Journal of Chemical Sciences最新文献

The resonant low-energy electron (LEE) induced scattering off biomolecules is proposed to undergo dissociative electron attachment (DEA) as one of the favoured pathways. In the current work, we have considered the citric acid molecule due to its biological relevance in the Krebs cycle, in which LEEs may affect and lead to metabolic dysfunction. To investigate the DEA pathway of citric acid, we implemented the local complex potential-based time-dependent wavepacket (LCP-TDWP) approach. From our calculation, we observed that the vertical attachment energy (VAE) of the citric acid system is found to be −1.17 eV, and the electron attaches itself to the 2-carboxylic acid group to form a transient negative ion (TNI) which further dissociates into a free radical and a radical anion. The lifetime for the TNI is around 1000 fs, with a maximum cross-section seen at 1.09 eV.

Graphical abstract

The interaction of low-energy electrons with citric acid can lead to dissociative electron attachment (DEA). In the current work, we used the local complex potential-based time-dependent wave packet (LCP-TDWP) approach to investigate DEA to citric acid. The time evolution of the probability density suggests the possibility of a boomerang model.

We present three related schemes to generate novel molecules based on seed molecule; all the methods use as input the voxelized representation of the seed molecule to generate the SMILES representation of the novel molecule. At heart of these methods are two networks (a) a variational auto encoder that uses a Riemannian metric to encode the latent space of (hence named RHVAE) and can use pharmacophoric requirements as additional input for decoder and (b) attentive captioning network (a type of recurring neural network) that can efficiently focus, capture and use the ‘content’ of input to generate the SMILES output of novel molecules. We analyze the performance of the three proposed methods. We demonstrate the generation of meaningful new molecules, by generating shapes through an auto encoder network which can then be passed to our attentive captioning network, while requiring smaller datasets for training and retaining similar performance to existing state-of-art methods.

Graphical abstract

SYNOPSIS Study demonstrates the generation of meaningful ligands using machine learning; specifically, an autoencoder that uses Remannian geometry represenation for its latent space whose output grid can be passed to a attentive captioning network. We demonstrate suggested schemes require smaller data sets for training while retaining similar performance as to state-of-art methods..The VAE model employed

The ultrafast solvent dynamics of glycerol and ethylene glycol (EG) in response to a sudden charge jump in two different solute probes, coumarin 153 (C153) and trans-2-[4-(dimethylamino)styryl] benzothiazole (DMASBT), were measured by employing streak camera-based detection system (temporal resolution ~2ps). Subsequently, the detection of time-dependent solvation of the excited solute was measured by appropriately combining the streak camera data with those from the time-correlated single photon counting (TCSPC) measurements (resolution ~90 ps). Interestingly, combined data for C153 provided dynamic Stokes shift magnitudes approximately double the magnitudes accessed via the streak camera alone for these two solute probes in glycerol and EG. The initial phase of solvation in EG was found to be too fast to be measured by the present streak camera-based detection set-up and missed nearly half of the total response. The relatively shorter average excited state fluorescence lifetime of DMASBT ((langle {tau }_{fl}rangle <0.5 mathrm{ns})) prohibited the detection of the (ge) 0.5 ns solvation component reported by C153 in glycerol, highlighting the importance of (langle {tau }_{fl}rangle) for complete measurements of polar solvation response via dynamic Stokes shift measurements. Inappropriate choice of fluorescent probe solute with shorter (langle {tau }_{fl}rangle) may therefore give rise to an unexpected solute dependence of polar solvation dynamics even when detection of the rapid initial decay is ensured through ultrafast measurements.

Graphical abstract

Graphical Abstract presenting schematically the measurements of the solvation response function by processing the relevant streak camera images and the time-correlated photon counting (TCSPC) data and appropriately combining them together.

The dissociation of the simplest Criegee intermediate (H(_2)COO) into formaldehyde (H(_2)CO) and oxygen atom (O) is very important in the atmospheric chemistry. In this study, we investigate the photodissociation of the O–O bond of H(_2)COO by simulating the dynamics of the process on the fitted multiconfigurational adiabatic potential energy surfaces (PESs). Tully’s fewest-switches surface hopping (FSSH) method is used for the simulation. The FSSH trajectories are initiated on the lowest optically-bright singlet excited state ((S_2)) and propagated along the O–O coordinate. Some of the trajectories end up on energetically lower PESs as a result of radiationless transfer through conical intersections. However, all the trajectories lead to O–O bond dissociation via one of the two channels. The simulation results demonstrate that the restricted O–O motion dissociates H(_2)COO into singlet fragments via the lower energy channel. The coupling of electronic states along O–O may account for this.

Graphical abstract

The photodissociation of simplest Criegee intermediate (H₂COO) into formaldehyde (H₂CO) and oxygen (O) was studied using Tully's fewest-switches surface hopping (FSSH). The simulation results demonstrate that the restricted O–O motion dissociates into singlet fragments via the lower energy channel.

In this paper we report non-enzymatic glucose oxidation with N, N′-Bis(2-hydroxybenzylidineamino) benzene gold (III) complex on reduced graphene oxide-gold (rGO-Au) nanoparticle coated modified copper (Cu) electrode. Potassium ferricyanide in 50 mM phosphate buffer solution (pH 7.0) was used as a mediator. The [(Salophen)Au]⁺ on rGO shows good catalytic property for the oxidation of glucose to gluconic acid (GA). The maximum current response produced by Au³⁺/Au⁺ redox potential was monitored by the linear sweep voltammetric method (LSV). As glucose concentration increases the current response at Au⁺³/Au⁺ redox potential decreases simultaneously. On catalytic oxidation of glucose to GA by the complex [(Salophen)Au]⁺, the solution pH reduces to 2.75, which results the decrease of current responses at the Au³⁺/Au⁺ working potential.

Graphical abstract

Direct oxidation of glucose to gluconic acid is achieved adopting non­enzytnatic technique by rGO based heterogeneous catalyst is reported in the present study. N,N'-Bis (2-hydroxy benzylidineatnino) benzene gold (III) complex on rGO-Au nanoparticles is used to fabricate the tnodified electrode. The oxidation mechanism is demonstrated. This work showed the potential of using [(Salophen)Au]⁺ Schiff base complex as a non­enzymatic substitute for glucose oxidize enzyme.

Strong green-emission is observed in the new Tb³⁺ activated Sr₆Y₂Al₄O₁₅ nanocrystalline material series fabricated via solution combustion methodology. A monoclinic crystal framework with space group I4/mcm (140) having irregularly shaped grains with an average size of 49 nm is formed. Morphological aspects are examined via scanning and transmission electron microscopy (SEM and TEM). On near-UV excitation, the photoluminescence spectrum presents a fair green-light production at 18382 cm^-1 wavenumbers reliable with the ⁵D₄→⁷F₅ electronic transition. The energy transfer phenomena are also discussed. The highest luminous intensity is observed for 5.0 mol% of Tb³⁺ composition with 282 nm excitation wavelength. d-d exchanges authorized the presence of the concentration quenching phenomenon. Diffuse reflectance spectroscopy was taken into use to explore the energy band gap which lies in the semiconductor domain. The CIE coordinates lay in the greenish zone of the chromaticity scheme, thus confirming their latent contention in pc-WLED fabrication and other advanced photonic applications.

Graphical abstract

Strong green-emission is observed in the new Tb³⁺ activated Sr₆Y₂Al₄O₁₅ nanocrystalline material series fabricated via solution combustion methodology. A monoclinic crystal framework with space group I4/mcm (140) having irregularly shaped grains with an average size of 49 nm is formed. On near-UV excitation, the photoluminescence spectrum presents a fair green-light production at 18382 cm^-1 wavenumbers reliable with the ⁵D₄→⁷F₅ electronic transition. The CIE coordinates lay in the greenish zone of the chromaticity scheme, thus confirming their latent contention in pc-WLED fabrication and other advanced photonic applications.

GUMBOS (group of uniform materials based on organic salts) are highly functional and tunable organic ionic materials that exhibit a solid state at room temperature, composed of oppositely charged bulky ions with high thermal stability. A variety of GUMBOS has been designed and synthesized by selecting appropriate ion pairs to use in targeted applications of different fields. Herein, parent DABCO-based GUMBOS were synthesized from the reaction of terpene such as (-)-menthol or (-)-borneol or (+)-fenchol and chloroacetic acid followed by DABCO. To formulate GUMBOS derivatives, the parent salt (with chloride counter-anion) was modified through an anion exchange metathesis process by taking different sodium/potassium salts. Structure elucidation was done through NMR, polarimeter, TGA, and GC-MS techniques. The synthesized ionic species were employed as organocatalysts in the enantioselective reduction reactions of various prochiral ketones to chiral alcohols. Low to good enantiomeric excess was obtained.

Graphical Abstract

The easily available and low-cost parent compounds i.e., terpenes and DABCO were used for the synthesis of GUMBOS through facile and simple synthetic routes. The salts were obtained with good yield, possessed optical activity, and had high thermal stability. Further, the organocatalytic role of salts was studied in asymmetric reduction reactions.

Sulforhodamine B (C₂₇H₃₀N₂O₇S₂) (SRB) is a fluorescent dye commonly used for in-vitro cytotoxicity monitoring, which under standard conditions, does not undergo natural degradation and remains in water as such. We report on mesoporous In₂S₃ as an efficient photocatalytic agent for the degradation of this dye. Mesoporous In₂S₃ nanopowders were synthesized using a wet chemistry approach at a temperature of 30 °C. The synthesized nanopowders had preferential orientation along the (222) plane with an average crystallite size of ~ 4 nm. The pore size in the nanopowdered material was found to vary with the stoichiometry of the precursor solution. The photocatalytic degradation efficiency was found to vary with the pore size of the In₂S₃ nanopowder. The highest rate constant of 4.58 x 10^-3 min^-1 for SRB degradation was recorded for the sample with an average pore size of 1.79 nm. The mesoporous In₂S₃ demonstrates a degradation efficiency of ~ 91% under direct sunlight (~720 lux) and ~ 42.3% under the halogen light source (320 lux).

Graphical abstract

The recent identification of the polycyclic aromatic hydrocarbon molecules, 1-cyanonaphthalene, and 2-cyanonaphthalene in the interstellar medium (ISM) requires laboratory support to understand the physicochemical nature of these molecules when they are present as icy mantles on cold dust grains. Therefore, we have carried out the infrared spectroscopic characterization of these molecules under astrochemical conditions. When deposited at 7 K, the spectra of the cyanonaphthalene ices were amorphous in nature. Upon warming to higher temperatures, cyanonaphthalene ices appear to remain amorphous until sublimation. Both sublimate at very high temperatures, 250-265 K, suggesting their presence on the ISM dust over a large temperature range such that they may influence the chemical complexity across the ISM.

Graphical abstract

SYNOPSIS Infrared spectroscopic characterization of cyanonaphthalene molecules under astrochemical conditions were carried. Cyanonaphthalene ices show no phase change upon warming. Cyanonaphthalene sublimation at very high temperatures, 250-265 K, suggests their presence on the ISM dust over a large temperature range and may further influence the chemical complexity.

Alchemical free energy calculations are widely used in predicting p(K_text{a}), and binding free energy calculations in biomolecular systems. These calculations are carried out using either Free Energy Perturbation (FEP) or Thermodynamic Integration (TI). Numerous efforts have been made to improve the accuracy and efficiency of such calculations, especially by boosting conformational sampling. In this paper, we use a technique that enhances the conformational sampling by temperature acceleration of collective variables for alchemical transformations and applies it to the prediction of p(K_text{a}) of the buried Asp(_{26}) residue in thioredoxin protein. We discuss the importance of enhanced sampling in the p(K_text{a}) calculations.

Graphical abstract

By using a computational technique that enhances the conformational sampling and alchemical transformation, we predict the pKa shift of the buried Asp26 residue in thioredoxin protein.