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European Journal of Medicinal Chemistry Feb 2015Solvation is a fundamental contribution in many biological processes and especially in molecular binding. Its estimation can be performed by means of several... (Review)
Review
Solvation is a fundamental contribution in many biological processes and especially in molecular binding. Its estimation can be performed by means of several computational approaches. The aim of this review is to give an overview of existing theories and methods to estimate solvent effects giving a specific focus on the category of implicit solvent models and their use in Molecular Dynamics. In many of these models, the solvent is considered as a continuum homogenous medium, while the solute can be represented at the atomic detail and at different levels of theory. Despite their degree of approximation, implicit methods are still widely employed due to their trade-off between accuracy and efficiency. Their derivation is rooted in the statistical mechanics and integral equations disciplines, some of the related details being provided here. Finally, methods that combine implicit solvent models and molecular dynamics simulation, are briefly described.
Topics: Models, Chemical; Molecular Dynamics Simulation; Solubility; Solutions; Solvents; Static Electricity; Thermodynamics
PubMed: 25193298
DOI: 10.1016/j.ejmech.2014.08.064 -
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 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 -
International Journal of Molecular... Jan 2022Fluorescent molecular assembly systems provide an exciting platform for creating stimuli-responsive nano- and microstructured materials with optical, electronic, and...
Fluorescent molecular assembly systems provide an exciting platform for creating stimuli-responsive nano- and microstructured materials with optical, electronic, and sensing functions. To understand the relationship between (i) the plausible molecular structures preferentially adopted depending on the solvent polarity (such as N,N-dimethylformamide [DMF], tetrahydrofuran [THF], and toluene), (ii) the resulting spectroscopic features, and (iii) self-assembled nano-, micro-, and macrostructures, we chose a sterically crowded triangular azo dye (3Bu) composed of a polar molecular core and three peripheral biphenyl wings. The chromophore changed the solution color from yellow to pink-red depending on the solvent polarity. In a yellow DMF solution, a considerable amount of the twisted azo form could be kept stable with the help of favorable intermolecular interactions with the solvent molecules. By varying the concentration of the DMF solution, the morphology of self-assembled structures was transformed from nanoparticles to micrometer-sized one-dimensional (1D) structures such as sticks and fibers. In a pink-red toluene solution, the periphery of the central ring became more planar. The resulting significant amount of the keto-hydrazone tautomer grew into micro- and millimeter-sized 1D structures. Interestingly, when THF-HO (1:1) mixtures were stored at a low temperature, elongated fibers were stacked sideways and eventually developed into anisotropic two-dimensional (2D) sheets. Notably, subsequent exposure of visible-light-irradiated sphere samples to solvent vapor resulted in reversible fluorescence off↔on switching accompanied by morphological restoration. These findings suggest that rational selection of organic dyes, solvents, and light is important for developing reusable fluorescent materials.
Topics: Azo Compounds; Coloring Agents; Crystallography, X-Ray; Light; Models, Molecular; Molecular Structure; Nanostructures; Solvents
PubMed: 35055154
DOI: 10.3390/ijms23020965 -
Briefings in Bioinformatics May 2022Characterizing RNA structures and functions have mostly been focused on 2D, secondary and 3D, tertiary structures. Recent advances in experimental and computational... (Review)
Review
Characterizing RNA structures and functions have mostly been focused on 2D, secondary and 3D, tertiary structures. Recent advances in experimental and computational techniques for probing or predicting RNA solvent accessibility make this 1D representation of tertiary structures an increasingly attractive feature to explore. Here, we provide a survey of these recent developments, which indicate the emergence of solvent accessibility as a simple 1D property, adding to secondary and tertiary structures for investigating complex structure-function relations of RNAs.
Topics: Nucleic Acid Conformation; RNA; Solvents
PubMed: 35348613
DOI: 10.1093/bib/bbac112 -
Molecules (Basel, Switzerland) Mar 2023A fast and straightforward reversed-phase dispersive liquid-liquid microextraction (RP-DLLME) using a deep eutectic solvent (DES) procedure to determine free tryptophan...
Deep Eutectic Solvent Based Reversed-Phase Dispersive Liquid-Liquid Microextraction and High-Performance Liquid Chromatography for the Determination of Free Tryptophan in Cold-Pressed Oils.
A fast and straightforward reversed-phase dispersive liquid-liquid microextraction (RP-DLLME) using a deep eutectic solvent (DES) procedure to determine free tryptophan in vegetable oils was developed. The influence of eight variables affecting the RP-DLLME efficiency has been studied by a multivariate approach. A Plackett-Burman design for screening the most influential variables followed by a central composite response surface methodology led to an optimum RP-DLLME setup for a 1 g oil sample: 9 mL hexane as the diluting solvent, vortex extraction with 0.45 mL of DES (choline chloride-urea) at 40 °C, without addition of salt, and centrifugation at 6000 rpm for 4.0 min. The reconstituted extract was directly injected into a high-performance liquid chromatography (HPLC) system working in the diode array mode. At the studied concentration levels, the obtained method detection limits (MDL) was 11 mg/kg, linearity in matrix-matched standards was R ≥ 0.997, relative standard deviations (RSD) was 7.8%, and average recovery was 93%. The combined use of the recently developed DES -based RP-DLLME and HPLC provides an innovative, efficient, cost-effective, and more sustainable method for the extraction and quantification of free tryptophan in oily food matrices. The method was employed to analyze cold-pressed oils from nine vegetables (Brazil nut, almond, cashew, hazelnut, peanut, pumpkin, sesame, sunflower, and walnut) for the first time. The results showed that free tryptophan was present in the range of 11-38 mg/100 g. This article is important for its contributions to the field of food analysis, and for its development of a new and efficient method for the determination of free tryptophan in complex matrices, which has the potential to be applied to other analytes and sample types.
Topics: Chromatography, High Pressure Liquid; Tryptophan; Deep Eutectic Solvents; Liquid Phase Microextraction; Plant Oils; Limit of Detection; Solvents
PubMed: 36903640
DOI: 10.3390/molecules28052395 -
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 -
The Journal of Physical Chemistry. B Aug 2022The ability to exploit carbonyl groups to measure electric fields in enzymes and other complex reactive environments by using the vibrational Stark effect has inspired...
The ability to exploit carbonyl groups to measure electric fields in enzymes and other complex reactive environments by using the vibrational Stark effect has inspired growing interest in how these fields can be measured, tuned, and ultimately designed. Previous studies have concentrated on the role of the solvent in tuning the fields exerted on the solute. Here, we explore instead the role of the solute electronic structure in modifying the local solvent organization and electric field exerted on the solute. By measuring the infrared absorption spectra of amide-containing molecules, as prototypical peptides, and contrasting them with non-amide carbonyls in a wide range of solvents, we show that these solutes experience notable differences in their frequency shifts in polar solvents. Using vibrational Stark spectroscopy and molecular dynamics simulations, we demonstrate that while some of these differences can be rationalized by using the distinct intrinsic Stark tuning rates of the solutes, the larger frequency shifts for amides and dimethylurea primarily result from the larger solvent electric fields experienced by their carbonyl groups. These larger fields arise due to their stronger -π conjugation, which results in larger C═O bond dipole moments that further induce substantial solvent organization. Using electronic structure calculations, we decompose the electric fields into contributions from solvent molecules that are in the first solvation shell and those from the bulk and show that both of these contributions are significant and become larger with enhanced conjugation in solutes. These results show that structural modifications of a solute can be used to tune both the solvent organization and electrostatic environment, indicating the importance of a solute-centric paradigm in modulating and designing the electrostatic environment in condensed-phase chemical processes.
Topics: Amides; Electronics; Solutions; Solvents; Static Electricity
PubMed: 35901512
DOI: 10.1021/acs.jpcb.2c03095 -
Progress in Nuclear Magnetic Resonance... 2022Solvent paramagnetic relaxation enhancement (sPRE) is a versatile nuclear magnetic resonance (NMR)-based method that allows characterization of the structure and... (Review)
Review
Solvent paramagnetic relaxation enhancement (sPRE) is a versatile nuclear magnetic resonance (NMR)-based method that allows characterization of the structure and dynamics of biomolecular systems through providing quantitative experimental information on solvent accessibility of NMR-active nuclei. Addition of soluble paramagnetic probes to the solution of a biomolecule leads to paramagnetic relaxation enhancement in a concentration-dependent manner. Here we review recent progress in the sPRE-based characterization of structural and dynamic properties of biomolecules and their complexes, and aim to deliver a comprehensive illustration of a growing number of applications of the method to various biological systems. We discuss the physical principles of sPRE measurements and provide an overview of available co-solute paramagnetic probes. We then explore how sPRE, in combination with complementary biophysical techniques, can further advance biomolecular structure determination, identification of interaction surfaces within protein complexes, and probing of conformational changes and low-population transient states, as well as deliver insights into weak, nonspecific, and transient interactions between proteins and co-solutes. In addition, we present examples of how the incorporation of solvent paramagnetic probes can improve the sensitivity of NMR experiments and discuss the prospects of applying sPRE to NMR metabolomics, drug discovery, and the study of intrinsically disordered proteins.
Topics: Solvents; Intrinsically Disordered Proteins; Magnetic Resonance Spectroscopy; Solutions; Nuclear Magnetic Resonance, Biomolecular
PubMed: 36496256
DOI: 10.1016/j.pnmrs.2022.09.001 -
ACS Applied Bio Materials Aug 2023This paper reports on the production of electro-spun nanofibers from softwood Kraft lignin without the need for polymer blending and/or chemical modification....
This paper reports on the production of electro-spun nanofibers from softwood Kraft lignin without the need for polymer blending and/or chemical modification. Commercially available softwood Kraft lignin was fractionated using acetone. The acetone-soluble lignin (AcSL) had an ash content of 0.06 wt %, a weight average molecular weight of 4250 g·mol along with the polydispersity index of 1.73. The corresponding values for as-received lignin (ARL) were 1.20 wt %, 6000 g·mol, and 2.22, respectively. The AcS was dissolved in a binary solvent consisting of acetone, and dimethyl sulfoxide (2:1, v/v) was selected for dissolving the AcSL. Conventional and custom-designed grounded electrode configurations were used to produce electro-spun neat lignin fibers that were randomly oriented or highly aligned, respectively. The diameter of the electro-spun fibers ranged from 1.12 to 1.46 μm. After vacuum drying at 140 °C for 6 h to remove the solvents and oxidation at 250 °C, the fibers were carbonized at 1000, 1200, and 1500 °C for 1 h. The carbonized fibers were unfused and void-free with an average diameter of 500 nm. Raman spectroscopy, scanning electron microscopy, and image analysis were used to characterize the carbonized fibers.
Topics: Solvents; Lignin; Acetone; Chemical Fractionation
PubMed: 37523247
DOI: 10.1021/acsabm.3c00278