Conformational Analysis of Conjugated Organic Materials: What Are My Heteroatoms Really Doing?

Organic semiconductor small molecules and polymers often incorporate heteroatoms into their chemical structures to affect the electronic properties of the material. A particular design philosophy has been to use these heteroatoms to influence torsional potentials, since the overlap of adjacent π-orbitals is most efficient in planar systems and is critical for charge delocalization in these systems. Since these design rules became popular, the messages from the earlier works have become lost in a sea of reports of "conformational locks", where the non-covalent interactions have relatively small contributions to planarizing torsional potentials. Greater influences can be found in the stabilization by extended conjugation, consideration of steric repulsion, and the interactions involving solubilizing chains and neighboring molecules or polymer chains in condensed phases.

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.

Ability of Peripheral H Bonds to Strengthen a Halogen Bond

Quantum calculations study the manner in which the involvement of a halogen atom as a proton acceptor in one or more H bonds (HBs) affects the strength of the halogen bond (XB) it can form with a nucleophile aligned with the X σ-hole. A variety of Lewis acids wherein X = F, Cl, Br, and I are attached to a tetrel atom C or Ge engaged in a XB with nucleophile NH₃. One, two, and three HF molecules were positioned perpendicular to the XB axis so that they could form a HB to the X atom. Each such HB strengthened the XB by an increment of 1 kcal/mol or more that does not attenuate as each new HB is added, potentially increasing the interaction energy manyfold. Additionally, the presence of one or more HBs facilitates the formation of a XB by molecules which are reluctant to engage in such a bond in the absence of these auxiliary interactions. Even the F atom, which avoids such a XB, can be coaxed to participate in a XB of moderate strength by one or more of these external HBs.

The Relevance of Experimental Charge Density Analysis in Unraveling Noncovalent Interactions in Molecular Crystals

The work carried out by our research group over the last couple of decades in the context of quantitative crystal engineering involves the analysis of intermolecular interactions such as carbon (tetrel) bonding, pnicogen bonding, chalcogen bonding, and halogen bonding using experimental charge density methodology is reviewed. The focus is to extract electron density distribution in the intermolecular space and to obtain guidelines to evaluate the strength and directionality of such interactions towards the design of molecular crystals with desired properties. Following the early studies on halogen bonding interactions, several "sigma-hole" interaction types with similar electrostatic origins have been explored in recent times for their strength, origin, and structural consequences. These include interactions such as carbon (tetrel) bonding, pnicogen bonding, chalcogen bonding, and halogen bonding. Experimental X-ray charge density analysis has proved to be a powerful tool in unraveling the strength and electronic origin of such interactions, providing insights beyond the theoretical estimates from gas-phase molecular dimer calculations. In this mini-review, we outline some selected contributions from the X-ray charge density studies to the field of non-covalent interactions (NCIs) involving elements of the groups 14-17 of the periodic table. Quantitative insights into the nature of these interactions obtained from the experimental electron density distribution and subsequent topological analysis by the quantum theory of atoms in molecules (QTAIM) have been discussed. A few notable examples of weak interactions have been presented in terms of their experimental charge density features. These examples reveal not only the strength and beauty of X-ray charge density multipole modeling as an advanced structural chemistry tool but also its utility in providing experimental benchmarks for the theoretical studies of weak interactions in crystals.

Rational Computational Design of Systems Exhibiting Strong Halogen Bonding Involving Fluorine in Bicyclic Diamine Derivatives

Perhaps the most controversial and rare aspect of the halogen bonding interaction is the potential of fluorine in compounds to serve as a halogen bond donor. In this note, we provide clear and convincing examples of hypothetical molecules in which fluorine is strongly halogen bonding in a metastable state. Of particular note is a polycyclic system inspired by Selectfluor, which has been controversially proposed to engage in halogen bonding.

On the Ability of Nitrogen to Serve as an Electron Acceptor in a Pnicogen Bond

Whereas pnicogen atoms like P and As have been shown repeatedly to act as electron acceptors in pnicogen bonds, the same is not true of the more electronegative first-row N atom. Quantum calculations assess whether N can serve in this capacity in such bonds and under what conditions. There is a positive π-hole belt that surrounds the central N atom in the linear arrangement of NNNF, NNN-CN, and NNO, which can engage a NH₃ base to form a pnicogen bond with binding energy between 3 and 5 kcal/mol. Within the context of a planar arrangement, the π-hole above the N in NO₂OF, N(CN)₃, and CF₃NO₂ is also capable of forming a pnicogen bond, the strongest of which amounts to 11 kcal/mol with NMe₃ as base. In their pyramidal geometry, NF₃ and N(NO₂)₃ engage with a base through the σ-hole on the central N, with variable binding energies between 2 and 9 kcal/mol. AIM and NBO provide somewhat different interpretations of the secondary interactions that occur in some of these complexes.

Azide···Oxygen Interaction: A Crystal Engineering Tool for Conformational Locking

We have designed, synthesized and crystallized 36 compounds, each containing an azide group and an oxygen atom separated by three bonds. Crystal structure analysis revealed that each of these molecules adopts a conformation in which the azide and oxygen groups orient syn to each other with a short O ··· N b  contact. Geometry-optimized structures [using  M06-2X/6-311G(d,p) level of theory ] also showed the syn conformation in all 36 of these cases, suggesting that this not merely a crystal packing effect. Quantum topological analysis using Bader's Atoms in Molecules (AIM) theory revealed bond paths and bond critical points (BCP) in these structures suggesting its nature and energetics to be similar to weak hydrogen bonding. The NCI-RDG plot clearly revealed the attractive interaction consisting of electrostatic or dispersive components in all the 36 systems. NBO analysis suggested a weak orbital-relaxation (charge-transfer) contribution of energy for a few  (sp2) O-donor systems. Natural population analysis (NPA) and molecular electrostatic potential mapping (MESP) of these crystal structures further revealed the existence of favorable azide-oxygen interaction.   A CSD search indicated the frequent and consistent occurrence of this interaction and its role dictating the syn conformation of azide and oxygen in molecules where these groups are separated by 2-4 bonds.

The crystal structure of 3,4-dichlorobenzoic acid chloride, C7H3Cl3O

C7H3Cl3O, monoclinic, P21/c (no. 14), a = 12.0518(15) Å, b = 9.7403(11) Å, c = 6.9562(9) Å, β = 99.047(4)°, V = 806.42(17) Å3, Z = 4, R gt (F) = 0.0316, wR ref (F 2) = 0.0793, T = 200 K.

Understanding noncovalent bonds and their controlling forces

The fundamental underpinnings of noncovalent bonds are presented, focusing on the σ-hole interactions that are closely related to the H-bond. Different means of assessing their strength and the factors that control it are discussed. The establishment of a noncovalent bond is monitored as the two subunits are brought together, allowing the electrostatic, charge redistribution, and other effects to slowly take hold. Methods are discussed that permit prediction as to which site an approaching nucleophile will be drawn, and the maximum number of bonds around a central atom in its normal or hypervalent states is assessed. The manner in which a pair of anions can be held together despite an overall Coulombic repulsion is explained. The possibility that first-row atoms can participate in such bonds is discussed, along with the introduction of a tetrel analog of the dihydrogen bond.

F-Halogen Bond: Conditions for Its Existence

The question as to whether the F atom can engage in a halogen bond (XB) remains unsettled. This issue is addressed via density functional theory calculations which pair a wide range of organic and inorganic F-acids with various sorts of Lewis bases. From an energetic perspective, perfluorinated hydrocarbons with sp, sp², or sp³ C-hybridization are unable to form an XB with an N-base, but a very weak bond can be formed if electron-withdrawing C≡N substituents are added to the acid. There is little improvement for inorganic acids O₂NF, FOF, ClF, BrF, SiF₄, or GeF₄, but F₂ is capable of a stronger XB of up to 5 kcal/mol. These results are consistent with a geometric criterion, which compares the intermolecular equilibrium distance with the sum of atomic van der Waals radii. The intensity of the σ-hole on the F atom has predictive value in that a V_s,max of at least 10-15 kcal/mol is required for XB formation. Adding a positive charge to the Lewis acid enhances the strength of any XB and even more so if the base is anionic. The acid-base interaction induces a contraction of the r(AF) covalent bond in the acid in most cases and a deshielding of the NMR signal of the F nucleus.

Synthesis, X-ray characterization and theoretical study of 3a,6:7,9a-diepoxybenzo[de]isoquinoline derivatives: on the importance of F⋯O interactions

This manuscript reports the synthesis, X-ray characterization and theoretical study of 3a,6:7,9a-diepoxybenzo[de]isoquinoline derivatives focusing on the importance of F···O interactions.

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.

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

Weak intermolecular interactions observed in crystalline materials are often influenced or forced by stronger interactions such as classical hydrogen bonds. Room temperature liquids offer a scenario where such strong interactions are absent so that the role and nature of the weak interactions can be studied more reliably. In this context, we have analyzed the common organic reagent benzoyl chloride (BC) and a series of its fluorinated derivatives using in situ cryocrystallography. The intermolecular interaction energies have been estimated and their topologies explored using energy framework analysis in a series of ten benzoyl chloride analogues, which reveal that the ππ stacking interactions serve as the primary building blocks in these crystal structures. The crystal packing is also stabilized by a variety of interaction motifs involving weak C-HO/F/Cl hydrogen bonds and FF, FCl, and ClCl interactions. It is found that fluorination alters the electrostatic nature of the benzoyl chlorides, with subsequent changes in the formation of different weak interaction motifs. The effects of fluorination on these weak intermolecular interactions have been systematically analyzed further via detailed inputs from a topological analysis of the electron density and Hirshfeld surface analysis.

Characterization of fluorine-centred `F...O' σ-hole interactions in the solid state

In the current study, the crystal structure of 1-(3-nitrophenyl)-2,2,2-trifluoroethanone (A1) and (E)-4-((4-fluorophenyl) diazenyl)phenol (A2) has been analyzed for the characterization of the presence of a `unique' and `rare' intermolecular C(sp3/sp2)—F...O contact, which has been observed to play a significant role in the crystal packing. Theoretical charge-density calculations have been performed to study the nature and strength associated with the existence of this intermolecular F...O contact, wherein the F atom is attached to ansp3-hybridized C atom in the case of A1 and to ansp2hybridized carbon in the case of A2. The crystal packing of the former contains two `electronically different' Csp3—F...O contacts which are present across and in between the layers of molecules. In the latter case, it is characterized by the presence of a very `short' (2.708 Å) and `highly directional' (168° at ∠C4—F1...O1 and 174° at ∠C10—O1...F1) Csp2—F...O contact. According to the Cambridge Structural Database (CSD) study, it is a rare example in molecular crystals. Topological features of F...O contacts in the solid state were compared with the gas-phase models. The two-dimensional and three-dimensional static deformation density obtained from theoretical multipole modeling confirm the presence of a charge depleted region on the F atoms. Minimization of the electrostatic repulsion between like charges are observed through subtle arrangements in the electronic environment in two of the short intermolecular F...O contacts. These contacts were investigated using inputs from pair energy decomposition analysis, Bader's quantum theory of atoms in molecules (QTAIM), Hirshfeld surface analysis, delocalization index, reduced density gradient (RDG) plot, electrostatic potential surface and distributed atomic polarizability. The intermolecular energy decomposition (PIXEL) and RDG–NCI (non-covalent interaction) analysis of the F...O contacts establish the interaction to be dispersive in nature. The mutual polarization of an O atom by fluorine andviceversaprovides real physical insights into the role of atomic polarizability in interacting atoms in molecules in crystals.

Fluorination promotes chalcogen bonding in crystalline solids

Flurorine promotes the electrophilicity of sulfur to the point that chalcogen bond formation affects the crystal packing in the solid.