Investigation of encapsulated water wire within self-assembled hydrophilic nanochannels, in a modified γ4-amino acid crystals: Tracking thermally induced changes of intermolecular interactions within a crystalline hydrate.

Nanostructures formed by the self-assembly of modified/unmodified amino acids have the potential to be useful in several biological/nonbiological applications. In that regard, the greater conformational space provided by γ-amino acids, owing to their additional backbone torsional degrees of freedom and enhanced proteolytic stability, compared to their α-counterparts, should be explored. Though, modified single amino acid-based nanomaterials such as nanobelts or hydrogels are developed by utilizing the monosubstituted γ-amino acids derived from the backbone homologation of phenylalanine (Phe). Examples of a single γ-amino acid-based porous nanostructure capable of accommodating solvent molecules are not really known. The crystal structures of a modified γ4(R)Phe residue, Boc-γ4(R)Phe-OH, at different temperatures, showed that hydrogen-bonded water molecules are forming a wire inside hydrophilic nanochannels. The dynamics of intermolecular interactions between the water wire and the inner wall of the channel with relation to the temperature change was investigated by analyzing the natural bonding orbital (NBO) calculation results performed with the single crystal structures obtained at different temperature points. The NBO results showed that from 325 K onward, the strength of water-water interactions in the water wire are getting weaker, whereas, for the water-inner wall interactions, it getting stronger, suggesting a favorable change in the orientation of water molecules with temperatures, for the latter.

Axial vs equatorial: Capturing the intramolecular charge transfer state geometry in conformational polymorphic crystals of a donor-bridge-acceptor dyad in nanosecond-time-scale.

Two conformational polymorphs of a donor-bridge-acceptor (D-B-A) dyad, p-(CH3)2N-C6H4-(CH2)2-(1-pyrenyl)/PyCHDMA, were studied, where the electron donor (D) moiety p-(CH3)2N-C6H4/DMA is connected through a bridging group (B), -CH2-CH2-, to the electron acceptor (A) moiety pyrene. Though molecular dyads like PyCHDMA have the potential to change solar energy into electrical current through the process of photoinduced intramolecular charge transfer (ICT), the major challenge is the real-time investigation of the photoinduced ICT process in crystals, necessary to design solid-state optoelectronic materials. The time-correlated single photon counting (TCSPC) measurements with the single crystals showed that the ICT state lifetime of the thermodynamic form, PyCHDMA1 (pyrene and DMA: axial), is ∼3 ns, whereas, for the kinetic form, PyCHDMA20 (pyrene and DMA: equatorial), it is ∼7 ns, while photoexcited with 375 nm radiation. The polymorphic crystals were photo-excited and subsequently probed with a pink Laue x-ray beam in time-resolved x-ray diffraction (TRXRD) measurements. The TRXRD results suggest that in the ICT state, due to electron transfer from the tertiary N-atom in DMA moiety to the bridging group and pyrene moiety, a decreased repulsion between the lone-pair and the bond-pair at N-atom induces planarity in the C-N-(CH3)2 moiety, in both polymorphs. The Natural Bond Orbital calculations and partial atomic charge analysis by Hirshfeld partitioning also corroborated the same. Although the interfragment charge transfer (IFCT) analysis using the TDDFT results showed that for the charge transfer excitation in both conformers, the electrons were transferred from the DMA moiety to mostly the pyrene moiety, the bridging group has little role to play in that.

Ultrafast sorting: Excimeric π-π stacking distinguishes pyrene-N-methylacetamide isomers on the ultrafast time scale.

Pyrene based molecules are inclined to form excimers through self-association upon photoexcitation. In this work, the pyrene core is functionalized with the N-methylacetamide group at the position 1 or 2 to develop pyren-1-methylacetamide (PyMA1) and pyren-2-methylacetamide (PyMA2), respectively. Upon photoexcitation with 345 nm, a portion of molecules in PyMA1 and PyMA2 solutions at ≥1.0 mM have formed static excimers. The steady state spectroscopic measurements suggest that, whether it is the dimerization of molecules in the ground state (GS) or in excimer formation, characteristic signs are more pronounced in PyMA1 than its isomeric counterpart, PyMA2. The shift of the excimer band in their respective emission spectra suggests that the extent of overlap in π-π stacking is greater for PyMA1 than for PyMA2 in the excited state. The optimized geometry of dimers in toluene shows that the overlapping area between the pyrene moieties in π-π stacking between the dimers is greater for PyMA1 than for PyMA2 in GS. The natural bond orbital analysis with the optimized GS geometries shows that the stabilization/interaction energy between the dimers in π-π stacking is higher in PyMA1 compared to PyMA2 in toluene. The transient absorption (TA) measurements in toluene over the fs-ps regime (fs-TA) showed that the formation of static excimers with pre-associated dimers in PyMA1 happens in ∼700 fs whereas the excimers for the pre-associated dimers in PyMA2 have formed in slightly slower time scale (∼1.95 ps). Contrary to what was observed in solution, the extent of overlap in π-π stacking is lower for PyMA1 dimers (∼17%) than for PyMA2 dimers (∼37%) in single crystals.

Pregabalin peptides: conformational comparison of γ3- and γ4-substituted γ-amino acids in αγααα pentapeptides.

Gamma-aminobutyric acid (GABA, gammaAbu), an unsubstituted gamma-amino acid, is an important inhibitory neurotransmitter in the mammalian brain. The role of GABA in the treatment of epilepsy has triggered a great deal of interest in substituted gamma-amino acids, which may serve as GABA analogs, acting as inhibitors of GABA aminotransferase. Pregabalin (Pgn), a well-known antiepileptic drug, is also a beta-substituted gamma3-amino acid. Pregabalin and gamma4Leu, an isomer of the pregabalin (Pgn) residue, both carrying the same isobutyryl group in the side chain, were introduced in the present study to have a comparison of their respective conformational differences as well as their role in influencing the overall conformation of the peptides, they are inserted in. Two alpha-gamma-alpha-alpha-alpha hybrid pentapeptides were designed that contain Aib-Pgn and Aib-gamma4Leu segments at the N terminus. The study provides a detailed analysis of the conformational properties and non-covalent interactions observed in the crystal structures of two polymorphs of the pentapeptide monohydrate, Boc-Aib-(S)Pgn-Leu-Phe-Val-OMe (C38H63N5O8·H2O) and the isomeric pentapeptide, Boc-Aib-gamma4(R)Leu-Leu-Phe-Val-OMe (C38H63N5O8), obtained from single crystal X-ray diffraction experiments.

Crystallographic characterization of the α,γ C12 helix in hybrid peptide sequences.

The solid-state conformations of two αγ hybrid peptides Boc-[Aib-γ(4) (R)Ile]4 -OMe 1 and Boc-[Aib-γ(4) (R)Ile]5 -OMe 2 are described. Peptides 1 and 2 adopt C12 -helical conformations in crystals. The structure of octapeptide 1 is stabilized by six intramolecular 4 → 1 hydrogen bonds, forming 12 atom C12 motifs. The structure of peptide 2 reveals the formation of eight successive C12 hydrogen-bonded turns. Average backbone dihedral angles for αγ C12 helices are peptide 1, Aib; φ (°) = -57.2 ± 0.8, ψ (°) = -44.5 ± 4.7; γ(4) (R)Ile; φ (°) = -127.3 ± 7.3, θ1 (°) = 58.5 ± 12.1, θ2 (°) = 67.6 ± 10.1, ψ (°) = -126.2 ± 16.1; peptide 2, Aib; φ (°) = -58.8 ± 5.1, ψ (°) = -40.3 ± 5.5; ψ(4) (R)Ile; φ (°) = -123.9 ± 2.7, θ1 (°) = 53.3 θ 4.9, θ 2 (°) = 61.2 ± 1.6, ψ (°) = -121.8 ± 5.1. The tendency of γ(4) -substituted residues to adopt gauche-gauche conformations about the C(α) -C(ß) and C(ß) -C(γ) bonds facilitates helical folding. The αγ C12 helix is a backbone expanded analog of α peptide 310 helix. The hydrogen bond parameters for α peptide 310 and α-helices are compared with those for αγ hybrid C12 helix. Copyright © 2016 European Peptide Society and John Wiley & Sons.

Directing peptide conformation with centrally positioned pre-organized dipeptide segments: studies of a 12-residue helix and ß-hairpin.

Secondary structure formation in oligopeptides can be induced by short nucleating segments with a high propensity to form hydrogen bonded turn conformations. Type I/III turns facilitate helical folding while type II'/I' turns favour hairpin formation. This principle is experimentally verified by studies of two designed dodecapeptides, Boc-Val-Phe-Leu-Phe-Val-Aib-Aib-Val-Phe-Leu-Phe-Val-OMe 1 and Boc-Val-Phe-Leu-Phe-Val-(D)Pro-(L)Pro-Val-Phe-Leu-Phe-Val-OMe 2. The N- and C-terminal flanking pentapeptide sequences in both cases are identical. Peptide 1 adopts a largely α-helical conformation in crystals, with a small 310 helical segment at the N-terminus. The overall helical fold is maintained in methanol solution as evidenced by NMR studies. Peptide 2 adopts an antiparallel ß-hairpin conformation stabilized by 6 interstrand hydrogen bonds. Key nuclear Overhauser effects (NOEs) provide evidence for the antiparallel ß-hairpin structure. Aromatic proton chemical shifts provide a clear distinction between the conformation of peptides 1 (helical) and 2 (ß-hairpin). The proximity of facing aromatic residues positioned at non-hydrogen bonding positions in the hairpin results in extensively ring current shifted proton resonances in peptide 2.

Structural dynamics of a thermally silent triiron(II) spin crossover defect grid complex.

The structural evolution of spin crossover (SCO) complexes during their spin transition at equilibrium and out-of-equilibrium conditions needs to be understood to enable their successful utilisation in displays, actuators and memory components. In this study, diffraction techniques were employed to study the structural changes accompanying the temperature increase and the light irradiation of a defect [2 × 2] triiron(II) metallogrid of the form [FeII3LH2(HLH)2](BF4)4·4MeCN (FE3), LH = 3,5-bis{6-(2,2'-bipyridyl)}pyrazole. Although a multi-temperature crystallographic investigation on single crystals evidenced that the compound does not exhibit a thermal spin transition, the structural analysis of the defect grid suggests that the flexibility of the grid, provided by a metal-devoid vertex, leads to interesting characteristics that can be used for intermolecular cooperativity in related thermally responsive systems. Time-resolved photocrystallography results reveal that upon excitation with a ps laser pulse, the defect grid shows the first two steps of the out-of-equilibrium process, namely the photoinduced and elastic steps, occurring at the ps and ns time scales, respectively. Similar to a previously reported [2 × 2] tetrairon(II) metallogrid, FE3 exhibits a local distortion of the entire grid during the photoinduced step and a long-range distortion of the lattice during the elastic step. Although the lifetime of the pure photoinduced high spin (HS) state is longer in the tetranuclear grid than in the defect grid, suggesting that the global nuclearity plays a crucial role for the lifetime of the photoinduced species, the influence of the co-crystalising solvent on the lifetime of the photoinduced HS state remains unknown. This study sheds light on the out-of-equilibrium dynamics of a thermally silent defect triiron SCO metallogrid.

Metal-to-metal communication during the spin state transition of a [2 × 2] Fe(II) metallogrid at equilibrium and out-of-equilibrium conditions.

Spin crossover (SCO) complexes are prototypes of materials with bi- or multi-stability in the solid state. The structural evolution during their spin transition is a key feature to establish the foundations of how to utilize this type of material. So far, ultrafast time-resolved structural investigations of SCO solids have been focused on monometallic complexes, though an increasing number of oligometallic SCO complexes showing cooperativity effects are being reported. Here, we used single crystal X-ray crystallography and time-resolved pink Laue photocrystallography to study the molecular reorganisation during the thermal and photoinduced SCO of a [2 × 2] tetranuclear metallogrid of the form [FeII4LMe4](BF4)4·2MeCN ([LMe]- = 4-methyl-3,5-bis{6-(2,2'-bipyridyl)}pyrazolate). A multitemperature crystallographic investigation on single crystals reveals an effective communication between the metal centres during thermal SCO, observed by the simultaneous transformation of the coordination polyhedra of both crystallographic-symmetry independent metal atoms accompanying the SCO in only one of them. Time-resolved photocrystallography results reveal the different molecular responses between mononuclear and oligonuclear complexes, after light irradiation with a picosecond laser pulse. While mononuclear SCO complexes reorganise once during the first nanosecond after excitation, the tetranuclear metallogrid exhibits a multiple structural rearrangement in the same span of time. Such behaviour is attributed to the elastic communication between metal atoms, which allows the propagation of a short-range elastic distortion over the entire Fe4 grid complex. The present study sheds light on the importance of strong elastic coupling of metal atoms during the correlated spin transition of oligometallic complexes.

Short- vs. long-range elastic distortion: structural dynamics of a [2 × 2] tetrairon(II) spin crossover grid complex observed by time-resolved X-Ray crystallography.

Spin crossover complexes (SCO) are among the most studied molecular switches due to their potential use in displays, sensors, actuators and memory components. A prerequisite to using these materials is the understanding of the structural changes following the spin transition at out-of-equilibrium conditions. So far, out-of-equilibrium studies in SCO solids have been focused on mononuclear complexes, though a growing number of oligonuclear SCO complexes showing cooperative effects are being reported. Here, we use time-resolved pink Laue crystallography to study the out-of-equilibrium dynamics of a [2 × 2] tetranuclear metallogrid of the form [FeII4LMe4](BF4)4·2MeCN ([LMe]- = 4-methyl-3,5-bis{6-(2,2'-bipyridyl)}pyrazolate). The out-of-equilibrium spin state switching induced by a ps laser pulse demonstrates that the metallogrid exhibits a multi-step response similar to that reported for mononuclear complexes. Contrary to the mononuclear complexes, the metallogrid shows two types of elastic distortions at different time scales. The first is a short-range distortion that propagates over the entire Fe4 grid complex during the ps time scale, and it is caused by the rearrangement of the coordination sphere of the photo-switching ion and the constant feedback between strongly linked metal ions. The second is a long-range distortion caused by the anisotropic expansion of the lattice during the ns time scale, observed in mononuclear materials. The structural analysis demonstrates that the long-range prevails over the short-range distortion, inducing the largest deformation of both the entire grid and the coordination sphere of each metal ion. The present study sheds light on the out-of -equilibrium dynamics of a non-cooperative oligonuclear complex.

Exploring the structural changes on excitation of a luminescent organic bromine-substituted complex by in-house time-resolved pump-probe diffraction.

The structural changes accompanying the excitation of the luminescent dibromobenzene derivative, 1,4-dibromo-2,5-bis(octyloxy)benzene, have been measured by in-house monochromatic time-resolved (TR) diffraction at 90 K. Results show an increment of the very short intermolecular Br•••Br contact distance from 3.290 Å to 3.380 Å. Calculations show the Br…Br interaction to be strongly repulsive in both the Ground and Excited states but significantly relaxed by the lengthening of the contact distance on excitation. The stability of the crystals is attributed to the many weak C-H···Br and C-H···π intermolecular interactions. The study described is the first practical application of In-House Time-Resolved diffraction, made possible by the continuing increase in the brightness of X-ray sources and the sensitivity of our detectors.

Solid state structure of p-bromo phenyl 4,5,7-tri-O-benzyl-ß-D-glycero-D-talo-septanoside and an analysis of non-covalent interactions.

The solid state structure of a new seven-membered sugar oxepane derivative, namely, p-bromo phenyl 4,5,7-tri-O-benzyl-ß-D-glycero-D-talo-septanoside is discussed, as determined through single crystal X-ray structural determination and in relation to their conformational features. The molecule adopts twist-chair as the preferred conformation, with conformational descriptor (O,1)TC(2,3). The solid state packing of molecules is governed by a rich network of non-covalent bonding originating from O-H⋯O, C-H⋯π, C-H⋯Br and aromatic π⋯π interactions that stabilize the packing of molecules in the crystal.

C11/C9 helices in crystals of αß hybrid peptides and switching structures between helix types by variation in the α-residue.

Close-packed helices with mixed hydrogen bond directionality are unprecedented in the structural chemistry of α-polypeptides. While NMR studies in solution state provide strong evidence for the occurrence of mixed helices in (ßß)n and (αß)n sequences, limited information is currently available in crystals. The peptide structures presented show the occurrence of C11/C9 helices in (αß)n peptides. Transitions between C11 and C11/C9 helices are observed upon varying the α-amino acid residue.

Dense network of O-H⋯O and C-H⋯O interactions in the solid state structure of n-pentyl-2-chloro-2-deoxy-α-D-manno-sept 3-uloside.

Single crystal X-ray structural analysis of a septanoside, namely, n-pentyl-2-chloro-2-deoxy sept-3-uloside (1) provides many finer details of the molecular structure, in addition to its preferred twist-chair conformation, namely, (5,6)TC3,4 conformation. Structural analysis reveals a dense network of O-H⋯O, C-H⋯O and van der Waals interactions that stabilize interdigitized, planar bi-layer structure of the crystal lattice.

C12 helices in long hybrid (αγ)n peptides composed entirely of unconstrained residues with proteinogenic side chains.

Unconstrained γ(4) amino acid residues derived by homologation of proteinogenic amino acids facilitate helical folding in hybrid (αγ)n sequences. The C12 helical conformation for the decapeptide, Boc-[Leu-γ(4)(R)Val]5-OMe, is established in crystals by X-ray diffraction. A regular C12 helix is demonstrated by NMR studies of the 18 residue peptide, Boc-[Leu-γ(4)(R)Val]9-OMe, and a designed 16 residue (αγ)n peptide, incorporating variable side chains. Unconstrained (αγ)n peptides show an unexpectedly high propensity for helical folding in long polypeptide sequences.

Unconstrained homooligomeric γ-peptides show high propensity for C14 helix formation.

Monosubstituted γ(4)-residues (γ(4)Leu, γ(4)Ile, and γ(4)Val) form helices even in short homooligomeric sequences. C14 helix formation is established by X-ray diffraction in homooligomeric (γ)n tetra-, hexa- and decapeptide sequences demonstrating the high propensity of γ residues, with proteinogenic side chains, to adopt locally folded conformations.

ß-Turn analogues in model αß-hybrid peptides: structural characterization of peptides containing ß(2,2)Ac6c and ß(3,3)Ac6c residues.

The effect of gem-dialkyl substituents on the backbone conformations of ß-amino acid residues in peptides has been investigated by using four model peptides: Boc-Xxx-ß(2,2)Ac(6)c(1-aminomethylcyclohexanecarboxylic acid)-NHMe (Xxx = Leu (1), Phe (2); Boc = tert-butyloxycarbonyl) and Boc-Xxx-ß(3,3)Ac(6)c(1-aminocyclohexaneacetic acid)-NHMe (Xxx = Leu (3), Phe (4)). Tetrasubstituted carbon atoms restrict the ranges of stereochemically allowed conformations about flanking single bonds. The crystal structure of Boc-Leu-ß(2,2)Ac(6)c-NHMe (1) established a C(11) hydrogen-bonded turn in the αß-hybrid sequence. The observed torsion angles (α(ϕ≈-60°, ψ≈-30°), ß(ϕ≈-90°, θ≈60°, ψ≈-90°)) corresponded to a C(11) helical turn, which was a backbone-expanded analogue of the type III ß turn in αα sequences. The crystal structure of the peptide Boc-Phe-ß(3,3)Ac(6)c-NHMe (4) established a C(11) hydrogen-bonded turn with distinctly different backbone torsion angles (α(ϕ≈-60°, ψ≈120°), ß(ϕ≈60°, θ≈60°, ψ≈-60°)), which corresponded to a backbone-expanded analogue of the type II ß turn observed in αα sequences. In peptide 4, the two molecules in the asymmetric unit adopted backbone torsion angles of opposite signs. In one of the molecules, the Phe residue adopted an unfavorable backbone conformation, with the energetic penalty being offset by a favorable aromatic interaction between proximal molecules in the crystal. NMR spectroscopy studies provided evidence for the maintenance of folded structures in solution in these αß-hybrid sequences.