Three-center Hydrogen Bonds 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.

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.

Crystal structures of five halido gold complexes involving piperidine or pyrrolidine as ligands or (protonated) as cations.

In bromido-(pyrrolidine-κN)gold(I) bis-(pyrrolidine-κN)gold(I) bromide, [AuBr(pyr)]·[Au(pyr)2]Br (pyr = pyrrolidine, C4H9N), 2, alternating [AuBr(pyr)] mol-ecules and [Au(pyr)2]+ cations are connected by aurophilic contacts to form infinite chains of residues parallel to the b axis. The chains are cross-linked by three N-H⋯Br- hydrogen bonds and an Au⋯Br contact to form a layer structure parallel to the ab plane. Tri-chlorido-(piperidine-κN)gold(III), [AuCl3(pip)] (pip = piperidine, C5H11N), 3, consists of mol-ecules with the expected square-planar coordination at the gold atom, which are connected by an N-H⋯Cl hydrogen bond and an Au⋯Cl contact to form a layer structure parallel to the ac plane. The structures of bis-(piperidinium) tetra-chlorido-aurate(III) chloride, (pipH)2[AuCl4]Cl, 4, and bis-(pyrrolidinium) tetra-bromido-aurate(III) bromide, (pyrH)2[AuBr4]Br, 6, are closely related but not isotypic. Compound 6 crystallizes in space group Ibam; the Au and two Br atoms of the anion lie in the mirror plane x, y, 0, whereas the bromide ions occupy special positions 0, 0.5, 0 and 0, 0.5, 0.25, with site symmetry 2/m. The NH2 group forms a hydrogen bond to one bromide ion, and also a three-centre hydrogen bond to the other bromide atom and to a metal-bonded Br atom. The packing involves chains of hydrogen-bonded pyrrolidinium and bromide ions parallel to the c axis, combined with a layer structure of [AuBr4]- and bromide anions, parallel to the ab plane and involving Au⋯Br and Br⋯Br contacts. Compound 4, however, crystallizes pseudosymmetrically in space group Iba2; two chlorine atoms of the anion lie on the twofold axis 0.5, 0.5, z, and there are two independent cations. The packing is closely similar to that of 6, but there are no N-H⋯Cl hydrogen bonds to metal-bonded chlorines. The contact distances Au⋯Cl are appreciably longer than their Au⋯Br counterparts in 6, whereas the Cl⋯Cl contact is much shorter than Br⋯Br in 6. Tri-bromido-(piperidine-κN)gold(III) crystallizes as its di-chloro-methane solvate, [AuBr3(pip)]·CH2Cl2, 7. It too displays a square-planar coordination at the gold atom. The packing involves hydrogen bonds N-H⋯Br, stacking of neighbouring AuBr3 units by Au⋯Br contacts, and a short Br⋯Br contact; these combine to form a layer structure parallel to the ac plane.

Crystal structures of five gold(I) complexes with methylpiperidine ligands

In bis(4-methylpiperidine-κN)gold(I) chloride, [Au(C6H13N)2]Cl (1), the methyl groups are, as expected, equatorial at the piperidine ring, but the Au atom is axial; this is the case for all five structures reported here, as is the expected linear coordination at the Au atom. Hydrogen bonding of the form N—H...Cl−...H—N leads to inversion-symmetric dimers, which are further connected by C—H...Au contacts. Bis(4-methylpiperidine-κN)gold(I) dichloridoaurate(I), [Au(C6H13N)2][AuCl2] (2), also forms inversion-symmetric dimers; these involve aurophilic interactions and three-centre hydrogen bonds of the form NH(...Cl)2. Bis(4-methylpiperidine-κN)gold(I) dibromidoaurate(I), [Au(C6H13N)2][AuBr2] (3), is isotypic to 2. The 1:1 adduct chlorido(4-methylpiperidine-κN)gold(I) bis(4-methylpiperidine-κN)gold(I) chloride, [Au(C6H13N)2]Cl·[AuCl(C6H13N)] (4), crystallizes as its dichloromethane solvate. The asymmetric unit contains two formula units, in each of which the chloride anion accepts a hydrogen bond from the cation and from the neutral molecule, and the two Au atoms are linked via an aurophilic interaction. A further hydrogen bond leads to inversion-symmetric dimers. The asymmetric unit of bis(2-methylpiperidine-κN)gold(I) chloride, [Au(C6H13N)2]Cl (5), contains two `half' cations, in which the Au atoms lie on twofold axes, and a chloride ion on a general position. Within each cation, the relative configurations at the atoms N and C2 (which bears the methyl substituent) are R,S. The twofold-symmetric dimer involves two N—H...Cl−...H—N units and an aurophilic contact between the two Au atoms.

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.

Crystal structure of 2-{[5-amino-1-(phenyl-sulfon-yl)-1H-pyrazol-3-yl]-oxy}-1-(4-methyl-phen-yl)ethan-1-one.

In the title compound, C18H17N3O4S, the pyrazole ring is planar, with the sulfur atom lying 0.558 (1) Å out of the ring plane. The NH2 group is involved in an intra-molecular hydrogen bond to a sulfonyl oxygen atom; its other hydrogen atom forms an asymmetric three-centre hydrogen bond to the two oxygen atoms of the -O-CH2-C=O- grouping, via the 21 screw axis, forming a ribbon structure parallel to the b axis. Translationally adjacent, coplanar ribbons form a layer parallel to (10).

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

Fifteen 4-(2-meth-oxy-phen-yl)piperazin-1-ium salts containing organic anions: supra-molecular assembly in zero, one, two and three dimensions.

Fifteen 4-(2-meth-oxy-phen-yl)piperazin-1-ium salts containing organic anions have been prepared and structurally characterized. In the isostructural 4-chloro-benzoate and 4-bromo-benzoate salts, C11H17N2O+·C7H4ClO2 - (I) and C11H17N2O+·C7H4BrO2 - (II), and the 4-iodo-benzoate salt C11H17N2O+·C7H4IO2 - (III), the ions are linked by N-H⋯O hydrogen bonds, forming centrosymmetric R 4 4(12) four-ion aggregates; a similar aggregate is formed in the 2-chloro-benzoate salt (V), isomeric with (I). In the 2-fluoro-benzoate salt C11H17N2O+·C7H4FO2 - (IV), and the isomorphous pair of salts, the 2-bromo-benzoate (VI), isomeric with (II) and 2-iodo-benzoate (VII), isomeric with (III), N-H⋯O and C-H⋯π(arene) interactions link the components into three-dimensional arrays. Four-ion R 4 4(12) aggregates are also found in the 2-methyl-benzoate, 4-amino-benzoate and 4-nitro-benzoate salts, C11H17N2O+·C8H7O2 - (VIII), C11H17N2O+·C7H6NO2 - (IX) and C11H17N2O+·C7H4NO4 - (X), but those in (IX) are linked into complex sheets by an additional N-H⋯O hydrogen bond. In the 3,5-dinitrobenzoate salt, C11H17N2O+·C7H3N2O6 -·2H2O (XI), N-H⋯O and O-H⋯O hydrogen bonds link the components into a complex ribbon structure. In the picrate salt, C11H17N2O+·C6H2N3O7 - (XII), the four-ion aggregates are linked into chains of rings by C-H⋯O hydrogen bonds. In the hydrogen maleate salt, C11H17N2O+·C4H3O4 - (XIII), two- and three-centre hydrogen bonds link the ions into a ribbon structure while both anions contain very short but asymmetric O-H⋯O hydrogen bonds, having O⋯O distances of 2.4447 (16) and 2.4707 (17) Å. O-H⋯O Hydrogen bonds link the anions in the hydrogen fumarate salt (XIV), isomeric with (XIII), into chains that are linked into sheets via N-H⋯O hydrogen bonds. In the hydrogen (2R,3R)-tartrate salt, C11H17N2O+·C4H5O6 -·1.698H2O (XV), the anions are linked into sheets by O-H⋯O hydrogen bonds. Comparisons are made with the structures of some related compounds.

The different modes of chiral [1,2,3]triazolo[5,1-b][1,3,4]thiadiazines: crystal packing, conformation investigation and cellular activity.

The crystal structures of four new chiral [1,2,3]triazolo[5,1-b][1,3,4]thiadiazines are described, namely, ethyl 5'-benzoyl-5'H,7'H-spiro[cyclohexane-1,6'-[1,2,3]triazolo[5,1-b][1,3,4]thiadiazine]-3'-carboxylate, C19H22N4O3S, ethyl 5'-(4-methoxybenzoyl)-5'H,7'H-spiro[cyclohexane-1,6'-[1,2,3]triazolo[5,1-b][1,3,4]thiadiazine]-3'-carboxylate, C20H24N4O4S, ethyl 6,6-dimethyl-5-(4-methylbenzoyl)-6,7-dihydro-5H-[1,2,3]triazolo[5,1-b][1,3,4]thiadiazine-3-carboxylate, C17H20N4O3S, and ethyl 5-benzoyl-6-(4-methoxyphenyl)-6,7-dihydro-5H-[1,2,3]triazolo[5,1-b][1,3,4]thiadiazine-3-carboxylate, C21H20N4O4S. The crystallographic data and cell activities of these four compounds and of the structures of three previously reported similar compounds, namely, ethyl 5'-(4-methylbenzoyl)-5'H,7'H-spiro[cyclopentane-1,6'-[1,2,3]triazolo[5,1-b][1,3,4]thiadiazine]-3'-carboxylate, C19H22N4O3S, ethyl 5'-(4-methoxybenzoyl)-5'H,7'H-spiro[cyclopentane-1,6'-[1,2,3]triazolo[5,1-b][1,3,4]thiadiazine]-3'-carboxylate, C19H22N4O4S, and ethyl 6-methyl-5-(4-methylbenzoyl)-6-phenyl-6,7-dihydro-5H-[1,2,3]triazolo[5,1-b][1,3,4]thiadiazine-3-carboxylate, C22H22N4O3S, are contrasted and compared. For both crystallization and an MTT assay, racemic mixtures of the corresponding [1,2,3]triazolo[5,1-b][1,3,4]thiadiazines were used. The main manner of molecular packing in these compounds is the organization of either enantiomeric pairs or dimers. In both cases, the formation of two three-centre hydrogen bonds can be detected resulting from intramolecular N-H...O and intermolecular N-H...O or N-H...N interactions. Molecules of different enantiomeric forms can also form chains through N-H...O hydrogen bonds or form layers between which only weak hydrophobic contacts exist. Unlike other [1,2,3]triazolo[5,1-b][1,3,4]thiadiazines, ethyl 5'-benzoyl-5'H,7'H-spiro[cyclohexane-1,6'-[1,2,3]triazolo[5,1-b][1,3,4]thiadiazine]-3'-carboxylate contains molecules of only the (R)-enantiomer; moreover, the N-H group does not participate in any significant intermolecular interactions. Molecular mechanics methods (force field OPLS3e) and the DFT B3LYP/6-31G+(d,p) method show that the compound forming enantiomeric pairs via weak N-H...N hydrogen bonds is subject to greater distortion of the geometry under the influence of the intermolecular interactions in the crystal. For intramolecular N-H...O and S...O interactions, an analysis of the noncovalent interactions (NCIs) was carried out. The cellular activities of the compounds were tested by evaluating their antiproliferative effect against two normal human cell lines and two cancer cell lines in terms of half-maximum inhibitory concentration (IC50). Some derivatives have been found to be very effective in inhibiting the growth of Hela cells at nanomolar and submicromolar concentrations with minimal cytotoxicity in relation to normal cells.

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).

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.

Ethyl 6′-cyano-7′-phenyl-1′,6′,7′,7a'-tetrahydro-3′H-spiro[indeno[1,2-b]quinoxaline-11,5′-pyrrolo[1,2-c]thiazole-6′-carboxylate

In the title compound, C22H22ClN4O2S, the angle between the mean planes of the indene ring and the quinoxaline ring system is 3.93 (11)°. The five-membered indene and thiazole rings both adopt envelope conformations while the pyrrole ring adopts a twisted conformation. The two acceptor O atoms form a chelated three-centred hydrogen bond with a phenyl C atom.

Intramolecular Natural Energy Decomposition Analysis: Applications to the Rational Design of Foldamers.

We describe an intramolecular version of the natural energy decomposition analysis (NEDA), with the aim of evaluating interactions between molecular fragments across covalent bonds. The electronic energy in intramolecular natural energy decomposition analysis (INEDA) is divided into electrical, core, and charge transfer components. The INEDA method describes the fragments using the nonfragmented electronic density, and, therefore, there are no limitations in how to choose the boundary orbital. We used INEDA to evaluate the interaction energies that give origin to barriers of rotation around Camide Caromatic (Cam Car ) and Namide Caromtaic (Nam Car ) bonds in arylamide-foldamer building blocks. We found that differences of barrier height between models with different ortho-aryl substituents stem from charge transfer and core interactions. In three-center hydrogen-bond (H-bond) models with an NH proton donor H-bound to two electronegative ortho-aryl substituents, the interaction energy of the three-center system is larger than in either of the two-center H-bond subsystem alone, indicating an increase of overall rigidity. The combination of INEDA and NEDA allows the evaluation of intermolecular and intramolecular interactions using a consistent theoretical framework. © 2018 Wiley Periodicals, Inc.

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.

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.