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Annual Review of Biophysics May 2019It would often be useful in computer simulations to use an implicit description of solvation effects, instead of explicitly representing the individual solvent... (Review)
Review
It would often be useful in computer simulations to use an implicit description of solvation effects, instead of explicitly representing the individual solvent molecules. Continuum dielectric models often work well in describing the thermodynamic aspects of aqueous solvation and can be very efficient compared to the explicit treatment of the solvent. Here, we review a particular class of so-called fast implicit solvent models, generalized Born (GB) models, which are widely used for molecular dynamics (MD) simulations of proteins and nucleic acids. These approaches model hydration effects and provide solvent-dependent forces with efficiencies comparable to molecular-mechanics calculations on the solute alone; as such, they can be incorporated into MD or other conformational searching strategies in a straightforward manner. The foundations of the GB model are reviewed, followed by examples of newer, emerging models and examples of important applications. We discuss their strengths and weaknesses, both for fidelity to the underlying continuum model and for the ability to replace explicit consideration of solvent molecules in macromolecular simulations.
Topics: Computer Simulation; Nucleic Acids; Proteins; Solvents; Thermodynamics
PubMed: 30857399
DOI: 10.1146/annurev-biophys-052118-115325 -
Annual Review of Chemical and... Jun 2021The most important developments in solvent-based fluid separations, separations involving at least one fluid phase, are reviewed. After a brief introduction and... (Review)
Review
The most important developments in solvent-based fluid separations, separations involving at least one fluid phase, are reviewed. After a brief introduction and discussion on general solvent trends observed in all fields of application, several specific fields are discussed. Important solvent trends include replacement of traditional molecular solvents by ionic liquids and deep eutectic solvents and, more recently, increasing discussion around bio-based solvents in some application fields. Furthermore, stimuli-responsive systems are discussed; the most significant developments in this field are seen for CO-switchable and redox-responsive solvents. Discussed fields of application include hydrocarbons separations, carbon capture, biorefineries, and metals separations. For all but the hydrocarbons separations, newly reported electrochemically mediated separations seem to offer exciting new windows of opportunities.
Topics: Ionic Liquids; Solvents
PubMed: 33852351
DOI: 10.1146/annurev-chembioeng-102620-015346 -
Acta Crystallographica. Section D,... May 2015The mother liquor from which a biomolecular crystal is grown will contain water, buffer molecules, native ligands and cofactors, crystallization precipitants and... (Review)
Review
The mother liquor from which a biomolecular crystal is grown will contain water, buffer molecules, native ligands and cofactors, crystallization precipitants and additives, various metal ions, and often small-molecule ligands or inhibitors. On average, about half the volume of a biomolecular crystal consists of this mother liquor, whose components form the disordered bulk solvent. Its scattering contributions can be exploited in initial phasing and must be included in crystal structure refinement as a bulk-solvent model. Concomitantly, distinct electron density originating from ordered solvent components must be correctly identified and represented as part of the atomic crystal structure model. Herein, are reviewed (i) probabilistic bulk-solvent content estimates, (ii) the use of bulk-solvent density modification in phase improvement, (iii) bulk-solvent models and refinement of bulk-solvent contributions and (iv) modelling and validation of ordered solvent constituents. A brief summary is provided of current tools for bulk-solvent analysis and refinement, as well as of modelling, refinement and analysis of ordered solvent components, including small-molecule ligands.
Topics: Crystallization; Crystallography, X-Ray; Macromolecular Substances; Models, Molecular; Solvents
PubMed: 25945568
DOI: 10.1107/S1399004715006045 -
Annual Review of Public Health 1988
Review
Topics: Absorption; Animals; Epidemiologic Methods; Humans; Nervous System; Solvents; Substance-Related Disorders
PubMed: 3288233
DOI: 10.1146/annurev.pu.09.050188.001255 -
Angewandte Chemie (International Ed. in... Jul 2022The experimental isolation of H-bond energetics from the typically dominant influence of the solvent remains challenging. Here we use synthetic molecular balances to...
The experimental isolation of H-bond energetics from the typically dominant influence of the solvent remains challenging. Here we use synthetic molecular balances to quantify amine/amide H-bonds in competitive solvents. Over 200 conformational free energy differences were determined using 24 H-bonding balances in 9 solvents spanning a wide polarity range. The correlations between experimental interaction energies and gas-phase computed energies exhibited wild solvent-dependent variation. However, excellent correlations were found between the same computed energies and the experimental data following empirical dissection of solvent effects using Hunter's α/β solvation model. In addition to facilitating the direct comparison of experimental and computational data, changes in the fitted donor and acceptor constants reveal the energetics of secondary local interactions such as competing H-bonds.
Topics: Amides; Hydrogen Bonding; Solvents; Thermodynamics
PubMed: 35608961
DOI: 10.1002/anie.202206604 -
Current Opinion in Biotechnology Jun 2012Bacteria have been found in all niches explored on Earth, their ubiquity derives from their enormous metabolic diversity and their capacity to adapt to changes in the... (Review)
Review
Bacteria have been found in all niches explored on Earth, their ubiquity derives from their enormous metabolic diversity and their capacity to adapt to changes in the environment. Some bacterial strains are able to thrive in the presence of high concentrations of toxic organic chemicals, such as aromatic compounds, aliphatic alcohols and solvents. The extrusion of these toxic compounds from the cell to the external medium represents the most relevant aspect in the solvent tolerance of bacteria, however, solvent tolerance is a multifactorial process that involves a wide range of genetic and physiological changes to overcome solvent damage. These additional elements include reduced membrane permeabilization, implementation of a stress response programme, and in some cases degradation of the toxic compound. We discuss the recent advances in our understanding of the mechanisms involved in solvent tolerance.
Topics: Bacterial Proteins; Environmental Pollutants; Gram-Negative Bacteria; Ion Pumps; Organic Chemicals; Solvents
PubMed: 22155018
DOI: 10.1016/j.copbio.2011.11.015 -
International Journal of Molecular... Mar 2022Greater awareness of environmental sustainability has driven many industries to transition from using synthetic organic solvents to greener solvents in their... (Review)
Review
Greater awareness of environmental sustainability has driven many industries to transition from using synthetic organic solvents to greener solvents in their manufacturing. Deep eutectic solvents (DESs) have emerged as a highly promising category of green solvents with well-demonstrated and wide-ranging applications, including their use as a solvent in extraction of small-molecule bioactive compounds for food and pharmaceutical applications. The use of DES as an extraction solvent of biological macromolecules, on the other hand, has not been as extensively studied. Thereby, the feasibility of employing DES for biomacromolecule extraction has not been well elucidated. To bridge this gap, this review provides an overview of DES with an emphasis on its unique physicochemical properties that make it an attractive green solvent (e.g., non-toxicity, biodegradability, ease of preparation, renewable, tailorable properties). Recent advances in DES extraction of three classes of biomacromolecules-i.e., proteins, carbohydrates, and lipids-were discussed and future research needs were identified. The importance of DES's properties-particularly its viscosity, polarity, molar ratio of DES components, and water addition-on the DES extraction's performance were discussed. Not unlike the findings from DES extraction of bioactive small molecules, DES extraction of biomacromolecules was concluded to be generally superior to extraction using synthetic organic solvents.
Topics: Deep Eutectic Solvents; Plant Extracts; Solvents; Water
PubMed: 35328803
DOI: 10.3390/ijms23063381 -
Bioresource Technology Feb 2023Demonstrated to be highly effective for lignocellulosic biomass pretreatment, deep eutectic solvent (DES) has attracted increasing attention owing to its advantages of... (Review)
Review
Demonstrated to be highly effective for lignocellulosic biomass pretreatment, deep eutectic solvent (DES) has attracted increasing attention owing to its advantages of simple synthesis, relatively low chemical cost, and better biocompatibility as compared to certain ionic liquids. Here we provide a critical review of the status of the design/selection of DES for the pretreatment of biomass feedstocks with an emphasis on the process intensification strategies: 1) integration of microwave, ultrasound, and high solid extrusion for pretreating biomass, 2) one-pot DES pretreatment, enzymatic hydrolysis, and fermentation, 3) strategies for DES recycling and product recovery; and 4) recent progress on molecular simulations toward understanding the interactions between DES and biomass compounds such as lignin and cellulose. Lastly, we provide perspectives toward cost-effective, continuous, high-solid, environmental-benign, and industrial-relevant applications and point to future research directions to address the challenges associated with DES pretreatment.
Topics: Biomass; Solvents; Cellulose; Lignin; Ionic Liquids; Hydrolysis
PubMed: 36442603
DOI: 10.1016/j.biortech.2022.128394 -
Small (Weinheim An Der Bergstrasse,... Oct 2022In this study, manganese-based multiply hierarchical chiral supraparticles (SPs), with an anisotropy factor (g-factor) of 0.102 and circular dichroism (CD) intensity of...
In this study, manganese-based multiply hierarchical chiral supraparticles (SPs), with an anisotropy factor (g-factor) of 0.102 and circular dichroism (CD) intensity of 260 mdeg at 530 nm, are successfully synthesized with polar-solvent-mediated strategies. Notably, the g-factor of the SPs is further enhanced to 0.121 by the addition of an external chiral solvent, generating a chiral biased environment, which increases their CD intensity to 320 mdeg at 500 nm. The mechanism underlying the different chirality is proposed to be a difference in the angle of tilt of ±33° between the two enantiomers of the chiral SPs, which involves a difference of ±7° between the orientation of individual nanoplatelets. Chiral solvents induce the angle between adjacent nanoplatelets to get smaller than the original structure that leads to their higher anisotropic value. These findings potentially provide a practical method for the construction of complex chiral superstructures and the regulation of chiroptical activity.
Topics: Solvents; Manganese; Circular Dichroism; Stereoisomerism; Ions
PubMed: 36108137
DOI: 10.1002/smll.202202741 -
Physical Chemistry Chemical Physics :... Aug 2022Deep eutectic solvents (DESs) as novel green solvents are potential options to replace inorganic acids for hydrometallurgy. Compared with inorganic acids, the... (Review)
Review
Deep eutectic solvents (DESs) as novel green solvents are potential options to replace inorganic acids for hydrometallurgy. Compared with inorganic acids, the physicochemical properties of DESs and their applications in recycling of spent lithium-ion batteries were summarized. The viscosity, metal solubility, toxicological properties and biodegradation of DESs depend on the hydrogen bond donor (HBD) and acceptor (HBA). The viscosity of ChCl-based DESs increased according to the HBD in the following order: alcohols < carboxylic acids < sugars < inorganic salts. The strongly coordinating HBDs increased the solubility of metal oxide surface complexation reactions followed by ligand exchange for chloride in the bulk solvent. Interestingly, the safety and degradability of DESs reported in the literature are superior to those of inorganic acids. Both DESs and inorganic acids have excellent metal leaching efficiencies (>99%). However, the reaction kinetics of DESs are 2-3 orders of magnitude slower than those of inorganic acids. A significant advantage of DESs is that they can be regenerated and recycled multiple times after recovering metals by electrochemical deposition or precipitation. In the future, the development of efficient and selective DESs still requires a lot of attention.
Topics: Deep Eutectic Solvents; Electric Power Supplies; Hydrogen Bonding; Ions; Lithium; Metals; Solvents
PubMed: 35938373
DOI: 10.1039/d1cp05968h