding a LBHB at this location. However, similar analysis of the Escherichia coli homologue YajL shows both residues may be protonated at the H-bonded oxygen atoms, potentially consistent with a LBHB. A Protein Data Bank-wide screen identifies candidate carboxylic acid H-bonds in approximately 14% of proteins, which are typically short [⟨dO-O⟩ = 2.542(2) Å]. Chemically similar H-bonds between hydroxylated residues (Ser/Thr/Tyr) and carboxylates show a trend of lengthening O-O distance with increasing H-bond donor pKa. This trend suggests that conventional electronic effects provide an adequate explanation for short, charge-assisted carboxylic acid-carboxylate H-bonds in proteins, without the need to invoke LBHBs in general. This study demonstrates that bond length analysis of atomic resolution X-ray crystal structures provides a useful experimental test of certain candidate LBHBs.
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Project description:Discovering the interaction mechanism and location of RNA binding proteins (RBPs) on RNA is critical for understanding gene expression regulation. Here, we apply selective 2’-hydroxyl acylation analyzed by primer extension (SHAPE) on in vivo transcripts to identify transcriptome-wide footprints (fSHAPE) on RNA when compared to protein-absent transcripts. Structural analyses indicate that fSHAPE precisely detects nucleotides whose base moieties hydrogen bond with protein and that fSHAPE patterns can predict binding sites of RBPs of interest. To illustrate, we demonstrate that fSHAPE correctly identifies known and novel iron response protein RNA elements. Furthermore, we enable selective interrogation of RNA-protein complexes by integrating SHAPE and fSHAPE with crosslinking and immunoprecipitation (eCLIP) of desired RBPs. To demonstrate, histone stem loop elements and their nucleotides that hydrogen bond with stem-loop binding protein were identified by SHAPE-eCLIP and fSHAPE-eCLIP. Together, these technologies greatly expand on strategies for understanding specific cellular RNA interactions in RNA-protein complexes.
2020-11-30 | GSE149767 | GEO
Project description:Regulating the states of hydrogen bonds in ionic liquids (ILs) is an effective way to improve their catalytic performance. In this paper, disulfonic-functionalized acidic ionic liquids (DSFAILs) were synthesized successfully, including novel SO3H-functionalized binuclear IL (bis[3-(CH2)3SO3H-1-(CH2)2-Im][HSO4]2). For the biodiesel synthesis, compared with the traditional ILs catalysts, DSFAILs bis[(3-(CH2)3SO3H-1-(CH2)2-Im][HSO4]2, [Im(N (CH2)3SO3H)2][HSO4]) had higher catalytic activity even under mild reaction conditions. Using the density functional theory (DFT) method, the role of hydrogen bonds in different SO3H-functionalized acidic ionic liquids (SFAILs) was explored. The forms of hydrogen bonds existing in different ILs directly determine their acidity. It suggested that the forming status of the active sites (hydrogen bonds) were diverse in different SFAILs. Also, deep ionization of the hydrogen atoms from the cation-anion strong interaction could increase the acidity and catalytic performance of SFAILs. From this, the structure-activity relationship between the SFAILs structures and the catalytic activity of methyl oleate synthesis was proposed. Besides, the experimental results also showed that bis[3-(CH2)3SO3H-1-(CH2)2-Im][HSO4]2 catalyst had a high catalytic activity to obtain methyl oleate and the catalyst could be separated easily owing to its larger molecular weight. However, [Im(N(CH2)3SO3H)2][HSO4] had a stronger acidity and a lower steric hindrance and thus a higher catalytic activity and was the optimal catalyst for the methyl oleate synthesis. In the presence of a small amount of catalyst (6 wt %) and at low reaction temperature (353 K), the methyl oleate yield could reach up to 93%. After six recycles of the catalyst, the methyl oleate yield remained at 90%.
| S-EPMC7271023 | biostudies-literature