Three-center Hydrogen Research Articles

Intramolecular lactam cross-linking of short oligoureas.

Oligourea foldamers are known to fold into 2.5-helices, stabilized by three-centered hydrogen bonds, which makes them conformationally more rigid than peptides. Nevertheless, the folding propensity and conformational stability in solution depend on the length of the oligomer, as well as the temperature, solvent, and so forth. In the peptide field, there are many approaches known for constraining the backbone in the folded conformation, including the stapling of side chains by disulfide bridges, lactam formation, ring closing metathesis reaction, and others. In this work, we linked side chains by lactam bridges of short oligoureas (four residues), containing Glu- and Lys-like residues. The designed oligoureas differed in the position of the Glu-like residue. Next, the conformational properties of linear and cyclic compounds were studied in protic solvent (methanol) by nuclear magnetic resonance and circular dichroism. Importantly, it was discovered that larger macrocycles (24-membered) are more tolerated with respect to the helical turn than smaller macrocycles (19-membered) under the studied conditions.

Multiple non-covalent-interaction-directed supramolecular double helices: the orthogonality of hydrogen, halogen and chalcogen bonding.

In this study, a benzoselenadiazole- and pyridine-bifunctionalized hydrogen-bonded arylamide foldamer was synthesized. A co-crystallization experiment with 1,4-diiodotetrafluorobenzene showed that a new type of supramolecular double helices, which were induced by three orthogonal interactions, namely, three-center hydrogen bonding (O⋯H⋯O), I⋯N halogen bonding and Se⋯N chalcogen bonding, have been constructed in the solid state. This work presents a novel instance of multiple non-covalent interactions that work together to construct supramolecular architectures.

Imaging of Single Molecular Behaviors Under Bifurcated Three-Centered Hydrogen Bonding.

The mechanism for interaction and bonding of single guest molecules with active sites fundamentally determines the sorption and subsequent catalytic processes occurring in host zeolitic frameworks. However, no real-space studies on these significant issues have been reported thus far, since atomically visualizing guest molecules and recognizing single Al T-sites in zeolites remain challenging. Here, we atomically resolved single thiophene probes interacting with acid T-sites in the ZSM-5 framework to study the bonding behaviors between them. The synergy of bifurcated three-centered hydrogen bonds and van der Waals interactions can "freeze" the near-horizontal thiophene and make it stable enough to be imaged. By combining the imaging results with simulations, direct atomic observations enabled us to precisely locate the single Al T-sites in individual straight channels. Then, we statistically found that the thiophene bonding probability of the T11 site is 15 times higher than that of the T6 site. For different acid T-sites, the variation in the interaction synergy changes the inner angle of the host-guest O-H···S hydrogen bond, thereby affecting the stability of the near-horizontal thiophene and leading to considerable bonding inhomogeneities.

Ab Initio Microkinetics of H2S Interactions with Clean and Sulfided Au(110) at Low Temperature: A Strong Assistance in Partial Dissociation from Single Sulfur Atoms

A microkinetic model built on first-principles calculations is developed to clarify an ongoing experimental controversy regarding whether hydrogen sulfide (H2S) molecules are intact or dissociated on pristine and S-covered Au(110) surfaces at 120 K. From the simulation, we prove that only associative adsorption of H2S on the defect-free, flat (110) facet of gold occurs in the exposure region under investigation, whereas its reaction with sulfur adsorbed as single atoms straightforwardly proceeds to yield relatively strongly bound SH radicals for the surface precovered with elemental S. The sulfur assistance of neighboring H2S to decompose is ascribed to the stability of the corresponding transition state in which three-center hydrogen bonding interactions are being formed. One-dimensional zigzag chains of divalent sulfur are shown as structural units of the c(2 × 4) superstructure observed experimentally in inactive sulfur islands for the S + H2S reaction. The sensitivity of H–S bond cleavage in surface H2S to the aggregation state of coadsorbed sulfur may, in part, be rationalized by the change in valency of these adatoms. This is the first time that a clear theoretical picture of the chemistry of H2S on such an open Au surface is provided, which is beneficial to elucidate more complicated reaction processes, such as sulfur-poisoning tolerance of gold nanocatalysts.

Synthesis, Characterizations, Crystal Structure, DFT, and Hirshfeld Surface Analysis of 4-Cyclohexyl-1-(thiophene-2-carbonyl)thiosemicarbazide

The crystal structure of the thiosemicarbazide derivative 4-cyclohexyl-1-(thiophene-2-carbonyl)thiosemicarbazide (ChtcTSC), C12H17N3OS2, is reported here. The title compound ChtcTSC has been characterized by various physicochemical techniques viz UV–Vis., Infrared, and NMR. It crystallizes in the monoclinic system having space group P21/c. The dihedral angle between the thiophene and cyclohexyl rings is 60.7(4)°. The crystal packing is established by intermolecular N–H⋯O packing interactions involving a three-center donor hydrogen bond between the keto oxygen atom of the thiophene group and H atoms belonging to the hydrazine group which links the molecules into chains along the (011) plane of the unit cell. Hydrogen bonds between the hydrazine hydrogen atom and one of the thiophene groups and C–H⋯Cg π -ring interactions provide added stability to the crystal packing. The fingerprint plots associated with Hirshfeld surface analysis indicate that there are different types of weak interactions viz. O⋯H–C, O⋯H–N, and S⋯H–C. The geometry optimization has been performed using the DFT method, and geometrical parameters thus obtained for ChtcTSC correlate with the single-crystal X-ray data. The TD-DFT study showed a small HOMO and LUMO energy gap of 2.869 eV. The electronic transition from the ground state to the excited state due to a transfer of electrons from HOMO to LUMO levels is mainly associated with the n → π* transition.Graphical AbstractThe crystal structure of 4-cyclohexyl-1-(thiophene-2-carbonyl)thiosemicarbazide (ChtcTSC) is reported here where the title compound ChtcTSC has been characterized by various physiochemical techniques including UV–Vis., Infrared, NMR, DFT and Hirshfeld surface analysis.

Glass-forming Schiff bases: Peculiar self-organizing systems with bifurcated hydrogen bonds

A combination of quantum computations with calorimetric, dielectric, infrared, and diffraction studies was used to dissect the nature of atypical bifurcated (three-centered) hydrogen bonds (BHBs). Based on the analysis of four glass-forming Schiff bases, this article experimentally proves that self-organization via BHBs may be prevalent in H-bonding systems. Moreover, it explicitly shows that even high screening of the proton-donor and proton-acceptor groups is not a sufficient obstacle to form the BHBs. Even highly sterically hindered Schiff bases form lasting centrosymmetric dimers via a pair of BHBs in the liquid and glass phases. The driving force for their medium-range-scale ordering tendency is a disorder in the molecular scaffold, strictly bound to the N…H…O bond character. As a result, the protons of the BHBs center gain translational freedom. Finally, it is shown that, contrary to the prevailing opinion, Schiff bases can be good glass-forming systems with high glass transition temperatures.

Spectroscopic and Structural Study of a New Conducting Pyrazolium Salt.

The increase in conductivity with temperature in 1H-pyrazol-2-ium 2,6-dicarboxybenzoate monohydrate was analyzed, and the influence of the mobility of the water was discussed in this study. The electric properties of the salt were studied using the impedance spectroscopy method. WB97XD/6-311++G(d,p) calculations were performed, and the quantum theory of atoms in molecules (QTAiM) approach and the Hirshfeld surface method were applied to analyze the hydrogen bond interaction. It was found that temperature influences the spectroscopic properties of pyrazolium salt, particularly the carbonyl and hydroxyl frequencies. The influence of water molecules, connected by three-center hydrogen bonds with co-planar tetrameters, on the formation of structural defects is also discussed in this report.

Supramolecular Assemblies Based on Intramolecular Three-Center Hydrogen Bond and their Applications

Supramolecular Assemblies Based on Intramolecular Three-Center Hydrogen Bond and their Applications

Reduction of a disulfide-constrained oligo-glutamate peptide triggers self-assembly of β2-type amyloid fibrils with the chiroptical properties determined by supramolecular chirality

Disulfide bonds prevent aggregation of globular proteins by stabilizing the native state. However, a disulfide bond within a disordered state may accelerate amyloidogenic nucleation by navigating fluctuating polypeptide chains towards an orderly assembly of β-sheets. Here, the self-assembly behavior of Glu-Cys-(Glu)4-Cys-Glu peptide (E6C2), in which an intrachain disulfide bond is engineered into an amyloidogenic homopolypeptide motif, is investigated. To this end, the Thioflavin T (ThT) fluorescence kinetic assay is combined with infrared spectroscopy, circular dichroism (CD), atomic force microscopy (AFM) and Raman scattering measurements. Regardless of whether the disulfide bond is intact or reduced, E6C2 monomers remain disordered within a broad range of pH. On the other hand, only reduced E6C2 self-assembles into amyloid fibrils with the unique infrared traits indicative of three-center hydrogen bonds involving main-chain carbonyl as a bifurcating acceptor and main-chain NH and side-chain –COOH groups as hydrogen donors: the bonding pattern observed in so-called β2-fibrils. AFM analysis of β2-E6C2 reveals tightly packed rectangular superstructures whose presence coincides with strong chiroptical properties. Our findings suggest that formation of chiral amyloid superstructures may be a generic process accessible to various substrates, and that the fully extended conformation of a poly-Glu chain is a condition sine qua non for self-assembly of β2-fibrils.

Glycerol as Alternative Co-Solvent for Water Extraction of Polyphenols from Carménère Pomace: Hot Pressurized Liquid Extraction and Computational Chemistry Calculations.

Glycerol is a co-solvent for water extraction that has been shown to be highly effective for obtaining polyphenol extracts under atmospheric conditions. However, its efficacy under subcritical conditions has not yet been studied. We assessed different water-glycerol mixtures (15%, 32.5%, and 50%) in a hot pressurized liquid extraction system (HPLE: 10 MPa) at 90 °C, 120 °C, and 150 °C to obtain extracts of low molecular weight polyphenols from Carménère grape pomace. Under the same extraction conditions, glycerol as a co-solvent achieved significantly higher yields in polyphenols than ethanol. Optimal extraction conditions were 150 °C, with 32.5% glycerol for flavonols and 50% for flavanols, stilbenes, and phenolic acids. Considering gallic acid as a model molecule, computational chemistry calculations were applied to explain some unusual extraction outcomes. Furthermore, glycerol, methanol, ethanol, and ethylene glycol were studied to establish an incipient structure–property relationship. The high extraction yields of gallic acid obtained with water and glycerol solvent mixtures can be explained not only by the additional hydrogen bonds between glycerol and gallic acid as compared with the other alcohols, but also because the third hydroxyl group allows the formation of a three-centered hydrogen bond, which intensifies the strongest glycerol and gallic acid hydrogen bond. The above occurs both in neutral and deprotonated gallic acid. Consequently, glycerol confers to the extraction solvent a higher solvation energy of polyphenols than ethanol.

Three new amidophosphoric acid esters with a P(O)[OCH2C(CH3)2CH2O] segment: X-ray diffraction, DFT, AIM and Hirshfeld surface investigations of bi- and tri-furcated (three and four-center) hydrogen bond interactions

AbstractStructural and packing features of three new amidophosphoric acid esters having a common partXP(O)[OCH2C(CH3)2CH2O], withX = [(CH3)3CNH] (1), [(CH3)2HCNH] (2) and [C6H11(CH3)N] (3), are investigated by single crystal X-ray diffraction. The results illustrate that the compounds1and3crystallize with one independent molecule in the asymmetric unit; whereas, for2, the compound crystallizes with three independent molecules in the asymmetric unit. The crystal structures are mostly stabilizedviatri-furcated hydrogen bond interactions (C–H · · ·)2(N–H · · ·)O=P in1and (C–H · · ·)3O=P in3, while the stability is given by bi-furcated hydrogen bond interactions (C–H · · ·)(N–H · · ·)O=P in2. For a better understanding of the nature, strength and energetics associated with the formation of the quoted multi-center hydrogen bond interactions, the Natural Bond Order (NBO) method from Density Functional Theory (DFT) and a topological analysis by means of Atoms In Molecules (AIM) and Hirshfeld surface procedures were performed. These studies reveal that the studied multi-center hydrogen bond interactions of the type O · · · H are favoured in the crystal packing displaying enrichment ratios larger than unity. The detailed nature of the different interactions in these multi-center interactions is studied for the first time in such compounds. It is shown that the N–H · · · O interaction is rather non-covalent closed-shell whereas the C–H · · · O interaction is more van der Waals closed-shell. Stronger hydrogen bond interactions are observed for a lower multiple H-atom acceptor oxygen in three-center hydrogen bond interactions (C–H · · ·)(N–H · · ·)O=P of2than for four-center interactions in1[i.e. (C–H · · ·)2(N–H · · ·)O=P] and3[i.e. (C–H · · ·)3O=P]. The better H-atom acceptability of the O atom of P=O compared with the esteric O atom is explained by the richers-character of the hybrid orbital of the O atom acceptor of P=O coupled with enhance of the polarization and charge. The obtained results are also confirmed by Molecular Electrostatic Potential (MEP).

Absolute control of helicity at the C-termini in quinoline oligoamide foldamers by chiral oxazolylaniline moieties

Absolute one-handed chiral quinoline tetramers andoctamers containing different oxazolylanilines at the C-terminus have been synthesized. The absolute one-handed sense and diastereomeric excess values were valued by 1H NMR. X-ray crystal diffractionand CD studies reveal that the S-oxazolylaniline always induces a P-handed helicity and the absolute helicity is driven by the stable three-center hydrogen bonding between protons in the amide and N atoms in oxazolylaniline and adjacent quinoline ring. CPL investigations demonstrated that S-CQn-a⿼d are CPL active and its glum values are dependent on its length. Interestingly, the sizes of the substituents in the chiral centers are different, however, they exert no effect on the dissymmetric factors gabs and glum of quinoline oligoamide foldamers.

Halogen Bond Asymmetry in Solution.

Halogen bonding is the noncovalent interaction of halogen atoms in which they act as electron acceptors. Whereas three-center hydrogen bond complexes, [D···H···D]+ where D is an electron donor, exist in solution as rapidly equilibrating asymmetric species, the analogous halogen bonds, [D···X···D]+, have been observed so far only to adopt static and symmetric geometries. Herein, we investigate whether halogen bond asymmetry, i.e., a [D–X···D]+ bond geometry, in which one of the D–X bonds is shorter and stronger, could be induced by modulation of electronic or steric factors. We have also attempted to convert a static three-center halogen bond complex into a mixture of rapidly exchanging asymmetric isomers, [D···X–D]+ ⇄ [D–X···D]+, corresponding to the preferred form of the analogous hydrogen bonded complexes. Using 15N NMR, IPE NMR, and DFT, we prove that a static, asymmetric geometry, [D–X···D]+, is obtained upon desymmetrization of the electron density of a complex. We demonstrate computationally that conversion into a dynamic mixture of asymmetric geometries, [D···X–D]+ ⇄ [D–X···D]+, is achievable upon increasing the donor–donor distance. However, due to the high energetic gain upon formation of the three-center-four-electron halogen bond, the assessed complex strongly prefers to form a dimer with two static and symmetric three-center halogen bonds over a dynamic and asymmetric halogen bonded form. Our observations indicate a vastly different preference in the secondary bonding of H+ and X+. Understanding the consequences of electronic and steric influences on the strength and geometry of the three-center halogen bond provides useful knowledge on chemical bonding and for the development of improved halonium transfer agents.

The intramolecular hydrogen bond as a unit of molecular electronics: Molecular switching controlled by overcrowded intramolecular three-centered hydrogen bond

The equilibrium geometry of the 2,5-bis-[2-(pyridin-2-yl)-vinyl]-1[Formula: see text]-pyrrole calculated at the MP2/6-311[Formula: see text]G([Formula: see text],[Formula: see text]) level of theory evidences the breaking of one of the components in the three-centered intramolecular hydrogen bond due to the steric strain. For this reason, the three-centered intramolecular hydrogen bonding turns out to be asymmetric interaction involving the major and minor components. However, the reversible switching between these components under an external impact is also possible. Two different stable states with unequal geometric and electronic structure are observed in the derivatives of the 2,5-bis-[2-(pyridin-2-yl)-vinyl]-1[Formula: see text]-pyrrole. These molecules represent novel molecular switches operating due to the pendulum-like transition between the nonequivalent two-centered components of the overcrowded three-centered intramolecular hydrogen bond. Implantation of hydrogen bond as a unit of the molecular scale device enhances potential of molecular electronics and could serve as a step towards the construction of artificial biological ensembles.

Site-selective As–P substitution and hydrogen bonding in the crystal structure of philipsburgite, Cu5Zn((As,P)O4)2(OH)6·H2O

Philipsburgite, Cu5Zn((As,P)O4)2(OH)6·H2O, from the Middle Pit, Gold Hill Mine, Tooele Co., Utah, USA, was studied by single-crystal X-ray diffraction and scanning electron microscopy. The empirical formula of the studied sample is (Cu4.69Zn1.23)(As0.86P0.18O4)2(OH)5.61·H2O, which agrees well with the previous reports on the mineral. Philipsburgite is monoclinic, P21/c, a = 12.385(6), b = 9.261(4), c = 10.770(5) A, β = 97.10(1)o, V = 1225.7(9) A3 (at 100 K), and Z = 4. The crystal structure was refined to R1 = 0.046 for 2563 unique observed reflections with |Fo| ≥ 4σF. The crystal structure of philipsburgite is isotypic to that of kipushite and can be considered as a complex three-dimensional framework consisting of two types of layers stacked parallel to the a-axis. The A-type layer is formed by the edge-sharing Jahn–Teller-distorted Cuφ6 octahedra [φ = O2−, (OH)−, H2O]. Two adjacent octahedral layers are linked via (As2O4) tetrahedra. The B-type layer is built by corner-sharing (ZnO4) and (As1O4) tetrahedra and is formed by the four- and eight-membered tetrahedral rings. The A:B ratio of the A and B layers is equal to 2:1. The hydrogen bonding network in philipsburgite is rather complex and consists of two- and three-center hydrogen bonds. The As1 site accommodates ca. 18% of P and is a preferable position for the P substitution in philipsburgite. The observed selectivity of the As1 site for P may indicate that, for the intermediate compositions with the P:As ratios close to 1:1, there is a fully ordered species with P prevalent at the As1 site and As prevalent at the As2 site. The intermediate composition would, therefore, be Cu5Zn(AsO4)(PO4)(OH)6·H2O and such a mineral can be considered as a separate species, according to the rules of the International Mineralogical Association (IMA). Philipsburgite should be considered as structurally complex with the Shannon information contents of 4.954 bits/atom and 614.320 bits/cell. The obvious reason for the structural complexity of the mineral is its modularity, i.e., the presence of two structurally distinct modules, the octahedral–tetrahedral (A) and tetrahedral (B) layers.

Theoretical Study of the Structure and Stability of Stepwise Hydrogenated Aluminum Clusters Al44H n (n = 1−24)

The energies and structural and spectroscopic characteristics of a series of model stepwise hydrogenated aluminum clusters Al44H n (n = 1−24) obtained by successive introduction of hydrogen atoms into various surface positions of the Al44 cluster have been calculated by the density functional theory method (B3LYP). According to these calculations, the [Al39] surface layer of the cage retains a closed “nested doll” shape with a pentaatomic inner core [Al5]. With increasing n, both the surface layer and the core tend to experience increasing asymmetric distortions. The surface is corrugated and undergoes significant axial and equatorial extensions and contractions, some of the Al−H two-center terminal bonds are transformed into threecenter hydrogen bridges, and some Al atoms are displaced from the surface layer to the outer sphere and are bound to the surface through hydrogen bridges. The inner core [Al5] at n = 24 loses its bipyramidal shape and shifts to the surface layer so that one or two of its atoms are “built-in” into the concave regions of the surface layer. The calculated average energies of Al−H bonds are within the range ~55.5 ± 2.5 kcal/mol. The averaged energies of the Al44H n → Al44Hn–2 + Н2 dissociation reactions with elimination of a hydrogen molecule are on the order of a few kilocalories per mole and are evidence of small exothermicity (or isothermicity) of these reactions. For the Al44H, Al44H2, and Al44H6 clusters as an example, the relative stabilities of isomers with terminal Al−H bonds in various nonequivalent positions of the [Al39] surface layer are compared.

Estimating the energy of intramolecular bifurcated (three-centered) hydrogen bond by X-ray, IR and 1H NMR spectroscopy, and QTAIM calculations

The structure of a series of the 2-substituted pyrroles containing the intramolecular NH⋯OC hydrogen bond and the 2,5-disubstituted pyrroles having the three-centered intramolecular CO⋯H(N)⋯OC hydrogen bond was studied by X-ray, IR, NMR spectroscopy, and quantum chemical calculations, including calculations in terms of Quantum Theory of Atoms in Molecules (QTAIM). The X-ray diffraction data show that the intramolecular rH … O and RN … O distances increase upon conversion from a two-centered hydrogen bond to a three-centered hydrogen bond, indicating a weakening of the last interaction. The topological parameters of the hydrogen bond obtained from the QTAIM calculations (electron density ρBCP and potential energy density V at the critical point of the hydrogen bond) made it possible to quantify the hydrogen bond energy in the studied compounds. The energy of intramolecular NH⋯OC hydrogen bond in the 2-substituted pyrroles is in the range from 5.5 to 6.0 kcal mol−1 (moderate hydrogen bond), whereas the energy of the components of the three-centered intramolecular CO⋯H(N)⋯OC hydrogen bond in the 2,5-disubstituted pyrroles is reduced to 2.5–3.5 kcal mol−1 (weak hydrogen bond). For weak components of the three-centered hydrogen bond, the principle of the additivity of effects on the spectral parameters influenced by the hydrogen bond (change in the vibration frequency of the NH bond, ΔνN‒H, and the chemical shift of bridge proton, ΔδNH) was proposed. For this reason, the ½ΔνN-H and ½ΔδNH values also were used for estimating the energy of the two-centered components of the three-centered CO⋯H(N)⋯OC hydrogen bond. These estimates are in good agreement with those obtained from the ρBCP and V parameters. Consequently, the ½ΔνN-H and ½ΔδNH parameters can be used as an energy descriptor for two-centered components in the case of a symmetric intramolecular three-centered hydrogen bond.

Synthesis and Verification of Fluorescent pH Probes Based on 2-Quinolone Platform

Intracellular pH plays an important role in biological events, including cell metabolism, signal transduction, cell growth, apoptosis and endocytosis. The development of simple and robust proton-recognizing fluorescent probes has been a research field of high interest. In this work, we describe the design and synthesis of a 2-quinolone Schiff base as a novel acidic fluorescent probe. The design strategy of the probe is based on non-classical hydrogen bonding in the form of an intramolecular three-centered hydrogen bond (THB). pH titrations at pHs 2 and 6 indicate that there is enhancement of fluorescence with increasing proton concentration. Additionally, no interference of metal ions such as Cu2+, Fe3+, Hg2+, Zn2+, Co2+, Cd2+ and Pb2+ ions were detected during the course of these titrations.

Controlling Helix Sense at N- and C-Termini in Quinoline Oligoamide Foldamers by β-Pinene-Derived Pyridyl Moieties.

A series of quinoline oligoamide foldamers bearing a β-pinene-derived pyridyl group at the N-terminus or the C-terminus were synthesized, and the efficiencies of chiral inductions have been evaluated by 1H NMR and CD spectra. The chiral inductions were quantitative when chiral pyridyl acid was appended at the N-terminus, but were inferior when chiral pyridyl amine was appended at the C-terminus. Unexpectedly, N-oxidation on the pyridine ring at the C-terminus does not notably enhance the chiral induction efficiency in spite of the presence of three-center hydrogen bonds.

Unveiling the three-center hydrogen bond dynamic behavior in ground and excited states

The behavior of three-centered hydrogen bond (THB) in excited state is unveiled firstly. The notion proposed in experiment that the THB configuration can be stable in solution has been verified. And one more stable configuration has been found which has two intramolecular hydrogen bonds compared with THB configuration. The analysis of optimization geometrical configurations shows that the THB weakens upon photoexcitation and is apparent weaker than the two-centered hydrogen bond. The reduced electron density gradient (RDG) maps indicate that the weakening of THB compared with two-centered hydrogen bond is due to the steric repulsion of hydrogen bond donors and acceptors. In addition, fluoresce spectra indicate that the 3-position substituent of coumarin has a large blue-shift on maximum fluorescence wavelength compared with the 7-aminocoumarin C500.