RESUMEN

The structures of the simplest symmetric primary ethers [(CnH2n+1)2O, n = 1-3] determined under high pressure revealed their conformational preferences and intermolecular interactions. In three new polymorphs of diethyl ether (C2H5)2O, high pressure promotes intermolecular CH...O contacts and enforces a conversion from the trans-trans conformer present in the α, ß and γ phases to the trans-gauche conformer, which is higher in energy by 6.4 kJ mol-1, in the δ phase. Two new polymorphs of dimethyl ether (CH3)2O display analogous transformations of the CH...O bonds. The crystal structure of di-n-propyl ether (C3H7)2O, determined for the first time, is remarkably stable over the whole pressure range investigated from 1.70 up to 5.30 GPa.

RESUMEN

Halogenidoantimonate(III) monohydrates of the (C4H12N2)[SbX5]·H2O (X = Cl, 1 or Br, 2) formula, crystallizing in the same monoclinic space group of P21/n, are isostructural, with an isostructurality index close to 99%. The single crystal X-ray diffraction data do not show any indication of phase transition in cooling these crystals from room temperature to 85 K. Both hybrid crystals are built up from [SbX6]3- octahedra that are joined together by a common edge forming isolated bioctahedral [Sb2X10]4- units, piperazine-1,4-diium (C4H12N2)2+ cations and water of crystallization molecules. These structural components are joined together by related but somewhat different O/N/C-H···X and N-H···O hydrogen bonded systems. The evolution of structural parameters, notably the secondary Sb-X bonds along with the associated X/Sb-Sb/X-X/Sb angles and O/N/C-H···X hydrogen bonds, as a function of ligand exchange and temperature, along with their influence on the irregularity of [SbX6]3- octahedra, was determined. The comparison of packing features and hydrogen bond parameters, additionally supported by the Hirshfeld surface analysis and data retrieved from the Cambridge Structural Database, demonstrates the hierarchy and importance of hydrogen bond interactions that influence the irregularity of single [SbX6]3- units.

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RESUMEN

In situ grown crystals of CF3I and CF3CH2I are dominated by II and FF interactions. Their co-crystals with benzene, (CF3I)2·C6H6 and CF3CH2I·C6H6, contain two completely different sets of intermolecular interactions. (CF3I)2·C6H6 shows a unique halogen-bond type: above-the-bond C-IπC6H6 interactions. CF3CH2I·C6H6 shows above-the-centre C-HπC6H6 interactions. These interactions are electrostatically dominated type II halogen bonds between single halogenoalkane molecules and weaker dispersion dominated interactions between the co-crystal components. The observed preferences for benzene for the two binding partners match with calculated molecular electrostatic potentials.

RESUMEN

Tetrachlorobenzenes represent one of the best known, but not yet fully understood, group of isomers of the structure-melting point relationship. The differences in melting temperatures of these structurally related compounds were rationalized in terms of the hierarchy and nature of formed noncovalent interactions, and the molecular aggregation that is influenced by molecular symmetry. The highest melting point is associated with the highly symmetric 1,2,4,5-tetrachlorobenzene isomer. The structures of less symmetrical 1,2,3,4-tetrachlorobenzene and 1,2,3,5-tetrachlorobenzene, determined at 270 and 90 K, show a distinct pattern of halogen bonds, characterized by the different numbers and types of interactions. The evolution of Cl...Cl/H distances with temperature indicates the attractive character of intermolecular interactions and their importance to the structural and thermodynamic parameters of isomeric compounds. The favoured Cl...Cl halogen bonds were found to play a decisive role in differentiating the melting temperatures of tetrachlorobenzene isomers. It was also found that, besides the molecular symmetry and ability to form specific intermolecular interactions, both the type and the distribution of interactions are the important factors responsible for the melting behaviour of the studied isomers. The observed preferences, in tetrachlorobenzenes, for the formation of specific noncovalent interactions correspond to the distribution of calculated partial atomic charges and to the magnitudes of electrostatic potential on the molecular surfaces as well as correlate with the enthalpy of melting parameters.

RESUMEN

The ability to intentionally construct, through different types of interactions, inorganic-organic hybrid materials with desired properties is the main goal of inorganic crystal engineering. The primary deformation, related to intrinsic interactions within inorganic substructure, and the secondary deformation, mainly caused by the hydrogen bond interactions, are both responsible for polyhedral distortions of halogenidoantimonates(III) with organic cations. The evolution of structural parameters, in particular the Sb-I secondary- and O/N/C-H...I hydrogen bonds, as a function of temperature assists in understanding the contribution of those two distortion factors to the irregularity of [SbI6]3- polyhedra. In tris(piperazine-1,4-diium) bis[hexaiodidoantimonate(III)] pentahydrate, (C4H12N2)3[SbI6]2·5H2O (TPBHP), where the isolated [SbI6]3- units were found, distortion is governed only by O/N/C-H...I hydrogen bonds, whereas in piperazine-1,4-diium bis[tetraiodidoantimonate(III)] tetrahydrate, (C4H12N2)[SbI4]2·4H2O (PBTT), both primary and O-H...I secondary factors cause the deformation of one-dimensional [{SbI4}n]n- chains. The larger in spatial dimensions piperazine-1,4-diium cations, in contrast to the smaller water of crystallization molecules, do not significantly contribute to the octahedral distortion, especially in PBTT. The formation of isolated [SbI6]3- ions in TPBHP is the result of specific second coordination sphere hydrogen bond interactions that stabilize the hybrid structure and simultaneously effectively separate and prevent [SbI6]3- units from mutual interactions. The temperature-induced changes, further supported by the analysis of data retrieved from the Cambridge Structural Database, illustrate the significance of both primary and secondary distortion factors on the deformation of octahedra. Also, a comparison of packing features in the studied hybrids with those in the non-metal containing piperazine-1,4-diium diiodide diiodine (C4H12N2)I2·I2 (PDD) confirms the importance and hierarchy of different types of interactions.

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A series of model compounds containing 3-amino-1H-pyrazole-5-carboxylic acid residue with N-terminal amide/urethane and C-terminal amide/hydrazide/ester groups were investigated by using NMR, Fourier transform infrared, and single-crystal X-ray diffraction methods, additionally supported by theoretical calculations. The studies demonstrate that the most preferred is the extended conformation with torsion angles ϕ and ψ close to ±180°. The studied 1H-pyrazole with N-terminal amide/urethane and C-terminal amide/hydrazide groups solely adopts this energetically favored conformation confirming rigidity of that structural motif. However, when the C-terminal ester group is present, the second conformation with torsion angles ϕ and ψ close to ±180° and 0°, respectively, is accessible. The conformational equilibrium is observed in NMR and Fourier transform infrared studies in solution in polar environment as well as in the crystal structures of other related compounds. The observed conformational preferences are clearly related to the presence of intramolecular interactions formed within the studied residue. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.

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Dehydrophenylalanine, ΔPhe, is the most commonly studied α,ß-dehydroamino acid. In nature, further modifications of the α,ß-dehydroamino acids were found, for example, replacement of the C-terminal amide group by oxazole ring. The conformational properties of oxazole-dehydrophenylalanine residue (ΔPhe-Ozl), both isomers Z and E, were investigated. To determine all possible conformations, theoretical calculations were performed using Ac-(Z/E)-ΔPhe-Ozl(4-Me) model compounds at M06-2X/6-31++G(d,p) level of theory. Ac-(Z/E)-ΔPhe-Ozl-4-COOEt compounds were synthesized and the conformational preferences of each isomer, Z and E, were investigated using FTIR and NMR-NOE in solutions of increasing polarity (CHCl3 , DMSO-d6). The solid-state low-temperature structures of Ac-(Z)-ΔPhe-Ozl-4-COOEt and its intermediate analog Ac-(Z)-ΔPhe-Ozn(4-OH)-4-COOEt were also determined. In a weakly polar environment, the ΔPhe-Ozl residue has a tendency to adopt the conformation ß2 with the calculated φ and ψ angles of -127° and 0° for the isomer Z and -170° and 26° for the isomer E. The increase of environment polarity favors the helical conformation α and the beta-turn like conformation ß, but the conformation ß2 seems to be still accessible. The (E)-ΔPhe-Ozl residue can be obtained from the isomer Z in photoisomerization reaction. However, hydroxyl-oxazoline-dehydrophenylalanine ΔPhe-Ozn(4-OH) decomposes in such conditions. Alternatively, (E)-ΔPhe-NH2 can be applied as a substrate in the Hantzsch reaction. © 2016 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 283-294, 2016.

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Oxazole ring occurs in numerous natural peptides, but conformational properties of the amino acid residue containing the oxazole ring in place of the C-terminal amide bond are poorly recognized. A series of model compounds constituted by the oxazole-amino acids occurring in nature, that is, oxazole-alanine (L-Ala-Ozl), oxazole-dehydroalanine (ΔAla-Ozl), and oxazole-dehydrobutyrine ((Z)-ΔAbu-Ozl), was investigated using theoretical calculations supported by FTIR and NMR spectra and single-crystal X-ray diffraction. It was found that the main feature of the studied oxazole-amino acids is the stable conformation ß2 with the torsion angles φ and ψ of -150°, -10° for L-Ala-Ozl, -180°, 0° for ΔAla-Ozl, and -120°, 0° for (Z)-ΔAbu-Ozl, respectively. The conformation ß2 is stabilized by the intramolecular N-H···N hydrogen bond and predominates in the low polar environment. In the case of the oxazole-dehydroamino acids, the π-electron conjugation that is spread on the oxazole ring and C(α)═C(ß) double bond is an additional stabilizing interaction. The tendency to adopt the conformation ß2 clearly decreases with increasing the polarity of environment, but still the oxazole-dehydroamino acids are considered to be more rigid and resistant to conformational changes.

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Directional Cl···Cl type I and II interactions govern the low-density aggregation of 1,1,2,2-tetrachloroethane molecules in synclinal conformation in the crystalline state at low temperature, whereas the dense molecular packing in high-pressure is achieved for the antiperiplanar conformers and electrostatically less favored Cl···Cl contacts. The mechanism of transformation between loose and dense associations involves the collapse of Cl···Cl contacts and conformational conversion.

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Two E isomers of α,ß-dehydro-phenylalanine, Ac-(E)-ΔPhe-NHMe (1a) and Ac-(E)-ΔPhe-NMe(2) (2a), have been synthesized and their low temperature structures determined by single-crystal X-ray diffraction. A systematic theoretical analysis was performed on these molecules and their Z isomers (1b and 2b). The ϕ,ψ potential energy surfaces were calculated at the MP2/6-31+G(d,p) and B3LYP/6-31+G(d,p) levels in the gas phase and at the B3LYP/6-31+G(d,p) level in the chloroform and water solutions with the SCRF-PCM method. All minima were fully optimized by the MP2 and DFT methods, and their relative stabilities were analyzed in terms of π-conjugation, internal H-bonds, and dipole-dipole interactions between carbonyl groups. The results indicate that all the studied compounds can adopt the conformation H (ϕ, ψ ≈ ±40°, ∓120°) which is atypical for standard amino acids residues. A different arrangement of the side chain in the E and Z isomers causes them to have different conformational preferences. In the presence of a polar solvent both Z isomers of ΔPhe (1b and 2b) are found to adopt the 3(10)-helical conformation (left- and right-handed are equally likely). On the other hand, this conformation is not accessible or highly energetic for E isomers of ΔPhe (1a and 2a). Those isomers have an intrinsic inclination to have an extended conformation. The conformational space of the Z isomers is much more restricted than that of the E derivative both in the gas phase and in solution. In the gas phase the E isomers of ΔPhe have lower energies than the Z ones, but in the aqueous solution the energy order is reversed.

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Dehydrobutyrine is the most naturally occurring dehydroamino acid. It is also the simplest dehydroamino acid having the geometrical isomers E/Z. To investigate its conformational properties, a theoretical analysis was performed on N-acetyl-alpha,beta-dehydrobutyrine N'-methylamides, Ac-(E)-DeltaAbu-NHMe and Ac-(Z)-DeltaAbu-NHMe, as well as the dehydrovaline derivative Ac-DeltaVal-NHMe. The phi, psi potential energy surfaces and the localised conformers were calculated at the B3LYP/6-311 + + G(d,p) level of theory both in vacuo and with inclusion of the solvent (chloroform, water) effect (SCRF method). The X-ray crystal structures of Ac-(Z)-DeltaAbu-NHMe and Ac-DeltaVal-NHMe were determined at 85 and 100 K, respectively. The solid-state conformational preferences for the studied residues have been analysed and compared with the other related structures. Despite the limitations imposed by the C(alpha) = C(beta) double bond on the topography of the side chains, the main chains of the studied dehydroamino acids are more flexible than in standard alanine. The studied dehydroamino acids differ in their conformational preferences, which depend on the polarity of the environment. This might be a reason why the nature quite precisely differentiates between DeltaVal and each of the DeltaAbu isomers, and why, particularly so with the latter, they are used as a conformational tool to influence the biological action of usually small, cyclic dehydropeptides.

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The factors influencing the distortion of inorganic anions in the structures of chloridoantimonates(III) with organic cations, in spite of numerous structural studies on those compounds, have not been clearly described and separated. The title compound, [(C(2)H(5))(2)NH(2)](3)[SbCl(6)], consisting of isolated distorted [SbCl(6)](3-) octahedra that have C(3) symmetry and [(C(2)H(5))(2)NH(2)](+) cations, unequivocally shows the role played by hydrogen bonding in the geometry variations of inorganic anions. The organic cations, which are linked to the inorganic substructure through N-H...Cl hydrogen bonds, are clearly responsible for the distortion of the octahedral coordination of Sb(III) in terms of differences (Delta) in both Sb-Cl bond lengths [Delta = 0.4667 (6) A] and Cl-Sb-Cl angles [Delta = 9.651 (17) degrees].

RESUMEN

Pressure-induced transformations between gauche-, gauche+ and transoid conformations have been evidenced by X-ray single-crystal diffraction for 1,1,2-trichloroethane, and the energies of intermolecular interactions, conformational conversion, and the latent heat have been determined.

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Isochoric and isobaric freezing of 1,1-dichloroethane, CH3CHCl2, mp=176.19 K, yielded the orthorhombic structure, space group Pnma, with the fully ordered molecules, in the staggered conformation, located on mirror planes. The CH3CHCl2 ambient-pressure (0.1 MPa) structures were determined at 160 and 100 K, whereas the 295 K high-pressure structures were determined at 0.59 and 1.51 GPa. At 0.1 MPa, all intermolecular distances are considerably longer than the sums of the van der Waals radii, and only a pressure of about 1.5 GPa squeezed the Cl...Cl and Cl...H contacts to distances commensurate with these sums. The exceptionally large difference between the melting points of isomeric 1,1- and 1,2-dichloroethane can be rationalized in terms of their molecular-packing efficiency. It has been shown that the location of atoms in molecules affects their intermolecular interactions, and hence their van der Waals radii are the function of molecular structures.

RESUMEN

Isomers 1,2-dichlorobenzene (o-DCB) and 1,3-dichlorobenzene (m-DCB) were high-pressure frozen in-situ in a Merrill-Bassett diamond-anvil cell and their structures determined at room temperature and at 0.18 (5) GPa for o-DCB, and 0.17 (5) GPa for m-DCB by single-crystal X-ray diffraction. The patterns of halogen...halogen intermolecular interactions in these structures can be considered to be the main cohesive forces responsible for the molecular arrangements in these crystals. The molecular packing of dichlorobenzene isomers, including three polymorphs of 1,4-dichlorobenzene (p-DCB), have been compared and relations between their molecular symmetry, packing arrangements, intermolecular interactions and melting points discussed. The topology of the crystal packing in dichlorobenzene isomers results from the interplay of the molecular shape, steric hindrances and intermolecular interactions. The non-planar arrangement of the dichlorobenzene molecules in the crystal structures can be justified by the distributions of the electrostatic potential on molecular surfaces, which determines electrostatic intermolecular interactions.

RESUMEN

The structure of N,N-dimethylethylenediammonium pentachloroantimonate(III), [(CH3)2NH(CH2)2NH3][SbCl5], NNDP, was investigated at 100 and 15 K at ambient pressure, as well as at pressures up to 4.00 GPa at room temperature in the diamond-anvil cell. The stable structure at low temperatures and low pressures consists of isolated [SbCl5]2- anions and [(CH3)2NH(CH2)2NH3]2+ cations. The inorganic anions have a distorted square pyramidal geometry. They are arranged in linear chains parallel to the c axis. In contrast to the low-temperature studies, where no phase transition was detected, pressure induces a P2(1)/c --> P2(1)/n phase transition between 0.55 and 1.00 GPa, accompanied by a doubling of the a unit-cell parameter. This solid-solid transition results from changes in the electron configuration of the Sb(III) atom and formation of the Sb-Cl bridging bonds between inorganic polyhedra to form, at approximately 1.0 GPa, isolated [Sb2Cl10]4- units consisting of [SbCl6]3- octahedra and [SbCl5]2- square pyramids connected by a common corner. The intermolecular distances continuously decrease with further increase in pressure, and at approximately 3.1 GPa, zigzag [{SbCl5}n]2n- chains containing corner-sharing [SbCl6]3- octahedra are formed. The unit-cell volume of NNDP decreases by 18.15% between room pressure and 4.00 GPa. The linear distortions of the [SbCl5]2- and [SbCl6]3- polyhedra decrease with increasing pressure and decreasing temperature and indicate a reduction in the stereochemical activity of the lone electron pair on the Sb(III) atom.

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The title molecule, C(11)H(12)O(3), is almost planar, with an average deviation of the C and O atoms from the least-squares plane of 0.146(4)A. The geometry about the C=C bond is trans. The phenyl ring and -COOCH(3) group are twisted with respect to the double bond by 9.3(3) and 5.6(5) degree, respectively. The endocyclic angle at the junction of the propenoate group and the phenyl ring is decreased from 120 degree by 2.6(2) degree, whereas two neighbouring angles around the ring are increased by 2.3(2) and 0.9(2) degree. This is probably associated with the charge-transfer interaction of the phenyl ring and -COOCH(3) group through the C=C double bond. The molecules are joined together through C-H...O hydrogen bonds between the methoxy and ester groups to form characteristic zigzag chains extended along the c axis.