Intermolecular Geometries Research Articles

Halogen Bond via an Electrophilic π-Hole on Halogen in Molecules: Does It Exist?

This study reveals a new non-covalent interaction called a π-hole halogen bond, which is directional and potentially non-linear compared to its sister analog (σ-hole halogen bond). A π-hole is shown here to be observed on the surface of halogen in halogenated molecules, which can be tempered to display the aptness to form a π-hole halogen bond with a series of electron density-rich sites (Lewis bases) hosted individually by 32 other partner molecules. The [MP2/aug-cc-pVTZ] level characteristics of the π-hole halogen bonds in 33 binary complexes obtained from the charge density approaches (quantum theory of intramolecular atoms, molecular electrostatic surface potential, independent gradient model (IGM-δginter)), intermolecular geometries and energies, and second-order hyperconjugative charge transfer analyses are discussed, which are similar to other non-covalent interactions. That a π-hole can be observed on halogen in halogenated molecules is substantiated by experimentally reported crystals documented in the Cambridge Crystal Structure Database. The importance of the π-hole halogen bond in the design and growth of chemical systems in synthetic chemistry, crystallography, and crystal engineering is yet to be fully explicated.

Relationship between molecular structure and corrugations in self-assembled polypeptoid nanosheets revealed by cryogenic electron microscopy

Designing conformationally dynamic molecules that self-assemble into predictable nanostructures remains an important unmet challenge. This paper describes how atomic-scale cryogenic transmission electron microscopy (cryo-TEM) can be used to explore the relationship between molecular structure and self-assembly of block copolymers. We examined sheetlike micelles formed in water using a series of diblock copolypeptoids with the same hydrophilic block and three distinct crystalline hydrophobic blocks. Our cryo-TEM images revealed all the structures share nansoscale features, but differ in their intermolecular packing geometries. Different molecular arrangements, parallel and antiparallel V-shaped crystal motifs, were revealed by two-dimensional atomic-scale through-plane images. However, images from tilted samples revealed an unexpected feature when the hydrophobic polypeptoid block comprised phenyl rings with substituted bromine atoms at the para position. The nanosheets contained atomic-scale corrugations that were absent in the other systems which comprised unsubstituted aliphatic and aromatic side chains. We hypothesize that these corrugations are due to the dipolar characteristics of the brominated phenyl group and interactions between this group and water molecules. Published by the American Physical Society 2024

Fast electron damage mechanism of epoxy resin studied by electron energy loss spectroscopy and electron diffraction.

The damage mechanism and exposure tolerance of epoxy resins to fast electrons remain unclear. We quantitatively investigated the effects of electron irradiation on a common epoxy resin by dose-dependent electron energy loss spectroscopy. The results show that sp3 states of nitrogen, oxygen, and their adjacent carbon atoms were converted to sp2 states, forming imine (C=N) and carbonyl (C=O) as the total electron dose increased. The sp3 to sp2 conversion mechanism was proposed. The epoxy resin was very sensitive to fast electrons and the original electronic states were maintained up to a total dose of ∼103e-nm-2 at a low temperature of 103K. Dose-dependent electron diffraction revealed that the intra- and intermolecular geometries changed below and around the total dose of ∼103e-nm-2.

The Tetrel Bond and Tetrel Halide Perovskite Semiconductors.

The ion pairs [Cs+•TtX3-] (Tt = Pb, Sn, Ge; X = I, Br, Cl) are the building blocks of all-inorganic cesium tetrel halide perovskites in 3D, CsTtX3, that are widely regarded as blockbuster materials for optoelectronic applications such as in solar cells. The 3D structures consist of an anionic inorganic tetrel halide framework stabilized by the cesium cations (Cs+). We use computational methods to show that the geometrical connectivity between the inorganic monoanions, [TtX3-]∞, that leads to the formation of the TtX64- octahedra and the 3D inorganic perovskite architecture is the result of the joint effect of polarization and coulombic forces driven by alkali and tetrel bonds. Depending on the nature and temperature phase of these perovskite systems, the Tt···X tetrel bonds are either indistinguishable or somehow distinguishable from Tt-X coordinate bonds. The calculation of the potential on the electrostatic surface of the Tt atom in molecular [Cs+•TtX3-] provides physical insight into why the negative anions [TtX3-] attract each other when in close proximity, leading to the formation of the CsTtX3 tetrel halide perovskites in the solid state. The inter-molecular (and inter-ionic) geometries, binding energies, and charge density-based topological properties of sixteen [Cs+•TtX3-] ion pairs, as well as some selected oligomers [Cs+•PbI3-]n (n = 2, 3, 4), are discussed.

Tetrel Bonding in Anion Recognition: A First Principles Investigation

Twenty-five molecule-anion complex systems [I4Tt···X-] (Tt = C, Si, Ge, Sn and Pb; X = F, Cl, Br, I and At) were examined using density functional theory (ωB97X-D) and ab initio (MP2 and CCSD) methods to demonstrate the ability of the tetrel atoms in molecular entities, I4Tt, to recognize the halide anions when in close proximity. The tetrel bond strength for the [I4C···X-] series and [I4Tt···X-] (Tt = Si, Sn; X = I, At), was weak-to-moderate, whereas that in the remaining 16 complexes was dative tetrel bond type with very large interaction energies and short Tt···X close contact distances. The basis set superposition error corrected interaction energies calculated with the highest-level theory applied, [CCSD(T)/def2-TZVPPD], ranged from -3.0 to -112.2 kcal mol-1. The significant variation in interaction energies was realized as a result of different levels of tetrel bonding environment between the interacting partners at the equilibrium geometries of the complex systems. Although the ωB97X-D computed intermolecular geometries and interaction energies of a majority of the [I4Tt···X-] complexes were close to those predicted by the highest level of theory, the MP2 results were shown to be misleading for some of these systems. To provide insight into the nature of the intermolecular chemical bonding environment in the 25 molecule-anion complexes investigated, we discussed the charge-density-based topological and isosurface features that emanated from the application of the quantum theory of atoms in molecules and independent gradient model approaches, respectively.

Analytic Gradients for the Long-Range-Corrected XYG3 Type of Doubly Hybrid Density Functionals: Theory, Implementation, and Assessment.

An analytic gradient algorithm for the long-range-corrected (lrc-) XYG3 type of doubly hybrid functionals has been derived and implemented. Due to the introduction of a long-range second-order perturbation (lrPT2) as the correction, the Z-vector equations need to be modified, where the construction of a unique total Lagrangian of the method is required. Geometry optimizations using lrc-XYG3 and lrc-XYGJ-OS have then been applied to the A21 data set that consists of 21 noncovalently interacting systems with CCSD(T) reference data for structures, in order to testify the idea of introducing lrPT2 for a better description of intermolecular interactions. While lrc-XYG3 was observed to offer a better description in dispersion-dominant systems as compared to the XYG3 functional, lrc-XYGJ-OS stands out with an overall better balanced performance in reproducing intermolecular geometries.

Chalcogen···Chalcogen Bonding in Molybdenum Disulfide, Molybdenum Diselenide and Molybdenum Ditelluride Dimers as Prototypes for a Basic Understanding of the Local Interfacial Chemical Bonding Environment in 2D Layered Transition Metal Dichalcogenides

An attempt was made, using computational methods, to understand whether the intermolecular interactions in the dimers of molybdenum dichalcogenides MoCh2 (Ch = chalcogen, element of group 16, especially S, Se and Te) and similar mixed-chalcogenide derivatives resemble the room temperature experimentally observed interactions in the interfacial regions of molybdenites and their other mixed-chalcogen derivatives. To this end, MP2(Full)/def2-TVZPPD level electronic structure calculations on nine dimer systems, including (MoCh2)2 and (MoChCh′2)2 (Ch, Ch′ = S, Se and Te), were carried out not only to demonstrate the energetic stability of these systems in the gas phase, but also to reproduce the intermolecular geometrical properties that resemble the interfacial geometries of 2D layered MoCh2 systems reported in the crystalline phase. Among the six DFT functionals (single and double hybrids) benchmarked against MP2(full), it was found that the double hybrid functional B2PLYPD3 has some ability to reproduce the intermolecular geometries and binding energies. The intermolecular geometries and binding energies of all nine dimers are discussed, together with the charge density topological aspects of the chemical bonding interactions that emerge from the application of the quantum theory of atoms in molecules (QTAIM), the isosurface topology of the reduced density gradient noncovalent index, interaction region indicator and independent gradient model (IGM) approaches. While the electrostatic surface potential model fails to explain the origin of the S···S interaction in the (MoS2)2 dimer, we show that the intermolecular bonding interactions in all nine dimers examined are a result of hyperconjugative charge transfer delocalizations between the lone-pair on (Ch/Ch′) and/or the π-orbitals of a Mo–Ch/Ch′ bond of one monomer and the dπ* anti-bonding orbitals of the same Mo–Ch/Ch′ bond in the second monomer during dimer formation, and vice versa. The HOMO–LUMO gaps calculated with the MN12-L functional were 0.9, 1.0, and 1.1 eV for MoTe2, MoSe2 and MoS2, respectively, which match very well with the solid-state theoretical (SCAN-rVV10)/experimental band gaps of 0.75/0.88, 0.90/1.09 and 0.93/1.23 eV of the corresponding systems, respectively. We observed that the gas phase dimers examined are perhaps prototypical for a basic understanding of the interfacial/inter-layer interactions in molybdenum-based dichalcogenides and their derivatives.

An ab initio study of some halogen-bonded complexes containing cyclic ethers

The binary complexes formed between the dihalogens fluorine, chlorine and bromine, and the cyclic ethers oxirane, oxetane, tetrahydrofuran and tetrahydropyran, have been studied by means of ab initio calculations at the second-order level of Møller–Plesset perturbation theory. The properties of interest are the interaction energies, the intermolecular geometries, the perturbations of the intramolecular dihalogen and ether geometries, the wavenumber shifts of the dihalogen and ether molecules, and the variations of the natural atomic charges resulting from complexation. The trends observed are discussed in terms of the physical properties of the interacting monomers, such as the polarizabilities of the dihalogen molecules and the gas phase basicities of the ethers.

A new monoclinic form of a Ru(II)/Fe(II) heterobimetallic complex: Conformation, Crystal packing and Hirshfeld surface

Herein, a new monoclinic form (C2/c), Form H-II, of the heterobimetallic cis-[RuCl2(dppf)(bipy)] complex was obtained and compared in terms of molecular conformation, as well as intra and intermolecular geometries with two orthorhombic forms (Pna21) previously reported, Form S and H-I. The crystal packing of Form H-II is based on weak intermolecular interactions that were explored by Hirshfeld surface and 2D-fingerprint plots analysis, revealing the presence of weak H…H, C…H, C…C and Cl…H contacts that stabilize the crystal structure. As can be seen, the Form H-II differs from hydrate form (Form H-I), according water molecule location and crystal self-assembly. This found emphasizes the versatility of the studied Ru(II)/Fe(II) heterobimetallic complex in the crystal engineering field.

Synthesis and characterization of a new class of phenothiazine molecules with 10H-substituted morpholine & piperidine derivatives: A structural insight

A series of 10H-substituted phenothiazine-based molecules were prepared by the base-catalyzed reactions. The synthesized compounds are characterized by Mass spectroscopy, NMR, and SCXRD to examine the role of different functional groups involved in the intermolecular interactions and conformational geometries. The crystal packing of the compounds is governed by O–H⋯O, C–H⋯O, and π–π interactions. A complete understanding of the intermolecular interactions is studied employing the Hirshfeld analysis, 2D Fingerprint plot. Furthermore, the density functional theory (DFT/B3LYP) method at the 6–311++G(d,p) basis set was performed to support and compare experimental & theoretical geometrical parameters of phenothiazine derivatives.

How Significant Are Unusual Protein-Ligand Interactions? Insights from Database Mining.

We present a new approach to derive interaction propensities of protein-ligand atom pairs from mining of the Protein Data Bank. To ensure solid statistics, we use a line-of-sight contact filter and normalize the observed frequency of hits by a statistical null model based on exposed surface areas of atom types in the protein-ligand binding site. This allows us to investigate which intermolecular interactions and geometries are found more often than expected by chance in protein-ligand complexes. We focus our study on some of the unusual interactions that were postulated to be favorable, including σ-hole bonding of halogen and sulfur atoms, weak hydrogen bonding with fluorine as acceptor, and different types of dipolar interactions. Our results confirm some and challenge other common assumptions on these interactions and highlight other contact types that are yet underexplored in structure-based drug design.

Singlet-Fission-Born Quintet State: Sublevel Selections and Trapping by Multiexciton Thermodynamics.

Singlet fission (SF) is expected to exceed the theoretical limit of the solar cell efficiency. Quintet (Q) state generation in triplet-triplet pair is essential for preventing the unwanted loss of SF-born multiexciton through singlet channels, although little is known on the primary multiexciton spin dynamics following the intermolecular SF. In this study, time-resolved EPR revealed the intermolecular multiexciton dynamics, energetics and geometries in aggregated 6,13-bis(triisopropylsilylethynyl)pentacene and 2-phenyl-6,11-bis(triisopropylsilylethynyl)tetracene in diluted frozen solution. We have demonstrated sublevel selective generations of excited quintet states (|Q0⟩, |Q-1⟩ and |Q-2⟩) by singlet-quintet (SQ) mixings during triplet-exciton diffusions within geminate multiexcitons. The present fundamental characteristics of the quintet generations shows strong impact of coexistence of molecularly ordered "hot spot" and disordered regions for exergonic SQ mixings driven by entropy, thereby paving a new avenue for rational designs of organic devices with controlled multiexciton dynamics by optimizing film morphologies.

Qualitative and quantitative analysis of intermolecular interactions in xanthenedione derivatives.

The existence of intermolecular interactions and the conformational geometry adopted by molecules are related to biological activity. Xanthenedione molecules are promising and emerging antioxidants and acetylcholinesterase inhibitors. To examine the role of different functional groups involved in the intermolecular interactions and conformational geometries adopted in xanthenediones, a series of three substituted xanthenediones have been crystallized [9-(3-hydroxyphenyl)-3,3,6,6-tetramethyl-3,4,5,6,7,9-hexahydro-1H-xanthene-1,8(2H)-dione, C23H26O4, 9-(5-bromo-2-methoxyphenyl)-3,3,6,6-tetramethyl-3,4,6,7-tetrahydro-2H-xanthene-1,8(5H,9H)-dione, C24H27BrO4, and 3,3,6,6-tetramethyl-9-(pyridin-2-yl)-3,4,6,7-tetrahydro-2H-xanthene-1,8(5H,9H)-dione, C22H25NO3] and their intermolecular interactions analyzed via Hirshfeld analysis. The results show that all the derivatives adopt the same structural conformation, where the central ring has a shallow boat conformation and the outer rings have a twisted boat conformation. The intermolecular interactions in the molecules are predominantly O-H...O, C-H...O and π-π interactions. The optimized structures of the derivatives from theoretical B3LYP/6-311G** calculations show a good correlation with the experimental structures. The lattice energy involved in the intermolecular interactions has been explored using PIXELC.

New Polymorphs of Perylene:Tetracyanoquinodimethane Charge Transfer Cocrystals

We report two hitherto unknown polymorphs of the charge transfer (CT) cocrystal perylene:tetracyanoquinodimethane (TCNQ) grown by physical vapor transport (PVT) in argon atmosphere. One of the polymorphs, named β, has stoichiometry 1:1 and adds to the three known structures with stoichiometry 1:1 (α), 2:1, and 3:1. Interestingly, below (280 ± 10) K the β structure undergoes a phase transition to what we refer to as the γ polymorph, with halving of the unit cell and reduction of symmetry from monoclinic to triclinic. Both new crystal structures present two alternating stacks with different intermolecular and intramolecular geometries. In stack S–I the perylene molecules show substantial deviations from planarity, with the angle between the naphthalene intramolecular moieties of 6.69°, and with the perylene and TCNQ molecular centroids shifted by 1.95 A. In the second stack, S-II, the perylene is planar, and the centroids almost coincident. Structural investigations on bond length complemented by vibrationa...

Characterization of Excimer Relaxation via Femtosecond Shortwave- and Mid-Infrared Spectroscopy.

Excimer formation plays a significant role in trapping excitons within organic molecular solids. Covalent dimers of perylene-3,4:9,10-bis(dicarboximide) (PDI) are useful model systems for studying these processes as their intermolecular geometries can be precisely tuned. Using femtosecond visible-pump infrared-probe (fsIR) spectroscopy in the shortwave- and mid-infrared regions, we characterize two PDI dimers with a cofacial and a slip-stacked geometry that are coupled through a triptycene bridge. In the mid-infrared region, fsIR spectra for the strongly coupled dimers are highly blue-shifted compared to spectra for monomeric 1*PDI. The perylene core stretching modes provide a directly observable probe of excimer relaxation, as they are particularly sensitive to this process, which is associated with a small blue shift of these modes in both dimers. The broad Frenkel-to-CT state electronic transition of the excimer, the edge of which has previously been detected in the NIR region, is now fully resolved to be much broader and to extend well into the shortwave infrared region for both dimers and is likely a generic feature of π-extended aromatic excimers.

Singlet Fission via an Excimer-Like Intermediate in 3,6-Bis(thiophen-2-yl)diketopyrrolopyrrole Derivatives.

Singlet fission (SF) in polycrystalline thin films of four 3,6-bis(thiophen-2-yl)diketopyrrolopyrrole (TDPP) chromophores with methyl (Me), n-hexyl (C6), triethylene glycol (TEG), and 2-ethylhexyl (EH) substituents at the 2,5-positions is found to involve an intermediate excimer-like state. The four different substituents yield four distinct intermolecular packing geometries, resulting in variable intermolecular charge transfer (CT) interactions in the solid. SF from the excimer state of Me, C6, TEG, and EH takes place in τSF = 22, 336, 195, and 1200 ps, respectively, to give triplet yields of 200%, 110%, 110%, and 70%, respectively. The transient spectra of the excimer-like state and its energetic proximity to the lowest excited singlet state in these derivatives suggests that this state may be the multiexciton (1)(T1T1) state that precedes formation of the uncorrelated triplet excitons. The excimer decay rates correlate well with the SF efficiencies and the degree of intermolecular donor-acceptor interactions resulting from π-stacking of the thiophene donor of one molecule with the DPP core acceptor in another molecule as observed in the crystal structures. Such interactions are found to also increase with the SF coupling energies, as calculated for each derivative. These structural and spectroscopic studies afford a better understanding of the electronic interactions that enhance SF in chromophores having strong intra- and intermolecular CT character.

The integration of solid-form informatics into solid-form selection.

To demonstrate how the use of structural informatics during drug development assists with the assessment of the risk of polymorphism and the selection of a commercial solid form. The application of structural chemistry knowledge derived from the hundreds of thousands of crystal structures contained in the Cambridge Structural Database to drug candidates is described. Examples given show the comparison of intermolecular geometries to database-derived statistics, the use of Full Interaction Maps to assess polymorph stability and the calculation of hydrogen bond propensities to provide assurance of a stable solid form. The software tools used are included in the Cambridge Structural Database System and the Solid Form Module of Mercury. The early identification of an unusual supramolecular motif in the development phase of maraviroc led to further experimental work to find the most stable polymorph. Analyses of two polymorphs of a pain candidate drug demonstrated how consideration of molecular conformation and intermolecular interactions were used for the assessment of relative stability. Informatics analysis confirmed that the solid form of crizotinib, a monomorphic system, had a low risk of polymorphism. The application of informatics-based assessment of new chemical entities complements experimental studies and provides a deeper understanding of the qualities of the structure. The information provided by structural analyses is incorporated into the assessment of risk. Informatics techniques are quick to apply and are straightforward to use, allowing an assessment of progressing drug candidates.

Hot Charge-Transfer States Determine Exciton Dissociation in the DTDCTB/C60 Complex for Organic Solar Cells: A Theoretical Insight

To understand charge-transfer (CT) processes at the donor/acceptor interface of DTDCTB/fullerene solar cells, we have investigated the electronic couplings and the rates for exciton-dissociation and charge-recombination processes based on two representative intermolecular geometries of the DTDCTB/C60 complex by means of quantum-chemical calculations. Consistent with the experimental measurements of the time scale of over subns or even ns for charge recombination (CR), the calculated CR rates are lower than 1010 s–1 and in most cases, below 109 s–1. The calculated rates for exciton dissociation into the CT ground state are mostly lower than 1010 s–1, which is, however, in sharp contrast with the ultrafast charge separation (∼100 fs) observed experimentally. Interestingly, our calculations point out that excitons are able to dissociate into a higher-energy excited CT state much faster, with the rates being as large as about 1012 and 1014 s–1 in all cases for excitons based on C60 and DTDCTB, respectively. Thus, exciton dissociation in the DTDCTB/C60 complex is determined by the hot CT states. As the excess energy of the excited CT state can facilitate the geminate electron and hole to further separate at the donor/acceptor interface, our theoretical results suggest that the high performance of the DTDCTB/fullerene-based solar cell can be mainly attributed to the fact that excitons dissociate via the hot CT states to effectively form mobile charge carriers.

Synthesis and Solid-State Polymerization of Diacetylene Derivatives with an N-Carbazolylphenyl Group

Abstract Four diacetylene derivatives with an N-carbazolylphenyl group as a donor moiety have been synthesized and subsequently characterized. These diacetylene derivatives undergo solid-state polymerization via UV irradiation, although these compounds have relatively large π-conjugated aromatic groups. The polymerization behaviors of these derivatives were confirmed by distinct absorption bands for polydiacetylenes. The reactive process is strongly influenced by the slightly differing side groups. Single crystal growth of the two compounds was successful and their crystal structure analyses revealed large differences in the molecular conformations and intermolecular geometries caused by a methylene unit. The HOMO population of the monomers is predominantly expressed in the phenyl carbazole unit, while each polymer showed differing HOMO energies with some polymers exhibiting high-lying HOMO levels.

Mapping the genome of meta-generalized gradient approximation density functionals: the search for B97M-V.

A meta-generalized gradient approximation density functional paired with the VV10 nonlocal correlation functional is presented. The functional form is selected from more than 10(10) choices carved out of a functional space of almost 10(40) possibilities. Raw data come from training a vast number of candidate functional forms on a comprehensive training set of 1095 data points and testing the resulting fits on a comprehensive primary test set of 1153 data points. Functional forms are ranked based on their ability to reproduce the data in both the training and primary test sets with minimum empiricism, and filtered based on a set of physical constraints and an often-overlooked condition of satisfactory numerical precision with medium-sized integration grids. The resulting optimal functional form has 4 linear exchange parameters, 4 linear same-spin correlation parameters, and 4 linear opposite-spin correlation parameters, for a total of 12 fitted parameters. The final density functional, B97M-V, is further assessed on a secondary test set of 212 data points, applied to several large systems including the coronene dimer and water clusters, tested for the accurate prediction of intramolecular and intermolecular geometries, verified to have a readily attainable basis set limit, and checked for grid sensitivity. Compared to existing density functionals, B97M-V is remarkably accurate for non-bonded interactions and very satisfactory for thermochemical quantities such as atomization energies, but inherits the demonstrable limitations of existing local density functionals for barrier heights.