Rapid and Automated Ab Initio Metabolite Collisional Cross Section Prediction from SMILES Input.

We implemented an ab initio CCS prediction workflow which incrementally refines generated structures using molecular mechanics, a deep learning potential, conformational clustering, and quantum mechanics (QM). Automating intermediate steps for a high performance computing (HPC) environment allows users to input the SMILES structure of small organic molecules and obtain a Boltzmann averaged collisional cross section (CCS) value as output. The CCS of a molecular species is a metric measured by ion mobility spectrometry (IMS) which can improve annotation of untargeted metabolomics experiments. We report only a minor drop in accuracy when we expedite the CCS calculation by replacing the QM geometry refinement step with a single-point energy calculation. Even though the workflow involves stochastic steps (i.e., conformation generation and clustering), the final CCS value was highly reproducible for multiple iterations on L-carnosine. Finally, we illustrate that the gas phase ensembles modeled for the workflow are intermediate files which can be used for the prediction of other properties such as aqueous phase nuclear magnetic resonance chemical shift prediction. The software is available at the following link: https://github.com/DasSusanta/snakemake_ccs.

In Silico Collision Cross Section Calculations to Aid Metabolite Annotation.

The interpretation of ion mobility coupled to mass spectrometry (IM-MS) data to predict unknown structures is challenging and depends on accurate theoretical estimates of the molecular ion collision cross section (CCS) against a buffer gas in a low or atmospheric pressure drift chamber. The sensitivity and reliability of computational prediction of CCS values depend on accurately modeling the molecular state over accessible conformations. In this work, we developed an efficient CCS computational workflow using a machine learning model in conjunction with standard DFT methods and CCS calculations. Furthermore, we have performed Traveling Wave IM-MS (TWIMS) experiments to validate the extant experimental values and assess uncertainties in experimentally measured CCS values. The developed workflow yielded accurate structural predictions and provides unique insights into the likely preferred conformation analyzed using IM-MS experiments. The complete workflow makes the computation of CCS values tractable for a large number of conformationally flexible metabolites with complex molecular structures.

Facile hydrothermal synthesis of novel Fe-Cu layered double hydroxide/biochar nanocomposite with enhanced sonocatalytic activity for degradation of cefazolin sodium.

This study reports the successful synthesis of Fe-Cu layered double hydroxide (Fe-Cu-LDH) /biochar (BC) nanocomposite by a hydrothermal method. The sonocatalytic performance of Fe-Cu-LDH/BC nanocomposite was investigated for the degradation of cefazolin sodium (CFZ), as a model emerging contaminant, from the solution. The physico-chemical properties of the synthesized samples were analyzed by X-ray diffraction (XRD), scanning electron microscopy (SEM), energy-dispersive x-ray spectroscopy (EDX), Brunauer-Emmett-Teller (BET), high-resolution transmission electron microscopy (HRTEM), X-ray photoelectron spectroscopy (XPS), Fourier transform infrared (FT-IR), and UV-Vis diffuse reflectance spectroscopy (DRS) analyses. The best sonocatalytic efficiency of 97.6% was achieved by using 1.0 g/L sonocatalyst, 0.1 mM CFZ, and an ultrasonic power of 300 W at pH = 6.5 (natural) within 80 min. Additionally, the effects of the addition of various oxidants, dissolved gases, and organic and inorganic scavengers on the degradation of CFZ were studied. Moreover, the possible sonocatalytic mechanism of the sonochemical degradation of CFZ in the presence of Fe-Cu-LDH/BC sonocatalyst was proposed based on the results of GC-MS analysis. The mineralization of CFZ solution was evaluated using COD and IC analyses. Finally, the reusability test of Fe-Cu-LDH/BC nanocomposite in the CFZ degradation revealed that almost 9% drop occurred after five successive cycles.

Photocatalytic degradation of gemifloxacin antibiotic using Zn-Co-LDH@biochar nanocomposite.

The aim of the present study was to investigate the photocatalytic performance of biochar (BC)-incorporated Zn-Co-layered double hydroxide (LDH) nanostructures in gemifloxacin (GMF) degradation as a model pharmaceutical pollutant. The as-prepared Zn-Co-LDH@BC showed high photocatalytic efficiency due to the enhanced separation of photo-generated charge carriers using cobalt hydroxide as well as inhibiting the agglomeration of LDH nanostructures by incorporation of BC. According to the results, 92.7% of GMF was degraded through photocatalysis in the presence of Zn-Co-LDH catalyst. The photocatalytic performance of BC-incorporated Zn-Co-LDH was highly dependent on the solute concentration and photocatalyst dosage. The addition of ethanol caused more inhibiting effect than that of benzoquinone (BQ), indicating the major role of •OH in decomposition of GMF compared to the negligible role of O2•-. A greater enhancement in the photocatalytic degradation of GMF was obtained when the photoreactor containing Zn-Co-LDH@BC nanostructures was oxygenated. Less than 10% drop in the removal efficiency of GMF was observed within five successive operational runs. The results of chemical oxygen demand (COD) analysis indicated the COD removal efficiency of about 80% within 200 min, indicating the acceptable mineralization of GMF. The reaction pathways were also proposed for the photocatalytic conversion of GMF under UV light irradiation.

Sonocatalytic activity of biochar-supported ZnO nanorods in degradation of gemifloxacin: Synergy study, effect of parameters and phytotoxicity evaluation.

This study focuses on the facile preparation of ZnO-biochar (ZnO-BC) nanocomposite prepared by the hydrothermal approach as an efficient sonocatalyst for degradation and mineralization of gemifloxacin (GMF). Morphological and textural characteristics of bare biochar (BC), ZnO nanorods (ZnO NRs) and ZnO-BC nanocomposite were investigated using TEM, SEM and BET analyses. Moreover, XRD, FTIR, EDX and UV-vis DRS analyses were performed to study the crystalline structure, functional groups, elemental composition and optical properties of the samples, respectively. ZnO-BC nanocomposite showed better sonocatalytic performance than BC and ZnO NRs owing to its huge surface area, narrow band gap and enhanced sonoluminescence phenomenon. These properties led to the synergetic ability of ultrasonic irradiation and catalytic activity of ZnO-BC to generate reactive species and subsequent radical reactions. In addition, the effect of the addition of various gases and scavengers on the removal of GMF was evaluated. The GC-MS analysis was used to verify the generation of some intermediates and a possible pathway was proposed accordingly. 83.7% COD removal efficiency was observed within 90 min treatment confirming efficient mineralization of GMF solution. The phytotoxicity test was carried out using Lemna minor and the results proved that after the treatment process, a considerable toxicity removal of the GMF solution had occured.

Synthesis of ZrO2 nanoparticles on pumice and tuff for sonocatalytic degradation of rifampin.

ZrO2-pumice and ZrO2-tuff nanocomposites were synthesized via a modified sol-gel method and used as efficient catalysts for sonocatalytic degradation of rifampin (RIF). The physico-chemical properties of the prepared catalysts were examined using XRF, SEM, EDX, FT-IR and BET analyses and compared to pure pumice and tuff samples. Subsequently, the efficacy of catalysts in degradation of RIF was assessed under various experimental conditions. Both ZrO2-pumice and ZrO2-tuff (1.5 g L-1) exhibited promising catalytic activity for sonocatalytic degradation of RIF at its initial concentration of 20 mg L-1, natural pH and under ultrasonic irradiation power of 300 W. In this condition, about 95% and 83% of RIF was removed through US/ZrO2-pumice and US/ZrO2-tuff processes, respectively. Furthermore, the influence of the addition of a number of scavengers, enhancers and gases on the degradation of RIF was studied. The pronounced degradation effectiveness of the catalysts under ultrasound irradiation could be assigned to their synergetic ability to produce reactive species and subsequent radical reactions. The intermediate products formed in the solution from degradation of RIF were also identified and a decomposition pathway was proposed using GC-MS, COD, TOC and IC analyses.

Sonocatalytic degradation of Reactive Yellow 39 using synthesized ZrO2 nanoparticles on biochar.

ZrO2-biochar (ZrO2-BC) nanocomposite was prepared by a modified sonochemical/sol-gel method. The physicochemical properties of the prepared nanocomposite were evaluated using scanning electron microscopy, energy-dispersive X-ray spectroscopy, X-ray fluorescence, Fourier transform infrared spectroscopy and Brunauer-Emmett-Teller model. The sonocatalytic performance of ZrO2-BC was investigated in sonochemical degradation of Reactive Yellow 39 (RY39). The high observed sonocatalytic activity of the ZrO2-BC sample could be interpreted by the mechanisms of sonoluminescence and hot spots. Parameters including ZrO2-BC dosage, solution pH, initial RY39 concentration and ultrasonic power were selected as the main operational parameters and their influence on RY39 degradation efficiency was examined. A 96.8% degradation efficiency was achieved with a ZrO2-BC dosage of 1.5g/L, pH of 6, initial RY39 concentration of 20mg/L and ultrasonic power of 300W. In the presence of OH radical scavengers, RY39 degradation was significantly inhibited, providing evidence for the key role of hydroxyl radicals in the process. The sonodegradation intermediates were identified using gas chromatography-mass spectroscopy and the possible decomposition route was proposed.