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Summary The structure and reactivity of silicon(IV), the second most abundant element in our Earth's crust, is determined by its invariant tetrahedral coordination geometry. Silicon(IV) with a square-planar configuration (ptSiIV) represents a transition state. Quantum theory supported the feasibility of stabilizing ptSiIV by structural constraint, but its isolation has not been achieved yet. Here, we present the synthesis and full characterization of the first square-planar coordinated silicon(IV). The planarity provokes an extremely low-lying unoccupied molecular orbital that induces unusual silicon redox chemistry and CH-agostic interactions. The small separation of the frontier molecular orbitals enables visible-light ligand-element charge transfer and bond-activation reactivity. Previously, such characteristics have been reserved for d-block metals or low-valent p-block elements. Planarization transfers them, for the first time, to a p-block element in the normal valence state., Graphical abstract, Highlights • The first square-planar silicon(IV) is isolated • A low-lying LUMO provokes CH-agostic interaction and visible-light absorption • Transition metals are mimicked without leaving the natural oxidation state, The bigger picture Tetrahedral silicon(IV) compounds are the building blocks of our Earth’s crust. Here, we describe the first species of silicon(IV) with a square-planar configuration. The structural deformation has substantial consequences for the compounds’ physicochemical properties and imparts features usually associated with transition metals. Upon planarization, the frontier molecular orbital gap shrinks by more than 50% and enables ligand-element charge transfer, CH-bond agostic interactions, and spontaneous reactivity with inert bonds. Small frontier molecular orbital gaps are critical for bond-activation reactivity, catalysis, and photochemistry with transition metals. Traditional approaches to mimic these characteristics with the more abundant p-block elements rely on unusual valence or oxidation states. With the realization of square-planar silicon(IV), these peculiarities start reaching p-block elements in their natural oxidation states., Our Earth’s crust is covered with compounds of silicon(IV). In each, tetracoordinated silicon(IV) arranges its four substituents in a tetrahedral fashion, while other environments are unknown. This work describes the isolation and properties of a molecular complex with square-planar silicon(IV). The flattened structural motif provokes a range of features that primes the second most abundant element for new applications in catalysis and materials science.

In comparison with the common-used electron donor (D)-electron acceptor (A) type symmetric polymers with regular structures, their asymmetric counterparts have received much less attention and seldom been applied in polymer solar cells. Since the precise modulation of π bridge can significantly influence the photoelectric properties of D-A type polymers, π bridges of tailorable thiophenes are introduced into benzodithiophene (BDT)-benzodithiophene-4,8-dione (BDD) copolymers in both symmetric and asymmetric patterns. Together with the halogen substituent of fluorine or chlorine on BDT, four polymer donors are designed and synthesized. As expected, PTB2T-F and PTB2T-Cl with the asymmetric π bridges of thiophene and hexyl-bithiophene exhibit better planarity, stronger intermolecular interaction and higher hole mobility than P2TB2T-F and P2TB2T-Cl with the symmetric π bridges of hexyl-bithiophene. The more suitable phase separation and optimized nanomorphology is determined by the reasonable miscibility between asymmetric polymer and acceptor, which is evaluated by Flory-Huggins interaction, contributing to the extremely higher performance than that of symmetric counterpart. Moreover, paired with IT-4F as the acceptor, PTB2T-F affords better device performances than the reference BDT-BDD polymer PM6 with the symmetry π bridge of thiophene. These results demonstrate that the precise modulation of asymmetric π bridges is a promising strategy to construct high-efficiency D-A type polymer donors.

The correlation of the rotation about the Cα-C' bond and the pyramidalization of the sp2-hybridized carbon atom C' and its three bonding partners to a flattened tetrahedron in the substructure Cβ-CαH-C'(═O)-OMe of substituted methyl acetates revealed that the two processes are not independent of each other but parts of a common molecular motion, as outlined in the preceding back-to-back paper. In the present study, we generalized the substructure to Xβ-CαH-C'(═Y)-Z with X, Y, and Z = O, N, C, and S, extending the analysis to several hundred thousand structures of the type carboxylates, carboxamides, ketones, imines, olefins, peptides, lactates, carbothioates, and phenyl derivatives, retrieved from the Cambridge Structural Database. ψ/θ Scatter plots of the individual structure points and their averaging in ψ/θav curves result in wavelike patterns with three maxima and minima and inversion symmetry at ψ = 0° and ±180 for a 360° rotation of Cβ about the Cα-C' bond. The pyramidalization of the sp2-hybridized group CαCiCoCo', which is part of the aromatic system, even disturbs the planarity of phenyl rings. Density functional theory calculations confirm the results of the CSD search.

The correlation of the rotation about the bond C'-Cα and the pyramidalization of the sp2 hybridized carbon atom C' and its three bonding partners to a flattened tetrahedron was investigated for the substructure Cβ-CαH-C'(═O)-OMe. A search in the Cambridge Structural Database (CSD) gave 15,295 structures with a substituted methyl acetate group at the end of the molecules. The scatter plot of the rotation angle ψ = O═C'-Cα-Cβ versus the pyramidalization angle θ = O(MeO)C'Cα and the ψ/θav curve show an unusual undulating pattern with three maxima and minima for a 360° rotation about the bond C'-Cα. There is no net chiral induction from the (Mψ)/(Pψ) conformations of the bond C'-Cα to the (Rθ)/(Sθ) configurations of the flattened tetrahedron because the contributions of the three maxima and minima cancel each other. The wavelike ψ/θav curve demonstrates that the rotation about the bond C'-Cα and the pyramidalization of the group C'(═O)(OMe)Cα are not independent processes. They are coupled with each other in one common molecular motion. The ψ/θav curve appears as the third harmonic of a sinusoidal fundamental frequency. DFT calculations of the propanoate anion, methyl propanoate, and methyl 2-methylpropanoate confirm the results of the CSD search.

An unexpected side product of a McMurry reaction was found to be a new [2.2]pyrenophane consisting of two pyrene units with different substitution patterns as well as different types and degrees of distortion from planarity. The new pyrenophane exhibits both monomer and intramolecular excimer fluorescence. Natural bond orbital (NBO) analysis revealed that there is an intramolecular charge-transfer interaction from the more distorted pyrene system to the less distorted one. The origin of the new pyrenophane was traced back to an impurity that was present a full five steps prior to the McMurry reaction from which it was isolated. The pathway to the pyrenophane shadowed that of the main synthetic route.

A helically twisted ribbon-shaped nanographene 3 containing four pentagons, eighteen hexagons and four heptagons was synthesized by a cascade of classical Scholl and non-classical Scholl-type cycloheptatriene formation reactions. In the pivotal step of the synthesis, ten carbon-carbon bonds and four cycloheptatriene rings were formed in one single operation in 11% yield. In this way, the fenestrindane core 1 was annelated with two m-quaterphenyl units 4 at opposite rims, generating a unique helically twisted structure 3 with D-2-symmetry. X-ray crystallography confirmed this [5.5.5.5]fenestrane-based molecular topology and revealed the aggregation of a pair of antipodal enantiomers, (M)-3 and (P)-3, in the solid state. The torsion angles, planarity of hexagons in the two tribenzo[fg,ij,rst]pentaphene substructures and the local aromaticity of the hexagons were studied based on the crystal data. The optical and electronic properties of compound 3 were investigated by UV/Vis and fluorescence spectroscopy and cyclic voltammetry. Based on the reactions of several partially cyclized intermediates and DFT calculations, a mechanistic sequence of the reaction pathways towards the formation of the nanographene 3 is proposed. In particular, factors that affect the relative ease and the role of hydride abstraction from one of the sp(3)-hybridized benzhydrylic bridgeheads, giving rise to cycloheptatrien-7-ol side products, are unfolded in this study. It is demonstrated that this side track occurs exclusively at the most highly conjugated pi-electron system formed and efficiently competes with the classical and non-classical Scholl cyclodehydrogenation reactions in the last stage of the reaction sequence.

Reaction of LiOCtBu2Ph with TlPF6 forms the dimeric Tl2(OCtBu2Ph)2 complex, a rare example of a homoleptic thallium alkoxide complex demonstrating formally two-coordinate metal centers. Characterization of Tl2(OCtBu2Ph)2 by 1H and 13C NMR spectroscopy and X-ray crystallography reveals the presence of two isomers differing by the mutual conformation of the alkoxide ligands, and by the planarity of the central Tl–O–Tl–O plane. Tl2(OCtBu2Ph)2 serves as a convenient precursor to the formation of old and new [M(OCtBu2Ph)n] complexes (M = Cr, Fe, Cu, Zn), including a rare example of T-shaped Zn(OCtBu2Ph)2(THF) complex, which could not be previously synthesized using more conventional LiOR/HOR precursors. The reaction of [Ru(cymene)Cl2]2 with Tl2(OCtBu2Ph)2 results in the formation of a ruthenium(II) alkoxide complex. For ruthenium, the initial coordination of the alkoxide triggers C–H activation at the ortho-H of [OCtBu2Ph] which results in its bidentate coordination. In addition to Tl2(OCtBu2Ph)2, related Tl2(OCtBu2(3,5-Me2C6H3))2 was also synthesized, characterized, and shown to exhibit similar reactivity with iron and ruthenium precursors. Synthetic, structural, and spectroscopic characterizations are presented.

Molecular engineering enabling reversible transformation between helical and planar conformations is described herein. Starting from easily available 2-(pyridin-2-yl)anilines and alkynes, a one-pot strategy is set up for the synthesis of aza[4]helicenes via two successive rhodium-catalyzed C–H activation/cyclizations. Helical pyrrolophenanthridiziniums can be transformed into planar conformations through the cleavage of acidic pyrrole N–H, leading to turn-off fluorescence. NMR spectra, single crystal X-ray diffraction and DFT calculations demonstrate that the formation of an intramolecular C–H⋯N hydrogen bond is beneficial to stabilize the pyrrole nitrogen anion of the planar molecule and provide increased planarity. The reversible conformation transformations can be finely adjusted by the electron-donating and -withdrawing groups on the π+-fused pyrrole skeleton in the physiological pH range, thus affording an opportunity for pH-controlled intracellular selective fluorescence imaging. Pyrrolophenanthridiziniums show turn-on fluorescence in lysosomes owing to the acidic environment of lysosomes and turn-off fluorescence out of lysosomes, indicating the occurrence of the deprotonation reaction outside lysosomes and the corresponding transformation from helical to planar conformations., One-pot synthesis of aza[4]helicenes is accomplished through two successive C–H activation/cyclizations, which exhibit on/off fluorescence switching through reversible transformation between helical and planar conformations.

In this text based on the 2018 Lonsdale lecture, beginning with early work by Kathleen Lonsdale, instructive examples are given of unusual and unexpected structures derived from X-ray crystallography, not all of which are genuine results., This feature article is derived from the author’s presentation of the Lonsdale lecture at the BCA Spring Meeting in 2018. One of the research results for which Kathleen Lonsdale is best known was her 1929 demonstration that the benzene ring in crystalline hexa­methyl­benzene is planar and has essentially hexagonal symmetry, resolving decades of dispute among organic chemists. More recent crystallographic studies of hexa­methyl­benzene have shown that there are actually small deviations from planarity. Such deviations for aromatic compounds may be due to electronic, steric, and/or intermolecular factors. Some substituted benzene molecules display remarkably large deviations, both from a planar ring structure and from regular hexagonal angular geometry around the ring. Starting from this specific connection with Kathleen Lonsdale’s research, a number of stories are recounted of structural distortions and deviations from expected results and explanations that have been suggested for them, across a wide range of chemical topics including macrocycles, metal clusters, unusual coordination geometry and isomerism. On the way we find genuine surprises and results that have led to new understanding, but also examples of poor experiments, misinterpretation of data, scientific bias and preconceived ideas, incompetence and even deliberate fraud. Some aspects of structure validation are discussed. While showcasing some interesting research in its own right, this account also serves an educational purpose.

Assuming aromaticity (cyclic continuous conjugation, planarity, and obeying the Huckel 4n + 2 rule), effects of one and two fused six-membered heterocyclic rings are investigated on the energy lowering (stabilization) of 22 novel singlet (s) and triplet (t) carbenes, at B3LYP/AUG-cc-pVTZ and M06-2X/AUG-cc-pVTZ. Results display that (1) exclusive of triplet pyridine-4-ylidene, and s and t states, other species appear as ground state, so every s Hammick carbene exhibits more stability than its corresponding t state; (2) the highest stability is demonstrated by unsubstituted pyridine-4-ylidene as reference carbene, and the lowest stability is shown by carbene situated between two nitrogen heteroatoms of two fused rings, in a “W” arrangement; (3) regarding the relationship between carbenic center (CC) and substituted heteroatom, the order of stabilization for fused rings is meta > para > ortho; (4) regardless of how organized, fusion of one six-membered ring, in a given arrangement, has more stabilizing effect than two six-membered rings; (5) contrary to our expectation, t Hammick carbenes show higher band gap (ΔEHOMO-LUMO) than their corresponding s species; (6) based on the NICS (nuclear independent chemical shift) results, the least stable carbene has the most aromaticity in its pyridine ring; and (7) according to proposed homomolecular isodesmotic reactions, all s states are stabilized via π-donor/σ-acceptor substitution more than the t states.

The stability and some characteristic bonding features of a variety of ligand (L)-stabilized phosphinidene complexes derived from adduct formation with halides, and both anionic or neutral O-donor bases were explored. Furthermore, the main features of L → P pnictogen bonding in such adducts were studied not only by using geometric criteria such as L-P bond distances and pyramidalization or planarity at P but also by turning the spotlight on bond-strength-related (including atoms-in-molecules-derived) parameters, thermodynamic stability dependence with electronic characteristics of the free ligand, and dative-bonding participation. We propose the new relative positions of the charge concentration band descriptor, τVSCC, which, together with the sign and magnitude of ∇2ρ at the bond critical point, constitutes the required criteria to differentiate L-P linkages as van der Waals interactions, dative bonding, or mostly covalent bonds.

Schiff base complexes derived from salicylaldehyde and ethylene-, propylene-, and trans-1,2-cyclohexane-diamines exhibit p-channel transistor properties. The Cu complexes are open-shell compounds, but the oxidation and the hole transport occur at the highest occupied molecular orbital, where the singly occupied molecular orbital (SOMO) does not participate in conduction. Although Ni complexes tend to show larger mobilities than Cu complexes owing to the molecular planarity, the presence of SOMO is not harmful to the transistor properties.

We report on a synthetic strategy for a series of thienothiophene-benzotriazole-based polymers—octyl-PTTBTz-F, Si-PTTBTz, and Si-PTTBTz-F—wherein conformational locks are introduced to induce intra- and intermolecular interactions (F···S, F···H–C, and C–F··· π F) for high backbone planarity and siloxane-terminated side chains are introduced to increase solubility. The three polymers were utilized as active layers in organic field-effect transistors, and the effects of thermal annealing on the polymer crystallinity and device performances were studied. Although the fluorine-atom-substituted octyl-PTTBTz-F showed a moderate hole mobility of up to 4.2 × 10−3 cm2 V−1 s−1 with enhanced molecular orientation because of conformational locks, it had poor solubility in common organic solvents. The Si-PTTBTz polymer with the siloxane-terminated side chains showed good solubility but inferior device performance with a hole mobility of up to 2.2 × 10−4 cm2 V−1 s−1. The rationally designed Si-PTTBTz-F polymer, which contains both fluorine atoms in the backbone and siloxane-terminated groups in the side chains, showed an excellent hole mobility of up to 0.11 cm2 V−1 s−1 and good solubility in common organic solvents.

Presented here are the synthesis, characterization and study (using single crystal X-ray diffraction, Raman scattering, quantum mechanics calculations) of the structures of a series of biphenyls substituted in positions 3, 3′, 4 and 4′ with a variety of R (R = methyl, acetyl, hexyl) groups connected to the biphenyl core through oxygen atoms. The molecular conformation, particularly the torsion angle between aromatic rings has been extensively studied both in the solid as well as in the liquid state. The results show that the compounds appearing as rigorously planar in the solid present instead a twisted conformation in the melt. The solid versus melt issue strongly suggests that the reasons for planarity are to be found in the packing restraints. A `rule of thumb' is suggested for the design of biphenyls with different molecular conformations, based on the selection of the OR substituent.

Two o-carboranyl compounds containing 1,2,4-triazole groups, each appended with an N-aryl ring (either N-phenyl or N-diisopropylphenyl), were strategically designed and prepared to elucidate the relationship between their structural orientation (planarity) and intramolecular charge transfer (ICT)-based radiative decay. The photophysical analysis of both compounds shows that the N-phenyl appended compound shows a much higher quantum yield and larger radiative decay constant for ICT-based emission in the rigid state (solution at 77 K and film) than those of the N-diisopropylphenyl appended compound, even exhibiting an additional ICT-based emission in solution at 298 K. Theoretical calculations on their ground and excited states indicate that the planarity of the N-aryl appended triazole moiety affects the efficiency of radiative decay for the ICT transition. These findings firmly establish a strong relationship between the planarity of the appended aryl groups relative to the triazole ring and ICT-based radiative decay in these o-carboranyl luminophores.

A family of hexaazamacrocyclic lanthanide complexes, [Ln(Ln)(NCS)3] (LnIII = Dy, Er; n = 1-3) has been synthesized and characterized by single-crystal X-ray diffraction, magnetic measurements and ab initio calculations. Macrocyclic ligands (Ln) differ in the lateral spacers, which are aliphatic chains with two and three carbons (for Ln, n = 1 and 2, respectively), and an aromatic ring for Ln = 3. Modification of the macrocycle spacer tunes planarity and rigidity of the equatorial coordination for both oblate (Dy) and prolate (Er) lanthanide ions. Ac-susceptibility studies showed that four of the six complexes are field induced single molecule magnets (SMMs). Trends in magnetic relaxation properties are rationalized with the aid of ab initio multireference calculations, highlighting the combined influence of macrocycle planarity, lanthanide electronic density distribution and intermolecular interactions for the achievement of slow demagnetization.

Two thiophene backbone-based hole-transporting polymers, namely, poly[(2,2′-bithiophene-5,5′-diyl)-alt-(5,7-bis(2-butyloctyl)-4H,8H-benzo[1,2-c:4,5-c′]dithiophene-4,8-dione-1,3-diyl)] (PT2-BDD) and poly[(3,3′-difluoro-[2,2′-bithiophene]-5,5′-diyl)-alt-(5,7-bis(2-butyloctyl)-4H,8H-benzo[1,2-c:4,5-c′]dithiophene-4,8-dione-1,3-diyl)] (PF2-BDD), were prepared by using electron-withdrawing pendant groups such as ketone and fluorine moieties. They both exhibited a planar backbone with efficient π conjugation, which is suitable for hole transport in organic thin-film transistors (OTFTs). However, the fluorinated one (i.e., PF2-BDD), despite its perfect backbone planarity and strong intra- and intermolecular interactions, could not enhance the OTFT performance; due to its solvent resistance, electron negativity, and random orientation, PF2-BDD showed 10 times lower hole mobility than the non-fluorinated polymer (i.e., PT2-BDD). Nonetheless, the two-dimensional grazing incidence X-ray diffraction and temperature-dependent absorption spectra of the synthesized polymers provided crucial information to understand the relationship between their hole transport behavior and molecular structure.

5-Methyl-2-[(2-nitrophenyl)amino]-3-thiophenecarbonitrile is a crystalline compound rich in conformational polymorphs largely owing to the flexible torsion angle that leads to distinct colors, earning it the moniker ROY (Red-Orange-Yellow). Guanidinium organosulfonate hydrogen-bonded frameworks form six crystalline inclusion compounds with ROY, described here, in which the framework limits conformational twisting out of plane. Three of the six inclusion compounds enforce greater planarity and π-conjugation than any of nine ROY polymorphs that have been characterized by single crystal X-ray diffraction.

Ordered domains play a central role in determining the properties of organic semiconductors, and thereby the performance of their devices. The molecules in these ordered domains are often characterized by planar backbone conformations. We investigate the influence of backbone planarity on the propensity to form ordered structures using a pair of model oligomers with electron poor benzothiadiazole moieties and electron rich thiophene units. The two oligomers differ by their central unit, where a bithiophene unit either allows for flexible twists (“TT”), or where it is bridged as a cyclopentadithiophene to provide a rigid planar connection (“CT”). Temperature dependent absorption and luminescence spectroscopy in solution along with atomistic simulations show that the more flexible TT readily forms aggregates upon cooling, while CT instead first forms non-emissive excimers and only forms aggregates below 200 K. Molecular dynamics simulations reveal that aggregation in TT can only be accounted for if TT takes on a planar conformation in the course of the aggregation process. The stronger intermolecular interaction in TT compared to the banana-shaped CT can then be related to the larger number of attractive intermolecular interactions between the various subunits. Thus, molecular flexibility is an important design parameter, as it determines the accessibility of ordered intermolecular structures and ultimately device performance.

An expedient two-step synthesis produces in good yield polyaromatic heptacyclic (hetero)arylated o-substituted s-aryltetrazines (s-Tz) directly from diphenyl s-tetrazine. This methodology overcomes the steric limitations of classical Pinner-like syntheses encountered for o-functionalized s-Tz. A single step palladium-catalyzed N-directed C–H bond tetrahalogenation is followed by a Pd-catalyzed Suzuki (hetero)arylation that is achieved simultaneously on four sites. The single crystal X-ray diffraction structure of the resulting typical polyaromatic heptacyclic aromatic compound 3,6-bis(2,6-diphenyl)-1,2,4,5-tetrazine (3) is analyzed, together with R-functionalized peripheral phenyl derivatives [R = p-t-Bu (4), and m-OMe (10)]. Generally, stacking interactions between aromatic rings can be considerably stronger if electron-depleted rings are combined with electron-rich ones. Thus, electron-poor heteroaromatic aryltetrazines are expected to interact with electron-rich phenyl aromatic rings from reduced π⋯π repulsion, rendering the formation of stacking networks more favorable. Herein, despite the presence of strongly electron-deficient heteroaromatic tetrazine cores, the disruption of planarity between the various aromatic rings involved precludes the expected stacking arrangement. Thus, packing organization is driven by weak hydrogen bonding with C–H⋯N short contacts (or C–H⋯O when possible). These new heptaaromatics, which incorporate for the first time an electron-attracting nitrogen-rich core are easily modifiable from cross-coupling reactions, and constitute a relevant structural and electronical alternative to the well-known and high value class of hexaphenylbenzenes.

The structure determination of a series of biphenylsilyloxonium cations through NMR and XRD studies, supported by DFT calculations was carried out, allowing to get insights into the origin of the oxygen pyramidalization in biphenyl and binaphthylsilyl oxoniums. Low barrier of inversion in the oxygenyl series points toward a key role of the biaryl axis in the inversion of configuration at the oxygen center.

The title compound comprises four crystallographically different mol­ecules that are composed of a 1,5-bis­(4-meth­oxy­phen­yl)penta-1,4-dien-3-ylidenyl group and a benzyl ring connected by a hydrazine-1-carbodi­thio­ate bridge. In the crystal, mol­ecules are connected into a three-dimensional network through C—H⋯O, N—H⋯S and C—H⋯π inter­actions., In the title hydrazinecarbodi­thio­ate derivative, C27H26N2O2S2, the asymmetric unit is comprised of four mol­ecules (Z = 8 and Z′ = 4). The 4-meth­oxy­phenyl rings are slightly twisted away from their attached olefinic double bonds [torsion angles = 5.9 (4)–19.6 (4)°]. The azomethine double bond has an s-trans configuration relative to one of the C=C bonds and an s-cis configuration relative to the other [C=C—C= N = 147.4 (6)–175.7 (2) and 15.3 (3)–37.4 (7)°, respectively]. The torsion angles between the azomethine C=N double bond and hydrazine-1-carbodi­thio­ate moiety indicate only small deviations from planarity, with torsion angles ranging from 0.9 (3) to 6.9 (3)° and from 174.9 (3) to 179.7 (2)°, respectively. The benzyl ring and the methyl­enesulfanyl moiety are almost perpendicular to each other, as indicated by their torsion angles [range 93.7 (3)–114.6 (2)°]. In the crystal, mol­ecules are linked by C—H⋯O, N—H⋯S and C—H⋯π(ring) hydrogen-bonding inter­actions into a three-dimensional network. Structural details of related benzyl hydrazine-1-carbodi­thio­ate are surveyed and compared with those of the title compound.

In the title com­pound, the dihedral angle between the planes of the bi­pyridine and carbazole moieties connected by an O atom is 68.45 (3)°. The bi­pyridine ring system, with two meth­oxy substituents, is approximately planar. The pyridine ring in the pyridyl-substituted carbazole fragment is tilted by 56.65 (4)° with respect to the mean plane of the carbazole moiety. The title com­pound exhibits a high energy gap and triplet energy., In the title com­pound, C29H22N4O3, the carbazole system forms a dihedral angle of 68.45 (3)° with the mean plane of the bi­pyridine ring system. The bi­pyridine ring system, with two meth­oxy substituents, is approximately planar (r.m.s. deviation = 0.0670 Å), with a dihedral angle of 7.91 (13)° between the planes of the two pyridine rings. Intra­molecular C—H⋯O/N hydrogen bonds may promote the planarity of the bipyridyl ring system. In the pyridyl-substituted carbazole fragment, the pyridine ring is tilted by 56.65 (4)° with respect to the mean plane of the carbazole system (r.m.s. deviation = 0.0191 Å). In the crystal, adjacent mol­ecules are connected via C—H⋯O/N hydrogen bonds and C—H⋯π inter­actions, resulting in the formation of a three-dimensional (3D) supra­molecular network. In addition, the 3D structure contains inter­molecular π–π stacking inter­actions, with centroid–centroid distances of 3.5634 (12) Å between pyridine rings. The title com­pound exhibits a high energy gap (3.48 eV) and triplet energy (2.64 eV), indicating that it could be a suitable host material in organic light-emitting diode (OLED) applications.

The title compound crystallizes in the monoclinic space group P21/c with three independent mol­ecules in the asymmetric unit. Two types of hydrogen-bonding inter­actions, C—H⋯O and N—H⋯O, are observed, as well as bifurcation of these inter­actions. The N—H⋯O inter­actions link mol­ecules to form infinite chains. The packing of mol­ecules in the unit cell shows a pattern of overlapping aromatic rings, forming column-like formations. π–π inter­actions are observed between the overlapping aromatic rings., The title compound, 2-(methyl­amino)­cyclo­hepta-2,4,6-trien-1-one, C8H9NO, crystallizes in the monoclinic space group P21/c, with three independent mol­ecules in the asymmetric unit. The planarity of the mol­ecules is indicated by planes fitted through the seven ring carbon atoms. Small deviations from the planes, with an extremal r.m.s. deviation of 0.0345 Å, are present. In complexes of transition metals with similar ligands, the large planar seven-membered aromatic rings have shown to improve the stability of the complex. Two types of hydrogen-bonding inter­actions, C—H⋯O and N—H⋯O, are observed, as well as bifurcation of these inter­actions. The N—H⋯O inter­actions link mol­ecules to form infinite chains. The packing of mol­ecules in the unit cell shows a pattern of overlapping aromatic rings, forming column-like formations. π–π inter­actions are observed between the overlapping aromatic rings at 3.4462 (19) Å from each other.

Luminescent silver(I) halogenido coordination polymers [Ag2X2(PPh3)2(bpy)] n (X = I, Br, Cl) have been prepared. The iodido and bromido complexes exhibit strong blue phosphorescence assignable to the 3π-π*-excited-state of bpy, whereas the chlorido complex shows luminescence thermochromism due to the π-π*-state of bpy and charge transfer from the {Ag2Cl2} core to the bpy π*-orbital. Taking advantage of their structural similarities, we prepared a series of mixed-halogenido silver(I) complexes [Ag2(X xX'(1- x))2(PPh3)2(bpy)] n (X, X' = I, Br, Cl) at varying molar fractions as solid solutions. The mixed-halogenido complexes are as strongly luminescent as their parent complexes. The detailed study of their structure and emissive properties revealed smooth energy migration between the luminescent units and modification of the luminescence properties based on the planarity of bpy.

The title compound shows a mol­ecular framework with the di­phenyl­ethyne unit slightly deviating from planarity and the l-alanine moieties adopting a distorted helical conformation. The crystal structure features a two-dimensional network supported by N—H⋯O and C—H⋯O hydrogen bonding., The di­phenyl­ethyne unit of the title mol­ecule, C24H24N2O6, deviates slightly from planarity. The l-alanine moieties adopt distorted helical conformations of opposite winding direction. Infinite ribbons of N—H⋯O=C-connected mol­ecules represent the basic supra­molecular entities of the crystal structure. These aggregates are linked by C—H⋯O hydrogen bonds involving the oxygen atoms of the methyl carboxyl­ate units. The crystal studied was refined as an inversion twin.

For poly(9,9-dioctylfuorene) (PFO), β phase (coplanar conformation with the intra-chain torsion angle of 165°) has a greater conjugation length and higher degree of order compared to those of α phase, which favors charge carrier transport. However, the highest content of β phase obtained so far is 45%. We propose to increase the content of β phase by promoting the solution aggregation of PFO molecules and extending film-forming time. For this purpose, 1,8-diiodooctane (DIO) is added to PFO o-xylene solution, which enhances the interaction of PFO chains and improves the planarity of PFO backbone, resulting in the formation of ordered aggregation. The aggregates act as nucleation centers to promote the formation of β phase. The content of β phase increases with increasing DIO concentration and reaches a platform of 39% as DIO is more than 4 vol%. Furthermore, the film is kept in a sealed environment with o-xylene atmosphere for 3 h, thus the PFO molecules have enough time to diffuse to the crystallization front and achieve disorder-order transition. As a result, the crystallinity of PFO is improved significantly and the content of β phase increases to 52%, reaching the highest value reported so far.

A theoretical study has been carried out at the M062X/6-311++G(d,p) computational level to search for a rationale on ligands' affinity toward α2-adrenoceptors by estimating the nature and strength of intramolecular hydrogen bonds potentially formed (by means of the QTAIM and NBO approaches) as well as the degree of deviation from planarity that could be observed in some of the compounds. Four different families have been studied: thiophen-2-yl, 3-carboxylatethiophen-2-yl esters, 3-cyanothiophen-2-yl, and 2-thiazolyl guanidinium derivatives. In the case of the thiophen-2-yl guanidines not substituted in the 3 position, nonplanarity was always observed, whereas in the thiazole series, intramolecular hydrogen bonds were identified between the guanidinium and the thiazole ring forcing the systems to planarity. Regarding the carboxylic esters, two different rotamers were found: quasi-planar and quasi-perpendicular systems with very similar energy. Both of these isomers can form different nets of intramolecular hydrogen bonds and other types of noncovalent interactions. Different physicochemical properties such as basicity, solubility, or lipophilicity were calculated for these systems, but no correlation to the degree of planarity was found. However, when comparing the α2-ARs affinity with the planarity of the molecules, a trend appears in the thiophen-2-yl guanidinium series indicating that lack of planarity seems to be optimal for α2-ARs engagement.

A new series of asymmetrical heterobimetallic azines [(η5-C5H5)Fe{(η5-C5H4) C(R) = N N C(R1)-(η5-C5H4)Re(CO)3}] (1–3) and symmetrical homobimetallic cyrhetrenyl azines [{(η5-C5H4) C(R) = N}Re(CO)3]2 (4, 5) have been synthesized and were spectroscopically characterized by FT-IR, NMR, EI-MS and cyclic voltammetry. The molecular structures of 1 and 4 were determined using single-crystal X-ray diffraction technique. Based on the oxidation potential of the ferrocenyl units and the high degree of planarity of the [(C5H4) C(H) = N N C(H)-(C5H4)] system in complex 1, we inferred electronic communication between the electron-withdrawing cyrhetrenyl groups through the π-conjugated azine bridge. The compounds display an (E,E)-configuration about the >C N- bond, an s-trans conformation for the N N bond and an anti-conformation for the two organometallic fragments.

Although various donor–acceptor (D–A) small molecules with high power conversion efficiency have been reported, D–A small molecules with high field-effect mobility are still rare. In this work, two new A–D–A small molecules with a rigid indacenodithieno[3,2-b]thiophene (IDTT) moiety as the central core and both ends capped with strong electron-withdrawing indole-2,3-dione (IDD) and N-substituted pyrrolo[2,3-b]pyridine-2,3-dione (IDD-N) were synthesized and characterized for applications in solution-processable organic field-effect transistors (OFETs). A N atom was introduced to the IDD units to enhance the planarity and structural ordering by noncovalent interactions, leading to a dramatic effect on the small molecule. The unsubstituted small molecule (IDTT–IDD) did not show any field-effect performance, whereas an encouraging hole mobility of 7.7 cm2 V–1 s–1 with an average mobility of 6.1 cm2 V–1 s–1 was obtained for solution-processable OFETs based on the N-substituted one (IDTT–IDD-N). This work provi...

Twofold Buchwald-Hartwig aminations selectively furnish three regioisomers of bis[1]benzothieno[1,4]thiazines; X-ray structure analyses and DFT calculations were corroborated for correlation of their electronic properties. All regioisomers outscore the parent compound phenothiazine with respect to a low-lying oxidation potential and reversible redox activity. The anti-anti bis[1]benzothieno[3,2-b:2',3'-e][1,4]thiazines possess the lowest oxidation potentials in this series and displayed pronounced green luminescence in solution (ΦF ≈20 %) and in the solid state. Syn-anti regioisomers were only weakly luminescent in solution, but showed aggregation-induced emission enhancement and solid-state luminescence. Most interestingly, X-ray structure analyses revealed that anti-anti derivatives have an amazingly coplanar structure of the pentacyclic anellated 1,4-thiazine system, emphasizing a structural similarity to heteroacenes. The calculated theoretical nucleus-independent chemical shifts additionally suggested that these 8π-electron core systems can be considered as the first electronically unbiased anellated 1,4-thiazines with antiaromatic character.

DFT calculations are presented for a series of tetrathiafulvalene (TTF) derivatives which, in association with tetracyano-p-quinodimethane (TCNQ) units, form π stacked, solid state compounds. The geometric and electronic features of eight differently substituted TTF units (some with two Se in place of S heteroatoms) are determined by DFT optimizations, each one bearing the 0, +1 and +2 charges. The minor deformations from planarity observed in the uncharged species disappear upon the electron removal. The delocalized π character of the HOMO with prevailing antibonding character between the C and S (Se) atoms justifies the geometric effects on the unit upon the release of the electrons and possibly the stacking of the units. Energy considerations indicate the parent TTF species is be less prone toward oxidation than its various derivatives. Finally, an important correlation emerges between the studied organic molecules and known square planar bis-dithiolene d8 metal complexes, also with propensity toward redox isomerism.

The co-assembly behavior of peptide-π-peptide and peptide-alkyl-peptide triblock molecules that form one-dimensional (1D) nanostructures under acidic, aqueous environments is dependent on the peptide sequence and the torsional constraints imposed within the nanomaterial volume. Although a hydrophilic tripeptide sequence (Asp-Asp-Asp, DDD-) previously promoted isolation/dilution of minority π-electron components in the matrix of aliphatic peptides, a β-sheet promoting sequence (Asp-Val-Val, DVV-) led to blocks of the two components distributed within larger 1D self-assembled nanostructures. Furthermore, torsional restrictions exerted on the oligoaromatic π-electron unit by the self-assembly process can lead to changes in its conformation (for example, planarity), which has ramifications on its functionality within the peptide matrix. Here, we study this impact on thiophene-based π-electron units with inherently different geometries, viz., relatively planar 2,2':5',2″:5″,2‴-quaterthiophene and 3″,4'-dimethyl-2,2':5',2″:5″,2‴-quaterthiophene, which is twisted at the core bithiophene unit due to the presence of two methyl groups. These peptides were co-assembled at 5 and 20 mol % with peptide- n-decyl-peptide triblock molecules, and the resultant assemblies were studied using UV-vis absorption, photoluminescence, and circular dichroism spectroscopies. We found that torsional restriction in dimethylated quaterthiophene units can impact the stacking behavior of these 1D peptide nanoassemblies and have consequences on their photophysical properties. Additionally, these insights help in the understanding of the dependence of the optoelectronic properties of these materials on both the intrinsic conformation of π-units and the geometric constraints imposed by their immediate local environment under aqueous conditions.

A novel oxygen-bridged triarylamine polycyclic unit based tris-cyclometalated heteroleptic iridium(iii) complex (Ir-NO) has been designed and prepared. Similar iridium(iii) complexes (Ir-N and Ir-O) have also been prepared for comparison. The single crystal structure indicates that the oxygen-bridged triarylamine polycyclic unit of Ir-NO shows certain planarity, resulting in obvious rigidity and interesting π-π stacking. Additionally, Ir-NO shows a larger redshift emission (586 nm) and a longer emission lifetime (628 ns) than Ir-N (525 nm, 344 ns) and Ir-O (543 nm, 436 ns), and the phosphorescence color can be tuned from green to orange. Electrochemical experiments and DFT calculations reveal that Ir-NO exhibits a high HOMO energy level and intraligand charge transfer (3ILCT) excited state properties, which is in contrast to the low HOMO energy level and metal-to-ligand charge transfer (3MLCT) excited state properties in Ir-N and Ir-O. This result can be attributed to the strong electron-donating ability of the unit.

The structural/geometrical features, multinuclear GIAO-NMR characteristics, tropicity, nucleus independent chemical shift NICS(1) and NICS(1)zz values, and NPA charge densities for phosphatriquinacene, its P-methylated phosphonium cation, the zwitterionic P-methylphosphaacepentalenide, and its conjugate acid have been modeled using DFT at the B3LYP/6-311++G(d,p) level of theory and are compared explicitly with computed data for the previously described aza-analogs at the same level of theory. By all investigated criteria, the phosphatriquinacene-based zwitterion is clearly aromatic but somewhat less so than the aza-analog. To probe the variations in anisotropic shielding effects, a number of other +P–R derivatives (R = H, F, CF3, iso-Pr, n-Pr, sec-Bu) were computed and compared with models. Extension of the study to the As-counterpart showed that by the same set of criteria, the arsa-bridged zwitterion is also aromatic. The relative aromaticity order in the main group family is N > P > As, which correlates with deviation from planarity of the annulene ring, as measured by the angle between the ring planes, i.e. (dr) N: 144.7°; P: 123.4°; As: 120.4°. Extension of the study to the dicationic group VI oxa- and thia-bridged analogs led to the same observation, i.e. relative aromaticity O > S. By contrast, an inverse correlation between planarity and aromaticity was found when comparing analogs from the same row of the periodic table, with relative aromaticity orders O > N and S > P. Including a solvation model (IEFPCM method) did not produce significant changes, although increasing solvent polarity led to slightly less negative NICS values and weaker anisotropic shielding.

To clarify the relationship between planarity and intramolecular charge transfer (ICT), two o-carboranyl compounds (TCB and FCB) containing different ortho-type terphenyl rings, namely, perfectly distorted or planar phenyl rings, were synthesised and fully characterised. Although the emission spectra of both compounds presented intriguing dual-emission patterns in solution at 298 or 77 K and in the film state, distorted TCB mostly showed locally excited emission, whereas planar FCB demonstrated intense emission corresponding to an ICT transition. Interestingly, the emission efficiencies and radiative decay constants of terphenyl-based o-carboranyl compounds were gradually enhanced by increasing the planarity of the terphenyl groups. These results verify the existence of a strong relationship between the planarity of appended aryl groups and ICT-based radiative decay in o-carborane-substituted compounds.

Newly developed fused-ring electron acceptors (FREAs) have proven to be an effective class of materials for extending the absorption window and boosting the efficiency of organic photovoltaics (OPVs). While numerous acceptors have been developed, there is surprisingly little structural diversity among high performance FREAs in literature. Of the high efficiency electron acceptors reported, the vast majority utilize derivatives of 2-(3-oxo-2,3-dihydroinden-1-ylidene)malononitrile (INCN) as the acceptor moiety. It has been postulated that the high electron mobility exhibited by FREA molecules with INCN end groups is a result of close π-π stacking between the neighboring planar INCN groups, forming an effective charge transport pathway between molecules. To explore this as a design rationale for electron acceptors, we synthesized a new fused-ring electron acceptor, IDTCF, which has methyl substituents out of plane to the conjugated acceptor backbone. These methyl groups hinder packing and expand the π-π stacking distance by ∼1 Å, but have little impact on the optical or electrochemical properties of the individual FREA molecule. The extra steric hindrance from the out of plane methyl substituents restricts packing and results in large amounts of geminate recombination, thus degrading the device performance. Our results show that intermolecular interactions (especially π-π stacking between end groups) play a crucial role in performance of FREAs. We demonstrated that the planarity of the acceptor unit is of paramount importance as even minor deviations in end group distance are enough to disrupt crystallinity and cripple device performance.

A family of eight π-extended push–pull coumarins with cross-conjugated (amide) and directly conjugated (p-phenylene, alkyne, alkene) bridges were synthesized through a convergent strategy. Using an experimentally calibrated computational protocol, their UV–Visible light absorption and emission spectra in solution were investigated. Remarkably, amide-, alkyne- and alkene-bridges undergo comparable vertical excitations. The different nature of these bridges manifests during excited-state relaxation and fluorescence. We predict that these molecules can serve as building blocks for p-type semiconductors with low reorganization energies, below 0.2 eV. Since solid-state self-assembly is crucial for this application, we examined the effect of the π-bridge over the supramolecular organization in this family of compounds to determine if stacking prevails in these π-extended coumarin derivatives. Amide and alkyne spacers allow coplanar conformations which crystallize readily; p-phenylene hinders planarity yet allows facile crystallization; alkene-bridged molecules eluded all crystallization attempts. All the crystals obtained feature dense face-to-face π-stacking with 3.5–3.7 A interlayer distances, expected to facilitate charge transfer processes in the solid state.

As the next neutral structure following Hückels rule, a planar and aromatic [10]annulene is ideal to study the link between ring size and aromaticity. However, the puckered geometry of the parent [10]annulene suggests that the aromatic stabilization energy is not sufficient to overcome the ring strain that exists when the system is forced into planarity. It has been shown computationally that this ring strain can be alleviated through the addition of two or more cyclopropane rings to the periphery, thereby creating theoretically aromatic structures. An alternative strategy to eliminating the issue of ring strain was demonstrated experimentally with the successful preparation of the highly aromatic 1,6-didehydro[10]annulene. However, the system rapidly cyclizes at -40°C to a naphthalene diradical due to the close proximity of the in-plane p-orbitals present in the system. Here we show that cyclopropanating one side of the unstable annulene successfully prevents the destabilizing cross-ring interaction while maintaining a highly aromatic structure. Remarkably, the formed [10]annulene is bench stable and can be stored for extended periods of time.

ConspectusThe concept of aromaticity is one of the most fundamental principles in chemistry. It is generally accepted that planarity is a prerequisite for aromaticity, and typically the more planar the geometry of an aromatic compound is, the stronger aromatic it is. However, it is not always the case, particularly when transition metals are involved in conjugation and electron delocalization of aromatic systems, i.e., metalla-aromatics. Because of the intrinsic nature of transition-metal orbitals, besides planar geometries, the most stable molecular structures of metalla-aromatic compounds could take nonplanar and even spiro geometries. In this Account, we outline several unprecedented types of metalla-aromatics developed recently in our research group.Around seven years ago, we found that 1,4-dilithio-1,3-butadienes, dilithio reagents with π-conjugation, could function as non-innocent ligands and react with low-valent transition-metal complexes, generating monocyclic metalla-aromatic compounds. Later on, by taking advantage of the unique behavior of dilithio reagents and the intrinsic nature of different transition metals, we have synthesized a series of metalla-aromatic compounds, of which four types are discussed here, and each of them represents the first of its kind. First, nearly planar aromatic dicupra[10]annulenes, a 10 π-electron aromatic system with two bridging Cu atoms participating in the orbital conjugation and electron delocalization, are synthesized by annulating two dilithio reagents with two Cu(I) complexes.Second, four kinds of spiro metalla-aromatics, featuring planar (with Pd, Pt, or Rh as the spiro atom) geometry with a whole 10π aromatic system, octahedral (tris-spiro metalla-aromatics with V as the spiro atom) geometry with an entire 40π Craig-Mobius aromatic system, tetrahedral (with Mn as the spiro atom) geometry having two independent and perpendicular 6π planar aromatic rings, and tetrahedral (with Mn as the spiro atom) geometry with one planar and one nonplanar 6π aromatic rings, respectively, are generated. In sharp contrast to spiroaromaticity with carbon acting as the spiro atom described in Organic Chemistry, the metal spiro atom herein takes part in orbital conjugation and electron delocalization.Third, nonplanar aromatic butadienyl diiron complexes are realized. Different from planar aromatic systems featuring delocalized π-type overlap, this nonplanar metalla-aromaticity is achieved by the novel σ-type overlap between the two Fe 3dxz orbitals and the butadienyl π orbital, forming a 6π aromatic system. Fourth, dinickelaferrocene, a ferrocene analogue with two aromatic nickeloles, is synthesized from our monocyclic aromatic dilithionickelole and FeBr2. The aromaticity of dinickelaferrocene and its nickelole ligands is realized by electron back-donation from the Fe 3d orbital to the π* orbital of nickeloles, which also deepens our understanding of the origin of aromaticity.The search for unprecedented and exciting aromatic systems, particularly with transition metals being involved, will continue to drive this intriguing research field forward. Given the synthetic strategies and various types of metalla-aromatics developed and described, diversified metalla-aromatics of interesting structures and reaction chemistry, novel chemical bonding modes, and useful functions can be expected.

The title compound, C13H10O2, crystallizes with two almost planar molecules in the asymmetric unit. In the crystal, slipped π–π stacking interactions help to establish the packing with the shortest centroid–centroid separation being 3.8195 (18) Å.

The title compound, C20H22BNO2, has a polarized π-system due to resonance between N—C(H)=C(H)—B and ionic N+=C(H)—C(H)=B− canonical structures. The dihedral angles between the ethenyl plane (r.m.s. deviation for C2H2 = 0.0333 Å) with the ethenyl-C(NC2-pyrrole) plane (r.m.s. deviation CNC2 0.0423 Å) and the ethenyl-C(BO2-1,3,2-dioxaborolane) plane (r.m.s. deviation BCO2 0.0082 Å) are 45.86 (8) and 37.47 (8)°, respectively, and are greater than those found for the previously reported E-isomer [Hatayama & Okuno (2012) Acta Cryst. E68, o84]. In comparison with the E-isomer, the reduced planarity of Z-isomer results in a decrease of the contribution of the N+=C(H)—C(H)=B− canonical structure.

This work describes a comparative molecular structure of two hydroxychlorochalcones with an emphasis on their planarity. Hirshfeld surface analysis investigates the effect of ortho- and para-chlorine substitution on supramolecular arrangement and physical chemical properties. The molecular conformation of 2′-hydroxy-4′,6′-dimethyl-2-chlorochalcone and 2′-hydroxy-4′,6′-dimethyl-4-chlorochalcone chalcones was obtained through DFT with the exchange-correlation functional M06-2X and the 6-311++G(2d,2p) basis set, and the results were compared with the experimental X-ray data in order to get insights on the effect of ortho- and para-chlorine substitution. The charge transfer into entire main carbon chain was also investigated using frontier molecular orbitals (HOMO and LUMO), NBO, and MEP map in order to describe the comparative conformational stability due to the resonance effect produced by π electron displacements. Finally, the intermolecular observed interactions were analyzed by QTAIM, with the M06-2X/6-311G++(d,p) theory level.

Isoindigo (IID) has been developed as an electron deficient moiety for high-performance conjugated organic materials, especially for constituting donor–acceptor (D-A) type conjugated polymers. To further enhance the planarity of IID unit to promote the associated intramolecular charge transfer (ICT) effect of the derived polymers, various of structural modifications have been performed in recent years. Herein, two heterocyclic ring-fused IID core structures, tetrafluorobenzene-centered IID (FBIID) and pyrazine-centered IID (PzIID), were developed and copolymerized with two common electron-rich moieties, 2,2′-bithiophene (2 T) and (E)-1,2-bis(thiophen-2-yl)ethene (TVT). The properties and structure-mobility relationship of the prepared four D-A type polymers, PFBIID-2 T, PFBIID-TVT, PPzIID-2 T, and PPzIID-TVT are systematically studied to elucidate the effect of the spacer structure in the heterocyclic ring-fused IID units. Both the simulation results and experimental analyses show that the PzIID-based polymers possess much higher planarity and mobility than the FBIID-based ones because of the less substituents on the pyrazine spacer, which reduces the steric hindrance within the structure. Finally, we show that the distinctly different planarity between FBIID and PzIID results in significantly different field-effect transistor (FET) mobility. Owing to the higher planarity and improved stacking and crystallinity of the polymer chains, the PzIID-derived polymers deliver much higher hole mobilities (μhs) of > 3 × 10 −4 (cm2 V−1 s−1) than the FBIID-derived polymers that show no conspicuous charge-transporting properties. This result clearly highlights the crucial role of the spacer structure in designing the heterocyclic ring-fused IID core structures.

This work describes molecular structures of chalcones 2'-Hydroxy-4',6'-dimethyl-2-chlorochalcone and 2'-Hydroxy-4',6'-dimethyl-4-chlorochalcone and overlap of these structures in order to detect the change in planarity. The Hirshfeld Surface analysis to investigate when the position of the atom the chlorine in the aromatic ring is changed and how does this change influence in the properties of the organic compound. The geometric molecular were obtained through the DFT/M06-2X/6-311++G(2d, 2p) theory level. Frontier Molecular Orbital, NBO and MEP map were determined, in order to observe the information related to charge transfer in the molecule. The interactions between the molecules were verified with the aid of QTAIM.

An extensive database study of hydrogen bonds in different protein environments showed systematic variations in donor-acceptor-acceptor antecedent angle (Ĥ) and donor-acceptor distance. Protein environments were characterized by depth (distance of amino acids from bulk solvent), secondary structure, and whether the donor/acceptor belongs to the main chain (MC) or side chain (SC) of amino acids. The MC-MC hydrogen bonds (whether in secondary structures or not) have Ĥ angles tightly restricted to a value of around 155°, which was distinctly different from other Ĥ angles. Quantum chemical calculations attribute this characteristic MC-MC Ĥ angle to the nature of the electron density distribution around the planar peptide bond. Additional classical simulations suggest a causal link between MC-MC Ĥ angle and the conformation of secondary structures in proteins. We also showed that donor-acceptor distances are environment dependent, which has implications on protein stability. Our results redefine hydrogen bond geometries in proteins and suggest useful refinements to existing molecular mechanics force fields., Graphical abstract Image 1, Highlights • Hydrogen bonds are known to stabilize the structures of proteins. • We investigated the hydrogen bond types involving the main and side chains of amino acids and their environments. • The different types have unique preferences for donor-acceptor distances as well as for the donor-acceptor-acceptor antecedent (Ĥ) angles. • Classical and quantum calculations implicate the electronic structure of the peptide bond as the origin of these differences. • This study explains the origin of secondary structures and is important for protein characterization and design.

The Ruhemann's Purple (RP) is a chromophore formed from ninhydrin reaction with amines mainly applied to develop latent fingerprints in forensic science. Further enhancement of RP photoluminescence is achieved thought post-treatment with transition metal salt (commonly ZnCl2 alcohol solution), due to the coordination of RP with the metal ion. The literature attributes this improvement to the RP planarity increase in the complex, suggesting this characteristic as important to the post-treatment success. In the present work, the experimentally reported ZnRP complexes and the isolated RP ligand were investigated at the ωB97XD/6-311++G(d,p)/LanL2DZ/IEFPCM(MeOH) level, and their geometrical parameters, complexation energies, and spectroscopic properties (harmonic vibrations and electronic spectrum) were evaluated and agree with the experimental data. The systematic variation of the RP planarity (tilt angle) showed that the lowest energy electronic transition is quite sensitive to RP of this torsion angle. However, the RP planarity increase corresponds to approximately 30% of the total band shift achieved in the complex formation. The results reinforce the importance of the metal ion in the photoluminesce property changing and draw attention to improvements on transition metal complexes design in the post-treatment of developed latent fingermarks.

A novel poly­morph of (E)-4-bromo-2-[(phenyl­imino)­meth­yl]phenol is reported, with a dihedral angle between the planes of the two aromatic rings of 45.6 (1)°, significantly different to that of the previously published poly­morph. The structure contains an intra­molecular O—H⋯N hydrogen bond forming an S(6) ring., A new poly­morph of (E)-4-bromo-2-[(phenyl­imino)­meth­yl]phenol, C13H10BrNO, is reported, together with a low-temperature structure determination of the previously published poly­morph. Both poly­morphs were found to have an intra­molecular O—H⋯N hydrogen bond between the phenol OH group and the imine N atom, forming an S(6) ring. The crystals were observed to have different colours at room temperature, with the previously published poly­morph being more orange and the new poly­morph more yellow. The planarity of the mol­ecule in the two poly­morphs was found to be significantly different, with dihedral angles (Φ) between the two aromatic rings for the previously published ‘orange’ poly­morph of Φ = 1.8 (2)° at 120 K, while the new ‘yellow’ poly­morph had Φ = 45.6 (1)° at 150 K. It was also observed that both poly­morphs displayed some degree of thermochromism and upon cooling the ‘orange’ poly­morph became more yellow, while the ‘yellow’ poly­morph became paler upon cooling.

Taking advantage of the known planarity of the N-acetyl group of N-acetylglucosamine, an analysis of the quality of carbohydrate structures found in the protein databank was performed. Few obvious defects of the local geometry of the carbonyl group were observed. However, the N-acetyl group was often found in the less favorable cis conformation (12% of the cases). It was also found severely twisted in numerous instances, especially in structures with a resolution poorer than 1.9 A determined between 2000 and 2015. Though the automated PDB-REDO procedure has proved able to improve nearly 85% of the structural models deposited to the PDB, and does prove able to cure most severely twisted conformations of the N-acetyl group, it fails to correct its high rate of cis conformations. More generally, for structures with a resolution poorer than 1.6 A, it produces N-acetylglucosamine models in slightly poorer agreement with experimental data, as measured using real-space correlation coefficients. Significant improvements are thus still needed, at least as far as this carbohydrate structure is concerned.

The geometry of arginine shows more complexity than is accommodated by the standard restraints., Crystallographic refinement of macromolecular structures relies on stereochemical restraints to mitigate the typically poor data-to-parameter ratio. For proteins, each amino acid has a unique set of geometry restraints which represent stereochemical information such as bond lengths, valence angles, torsion angles, dihedrals and planes. It has been shown that the geometry in refined structures can differ significantly from that present in libraries; for example, it was recently reported that the guanidinium moiety in arginine is not symmetric. In this work, the asymmetry of the N∊—Cζ—Nη1 and N∊—Cζ—Nη2 valence angles in the guanidinium moiety is confirmed. In addition, it was found that the Cδ atom can deviate significantly (more than 20°) from the guanidinium plane. This requires the relaxation of the planar restraint for the Cδ atom, as it otherwise causes the other atoms in the group to compensate by distorting the guanidinium core plane. A new set of restraints for the arginine side chain have therefore been formulated, and are available in the software package Phenix, that take into account the asymmetry of the group and the planar deviation of the Cδ atom. This is an example of the need to regularly revisit the geometric restraint libraries used in macromolecular refinement so that they reflect the best knowledge of the structural chemistry of their components available at the time.