Attractions and Repulsions in Molecular Crystals: What Can Be Learned from the Crystal Structures of Condensed Ring Aromatic Hydrocarbons?

Programming heterometallic 4f-4f' helicates under thermodynamic control: the circle is complete

Three non-symmetrical segmental ligand strands L4 can be wrapped around a linear sequence of one Zn2+ and two trivalent lanthanide cations Ln3+ to give quantitatively directional [ZnLn2(L4)3]8+ triple-stranded helicates in the solid state and in solution. NMR speciations in CD3CN show negligible decomplexation at a millimolar concentration and the latter helicate can be thus safely considered as a preorganized C3-symmetrical HHH-[(L43Zn)(LnA)(2-n)(LnB)n]8+ platform in which the thermodynamic properties of (i) lanthanide permutation between the central N9 and the terminal N6O3 binding sites and (ii) exchange processes between homo- and heterolanthanide helicates are easy to access (Ln = La, Eu, Lu). Deviations from statistical distributions could be programmed by exploiting specific site recognition and intermetallic pair interactions. Considering the challenging La3+ : Eu3+ ionic pair, for which the sizes of the two cations differ by only 8%, a remarkable excess (70%) of the heterolanthanide is produced, together with a preference for the formation of the isomer where the largest lanthanum cation lies in the central N9 site ([(La)(Eu)] : [(Eu)(La)] = 9 : 1). This rare design and its rational programming pave the way for the preparation of directional light-converters and/or molecular Q-bits at the (supra)molecular level.

Theoretical Investigation of Linear Relationships between the Dihedral Torsion Angles and Diosmium Bond Distances in Diosmium Sawhorse Complexes

Strong linear relationships between their Ceq-Os-Os-Ceq dihedral angles and their Os-Os bond distances in diosmium sawhorse complexes Os2(u-O2CR)2(CO)4L2 (L = CO and/or PR3) form two trendlines depending upon the presence or absence of terminal phosphines. These trends appear unrelated to the basicity of the bridging ligand or the number of phosphines. The mathematical derivation of the relationship between the O-Os-Os-O dihedral angle and the Os-Os bond distance shows how the other geometric parameters affect this relationship. Optimized density functional theory (DFT) structures reveal a similar strong linear correlation, where more electron-donating ligands render shorter Os-Os bond distances and larger dihedral angles, but these results form a single trendline. Computational scans of individual parameters show that the Os-Os bond responds strongly to changes in the dihedral angles, but the dihedral angles only respond weakly to changes in the Os-Os bond distance because the Os-Os-O bond angle links and modifies their direct coupling. Solid-state analysis of their structures, including DFT geometry optimizations, shows that phosphines protect the Os-Os bond distance from packing influences along the Os-Os axis, while in complexes without phosphines, packing compresses the Os-Os bond and the weak dihedral responses create the second trendline.

Realizing long range π-conjugation in phenanthrene and phenanthrene-based molecular crystals for anomalous piezoluminescence

Unlike the known aggregation-caused quenching (ACQ) that the enhancement of π-π interactions in rigid organic molecules usually decreases the luminescent emission, here we show that an intermolecular "head-to-head" π-π interaction in the phenanthrene crystal, forming the so-called "transannular effect", could result in a higher degree of electron delocalization and thus photoluminescent emission enhancement. Such a transannular effect is molecular configuration and stacking dependent, which is absent in the isomers of phenanthrene but can be realized again in the designed phenanthrene-based cocrystals. The transannular effect becomes more significant upon compression and causes anomalous piezoluminescent enhancement in the crystals. Our findings thus provide new insights into the effects of π-π interactions on luminescence emission and also offer new pathways for designing efficient aggregation-induced emission (AIE) materials to advance their applications.

Molecular dynamics investigation of benzoic acid in confined spaces

Classical molecular dynamics simulations are carried out to investigate the aggregation of supercooled benzoic acid in confined spaces. Nanocavities, nanotubes and nanolayers are defined by restricting the periodicity of the simulation to zero, one or two dimensions, with boundaries set by adjustable, general, and computationally cheap van der Waals barriers. The effect of different confinement geometries is explored. It is found that the confinement impacts the liquid collective dynamics, strengthening the correlations that affect the motion of distant molecules. Overall, confinement determines up to a tenfold increase of the viscosity of the liquid and strongly slows down the rotational correlation times. Aggregation mediated by interactions with the walls and partial polarization of the liquid are observed. Additionally, transitions to high-density liquid states occur when stiffer barriers are used. In general, a reduced accessible amount of phase space fosters the struggle for a closer packing to relieve unfavorable atom-atom contacts, while maximizing the attractive ones. In benzoic acid, this implies that the hydrogen bond network is organized more efficiently in high density states.

Synthesis and Structural Properties of Adamantane-Substituted Amines and Amides Containing an Additional Adamantane, Azaadamantane or Diamantane Moiety

Introduction of adamantane moieties on diamondoids such as adamantane, 2-azaadamantane or diamantane by amide formation and reduction to the corresponding amine was performed in a straightforward and easy way by amidation under Schotten-Baumann conditions and reduction with BH3  ⋅ THF. The obtained amides and amines were studied in terms of structural properties towards the perspective of transformation into nanodiamonds. Crystal structure and dynamic NMR experiments of the most crowded amide obtained gave structural insights into the effect of bulkiness and steric strain on out-of-planarity of amide bonds (16.0°) and the kinetics and thermodynamics of amide bond rotation (ΔG≠ 298K =11.5-13.3 kcal ⋅ mol-1 ).

Combined Computational/Experimental Investigation of new cocrystals of the drug bosentan

We report the discovery of new cocrystals of bosentan, a drug used in the treatment of pulmonary artery hypertension, with succinic acid, resorcinol and 4-hydroxybenzoic acid through a combined virtual/experimental...

Experimental and computational evidence for a stabilising C–Cl(lone-pair)⋯π(chelate-ring) interaction

Stabilising C–Cl(lone-pair)⋯π(chelate ring) interactions are described.

A new supramolecular heterosynthon [C–I⋯OC(carboxylate)] at work: engineering copper acetate cocrystals

Carboxylate–iodine supramolecular heterosynthons in combination with energy frameworks can be reliably applied in engineering hybrid metal-carboxylate cocrystals.

Experimental Approach to the Study of Anharmonicity in the Infrared Spectrum of Pyrene from 14 to 723 K

Quantifying the effect of anharmonicity on the infrared spectrum of large molecules such as polycyclic aromatic hydrocarbons (PAHs) at high temperatures is the focus of a number of theoretical and experimental studies, many of them motivated by astrophysical applications. We recorded the IR spectrum of pyrene C16H10 microcrystals embedded in KBr pellets over a wide range of temperatures (14-723 K) and studied the evolution of band positions, widths, and integrated intensities with temperature. We identified jumps for some of the spectral characteristics of some bands in the 423-473 K range. These were attributed to a change of phase from crystal to molten in condensed pyrene, which appears to affect more strongly bands involving large CH motions. Empirical anharmonicity factors that quantify the linear evolution of band positions and widths with temperature for values larger than ∼150-250 K, depending on the band, were retrieved from both phases and averaged to provide recommended values for these anharmonicity factors. The derived values were found to be consistent with available gas phase data. We conclude about the relevance of the methodology to produce data that can be compared with calculated anharmonic IR spectra and provide input for models that simulate the IR emission of astro-PAHs.

Rigorous control of vesicle-forming lipid pKa by fluorine-conjugated bioisosteres for gene-silencing with siRNA

While the influence of pK_a provided by amine-containing materials in siRNA delivery vectors for use in gene-silencing has been widely studied, there are little reports in which amine pK_a is controlled rigorously by using bioisosteres and its effect on gene-silencing. Here, we report that amine pK_a could be rigorously controlled by replacement of hydrogen atom(s) with fluorine atom(s). A series of mono- and di-amine lipids with a different number of fluorine atoms were synthesized. The pK_a of the polyamine lipids was shifted to a lower value with an increase in the number of fluorine atoms. The optimal pK_a for high gene-silencing efficiency varied according to the number of amine residues in the polyamine lipid. Whereas the endosomal escape ability of mono-amine lipid-containing lipid vesicles (LVs) depended on the pK_a, that of all tested di-amine lipid-containing LVs showed equal membrane-destabilizing activity. LVs showing moderately weak interactions with siRNA facilitated cytoplasmic release of siRNA, resulting in strong gene-silencing. These findings indicate that appropriate amine pK_a engineering depending on the number of amines is important for the induction of effective RNA interference.

How Au Outperforms Pt in the Catalytic Reduction of Methane towards Ethane and Molecular Hydrogen

Within the context of a "hydrogen economy", it is paramount to guarantee a stable supply of molecular hydrogen to devices such as fuel cells. At the same time, catalytic conversion of the environmentally harmful methane into ethane, with a significantly lower Global Warming Potential, turns into a highly desirable challenge. Herein we propose a first-step novel proof-of-concept mechanism to accomplish both tasks simultaneously. For that purpose we provide transition-state barriers and reaction Helmholtz free energies obtained from first-principles Density Functional Theory by taking account vibrations for 2CH₄(g) → C₂H₆(g) + H₂(g) to show that molecular hydrogen can be produced by subnanometer Pt₃₈ and Au₃₈ nanoparticles from natural gas. Interestingly, the active sites for the reaction are located on different planes on the two nanoparticles, effectively differentiating the working principle of the two metals. The analysis shows that the complete cycle to reduce CH₄ can be performed on Au and Pt with similar efficiencies, but Au requires only half the working temperature of Pt. This substantial decrease of temperature can be traced back to several intermediate steps, but most crucially to the final one where the catalyst must be cleaned from H(⋆) to be able to restart the catalytic cycle. This simple study case provides useful guidelines to capitalize on finite-size effects in small nanoparticles for the design of new and more efficient catalysts. Interestingly, present results obtained for the intermediate steps of the catalytic cycle show an excellent agreement with previous experimental evidence. Finally, we stress the importance of including the final cleaning steps to start a new fresh catalytic cycle.

Modelling of adsorption and intercalation of hydrogen on/into tungsten disulphide multilayers and multiwall nanotubes

Understanding the interaction of hydrogen with layered materials is crucial in the fields of sensors, catalysis, fuel cells and hydrogen storage, among others. Density functional theory, improved by the introduction of van der Waals dispersion forces, provides an efficient and practical workbench to investigate the interaction of molecular and atomic hydrogen with WS2 multilayers and nanotubes. We find that H2 physisorbs on the surface of those materials on top of W atoms, while atomic H chemisorbs on top of S atoms. In the case of nanotubes, the chemisorption strength is sensitive to the nanotube diameter. Diffusion of H2 on the surface of WS2 encounters quite small activation barriers whose magnitude helps to explain previous and new experimental results for the observed dependence of the hydrogen concentration with temperature. Intercalation of H2 between adjacent planar WS2 layers reveals an endothermic character. Intercalating H atoms is energetically favorable, but the intercalation energy does not compensate for the cost of dissociating the molecules. When H2 molecules are intercalated between the walls of a double wall nanotube, the rigid confinement induces the dissociation of the confined molecules. A remarkable result is that the presence of a full H2 monolayer adsorbed on top of the first WS2 layer of a WS2 multilayer system strongly facilitates the intercalation of H2 between WS2 layers underneath. This opens up an additional gate to intercalation processes.

Pillars of crystal engineering: crystal energies and symmetry operators

Molecular pairs with top-ranking interaction energy are sorted out for 1235 organic crystal structures, in relationship with the corresponding symmetry operators. Top pairing energies compare with 20–40% of the total lattice energies (see figure).

Competition between intermolecular hydrogen bonding and stacking in the crystals of 4-Hydroxy-N-(pyridin-2-yl)-2,2-dioxo-1H-2λ6,1-benzothiazine-3-carboxamides

The traditional crystal packing study based on the analysis of geometrical characteristics of intermolecular interactions is found to be not informative enough. The application of quantum-chemical calculations for the evaluation of pairwise interaction energies between molecules allows to get much more information about supramolecular architecture. The staking interactions between π-systems of neighboring molecules form the building unit of the crystal packing in the absence of any strong interactions as well as in the presence of the N–H…O classical hydrogen bond. Unexpectedly the hydrogen bonds play the secondary role in the crystal packing formation as compared to stacking. Analysis of the total interaction energy of the basic molecule with all the molecules of its first coordination sphere and the pairwise interaction energies allows to evaluate the extent of crystal isotropy from point of view of interaction energies.

Br...Br and van der Waals interactions along a homologous series: crystal packing of 1,2-dibromo-4,5-dialkoxybenzenes

The crystalline structures of four homologues of the 1,2-dibromo-4,5-dialkoxybenzene series [Br2C6H2(OCnH2n + 1)2forn= 2, 12, 14 and 18] have been solved by means of single-crystal crystallography. Comparison along the series, including the previously reportedn= 10 andn= 16 derivatives, shows a clear metric trend (bandcessentially fixed along the series andagrowing linearly withn), in spite of some subtle differences in space groups and/or packing modes. A uniform packing pattern for the aliphatic chains has been found for then= 12 to 18 homologues, which slightly differs from that of then= 10 derivative. The crystalline structures of all the higher homologues (n= 10–18) seem to arise from van der Waals interchain interactions and, to a lesser extent, type II Br...Br interactions. The dominant role of interchain interactions provides direct structural support for the usual interpretation of melting point trends like that found along this series.Atoms in Molecules(AIM) analysis allows a comparison of the relative magnitude of the interchain and Br...Br interactions, an analysis validated by the measured melting enthalpies.

Structural systematics of aryl-1,3-dithiane derivatives: crystal and energy-minimised structures, and Hirshfeld surface analysis

The crystal structure analysis of three aryl-1,3-dithiane derivatives, with aryl=4-methylphenyl (1), 4-chlorophenyl (2) and 2,4-dichlorophenyl (3), shows the three molecules to have very similar conformations, with the aryl ring lying on an approximate mirror plane that bisects the dithiane ring which adopts a chair conformation; the energy-minimised structures are consistent with the experimental structures. The greater barrier to rotation about the methine-C–C(ipso) bond in 3, cf. 1 and 2, is related to unfavourable intramolecular S···Cl interactions in the putative transition state. The molecular packing in 1–3, while globally similar, are distinct, being based on combinations of identifiable C–H···π(arene), C–H···S and C–Cl···π(arene) interactions. The lack of isostructural relationships points to the significance of the identified intermolecular interactions to direct molecular packing.

Crystal Fluidity Reflected by Fast Rotational Motion at the Core, Branches, and Peripheral Aromatic Groups of a Dendrimeric Molecular Rotor

Low packing densities are key structural features of amphidynamic crystals built with static and mobile components. Here we report a loosely packed crystal of dendrimeric rotor 2 and the fast dynamics of all its aromatic groups, both resulting from the hyperbranched structure of the molecule. Compound 2 was synthesized with a convergent strategy to construct a central phenylene core with stators consisting of two layers of triarylmethyl groups. Single crystal X-ray diffraction analysis confirmed a low-density packing structure consisting of one molecule of 2 and approximately eight solvent molecules per unit cell. Three isotopologues of 2 were synthesized to study the motion of each segment of the molecule in the solid state using variable temperature quadrupolar echo (2)H NMR spectroscopy. Line shape analysis of the spectra reveals that the central phenylene, the six branch phenylenes, and the 18 periphery phenyls all display megahertz rotational dynamics in the crystals at ambient temperature. Arrhenius analysis of the data gives similar activation energies and pre-exponential factors for different parts of the structure. The observed pre-exponential factors are 4-6 orders of magnitude greater than those of elementary site-exchange processes, indicating that the dynamics are not dictated by static energetic potentials. Instead, the activation energies for rotations in the crystals of 2 are controlled by temperature dependent local structural fluctuations and crystal fluidity.

Molecular crystals by design?

In this Viewpoint, the impact of the paper published by Gautam R. Desiraju and Angelo Gavezzotti (J. Chem. Soc., Chem. Commun., 1989, 621) upon the development of Crystal Engineering, now recognised a key discipline in contemporary chemical/pharmaceutical/materials science, is discussed.

An efficient algorithm for multipole energies and derivatives based on spherical harmonics and extensions to particle mesh Ewald

Next-generation molecular force fields deliver accurate descriptions of non-covalent interactions by employing more elaborate functional forms than their predecessors. Much work has been dedicated to improving the description of the electrostatic potential (ESP) generated by these force fields. A common approach to improving the ESP is by augmenting the point charges on each center with higher-order multipole moments. The resulting anisotropy greatly improves the directionality of the non-covalent bonding, with a concomitant increase in computational cost. In this work, we develop an efficient strategy for enumerating multipole interactions, by casting an efficient spherical harmonic based approach within a particle mesh Ewald (PME) framework. Although the derivation involves lengthy algebra, the final expressions are relatively compact, yielding an approach that can efficiently handle both finite and periodic systems without imposing any approximations beyond PME. Forces and torques are readily obtained, making our method well suited to modern molecular dynamics simulations.

The importance of Au⋯π(aryl) interactions in the formation of spherical aggregates in binuclear phosphane gold(i) complexes of a bipodal thiocarbamate dianion: a combined crystallographic and computational study, and anti-microbial activity

Compact molecular structures of antimicrobial (R₃PAu)₂L (R = Et (1), Ph ((2) and Cy ((3); LH₂ = {1,4-[MeOC(S)-N(H)]₂C₆H₄}), arise from intramolecular Au⋯π(aryl) interactions, proven by theory to be attractive and 12 kcal mol^–1 more stable than anticipated Au⋯O interactions.

The nature of the C–Br⋯Br–C intermolecular interactions found in molecular crystals: a general theoretical-database study

The properties of C–Br⋯Br–C interactions have been determined by doing MP2 theoretical calculations on model dimers and on dimers taken from the Cambridge Structural Database (presenting Br⋯Br distances within the 3.0 to 4.5 Å range).

Etching of graphene in a Hydrogen-rich Atmosphere towards the Formation of Hydrocarbons in Circumstellar Clouds

We describe a mechanism that explains the formation of hydrocarbons and hydrocarbyls from hydrogenated graphene/graphite; hard C-C bonds are weakened and broken by the synergistic effect of chemisorbed hydrogen and high temperature vibrations. Total energies, optimized structures, and transition states are obtained from Density Functional Theory simulations. These values have been used to determine the Boltzman probability for a thermal fluctuation to overcome the kinetic barriers, yielding the time scale for an event to occur. This mechanism can be used to rationalize the possible routes for the creation of small hydrocarbons and hydrocarbyls from etched graphene/graphite in stellar regions.

Virtual screening: an in silico tool for interlacing the chemical universe with the proteome

In silico screening both in the forward (traditional virtual screening) and reverse sense (inverse virtual screening (IVS)) are helpful techniques for interlacing the chemical universe of small molecules with the proteome. The former, which is using a protein structure and a large chemical database, is well-known by the scientific community. We have chosen here to provide an overview on the latter, focusing on validation and target prioritization strategies. By comparing it to complementary or alternative wet-lab approaches, we put IVS in the broader context of chemical genomics, target discovery and drug design. By giving examples from the literature and an own example on how to validate the approach, we provide guidance on the issues related to IVS.

Nanoindentation in crystal engineering: quantifying mechanical properties of molecular crystals

Nanoindentation is a technique for measuring the elastic modulus and hardness of small amounts of materials. This method, which has been used extensively for characterizing metallic and inorganic solids, is now being applied to organic and metal-organic crystals, and has also become relevant to the subject of crystal engineering, which is concerned with the design of molecular solids with desired properties and functions. Through nanoindentation it is possible to correlate molecular-level properties such as crystal packing, interaction characteristics, and the inherent anisotropy with micro/macroscopic events such as desolvation, domain coexistence, layer migration, polymorphism, and solid-state reactivity. Recent developments and exciting opportunities in this area are highlighted in this Minireview.