Cl···Cl interactions in molecular crystals: insights from the theoretical charge density analysis

Confinement and Separation of Benzene from an Azeotropic Mixture Using a Chlorinated B←N Adduct

Separations of azeotropic mixtures are typically carried out using energy-demanding processes (e.g., distillation). Here, we report the capacity of a self-assembled chlorinated boronic ester-based adduct to confine acetonitrile and benzene in channels upon crystallization. The solvent confinement occurs via a combination of hydrogen bonding and [π···π] interactions. Quantitative separation of benzene from an azeotropic 1:1 mixture of a benzene/acetonitrile (v/v), and methanol is achieved through crystallization with the chlorinated adduct by complementary [C-H···O] and [C-H···π] interactions. Inclusion behavior is rationalized by molecular modeling and crystallographic analysis. The chlorinated boronic ester adduct shows the potential of modularity via isosteric substitution for the separation of challenging chemical mixtures (e.g., azeotropes).

Dioxygen-halogen bonding exemplified by crystalline peroxosolvates of N,N'-bis(haloacetyl) bispidines

The halogen bonding in molecular crystals and supramolecular assemblies has been widely investigated. Special attention is given to the molecular structures capable of simultaneously exhibiting different types of non-covalent interactions, including conventional hydrogen bonds and halogen bonds. This paper systematically analyzes crystalline peroxosolvates of bispidine-based bis-amide derivatives, containing haloacetic acid residues, namely previously reported 1,1'-(1,5-dimethyl-3,7-diazabicyclo[3.3.1]nonane-3,7-diyl)bis(2-iodooethanone) peroxosolvate C13H20I2N2O2·H2O2 (1) and four new crystalline compounds, 1,1'-(1,5-dimethyl-3,7-diazabicyclo[3.3.1]nonane-3,7-diyl)bis(2-bromoethanone) peroxosolvate C13H20Br2N2O2·H2O2 (2), 1,1'-(9-hydroperoxy-9-hydroxy-1,5-dimethyl-3,7-diazabicyclo[3.3.1]nonane-3,7-diyl)bis(2-iodoethanone) peroxosolvate C13H20I2N2O5·0.5H2O2 (3), 1,1'-(9-hydroperoxy-9-hydroxy-1,5-dimethyl-3,7-diazabicyclo[3.3.1]nonane-3,7-diyl)bis(2-bromoethanone) peroxosolvate C13H20Br2N2O5·H2O2 (4), and 1,1'-(9-hydroperoxy-9-hydroxy-1,5-dimethyl-3,7-diazabicyclo[3.3.1]nonane-3,7-diyl)bis(2-chloroethanone) peroxosolvate C13H20Cl2N2O5·H2O2 (5). Compounds 2-5 were synthesized for the first time and their crystal structures were determined by single-crystal X-ray diffractometry (SCXRD). To the best of our knowledge, 3-5 are unprecedented crystalline hydrogen peroxide adducts of organic hydroperoxides (R-OOH). Short intermolecular contacts between halogen and hydroperoxo oxygen atoms were found in 1-3. The halogen bonding of C-I(Br) fragments with dioxygen species in compounds 1-3 as well as in the previously reported cocrystal of diacetone diperoxide with triodotrinitrobenzene (6) was identified through reduced density gradient analysis, Hirshfeld surface analysis, and Bader analysis of crystalline electron density. The interactions were quantified using the electron density topological properties acquired from the periodic DFT calculations and evaluated to lie in the range of 9-19 kJ mol-1. A distinctive spectral feature was revealed for this type of interaction, involving a red shift of the characteristic O-O stretching vibration by about 6 cm-1, which appeared in IR spectra as a narrow low-intensity band in the region 837-872 cm-1.

Bispidine as a Versatile Scaffold: From Topological Hosts to Transmembrane Transporters

The development of designer topological structures is a synthetically challenging endeavor. We present herein bispidine as a platform for the design of molecules with various topologies and functions. The bispidine-based acyclic molecule, which shows intriguing S-shape topology, is discussed. Single-crystal X-ray diffraction studies revealed that this molecule exists in the solid state as two conformational enantiomers. In addition, bispidine-based designer macrocycles were synthesized and investigated for ionophoric properties. Patch clamp experiments revealed that these macrocycles transport both anions and cations non-specifically with at least tenfold higher chloride conductance over the cations under the given experimental conditions. Ultramicroscopy and single-crystal X-ray crystallographic studies indicated that the self-assembling macrocycle forms a tubular assembly. Our design highlights the use of unconventional dihydrogen interactions in nanotube fabrication.

Virtual Screening, Structural Analysis, and Formation Thermodynamics of Carbamazepine Cocrystals

In this study, the existing set of carbamazepine (CBZ) cocrystals was extended through the successful combination of the drug with the positional isomers of acetamidobenzoic acid. The structural and energetic features of the CBZ cocrystals with 3- and 4-acetamidobenzoic acids were elucidated via single-crystal X-ray diffraction followed by QTAIMC analysis. The ability of three fundamentally different virtual screening methods to predict the correct cocrystallization outcome for CBZ was assessed based on the new experimental results obtained in this study and data available in the literature. It was found that the hydrogen bond propensity model performed the worst in distinguishing positive and negative results of CBZ cocrystallization experiments with 87 coformers, attaining an accuracy value lower than random guessing. The method that utilizes molecular electrostatic potential maps and the machine learning approach named CCGNet exhibited comparable results in terms of prediction metrics, albeit the latter resulted in superior specificity and overall accuracy while requiring no time-consuming DFT computations. In addition, formation thermodynamic parameters for the newly obtained CBZ cocrystals with 3- and 4-acetamidobenzoic acids were evaluated using temperature dependences of the cocrystallization Gibbs energy. The cocrystallization reactions between CBZ and the selected coformers were found to be enthalpy-driven, with entropy terms being statistically different from zero. The observed difference in dissolution behavior of the cocrystals in aqueous media was thought to be caused by variations in their thermodynamic stability.

Characterization of non-covalent contacts in mono- and di-halo substituted acetaldehydes: probing the substitution effects of electron donating and withdrawing groups

In the current work, a systematic evaluation of the different types of non-covalent interactions (NCIs) in acetaldehyde dimers, including dimers of mono-halo (XCH₂CHO)₂, di-halo (X₂CHCHO)₂ and tri-halo substituted (X₃CCHO)₂ acetaldehydes via the associated stabilization energy of these dimers has been performed. Furthermore, a topological analysis of the electron density based on the quantum theory of atoms in molecules (QTAIM) and non-covalent interaction reduced density gradient (NCI-RDG) isosurfaces has also been performed to evaluate the nature of these NCIs. The geometrical and electronic characteristics have been evaluated via the presence of different electron-donating groups (EDGs) and electron-withdrawing groups (EWGs) or substituents in dimers of these molecules, namely, XCH(Y)CHO and X₂C(Y)CHO (wherein X = -F, -Cl, and -Br and Y = -SO₃H, -CN, -NO₂, -NH₂, -CH₃, -OCH₃, and -SMe₃). The C-H⋯O, C-H⋯X, X⋯X, X⋯O and C⋯O tetrel bonded contacts have been recognized to play an important role in the stabilization of the formed dimers. This study also establishes the fact that the overall stability of the dimeric assemblies is governed by the contributions from the mutual and complex interplay of a variety of interactions in the investigated dimers. Hence considerations based on strong H-bond donor-acceptor characteristics hold relevance for simple systems only, but slight alteration in the electronic environment can affect the overall stabilization energies of the system being investigated and the nature of the interactions that contribute towards the same.

Halogen-Halogen Nonbonded Interactions

Halogen-halogen nonbonded interactions were studied for methyl halides and phenyl halides using both B3LYP and MP2 along with 6-311+G* and aug-cc-pVTZ. With the methyl halides, the linear approach was found to lead to little stabilization, whereas the "90°" approach gave 1-2 kcal/mol. This modest stabilization was due to long-range electron correlation effects. The lowest-energy arrangement had the molecules side-by-side, with the major stabilization being derived from halogen-hydrogen interactions. The results for methyl bromide were quite similar. Chlorobenzene dimer with the 90° orientation gave a small stabilization energy, but the best arrangement had the two benzene rings oriented over each other. The meta orientation of the chlorines had a lower energy than ortho or para. The dimerization energy was larger than that for two benzene rings sitting directly above each other, suggesting that whereas Cl···Cl interaction is not very important, the effect of the halogen on the electron distribution does have an effect. This suggests that much of the crystallographic results for these compounds may not be due to halogen-halogen interactions but rather the interaction between the substituted benzene rings along with crystal forces.

Modeling of Solute-Solvent Interactions Using an External Electric Field-From Tautomeric Equilibrium in Nonpolar Solvents to the Dissociation of Alkali Metal Halides

An implicit account of the solvent effect can be carried out using traditional static quantum chemistry calculations by applying an external electric field to the studied molecular system. This approach allows one to distinguish between the effects of the macroscopic reaction field of the solvent and specific solute-solvent interactions. In this study, we report on the dependence of the simulation results on the use of the polarizable continuum approximation and on the importance of the solvent effect in nonpolar solvents. The latter was demonstrated using experimental data on tautomeric equilibria between the pyridone and hydroxypyridine forms of 2,6-di-tert-butyl-4-hydroxy-pyridine in cyclohexane and chloroform.

Novel cocrystals of the potent 1,2,4-thiadiazole-based neuroprotector with carboxylic acids: virtual screening, crystal structures and solubility performance

Five new multicomponent solid forms of the biologically active 1,2,4-thiadiazole derivative (TDZH) with dicarboxylic and hydroxybenzoic acids have been discovered by combined virtual/experimental cocrystal screening.

Exploring the solid form landscape of the antifungal drug isavuconazole: crystal structure analysis, phase transformation behavior and dissolution performance

Phase transformation of ISV solid forms during dissolution.

London dispersion-driven hetero-aryl-aryl interactions in 1,2-diaryldisilanes

Non-covalent aryl-aryl interactions for the molecular structures of three 1,2-diaryltetramethyldisilanes X5C6-(SiMe2)2-C6Y5 (X ≠ Y; X, Y = H, F, Cl) were studied by single crystal X-ray and gas electron diffraction as well as by SAPT calculations. Aryl-aryl interactions cause all to adopt exclusively rather untypical eclipsed syn-conformers in the gas phase, and C6F5-(SiMe2)2-C6Cl5 also in the solid state.

Aryl-Aryl Interactions in (Aryl-Perhalogenated) 1,2-Diaryldisilanes

Three 1,2-diaryltetramethyldisilanes X5 C6 -(SiMe2 )2 -C6 X5 with two C6 H5 , C6 F5 , or C6 Cl5 groups were studied concerning the importance of London dispersion driven interactions between their aryl groups. They were prepared from 1,2-dichlorotetramethyldisilane by salt elimination. Their structures were determined in the solid state by X-ray diffraction and for free molecules by gas electron-diffraction. The solid-state structures of the fluorinated and chlorinated derivatives are dominated by aryl-aryl interactions. Unexpectedly, Cl5 C6 -(SiMe2 )2 -C6 Cl5 exists exclusively as an eclipsed syn-conformer in the gas phase with strongly distorted Si-C6 Cl5 units due to strong intramolecular interactions. In contrast, F5 C6 -(SiMe2 )2 -C6 F5 reveals weaker interactions. The contributions to the total interaction energy were analyzed by SAPT calculations.

Existence of untypical halogen-involving interactions in crystal packings: a statistical and first-principles study

There is a common perception by the scientific community that a halogen-involving interaction forms when the distance between the donor atom and the acceptor atom is less than the sum of their van der Waals (vdW) radii.

Relationships between Interaction Energy and Electron Density Properties for Homo Halogen Bonds of the [(A)nY-X···X-Z(B)m] Type (X = Cl, Br, I)

Relationships between interaction energy (Eint) and electron density properties at the X···X bond critical point or the d(X···X) distance were established for the large set of structures [(A)nY-X···X-Z(B)m] bearing the halogen bonds Cl···Cl, Br···Br, and I···I (640 structures in total). The best estimator of Eint is the kinetic energy density (Gb), which reasonably approximates the whole set of the structures as -Eint = 0.128Gb2 - 0.82Gb + 1.66 (R2 = 0.91, mean absolute deviation 0.39 kcal/mol) and demonstrates low dispersion. The potential and kinetic energy densities, electron density, and the d(X···X) distance behave similarly as estimators of Eint for the individual series Cl···Cl, Br···Br, and I···I. A number of the Eint(property) correlations are recommended for the practical application in the express estimates of the strength of the homo-halogen bonds.

Relative stability of the cis and trans isomers of octahedral cobalt(iii) complexes of the type [Co(N2O2)X2] with tetradentate salen type Schiff bases: a combined theoretical and experimental study

Energies of cis and trans isomers of a series of octahedral cobalt(iii) complexes with salen type Schiff bases have been estimated by DFT calculations.

The QM/MM-QTAIM approach reveals the nature of the different reactivity of cephalosporins in the active site of L1 metallo-β-lactamase

We combine the QM/MM and the QTAIM approaches to predict the reactivity of cephalosporins in the active site of L1 metallo-β-lactamase.

Solving the enigma of weak fluorine contacts in the solid state: a periodic DFT study of fluorinated organic crystals

The nature and strength of weak interactions with organic fluorine in the solid state are revealed by periodic density functional theory (periodic DFT) calculations coupled with experimental data on the structure and sublimation thermodynamics of crystalline organofluorine compounds. To minimize other intermolecular interactions, several sets of crystals of perfluorinated and partially fluorinated organic molecules are considered. This allows us to establish the theoretical levels providing an adequate description of the metric and electron-density parameters of the C–F⋯F–C interactions and the sublimation enthalpy of crystalline perfluorinated compounds. A detailed comparison of the C–F⋯F–C and C–H⋯F–C interactions is performed using the relaxed molecular geometry in the studied crystals. The change in the crystalline packing of aromatic compounds during their partial fluorination points to the structure-directing role of C–H⋯F–C interactions due to the dominant electrostatic contribution to these contacts. C–H⋯F–C and C–H⋯O interactions are found to be identical in nature and comparable in energy. The factors that determine the contribution of these interactions to the crystal packing are revealed. The reliability of the results is confirmed by considering the superposition of the electrostatic potential and electron density gradient fields in the area of the investigated intermolecular interactions.

The nature and strength of weak C–H⋯F–C and C–F⋯F–C interactions and their role in organofluorine molecular crystals were studied using periodic DFT coupled with CSD data mining and experimental sublimation enthalpies.

Hypercoordinated Oligosilanes Based on Aminotrisphenols

The hypercoordinated silicon chlorides ClSi[(o-OC₆H₄)₃N] (3) and ClSi[(OC₆H₂Me₂CH₂)₃N] (5) were used for the synthesis of catenated derivatives (Me₃Si)₃SiSi[(o-OC₆H₄)₃N] (9), (Me₃Si)₃SiSiMe₂SiMe₂Si(SiMe₃)₂Si[(o-OC₆H₄)₃N] (11), and (Me₃Si)₃SiSi[(OC₆H₂Me₂CH₂)₃N] (13) in reactions with (Me₃Si)₃SiK·THF (7) or (Me₃Si)₃SiK·[18-crown-6] (8). It was found that the nature of the (Me₃Si)₃SiK solvate determines the product of interaction, resulting in the formation of (Me₃Si)₃Si(CH₂)₄OSi[(OC₆H₂Me₂CH₂)₃N] (12) or 13. Compounds obtained were characterized using multinuclear NMR and UV-vis spectroscopy and mass spectrometry. The molecular structures of 3, 9, and 11-13 were investigated by single-crystal X-ray analysis, featuring hypercoordinated Si atoms in a trigonal-bipyramidal coordination environment with O atoms in the equatorial plane. The structure of the side product [N(CH₂C₆H₂Me₂O)₃Si]₂O (6) was also studied, indicating highly tetrahedrally distorted trigonal-bipyramidal environment at the Si atoms, which was confirmed by crystal density functional theory calculations indicating the very weak Si ← N interaction. The Si···N interatomic distances span a broad range (2.23-2.78 Å). The dependence of structural and NMR parameters for hypercoordinated catenated compounds from the type of the ligand was established.

Hydration of the Carboxylate Group in Anti-Inflammatory Drugs: ATR-IR and Computational Studies of Aqueous Solution of Sodium Diclofenac

Diclofenac (active ingredient of Voltaren) has a significant, multifaceted role in medicine, pharmacy, and biochemistry. Its physical properties and impact on biomolecular structures still attract essential scientific interest. However, its interaction with water has not been described yet at the molecular level. In the present study, we shed light on the interaction between the steric hindrance (the intramolecular N-H···O bond, etc.) carboxylate group (-CO₂^-) with water. Aqueous solution of sodium declofenac is investigated using attenuated total reflection-infrared (ATR-IR) and computational approaches, i.e., classical molecular dynamics (MD) simulations and density functional theory (DFT). Our coupled classical MD simulations, DFT calculations, and ATR-IR spectroscopy results indicated that the -CO₂^- group of the diclofenac anion undergoes strong specific interactions with the water molecules. The combined experimental and theoretical techniques provide significant insights into the spectroscopic manifestation of these interactions and the structure of the hydration shell of the -CO₂^- group. Moreover, the developed methodology for the theoretical analysis of the ATR-IR spectrum could serve as a template for the future IR/Raman studies of the strong interaction between the steric hindrance -CO₂^- group of bioactive molecules with the water molecules in dilute aqueous solutions.

Synthesis, characterization and crystal structure of 2-chloroethyl(methylsulfonyl)methanesulfonate

This is a study of structure – reactivity relationship of clomesone.

Supra-molecular inter-actions in the 1:2 co-crystal of 4,4'-bipyridine and 3-chloro-thio-phene-2-carb-oxy-lic acid

The asymmetric unit of the title compound, 2C5H3ClO2S·C10H8N2, is comprised of a mol-ecule of 3-chloro-thio-phene-2-carb-oxy-lic acid (3TPC) and half of a mol-ecule of 4,4'-bi-pyridine (BPY). A distinctive O-H⋯N-based synthon is present. Cl⋯Cl and π-π stacking inter-actions further stabilize the crystal structure, forming a two-dimensional network parallel to the bc plane.

Asymmetric bifurcated halogen bonds

Halogen bonding (XB) is being extensively explored for its potential use in advanced materials and drug design. Despite significant progress in describing this interaction by theoretical and experimental methods, the chemical nature remains somewhat elusive, and it seems to vary with the selected system. In this work we present a detailed DFT analysis of three-center asymmetric halogen bond (XB) formed between dihalogen molecules and variously 4-substituted 1,2-dimethoxybenzene. The energy decomposition, orbital, and electron density analyses suggest that the contribution of electrostatic stabilization is comparable with that of non-electrostatic factors. Both terms increase parallel with increasing negative charge of the electron donor molecule in our model systems. Depending on the orientation of the dihalogen molecules, this bifurcated interaction may be classified as 'σ-hole - lone pair' or 'σ-hole - π' halogen bonds. Arrangement of the XB investigated here deviates significantly from a recent IUPAC definition of XB and, in analogy to the hydrogen bonding, the term bifurcated halogen bond (BXB) seems to be appropriate for this type of interaction.

Using non-covalent interactions to direct regioselective 2+2 photocycloaddition within a macrocyclic cavitand

A cavitand mediated approach involving host–guest and guest–guest interactions has been developed to direct regioselective photocycloaddition of non-symmetric alkenes wherein a complete reversal in selectivity is achievable.

Halogenated tennimides and trezimides: impact of halogen bonding and solvent role on porous network formation and inclusion

The role of halogenated and aprotic solvents in macrocyclic structures is assessed in terms of halogen and hydrogen bonding interactions.

Hydrogen-bonding networks of purine derivatives and their bilayers for guest intercalation

6-Chloro-9-propyl-purin-2-amine (pr-GCl) forms two-dimensional hydrogen-bonded networks which in turn stack via π–π interactions, leading to the formation of bilayers that can accommodate organic guest molecules.

Theoretical study of intermolecular interactions in crystalline arene–perhaloarene adducts in terms of the electron density

The intermolecular interactions in C₆X₆–arene crystals (X = F, Cl) and the halogen substitution effect can be quantified by the electron density.

Crystal structure of 3-chloro-N-(2-nitro-phen-yl)benzamide

In the title compound, C13H9ClN2O3, the mean plane of the central amide fragment (r.m.s. deviation = 0.016 Å) subtends dihedral angles of 15.2 (2) and 8.2 (2)° with the chloro- and nitro-substituted benzene rings, respectively. An intra-molecular N-H⋯O hydrogen bond generates an S(6) ring. In the crystal, mol-ecules are linked by weak C-H⋯O hydrogen bonds, forming C(7) chains which propagate along [010], but no Cl⋯Cl short contacts are observed.

Influence of Secondary Interactions on the Structure, Sublimation Thermodynamics, and Solubility of Salicylate:4-Hydroxybenzamide Cocrystals. Combined Experimental and Theoretical Study

Cocrystal screening of 4-hydroxybenzamide with a number of salicylates (salicylic acid, SA; 4-aminosalicylic acid, PASA; acetylsalicylic acid, ASA; and salicylsalicylic acid, SSA) was conducted to confirm the formation of two cocrystals, [SA+4-OHBZA] (1:1) and [PASA+4-OHBZA] (1:1). Their structures were determined using single-crystal X-ray diffraction, and the hydrogen-bond network topology was studied. Thermodynamic characteristics of salicylic acid cocrystal sublimation were obtained experimentally. It was proved that PASA cocrystallization with 4-OHBZA makes the drug more stable and prevents the irreversible process of decarboxylation of PASA resulting in formation of toxic 3-aminophenol. The pattern of non-covalent interactions in the cocrystals is described quantitatively using solid-state density functional theory followed by Bader analysis of the periodic electron density. It has been found that the total energy of secondary interactions between synthon atoms and the side hydroxyl group of the acid molecule in [SA+4-OHBZA] (1:1) and [PASA+4-OHBZA] (1:1) cocrystals is comparable to the energy of the primary acid-amide heterosynthon. The theoretical value of the sublimation enthalpy of [SA+4-OHBZA], 231 kJ/mol, agrees fairly well with the experimental one, 272 kJ/mol. The dissolution experiments with [SA+4-OHBZA] have proved that the relatively large cocrystal stability in relation to the stability of its components has a negative effect on the dissolution rate and equilibrium solubility. The [PASA+4-OHBZA] (1:1) cocrystal showed an enhancement of apparent solubility compared to that of the corresponding pure active pharmaceutical ingredient, while their intrinsic dissolution rates are comparable.

Saccharin salts of biologically active hydrazone derivatives

Crystal structures, solubility and formation thermodynamics of saccharin salts with biologically active hydrazone derivatives were investigated.

The applicability of the dimeric heterosynthon concept to molecules with equivalent binding sites. A DFT study of crystalline urea–H2O2

The limited applicability of the dimeric heterosynthon concept to a two-component urea–H₂O₂crystal is reported.

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).

Salicylamide cocrystals: screening, crystal structure, sublimation thermodynamics, dissolution, and solid-state DFT calculations

A new cocrystal of 2-hydroxybenzamide (A) with 4-acetamidobenzoic acid (B) has been obtained by the DSC screening method. Thermophysical analysis of the aggregate [A:B] has been conducted and a fusion diagram has been plotted. Cocrystal formation from melts was studied by using thermomicroscopy. A cocrystal single-crystal was grown and its crystal structure was determined. The pattern of noncovalent interactions has been quantified using the solid-state DFT computations coupled with the Bader analysis of the periodic electron density. The sublimation processes of A-B cocrystal have been studied and its thermodynamic functions have been calculated. The classical method of substance transfer by inert gas-carrier was chosen to investigate sublimation processes experimentally. The lattice energy is found to be 143 ± 4 kJ/mol. It is lower than the sum of the corresponding values of the cocrystal pure components. The theoretical value of the lattice energy, 156 kJ/mol, is in reasonable agreement with the experimental one. A ternary phase diagram of solubility (A-B-ethanol) has been plotted and the areas with solutions for growing thermodynamically stable cocrystals have been determined.