Hydrogen-bonding Modes Research Articles

Azocarboxamide-enabled enantioselective regiodivergent unsymmetrical 1,2-diaminations

Enantioenriched unsymmetrical vicinal diamines are important basic structural motifs. While catalytic asymmetric intermolecular 1,2-diamination of carbon–carbon double bonds represents the most straightforward approach for preparing enantioenriched vicinal-diamine-containing heterocycles, these reactions are often limited to the installation of undifferentiated amino functionalities through metal catalysis and/or the use of stoichiometric amounts of oxidants. Here, we report organocatalytic enantioselective unsymmetrical 1,2-diaminations based on the rational design of a bifunctional 1,2-diamination reagent, namely, azocarboxamides (ACAs). Under the catalysis of chiral phosphoric acid, unsymmetrical 1,2-diaminations of ACAs with various electron-rich double bonds readily occur in a regiodivergent manner. Indoles prefer dual hydrogen-bonding mode to give dearomative (4 + 2) products, and 3-vinylindoles and azlactones are inclined to undergo unsymmetrical 1,2-diamination via the (3 + 2) process. DFT calculations are performed to reveal the reaction mechanism and the origin of the regio- and enantioselectivity. Guided by computational design, we are able to reverse the regioselectivity of the dearomative unsymmetrical 1,2-diamination of indoles using Lewis acid catalysis.

Molecular dynamics simulation of nanocellulose and cement matrix composites

The interfacial properties of nanocellulose and cement matrix are the key factors affecting the mechanical properties of composite materials. However, it is challenging to study the interface combination through conventional experiments and microscopic characterization techniques. Molecular dynamics simulation (MD), as a nanoscale analytical method, can be used to calculate and analyze the strength, deformation, destruction and interfacial interaction of materials on the atomic scale. Since the existing methods of C-S-H modeling and fiber pull-out from the matrix in molecular dynamics simulations were not suitable for cellulose/C-S-H composite models. In this paper, a molecular dynamics simulation method for nanocellulose cement matrix composites was proposed. Based on the embedded composite model, the tensile stress-strain, interfacial interaction energy, hydrogen bond, and interface failure mode were studied when cellulose was pulled out of the matrix. The results showed that adding cellulose could improve the local ductility and tensile strength of cement matrix materials. The interfacial interaction energy between cellulose and C-S-H was approximately −1.09 J/m2, which was much higher than that between carbon nanotubes and C-S-H. Cellulose would adsorb hydrogen and oxygen atoms on H2O, OH− and silica tetrahedron in C-S-H. In the pull-out simulation of cellulose in C-S-H, C-S-H on the surface of cellulose would be destroyed and attached to the cellulose surface and moved along with it, indicating that cellulose could play a good bridging role in the matrix. The simulation results revealed the action mechanism of cellulose in cement matrix materials.

Renewed spectroscopic and theoretical research of hydrogen bonding in ascorbic acid

The studies of two isomers of ascorbic acid and their deuteroanalogues, presented in the paper, have been accomplished by vibrational spectroscopy methods and quantum-chemical simulations. The spectroscopic research of L-ascorbic and D-isoascorbic acids have been carried out by the infrared (IR) and Raman (R) techniques. On the basis of the obtained results the spectral interpretation of the hydrogen bonded groups of ascorbic acids has been performed. Car-Parrinello Molecular Dynamics (CPMD) and Density Functional Theory (DFT) have been employed to support spectroscopic experimental findings and shed light onto the bridged proton dynamics in the L- and D- isomers of ascorbic acids. The accurate assignments of the hydrogen bond modes have been accomplished with the application of deuterosubstitution, CPMD-solid state simulations and Potential Energy Distribution (PED) analysis. The spectral and structural results have shown that dependency ν(OH) = f(γ(OH)) is the most common for the OHO hydrogen bond, whereas dependency d(OO) = f(γ(OH)) differs as for the ionic and resonance assisted hydrogen bonds.

A molecular insight into the development of sensitive glucometers along with DFT investigation of glucose adsorption by a beryllium oxide particle

A molecular insight into the sensitive glucometers along with examining the adsorption of glucose (GLU) with the assistance of a representative beryllium-oxide (BeO)-particle (BOP) was provided in this work. Quantum density functional theory (DFT) calculations were performed for optimizing the models and obtaining their required information. The results indicated the possibility of formations of six interacting configurations of GLU@BOP complexes, I - VI, with the existence of H⋯O and O⋯Be interactions from GLU to BOP, with a detected mode of non-classical hydrogen bond in two of the complexes. The results of interaction strengths and frontier molecular orbitals variations indicated possibilities of formations of reasonable complexes. The existence of non-covalent physical interactions helped approach a recovery time for employing the BOP in a re-adsorption process besides indicating different conductance levels. Consequently, the models of GLU@BOP complexes were found suitable for working in a sensitive adoption of GLU for developing sensitive glucometers.

Molecular soldered COF membrane with crystalline-amorphous heterointerface for fast organic solvent nanofiltration

Covalent organic frameworks (COFs) featuring high porosity and well-defined pore structures are attractive candidates for organic solvent nanofiltration (OSN). However, preparing defect-free COF membrane and manipulating pore size for precise molecular separation in OSN remains a significant challenge. Herein, we address this challenge by developing composite membranes through molecular soldering a benzimidazole-linked polymer (BILP-101x) onto a continuous ACOF-1 membrane. The shared monomer of ACOF-1 and BILP-101x promotes good compatibility, allowing the amorphous BILP-101x chemically stitch the grain boundary defects of the crystalline ACOF-1 layer and create narrow, staggered pores at the interface, thereby enhancing the OSN performance. Non-equilibrium molecular dynamics simulations were employed to reproduce and explain the permeability order of the solvents and dyes, revealing a hydrogen-bond cluster permeation mode for alcohols. Furthermore, the optimized BILP-101x/ACOF-1 composite membrane exhibits excellent ethanol permeance (13.2 ​L ​m−2 ​h−1 bar−1) and outstanding rejection towards various dye molecules, together with desirable and stable OSN performance under continuous filtration operation. This work opens a new avenue for improving the separation performance of continuous COF membranes in OSN applications.

Intermolecular hydrogen bonding behavior of amino acid radical cations.

Amino acid and peptide radicals are of broad interest due to their roles in biochemical oxidative damage, pathogenesis and protein radical catalysis, among others. Using density functional theory (DFT) calculations at the ωB97X-D/def2-QZVPPD//ωB97X-D/def2-TZVPP level of theory, we systematically investigated the hydrogen bonding between water and fourteen α-amino acids (Ala, Asn, Cys, Gln, Gly, His, Met, Phe, Pro, Sel, Ser, Thr, Trp, and Tyr) in both neutral and radical cation forms. For all amino acids surveyed, stronger hydrogen-bonding interactions with water were observed upon single-electron oxidation, with the greatest increases in hydrogen-bonding strength occurring in Gly, Ala and His. We demonstrate that the side chain has a significant impact on the most favorable hydrogen-bonding modes experienced by amino acid radical cations. Our computations also explored the fragmentation of amino acid radical cations through the loss of a COOH radical facilitated by hydrogen bonding. The most favorable pathways provided stabilization of the resulting cationic fragments through hydrogen bonding, resulting in more favorable thermodynamics for the fragmentation process. These results indicate that non-covalent interactions with the environment have a profound impact on the structure and chemical fate of oxidized amino acids.

How Ligands Interact with the Kinase Hinge.

ATP-competitive kinase inhibitors form hydrogen bond interactions with the kinase hinge region at the adenine binding site. Thus, it is crucial to explore hinge-ligand recognition as part of a rational drug design strategy. Here, harnessing known ligand-bound kinase structures and experimental assay resources, we first created a kinase structure-assay database (KSAD) containing 2705 nM ligand-bound kinase complexes. Then, using KSAD, we systematically investigate hinge-ligand binding patterns using interaction fingerprints, thereby delineating 15 different hydrogen-bond interaction modes. We believe these results will be valuable for de novo drug design and/or scaffold hopping of kinase-targeted drugs.

Main Group Molecular Switches with Swivel Bifurcated to Trifurcated Hydrogen Bond Mode of Action.

Artificial molecular machines have captured the full attention of the scientific community since Jean-Pierre Sauvage, Fraser Stoddart, and Ben Feringa were awarded the 2016 Nobel Prize in Chemistry. The past and current developments in molecular machinery (rotaxanes, rotors, and switches) primarily rely on organic-based compounds as molecular building blocks for their assembly and future development. In contrast, the main group chemical space has not been traditionally part of the molecular machine domain. The oxidation states and valency ranges within the p-block provide a tremendous wealth of structures with various chemical properties. Such chemical diversity─when implemented in molecular machines─could become a transformative force in the field. Within this context, we have rationally designed a series of NH-bridged acyclic dimeric cyclodiphosphazane species, [(μ-NH){PE(μ-NtBu)2PE(NHtBu)}2] (E = O and S), bis-PV2N2, displaying bimodal bifurcated R21(8) and trifurcated R31(8,8) hydrogen bonding motifs. The reported species reversibly switch their topological arrangement in the presence and absence of anions. Our results underscore these species as versatile building blocks for molecular machines and switches, as well as supramolecular chemistry and crystal engineering based on cyclophosphazane frameworks.

Visible-Light Organophotoredox-Mediated [3 + 2] Cycloaddition of Arylcyclopropylamine with Structurally Diverse Olefins for the Construction of Cyclopentylamines and Spiro[4.n] Skeletons.

We developed a visible-light-mediated [3 + 2] cycloaddition of arylcyclopropylamine with structurally diverse olefins using QXPT-NPh as a highly efficient organic photoredox catalyst. We first achieved the use of various alkyl-substituted alkenes in intermolecular [3 + 2] cycloadditions with cyclopropylamine. We also developed a general and efficient strategy for the construction of structurally diverse cyclopentane-based spiro[4.n] skeletons with 1,3-difunctional groups, which broadly exist in natural products and synthetic molecules. Furthermore, we proposed a hydrogen-bond mode between the arylcyclopropylamine and the photocatalyst QXPT-NPh.

Trimethylamine Probes Isolated Silicon Dangling Bonds and Surface Hydroxyls of (H,OH)-Si(001)

To better understand why amines catalyze the reactivity of SiOH with silanes, we examined the adsorption of trimethylamine under a low pressure (10–9–10–8 mbar) and a low temperature (105–160 K) on water-terminated (H,OH)-Si(001), which is both a model surface for adsorption studies and a promising starting substrate for atomic layer deposition. Trimethylamine bonding configurations were determined by combining real-time synchrotron radiation X-ray photoelectron spectroscopy (XPS) and high-resolution electron energy loss spectroscopy (HREELS) with density functional theory (DFT) calculations of core-level ionization energies and vibrational spectra. Both spectroscopies showed that the majority of species are trimethylamine molecules making acceptor H bonds with surface hydroxyls. Moreover, HREELS indicated that the hydrogen-bonding modes (single and double hydrogen acceptor bonds) depend on temperature and/or coverage, which may in turn affect the weakening of the O–H bond, and hence the catalytic effects of trimethylamine. XPS also clearly detected a minority species, trimethylamine, datively bonded to the isolated silicon dangling bonds (a few 1/100th of a monolayer). This species is prone to breaking, and a detailed analysis of the reaction products was made. The reactivity of the electrically active isolated silicon dangling bonds with the amine may impact the Fermi-level position in the gap.

Modulating the Structures and Magnetic Properties of Dy(III) Single-Molecule Magnets through Acid-Base Regulation.

Chemical modulation on the structures and physical properties of the coordination complexes is of great interest for the preparation of new functional materials. By changing the acidity or basicity of the reaction medium, the deprotonation degree of a multidentate ligand with multiple active protons, H4daps (H4daps = N',N'″-((1E,1'E)-pyridine-2,6-diylbis(ethan-1-yl-1-ylidene))bis(2-hydroxybenzohydrazide)), can be regulated on purpose. With this ligand of different deprotonation and charges, three new DyIII complexes ([Dy(H3daps)(CH3COO)2(EtOH)]·CH3COOH (1Dy), [Dy2(H2daps)2(EtOH)2(H2O)2(MeOH)2](CF3SO3)2·(H2O)2 (2Dy), and [Dy3(H1daps)2(H2daps)(μ3-OH)(EtOH)(H2O)] (3Dy)) of different nuclearities (mono-, di-, and trinuclear for 1Dy to 3Dy, respectively) have been synthesized and characterized structurally and magnetically. Analyses on the related bond lengths and resulting hydrogen bond modes in the complexes provide the details of the deprotonation position and the charge of the ligands, which can be in the form of H3daps-, H2daps2-, and H1daps3-. Interestingly, the more deprotonated ligand can act as a bridging ligand between the DyIII centers using the phenol and/or carbonyl oxygen atoms, which leads to the multinuclear structures. Magnetic studies on these complexes revealed that complex 1Dy is a field-induced single-molecule magnet (SMM), while complexes 2Dy and 3Dy show SMM behavior under a zero dc field.

Theoretical Study of Proton Tunneling in the Imidazole–Imidazolium Complex

Proton tunneling in the hydrogen-bonded imidazole–imidazolium complex ion has been studied theoretically. Ab initio CASSCF/6-311++G(d,p) calculations concerning geometry optimization and vibrational frequencies have been carried out for equilibrium and transition state structures of the system. Two-dimensional double-well model potentials were constructed on the basis of ab initio results and used to analyze the proton dynamics in the hydrogen bond and the influence of the excitation of low-frequency hydrogen-bond vibrations on the proton tunneling splittings. The energy of tunneling-split vibrational sublevels of the high-frequency tunneling mode have been calculated for its ground and first excited vibrational state for the series of excitations of the coupled low-frequency intramolecular hydrogen-bond modes. The promoting and suppressing effect of the low-frequency modes on the proton splittings was shown in the ground and first excited vibrational state of the tunneling mode. The vibrational sublevels form the two separate semicontinuous bands between which the absorption transitions may occur. This mechanism explains the experimentally observed splitting and doublet-component broadening of the high-frequency N–H stretching infrared (IR) absorption band.

Constructing π-Stacked Supramolecular Cage Based Hierarchical Self-Assemblies via π···π Stacking and Hydrogen Bonding.

Constructing supramolecular cages with multiple subunits via weak intermolecular interactions is a long-standing challenge in chemistry. So far, π-stacked supramolecular cages still remain unexplored. Here, we report a series of π-stacked cage based hierarchical self-assemblies. The π-stacked cage (π-MX-cage) is assembled from 16 [MXL]+ ions (M = Mn2+, Co2+; X = Br-, SCN-, Cl-; and L = tris(2-benzimidazolylmethyl)amine) via 18 intermolecular π-stacking interactions. The tetrahedral cage, consisting of four [MXL]+ ions as the vertexes and six pairs of [MXL]+ ions as the edges, features 48 exterior N-H hydrogen bond donors for hydrogen bond formation with guest molecules. By variation of the M2+/X- pair, the π-MX-cage demonstrates unique versatility for incorporating a wide variety of species via different hydrogen-bonding modes during the assembly of hierarchical superstructures. In specific, the π-MnBr-cages encapsulate acetonitrile (CH3CN) or cis-1,3,5-cyclohexanetricarbonitrile (cis-HTN) molecules in the central voids, while a core-shell tetrahedral inorganic cluster [Mn(H2O)6]@([Mn(H2O)4]4[Br42-]6) (Mn@Mn4-cage) is captured within the interstitial regions between cages. The π-CoSCN-cages are capable of stabilizing reactive sulfur-containing species, such as S2O42-, S2O62-, and HSO3- ions, in the hierarchical superstructure. Finally, H2PO4- ions are incorporated between π-CoCl-cages, resulting in an inorganic mesoporous framework. These results provide insights into further exploring the chemistry and hierarchical assembly of supramolecular cages based on π-π stacking intermolecular interactions.

Bicyclic Guanidine-Catalyzed Asymmetric Cycloaddition Reaction of Anthrones-Bifunctional Binding Modes and Origin of Stereoselectivity.

We report a computational analysis of the [5,5] bicyclic guanidine-catalyzed asymmetric cycloaddition reaction of anthrones. Based on extensive conformational search of key intermediates and transition states on the potential energy surface and density functional theory calculations, we studied five plausible binding modes between the guanidine catalyst and substrates for this reaction. Our results indicate that the most favorable pathway is a stepwise conjugate addition-Aldol sequence via the dual hydrogen-bond binding mode. The predicted level of enantioselectivity is in good agreement with experimental values. Trends in variation of substrates and catalysts have also been reproduced by our calculations. Decomposition analysis revealed the significance of aromatic interactions in stabilizing the key enantioselectivity-determining transition state structures.

Manipulating Light-Induced Dynamic Macro-Movement and Static Photonic Properties within 1D Isostructural Hydrogen-Bonded Molecular Cocrystals.

Smart molecular crystals with light-driven mechanical responses have received interest owing to their potential uses in molecular machines, artificial muscles, and biomimetics. However, challenges remain in control over both the dynamic photo-mechanical behaviors and static photonic properties of molecular crystals based on the same molecule. Herein, we show the construction of isostructural co-crystals allows their light-induced cracking and jumping behaviors (photosalient effect) to be controlled. Hydrogen-bonded co-crystals from 4-(1-naphthylvinyl)pyridine (NVP) with co-formers (tetrafluoro-4-hydroxybenzoic acid (THA) and tetrafluorobenzoic acid (TA)) crystallize as isostructural crystals, but have different static and dynamic photo-mechanical behaviors. These differences are due to alternations in the orientation of NVP and hydrogen-bonding modes of the co-formers. After light activation, the 1D NVP-TA crystal splits and shears off within 1 s. For NVP-THA, its photostability and high quantum yield give novel photonic properties, including low optical waveguide loss, highly polarized anisotropy, and efficient up-conversion fluorescence.

Towards the use of (pseudo) nucleobase substituted amphiphiles as DNA nucleotide mimics and antimicrobial agents

ABSTRACT Here we present the synthesis of complementary (pseudo) nucleobase appended Supramolecular Self-associating Amphiphilic (SSA) salts and, establish the potential for this molecular construct to produce a new class of DNA inspired synthetic structures/materials. The anionic component of this class of amphiphile contains multiple hydrogen bond donating and accepting functionalities, meaning that these systems can access multiple self-associative hydrogen-bonding modes simultaneously. Herein, we characterise the self-associative properties of these DNA inspired amphiphiles in the solid state, solution state and gas phase. Finally, we investigate the potential of these amphiphilic salts to act as antimicrobial agents against model Gram-positive (methicillin-resistant Staphylococcus aureus – MRSA) and Gram-negative (Escherichia coli – E. coli) bacteria.

Electrophilic Hypervalent Trifluoromethylthio-Iodine(III) Reagent.

Herein we report the design and synthesis of hypervalent trifluoromethylthio-iodine(III) reagent 1 and the elucidation of its structure by NMR spectroscopy and X-ray crystallography. The trifluoromethylthiolation reactions of 1 with various nucleophiles were explored, and this compound was found to be a versatile electrophilic reagent for the transfer of a trifluoromethylthio group (-SCF3). The hydrogen-bonding mode responsible for the activation of 1 by the solvent 1,1,1,3,3,3-hexafluoro-2-propanol was investigated both experimentally and computationally.

Monoalkylation of aniline with trichloroacetimidate catalyzed by (±)-camphorsulfonic acid through an SN1 reaction based on dual hydrogen-bonding activation modes

Herein, the monoalkylation of anilines with trichloroacetimidates catalyzed by CSA was investigated theoretically, and it was found that the reaction occurred through an SN1 reaction involving the dual hydrogen-bonding activation modes.

Electrostatic Investigation of 4-Dicyanomethylene-2,6-dimethyl-4H-pyran (DDP) Dye with Amide Derivatives in Water.

Cyclic voltammetry (CV) studies of 4-dicyanomethylene-2,6-4H-pyran (DDP) dye with alkyl-substituted amides were carried out in an aqueous solution. Formamide and substituted amide interaction with DDP dye were characterized by fluorescence spectral techniques in an aqueous solution, but the electrochemical nature and the interaction at the interface region between dye–amide remains largely unexplored. The introduction of formamide to DDP dye exhibits an increase in the peak current accompanied with potential values gradually shifting more toward a less positive region. A large variation in the current–potential characteristics is observed in alkyl-substituted amides. The cyclic voltammograms of alkyl amides are found to be entirely different from each other. The role of alkyl substitution in the amide molecular framework influences the reduction potential of the dye in an aqueous medium. The mode of interaction of the dye with alkyl-substituted amides is predominantly due to the electrostatic behavior, even though hydrogen-bonding interactions coexist throughout the aqueous phase. The binding constant parameter (K), free-energy changes (ΔG), and the variation in the potential behavior of the dye in the presence of formamide and alkyl amides authenticate that the nature of interaction operates by both hydrogen-bonding mode and electrostatic interactions. Electrochemical techniques when coupled with fluorescence methods provide an efficient method of determining the interaction at the bulk and the interface regions of a water-soluble dye with nonfluorophoric solutes.

Interfacial assembled Langmuir films of isomeric lipid derivative: Effect of hydrogen bond and chirality transfer

The assembled behaviors of three isomeric L-glutamic lipid derivatives at the water/air interface are different via Langmuir-Blodgett method. Various nanostructures were formed by different mode of hydrogen bond. In the mode of intramolecular hydrogen bond interaction, relative long and thin nanowire appeared. If intermolecular hydrogen bond interaction plays an important role, short nanorod nanostructures were obtained. While both intra- and inter-molecular hydrogen bond interactions exist, the morphology exhibits the mixture of nanowire and nanosheet. In the case of tetrakis (4-sulfonatonphenyl)-porphine (TPPS) added to the subphase, the nanostructures of self-assembly change obviously and achiral TPPS can be induced to appear supramolecular chirality, which due to the interaction between TPPS and the chiral lipid. And the opposite supramolecular chirality ascribed to TPPS can be induced by the origin chirality of lipids.