Synthetic and Structural Studies of 1,8‐Chalcogen Naphthalene Derivatives

Four novel 1,8‐disubstituted naphthalene derivatives 4 – 7 that contain chalcogen atoms occupying the peri positions have been prepared and fully characterised by using X‐ray crystallography, multinuclear NMR spectroscopy, IR spectroscopy and MS. Molecular distortion due to noncovalent substituent interactions was studied as a function of the bulk of the interacting chalcogen atoms and the size and nature of the alkyl group attached to them. X‐ray data for 4 – 7 was compared to the series of known 1,8‐bis(phenylchalcogeno)naphthalenes 1 – 3 , which were themselves prepared from novel synthetic routes. A general increase in the E???E′ distance was observed for molecules containing bulkier atoms at the peri positions. The decreased S???S distance from phenyl‐ 1 and ethyl‐ 4 analogues is ascribed to a weaker chalcogen lone pair–lone pair repulsion acting in the ethyl analogue due to the presence of two equatorial S(naphthyl) ring conformations. Two novel peri‐substituted naphthalene sulfoxides of 1 , Nap(O?SPh)(SPh) 8 and Nap(O?SPh)₂ 9 , which contain different valence states of sulfur, were prepared and fully characterised by using X‐ray crystallography and multinuclear NMR spectroscopy, IR spectroscopy and MS. Molecular structures were analysed by using naphthalene ring torsions, peri‐atom displacement, splay angle magnitude, S???S interactions, aromatic ring orientations and quasi‐linear O?S???S arrangements. The axial S(naphthyl) rings in 8 and 9 are unfavourable for S???S contacts due to stronger chalcogen lone pair–lone pair repulsion. Although quasi‐linear O?S???S alignments suggest attractive interaction is conceivable, analysis of the B3LYP wavefunctions affords no evidence for direct bonding interactions between the S atoms.     

Carbonyl Activation by Selenium- and Tellurium-Based Chalcogen Bonding in a Michael Addition Reaction

In the last years the use of chalcogen bonding—the noncovalent interaction involving electrophilic chalcogen centers—in noncovalent organocatalysis has received increased interest, particularly regarding the use of intermolecular Lewis acids. Herein, we present the first use of tellurium-based catalysts for the activation of a carbonyl compound (and only the second such activation by chalcogen bonding in general). As benchmark reaction, the Michael-type addition between trans-crotonophenone and 1-methylindole (and its derivatives) was investigated in the presence of various catalyst candidates. Whereas non-chalcogen-bonding reference compounds were inactive, strong rate accelerations of up to 1000 could be achieved by bidentate triazolium-based chalcogen bond donors, with product yields of >90 % within 2 h of reaction time. Organotellurium derivatives were markedly more active than their selenium and sulphur analogues and non-coordinating counterions like BAr^F₄ provide the strongest dicationic catalysts.     

Hydrogen-Bond Structure and Dynamics of TADDOL Asymmetric Organocatalysts Correlate with Catalytic Activity

The catalytic efficiency of diol-based organocatalysts has been shown to strongly depend on the diols molecular structure including hydrogen-bonding, yet, the underlying molecular-level origins have remained elusive. Herein a study on the inter- and intramolecular hydrogen-bonding of two isomeric diol-based catalysts (TADDOLs) in solution is presented: 1-Naphthyl substituted TADDOL (1nTADDOL), which exhibits high catalytic efficiency, and 2-naphthyl substituted TADDOL (2nTADDOL), which is a poor catalyst. Using nuclear magnetic resonance and infrared spectroscopy, comparable hydrogen-bond strengths for both TADDOLs in solution were found, however, significantly slower bonding dynamics for 1nTADDOL. In aromatic solvents, 1nTADDOL forms less, but longer-lived, intermolecular OH⋅⋅⋅π bonds to solvent molecules, as compared to 2nTADDOL. Thus, rather than previously suggested differences in intermolecular hydrogen-bonding strengths, the results suggest that the hydrogen-bonding kinetics and entropies differ for both TADDOLs, which also explains their vastly different catalytic activities.     

Synthesis and Characterization of Ba[CoSO]: Magnetic Complexity in the Presence of Chalcogen Ordering

Barium thio‐oxocobaltate(II), Ba[CoS_2/2O_2/2], was synthesized by the reaction of equimolar amounts of BaO, Co, and S in closed silica ampoules. The title compound (Cmcm, a=3.98808(3), b=12.75518(9), c=6.10697(4) Å) is isostructural to Ba[ZnSO]. The use of soft X‐ray absorption spectroscopy confirmed that cobalt is in the oxidation state +2 and tetrahedrally coordinated. Its coordination consists of two sulfur and two oxygen atoms in an ordered fashion. High‐temperature magnetic susceptibility data indicate strong low‐dimensional spin–spin interactions, which are suggested to be closely related to the layer‐type crystal structure and perhaps the ordered distribution of sulfur and oxygen. Antiferromagnetic ordering below T_N=222 K is observed as an anomaly in the specific heat, coinciding with a significant lowering of the magnetic susceptibility. Density functional theory calculations within a generalized‐gradient approximation (GGA)+U approach identify an antiferromagnetic ground state within the square‐like two‐dimensional layers of Co, and antiferromagnetic correlations for nearest and next nearest neighbors along bonds mediated by oxygen or sulfur. However, this magnetic state is subject to frustration by relatively strong interlayer couplings.     

A Quantitative Molecular Orbital Perspective of the Chalcogen Bond

We have quantum chemically analyzed the structure and stability of archetypal chalcogen-bonded model complexes D₂Ch⋅⋅⋅A⁻ (Ch = O, S, Se, Te; D, A = F, Cl, Br) using relativistic density functional theory at ZORA-M06/QZ4P. Our purpose is twofold: (i) to compute accurate trends in chalcogen-bond strength based on a set of consistent data; and (ii) to rationalize these trends in terms of detailed analyses of the bonding mechanism based on quantitative Kohn-Sham molecular orbital (KS-MO) theory in combination with a canonical energy decomposition analysis (EDA). At odds with the commonly accepted view of chalcogen bonding as a predominantly electrostatic phenomenon, we find that chalcogen bonds, just as hydrogen and halogen bonds, have a significant covalent character stemming from strong HOMO−LUMO interactions. Besides providing significantly to the bond strength, these orbital interactions are also manifested by the structural distortions they induce as well as the associated charge transfer from A⁻ to D₂Ch.     

Synthesis of Dibenzochalcogenaborins and Systematic Comparisons of Their Optical Properties by Changing a Bridging Chalcogen Atom

Novel hetero‐π‐conjugated compounds (dibenzochalcogenaborins) with the same molecular framework, bearing a boron atom as an acceptor and chalcogen atoms as a donor, were synthesized, and systematic comparisons among these molecules were performed. X‐ray crystallographic analysis of these molecules showed similar structures with high planarity. UV/Vis spectroscopy and theoretical calculations revealed that the absorption maxima and the HOMO–LUMO gap changed by systematically changing the bridging chalcogen atom. Dibenzooxaborin and dibenzothiaborin showed fluorescence emission both in solution and in the solid state with a small Stokes shift, indicating the high rigidity of these compounds. On the other hand, dibenzoselenaborin exhibited a very weak fluorescence as a result of the heavy atom effect.     

Controlling the conformation of arylamides: computational studies of intramolecular hydrogen bonds between amides and ethers or thioethers

The role of an ortho-alkylthioether group in controlling the conformation around the ring-N bonds of meta-connected arylamide oligomers is studied. Density functional theory (DFT) geometries of model compounds, including acetanilide, an ether acetanilide, and a thioether acetanilide, and their corresponding diamides, show that for either monoamide or diamide the alkyl side chain of the thioether should be perpendicular to the aryl plane, whereas for the ether monoamide, the alkyl side chain is in the aryl plane. DFT ring-N torsional potentials and constrained geometries of the model compounds demonstrate that carbonyl-S repulsion leads to a high torsional barrier and that intramolecular N-H...S and C-H...O hydrogen bonds and ring-amide conjugation lead to N-H having a preferred orientation in the benzene plane pointing towards S. The N-H bond lengthens and the ortho-ring C-H bond shortens in a regular pattern in the approach to the preferred orientation. Calculated IR frequencies for the N-H stretch show a clear red shift between model compounds without and with the thioether side chain.     

Kinetic,Spectroscopic, and Theoretical Assessment of Associative and Dissociative Methanol Dehydration Routes in Zeolites

Mechanistic interpretations of rates and in situ IR spectra combined with density functionals that account for van der Waals interactions of intermediates and transition states within confining voids show that associative routes mediate the formation of dimethyl ether from methanol on zeolitic acids at the temperatures and pressures of practical dehydration catalysis. Methoxy‐mediated dissociative routes become prevalent at higher temperatures and lower pressures, because they involve smaller transition states with higher enthalpy, but also higher entropy, than those in associative routes. These enthalpy–entropy trade‐offs merely reflect the intervening role of temperature in activation free energies and the prevalence of more complex transition states at low temperatures and high pressures. This work provides a foundation for further inquiry into the contributions of H‐bonded methanol and methoxy species in homologation and hydrocarbon synthesis reactions from methanol.     

Charge-Assisted Chalcogen Bonds: CSD and DFT Analyses and Biological Implication in Glucosidase Inhibitors

This study reports a combined Cambridge Structural Database and theoretical DFT study of charge assisted chalcogen bonds involving sulfonium, selenonium, and telluronium cations. The chalcogen bond has been recently defined by IUPAC as the net attractive interaction between an electrophilic region associated with a chalcogen atom in a molecular entity and a nucleophilic region in another, or the same, molecular entity. Divalent chalcogen atoms typically have up to two σ-holes and forms up to two ChBs; the same holds for tetravalent chalcogens which adopt a seesaw arrangement. In sulfonium, selenonium, and telluronium salts chalcogen atoms form three covalent bonds, three σ-holes are located opposite to these bonds, and up to three charge assisted ChBs can be formed between these holes and the counterions. The covalent bond arrangement around these chalcogen atoms is similar to trivalent pnictogen atoms and translates into a similar pattern of noncovalent interactions. We have found and studied this type of charge-assisted chalcogen bonds in various sulfonium ion-containing inhibitors of glucosidase, for example, salacinol and kotalanol.     

Structures of Trichloromethyl Thiocyanate,CCl3SCN,in Gaseous and Crystalline State

Trichloromethyl thiocyanate, CCl₃SCN, was structurally studied in both the gas and crystal phases by means of gas electron diffraction (GED) and single‐crystal X‐ray diffraction (XRD), respectively. Both experimental studies and quantum chemical calculations indicate a staggered orientation of the CCl₃ group relative to the SCN group. This conclusion is supported by the similarity of the C?SCN bond length to that of the anti‐structure of CH₂ClSCN (Berrueta Martínez et al. Phys. Chem. Chem. Phys. 2015, 17, 15805–15812). 1 Bond lengths and angles are similar for gas and crystal CCl₃SCN structures; however, the crystal structure presents different intermolecular interactions. These include halogen and chalcogen type interactions, the geometry of which was studied. Characteristic C‐Y???N angles (Y=Cl or S) close to 180° provide evidence for typical σ‐hole interactions along the halogen/chalcogen?carbon bond in N???Cl and N???S, intermolecular units.     

Radical Anions,Radical-Anion Salts,and Anionic Complexes of 2,1,3-Benzochalcogenadiazoles

By means of cyclic voltammetry (CV) and DFT calculations, it was found that the electron-acceptor ability of 2,1,3-benzochalcogenadiazoles 1 – 3 (chalcogen: S, Se, and Te, respectively) increases with increasing atomic number of the chalcogen. This trend is nontrivial, since it contradicts the electronegativity and atomic electron affinity of the chalcogens. In contrast to radical anions (RAs) [ 1 ]^.− and [ 2 ]^.−, RA [ 3 ]^.− was not detected by EPR spectroscopy under CV conditions. Chemical reduction of 1 – 3 was performed and new thermally stable RA salts [K(THF)]⁺[ 2 ]^.− ( 8 ) and [K(18-crown-6)]⁺[ 2 ]^.− ( 9 ) were isolated in addition to known salt [K(THF)]⁺[ 1 ]^.− ( 7 ). On contact with air, RAs [ 1 ]^.− and [ 2 ]^.− underwent fast decomposition in solution with the formation of anions [ECN]⁻, which were isolated in the form of salts [K(18-crown-6)]⁺[ECN]⁻ ( 10 , E=S; 11 , E=Se). In the case of 3 , RA [ 3 ]^.− was detected by EPR spectroscopy as the first representative of tellurium–nitrogen π-heterocyclic RAs but not isolated. Instead, salt [K(18-crown-6)]⁺₂[ 3 -Te₂]²⁻ ( 12 ) featuring a new anionic complex with coordinate Te−Te bond was obtained. On contact with air, salt 12 transformed into salt [K(18-crown-6)]⁺₂[ 3 -Te₄- 3 ]²⁻ ( 13 ) containing an anionic complex with two coordinate Te−Te bonds. The structures of 8 – 13 were confirmed by XRD, and the nature of the Te−Te coordinate bond in [ 3 -Te₂]²⁻ and [ 3 -Te₄- 3 ]²⁻ was studied by DFT calculations and QTAIM analysis.     

Monomer versus alcohol activation in the 4-dimethylaminopyridine-catalyzed ring-opening polymerization of lactide and lactic O-carboxylic anhydride

Model reactions for the 4-dimethylaminopyridine (DMAP)-catalyzed ring-opening polymerization of lactide and the corresponding lactic O-carboxylic anhydride (lacOCA) have been studied computationally at the B3LYP/6-31G(d) level of theory. The solvent effect of dichloromethane was taken into account through PCM/SCRF single-point calculations at the B3LYP/6-31G(d) level of theory. In marked contrast with that predicted for the reaction of alcohols with acetic anhydride, the mechanism in which nucleophilic activation of the monomer involving acylpyridinium intermediates was found to be energetically less favorable than the base activation of the alcohol through hydrogen bonding. The concerted pathway for the ring-opening of lactide and lacOCA was shown to compete with the traditional stepwise mechanism involving tetrahedral intermediates. Furthermore, DMAP is proposed to act as a bifunctional catalyst through its basic nitrogen center and an acidic ortho-hydrogen atom.     

Experimental and theoretical charge density study of the neurotransmitter taurine

The experimental electron density distribution in taurine, 2-aminoethane sulfonic acid, 1, has been determined from high-resolution X-ray diffraction data collected at a temperature of 100 K. Taurine crystallizes as a zwitterion in the monoclinic space group P2(1)/c. Topological analysis of the experimental electron density and a comparison with high-level theoretical gas-phase calculations show that the crystal environment has a significant influence on the electronic configuration of the sulfonate moiety in 1, which in the crystal is more delocalized than in the gas phase. This crystal effect is mainly due to hydrogen bonding.     

Central‐Atom Size Effects on the Methyl Torsions of Group XIV Tetratolyls

The Group XIV tetratolyl series X(C₆H₄‐CH₃)₄ (X=C, Si, Ge, Sn, Pb) were studied by using inelastic neutron scattering to measure the low‐energy phonon spectra to directly access the methyl‐group torsional modes. The effect of increased molecular radius as a function of the size of the central atom was shown to have direct influence on the methyl dynamics, reinforced with the findings of molecular dynamics and contact surface calculations, based upon the solid‐state structures. The torsional modes in the lightest analogue were found to be predominantly intramolecular: the Si and Ge analogues have a high degree of intermolecular methyl–methyl group interactions, whilst the heaviest analogues (Sn and Pb) showed pronounced intermolecular methyl interactions with the whole phonon bath of the lattice modes.     

Formation of T‐Shaped versus Charge‐Transfer Molecular Adducts in the Reactions Between Bis(thiocarbonyl) Donors and Br2 and I2

The reactions of 4,5,6,7‐tetrathiocino‐[1,2‐b:3,4‐b′]‐1,3,8,10‐tetrasubstituted‐diimidazolyl‐2,9‐dithiones (R₂,R′₂‐todit; 1 : R=R′=Et; 2 : R=R′=Ph; 3 : R=Et, R′=Ph) with Br₂ exclusively afforded 1:1 and 1:2 “T‐shaped” adducts, as established by FT‐Raman spectroscopy and single‐crystal X‐ray diffraction in the case of complex 1? 2 Br₂. On the other hand, the reactions of compounds 1 – 3 with molecular I₂ provided charge‐transfer (CT) “spoke” adducts, among which the solvated species 3? 2 I₂ ? (1?x)I₂ ? x CH₂Cl₂ (x=0.94) and ( 3 )₂ ? 7 I₂ ? x CH₂Cl_2, (x=0.66) were structurally characterized. The nature of all of the reaction products was elucidated based on elemental analysis and FT‐Raman spectroscopy and supported by theoretical calculations at the DFT level.     

Synthesis,Coordination Chemistry and Bonding of Strong N‐Donor Ligands Incorporating the 1H‐Pyridin‐(2E)‐Ylidene (PYE) Motif

A range of N‐donor ligands based on the 1H‐pyridin‐(2E)‐ylidene (PYE) motif have been prepared, including achiral and chiral examples. The ligands incorporate one to three PYE groups that coordinate to a metal through the exocyclic nitrogen atom of each PYE moiety, and the resulting metal complexes have been characterised by methods including single‐crystal X‐ray diffraction and NMR spectroscopy to examine metal–ligand bonding and ligand dynamics. Upon coordination of a PYE ligand to a proton or metal‐complex fragment, the solid‐state structures, NMR spectroscopy and DFT studies indicate that charge redistribution occurs within the PYE heterocyclic ring to give a contribution from a pyridinium–amido‐type resonance structure. Additional IR spectroscopy and computational studies suggest that PYE ligands are strong donor ligands. NMR spectroscopy shows that for metal complexes there is restricted motion about the exocyclic C? N bond, which projects the heterocyclic N‐substituent in the vicinity of the metal atom causing restricted motion in chelating‐ligand derivatives. Solid‐state structures and DFT calculations also show significant steric congestion and secondary metal–ligand interactions between the metal and ligand C? H bonds.     

Mechanism, regioselectivity, and the kinetics of phosphine-catalyzed [3+2] cycloaddition reactions of allenoates and electron-deficient alkenes

With the aid of computations and experiments, the detailed mechanism of the phosphine-catalyzed [3+2] cycloaddition reactions of allenoates and electron-deficient alkenes has been investigated. It was found that this reaction includes four consecutive processes: 1) In situ generation of a 1,3-dipole from allenoate and phosphine, 2) stepwise [3+2] cycloaddition, 3) a water-catalyzed [1,2]-hydrogen shift, and 4) elimination of the phosphine catalyst. In situ generation of the 1,3-dipole is key to all nucleophilic phosphine-catalyzed reactions. Through a kinetic study we have shown that the generation of the 1,3-dipole is the rate-determining step of the phosphine-catalyzed [3+2] cycloaddition reaction of allenoates and electron-deficient alkenes. DFT calculations and FMO analysis revealed that an electron-withdrawing group is required in the allene to ensure the generation of the 1,3-dipole kinetically and thermodynamically. Atoms-in-molecules (AIM) theory was used to analyze the stability of the 1,3-dipole. The regioselectivity of the [3+2] cycloaddition can be rationalized very well by FMO and AIM theories. Isotopic labeling experiments combined with DFT calculations showed that the commonly accepted intramolecular [1,2]-proton shift should be corrected to a water-catalyzed [1,2]-proton shift. Additional isotopic labeling experiments of the hetero-[3+2] cycloaddition of allenoates and electron-deficient imines further support this finding. This investigation has also been extended to the study of the phosphine-catalyzed [3+2] cycloaddition reaction of alkynoates as the three-carbon synthon, which showed that the generation of the 1,3-dipole in this reaction also occurs by a water-catalyzed process.     

Modified Guanines as Constituents of Smart Ligands for Nucleic Acid Quadruplexes

Repetitive guanine‐rich nucleic acid sequences play a crucial role in maintaining genome stability and the cell life cycle and represent potential targets for regulatory drugs. Recently, it has been demonstrated that guanine‐based ligands with a porphyrin core can be used as markers of G‐quadruplex assemblies in cell tissues. Herein, model systems of guanine‐based ligands are explored by DFT methods. The energies of formation of modified guanine tetrads and those of modified tetrads stacked on the top of natural guanine tetrads have been calculated. The interaction energy has been decomposed into contributions from hydrogen bonding, stacking, and ion coordination and a twist–rise potential energy scan has been performed to find the individual local minima. Energy decomposition analysis reveals the impact of various substituents (F, Cl, Br, I, Me, NMe₂) on individual energy terms. In addition, cooperative reinforcement in forming the modified and stacked tetrads, as well as the frontier orbitals participating in the hydrogen‐bonding framework involving the HOMO–LUMO gap between the occupied σ_HOMO on the proton‐accepting C=O and =N? groups and unoccupied σ_LUMO on the N?H groups, has been studied. The investigated systems are demonstrated to have a potential in ligand development, mainly due to stacking enhancement compared with natural guanine, which is used as a reference.