Microscopic Structure of Neat Linear Alkylamine Liquids: An X-Ray Scattering and Computer Simulation Study

Linear amines, from propylamine to nonylamine, are studied under ambient conditions by X-ray scattering and molecular dynamics simulations of various force field models. The major finding is that the prepeak in alkylamines is about 1 order of magnitude weaker than that in alkanols, hence suggesting much weaker hydrogen bonding-induced clustering of the amine groups than for the hydroxyl groups. Computer simulation studies reveal that the OPLS-UA model reproduces the prepeak, but with larger amplitudes, while the GROMOS-UA and CHARMM-AA force fields show almost no prepeak. Simulations of all models show the existence of hydrogen-bonded clusters, equally confirmed by the prominent prepeak of the structure factor between the nitrogen atoms. The hydrogen bond strength, as modeled by the Coulomb association in classical force field models, is about the same order of magnitude for both systems. Then, one may ask what is the origin of the weaker prepeak in alkylamines? Simulation data reveal that the existence of the prepeak is controlled through the cancellation of the positive contributions from the charged group correlations by the negative contributions from the cross charged-uncharged correlations. The C2v symmetry of the amine headgroup hinders clustering, which favors cross correlations with the tail atoms. This is opposite to alkanols where the symmetry of the hydroxyl headgroup favors clustering and hinders cross correlations with the alkyl tail. This competition between charged and uncharged atomic groups appears as a general mechanism to explain the existence of scattering prepeaks, including their position and amplitude.

Binding energies of ethanol and ethylamine on interstellar water ices: synergy between theory and experiments

Experimental and computational chemistry are two disciplines used to conduct research in astrochemistry, providing essential reference data for both astronomical observations and modeling. These approaches not only mutually support each other, but also serve as complementary tools to overcome their respective limitations. Leveraging on such synergy, we characterized the binding energies (BEs) of ethanol (CH3CH2OH) and ethylamine (CH3CH2NH2), two interstellar complex organic molecules (iCOMs), on crystalline and amorphous water ices through density functional theory (DFT) calculations and temperature-programmed desorption (TPD) experiments. Experimentally, CH3CH2OH and CH3CH2NH2 behave similarly, in which desorption temperatures are higher on the water ices than on a bare gold surface. Computed cohesive energies of pure ethanol and ethylamine bulk structures allow describing of the BEs of the pure species deposited on the gold surface, as extracted from the TPD curve analyses. The BEs of submonolayer coverages of CH3CH2OH and CH3CH2NH2 on the water ices cannot be directly extracted from TPD due to their co-desorption with water, but they are computed through DFT calculations, and found to be greater than the cohesive energy of water. The behaviour of CH3CH2OH and CH3CH2NH2 is different when depositing adsorbate multilayers on the amorphous ice, in that, according to their computed cohesive energies, ethylamine layers present weaker interactions compared to ethanol and water. Finally, from the computed BEs of ethanol, ethylamine and water, we can infer that the snow-lines of these three species in protoplanetary disks will be situated at different distances from the central star. It appears that a fraction of ethanol and ethylamine is already frozen on the grains in the water snow-lines, causing their incorporation in water-rich planetesimals.

Linking solid-state phenomena via energy differences in `archetype crystal structures'

Categorization underlies understanding. Conceptualizing solid-state structures of organic molecules with `archetype crystal structures' bridges established categories of disorder, polymorphism and solid solutions and is herein extended to special position and high-Z' structures. The concept was developed in the context of disorder modelling [Dittrich, B. (2021). IUCrJ, 8, 305-318] and relies on adding quantum chemical energy differences between disorder components to other criteria as an explanation as to why disorder - and disappearing disorder - occurs in an average structure. Part of the concept is that disorder, as probed by diffraction, affects entire molecules, rather than just the parts of a molecule with differing conformations, and the finding that an R·T energy difference between disorder archetypes is usually not exceeded. An illustrative example combining disorder and special positions is the crystal structure of oestradiol hemihydrate analysed here, where its space-group/subgroup relationship is required to explain its disorder of hydrogen-bonded hydrogen atoms. In addition, we show how high-Z' structures can also be analysed energetically and understood via archetypes: high-Z' structures occur when an energy gain from combining different rather than overall alike conformations in a crystal significantly exceeds R·T, and this finding is discussed in the context of earlier explanations in the literature. Twinning is not related to archetype structures since it involves macroscopic domains of the same crystal structure. Archetype crystal structures are distinguished from crystal structure prediction trial structures in that an experimental reference structure is required for them. Categorization into archetype structures also has practical relevance, leading to a new practice of disorder modelling in experimental least-squares refinement alluded to in the above-mentioned publication.

Hydrogen-Bonding Motifs in Adducts of Allylamine with the 10 Simplest n-Alcohols: Single-Crystal X-ray Diffraction Studies and Computational Analysis

In this paper, we analyzed the homologous series of 10 allylamine adducts with n-alcohols from methanol to decanol. These are the first adduct structures containing aliphatic n-alcohols and an aliphatic amine as co-formers. While all of the ingredients are liquids under ambient conditions, the phases were synthesized with the use of the in situ crystallization technique assisted by IR laser-focused radiation at atmospheric pressure. The structures were characterized by single-crystal X-ray diffraction. All of the phases contain the amine and alcohol in a 1:1 ratio. The architecture of the structures, based on hydrogen-bonding interactions between NH₂ and OH moieties, depends on the size of the alcohol and changes in a systematic way. The three smallest alcohol adducts contain centrosymmetric layers of molecules of the L4(4)8(8) type. The next four alcohol adducts have the T4(2) topology. The structures with the biggest alcohols contain non-centrosymmetric L6(6) layers. The structural investigations were supported by periodic DFT calculations at the B3LYP/pobTZVP level. The cohesive and adhesive energies made up of layer (E _lbe) and ribbon (E _rbe) binding energies were used to predict which type of architecture can be formed. The thermal stabilities of the adducts correlate with the melting points of the co-forming alcohols, with no evident relation to the adduct architecture.

Photocrosslinkable methacrylated gelatin hydrogel as a cell-friendly injectable delivery system for chlorhexidine in regenerative endodontics

OBJECTIVES

This work sought to formulate photocrosslinkable chlorhexidine (CHX)-laden methacrylated gelatin (CHX/GelMA) hydrogels with broad spectrum of action against endodontic pathogens as a clinically viable cell-friendly disinfection therapy prior to regenerative endodontics procedures.

METHODS

CHX/GelMA hydrogel formulations were successfully synthesized using CHX concentrations between 0.12 % and 5 % w/v. Hydrogel microstructure was evaluated by scanning electron microscopy (SEM). Swelling and enzymatic degradation were assessed to determine microenvironmental effects. Compression test was performed to investigate the influence of CHX incorporation on the hydrogels' biomechanics. The antimicrobial and anti-biofilm potential of the formulated hydrogels were assessed using agar diffusion assays and a microcosms biofilm model, respectively. The cytocompatibility was evaluated by exposing stem cells from human exfoliated deciduous teeth (SHEDs) to hydrogel extracts (i.e., leachable byproducts obtained from overtime hydrogel incubation in phosphate buffer saline). The data were analyzed using One- and Two-way ANOVA and Tukey's test (α = 0.05).

RESULTS

CHX/GelMA hydrogels were effectively prepared. NMR spectroscopy confirmed the incorporation of CHX into GelMA. The addition of CHX did not change the micromorphology (pore size) nor the swelling profile (p > 0.05). CHX incorporation reduced the degradation rate of the hydrogels (p < 0.001); whereas, it contributed to increased compressive modulus (p < 0.05). Regarding the antimicrobial properties, the incorporation of CHX showed a statistically significant decrease in the number of bacteria colonies at 0.12 % and 0.5 % concentration (p < 0.001) and completely inhibited the growth of biofilm at concentration levels 1 %, 2 %, and 5 %. Meanwhile, the addition of CHX, regardless of the concentration, did not lead to cell toxicity, as cell viability values were above 70 %.

SIGNIFICANCE

The addition of CHX into GelMA showed significant antimicrobial action against the pathogens tested, even at low concentrations, with the potential to be used as a cell-friendly injectable drug delivery system for root canal disinfection prior to regenerative endodontics.

Infrared Spectral Intensities of Amine Ices, Precursors to Amino Acids

Here, we address the paucity of infrared (IR) spectral data needed to quantify low-temperature experiments with amine ices, such as the formation of amino acids, by reporting new IR results on solid phases of methylamine (CH₃NH₂) and ethylamine (CH₃CH₂NH₂), precursors to glycine and alanine, respectively. Mid-IR band strengths and absorption coefficients for CH₃NH₂ and CH₃CH₂NH₂, in both amorphous and crystalline forms, are presented, along with measurements of a density and refractive index (670 nm) for each. For these same compounds, we also have calculated IR optical constants, and they are being made available in electronic form. Some applications of our new results are described along with proposals for future investigations. Suggestions are made related to the methods employed in such work, and particularly to the application of Beer's Law to the IR study of compounds of astrobiological interest. Comments are also included on the methods used, and the results presented in a recently published work on amino-acid IR intensities.

The effect of alkylation on the micro-solvation of ethers revealed by highly localized water librational motion

The specific far-infrared spectral signatures associated with highly localized large-amplitude out-of-plane librational motion of water molecules have recently been demonstrated to provide sensitive spectroscopic probes for the micro-solvation of organic molecules [Mihrin et al., Phys. Chem. Chem. Phys. 21(4), 1717 (2019)]. The present work employs this direct far-infrared spectroscopic approach to investigate the non-covalent intermolecular forces involved in the micro-solvation of a selection of seven ether molecules with systematically varied alkyl substituents: dimethyl ether, diethyl ether, diisopropyl ether, ethyl methyl ether, t-butyl methyl ether, and t-butyl ethyl ether. The ranking of the observed out-of-plane water librational band signatures for this selected series of ether–water complexes embedded in inert neon matrices at 4 K reveals information about the interplay of directional intermolecular hydrogen bond motifs and non-directional and long-range dispersion interactions for the micro-solvated structures. These far-infrared observables differentiate minor subtle effects introduced by specific alkyl substituents and serve as rigorous experimental benchmarks for modern quantum chemical methodologies of various levels of scalability, which often fail to accurately predict the structural variations and corresponding vibrational signatures of the closely related systems. The accurate interaction energies of the series of ether–water complexes have been predicted by the domain based local pair natural orbital coupled cluster theory with single-, double-, and perturbative triple excitations, followed by a local energy decomposition analysis of the energy components. In some cases, the secondary dispersion forces are in direct competition with the primary intermolecular hydrogen bonds as witnessed by the specific out-of-plane librational signatures.

Phase Transitions in Low-Dimensional Layered Double Perovskites: The Role of the Organic Moieties

Halide double perovskites are an interesting alternative to Pb-containing counterparts as active materials in optoelectronic devices. Low-dimensional double perovskites are fabricated by introducing large organic cations, resulting in organic/inorganic architectures with one or more inorganic octahedra layers separated by organic cations. Here, we synthesized layered double perovskites based on 3D Cs2AgBiBr6, consisting of double (2L) or single (1L) inorganic octahedra layers, using ammonium cations of different sizes and chemical structures. Temperature-dependent Raman spectroscopy revealed phase transition signatures in both inorganic lattice and organic moieties by detecting variations in their vibrational modes. Changes in the conformational arrangement of the organic cations to an ordered state coincided with a phase transition in the 1L systems with the shortest ammonium moieties. Significant changes of photoluminescence intensity observed around the transition temperature suggest that optical properties may be affected by the octahedral tilts emerging at the phase transition.

Non-noble metallic Cu with three different roles in a Cu doped ZnO/Cu/g-C3N4 heterostructure for enhanced Z-scheme photocatalytic activity

Cu serves as a co-catalyst, an electron mediator, and a dopant leading to a high enhancement in the photocatalytic activity of Cu-ZnO/Cu/g-C₃N₄ Z-scheme photocatalyst.

A Million Crystal Structures: The Whole Is Greater than the Sum of Its Parts

The founding in 1965 of what is now called the Cambridge Structural Database (CSD) has reaped dividends in numerous and diverse areas of chemical research. Each of the million or so crystal structures in the database was solved for its own particular reason, but collected together, the structures can be reused to address a multitude of new problems. In this Review, which is focused mainly on the last 10 years, we chronicle the contribution of the CSD to research into molecular geometries, molecular interactions, and molecular assemblies and demonstrate its value in the design of biologically active molecules and the solid forms in which they are delivered. Its potential in other commercially relevant areas is described, including gas storage and delivery, thin films, and (opto)electronics. The CSD also aids the solution of new crystal structures. Because no scientific instrument is without shortcomings, the limitations of CSD research are assessed. We emphasize the importance of maintaining database quality: notwithstanding the arrival of big data and machine learning, it remains perilous to ignore the principle of garbage in, garbage out. Finally, we explain why the CSD must evolve with the world around it to ensure it remains fit for purpose in the years ahead.

Face indexing and shape analysis of salicylamide crystals grown in different solvents

The effect of solvent on salicylamide's crystal habit was investigated. It is deduced that ethyl acetate is adsorbed more strongly on the faces, the increased size of which, can explain the shape change.

Revealing Photoluminescence Modulation from Layered Halide Perovskite Microcrystals upon Cyclic Compression

Halide perovskites show promise for high-efficiency solar energy conversion and light-emitting diode devices owing to their bandgap, which falls within the visible optical range. However, due to their rigidity, GPa pressures are necessary to control the complex interplay between their electronic and crystallographic structure. Layered perovskites are likely to be controlled using much lower pressures by exploiting the optical anisotropy of the embedded organic molecules in the structure. This work introduces layered perovskite microplatelets and demonstrates the extreme sensitivity of their emission to cyclic mechanical loading in the range of tens of MPa. A drastic change in their emission is observed in situ, from near-white to an enhanced blue color. This process is reversible, as is evident from a hysteresis loop in the photoluminescence (PL) intensity of the microplatelets. A combination of experimental analysis and computational modelling shows that such behavior cannot be attributed to changes in the crystallographic structure of the flakes. Instead, it suggests that, thanks to their structural anisotropy, microplate alignment and reorientation are responsible for the observed PL modulation. The possibility to tune the optical emission of layered perovskite crystals via low pressures makes them highly interesting as active materials in applications where stress sensing or light modulation is desired.

Temperature-induced first-order displacive phase transition of isonicotinamide-4-methoxybenzoic acid co-crystal

Isonicotinamide–4-methoxybenzoic acid co-crystal (1), C6H6N2O·C8H8O3, is formed through slow evaporation from methanol solution and it undergoes a first-order isosymmetry (monoclinicI2/a↔ monoclinicI2/a) structural phase transition atTc= 142.5 (5) K, which has been confirmed by an abrupt jump of crystallographic interaxial angle β from variable-temperature single-crystal XRD and small heat hysteresis (6.25 K) in differential scanning calorimetry measurement. The three-dimensional X-ray crystal structures of (1) at the low-temperature phase (LTP) (100, 140 and 142 K) and the high-temperature phase (HTP) (143, 150, 200, 250 and 300 K) were solved and refined as a simple non-disordered model with finalR[F2> 2σ(F2)] ≃ 0.05. The asymmetric unit of (1) consists of crystallographically independent 4-methoxybenzoic acid (A) and isonicotinamide (B) molecules in both enantiotropic phases. MoleculeAadopts a `near-hydroxyl' conformation in which the hydroxyl and methoxy groups are positioned on the same side. Both `near-hydroxyl' and `near-carbonyl' molecular conformations possess minimum conformational energies with an energy difference of < 0.15 kJ mol−1from a potential energy surface scan. In the crystal, molecules are joined into linearABBAarrays by intermolecular N—H...O and O—H...N hydrogen bonds which were preserved in both phases. However, theseABBAarrays are displaced from planarity upon LTP-to-HTP transition and the changes in inter-array interactions are observed in two-dimensional fingerprint plots of their Hirshfeld surfaces. ThePIXELenergies of each molecular pair in both phases were calculated to investigate the difference in intermolecular interaction energies before and after the displacement ofABBAarrays from planarity, which directly leads to the single-crystal-to-single-crystal phase transition of (1).

Specific energy contributions from competing hydrogen-bonded structures in six polymorphs of phenobarbital

Background

In solid state structures of organic molecules, identical sets of H-bond donor and acceptor functions can result in a range of distinct H-bond connectivity modes. Specifically, competing H-bond structures (HBSs) may differ in the quantitative proportion between one-point and multiple-point H-bond connections. For an assessment of such HBSs, the effects of their internal as well as external (packing) interactions need to be taken into consideration. The semi-classical density sums (SCDS-PIXEL) method, which enables the calculation of interaction energies for molecule–molecule pairs, was used to investigate six polymorphs of phenobarbital (Pbtl) with different quantitative proportions of one-point and two-point H-bond connections.

Results

The structures of polymorphs V and VI of Pbtl were determined from single crystal data. Two-point H-bond connections are inherently inflexible in their geometry and lie within a small PIXEL energy range (−45.7 to −49.7 kJ mol⁻¹). One-point H-bond connections are geometrically less restricted and subsequently show large variations in their dispersion terms and total energies (−23.1 to −40.5 kJ mol⁻¹). The comparison of sums of interaction energies in small clusters containing only the strongest intermolecular interactions showed an advantage for compact HBSs with multiple-point connections, whereas alternative HBSs based on one-point connections may enable more favourable overall packing interactions (i.e. V vs. III). Energy penalties associated with experimental intramolecular geometries relative to the global conformational energy minimum were calculated and used to correct total PIXEL energies. The estimated order of stabilities (based on PIXEL energies) is III > I > II > VI > X > V, with a difference of just 1.7 kJ mol⁻¹ between the three most stable forms.

Conclusions

For an analysis of competing HBSs, one has to consider the contributions from internal H-bond and non-H-bond interactions, from the packing of multiple HBS instances and intramolecular energy penalties. A compact HBS based on multiple-point H-bond connections should typically lead to more packing alternatives and ultimately to a larger number of viable low-energy structures than a competing one-point HBS (i.e. dimer vs. catemer). Coulombic interaction energies associated with typical short intermolecular C–H···O contact geometries are small in comparison with dispersion effects associated with the packing complementary molecular shapes.Graphical abstract

A systematic structural study of halogen bonding versus hydrogen bonding within competitive supramolecular systems

As halogen bonds gain prevalence in supramolecular synthesis and materials chemistry, it has become necessary to examine more closely how such interactions compete with or complement hydrogen bonds whenever both are present within the same system. As hydrogen and halogen bonds have several fundamental features in common, it is often difficult to predict which will be the primary interaction in a supramolecular system, especially as they have comparable strength and geometric requirements. To address this challenge, a series of molecules containing both hydrogen- and halogen-bond donors were co-crystallized with various monotopic, ditopic symmetric and ditopic asymmetric acceptor molecules. The outcome of each reaction was examined using IR spectroscopy and, whenever possible, single-crystal X-ray diffraction. 24 crystal structures were obtained and subsequently analyzed, and the synthon preferences of the competing hydrogen- and halogen-bond donors were rationalized against a background of calculated molecular electrostatic potential values. It has been shown that readily accessible electrostatic potentials can offer useful practical guidelines for predicting the most likely primary synthons in these co-crystals as long as the potential differences are weighted appropriately.

A charge density study of π-delocalization and intermolecular interactions

The location of bond critical points (red dots) and its associated bond path (black line) provide the evidence on the existence of the weak intermolecular interactions of the π–π interactions between triazole rings of atrz molecules in crystal with the close ring distance of 3.17 Å.

Accurate and Efficient Model Energies for Exploring Intermolecular Interactions in Molecular Crystals

The energy of interaction between molecules is commonly expressed in terms of four key components: electrostatic, polarization, dispersion, and exchange-repulsion. Using monomer wave functions to obtain accurate estimates of electrostatic, polarization, and repulsion energies along with Grimme's dispersion corrections, a series of energy models are derived by fitting to dispersion-corrected DFT energies for a large number of molecular pairs extracted from organic and inorganic molecular crystals. The best performing model reproduces B3LYP-D2/6-31G(d,p) counterpoise-corrected energies with a mean absolute deviation (MAD) of just over 1 kJ mol(-1) but in considerably less computation time. It also performs surprisingly well against benchmark CCSD(T)/CBS energies, with a MAD of 2.5 kJ mol(-1) for a combined data set including Hobza's X40, S22, A24, and S66 dimers. Two of these energy models, the most accurate and the fastest, are expected to find widespread application in investigations of molecular crystals.