Energy frameworks and a topological analysis of the supramolecular features in in situ cryocrystallized liquids: tuning the weak interaction landscape via fluorination

5-Aminoisophthalate-based kojic acid-appended bis-1,2,3-triazole: a fluorescent chemosensor for Cu2+ sensing and in silico study

A new, easy-to-prepare, and highly selective fluorescent chemosensor, i.e., 5-aminoisophthalate-based kojic acid-appended bis-1,2,3-triazole, was synthesized from an alkyne of 5-aminoisophthalic acid and azido-kojic acid using Cu(i)-catalyzed click chemistry and then successfully characterized. The alkyne structure of 5-aminoisophthalic acid, 1, was supported by the single-crystal X-ray crystallographic data. The fluorescent probe 3 was found to be highly selective for Cu2+ ions supported by the Job's plot with a stoichiometric ligand : metal ratio of 2 : 1, exhibiting almost a two-fold enhancement in the emission intensity upon the addition of Cu2+ ions (0-25 μM) with a detection limit of 8.82 μM. A comparison with LODs from previously developed chemosensors for Cu2+ ions was also conducted. Reversibility analysis indicated that probe 3 could be used as both a reusable sensor and as a scavenger of copper ions. DFT calculations with the basis sets B3LYP/6-311G(d,p) and LanL2DZ were employed for geometrical optimizations of structures of the alkyne 1, azide 2, probe 3, and complex 3.Cu2+. Hirshfeld surface analysis revealed significant intermolecular interactions in compound 1. Additionally, molecular docking for the antimicrobial activity showed the better antibacterial efficacy of probe 3.

Supramolecular assemblies in the molecular complexes of 4-cyanophenylboronic acid with different N-donor ligands

Molecular complexes of 4-cyanophenylboronic acid (CB) with various N-donor compounds having different conformational features, for example, rigid (1,10-phenanthroline (110phen), 4,7-phenanthroline (47phen), 1,7-phenanthroline (17phen) and acridine (acr)) and linear (1,2-bis(4-pyridyl)ethane (bpyea), 1,2-bis(4-pyridyl)ethene (bpyee) and 4,4'-azopyridine (azopy)), have been reported. In all complexes, the -B(OH)2 moiety is found to be in a syn-anti confirmation, with the exception of structures containing 110phen, bpyee, and azopy, wherein, syn-syn conformation is observed. Further, CB molecules remain intact in all structures except in the complexes with some linear N-donor ligands, wherein -B(OH)2 transforms to monoester (-B(OH)(OCH3)) prior to the formation of corresponding molecular complexes. In such boronic monoester complexes, the conformation of -B(OH)(OCH3) is syn-anti with respect to the -OH and -OCH3 groups. Also, complexes mediated by azopy and bpyee exist in both hydrated and anhydrous forms. In these anhydrous structures, the recognition pattern is through homomeric (juxtaposed -CN and -B(OH)2) as well as heteromeric (between hetero N-atom and -B(OH)2) O-H⋯N hydrogen bonds, while only heteromeric O-H⋯N hydrogen bonds hold co-formers in all other structures. Depending upon the conformational features of both co-formers, molecules are packed in crystal lattices in the form of stacked layers, helical chains, and crossed ribbons. All structures are fully characterized by single-crystal X-ray diffraction and phase purity is established by powder X-ray diffraction. Additionally, correlation among structures is explained by calculating a similarity index and performing a Hirshfeld surface analysis to quantify the strength and effectiveness of different types of intermolecular bonds that stabilize these structures along with the presentation of energy frameworks, representing the strength of the interactions in the form gradient cylinders. Also, the morphology of each complex was computed by BFDH methodology to correlate with the actual crystal morphology and packing arrangement.

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.

Low-Molecular-Weight Organogelators Based on N-dodecanoyl-L-amino Acids-Energy Frameworks and Supramolecular Synthons

Lauric acid was used to synthesize the low-molecular-weight organogelators (LMOGs), derivatives of two endogenous (L)-alanine, (L)-leucine, and three exogenous (L)-valine, (L)-phenylalanine, and (L)-proline amino acids. The nature of processes responsible for the gel formation both in polar and in apolar solvents of such compounds is still under investigation. Knowing that the organization of surfactant molecules affects the properties of nano scale materials and gels, we decided to elucidate this problem using crystallographic diffraction and energy frameworks analysis. The single crystals of the mentioned compounds were produced successfully from heptane/^tBuOMe mixture. The compounds form lamellar self-assemblies in crystals. The energetic landscapes of single crystals of a series of studied amphiphilic gelators have been analyzed to explore the gelling properties. The presented results may be used as model systems to understand which supramolecular interactions observed in the solid state and what energy contributions are desired in the designing of new low-molecular-weight organic gelators.

Structure, Optical and Magnetic Properties of Two Isomeric 2-Bromomethylpyridine Cu(II) Complexes [Cu(C6H9NBr)2(NO3)2] with Very Different Binding Motives

Two isomeric 2-bromomethylpyridine Cu(II) complexes [Cu(C₆H₉NBr)₂(NO₃)₂] with 2-bromo-5-methylpyridine (L¹) and 2-bromo-4-methylpyridine (L²) were synthesized as air-stable blue materials in good yields. The crystal structures were different with [Cu(L¹)₂(NO₃)₂] (CuL¹) crystallizing in the monoclinic space group P2₁/c, while the 4-methyl derivative CuL² was solved and refined in triclinic P1¯. The orientation of the Br substituents in the molecular structure (anti (CuL¹) vs. syn (CuL²) conformations) and the geometry around Cu(II) in an overall 4 + 2 distorted coordination was very different with two secondary (axially elongated) Cu-O bonds on each side of the CuN₂O₂ basal plane in CuL¹ or both on one side in CuL². The two Br substituents in CuL² come quite close to the Cu(II) centers and to each other (Br⋯Br ~3.7 Å). Regardless of these differences, the thermal behavior (TG/DTA) of both materials is very similar with decomposition starting at around 160 °C and CuO as the final product. In contrast to this, FT-IR and Raman frequencies are markedly different for the two isomers and the UV-vis absorption spectra in solution show marked differences in the π-π* absorptions at 263 (CuL²) or 270 (CuL¹) nm and in the ligand-to-metal charge transfer bands at around 320 nm which are pronounced for CuL¹ with the higher symmetry at the Cu(II) center, but very weak for CuL². The T-dependent susceptibility measurements also show very similar results (µ_eff = 1.98 µ_B for CuL¹ and 2.00 µ_B for CuL² and very small Curie-Weiss constants of about -1. The EPR spectra of both complexes show axial symmetry, very similar averaged g values of 2.123 and 2.125, respectively, and no hyper-fine splitting.

Structure-property relationship in thioxotriaza-spiro derivative: Crystal structure and molecular docking analysis against SARS-CoV-2 main protease

Detailed structural and non-covalent interactions in thioxotriaza-spiroderivative (DZ2) are investigated by single crystal structure anslysis and computational approaches. Its results were compared with the previously reported spiroderivative (DZ1). The crystal structure analysis revealed various C–H…O, N–H…O, C–H…N and N–H…S hydrogen bonds involved in constructing several dimeric motifs to stabilize the crystal packing. The differences and similarities in the relative contribution of non-covalent interactions in DZ1 and DZ2 compounds are compared using the Hirshfeld surface analysis and 2D fingerprint plots. The binding energies of specific molecular pairs and homodimers have been obtained using molecule–molecule interaction energy calculation. The hierarchy and topology of pair-wise intermolecular interactions are visualized through energy frameworks. The nature and strength of intra and intermolecular interactions were characterized using non-covalent interaction index analysis and the quantum theory of atoms in molecule approach. Further, molecular docking of compounds (DZ1 and DZ2) with SARS-CoV-2 main protease for COVID-19 is performed. And the superposition of these ligands and inhibitor N3, which is docked into the binding pocket of 7BQY, is presented. The binding affinity of −6.7 kcal/mol is observed, attributed to hydrogen bonding and hydrophobic interactions between the ligand and the amino acid residues of the receptor.

Deformation-induced phosphorescence shift in a 2D elastically flexible organic single crystal: role of chalcogen-centered weak interactions

Mechanically responsive organic luminescent crystals are one of the promising choices of materials for flexible photonic devices. However, the change in phosphorescence emission as a function of the flexibility of a crystal has never been reported. Our current findings demonstrate two-dimensional (2D) and one-dimensional (1D) macroscopic elastic deformability, under mechanical stress, in elastically flexible single crystals of dibenzothiophene, and its brominated derivative, respectively. Unlike the presence of dual fluorescence (FL) and room temperature phosphorescence (RTP) in dibenzothiophene single crystals, the derivative was found to show only RTP. Interestingly, upon elastic deformation, single crystals of the dual emissive dibenzothiophene show a noticeable blue shift (∼20 nm) of RTP emission when compared to their pristine crystals (straight and naturally bent). However, their FL peaks remain nearly unchanged irrespective of the crystal deformation. A hierarchy of structure-elastic functionality to RTP modulation has been quantitatively mapped by rationalizing the role of chalcogen-involved weak interactions.

In response to macroscopic elastical bending, single crystals of dual emissive dibenzothiophene depict a significant blue shift (∼20 nm) of RTP emission when compared to their pristine crystals (straight and naturally bent).

Cocrystals Based on 4,4’-bipyridine: Influence of Crystal Packing on Melting Point

The reactions of piperonylic acid (HPip) and cinnamic acid (HCinn) with 4,4’-bipyridine (4,4’-bipy) have been assayed using the same synthetic methodology, yielding two binary cocrystals with different acid:4,4’-bipy molar ratios, (HPip)(4,4’-bipy) (1) and (HCinn)2(4,4’-bipy) (2). The melting point (m.p.) of these cocrystals have been measured and a remarkable difference (ΔT ≈ 78 °C) between them was observed. Moreover, the two cocrystals have been characterized by powder X-ray diffraction (PXRD), elemental analysis (EA), FTIR-ATR, 1H NMR spectroscopies, and single-crystal X-ray diffraction. The study of their structural packings via Hirshfeld surface analysis and energy frameworks revealed the important contribution of the π···π and C-H···π interactions to the formation of different structural packing motifs, this being the main reason for the difference of m.p. between them. Moreover, it has been observed that 1 and 2 presented the same packing motifs as the crystal structure of their corresponding carboxylic acids, but 1 and 2 showed lower m.p. than those of the carboxylic acids, which could be related to the lower strength of the acid-pyridine heterosynthons respect to the acid-acid homosynthons in the crystal structures.

Elastic anisotropy of mechanically responsive molecular solids

Unique mechanical properties in molecular solids arise from a specific combination of structure and interaction anisotropy. Powder Brillouin light scattering offers new insight into the latter contribution to test current models for mechanical design.

Mapping the cooperativity pathways in spin crossover complexes

Crystal packing energy calculations are applied to the [Fe(PM-L)₂(NCS)₂] family of spin crossover (SCO) complexes (PM-L = 4-substituted derivatives of the N-(2-pyridylmethylene)-4-aminobiphenyl ligand) with the aim of relating quantitatively the cooperativity of observed SCO transitions to intermolecular interactions in the crystal structures. This approach reveals a linear variation of the transition abruptness with the sum of the magnitudes of the interaction energy changes within the first molecular coordination sphere in the crystal structure. Abrupt transitions are associated with the presence of significant stabilising and destabilising changes in intermolecular interaction energies. While the numerical trend established for the PM-L family does not directly extend to other classes of SCO complex in which the intermolecular interactions may be very different, a plot of transition abruptness against the range of interaction energy changes normalised by the largest change shows a clustering of complexes with similar transition abruptness. The changes in intermolecular interactions are conveniently visualised using energy difference frameworks, which illustrate the cooperativity pathways of an SCO transition.

The abruptness of spin crossover (SCO) is related to intermolecular energy changes occurring over the course of an SCO transition. Crossover is abrupt when SCO-induced strain is accommodated synergistically in a few key interactions.

The borderline: exploring the structural landscape of triptycene in cocrystallization with ferrocene

When the effective packing of triptycene (TripH)–ferrocene chain oligomers in their cocrystal could not be achieved, we reached a borderline at the structural landscape of TripH, where the packing of TripH molecules reproduces the pattern in the native TripH crystal.

Exploring the Effect of the Irradiation Time on Photosensitized Dendrimer-Based Nanoaggregates for Potential Applications in Light-Driven Water Photoreduction

Fourth generation polyamidoamine dendrimer (PAMAM, G4) modified with fluorescein units (F) at the periphery and Pt nanoparticles stabilized by L-ascorbate were prepared. These dendrimers modified with hydrophobic fluorescein were used to achieve self-assembling structures, giving rise to the formation of nanoaggregates in water. The photoactive fluorescein units were mainly used as photosensitizer units in the process of the catalytic photoreduction of water propitiated by light. Complementarily, Pt-ascorbate nanoparticles acted as the active sites to generate H2. Importantly, the study of the functional, optical, surface potential and morphological properties of the photosensitized dendrimer aggregates at different irradiation times allowed for insights to be gained into the behavior of these systems. Thus, the resultant photosensitized PAMAM-fluorescein (G4-F) nanoaggregates (NG) were conveniently applied to light-driven water photoreduction along with sodium L-ascorbate and methyl viologen as the sacrificial reagent and electron relay agent, respectively. Notably, these aggregates exhibited appropriate stability and catalytic activity over time for hydrogen production. Additionally, in order to propose a potential use of these types of systems, the in situ generated H2 was able to reduce a certain amount of methylene blue (MB). Finally, theoretical electronic analyses provided insights into the possible excited states of the fluorescein molecules that could intervene in the global mechanism of H2 generation.

Guest Solvent-dependence of the Nanomechanical Response in Substituted Dihydropyrimidinone Crystals

The nanomechanical responses of two crystalline phases of a dihydropyrimidine analogue (1) were similar irrespective of the presence (or absence) of the guest solvent. In contrast, the mechanical responses of two differently solvated forms of the second related (2) crystals were significantly different. These contrasting behaviors are rationalized in terms of intermolecular interactions and energy distributions.

Energy framework approach to the supramolecular reactions: interplay of the secondary bonding interaction in Ph2E2 (E = Se, Te)/p-I-C6F4-I co-crystals

Persistent packing patterns found in pure diorgano-dichalcogenides (Ph₂E₂) and their co-crystals suggest new, energy-based visualization and description of co-crystal formation.

Evaluating the importance of fractional Z′ polymorphs in a trifluoromethylated N,N′-diphenyloxalamide derivative

A curious case of crystal dimorphism reveals an adjusted fractional number of molecules in their respective crystallographic asymmetric units.

Crystal packing analysis of in situ cryocrystallized 2,2,2-tri-fluoro-aceto-phenone

Crystals of the liquid compound 2,2,2-tri-fluoro-aceto-phenone (TFAP, C8H5F3O) were obtained using the state-of-art in situ cryocrystallization technique. TFAP crystallizes in the monoclinic space group C2/c, and its crystal structure is mainly stabilized by a set of C-H⋯F, C-H⋯O, F⋯F and F⋯O supra-molecular contacts. The overall mol-ecular arrangement shows the formation of mol-ecular sheets parallel to the bc plane, which are in turn stacked along the a-axis direction. The weak inter-actions have been studied thoroughly, performing both a Hirshfeld surface analysis and theoretical calculations, to obtain the inter-molecular inter-action energies. A structural comparison of this compound with the previously reported substituted analogs was also carried out, showing a qualitative difference in terms of packing behaviour.

Revealing Factors Influencing the Fluorine-Centered Non-Covalent Interactions in Some Fluorine-Substituted Molecular Complexes: Insights from First-Principles Studies

We examine the equilibrium structure and properties of six fully or partially fluorinated hydrocarbons and several of their binary complexes using computational methods. In the monomers, the electrostatic surface of the fluorine is predicted to be either entirely negative or weakly positive. However, its lateral sites are always negative. This enables the fluorine to display an anisotropic distribution of charge density on its electrostatic surface. While this is the electrostatic surface scenario of the fluorine atom, its negative sites in some of these monomers are shown to have the potential to engage in attractive engagements with the negative site(s) on the same atom in another molecule of the same type, or a molecule of a different type, to form bimolecular complexes. This is revealed by analyzing the results of current state-of-the-art computational approaches such as DFT, together with those obtained from the quantum theory of atoms in molecules, molecular electrostatic surface potential and symmetry adapted perturbation theories. We demonstrate that the intermolecular interaction energy arising in part from the universal London dispersion, which has been underappreciated for decades, is an essential factor in explaining the attraction between the negative sites, although energy arising from polarization strengthens the extent of the intermolecular interactions in these complexes.

Quantitative analysis of solid-state diversity in trifluoromethylated phenylhydrazones

The cooperative roles of various structural motifs associated with the presence of different intermolecular interactions in the formation of molecular crystals are investigated in a series of trifluoromethylated phenylhydrazones. Out of the six compounds analysed, two exhibit three-dimensional structural similarities with geometrically equivalent building blocks, while a third exists as two polymorphic forms crystallized from ethanol solutions at low temperature (277 K) and room temperature (298 K), respectively. The compounds were characterized via single-crystal and powder X-ray diffraction techniques and differential scanning calorimetry. In the absence of any strong hydrogen bonding, the supramolecular constructs are primarily stabilized via molecular pairs with a high dispersion-energy contribution, due to the presence of molecular stacking along the molecular backbone along with C-H...π interactions in the solid state, in preference to an electrostatic contribution. The interaction energies for the most stabilizing molecular building blocks are in the range -29 to -43 kJ mol^-1. In addition, weak N-H...F, C-H...F and N-H...C interactions and F...F, F...C, F...N and C...N contacts act as secondary motifs, providing additional stability to the crystal packing. The overall molecular arrangements are carefully analysed in terms of their nature and energetics, and the roles of different molecular pairs towards the crystal structure are delineated. A topological study using the quantum theory of atoms in molecules was used to characterize all the atomic interactions in the solid state. It established the presence of (3, -1) bond critical points and the closed-shell nature of all the interactions.

CrystalExplorer model energies and energy frameworks: extension to metal coordination compounds, organic salts, solvates and open-shell systems

The application domain of accurate and efficient CE-B3LYP and CE-HF model energies for intermolecular interactions in molecular crystals is extended by calibration against density functional results for 1794 molecule/ion pairs extracted from 171 crystal structures. The mean absolute deviation of CE-B3LYP model energies from DFT values is a modest 2.4 kJ mol-1 for pairwise energies that span a range of 3.75 MJ mol-1. The new sets of scale factors determined by fitting to counterpoise-corrected DFT calculations result in minimal changes from previous energy values. Coupled with the use of separate polarizabilities for interactions involving monatomic ions, these model energies can now be applied with confidence to a vast number of molecular crystals. Energy frameworks have been enhanced to represent the destabilizing interactions that are important for molecules with large dipole moments and organic salts. Applications to a variety of molecular crystals are presented in detail to highlight the utility and promise of these tools.