Crystallography Aided by Atomic Core-Level Binding Energies: Proton Transfer versus Hydrogen Bonding in Organic Crystal Structures

Ionic bond or hydrogen bridge? Br?nsted proton transfer to nitrogen acceptors in organic crystals causes strong N1s core-level binding energy shifts. A study of 15 organic cocrystal and salt systems shows that standard X-ray photoelectron spectroscopy (XPS) can be used as a complementary method to X-ray crystallography for distinguishing proton transfer from H-bonding in organic condensed matter.     

Segmental,Domain‐Selective Perdeuteration and Small‐Angle Neutron Scattering for Structural Analysis of Multi‐Domain Proteins

Multi‐domain proteins play critical roles in fine‐tuning essential processes in cellular signaling and gene regulation. Typically, multiple globular domains that are connected by flexible linkers undergo dynamic rearrangements upon binding to protein, DNA or RNA ligands. RNA binding proteins (RBPs) represent an important class of multi‐domain proteins, which regulate gene expression by recognizing linear or structured RNA sequence motifs. Here, we employ segmental perdeuteration of the three RNA recognition motif (RRM) domains in the RBP TIA‐1 using Sortase A mediated protein ligation. We show that domain‐selective perdeuteration combined with contrast‐matched small‐angle neutron scattering (SANS), SAXS and computational modeling provides valuable information to precisely define relative domain arrangements. The approach is generally applicable to study conformational arrangements of individual domains in multi‐domain proteins and changes induced by ligand binding.     

Conformational Change from a Twisted Figure‐Eight to an Open‐Extended Structure in Doubly Fused 36π Core‐Modified Octaphyrins Triggered by Protonation: Implication on Photodynamics and Aromaticity

Two examples of core‐modified 36π doubly fused octaphyrins that undergo a conformational change from a twisted figure‐eight to an open‐extended structure induced by protonation are reported. Syntheses of the two octaphyrins (in which Ar=mesityl or tolyl) were achieved by a simple acid‐catalyzed condensation of dipyrrane unit containing an electron‐rich, rigid dithienothiophene (DTT) core with pentafluorobenzaldehyde followed by oxidation with 2,3‐dichloro‐5,6‐dicyano‐1,4‐benzoquinone (DDQ). The single‐crystal X‐ray structure of the octaphyrin (in which Ar=mesityl) shows a figure‐eight twisted conformation of the expanded porphyrin skeleton with two DTT moieties oriented in a staggered conformation with a π‐cloud distance of 3.7 Å. Spectroscopic and quantum mechanical calculations reveal that both octaphyrins conform to a [4n]π nonaromatic electronic structure. Protonation of the pyrrole nitrogen atoms of the octaphyrins results in dramatic structural change, which led to 1) a large redshift and sharpening of absorption bands in electronic absorption spectrum, 2) a large change in chemical shift of pyrrole β‐CH and ? NH protons in the ¹H NMR spectrum, 3) a small increase in singlet lifetimes, and 4) a moderate increase in two‐photon absorption cross‐section values. Furthermore, nucleus‐independent chemical shift (NICS) values calculated at various geometrical positions show positive values and anisotropy‐induced current density (AICD) plots indicate paratropic ring‐currents for the diprotonated form of the octaphyrin (in which Ar=tolyl); the single‐crystal X‐ray structure of the diprotonated form of the octaphyrin shows an extended structure in which one of the pyrrole ring of each dipyrrin subunit undergoes a 180 ° ring‐flip. Four trifluoroacetic acid (TFA) molecules are bound above and below the molecular plane defined by meso‐carbon atoms and are held by N? H ??? O, N? H ??? F, and C? H ??? F intermolecular hydrogen‐bonding interactions. The extended‐open structure upon protonation allows π‐delocalization and the electronic structure conforms to a [4n]π Hückel antiaromatic in the diprotonated state.     

The Structure of 2‐[(1S)‐(+)‐10‐camphorsulfonamino]‐6‐aminopyridine in the Solid State and in Solution; Unprecedented Cocrystallization of Four Stereoisomers

The solid and solution structures of a new optically active aminopyridine compound, 2‐[(1S)‐(+)‐10‐camphorsulfonamino]‐6‐aminopyridine [(S)‐csaap], 1 , are reported. Crystal data: space group P2₁, a = 8.9729 (5), b = 10.9447 (6), c = 36.693 (2) Å, β = 96.435 (1)°, V = 3580.8 (3) ų, Z = 8, R₁ = 0.0673 and wR₂ = 0.1600 with I > 2σ(I). This chiral compound shows an unprecedented cocrystallization of four stereoisomers, which are characterized by X‐ray crystallography and NMR spectroscopy.     

Host Perturbation in a β‐Hydroquinone Clathrate Studied by Combined X‐ray/Neutron Charge‐Density Analysis: Implications for Molecular Inclusion in Supramolecular Entities

X‐ray/neutron (X/N) diffraction data measured at very low temperature (15 K) in conjunction with ab initio theoretical calculations were used to model the crystal charge density (CD) of the host–guest complex of hydroquinone (HQ) and acetonitrile. Due to pseudosymmetry, information about the ordering of the acetonitrile molecules within the HQ cavities is present only in almost extinct, very weak diffraction data, which cannot be measured with sufficient accuracy even by using the brightest X‐ray and neutron sources available, and the CD model of the guest molecule was ultimately based on theoretical calculations. On the other hand, the CD of the HQ host structure is well determined by the experimental data. The neutron diffraction data provide hydrogen anisotropic thermal parameters and positions, which are important to obtain a reliable CD for this light‐atom‐only crystal. Atomic displacement parameters obtained independently from the X‐ray and neutron diffraction data show excellent agreement with a |ΔU| value of 0.00058 Ų indicating outstanding data quality. The CD and especially the derived electrostatic properties clearly reveal increased polarization of the HQ molecules in the host–guest complex compared with the HQ molecules in the empty HQ apohost crystal structure. It was found that the origin of the increased polarization is inclusion of the acetonitrile molecule, whereas the change in geometry of the HQ host structure following inclusion of the guest has very little effect on the electrostatic potential. The fact that guest inclusion has a profound effect on the electrostatic potential suggests that nonpolarizable force fields may be unsuitable for molecular dynamics simulations of host–guest interaction (e.g., in protein–drug complexes), at least for polar molecules.     

Synthesis,Spectroscopy, X‐ray Crystallography,and DFT Computations of Nanosized Phosphazenes

Nanoparticles of nine phosphazenes with general formula 4‐CH₃C₆H₄S(O)₂N=PX₃ [X = Cl ( A ), NC₄H₈ ( 1 ), NC₆H₁₂ ( 2 ), NC₄H₈N–C(O)OC₂H₅ ( 3 ), NC₄H₈N–C(O)OC₆H₅ ( 4 ), NC₄H₈O ( 5 ), NHCH₂–C₄H₇O ( 6 ), N(CH₃)(C₆H₁₁) ( 7 ), NHCH₂–C₆H₅ ( 8 ), and 2‐NH‐NC₅H₄ ( 9 )] were synthesized using ultrasonic method and characterized by ¹H, ¹³C, ³¹P NMR, FT‐IR, fluorescence, as well as UV/Vis spectroscopy and additionally with XRD, FE‐SEM, N₂ sorption, and elemental analysis. The ³¹P NMR spectra of compounds 1 – 9 reveal the most up field shift δ(³¹P) for 9 at –11.45 ppm reflecting the most electron donation of 2‐aminopyridinyl rings through resonance to the phosphorus atom. The ¹H, ¹³C NMR spectra of 7 exhibit two sets of signals for the hydrogen and carbon atoms of its two isomers present in the solution state in 1:4 ratio. The FE‐SEM micrographs illustrate that the nanoparticles of compounds 1 – 9 have spherical morphology and a size of 27–42 nm. From the XRD patterns, the crystal sizes were estimated to about 24–86 nm. The highest bandgap was measured for 3 (3.81 eV) whereas the smallest was measured for 8 (3.50 eV). The structures of two polymorphs of compound 5 ( 5 , 5′ ) were determined by X‐ray crystallography at 120 K. Both of these polymorphs are triclinic with P1 space group but 5 has a doubled unit cell volume and two symmetrically independent molecules ( 5a and 5b ). In structures 5a and 5′ , the phosphorus and all endocyclic atoms of two morpholinyl rings display disorder, whereas the molecule 5b does not show disorder. The strong intermolecular O–H ··· O hydrogen bonds plus weak intermolecular C–H ··· O and C–H ··· N interactions create three‐dimensional polymers in the crystalline networks of 5 and 5′ . The DFT computations illustrate that molecule 5b is more stable than 5a by –1.1062 and –0.9779 kcal · mol^–1 at B3LYP and B3PW91 levels, respectively. The NBO calculations presented sp³d hybridization for phosphorus and sulfur atoms and sp², sp³ hybrids for the nitrogen and oxygen atoms.     

Synthesis and X‐ray Crystallography of Two Lead(II) Decahydro‐closo‐Decaborate Hydrates

The reaction of Pb[CO₃] with an aqueous solution of (H₃O)₂[B₁₀H₁₀] in an equimolar ratio leads to two lead(II) decahydro‐closo‐decaborate hydrates both as triclinic, pale yellow single crystals. The water‐rich compound with the formula [Pb(H₂O)₃]₂Pb[B₁₀H₁₀]₃ · 5.5H₂O crystallizes in the space group P1 (a = 711.72(4), b = 1243.14(8), c = 2064.83(12) pm, α = 81.806(3), β = 83.795(3), γ = 80.909(3)°) with Z = 2. The compound with the lower water content, [Pb(H₂O)₃]Pb[B₁₀H₁₀]₂ · 1.5H₂O, also crystallizes in P1 (a = 718.46(4), b = 1288.75(8), c = 1279.91(8) pm, α = 70.145(3), β = 75.976(3), γ = 80.324(3)°) with Z = 2. Both structures can be described as layered arrangements and contain one Pb²⁺ cation each, which is only coordinated by the hydridic hydrogen atoms of the hydroborate anions. All the others are primarily surrounded by three water molecules in a non‐planar fashion and additional hydrogen atoms of [B₁₀H₁₀]^2– anions. The non‐lead‐bonded crystal water molecules in both structures are all connected via hydrogen bonds to the water molecules, which coordinate the Pb²⁺ cations, as well as via non‐classical hydrogen bonds to the cluster anions and reside between the layers. The [B₁₀H₁₀]^2– anions show only slight distortions from their ideal shape as bicapped square antiprisms.     

The Structure of Bis[N‐6‐aminopyridyl‐N‐(1S)‐(+)‐10‐camphorsulfonylamino]palladium in the Solid State and in Solution

The complex, bis[N‐6‐aminopyridyl‐N‐(1S)‐(+)‐10‐camphorsulfonylamino]palladium, Pd[(S)‐APCS]₂, 1 , was prepared by reaction of 2‐[(1S)‐(+)‐10‐camphorsulfonamino]‐6‐aminopyridine with PdCl₂ in THF. Complex 1 has been characterized by spectroscopic methods and its structure has been determined by X‐ray crystallography. Crystal data: space group C2, a= 16.082 (2), b = 17.104 (2), c = 13.051 (2)Å, β = 99.95 (1)°, V = 3535.9 (8) ų, Z = 2 with final residuals R1 = 0.0491 and wR2 = 0.0944. Two independent molecules, (S,S)‐Pd[(S)‐APCS]2, 1a , and (R,R)‐Pd[(S)‐APCS]2, 1b , were found in each asymmetric unit, which exchange to each other via a series of nitrogen inversion and C‐C bond rotation. The inversion energy (ΔGc₁^≠) and the energy barrier (δGc₂^≠) were 11.5 ± 0.1 Kcal mol^?1 at 246 K and 9.8 ± 0.1 Kcal mol^?1 at 199 K, respectively, calculated by dynamic NMR data.     

Hydrogen‐Bonded Complexes between 4‐Alkoxystilbazoles and Fluorophenols: Solid‐State Structures and Liquid Crystallinity

48 new hydrogen‐bonded complexes have been prepared by combining 16 fluorophenols of general formula C₆F_nH_5?nOH with three different alkoxystilbazoles (butyloxy‐, octyloxy‐ and dodecyloxy‐). Single‐crystal X‐ray structures were obtained for 10 of the 16 complexes of octyloxystilbazole from which it was found that most of the structures could be collected into one of two groups according to both the motif shown by the complex and by the solid‐state packing. Because all but one crystallised in the P$\bar 1$ space group, meaningful comparisons could be drawn and it was observed that six structures were extremely close in nature so that significant molecular overlap was found. On this basis, doubt is cast on the significance of some of the weaker intermolecular contacts found in the solid state. 40 of the new complexes showed liquid‐crystal properties and it was found that although complexes of butyloxystilbazole were all nematic, almost all of those with dodecyloxystilbazole showed a smectic A (SmA) phase. Complexes of octyloxystilbazole showed a mixture of both. Structure/property correlations showed that clearing points were independent of the pK_a of the phenol. The most stable mesophases were found when the fluorophenol contained a fluorine at the 2‐position, which was interpreted in terms of the formation of an intramolecular H???F hydrogen bond to give a six‐membered ring linking the two components into a stable, coplanar conformation. The least stable mesophases were found when no such ring formation was possible and the phenol was relatively free to move.     

Unraveling the Crystal Structure of Lanthanide–Murexide Complexes: Use of an Ancient Complexometry Indicator as a Near‐Infrared‐Emitting Single‐Ion Magnet

Herein, we provide some structural evidence of the complexation color‐change of murexide solutions in presence of lanthanide, which has been used for decades in complexometric studies. For Ln=Sm to Lu and Y, the compounds crystallize as monomeric [Ln(Murex)₃] ? 11 H₂O with an N3O6 tricapped square‐antiprism environment, which are stable up to 250 °C. Single‐ion magnet (SIM) behavior is then observed on the Yb^III derivative in an original nine‐coordinated environment. In‐field slow relaxation (Δ=(15.6±1) K; τ₀=2.73×10^?6 s) is observed with a very narrow distribution of the relaxation time (α_max=0.09). Magnetic and photophysical properties can be correlated. On one hand the analysis of NIR emission spectrum permits to have access to crystal field parameters and to compare them with those extracted from dc measurements. On the other hand, magnetic measurements permit to identify the nature of the M _J states involved in the ²F_5/2→²F_7/2 luminescence spectrum. The gap between the low‐lying states is in agreement with the energy barrier obtained from magnetic slow‐relaxation measurement.     

Multinuclear Solid‐State Magnetic Resonance as a Sensitive Probe of Structural Changes upon the Occurrence of Halogen Bonding in Co‐crystals

Although the understanding of intermolecular interactions, such as hydrogen bonding, is relatively well‐developed, many additional weak interactions work both in tandem and competitively to stabilize a given crystal structure. Due to a wide array of potential applications, a substantial effort has been invested in understanding the halogen bond. Here, we explore the utility of multinuclear (¹³C, ^14/15N, ¹⁹F, and ¹²⁷I) solid‐state magnetic resonance experiments in characterizing the electronic and structural changes which take place upon the formation of five halogen‐bonded co‐crystalline product materials. Single‐crystal X‐ray diffraction (XRD) structures of three novel co‐crystals which exhibit a 1:1 stoichiometry between decamethonium diiodide (i.e., [(CH₃)₃N⁺(CH₂)₁₀N⁺(CH₃)₃][2 I^?]) and different para‐dihalogen‐substituted benzene moieties (i.e., p‐C₆X₂Y₄, X=Br, I; Y=H, F) are presented. ¹³C and ¹⁵N NMR experiments carried out on these and related systems validate sample purity, but also serve as indirect probes of the formation of a halogen bond in the co‐crystal complexes in the solid state. Long‐range changes in the electronic environment, which manifest through changes in the electric field gradient (EFG) tensor, are quantitatively measured using ¹⁴N NMR spectroscopy, with a systematic decrease in the ¹⁴N quadrupolar coupling constant (C_Q) observed upon halogen bond formation. Attempts at ¹²⁷I solid‐state NMR spectroscopy experiments are presented and variable‐temperature ¹⁹F NMR experiments are used to distinguish between dynamic and static disorder in selected product materials, which could not be conclusively established using solely XRD. Quantum chemical calculations using the gauge‐including projector augmented‐wave (GIPAW) or relativistic zeroth‐order regular approximation (ZORA) density functional theory (DFT) approaches complement the experimental NMR measurements and provide theoretical corroboration for the changes in NMR parameters observed upon the formation of a halogen bond.     

Unprecedented Electron‐Poor Octahedral Ta6 Clusters in a Solid‐State Compound: Synthesis,Characterisations and Theoretical Investigations of Cs2BaTa6Br15O3

The crystal structure of Cs₂BaTa₆Br₁₅O₃ has been elucidated by using synchrotron X‐ray powder diffraction and absorption experiments. It is built from edge‐bridged octahedral [(Ta₆${{\rm Br}{{{\rm i}\hfill \atop 9\hfill}}}$ ${{\rm O}{{{\rm i}\hfill \atop 3\hfill}}}$ )${{\rm Br}{{{\rm a}\hfill \atop 6\hfill}}}$ ]^4? cluster units with a singular poor metallic electron (ME) count equal to thirteen. This leads to a paramagnetic behaviour related to one unpaired electron. The arrangement of the Ta₆ clusters is similar to that of Cs₂LaTa₆Br₁₅O₃ exhibiting 14‐MEs per [(Ta₆${{\rm Br}{{{\rm i}\hfill \atop 9\hfill}}}$ ${{\rm O}{{{\rm i}\hfill \atop 3\hfill}}}$ )${{\rm Br}{{{\rm a}\hfill \atop 6\hfill}}}$ ]^5? motif. The poorer electron‐count cluster presents longer metal–metal distances as foreseen according to the electronic structure of edge‐bridged hexanuclear cluster. Density functional theory (DFT) calculations on molecular models were used to rationalise the structural properties of 13‐ and 14‐ME clusters. Periodic DFT calculations demonstrate that the electronic structure of these solid‐state compounds is related to those of the discrete octahedral units. Oxygen–barium interactions seem to prevent the geometry of the octahedral cluster to strongly distort, allowing stabilisation of this unprecedented electron‐poor Ta₆ cluster in the solid state.