Tuhin S. Khan

On the mechanism of retro-Diels–Alder reaction of partially saturated 2-pyrones to produce biorenewable chemicals

Partially saturated 2-pyrone molecules undergo ring-opening and decarboxylation via retro-Diels–Alder (rDA) reaction. Density functional theory (DFT) simulations were utilized to calculate the intrinsic activation barrier and reaction energies of the steps involved in rDA reaction of biomass-derived 5,6-dihydro-4-hydroxy-6-methylpyran-2-one (5DHHMP), 4-hydroxy-3,6-dimethyl-pyran-2-one (4HDMP) and 4-hydroxy-6-(2-oxo-propyl)-3,6-dihydro-pyran-2-one (4HOPP). The rDA reaction of the three molecules in water proceeds in two steps via the formation of a zwitterionic intermediate. The calculated activation barrier (Ea = 61 kJ mol−1) for the rDA reaction of 5DHHMP in water compares well with the experimentally measured value. In the absence of hydrogen bonding interactions such as in the solvent n-hexane and gas-phase, the rDA reaction is concerted and activation barriers of the three molecules were estimated to be relatively higher. Substituents at C6, C4 and C3 position in partially saturated 2-pyrones showed a clear effect on the reactivity of the molecules which was correlated back to the resultant normal electron demand frontier molecular orbital (FMO) gap of the product diene and dienophile. The electronic and geometric (steric) effects of the substituents were separated by including several other structurally similar molecules having variations in the position, type and number of substituents. In general, the electronic effect of the substituents follow a linear trend, where FMO gap for normal electron demand serves as a good descriptor of the reactivity. The geometric effect was represented on a linear scale to quantify the steric hindrance offered by the methyl substituents. Molecules having no hydroxyl substituent at C4 such as 6-methyl-3,6-dihydro-2H-pyran-2-one (4HMTHP) and 4,6,6-trimethyl-3,6-dihydro-2H-pyran-2-one (DTMP) showed a concerted route for rDA reaction in water without the formation of the intermediate. The rates of rDA reaction of the molecules were observed to be accelerated in water as compared to n-hexane. In solvents, the reactivity of the molecule doesnt correlate to the FMO gap of the products, likely due to the differential stabilization of the reactant and transition state. In general, polar solvents (water, DMSO, ethanol and methanol) were calculated to show lesser activation energy despite of a greater FMO gap as compared to non-polar solvents (n-hexane). In a solvent, the rDA reaction of the molecules follows a Bronsted–Evans–Polanyi (BEP) relationship. In presence of a Bronsted acid catalyst the rDA reaction of 5DHHMP proceeds via the formation of an oxocarbenium ion which further helps in facilitating the reaction with a significantly reduced activation barrier (Ea = 15 kJ mol−1).

Reactivity descriptor for the retro Diels–Alder reaction of partially saturated 2-pyrones: DFT study on substituents and solvent effects

The retro-Diels–Alder (rDA) reaction of partially saturated 2-pyrone molecules to form the 1,3-butadiene backbone and CO2 was studied using density functional theory (DFT) calculations in vapor-phase, polar and non-polar solvents. The activation barriers for the ring-opening and decarboxylation of the molecules were correlated to the type of substituent present on the 2-pyrone ring. In the vapor-phase, the electronic effect of substituents led to a linear scaling relationship between the calculated activation barrier and corresponding frontier molecular orbital (FMO) gap of the product diene and CO2. A new descriptor was proposed as the average of the ionization potential (IP) of the diene and the electron affinity (EA) of the dienophile to describe the activation energy trend. Solvents were calculated to reduce the activation barriers by stabilizing the polar transition state by as much as 40 kJ mol−1, wherein polar solvents were calculated to reduce the barrier more than the non-polar solvents. The rDA reaction activation barrier in the solvent decreases in the following order: vapor-phase > n-hexane > benzene > acetone > methanol > water. The effect of solvents in rDA reactivity trends was successfully described for the first time through a single descriptor, the FMO gap. The existence of a Bronsted–Evans–Polanyi (BEP) relationship was established for the rDA reaction over different solvents. In solvents, the FMO gap, (IPdiene + EAdienophile)/2 and BEP relationship were proposed as the reactivity descriptors for the rDA reaction of 2-pyrones.

Water Rearrangements upon Disorder-to-Order Amyloid Transition.

Water plays a critical role in governing the intricate balance between chain-chain and chain-solvent interactions during protein folding, misfolding, and aggregation. Previous studies have indicated the presence of different types of water in folded (globular) proteins. In this work, using femtosecond and picosecond time-resolved fluorescence measurements, we have characterized the solvation dynamics from ultrafast to ultraslow time scale both in the monomeric state and in the amyloid state of an intrinsically disordered protein, namely κ-casein. Monomeric κ-casein adopts a compact disordered state under physiological conditions and is capable of spontaneously aggregating into highly ordered β-rich amyloid fibrils. Our results indicate that the mobility of biological water (type I) gets restrained as a result of conformational sequestration during amyloid formation. Additionally, a significant decrease in the bulk water component with a concomitant increase in the ultraslow component revealed the ordering of trapped interstitial water (type II) upon disorder-to-order amyloid transition. Our results provide an experimental underpinning of significant water rearrangements associated with both chain desolvation and water confinement upon amyloid formation.

First-Principle Microkinetic Modeling of Ethanol Dehydrogenation on Metal Catalyst Surfaces in Non-oxidative Environment: Design of Bimetallic Alloys

An ab-initio microkinetic model (MKM) was developed to understand the reactivity trend in transitional metal catalysts which are often used for non-oxidative conversion of alcohols to produce aldehydes. The MKM utilized ethanol reaction on the step sites of the catalyst, to calculate the turnover frequency (TOFs) for the production of acetaldehyde at 423xa0K. At these conditions, Cu showed the highest activity (TOFu2009~u2009102xa0s−1), followed by Pt (TOFu2009~u2009101xa0s−1). This explains why Cu, being the cheaper metal, is the ‘catalyst of choice’ for this reaction. Pd was the other most active (TOFu2009~u200910−u20091xa0s−u20091) catalyst, however, its activity was lesser than that of Cu and Pt. Rest of the metals screened (Co, Ni, Ag, Au, Rh, Ru, Re) showed low or negligible conversion for this reaction at 423xa0K. Interestingly, in the non-oxidative environment, the three most reactive metals (Cu, Pt and Pd) were also selective towards acetaldehyde production. At a higher temperature (473xa0K) and assuming around 10% conversion over the length of a packed-bed reactor, an appreciable TOF (~u200910−u20092xa0s−u20091) towards the aldehyde was calculated for other metals such as Co, Ni, Ag and Au. While Pt was the most active catalyst (TOFu2009~u2009104xa0s−1), the TOF on Cu remained high (TOFu2009~u2009103xa0s−1), to yield the desired aldehyde product. The trend in calculated TOF at 473xa0K followed the order; Ptu2009>u2009Cuu2009>u2009Pdu2009>u2009Cou2009>u2009Niu2009>u2009Agu2009>u2009Auu2009>u2009Rhu2009>u2009Ruu2009>u2009Re. Out of all the metals studied only Ag and Au were found to be selective towards ethylene, rest other metals were selective towards the aldehyde product. The surface of most of the metal catalysts (Pt, Pd, Co, Ni, Rh, Ru, Re) was covered with the intermediate CH3CO at both the temperatures (423xa0K and 473xa0K) studied. In contrast, only the surface of Cu was covered with the intermediate CH3CH2O, suggesting difficult C–H bond activation on Cu. Motivated from this monometallic reactivity trend, surface design of bimetallic alloys, based on Cu were explored for this reaction. Alloying Cu with a metal commonly used for C–H bond activation (such as Ni, Pd, Pt, Rh) was calculated to show high reactivity (TOFu2009>u2009103xa0s−1) for the aldehyde production. Following a similar rationale, one may think of tuning the reactivity of Ni itself by allowing the reaction to stop at CH3CHO, before undergoing further C–H bond activation. We suggest Ni alloying with Sn for moderating the surface catalytic activity of Ni, which was calculated to show high TOF (>u2009103xa0s−1) for this reaction.Graphical Abstract

Understanding the Nature of Amino Acid Interactions with Pd(111) or Pd–Au Bimetallic Catalysts in the Aqueous Phase

The interaction of methionine (Met) with different bimetallic-segregated surfaces comprising a uniform distribution of strips and islands of Au on the Pd(111) surface was examined using molecular dynamics (MD) simulations. Out of all the segregated and uniformly doped surfaces studied, the design of Pd-Au islands showed some reduction in the interaction energy (Eint = -43.7 kJ/mol) as compared to that of the pure Pd(111) surface (Eint = -50 kJ/mol) for a single Met molecule. However, at a higher coverage of 9 Met molecules/simulation cell, none of the Pd-Au alloy surfaces showed any improvement as compared to the Pd(111) surface. In order to develop a comprehensive understanding of the nature of the nonbonded interaction of aqueous biogenic impurities with the Pd catalyst surface, the MD study was extended to include a variety of aliphatic, S-containing, aromatic, and polar amino acids. The potential of mean force (PMF) profiles were observed to be distinct for each class of amino acids with substantial differences among amino acids with acidic and basic side chains. The side chains of all the polar and aromatic amino acids showed direct contact with the surface while aliphatic amino acids had their hydrophobic side chain aligned away from the surface. Interestingly, lysine (Lys) and tyrosine (Tyr) were the only two amino acids which interacted preferentially via the distant backbone nitrogen and backbone oxygen, respectively, despite their side chains being in direct contact with the metal surface. The strength of interaction was correlated with the size of the amino acid; the interaction energies were observed to be the maximum for large molecules such as arginine (Arg, Eint = -87.7 kJ/mol) and tryptophan (Trp, Eint = -73.4 kJ/mol), while it was a minimum for aliphatic amino acids such as alanine (Ala, Eint = -10.9 kJ/mol). The study is focused on examining the sensitivity of the choice of the preferential interaction site, conformational preferences, and interaction energies to the side-chain specificity.

Crystal structure and UV spectra of a 1,2-disubstituted benzimidazolium chloride

1-(2-Hydroxybenzyl)-2-(2-hydroxyphenyl)-1H-benzimidazol-3-ium chloride, C20H17N2O2 +·Cl−, is prepared by reaction of salicylaldehyde with o-phenylenediamine in the presence of trimethylsilyl chloride acting as a source of HCl. As a result of steric hindrance, the cation in the crystal is far from planar: the benzimidazole ring system makes dihedral angles of 55.49u2005(9) and 81.36u2005(8)° with the planes of the phenolic groups. The crystal packing is dominated by the O—H⋯Cl and N—H⋯Cl hydrogen bonds. The title compound exhibits two transitions in the UV region, which are revealed in the solid state and solution spectra as an absorption maximum at 280u2005nm and a shoulder at 320u2005nm. According to the results of TD–DFT calculation, both transitions have a π–π* nature and the molecular orbitals involved in these transitions are mostly localized on the benzimidazole ring system and on the phenyl ring attached to it at the 2-position.

The exclusive response of LSPR in uncapped gold nanoparticles towards silver ions and gold chloride ions

We report a significant modulation of the plasmon peak of a bare gold nanoparticle system after treatment with Ag+ or [AuCl4]− ions. The shift is highly selective to the presence of Ag+/[AuCl4]− metal ions and is not observed when other ions (Cu2+, Cd2+, Ce2+, Hg2+, Na+ and K+) are tested. The value of the red shift depends on the concentration of ions. As compared to Ag+ ions, the shift is larger in the presence of [AuCl4]− ions. We attribute the red-shift in plasmon to the formation of atomic clusters of Ag or Au and a change in relaxation times of hot electrons at the gold nanoparticle surface after treatment with Ag+ or [AuCl4]− ions. The red-shift is also sensitive to capping on gold nanoparticles, and silver ions do not shift the LSPR when gold nanoparticles are capped with citrate. The study of the effect of ions on the plasmon of AuNPs is significant from the viewpoint of designing highly selective AuNP based gold and silver ion sensors. The role of charge transfer and changes in electron dynamics, which lead to shifting of the localized surface plasmon resonance in AuNPs, has been exemplified as well. The versatility of the sensing approach has been tested in both solution-based and substrate-based configurations.