Nisanth N. Nair

High Proton Conductivity by a Metal–Organic Framework Incorporating Zn8O Clusters with Aligned Imidazolium Groups Decorating the Channels

A novel metal-organic framework, [{(Zn(0.25))(8)(O)}Zn(6)(L)(12)(H(2)O)(29)(DMF)(69)(NO(3))(2)](n) (1) {H(2)L = 1,3-bis(4-carboxyphenyl)imidazolium}, has been synthesized under solvothermal conditions in good yield. It shows a Zn(8)O cluster that is coordinated to six ligands and forms an overall three-dimensional structure with channels along the crystallographic a and b axes. The imidazolium groups of the ligand moiety are aligned in the channels. The channels are not empty but are occupied by a large number of DMF and water molecules. Upon heating, these solvent molecules can be removed without breakdown of the overall structure of the framework as shown by variable-temperature powder X-ray diffraction patterns. Of great interest is the fact that the compound exhibits high proton conductivity with a low activation energy that is comparable to those of Nafion presently used in fuel cells.

Twist Does a Twist to the Reactivity: Stoichiometric and Catalytic Oxidations with Twisted Tetramethyl-IBX

The methyl groups in TetMe-IBX lower the activation energy corresponding to the rate-determining hypervalent twisting (theoretical calculations), and the steric relay between successive methyl groups twists the structure, which manifests in significant solubility in common organic solvents. Consequently, oxidations of alcohols and sulfides occur at room temperature in common organic solvents. In situ generation of the reactive TetMe-IBX from its precursor iodo-acid, i.e., 3,4,5,6-tetramethyl-2-iodobenzoic acid, in the presence of oxone as a co-oxidant facilitates the oxidation of diverse alcohols at room temperature.

Influence of extreme thermodynamic conditions and pyrite surfaces on peptide synthesis in aqueous media.

Free energy landscapes and reaction mechanisms underlying the synthesis of diglycine in water were studied computationally. It was found that amino acid activation by carbonyl sulfide, leading to the formation of a cyclic alpha-amino acid N-carboxyanhydride (NCA, or Leuchs anhydride), preferentially follows an indirect pathway that involves an isocyanate intermediate. Extreme temperature and pressure conditions accelerate peptidization greatly compared to the ambient bulk water environment and are shown to favor, in general, concerted versus stepwise mechanisms. Finally, a pyrite surface, FeS2 (001), is found to lower reaction barriers further by decreasing fluctuations and by assisting the preformation of the cyclic five-membered NCA ring due to scaffolding.

Excited State Relaxation Dynamics of Model Green Fluorescent Protein Chromophore Analogs: Evidence for Cis–Trans Isomerism

Two green fluorescent protein (GFP) chromophore analogs (4Z)-4-(N,N-dimethylaminobenzylidene)-1-methyl-2-phenyl-1,4-dihydro-5H-imidazolin-5-one (DMPI) and (4Z)-4-(N,N-diphenylaminobenzylidene)-1-methyl-2-phenyl-1,4-dihydro-5H-imidazolin-5-one (DPMPI) were investigated using femtosecond fluorescence up-conversion spectroscopy and quantum chemical calculations with the results being substantiated by HPLC and NMR measurements. The femtosecond fluorescence transients are found to be biexponential in nature and the time constants exhibit a significant dependence on solvent viscosity and polarity. A multicoordinate relaxation mechanism is proposed for the excited state relaxation behavior of the model GFP analogs. The first time component (τ(1)) was assigned to the formation of twisted intramolecular charge transfer (TICT) state along the rotational coordinate of N-substituted amine group. Time resolved intensity normalized and area normalized emission spectra (TRES and TRANES) were constructed to authenticate the occurrence of TICT state in subpicosecond time scale. Another picosecond time component (τ(2)) was attributed to internal conversion via large amplitude motion along the exomethylenic double bond which has been enunciated by quantum chemical calculations. Quantum chemical calculation also forbids the involvement of hula-twist because of high activation barrier of twisting. HPLC profiles and proton-NMR measurements of the irradiated analogs confirm the presence of Z and E isomers, whose possibility of formation can be accomplished only by the rotation along the exomethylenic double bond. The present observations can be extended to p-HBDI in order to understand the role of protein scaffold in reducing the nonradiative pathways, leading to highly luminescent nature of GFP.

Rh1/γ‐Al2O3 Single‐Atom Catalysis of O2 Activation and CO Oxidation: Mechanism, Effects of Hydration, Oxidation State, and Cluster Size

The single‐atom catalysis of O2 activation and CO oxidation with Rh1 supported on γ‐Al2O3 is investigated here through ab initio molecular dynamics techniques. We scrutinize the molecular details of the mechanism for the full catalytic cycle that involves the oxidation of two CO molecules in succession. The effect of the surface hydration and oxidation state of Rh on the kinetics of O2 activation and CO oxidation is presented. We also report here the catalytic activity of experimentally intercepted RhI(CO)2 on γ‐Al2O3. Furthermore, we delineate the importance of single‐atom catalysis by comparing the performance of the Rh6/Al2O3 catalyst. A molecular level understanding of the differential reactivity on hydration, on oxidation, and of a larger Rh cluster size is reported.

Peptide Synthesis in Aqueous Environments : The Role of Extreme Conditions on Amino Acid Activation

The free energy surfaces and reaction mechanisms underlying the activation of amino acids by COS in bulk water at ambient conditions as well as extreme temperature-pressure thermodynamic conditions were studied using accelerated ab initio molecular dynamics. The results for the reaction sequence leading from glycine to its activated form, a so-called Leuchs anhydride or alpha-amino acid N-carboxyanhydride (NCA), suggest that extreme conditions not far from the critical point of water may favor the formation of this activated species. This is traced back to appropriately affecting relative stabilities of neutral versus charged or zwitterionic molecular species which shifts equilibria, affects relative barriers, and thus modifies reaction rates. Furthermore, it is shown that the N-carboxyanhydride of glycine is not formed from N-thiocarboxyl glycine by its direct cyclization, but instead an indirect mechanism, the so-called isocyanate route, is clearly preferred at both conditions. The work quantitatively underpins the impact of extreme solvent conditions on the investigated organic reactions in aqueous media which implies that the presented results are of relevance to fields such as prebiotic chemistry and green chemistry.

Dynamical magnetostructural properties of Anabaena ferredoxin

A mixed quantum/classical investigation of the dynamical magnetostructural properties, that is, “magnetodynamics,” of oxidized Anabaena PCC7119 ferredoxin is carried out at room temperature in two distinct conformational states. This protein hosts a [2Fe–2S] cluster in which two iron centers are antiferromagnetically coupled to an overall low-spin electronic ground state that has a genuine multireference character. To study the magnetodynamics of this prosthetic group, an approximate spin projection method is formulated in the framework of density functional theory that allows for multideterminant ab initio molecular dynamics simulations to be carried out efficiently. By using this scheme, the influence of both thermal fluctuations and conformational motion on the structure of the [2Fe–2S] cluster and on the dynamics of the antiferromagnetic coupling constant, J(t), has been investigated. In addition to demonstrating how sensitively the shape of the [2Fe–2S] core itself is affected by hydrogen bonding, the analyses reveal a complex dynamical coupling of J to both local vibrations and large-amplitude motion. It is shown that this interplay can be understood in terms of specific vibrational modes and distinct hydrogen-bonding patterns between the iron–sulfur cluster and the protein backbone, respectively. This implies going beyond the Goodenough–Kanamori rules for angular magnetostructural correlations of oxidized iron–sulfur prosthetic groups.

Molecular dynamics investigation of oxygen vacancy diffusion in rutile

Oxygen vacancy diffusion in rutile was studied by Born-Oppenheimer molecular dynamics techniques in the framework of the semiempirical molecular orbital method MSINDO. Migration of an oxygen vacancy from the rutile (110) surface towards the bulk was simulated. The metadynamics technique was employed to accelerate the diffusion processes. In this way, transition state structures and activation energies for the diffusion processes were obtained. Rate constants and the time scale of diffusion processes were estimated for different temperatures using the calculated activation energy. It was found that the vacancies in the bulk are less stable than on the surface. The feasibility of oxygen vacancy diffusion under experimental conditions is discussed.

Molecular dynamics implementation in MSINDO: Study of silicon clusters

Born–Oppenheimer molecular dynamics is implemented in the semiempirical self‐consistent field molecular orbital method MSINDO. The method is employed for the investigation of the structure and dynamics of silicon clusters of various sizes. The reliability of the present parameterization for silicon compounds is demonstrated by a comparison of the results of simulated annealing and of density functional calculations of Sin clusters (n = 5–7). The melting behavior of the Si7 cluster is investigated and the MSINDO results are compared to previous high‐level calculations. The efficiency of the present approach for the treatment of large systems is demonstrated by an extensive simulated annealing study of the Si45 and Si60 clusters. New Si45 and Si60 structures are found and evaluated. The relative stability of various energy minimum structures is compared with density functional calculations and available literature data.

Ligand exchanges and hydroxypalladation reactions of the Wacker process in aqueous solution at high Cl⁻ concentration.

Reaction mechanisms and associated free energies of various reaction steps involved in the Wacker process in aqueous acidic conditions at high Cl(-) concentration were investigated using accelerated ab initio molecular dynamics techniques. Several ligand exchange reactions of the catalytic precursor [PdCl(4)](2-) and nucleophilic attack of water at Pd-coordinated ethene (hydroxypalladation) were looked at in great molecular level detail. This work underlines the key role of the trans effect of Pd-coordinated ethene in the structure and dynamics of solvated Pd(II) complexes. Irrespective of Cl or water ligation at the trans position, the hydroxypalladation proceeds through an anti mechanism where an outer-sphere water attacks an ethene carbon atom in an anti fashion. Extensive molecular dynamics simulations were used to analyze various reaction mechanisms and unravel the stereochemistry of the crucial hydroxypalladation step.