Excited state property of hardly photodissociable heme-CO adduct studied by time-dependent density functional theory

While most of CO-bound hemes are easily photodissociated with a quantum yield of nearly unity, we occasionally encounter a CO-heme which appears hardly photodissociable under the ordinary measurement conditions of resonance Raman spectra using CW laser excitation and a spinning cell. This study aims to understand such hemes theoretically, that is, the excited-state properties of the five-coordinate heme-CO adduct (5cH) as well as the 6c heme-CO adduct (6cH) with a weak axial ligand. Using a hybrid density functional theory, we scrutinized the properties of the ground and excited spin states of the computational models of a 5cH and a water-ligated 6cH (6cH-H(2)O) and compared these properties with those of a photodissociable imidazole-ligated 6cH (6cH-Im). Jahn-Teller softening for the Fe-C-O bending potential in the a(1)-e excited state was suggested. The excited-state properties of 6cH-Im and 5cH were further studied with time-dependent DFT theory. The reaction products of 6cH-Im and 5cH were assumed to be quintet and triplet states, respectively. According to the time-dependent DFT calculations, the Q excited state of 6cH-Im, which is initially a pure pi-pi state, crosses the Fe-CO dissociative state (2A') without large elongation of the Fe-CO bond. In contrast, the Q state of the 5cH does not cross the Fe-CO dissociative state but results in the formation of the excited spin state with a bent Fe-C-O. Consequently, photoisomerization from linear to bent Fe-C-O in the 5cH is a likely mechanism for apparent nonphotodissociation.     

New strategies for exploring RNA's 2'-OH expose the importance of solvent during group II intron catalysis

The 2'-hydroxyl group contributes inextricably to the functional behavior of many RNA molecules, fulfilling numerous essential chemical roles. To assess how hydroxyl groups impart functional behavior to RNA, we developed a series of experimental strategies using an array of nucleoside analogs. These strategies provide the means to investigate whether a hydroxyl group influences function directly (via hydrogen bonding or metal ion coordination), indirectly (via space-filling capacity, inductive effects, and sugar conformation), or through interactions with solvent. The nucleoside analogs span a broad range of chemical diversity, such that quantitative structure activity relationships (QSAR) now become possible in the exploration of RNA biology. We employed these strategies to investigate the spliced exons reopening (SER) reaction of the group II intron. Our results suggest that the cleavage site 2'-hydroxyl may mediate an interaction with a water molecule.     

Polymer‐Chlorambucil Drug Conjugates: A Dynamic Platform of Anticancer Drug Delivery

Recently, polymer drug conjugates (PDCs) have attracted considerable attention in the treatment of cancer. In this work, a simple strategy has been developed to make PDCs of an antitumor alkylating agent, chlorambucil, using a biocompatible disulphide linker. Chlorambucil‐based chain transfer agent was used to prepare various homopolymers and block copolymers in a controlled fashion via reversible addition–fragmentation chain transfer polymerization. Chlorambucil conjugated block copolymer, poly(polyethylene glycol monomethyl ether methacrylate)‐b‐poly(methyl methacrylate), formed nanoaggregates in aqueous solutions, which are characterized by dynamic light scattering and field emission‐scanning electron microscopy. Finally, the simplicity of the design is exemplified by performing a release study of chlorambucil under reducing condition by using D,L‐dithiothreitol.

     

Ionic liquid-assisted carboxylation of amines by CO2: a mechanistic consideration

The catalytic roles of ionic liquids (ILs) in the syntheses of 1,3-disubstituted ureas from the carboxylation of amines by CO(2) were experimentally and theoretically investigated. The carboxylation reaction of n-butylamine was greatly facilitated by the presence of an IL and the catalytic activity of the IL was strongly affected by the nucleophilicity of the anion. Computational study on the mechanistic aspects of the carboxylation with methylamine with or without the presence of an IL, 1-ethyl-3-methylimidazolium chloride, implies that the activation energies of the transition states and the intermediate ionic species could be lowered significantly through the multi-interactions of the carbonyl group of CO(2) with both cations and anions of the ILs.     

Redox isomerization via azomethine ylide intermediates: N-alkyl indoles from indolines and aldehydes

Indolines react with aromatic and heteroaromatic aldehydes to yield N-alkyl indoles in a benzoic acid catalyzed redox isomerization reaction. Azomethine ylides are intermediates in this process which was established by intramolecular [3 + 2] trapping experiments.     

Marginal states in a cubic autocatalytic reaction

Marginal steady state belongs to a special class of states in nonlinear dynamics. To realize this state we consider a cubic autocatalytic reaction A + 2B → 3B in a continuous-stirred-tank-reactor, where the flow rate of the reactant A can be controlled to manipulate the dynamical behavior of the open system. We demonstrate that when the flow rate is weakly noisy the autocatalytic reaction admits of a steady state which is marginal in nature and is surrounded by infinite number of periodic trajectories. When the uncatalyzed reaction A → B is included in the reaction scheme, there exists a marginal steady state which is a critical state corresponding to the point of transition between the flow branch and the equilibrium branch, similar to gas-liquid critical point of transition. This state loses its stability in the weak noise limit.     

Structural dynamics and energy flow in Rydberg-excited clusters of N,N-dimethylisopropylamine

In molecular beams, the tertiary amine N,N-dimethylisopropyl amine can form molecular clusters that are evident in photoelectron and mass spectra obtained upon resonant multiphoton ionization via the 3p and 3s Rydberg states. By delaying the ionization pulse from the excitation pulse we follow, in time, the ultrafast energy relaxation dynamics of the 3p to 3s internal conversion and the ensuing cluster evaporation, proton transfer, and structural dynamics. While evaporation of the cluster occurs in the 3s Rydberg state, proton transfer dominates on the ion surface. The mass-spectrum shows protonated species that arise from a proton transfer from the alpha-carbon of the neutral parent molecule to the N-atom of its ionized partner in the dimer. DFT calculations support the proton transfer mechanism between tightly bonded cluster components. The photoelectron spectrum shows broad peaks, ascribed to molecular clusters, which have an instantaneous shift of about 0.5 eV toward lower binding energies. That shift is attributed to the charge redistribution associated with the induced dipoles in surrounding cluster molecules. A time-dependent shift that decreases the Rydberg electron binding energy by a further 0.4 eV arises from the structural reorganization of the cluster solvent molecules as they react to the sudden creation of a charge.     

Amplitude equations for breathing spiral waves in a forced reaction-diffusion system

Based on a multiple scale analysis of a forced reaction-diffusion system leading to amplitude equations, we explain the existence of spiral wave and its photo-induced spatiotemporal behavior in chlorine dioxide-iodine-malonic acid system. When the photo-illumination intensity is modulated, breathing of spiral is observed in which the period of breathing is identical to the period of forcing. We have also derived the condition for breakup and suppression of spiral wave by periodic illumination. The numerical simulations agree well with our analytical treatment.     

Remarkably stable amphiphilic random copolymer assemblies: A structure–property relationship study

Synthesis of a library of amphiphilic random copolymers from a single reactive pre‐polymer and their self‐assembly is reported. Post‐polymerization modifications of the parent polymer containing pendant N‐hydroxy succinimide (NHS) ester groups with various oligooxyethylene (OE) amines produce amphiphilic random copolymers with same degree of polymerization and equal extent of randomness. ¹H‐NMR and FT‐IR data indicate quantitative substitution in all cases. The critical aggregation concentration (CAC) for all the polymers is estimated to be in the range of 10^?5 M. Stability of these nano‐aggregates is studied by photoluminescence using time dependent F—rster Resonance Energy Transfer (FRET) between co‐encapsulated lipophilic dyes namely DiO and DiI in the hydrophobic pocket of the aggregates. These studies suggest remarkably high stability for all systems. However those with shorter hydrophilic pendant chains are found to be even more robust. Morphology is examined by high resolution transmission electron microscopy (HRTEM) which reveals multi‐micellar clusters and vesicles for polymers containing short and longer OE segments, respectively. Encapsulation efficacy is tested with both hydrophobic and hydrophilic guest molecules. All of them can encapsulate hydrophobic guest pyrene while a hydrophilic dye Calcein can be sequestered only in vesicle forming polymers. Lower critical solution temperature (LCST) is exhibited by only one polymer that contains the shortest OE chains. All polymers exhibit excellent cell viability as determined by MTT assay. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2013 , 51, 4932–4943     

Study of transfer of trace elements from soil to medicinal plants in the environment of Mangalore

The concentration of five trace elements Cr, As, Pb, Rb and Sr in seven medicinal plants Garcinia indica, Ficus benghalensis, Flacartia Montana, Nyctanthes arbor-tristis, Morinda citrifolia, Ficus recemosa, Barringtonia acutangula and associated soils were analyzed using ICP-MS. In plant the elemental concentrations of Cr, Pb, Rb and Sr vary widely and in soil the elemental concentrations of Cr, As and Sr showed wide variation. Selective enrichment of elements Rb and Sr was observed in some plants. The soil to plant transfer ratio was significant for Sr. The results of these systematic investigations are presented and discussed in this paper.