C−H···X Hydrogen Bonds of Acetylene, Ethylene, and Ethane with First- and Second-Row Hydrides

Molecular Mechanisms behind Acetylene Adsorption and Selectivity in Functional Porous Materials

Since its first industrial production in 1890s, acetylene has played a vital role in manufacturing a wide spectrum of materials. Although current methods and infrastructures for various segments of acetylene industries are well-established, with emerging functional porous materials that enabled desired selectivity toward target molecules, it is of timely interest to develop new efficient technologies to promote safer acetylene processes with a higher energy efficiency and lower carbon footprint. In this Minireview, we, from the perspective of materials chemistry, review state-of-the-art examples of advanced porous materials, namely metal-organic frameworks and decorated zeolites, that have been applied to the purification and storage of acetylene. We also discuss the challenges on the roadmap of translational research in the development of new solid sorbent-based separation technologies and highlight areas which require future research efforts.

Amino-Functionalised Hybrid Ultramicroporous Materials that Enable Single-Step Ethylene Purification from a Ternary Mixture

Pyrazine-linked hybrid ultramicroporous (pore size <7 Å) materials (HUMs) offer benchmark performance for trace carbon capture thanks to strong selectivity for CO2 over small gas molecules, including light hydrocarbons. That the prototypal pyrazine-linked HUMs are amenable to crystal engineering has enabled second generation HUMs to supersede the performance of the parent HUM, SIFSIX-3-Zn, mainly through substitution of the metal and/or the inorganic pillar. Herein, we report that two isostructural aminopyrazine-linked HUMs, MFSIX-17-Ni (17=aminopyrazine; M=Si, Ti), which we had anticipated would offer even stronger affinity for CO2 than their pyrazine analogs, unexpectedly exhibit reduced CO2 affinity but enhanced C2 H2 affinity. MFSIX-17-Ni are consequently the first physisorbents that enable single-step production of polymer-grade ethylene (>99.95 % for SIFSIX-17-Ni) from a ternary equimolar mixture of ethylene, acetylene and CO2 thanks to coadsorption of the latter two gases. We attribute this performance to the very different binding sites in MFSIX-17-Ni versus SIFSIX-3-Zn.

Theoretical insight into the hybridization effect of donor and acceptor atoms on the cooperativity of C-H···N hydrogen bonds

In the present work, the influence of hybridization on cooperativity between C-H···N hydrogen bonds is theoretically investigated. Here, C₂H₆, C₂H₄, and C₂H₂ are considered as hydrogen bonding donor while NH₃, N₂H₄, N₂H₂, and N₂ act as the hydrogen bonding acceptor. The calculations are performed at MP2/aug-cc-pVTZ level. It is observed that the stability of systems is amplified as C(sp) > C(sp²) > C(sp³) and also N(sp³) > N(sp²) > N(sp). The role of interaction and deformation energies on the stability of the systems is examined. The results indicate the contribution of interaction energy is dominant in all complexes. The strength of C-H···N hydrogen bond is estimated using interaction energy. In agreement with cooperative energies, the C-H···N hydrogen bond is respectively weakened/strengthened in the triads containing C(sp) and C(sp²)/C(sp³) where two hydrogen bonds coexist. On the other hand, the C-H···N hydrogen bond is strengthened in the ternary systems including N(sp³) and N(sp²) while an opposite behavior is obtained in the triad having N(sp).

Spectroscopic and Theoretical Study of Spin-Dependent Electron Transfer in an Iron(III) Superoxo Complex

It was shown previously (J. Am. Chem. Soc. 2014, 136, 10846) that bubbling of O2 into a solution of Fe(II)(BDPP) (H2BDPP = 2,6-bis[[(S)-2-(diphenylhydroxymethyl)-1-pyrrolidinyl]methyl]pyridine) in tetrahydrofuran at -80 °C generates a high-spin (SFe = (5)/2) iron(III) superoxo adduct, 1. Mössbauer studies revealed that 1 is an exchange-coupled system, [Formula: see text], where SR = (1)/2 is the spin of the superoxo radical, of which the spectra were not well enough resolved to determine whether the coupling was ferromagnetic (S = 3 ground state) or antiferromagnetic (S = 2). The glass-forming 2-methyltetrahydrofuran solvent yields highly resolved Mössbauer spectra from which the following data have been extracted: (i) the ground state of 1 has S = 3 (J < 0); (ii) |J| > 15 cm(-1); (iii) the zero-field-splitting parameters are D = -1.1 cm(-1) and E/D = 0.02; (iv) the major component of the electric-field-gradient tensor is tilted ≈7° relative to the easy axis of magnetization determined by the MS = ±3 and ±2 doublets. The excited-state MS = ±2 doublet yields a narrow parallel-mode electron paramagnetic resonance signal at g = 8.03, which was used to probe the magnetic hyperfine splitting of (17)O-enriched O2. A theoretical model that considers spin-dependent electron transfer for the cases where the doubly occupied π* orbital of the superoxo ligand is either "in" or "out" of the plane defined by the bent Fe-OO moiety correctly predicts that 1 has an S = 3 ground state, in contrast to the density functional theory calculations for 1, which give a ground state with both the wrong spin and orbital configuration. This failure has been traced to a basis set superposition error in the interactions between the superoxo moiety and the adjacent five-membered rings of the BDPP ligand and signals a fundamental problem in the quantum chemistry of O2 activation.

Cerium-based M4L4 tetrahedra as molecular flasks for selective reaction prompting and luminescent reaction tracing

The application of metal-organic polyhedra as "molecular flasks" has precipitated a surge of interest in the reactivity and property of molecules within well-defined spaces. Inspired by the structures of the natural enzymatic pockets, three metal-organic neutral molecular tetrahedral, Ce-TTS, Ce-TNS and Ce-TBS (H6TTS: N',N'',N'''-nitrilotris-4,4',4''-(2-hydroxybenzylidene)-benzohydrazide; H6TNS: N',N'',N'''-nitrilotris-6,6',6''-(2-hydroxybenzylidene)-2-naphthohydrazide; H6TBS: 1,3,5-phenyltris-4,4',4''-(2-hydroxybenzylidene)benzohydrazide), which exhibit different size of the edges and cavities, were achieved through self-assembly by incorporating robust amide-containing tridentate chelating sites into the fragments of the ligands. They acted as molecular flasks to prompt the cyanosilylation of aldehydes with excellent selectivity towards the substrates size. The amide groups worked as trigger sites and catalytic driven forces to achieve efficient guest interactions, enforcing the substrates proximity within the cavity. Experiments on catalysts with the different cavity radii and substrates with the different molecular size demonstrated that the catalytic performance exhibited enzymatical catalytic mechanism and occurred in the molecular flask. These amides were also able to amplify guest-bonding events into the measurable outputs for the detection of concentration variations of the substrates, providing the possibility for metal-organic hosts to work as smart molecular flasks for the luminescent tracing of catalytic reactions.

Non linear optical analyses of hexamine: phenol cocrystals based on hydrogen bonding: a comparative study

Fourier-Transform Infrared (FT-IR) spectroscopy supported by Raman spectroscopy has been employed to explain the conventional and unconventional hydrogen bonding present in the 4,4'thiodiphenol: hexamine and 4,4'sulfonyldiphenol: hexamine cocrystals. The possible internal and external vibrational modes are predicted through factor group analysis. Influence of intra molecular charge transfer (ICT) interaction caused by the strong ionic ground state hydrogen bonding between charged species, giving rise to a non centro symmetric structure which is a criterion for second harmonic generation (SHG) efficiency has been discussed. Intense low wave number hydrogen bond vibrations in Raman which arise due to electron-phonon coupling are analyzed. Optical quality of adducts is identified through UV-Vis analysis. The second harmonic generation efficiency of both adducts is determined by Kurtz-Perry method.

Stereospecificity of (1) H, (13) C and (15) N shielding constants in the isomers of methylglyoxal bisdimethylhydrazone: problem with configurational assignment based on (1) H chemical shifts

In the (13) C NMR spectra of methylglyoxal bisdimethylhydrazone, the (13) C-5 signal is shifted to higher frequencies, while the (13) C-6 signal is shifted to lower frequencies on going from the EE to ZE isomer following the trend found previously. Surprisingly, the (1) H-6 chemical shift and (1) J(C-6,H-6) coupling constant are noticeably larger in the ZE isomer than in the EE isomer, although the configuration around the -CH═N- bond does not change. This paradox can be rationalized by the C-H⋯N intramolecular hydrogen bond in the ZE isomer, which is found from the quantum-chemical calculations including Bader's quantum theory of atoms in molecules analysis. This hydrogen bond results in the increase of δ((1) H-6) and (1) J(C-6,H-6) parameters. The effect of the C-H⋯N hydrogen bond on the (1) H shielding and one-bond (13) C-(1) H coupling complicates the configurational assignment of the considered compound because of these spectral parameters. The (1) H, (13) C and (15) N chemical shifts of the 2- and 8-(CH(3) )(2) N groups attached to the -C(CH(3) )═N- and -CH═N- moieties, respectively, reveal pronounced difference. The ab initio calculations show that the 8-(CH(3) )(2) N group conjugate effectively with the π-framework, and the 2-(CH(3) )(2) N group twisted out from the plane of the backbone and loses conjugation. As a result, the degree of charge transfer from the N-2- and N-8- nitrogen lone pairs to the π-framework varies, which affects the (1) H, (13) C and (15) N shieldings.

On the Structure and Geometry of Biomolecular Binding Motifs (Hydrogen-Bonding, Stacking, X-H···π): WFT and DFT Calculations

The strengths of noncovalent interactions are generally very sensitive to a number of geometric parameters. Among the most important of these parameters is the separation between the interacting moieties (in the case of an intermolecular interaction, this would be the intermolecular separation). Most works seeking to characterize the properties of intermolecular interactions are mainly concerned with binding energies obtained at the potential energy minimum (as determined at some particular level of theory). In this work, in order to extend our understanding of these types of noncovalent interactions, we investigate the distance dependence of several types of intermolecular interactions, these are hydrogen bonds, stacking interactions, dispersion interactions, and X-H···π interactions. There are several methods that have traditionally been used to treat noncovalent interactions as well as many new methods that have emerged within the past three or four years. Here we obtain reference data using estimated CCSD(T) values at the complete basis set limit (using the CBS(T) method); potential energy curves are also produced using several other methods thought to be accurate for intermolecular interactions, these are MP2/cc-pVTZ, MP2/aug-cc-pVDZ, MP2/6-31G*(0.25), SCS(MI)-MP2/cc-pVTZ, estimated MP2.5/CBS, DFT-SAPT/aug-cc-pVTZ, DFT/M06-2X/6-311+G(2df,2p), and DFT-D/TPSS/6-311++G(3df,3pd). The basis set superposition error is systematically considered throughout the study. It is found that the MP2.5 and DFT-SAPT methods, which are both quite computationally intensive, produce potential energy curves that are in very good agreement to those of the reference method. Among the MP2 techniques, which can be said to be of medium computational expense, the best results are obtained with MP2/cc-pVTZ and SCS(MI)-MP2/cc-pVTZ. DFT-D/TPSS/6-311++G(3df,3pd) is the DFT-based method that can be said to give the most well-balanced description of intermolecular interactions.

On the importance of ribose orientation in the substrate activation of the coenzyme B12-dependent mutases

The degree to which the corrin ring portion of coenzyme B(12) can facilitate the H-atom-abstraction step in the glutamate mutase (GM)-catalyzed reaction of (S)-glutamate has been investigated with density functional theory. The crystal structure of GM identifies two possible orientations of the ribose portion of coenzyme B(12). In one orientation (A), the OH groups of the ribose extend away from the corrin ring, whereas in the other orientation (B) the OH groups, especially that involving O3', are instead directed towards the corrin ring. Our calculations identify a sizable stabilization amounting to about 30 kJ mol(-1) in the transition structure (TS) complex corresponding to orientation B (TS(B)CorIm). In the TS complex where the ribose instead is positioned in orientation A, no such effect is manifested. The observed stabilization in TS(B)CorIm appears to be the result of favorable interactions involving O3' and the corrin ring, including a C-HO hydrogen bond. We find that the degree of stabilization is not particularly sensitive to the Co-C distance. Our calculations show that any potential stabilization afforded to the H-atom-abstraction step by coenzyme B(12) is sensitive to the orientation of the ribose moiety.

Bis(terpyridine)-based surface template structures on graphite: a force field and DFT study

Host-guest networks formed by ordered organic layers are promising candidates for applications in molecular storage and quantum computing. We have studied 2-dimensionally ordered surface template structures of bis(terpyridine)-derived molecules (BTPs) on graphite using force field and DFT methods and compared the results to recent experimental observations. In order to determine the force field best suited for surface calculations, bond lengths and angles, torsional potentials, adsorption and stacking energies of smaller aromatic molecules were calculated with different force fields (Compass, UFF, Dreiding and CVFF). Density functional perturbation theory calculations were used to study the intermolecular interactions between 3,3'-BTP molecules. Structural properties, adsorption energies and rotational barriers of the 3,3'-BTP surface structure and its host-guest systems with phthalocyanine (PcH(2)) or excess 3,3'-BTP as guest molecules have been addressed. In addition, STM images of oligopyridine and phthalocyanine molecules were simulated based on periodic and local density functional theory calculations.

C-H...N and C-H...O intramolecular hydrogen bonding effects in the 1H, 13C and 15N NMR spectra of the configurational isomers of 1-vinylpyrrole-2-carbaldehyde oxime substantiated by DFT calculations

According to the (1)H, (13)C and (15)N NMR spectroscopic data and DFT calculations, the E-isomer of 1-vinylpyrrole-2-carbaldehyde adopts preferable conformation with the anti-orientation of the vinyl group relative to the carbaldehyde oxime group and with the syn-arrangement of the carbaldehyde oxime group with reference to the pyrrole ring. This conformation is stabilized by the C-H...N intramolecular hydrogen bond between the alpha-hydrogen of the vinyl group and the oxime group nitrogen, which causes a pronounced high-frequency shift of the alpha-hydrogen signal in (1)H NMR (approximately 0.5 ppm) and an increase in the corresponding one-bond (13)C-(1)H coupling constant (ca 4 Hz). In the Z-isomer, the carbaldehyde oxime group turns to the anti-position with respect to the pyrrole ring. The C-H...O intramolecular hydrogen bond between the H-3 hydrogen of the pyrrole ring and the oxime group oxygen is realized in this case. Due to such hydrogen bonding, the H-3 hydrogen resonance is shifted to a higher frequency by about 1 ppm and the one-bond (13)C-(1)H coupling constant for this proton increases by approximately 5 Hz.

Prediction of partition coefficients by multiscale hybrid atomic-level/coarse-grain simulations

Coarse-grain models are becoming an increasingly important tool in computer simulations of a wide variety of molecular processes. In many instances it is, however, desirable to describe key portions of a molecular system at the atomic level. There is therefore a strong interest in the development of simulation methodologies that allow representations of matter with mixed granularities in a multiscale fashion. We report here a strategy to conduct mixed atomic-level and coarse-grain simulations of molecular systems with a recently developed coarse-grain model. The methodology is validated by computing partition coefficients of small molecules described in atomic detail and solvated by water or octane, both of which are represented by coarse-grain models. Because the present coarse-grain force field retains electrostatic interactions, the simplified solvent particles can interact realistically with the all-atom solutes. The partition coefficients computed by this approach rival the accuracy of fully atomistic simulations and are obtained at a fraction of their computational cost. The present methodology is simple, robust and applicable to a wide variety of molecular systems.

Strength of Calpha-H...O=C hydrogen bonds in transmembrane proteins

A large number of Calpha-H...O contacts are present in transmembrane protein structures, but contribution of such interactions to protein stability is still not well understood. According to previous ab initio quantum calculations, the stabilization energy of a Calpha-H...O contact is about 2-3 kcal/mol. However, experimental studies on two different Calpha-H...O hydrogen bonds present in transmembrane proteins lead to conclusions that one contact is only weakly stabilizing and the other is not even stabilizing. We note that most previous computational studies were on optimized geometries of isolated molecules, but the experimental measurements were on those in the structural context of transmembrane proteins. In the present study, 263 Calpha-H...O=C contacts in alpha-helical transmembrane proteins were extracted from X-ray crystal structures, and interaction energies were calculated with quantum mechanical methods. The average stabilization energy of a Calpha-H...O=C interaction was computed to be 1.4 kcal/mol. About 13% of contacts were stabilizing by more than 3 kcal/mol, and about 11% were destabilizing. Analysis of the relationships between energy and structure revealed four interaction patterns: three types of attractive cases in which additional Calpha-H...O or N-H...O contact is present and a type of repulsive case in which repulsion between two carbonyl oxygen atoms occur. Contribution of Calpha-H...O=C contacts to protein stability is roughly estimated to be greater than 5 kcal/mol per helix pair for about 16% of transmembrane helices but for only 3% of soluble protein helices. The contribution would be larger if Calpha-H...O contacts involving side chain oxygen were also considered.

Gas-phase basicities of polyfunctional molecules. Part 1: Theory and methods

The experimental and theoretical methods of determination of gas-phase basicities, proton affinities and protonation entropies are presented in a tutorial form. Particularities and limitations of these methods when applied to polyfunctional molecules are emphasized. Structural effects during the protonation process in the gas-phase and their consequences on the corresponding thermochemistry are reviewed and classified. The role of the nature of the basic site (protonation on non-bonded electron pairs or on pi-electron systems) and of substituent effects (electrostatic and resonance) are first examined. Then, linear correlations observed between gas-phase basicities and ionization energies or substituent constants are recalled. Hydrogen bonding plays a special part in proton transfer reactions and in the protonation characteristics of polyfunctional molecules. A survey of the main properties of intermolecular and intramolecular hydrogen bonding in both neutral and protonated species is proposed. Consequences on the protonation thermochemistry, particularly of polyfunctional molecules are discussed. Finally, chemical reactions which may potentially occur inside protonated clusters during the measurement of gas-phase basicities or inside a protonated polyfunctional molecule is examined. Examples of bond dissociations with hydride or alkyl migrations, proton transport catalysis, tautomerization, cyclization, ring opening and nucleophilic substitution are presented to illustrate the potentially complex chemistry that may accompany the protonation of polyfunctional molecules.

Assembly of lipids and proteins into lipoprotein particles

The self-assembly of reconstituted discoidal high-density lipoproteins, known as nanodiscs, was studied using coarse-grained molecular dynamics and small-angle X-ray scattering. In humans, high-density lipoprotein particles transport cholesterol in the blood and facilitate the removal of excess cholesterol from the body. Native high-density lipoprotein exhibits a wide variety of shapes and sizes, forming lipid-free/poor, nascent discoidal, and mature spherical particles. Little is known about how these lipoprotein particles assemble and transform from one state to another. Multiple 10 micros coarse-grained simulations reveal the assembly of discoidal high-density lipoprotein particles from disordered protein-lipid complexes. Small-angle X-ray scattering patterns were calculated from the final assembled structures and compared with experimental measurements carried out for this study to verify the accuracy of the coarse-grained simulations. Results show that hydrophobic interactions assemble, within several microseconds, the amphipathic helical proteins and lipids into roughly discoidal particles, while the proteins assume a final approximate double-belt configuration on a slower time scale.

The bilayer-vesicle transition is entropy driven

Self-assembled bilayer membranes have a remarkable inclination to form closed shells or vesicles. This bilayer-vesicle transition has been shown experimentally and by various kinds of computer simulation techniques. Here we study this transition using coarse-grained molecular dynamics. The advantage of this simulation technique is that it allows for a detailed analysis of the transition, such as changes of the internal energy. Generally it is assumed that the bilayer-vesicle transition is driven by minimization of the edge energy. However, our simulations, which include solvent particles, show an increase in the potential energy of the system during the transition, implicating that the transition is not energy but entropy driven.