Eluvathingal D. Jemmis

Double aromaticity: aromaticity in orthogonal planes. The 3,5-dehydrophenyl cation.

Abstract The D 3h 3,5-dehydrophenyl cation (I), which may represent the structure of C 6 H 3 ions observed mass spectroscopically, illustrates double aromaticity : two different aromatic systems in orthogonal planes.

Ab initio structures of allyllithium

Abstract Complete optimization of classical and nonclassical allyllithium structures at the RHF/STO-3G level with subsequent RHF/4-31G and RHF/6-31G calculations confirms the C s , bridged species to have the lowest energy. The allyl fragment of this structure is significantly distorted from a planar arrangement in order to enhance bonding between the allyl anion HOMO (on C(1), C(3)) and the lithium p -orbital with axis parallel to C(1)–C(3).

Reactions of group 4 metallocene alkyne complexes with carbodiimides: experimental and theoretical studies of the structure and bonding of five-membered hetero-metallacycloallenes.

The reaction of the low-valent metallocene(II) sources Cp(2)Ti(η(2)-Me(3)SiC(2)SiMe(3)) (7) and Cp(2)Zr(py)(η(2)-Me(3)SiC(2)SiMe(3)) (11, Cp = η(5)-cyclopentadienyl, py = pyridine) with carbodiimides RN═C═NR (R = Cy, i-Pr, p-Tol) leads to the formation of five membered hetero-metallacycloallenes Cp(2)M{Me(3)SiC═C═C[N(SiMe(3))(R)]-N(R)} (9M-R) (M = Ti, R = i-Pr; M = Zr, R = Cy, i-Pr, p-Tol). Elimination of the alkyne (as the hitherto known reactivity of titanocene and zirconocene alkyne complexes would suggest) was not observed. The molecular structures of the obtained complexes were confirmed by X-ray studies. Moreover, the structure and bonding of the complexes 9Zr-Cy and 9Zr-p-Tol was investigated by DFT calculations.

Hypercarbons in polyhedral structures

Though carbon is mostly tetravalent and tetracoordinated, there are several examples where the coordination number exceeds four. Structural varieties that exhibit hypercarbons in polyhedral structures such as polyhedral carboranes, sandwich complexes, encapsulated polyhedral structures and novel planar aromatic systems with atoms embedded in the middle are reviewed here. The structural variety anticipated with hypercoordinate carbon among carboranes is large as there are many modes of condensation that could lead to large number of new patterns. The relative stabilities of positional isomers of polyhedral carboranes, sandwich structures, and endohedral carboranes are briefly described. The mno rule accounts for the variety of structural patterns. Wheel-shaped and planar hypercoordinated molecules are recent theoretical developments in this area.

Mechanism of gallic acid biosynthesis in bacteria (Escherichia coli) and walnut (Juglans regia)

Gallic acid (GA), a key intermediate in the synthesis of plant hydrolysable tannins, is also a primary anti-inflammatory, cardio-protective agent found in wine, tea, and cocoa. In this publication, we reveal the identity of a gene and encoded protein essential for GA synthesis. Although it has long been recognized that plants, bacteria, and fungi synthesize and accumulate GA, the pathway leading to its synthesis was largely unknown. Here we provide evidence that shikimate dehydrogenase (SDH), a shikimate pathway enzyme essential for aromatic amino acid synthesis, is also required for GA production. Escherichia coli (E. coli) aroE mutants lacking a functional SDH can be complemented with the plant enzyme such that they grew on media lacking aromatic amino acids and produced GA in vitro. Transgenic Nicotianatabacum lines expressing a Juglans regia SDH exhibited a 500% increase in GA accumulation. The J. regia and E. coli SDH was purified via overexpression in E. coli and used to measure substrate and cofactor kinetics, following reduction of NADP+ to NADPH. Reversed-phase liquid chromatography coupled to electrospray mass spectrometry (RP-LC/ESI–MS) was used to quantify and validate GA production through dehydrogenation of 3-dehydroshikimate (3-DHS) by purified E. coli and J. regia SDH when shikimic acid (SA) or 3-DHS were used as substrates and NADP+ as cofactor. Finally, we show that purified E. coli and J. regia SDH produced GA in vitro.

Which One Is Preferred: Myers-Saito Cyclization of Ene-Yne-Allene or Garratt-Braverman Cyclization of Conjugated Bisallenic Sulfone? A Theoretical and Experimental Study

A competitive scenario between Myers-Saito (MS) and Garratt-Braverman (GB) cyclization has been created in a molecule. High-level computations indicate a preference for GB over MS cyclization. The activation energies for the rate-determining steps of the GB and MS cyclizations were found to be the same (24.4 kcal/mol) at the B3LYP/6-31G* level of theory; thus, from the kinetic point of view, both reactions are feasible. However, the main biradical intermediate GB2 of the GB reaction is 6.2 kcal/mol lower in energy than the biradical MS2, which is the main intermediate of MS reaction, so GB cyclization is thermodynamically favored over MS cyclization. To verify the prediction by computational techniques, bisenediynyl sulfones 1-4 and bisenediynyl sulfoxide 17 were synthesized. Under basic conditions, these molecules isomerized to a system possessing both the ene-yne-allene and the bisallenic sulfone. The isolation of only one product, identified as the corresponding naphthalene- or benzene-fused sulfone 8-11, indicated the occurrence of GB cyclization as the sole reaction pathway. No product corresponding to the MS cyclization pathway could be isolated. Though the theoretical prediction showed a preference for the GB pathway over the MS pathway, the exclusive preference for GB over MS cyclization is very striking. Further analysis showed that the intramolecular self-quenching nature of the GB pathway may play an important role in the complete preference for this reaction. Apart from the mechanistic studies, these sulfones showed DNA cleavage activity that had an inverse relation with the reactivity order. Our findings are important for the design of artificial DNA-cleaving agents.

Subtype Selectivity in Phosphodiesterase 4 (PDE4): A Bottleneck in Rational Drug Design

Subtype selectivity of phosphodiesterase 4 (PDE4) has been proposed to be the most salient feature for the development of drugs for asthma and inflammation. The present review provides an account of various strategies to overcome the side effects of the PDE4 inhibitors. Subtype selectivity and recent developments of molecular modeling approaches towards PDE4 were addressed using QSAR and docking, followed by a detailed structural analysis of more than three dozen available X-ray structures of PDE4B and PDE4D. Usually, the lack of a 3-dimensional structure of a target protein is a bottleneck for rational drug design approaches. However, in this case the availability of 39 X-ray structures along with co-crystals has not improved the therapeutic ratio of drugs through rational drug design approaches. The investigation of structures led to find significant variations in the M-loop region, which is the integral part of the active site of PDE4B and PDE4D. These differences can be accounted for by varying conformation of the Pro(430) residue and a Thr(436)/Asn(362) mutation in the M-loop that causes variations in adjacent residue properties and also the pattern of hydrogen-bonding interactions. The impact of the M-loop region on inhibitor binding has been further scrutinized by MOLCAD surfaces and hydrophobicity. These have shown that PDE4B is more hydrophobic in nature than PDE4D in the M-loop region. A review of the above aspects given the emphasis on a new PDE4 inhibitor which can access both metal and solvent pockets may possibly lead to ligands with enhanced potency. The lining of the Q2 pocket that involves the M-loop region may be considered for the design of potent subtype-selective inhibitors.

An ab initio and matrix isolation infrared study of the 1:1 C2H2–CHCl3 adduct

Abstract The details of weak C–H⋯π interactions that control several inter and intramolecular structures have been studied experimentally and theoretically for the 1:1 C2H2–CHCl3 adduct. The adduct was generated by depositing acetylene and chloroform in an argon matrix and a 1:1 complex of these species was identified using infrared spectroscopy. Formation of the adduct was evidenced by shifts in the vibrational frequencies compared to C2H2 and CHCl3 species. The molecular structure, vibrational frequencies and stabilization energies of the complex were predicted at the MP2/6-311+G(d,p) and B3LYP/6-311+G(d,p) levels. Both the computational and experimental data indicate that the C2H2–CHCl3 complex has a weak hydrogen bond involving a C–H⋯π interaction, where the C2H2 acts as a proton acceptor and the CHCl3 as the proton donor. In addition, there also appears to be a secondary interaction between one of the chlorine atoms of CHCl3 and a hydrogen in C2H2. The combination of the C–H⋯π interaction and the secondary Cl⋯H interaction determines the structure and the energetics of the C2H2–CHCl3 complex. In addition to the vibrational assignments for the C2H2–CHCl3 complex we have also observed and assigned features owing to the proton accepting C2H2 submolecule in the acetylene dimer.

Metallacyclocumulenes: A Theoretical Perspective on the Structure, Bonding, and Reactivity

Conspectus Transition metals help to stabilize highly strained organic fragments. Metallacycles, especially unsaturated ones, provide much variety in this area. We had a sustained interest in understanding new C-C bond formation reactions affected by binuclear transition metal fragments Cp2M. One such study led to the exploration of the bimetallic C-C cleavage and coupled complexes, where the acetylide ligands bridge two metal atoms. The underlying M-C interaction in these complexes inspired the synthesis of a five-membered cyclocumulene complex, which opened a new phase in organometallic chemistry. The metallacyclocumulene produces a variety of C-C cleavage and coupled products including a radialene complex. Group 4 metallocenes have thus unlocked a fascinating chemistry by stabilizing strained unsaturated C4 organic fragments in the form of five-membered metallacyclocumulenes, metallacyclopentynes, and metallacycloallenes. Over the years, we have carried out a comprehensive theoretical study to understand the unusual stability and reactivity of these metallacycles. The unique (M-Cβ) interaction of the internal carbon atoms with the metal atom is the reason for unusual stability of the metallacycles. We have also shown that there is a definite dependence of the C-C coupling and cleavage reactions on the metal of metallacyclocumulenes. It demonstrates unexpected reaction pathways for these reactions. Based on this understanding, we have predicted and unraveled the stabilization factors of an unusual four-membered metallacycloallene complex. Indeed, our prediction about a four-membered heterometallacycle has led to an interesting bonding situation, which is experimentally realized. This type of M-C bonding is intriguing from a fundamental perspective and has great relevance in synthesizing unusual structures with interesting properties. In this Account, we first give a short prologue of what led to the present study and describe the salient features of the structure and bonding of the metallacyclocumulenes. The unusual reaction pathway of this metallacycle is explored next. Similar features of the metallacyclopentynes and metallacycloallenes are briefly mentioned. Then, we discuss the exploitation of the unique M-C bonding to design some exotic molecules such as a four-membered metallacycloallene complex. Our efforts to build a conceptual framework to understand these metallacycles and to exploit their chemistry continue.

Synthesis, characterization, and electronic structure of new type of heterometallic boride clusters.

The reaction of [Cp*TaCl(4)], 1 (Cp* = η(5)-C(5)Me(5)), with [LiBH(4)·THF] at -78 °C, followed by thermolysis in the presence of excess [BH(3)·THF], results in the formation of the oxatantalaborane cluster [(Cp*Ta)(2)B(4)H(10)O], 2 in moderate yield. Compound 2 is a notable example of an oxatantalaborane cluster where oxygen is contiguously bound to both the metal and boron. Upon availability of 2, a room temperature reaction was performed with [Fe(2)(CO)(9)], which led to the isolation of [(Cp*Ta)(2)B(2)H(4)O{H(2)Fe(2)(CO)(6)BH}], 3. Compound 3 is an unusual heterometallic boride cluster in which the [Ta(2)Fe(2)] atoms define a butterfly framework with one boron atom lying in a semi-interstitial position. Likewise, the diselenamolybdaborane, [(Cp*Mo)(2)B(4)H(4)Se(2)], 4 was treated with an excess of [Fe(2)(CO)(9)] to afford the heterometallic boride cluster [(Cp*MoSe)(2)Fe(6)(CO)(13)B(2)(BH)(2)], 5. The cluster core of 5 consists of a cubane [Mo(2)Se(2)Fe(2)B(2)] and a tricapped trigonal prism [Fe(6)B(3)] fused together with four atoms held in common between the two subclusters. In the tricapped trigonal prism subunit, one of the boron atoms is completely encapsulated and bonded to six iron and two boron atoms. Compounds 2, 3, and 5 have been characterized by mass spectrometry, IR, (1)H, (11)B, (13)C NMR spectroscopy, and the geometric structures were unequivocally established by crystallographic analysis. The density functional theory calculations yielded geometries that are in close agreement with the observed structures. Furthermore, the calculated (11)B NMR chemical shifts also support the structural characterization of the compounds. Natural bond order analysis and Wiberg bond indices are used to gain insight into the bonding patterns of the observed geometries of 2, 3, and 5.