Exploring the C–H…O Interactions in Glycoproteins

Glycoproteins are an important class of proteins that play a significant role in many cellular events. In the present study, we analyze the influence of C–H…O interactions in relation to other environmental preferences in glycoproteins. CH…O interactions are now accepted as a genuine hydrogen bond. Main chain–main chain interactions are predominant. Proline residues stabilize strands by C–H…O interactions in glycoproteins. Majority of the C–H…O interacting residues were conserved and had one or more stabilization centers. CH…O interactions might be responsible for the global conformational stability, since long-range CH…O contacts were predominant. The results presented in this study might be useful for structural stability studies in glycoproteins.     

On the Relative Importance of O–H/π Interactions in 7-Norbornenols

The geometries of the two H–O–C rotamers of synand two of anti-7-norbornenol have been optimized at the ab initio HF/6-31G** and B3LYP hybrid HF-DFT levels of theory by using a 6-31G** basis set. Contrary to an earlier report, we find that the (nongeometry constrained) anti-trans isomer (1d) is predicted to be more stable than the corresponding syn-cis form (1a). The increased stability of 1d vis-à-vis 1a can be accounted for in terms of relative H(1)–C(2)–O(3)–H(4) torsion energy effects. The computational results indicate that the hydroxyl proton in 1a enters into intramolecular hydrogen bonding with the proximate C=C bond. Supporting evidence for this conclusion resides in the fact that the 1a is predicted to possess the lowest O–H stretching frequency, a result that can be attributed to -hydrogen bonding.     

Structural variability of Ag(I) metal–organic networks: C–H⋯π and metal⋯π interactions

The synthesis and X-ray structural characterization of two silver(I) coordination polymers, [Ag₂(bpp)₂(Phdac)]·5H₂O (1) and [Ag₂(bpp)(HSSal)] (2), are reported, where bpp = 4,4′-trimethylene dipyridine, H₂Phdac = 1,4-phenylenediacetic acid, and H₃SSal = 5-sulfosalicylic acid. X-ray crystallography reveals that the structures are stabilized through hydrogen bonding interactions. The C–H?π and metal?π interactions of aromatic molecules play a crucial role in building a layered framework. Intricate combinations of the weak non-covalent interactions have been analyzed to explore cooperativity and competitiveness in the solid-state structures.     

Quantum Chemical Study on the Structural Characteristics and Stability of AlS_n~± Clusters

The geometric configurations and electronic structures of AlSn ±(n = 1~10) clusters were studied by the B3LYP(DFT) method at the 6-311G** level. The changing rules of the ground state structure features, charge transfer and bonding characteristics of the aluminum-sulfur doped clusters were discussed in detail. The ground states of AlSn ±(n 2) are all AlcoreSshell planar or solid double ring structures formed by inserting one Al atom to the Sm and Sn-m(mn) rings at the same time. Their molecular orbitals are mainly composed of Al s- and p-states mixed with S p-states. Finally, the stabilities of AlSn ± clusters have been obtained by analyzing the energy of the ground state structures.     

The Influence of C(sp3)H–Selenium Interactions on the 77Se NMR Quantification of the π-Accepting Properties of Carbenes

Selenium NMR has become a standard tool for scaling the π-accepting character of carbenes. Herein, we highlight that non-classical hydrogen bonding (NCHB), likely resulting from hyperconjugation, can play a significant role in the carbene–selenium ⁷⁷Se NMR chemical shift, thus triggering a non-linear behavior of the Se-Scale.     

Role of Pectin Substances in the Structural Organization of the Flax Fiber–Montmorillonite Hybrid Sorbent

The degree of immobilization of montmorillonite on flax fiber was determined experimentally, and the effect of the nonadditive increase in the sorption capacity of the biocomponent material was evaluated. Studies of pectin–montmorillonite model systems using methods of laser diffraction, X-ray diffraction, and gas adsorption revealed the formation of associate pairs with an equivalent increase in the pectin particle size, a threefold increase in the interlayer distance in the mineral structure, and a superadditive increase in the pore structure parameters. These effects prove formation of hybrid composites with limited intercalation of pectin polymer chains.     

Exploring Caffeine–Phenol Interactions by the Inseparable Duet of Experimental and Theoretical Data

Intermolecular interactions are difficult to model, especially in systems formed by multiple interactions. Such is the case of caffeine–phenol. Structural data has been extracted by using mass-resolved excitation spectroscopy and double resonance techniques. Then the predictions of seven different computational methods have been explored to discover structural and energetic discrepancies between them that may even result in different assignments of the system. The results presented herein highlight the difficulty of constructing functionals to model systems with several competing interactions, and raise awareness of problems with assignments of complex systems with limited experimental information that rely exclusively on energetic data.     

Novel Intermolecular C-H…π Interactions from a One-dimensional Chain:Synthesis and Crystal Structure of a Ladder Dibenzyl Tin Carboxylate

The title ladder organotin carboxylate,{[(C6H5CH2)2Sn]4(p-NH2C6H4-COO)2O2(OCH3)2}·0.5H2O 1,has been synthesized and structurally characterized by elemental analyses,IR and single-crystal X-ray diffraction analysis.Complex 1 is located across on an inversion center and displays a Sn4O4 ladder-like structure with a one-dimensional supramolecular chain through C-H…π interactions.In the asymmetric unit two Sn(Ⅳ) atoms assume similar trigonal bipyramidal coordination geometry.Two aminobenzoate groups coordinate to the terminal Sn(Ⅳ) atoms.The deprotonated methanol molecule bridges two independent Sn(Ⅳ) atoms.A half of lattice water molecule is disorderly filled in the cavity formed by Sn(Ⅳ) complexes.     

Chalcogen Bonding “2S–2N Squares” versus Competing Interactions: Exploring the Recognition Properties of Sulfur

Chalcogen bonding (CB) is the focus of increased attention for its applications in medicinal chemistry, materials science, and crystal engineering. However, the origin of sulfur's recognition properties remains controversial, and experimental evidence for supporting theories is still emerging. Here, a comprehensive evaluation of sulfur CB interactions is presented by investigating 2,1,3-benzothiadiazole X-ray crystallographic structures gathered from the Cambridge Structure Database (CSD), Protein Data Bank (PDB), and own laboratory findings. Through the systematic analysis of substituent effects on a subset library of over thirty benzothiadiazole derivatives, the competing interactions have been categorized into four main classes, namely 2S–2N CB square, halogen bonding (XB), S ⋅⋅⋅ S, and hydrogen-bonding (HB). A geometric model is employed to characterize the 2S–2N CB square motifs and discuss the role of electrostatic, dipole, and orbital contributions toward the interaction.     

Extending the Structures of the p-Sulfonatothiacalix[4]arene Dimers Through Second-sphere Coordination and π…π Stacking Interactions

Reactions of cobalt(II) nitrate or zinc(II) nitrate, tetrasodium p-sulfonatothiacalix[4]arene (Na₄H₄TCAS), and methylviologen dihexafluorophosphate (MV(PF₆)₂) afforded two isomorphous complexes, {[M(H₂O)₆]^2 + [MV]^2 + [(MV)₂M₂(H₂O)₄(H₂TCAS)₂]^4 ? }·14H₂O (M = Co, 1; Zn, 2). In these two complexes, each two thiacalixarenes form a dimer with C _i symmetry through the coordination of sulfonate groups, and the above dimers further extend their structures through second-sphere coordination and π…π stacking interactions into three-dimension nets.     

Direct Catalytic Conversion of Ethanol to C5+ Ketones: Role of Pd–Zn Alloy on Catalytic Activity and Stability

Ethanol can be used as a platform molecule for synthesizing valuable chemicals and fuel precursors. Direct synthesis of C₅₊ ketones, building blocks for lubricants and hydrocarbon fuels, from ethanol was achieved over a stable Pd-promoted ZnO-ZrO₂ catalyst. The sequence of reaction steps involved in the C₅₊ ketone formation from ethanol was determined. The key reaction steps were found to be the in situ generation of the acetone intermediate and the cross-aldol condensation between the reaction intermediates acetaldehyde and acetone. The formation of a Pd–Zn alloy in situ was identified to be the critical factor in maintaining high yield to the C₅₊ ketones and the stability of the catalyst. A yield of >70 % to C₅₊ ketones was achieved over a 0.1 % Pd-ZnO-ZrO₂ mixed oxide catalyst, and the catalyst was demonstrated to be stable beyond 2000 hours on stream without any catalyst deactivation.     

Infrared study of NH…π hydrogen bonding. N-tert-butylformamide - aromatic donor systems

The present paper reports the results of an infrared study in the region of the fundamental NH stretching vibration for the twelve N-tert-butylformamide - aromatic hydrocarbon systems. The thermodynamic properties for 1:1 NtBFA - aromatic donor complexes are given. The contribution of the charge transfer mechanism to the hydrogen bonding in the studied systems is considered. The experimental and the calculated intermolecular transition moments are compared and the best agreement is obtained for 2.65 Å hydrogen bond length.     

Origin of the Aggregation-Induced Phosphorescence of Platinum(II) Complexes: The Role of Metal–Metal Interactions on Emission Decay in the Crystalline State

Discerning the origins of the phosphorescent aggregation-induced emission (AIE) from Pt(II) complexes is crucial for developing the broader range of photo-functional materials. Over the past few decades, several mechanisms of phosphorescent AIE have been proposed, however, not have been directly elucidated. Herein, we describe phosphorescence and deactivation processes of four class of AIE active Pt(II) complexes in the crystalline state based on experimental and theoretical investigation. These complexes show metal-to-ligand and/or metal−metal-to-ligand charge transfer emission in crystalline state with different heat resistance against thermal emission quenching. The calculated energy profiles including the minimum energy crossing point between S₀ and T₁ states were consistent with the heat resistant properties, which provided the mechanism for AIE expression. Furthermore, we have clarified the role of metal-metal interaction in AIE by comparing two computational models.     

Recent strategic advances for the activation of benzylic C–H bonds for the formation of C–C bonds

Alkylarenes, obtained from abundant hydrocarbon feedstock sources, are an attractive starting material for the formation of complex molecular architectures. Conventional activation strategies of the relatively inert sp³-hybridized benzylic C–H bonds usually require relatively harsh conditions and are difficult to apply to the synthesis of fine chemicals. The present review describes recent strategic advances for the activation of benzylic C–H bonds for the catalytic formation of C–C bonds. In particular, two activation methods, i.e., strategies that generate benzylic radicals or benzyl anions, are discussed.     

Mini-review on the functionalization of C–H bond to C-X linkage via metalla-electrocatalyzed tool

To date, the C–H activation protocol and its functionalization of bonds via transition metal have witnessed major attention in coordination chemistry as they eliminate the pre-functionalization of the substrate. Conventional approaches use a stoichiometric amount of chemical oxidants which are toxic under mild conditions. This will create a major problem in C–H functionalization reactions that involve a selective issue of reductive elimination from metal center to form a significant amount of by-product (waste) in large amount which is difficult to separate and thus reduce atom economy and sustainability of the reaction medium. This will limit catalyst turnover and thus, decreases the reaction rate. To avoid this, there is an urgent need for renewable resources which bring about the functionalization of the C–H bond. Metalla-electro catalyzed is the cleanest tool on the platform of C–H activation chemistry. Here, electricity was being involved as a clean surrogate of chemical oxidant and holds unleashed potential for an oxidative protocol of C–H activation with unmet site selectivity. This mini-review pay attention to the C–H functionalization of the bond to C–C, C–N, and C-Miscellaneous (P, O, and S) bond linkage by employing different transition metal {precious (Pd, Rh, Ru, and Ir)} and {earth-abundant (Mn, Ni, Co, and Cu)} using the electrochemical tool. Such metalla-electro catalyzed tools are helpful to those who were not being trained electrochemists but can unleash this potential benefit in various sustainable organic transformations.     

Importance of aliphatic C–H hydrogen bonding on anion recognition

We have designed and synthesised new anion receptors 1 and 2, both of their C–H groups were at the α positions to carbonyl groups and further polarised by the attached polarising substituents. This enabled us to study hydrogen bonding donor ability of C–H bonds. The polarising substituents are electron withdrawing cyano group for host 1, while charged pyridinium group for host 2. As expected from charge effects, host 2 shows roughly an order of magnitude higher binding constants against various anion guests than those of receptor 1. Since the magnitude of polarisation change should be greatest for C–H group among various hydrogen bonding groups, this indicates the importance of C–H hydrogen bonding. In contrast, the relative order of binding constants was the same for both host 1 and 2. The order of association constants was found to be (CH₃)₂POO^? > CH₃COO^? > C₆H₅COO^? > Cl^? > Br^?. DFT calculation results were in good agreement with experimental binding constants and confirmed the importance of charged group substitution. In addition, receptor 1 showed the highest association constant for dimethyl phosphinate, which is implicated in many metabolic diseases.     

Vibrational phase relaxation of O–H stretch in bulk water: Role of large amplitude angular jumps and negative cross-correlations among the forces on the O–H bond

The ultrafast vibrational phase relaxation of O–H stretch in bulk water is investigated in molecular dynamics simulations. The dephasing time (T₂) of the O–H stretch in bulk water calculated from the frequency fluctuation time correlation function (C_ω(t)) is in the range of 70–80 femtosecond (fs), which is comparable to the characteristic timescale obtained from the vibrational echo peak shift measurements using infrared photon echo [W.P. de Boeij, M.S. Pshenichnikov, D.A. Wiersma, Ann. Rev. Phys. Chem. 49 (1998) 99]. The ultrafast decay of C_ω(t) is found to be responsible for the ultrashort T₂ in bulk water. Careful analysis reveals the following two interesting reasons for the ultrafast decay of C_ω(t). (A) The large amplitude angular jumps of water molecules (within 30–40 fs time duration) provide a large scale contribution to the mean square vibrational frequency fluctuation and gives rise to the rapid spectral diffusion on 100 fs time scale. (B) The projected force, due to all the atoms of the solvent molecules on the oxygen (F_O(t)) and hydrogen (F_H(t)) atom of the O–H bond exhibit a large negative cross-correlation (NCC). We further find that this NCC is partly responsible for a weak, non-Arrhenius temperature dependence of the dephasing rate.     

Disruptive influence of the host cage C60 on the guest He–H+ bond and bonding in H3+

Although a helium atom prefers to stay at the centre of a fullerene (C₆₀) cage and a proton binds with one of the carbon atoms from inside, DFT(MN15)/cc-pVTZ and DLPNO-MP2/def2-TZVP calculations show that the helium atom and the proton in HeH⁺ prefer to stay away from the centre of the cage, weakening the He–H⁺ covalent bond considerably. Both the helium atom and the proton exhibit noncovalent interactions with the carbon atoms of two pentagons at the opposite ends of the fullerene cage. Our calculations also show that a linear arrangement of H₃⁺ (inside C₆₀), pointing towards the centres of two pentagons opposite to each other, with the proton breaking away from H_2, is energetically more favored over the equilateral triangle geometry of free H₃⁺.