1-Butanol as a Solvent for Efficient Extraction of Polar Compounds from Aqueous Medium: Theoretical and Practical Aspects

Atomic-Scale Characterization of Microscale Battery Particles Enabled by a High-Throughput Focused Ion Beam Milling Technique

The cathode materials in lithium-ion batteries (LIBs) require improvements to address issues such as surface degradation, short-circuiting, and the formation of dendrites. One such method for addressing these issues is using surface coatings. Coatings can be sought to improve the durability of cathode materials, but the characterization of the uniformity and stability of the coating is important to assess the performance and lifetime of these materials. For microscale particles, there are, however, challenges associated with characterizing their surface modifications by transmission electron microscopy (TEM) techniques due to the size of these particles. Often, techniques such as focused ion beam (FIB)-assisted lift-out can be used to prepare thin cross sections to enable TEM analysis, but these techniques are very time-consuming and have a relatively low throughput. The work outlined herein demonstrates a FIB technique with direct support of microscale cathode materials on a TEM grid that increases sample throughput and reduces the processing time by 60-80% (i.e., from >5 to ∼1.5 h). The demonstrated workflow incorporates an air-liquid particle assembly followed by direct particle transfer to a TEM grid, FIB milling, and subsequent TEM analysis, which was illustrated with lithium nickel cobalt aluminum oxide particles and lithium manganese nickel oxide particles. These TEM analyses included mapping the elemental composition of cross sections of the microscale particles using energy-dispersive X-ray spectroscopy. The methods developed in this study can be extended to high-throughput characterization of additional LIB cathode materials (e.g., new compositions, coating, end-of-life studies), as well as to other microparticles and their coatings as prepared for a variety of applications.

Volatile organic compounds: A threat to the environment and health hazards to living organisms - A review

Volatile organic compounds (VOCs) are the organic compounds having a minimum vapor pressure of 0.13 kPa at standard temperature and pressure (293 K, 101 kPa). Being used as a solvent for organic and inorganic compounds, they have a wide range of applications. Most of the VOCs are non-biodegradable and very easily become component of the environment and deplete its purity. It also deteriorates the water quality index of the water bodies, impairs the physiology of living beings, enters the food chain by bio-magnification and degrades, decomposes and manipulates the physiology of living organisms. To unveil the adverse impacts of volatile organic compounds (VOCs) and their rapid eruption and interference in the living world, a review has been designed. This review presents an insight into the currently available VOCs, their sources, applications, sampling methods, analytic procedures, imposition on the health of aquatic and terrestrial communities and their contamination of the environment. Elaboration has been done on representation of toxicological effects of VOCs on vertebrates, invertebrates, and birds. Subsequently, the role of environmental agencies in the protection of environment has also been illustrated.

Rapid Multi-Omics Sample Preparation for Mass Spectrometry

Multi-omics analysis is a powerful and increasingly utilized approach to gain insight into complex biological systems. One major hindrance with multi-omics, however, is the lengthy and wasteful sample preparation process. Preparing samples for mass spectrometry (MS)-based multi-omics involves extraction of metabolites and lipids with organic solvents, precipitation of proteins, and overnight digestion of proteins. These existing workflows are disparate and laborious. Here, we present a simple, efficient, and unified approach to prepare lipids, metabolites, and proteins for MS analysis. Our approach, termed the Bead-enabled Accelerated Monophasic Multi-omics (BAMM) method, combines an n-butanol-based monophasic extraction with unmodified magnetic beads and accelerated protein digestion. We demonstrate that the BAMM method affords comparable depth, quantitative reproducibility, and recovery of biomolecules as state-of-the-art multi-omics methods (e.g., Matyash extraction and overnight protein digestion). However, the BAMM method only requires about 3 h to perform, which saves 11 steps and 19 h on average compared to published multi-omics methods. Furthermore, we validate the BAMM method for multiple sample types and formats (biofluid, culture plate, and pellet) and show that in all cases, it produces high biomolecular coverage and data quality.

Sustainable Use of Apple Pomace (AP) in Different Industrial Sectors

In many countries, apple pomace (AP) is one of the most produced types of agri-food waste (globally, it is produced at a rate of ~4 million tons/year). If not managed properly, such bio-organic waste can cause serious pollution of the natural environment and public health hazards, mainly due to the risk of microbial contamination. This review shows that AP can be successfully reused in different industrial sectors—for example, as a source of energy and bio-materials—according to the idea of sustainable development. The recovered active compounds from AP can be applied as preservatives, antioxidants, anti-corrosion agents, wood protectors or biopolymers. Raw or processed forms of AP can also be considered as feedstocks for various bioenergy applications such as the production of intermediate bioenergy carriers (e.g., biogas and pyrolysis oil), and materials (e.g., biochar and activated carbon). In the future, AP and its active ingredients can be of great use due to their non-toxicity, biodegradability and biocompatibility. Given the increasing mass of produced AP, the commercial applications of AP could have a huge economic impact in the future.

Recovery of N-Butanol from a Complex Five-Component Reactive Azeotropic Mixture

This paper proposes a concept of a process design for the separation and recovery of n-butanol from a five-component mixture, consisting of n-butanol, isobutanol, formaldehyde, water and methanol. The mixture is a common waste stream in the production of butylated amino resins; therefore, recovery of n-butanol is crucial to the efficiency of the process. The results show that up to 94% of the n-butanol present in the waste stream can be recovered. Under the studied conditions, 99.76% pure n-butanol can be obtained, while formaldehyde, water and methanol are present only in traces. The energy intensity of the process is estimated at 2.42 MJ/kg of purified n-butanol. The economic analysis of the process shows that the process is economically viable over a wide range of production capacities, as evidenced by high net present values and high return on investment values.

Photophysics of faecal pigments stercobilin and urobilin in aliphatic alcohols: introduction of a sensitive method for their detection using solvent phase extraction and fluorometry

Faecal pigments (FPs) are ubiquitous in the environment and are a primary contaminant in groundwater and surface water. This article presents a new analytical paradigm by a fluorescence coupled extraction-based method involving FP fluorescence enhancement and minimization of background fluorescence for high sensitivity detection. FPs show higher fluorescence intensity in aliphatic alcohols due to the breaking down of higher-order H-aggregates into lower-order H-aggregates (dimers). DFT studies using the B3LYP functional and LANL2DZ basis set show π-π stacking and hydrogen-bonding contributions towards forming H-aggregated dimers of FPs in the implicit and explicit solvent environments of 1-hexanol. This study is the first report on the extractability of FPs using 1-hexanol as an efficient extraction medium in comparison to higher-order aliphatic alcohols (1-butanol, 1-hexanol and 1-octanol). Furthermore, FP-Zn(II) complexes in 1-hexanol medium significantly enhance the fluorescence emission intensity (∼14-17 times), and the emission intensity remains stable over time. This further helps to increase the detection limit of FPs in the picomolar to sub-picomolar concentration range. This study proposes a protocol involving extraction of FPs by 1-hexanol followed by the complexation of FPs with Zn(II) in the alcohol media and subsequent fluorimetric detection of the FP-Zn(II) complex with a high level of sensitivity, enabled by reduced interference from the background fluorescence of humic acid. The complexation behaviour of FPs with various metal salts was also examined, which provided an understanding of the fluorescence behaviour of FPs with various other metal ions commonly present in natural environmental water. The proposed analytical method has been further validated using real water samples.

The isolation of water-soluble natural products - challenges, strategies and perspectives

Covering period: up to 2019Water-soluble natural products constitute a relevant group of secondary metabolites notably known for presenting potent biological activities. Examples are aminoglycosides, β-lactam antibiotics, saponins of both terrestrial and marine origin, and marine toxins. Although extensively investigated in the past, particularly during the golden age of antibiotics, hydrophilic fractions have been less scrutinized during the last few decades. This review addresses the possible reasons on why water-soluble metabolites are now under investigated and describes approaches and strategies for the isolation of these natural compounds. It presents examples of several classes of hydrosoluble natural products and how they have been isolated. Novel stationary phases and chromatography techniques are also reviewed, providing a perspective towards a renaissance in the investigation of water-soluble natural products.

Efficient Alchemical Intermediate States in Free Energy Calculations Using λ-Enveloping Distribution Sampling

Alchemical free energy calculations generally require intermediate states along a coupling parameter λ to establish sufficient phase space overlap for obtaining converged results. Such intermediate states can also be engineered to lower the energy barriers and, consequently, reduce the required sampling time. The recently introduced λ-enveloping distribution sampling (λ-EDS) scheme combines the properties of the minimum variance pathway and the EDS methods to improve sampling and allow for larger steps along the alchemical pathway compared to conventional approaches. This scheme also eliminates the need for soft-core potentials and retains the behavior of conventional λ-intermediate states as a limiting case. In this study, an automated procedure is developed to select the parameters of λ-EDS for optimal performance. The underlying theory is illustrated based on simulations of simple test systems (bond length changes in harmonic oscillators, mutations of dihedral angles, and charge creation in water), as well as on the calculation of the absolute hydration free energies of 12 small organic molecules.

Coarse-grained force-field for large scale molecular dynamics simulations of polyacrylamide and polyacrylamide-gels based on quantum mechanics

Developing a coarse-grained force field for polyacrylamide based on quantum mechanics equation of state.

An Alternative to Conventional λ-Intermediate States in Alchemical Free Energy Calculations: λ-Enveloping Distribution Sampling

Alchemical free energy calculations typically rely on intermediate states to bridge between the relevant phase spaces of the two end states. These intermediate states are usually created by mixing the energies or parameters of the end states according to a coupling parameter λ. The choice of the procedure has a strong impact on the efficiency of the calculation, as it affects both the encountered energy barriers and the phase space overlap between the states. The present work builds on the connection between the minimum variance pathway (MVP) and enveloping distribution sampling (EDS). It is shown that both methods can be regarded as special cases of a common scheme referred to as λ-EDS, which can also reproduce the behavior of conventional λ-intermediate states. A particularly attractive feature of λ-EDS is its ability to emulate the use of soft core potentials (SCP) while avoiding the associated computational overhead when applying efficient free energy estimators such as the multistate Bennett's acceptance ratio (MBAR). The method is illustrated for both relative and absolute free energy calculations considering five benchmark systems. The first two systems (charge inversion and cavity creation in a dipolar solvent) demonstrate the use of λ-EDS as an alternative coupling scheme in the context of thermodynamic integration (TI). The three other systems (change of bond length, change of dihedral angles, and cavity creation in water) investigate the efficiency and optimal choice of parameters in the context of free energy perturbation (FEP) and Bennett's acceptance ratio (BAR). It is shown that λ-EDS allows larger steps along the alchemical pathway than conventional intermediate states.

High-Throughput Fluorescence Assay for Ketone Detection and Its Applications in Enzyme Mining and Protein Engineering

Ketones are of great importance as building blocks in synthetic organic chemistry and biocatalysis. Most ketones cannot easily be quantitatively assayed due to the lack of visible photometric properties. Effective high-throughput assay (HTA) development is therefore necessary for ketone determination. Inspired by previous works of an aldehyde assay based on 2-amino benzamidoxime derivatives, we developed a colorimetric method for rapid a HTA of structurally diverse ketones by using para-methoxy-2-amino benzamidoxime (PMA). This PMA-based method is characterized by high sensitivity manner (μM) with low background, as checked by gas chromatography (GC). It can be used for quantitatively monitoring ketones by fluorescence screening in microtiter plates. Furthermore, this HTA method was employed in mining alcohol dehydrogenases (ADHs), and in directed evolution aimed at enhancing ADH activity in the catalytic transformation of alcohols to ketones. This work provides a general tool for ketone detection in biocatalyst development.

Ligand and additive free aerobic synthesis of diynes using Pd–CuFe2O4magnetic nanoparticles as an efficient reusable catalyst

Herein, we present the synthesis of Pd–CuFe₂O₄magnetic nanoparticles as an efficient and recyclable catalyst for the oxidative homocoupling of various terminal alkynes to form symmetric 1,3-diynes.

Calculation of the water-octanol partition coefficient of cholesterol for SPC, TIP3P, and TIP4P water

We present a numerical study of the relative solubility of cholesterol in octanol and water. Our calculations allow us to compare the accuracy of the computed values of the excess chemical potential of cholesterol for several widely used water models (SPC, TIP3P, and TIP4P). We compute the excess solvation free energies by means of a cavity-based method [L. Li et al., J. Chem. Phys. 146(21), 214110 (2017)] which allows for the calculation of the excess chemical potential of a large molecule in a dense solvent phase. For the calculation of the relative solubility ("partition coefficient," log₁₀ P o / w ) of cholesterol between octanol and water, we use the OPLS/AA force field in combination with the SPC, TIP3P, and TIP4P water models. For all water models studied, our results reproduce the experimental observation that cholesterol is less soluble in water than in octanol. While the experimental value for the partition coefficient is log₁₀ P o / w = 3.7, SPC, TIP3P, and TIP4P give us a value of log₁₀ P o / w = 4.5, 4.6, and 2.9, respectively. Therefore, although the results for the studied water models in combination with the OPLS/AA force field are acceptable, further work to improve the accuracy of current force fields is needed.

A Comparison of QM/MM Simulations with and without the Drude Oscillator Model Based on Hydration Free Energies of Simple Solutes

Maintaining a proper balance between specific intermolecular interactions and non-specific solvent interactions is of critical importance in molecular simulations, especially when predicting binding affinities or reaction rates in the condensed phase. The most rigorous metric for characterizing solvent affinity are solvation free energies, which correspond to a transfer from the gas phase into solution. Due to the drastic change of the electrostatic environment during this process, it is also a stringent test of polarization response in the model. Here, we employ both the CHARMM fixed charge and polarizable force fields to predict hydration free energies of twelve simple solutes. The resulting classical ensembles are then reweighted to obtain QM/MM hydration free energies using a variety of QM methods, including MP2, Hartree⁻Fock, density functional methods (BLYP, B3LYP, M06-2X) and semi-empirical methods (OM2 and AM1 ). Our simulations test the compatibility of quantum-mechanical methods with molecular-mechanical water models and solute Lennard⁻Jones parameters. In all cases, the resulting QM/MM hydration free energies were inferior to purely classical results, with the QM/MM Drude force field predictions being only marginally better than the QM/MM fixed charge results. In addition, the QM/MM results for different quantum methods are highly divergent, with almost inverted trends for polarizable and fixed charge water models. While this does not necessarily imply deficiencies in the QM models themselves, it underscores the need to develop consistent and balanced QM/MM interactions. Both the QM and the MM component of a QM/MM simulation have to match, in order to avoid artifacts due to biased solute⁻solvent interactions. Finally, we discuss strategies to improve the convergence and efficiency of multi-scale free energy simulations by automatically adapting the molecular-mechanics force field to the target quantum method.