Exploring nucleoside hydrolase catalysis in silico: molecular dynamics study of enzyme-bound substrate and transition state

The mechanism of action of inosine-uridine nucleoside hydrolase has been investigated by long-term molecular dynamics (MD) simulation in TIP3P water using stochastic boundary conditions. Five MD studies have been performed with enzyme substrate complex (E.S), enzyme substrate complex with protonated His241 (EH.S), enzyme transition state complex (E.TS), enzyme transition state complex with protonated His241 (EH.TS), and His241Ala transition state complex E(H241A).TS. Special attention has been given to the role of His241, which has been considered as the general acid catalyst to assist departure of the leaving nucleobase on the basis of its location in the active site in the X-ray crystal structure (). Yet on the basis of the location in the active site, Tyr229 is closer to the aniline ring of pAPIR as compared to His241. On initiation of MD simulations, His241 does not approach the nucleobase in the structures of EH.S, E.S, EH.TS, and E.TS. In the solvated enzyme, Tyr229, which is a member of the hydrogen bonding network inosine O2'.Asp14.His241.Tyr229.inosine N7, serves as a proton source to the leaving nucleobase. The loss of significant activity of His241Ala mutant is shown to be related to the disruption of the above hydrogen bonded network and the distancing of Tyr229 from inosine N7. The structures of the enzyme complexes with substrate or TS are not visibly altered on protonation of His241, a most unusual outcome. The bell-shaped pH dependence upon pK(app)'s of 7.1 and 9.1 may be attributed to the necessity of the dissociation of Asp10 or Asp15 and the acid form of Tyr229, respectively. In TS, the residue Ile81 migrated closer, whereas Arg233 moved away from the nucleobase. The probability of ribooxocarbenium ion stabilization by Asn168 and Asp14 is discussed. The Asp14-CO(2)(-) is hydrogen bonded to the ribose 2'-OH for 96% of the MD simulation time. Nucleophilic addition of water138 to ribooxocarbenium ion is suggested to be assisted by the proton shuttle from water138 --> Asp10 --> Asp15 --> water pool. An anticorrelation motion between Tyr229-OH and Asn168-OD1 in EH.S and E.S is observed. The relationship of this anticorrelated motion to mechanism, if any, deserves further exploration, perhaps the formation of a near attack conformation.     

A Tandem In Situ Peptide Cyclization through Trifluoroacetic Acid Cleavage

We present a new approach for peptide cyclization during solid phase synthesis under highly acidic conditions. Our approach involves simultaneous in situ deprotection, cyclization and trifluoroacetic acid (TFA) cleavage of the peptide, which is achieved by forming an amide bond between a lysine side chain and a succinic acid linker at the peptide N‐terminus. The reaction proceeds via a highly active succinimide intermediate, which was isolated and characterized. The structure of a model cyclic peptide was solved by NMR spectroscopy. Theoretical calculations support the proposed mechanism of cyclization. Our new methodology is applicable for the formation of macrocycles in solid‐phase synthesis of peptides and organic molecules.     

BOUNDARY TREATMENT AND AN EFFICIENT PRESSURE ALGORITHM FOR INTERNAL TURBULENT FLOWS USING THE PDF METHOD

The generalized Langevin model, which is used to model the motion of stochastic particles in the velocity–composition joint probability density function (PDF) method for reacting turbulent flows, has been extended to incorporate solid wall effects. Anisotropy of Reynolds stresses in the near-wall region has been addressed. Numerical experiments have been performed to demonstrate that the forces in the near-wall region of a turbulent flow cause the stochastic particles approachi ng a solid wall to reverse their direction of motion normal to the wall and thereby, leave the near-wall layer. This new boundary treatment has subsequently been implemented in a full-scale problem to prove its validity. The test problem considered here is that of an isothermal, non-reacting turbulent flow in a two-dimensional channel with plug inflow and a fixed back-pressure. An efficient pressure correction method, developed in the spirit of the PISO algorithm, has been implemented. The pressure correction strategy is easy to implement and is completely consistent with the time- marching scheme used for the solution of the Lagrangian momentum equations. The results show remarkable agreement with both k–ϵ and algebraic Reynolds stress model calculations for the primary velocity. The secondary flow velocity and the turbulent moments are in better agreement with the algebraic Reynolds stress model predictions than the k– ϵ predictions. © 1997 by John Wiley & Sons, Ltd.     

Thermodynamics of Lema$$\hat{i}$$ tre−Tolman−Bondi Model

Here we consider our universe as inhomogeneous spherically symmetric Lema [^(i)]{\hat{i}} tre−Tolman−Bondi Model and analyze the thermodynamics of this model of the universe. The trapping horizon is calculated and is found to coincide with the apparent horizon. The Einstein field equations are shown to be equivalent with the unified first law of thermodynamics. Finally assuming the first law of thermodynamics validity of the generalized second law of thermodynamics is examined at the apparent horizon for the perfect fluid and at the event horizon for holographic dark energy.     

Hall effects on hydromagnetic falling liquid film

An investigation is made of flow of an electrically conducting falling liquid film over a smooth vertical surface taking Hall effects into account, the liquid being permeated by a transverse magnetic field. Consideration of Hall current into the flow indicates a similarity between the flow of a rotating liquid and that due to the non-rotating system in presence of Hall currents. Discussion has been made for electrically conducting falling film in presence of cross-flow due to hall effect in non-rotating system.     

SANS investigation on evolution of pore morphology for varying sintering time in porous ceria

Precipitates of ceria were synthesized by homogeneous precipitation method using cerium nitrate and hexamethylenetetramine at 80°C. The precipitates were ground to fine particles of average size ∼0.7 μm. Circular disks with 10 mm diameter, 2 and 3 mm thickness were prepared from the green compacts by sintering at 1300° C for three different sintering times. Evolution of the pore structures in these specimens with sintering time was investigated by small-angle neutron scattering (SANS). The results show that the peak of the pore size distribution shifts towards the larger size with increasing sintering time although the extent of porosity decreases. This indicates that finer pores are eliminated from the system at a faster rate than the coarser ones as sintering proceeds and some of the finer pores coalesce to form bigger ones.     

Raman imaging and stress quantification in self‐assembled graphene oxide fiber ‘Latin Letters’

To probe the intrinsic stress distribution in terms of spatial Raman shift (ω) and change in the phonon linewidth (Γ), here we analyze self‐assembled graphene oxide fibers (GOF) ‘Latin letters’ by confocal Raman spectroscopy. The self‐assembly of GOF ‘Latin letters’ has been explained through surface tension, π–π stacking, van der Waals interaction at the air–water interface and by systematic time‐dependent investigation using field emission scanning electron microscopy analysis. Intrinsic residual stress due to structural joints and bending is playing a distinct role affecting the E_2g mode (G band) at and away from the physical interface of GOF segments with broadening of phonon linewidth, indicating prominent phonon softening. Linescan across an interface of the GOF ‘letters’ reveals Raman shift to lower wavenumber in all cases but more so in ‘Z’ fiber exhibiting a broader region. Furthermore, intrinsic stress homogeneity is observed for ‘G’ fiber distributed throughout its curvature with negligible shift corresponding to E_2g mode vibration. This article demonstrates the significance of morphology in stress distribution across the self‐assembled and ‘smart‐integrable’ GOF ‘Latin letters’. Copyright © 2016 John Wiley & Sons, Ltd.     

The origin of the ligand-controlled regioselectivity in Rh-catalyzed [(2 + 2) + 2] carbocyclizations: steric vs. stereoelectronic effects

Density functional theory calculations demonstrate that the reversal of regiochemical outcome of the addition for substituted methyl propiolates in the rhodium-catalyzed [(2 + 2) + 2] carbocyclization with PPh₃ and (S)-xyl-binap as ligands is both electronically and sterically controlled. For example, the ester functionality polarizes the alkyne π* orbital to favor overlap of the methyl-substituted terminus of the alkyne with the p_π-orbital of the alkenyl fragment of the rhodacycle during alkyne insertion with PPh₃ as the ligand. In contrast, the sterically demanding xyl-binap ligand cannot accommodate the analogous alkyne orientation, thereby forcing insertion to occur at the sterically preferred ester terminus, overriding the electronically preferred orientation for alkyne insertion.     

Conformational and electronic consequences in crafting extended, π-conjugated, light-harvesting macrocycles

The synthesis of a new series of free‐base, Ni^II and Zn^II 2,3,12,13‐tetra(ethynyl)‐5,10,15,20‐tetraphenyl porphyrins is described. Upon heating, two of the four ethynyl moieties undergo Bergman cyclization to afford the monocyclized 2,3‐diethynyl‐5,20‐diphenylpiceno[10,11,12,13,14,15‐jklmn]porphyrin in 30 %, 10 %, and trace yields, respectively. The structures of all products were investigated by using quantum chemical calculations and the free‐base analogue was isolated and crystallized; all compounds show significant deviation from the idealized planar structure. No fully‐cyclized bispiceno[20,1,2,3,4,5,10,11,12,13,14,15‐fghij]porphyrin was isolated from the reaction mixture. To understand why only two of the four enthynyl groups undergo Bergman cyclization, the reaction coordinates were examined by using DFT at the PWPW91/cc‐pVTZ(‐f) level coupled to a continuum solvation model. The barrier to cyclization of the second pair of ethynyl groups was found to be 5.5 kcal mol^?1 higher than the first, suggesting a negative cooperative effect and significantly slower rate for the second cyclization. Cyclization reactions for model porphyrin–enediynes with ethene‐ and H‐functionality substitutions at the meso‐phenyl rings were also examined, and found to have a similar barrier to diradical formation for the second cyclization event as for the first in these highly planar molecules. By enforcing an artificial 30° cant in two of the pyrrole rings of the porphyrin, the second barrier was increased by 2 kcal mol^?1 in the ethene model system; this suggests that the disruption of the π conjugation of the extended porphyrin structure is the cause of the increased barrier to the second cyclization event.     

Computationally designed and experimentally confirmed diastereoselective rhodium-catalyzed Pauson-Khand reaction at room temperature

The computational analysis of the rhodium-catalyzed Pauson-Khand reaction indicates that the key transition state is highly charge-polarized, wherein different diastereoisomers have distinctively different charge polarization patterns. Experimental studies demonstrate that chloro-enynes provide the optimal σ-electron-withdrawing group to promote polarization and thereby reduce the activation barrier to provide a highly diastereoselective reaction at room temperature.