A. Nijamudheen

Molecular Balances Based on Aliphatic CH−π and Lone-Pair−π Interactions

CH···π and lone-pair···π interactions are estimated for a series of conformationally dynamic bicyclic N-aryliimides. On the basis of their strengths and mutual synergy/competition, the molecules prefer a folded/unfolded conformation. Calculations suggest strategies to selectively isolate the folded form by increasing the strength of the attractive CH···π interaction or removing the lone-pair···π repulsion. While the barrier for the folded ⇄ unfolded transformation is too large to conformationally lock the molecules in either of the conformers, the dynamics for hopping of the alkyl group across rings and tumbling over the rings are found to be facile in the folded conformation.

Understanding the Mechanisms of Unusually Fast HH, CH, and CC Bond Reductive Eliminations from Gold(III) Complexes

Carbon-carbon bond reductive elimination from gold(III) complexes are known to be very slow and require high temperatures. Recently, Toste and co-workers have demonstrated extremely rapid CC reductive elimination from cis-[AuPPh3 (4-F-C6 H4 )2 Cl] even at low temperatures. We have performed DFT calculations to understand the mechanistic pathway for these novel reductive elimination reactions. Direct dynamics calculations inclusive of quantum mechanical tunneling showed significant contribution of heavy-atom tunneling (>25 %) at the experimental reaction temperatures. In the absence of any competing side reactions, such as phosphine exchange/dissociation, the complex cis-[Au(PPh3 )2 (4-F-C6 H4 )2 ](+) was shown to undergo ultrafast reductive elimination. Calculations also revealed very facile, concerted mechanisms for HH, CH, and CC bond reductive elimination from a range of neutral and cationic gold(III) centers, except for the coupling of sp(3) carbon atoms. Metal-carbon bond strengths in the transition states that originate from attractive orbital interactions control the feasibility of a concerted reductive elimination mechanism. Calculations for the formation of methane from complex cis-[AuPPh3 (H)CH3 ](+) predict that at -52 °C, about 82 % of the reaction occurs by hydrogen-atom tunneling. Tunneling leads to subtle effects on the reaction rates, such as large primary kinetic isotope effects (KIE) and a strong violation of the rule of the geometric mean of the primary and secondary KIEs.

Topochemical Transformations of CaX2 (X=C, Si, Ge) to Form Free-Standing Two-Dimensional Materials.

Topochemical transformations of layered materials CaX2 (X=Si, Ge) are the method of choice for the high-yield synthesis of pristine, defect-free two-dimensional systems silicane and germanane, which have advanced electronic properties. Based on solid-state dispersion-corrected calculations, mechanisms for such transformations are elucidated that provide an in-depth understanding of phase transition in these layered materials. While formation of such layered materials is highly favorable for silicane and germanane, a barrier of 1.2 eV in the case of graphane precludes its synthesis from CaC2 topochemically. The energy penalty required for distorting linear acetylene into a trans-bent geometry accounts for this barrier. In contrast it is highly favorable in the heavier analogues, resulting in barrierless topochemical generation of silicane and germanane. Photochemical generation of the trans-bent structure of acetylene in its first excited state (S1 ) can directly generate graphane through a barrierless condensation. Unlike the buckled structure of silicene, the phase-h of CaSi2 with perfectly planar silicene layers exhibits the Dirac cones at the high symmetry points K and H. Interestingly, topochemical acidification of the cubic phase of calcium carbide is predicted to generate the previously elusive platonic hydrocarbon, tetrahedrane.

Aminoindolines versus quinolines: mechanistic insights into the reaction between 2-aminobenzaldehydes and terminal alkynes in the presence of metals and secondary amines.

DFT computational studies in the cyclization of aminoalkyne (see structure), which is generated in situ by 2-aminobenzaldehydes and terminal alkynes in the presence of metals and secondary amines, has been investigated. The study revealed that the mode of cyclization (exo vs endo) depends on the protecting group on nitrogen, the oxidation state of copper, and substitution on alkyne.

Strain Control: Reversible H2 Activation and H2/D2 Exchange in Pt Complexes

Experiments have indicated that bulky ligands are required for efficient H2 activation by Pt-Sn complexes. Herein, we unravel the mechanisms for a Pt-Sn complex, Pt(Sn(t)Bu3)2(CN(t)Bu)2 (1a), catalyzed reversible H2 activation. Among a number of Pt-Sn catalysts used to model H2 activation and H2/D2 exchange reactions, only 1a with large strain was found to be suitable because the addition of H2 to 1a requires lowest distortion energy, minimal structural changes, and smallest entropy of activation. The activity of this Pt-Sn complex was compared vis-à-vis its Pt-Ge and Pt-Si analogues, and we predicted that strained Pt-Ge complex can efficiently activate H2 reversibly. Direct dynamics calculations for the rate of reductive elimination of H2, HD, and D2 from Pt(Sn(t)Bu3)(CN(t)Bu)2H3 (4a) and Pt(Sn(t)Bu3)(CN(t)Bu)2HD2 (4a([2D])) shows that H/D atom tunneling contributes significantly, which leads to an enhanced kinetic isotope effect. Strain control is suggested as a design concept in H2 activation.

Janus all-cis-1,2,3,4,5,6-Hexafluorocyclohexane: A Molecular Motif for Aggregation-Induced Enhanced Polarization.

Recently synthesized all-cis-1,2,3,4,5,6-hexafluorocyclohexane is the least stable among all possible configurational isomers of 1,2,3,4,5,6-hexafluorocyclohexane. This molecule has a remarkably large dipole moment (6.2 D) as well as high facial polarization. Solid-state, dispersion-corrected DFT (DFT-D3) calculations are performed on the crystalline phase of all-cis-1,2,3,4,5,6- hexafluorocyclohexane, which reveal that dispersion interactions play a crucial role in its stabilization. A number of thermodynamically favorable orientations of dimers, trimers and tetramers are demonstrated for this molecule. Parallel-stacked aggregates, from dimers to higher-order aggregates, which are absent in the crystal, are found to be thermodynamically most favorable due to the presence of strong short-range C-H⋅⋅⋅F-C intermolecular hydrogen-bonding networks. Because of their cooperative nature, binding energies, dipole moments, and polarizations per molecule increase from monomer to tetramer, whereas the HOMO-LUMO gaps follow the opposite trend. Based on the DFT-D3 calculations, it is proposed that this parallel-stacked arrangement can be further extended to prepare stable a 1D crystal such that a large dipole moment and macroscopic polarizations can arise, which might be useful in designing electronic and nonlinear optical devices. Because the molecule has conformational flexibility, the potential energy surface is investigated for ring flipping and the effects of fluorine substitution are studied by comparing the barrier with respect to cyclohexane and all-cis-1,2,3-trifluorocyclohexane.

Pattern Formation Due to Fluorination on Graphene Fragments: Structures, Hopping Behavior, and Magnetic Properties

Structures and mechanism of pattern formation for the radical fluorination on selected polyaromatic hydrocarbons (PAH) has been studied using density functional theory (DFT) methods. Our study reveals that the F(•) radical addition occurs preferentially at the edges of PAHs followed by the hopping of F(•) to the center due to the fluxional nature of C-F bond. F(•) migrates preferentially over the C-C bonds having a lower barrier than that over the aromatic π-cloud in cases of monofluorinated PAHs. Addition of a second F radical can stabilize the system, cooperatively. When two F(•) are added to the adjacent C atoms, it forms the minimum energy patterns. However, the addition of two fluorine radicals at the meta position of the same aromatic ring would lead to the stabilization of the triplet state compared to the singlet ground state. Therefore, depending on the sites of F(•) addition, these structures exhibit ferromagnetic/antiferromagnetic ground states. Considering the low barrier heights for the F(•) hopping, these systems are predicted to be in a dynamic equilibrium with their less stable ferromagnetic states. Our study also provides an atomistic understanding of the well-known rate determining state for the fluorine pattern formation in graphene and CNT.

Half-sandwich Ru(η6-C6H6) complexes with chiral aroylthioureas for enhanced asymmetric transfer hydrogenation of ketones – experimental and theoretical studies

The reactions of [RuCl2(η6-C6H6)]2 with chiral aroylthiourea ligands yielded pseudo-octahedral half-sandwich “piano-stool” complexes. All the Ru(II) complexes were characterized by analytical and spectral (UV-visible, FT-IR, 1H NMR and 13C NMR) studies. The molecular structures of the ligands (L2 and L4) and the complexes (2, 4 and 5) were confirmed by single crystal XRD. All the complexes were successfully screened as catalysts for the asymmetric transfer hydrogenation (ATH) of ketones using 2-propanol as the hydrogen source in the presence of KOH. The ATH reactions proceeded with excellent yields (up to 99%) and very good enantioselectivity (up to 99% ee). The scope of the present catalytic system was extended to substituted aromatic ketones and few hetero-aromatic ketones. Density functional theory (DFT) calculations predicted non-classical, concerted transition states for the ATH reactions. The catalytic activity of Ru–benzene complexes toward asymmetric reduction of ketones was significantly higher compared to that of p-cymene complex analogues. Such enhanced efficiency and product selectivity of Ru–benzene complexes compared to those of Ru–p-cymene complexes were rationalized by the computational study.

Analyte interactions with a new ditopic dansylamide-nitrobenzoxadiazole dyad: a combined photophysical, NMR, and theoretical (DFT) study.

We report herein the synthesis and photophysical studies on a new multicomponent chemosensor dyad comprising two fluorescing units, dansylamide (DANS) and nitrobenzoxadiazole (NBD). The system has been developed to investigate receptor-analyte binding interactions in the presence of both cations and anions in a single molecular system. A dimethyl amino (in the DANS unit) group is used as a receptor for cations, and acidic hydrogens of sulfonamide and the NBD group are used as receptors for anions. The system is characterized by conventional analytical techniques. The photophysical properties of this supramolecular system in the absence and presence of various metal ions and nonmetal ions as additives are investigated in an acetonitrile medium. Utility of this system in an aqueous medium has also been demonstrated. The absorption and fluorescence spectrum of the molecular system consists of a broad band typical of an intramolecular charge-transfer (ICT) transition. A low quantum yield and lifetime of the NBD moiety in the present dyad indicates photoinduced electron transfer (PET) between DANS and the NBD moiety. The fluorescence intensity of the system is found to decrease in the presence of fluoride and acetate anions; however, the quenching is found to be much higher for fluoride. This quenching behavior is attributed to the enhanced PET from the anion receptor to the fluorophore moiety. The mechanistic aspect of the fluoride ion signaling behavior has also been studied by infrared (IR) and (1)H NMR experiments. The hydrogen bonding interaction between the acidic NH protons of the DPN moiety and F(-) is found to be primarily responsible for the fluoride selective signaling behavior. While investigating the cation signaling behavior, contrary to anions, significant fluorescence enhancement has been observed only in the presence of transition-metal ions. This behavior is rationalized by considering the disruption of PET communication between DANS and the NBD moiety due to transition-metal ion binding. Theoretical (density functional theory) studies are also performed for the better understanding of the receptor-analyte interaction. Interestingly, negative cooperativity in binding is observed when the interaction of this system is studied in the presence of both Zn(2+) and F(-). Fluorescence microscopy studies also revealed that the newly developed fluorescent sensor system can be employed as an imaging probe in live cells.

Color polymorphism: Understanding the diverse solid-state packing and color in dimethyl-3,6-dichloro-2,5-dihydroxyterephthalate

Dimethyl-3,6-dichloro-2,5-dihydroxyterephthalate (MCHT) is known to exist in three differently packed crystals having three different colors, namely yellow (Y), light yellow (LY), and white (W). Apart from the difference in their color, the molecules in the crystals also differ in their intramolecular O-H⋅⋅⋅O and O-H⋅⋅⋅Cl hydrogen bonds. Time-dependent DFT calculations reveal the role of the various types of hydrogen bonds in controlling the color of the polymorphs. Mechanistic pathways that lead to such transformations in the crystal are elucidated by solid-state dispersion-corrected DFT studies. Relative stabilities of the various polymorphs rationalize the experimentally observed transformations between them. Calculations reveal that the minimum-energy pathway for the conversion of the Y form to a W form is through stepwise disrotatory motion of the two -OH groups through a hybrid intermediate having one intramolecular OH⋅⋅⋅O and one O-H⋅⋅⋅Cl bond. The LY form is shown to exist on the higher-energy pathway involving a concerted Y→W transformation.