Ion Pair Formation and Solvation Energies in Solutions of Alkali Halides in Dimethyl Sulfoxide. II. Model Calculations

1975 ◽  
Vol 53 (7) ◽  
pp. 1007-1018 ◽  
Author(s):  
Merrill S. Goldenberg ◽  
Peeter Kruus ◽  
Stephen K. F. Luk

Energy calculations were carried out on models of molecular-level structures likely to be present in solutions of alkali halides in dimethyl sulfoxide (DMSO). Classical electrostatic interactions were assumed, and polarization of a DMSO molecule was assumed due to the fields of the ions only. The validity of this assumption was tested. DMSO molecules were represented by increasingly detailed models, with most calculations carried out with each molecule represented by 10 point charges and 9 polarizable bonds. A program including up to 14 such molecules and two ions was used for energy and distance calculations, and is made available. Polarization effects are as important as interactions between permanent charges for energy calculations. The configurations of minimum energy determined by classical electrostatics often do not involve overlap of the "hard-sphere radii" of neighboring species, so that the neglect of quantum mechanical repulsive forces seems justified. Energy cycles using the calculated energies for ion–solvent complexes predicted experimental cation enthalpies with some success. The form of the potential for vibration of a cation in a solvent shell was investigated and found in cases not to have an energy minimum at the shell center. Calculations including next-nearest solvating DMSO's indicate a rather loose structure. An energy profile for an anion moving from a solvent-separated ion pair position to a contact-ion pair position is presented.

1979 ◽  
Vol 57 (5) ◽  
pp. 538-551 ◽  
Author(s):  
Peeter Kruus ◽  
Barbara E. Poppe

A model of solutions of alkali halides in DMSO is developed. Each ion is described by a radius, a charge, a polarizability, and an exponential repulsion parameter. Each molecule is described by a polarizability, charges, 6-12 energy parameters, and 6-12 distance parameters centered on each of the 10 atoms in the molecule. The model is applied to calculate (i) the vaporization energy of solvent molecules, (ii) single ion solvation energies and configurations of the solvating molecules, and (iii) the energy as a function of reaction coordinate for the formation of an ion pair. The energies and configurations are obtained by allowing the systems to relax to minimum energy configurations by allowing motion of the molecules. The results of (i) give a vaporization energy 60% of the experimental. The results of (ii) give solvation energies in reasonable agreement with the experimental, and configurations which are reasonable from the point of view of mobilities of ions. The results of (iii) show the presence of a distinct solvent separated ion pair which actually has an energy lower than the contact ion pair. Advantages and problems involved in using this approach to model solutions are discussed.


1971 ◽  
Vol 49 (19) ◽  
pp. 3107-3113 ◽  
Author(s):  
D. R. Dickson ◽  
P. Kruus

The ultrasonic absorption of dimethyl sulfoxide solutions of several alkali halides has been studied in the frequency range 1.5 to 52 MHz. An excess absorption, relaxing between 3 and 8 MHz, was observed. The relaxation was assigned to the final step in the stepwise formation of a contact ion pair, with the relaxation frequency controlled by the rate of movement of a solvent molecule rather than an ion. Data on the system water – dimethyl sulfoxide are also presented and the effect of water on the relaxation discussed.


Author(s):  
Vasily Bulatov ◽  
Wei Cai

Free energy is of central importance for understanding the properties of physical systems at finite temperatures. While in the zero temperature limit the system should evolve to a state of minimum energy (Section 2.3), this is not necessarily the case at a finite temperature. When an open system exchanges energy with the outside world (a thermostat) and maintains a constant temperature, its evolution proceeds towards minimizing its free energy. For example, a crystal turns into a liquid when the temperature exceeds its melting temperature precisely because the free energy of the liquid state becomes lower than that of the crystalline state. In the context of dislocation simulations, free energy is all important when one has to decide which of the possible core configurations the dislocation is likely to adopt at a given temperature.


Soft Matter ◽  
2019 ◽  
Vol 15 (40) ◽  
pp. 8051-8058 ◽  
Author(s):  
Kyu Hwan Choi ◽  
Dong Woo Kang ◽  
Kyung Hak Kim ◽  
Jiwon Kim ◽  
Youngbok Lee ◽  
...  

Strong electrostatic repulsive forces between PMMA particles in CHB/decane mixtures were directly measured with optical laser tweezers.


1980 ◽  
Vol 58 (6) ◽  
pp. 559-566 ◽  
Author(s):  
Paul G. Mezey ◽  
Anil Kapur

Conformational properties of dimethyl sulfoxide (DMSO) have been studied by abinitio molecular orbital method, using various gaussian basis sets. Polarization d functions are essential in reproducing the correct experimental geometry. Barriers to pyramidal inversion on sulfur and Me—S bond rotation have been calculated. The calculated asymmetric S—Me stretching potential indicates that minor intermolecular interactions may cause considerable geometric distortions in the DMSO molecule. These distortions are likely to contribute to the versatile biochemical effects of DMSO.


Materials ◽  
2021 ◽  
Vol 14 (24) ◽  
pp. 7701
Author(s):  
Karthik Rathinam ◽  
Xinwei Kou ◽  
Ralph Hobby ◽  
Stefan Panglisch

The wide use of alizarin red S (ARS), a typical anthraquinone dye, has led to its continued accumulation in the aquatic environment, which causes mutagenic and carcinogenic effects on organisms. Therefore, this study focused on the removal of ARS dye by adsorption onto a magnetic chitosan core–shell network (MCN). The successful synthesis of the MCN was confirmed by ATR-FTIR, SEM, and EDX analysis. The influence of several parameters on the removal of ARS dye by the MCN revealed that the adsorption process reached equilibrium after 60 min, pH played a major role, and electrostatic interactions dominated for the ARS dye removal under acidic conditions. The adsorption data were described well by the Langmuir isotherm and a pseudo-second order kinetic model. In addition to the preferable adsorption of hydrophobic dissolved organic matter (DOM) fractions onto the MCN, the electrostatic repulsive forces between the previously adsorbed DOM onto MCN and ARS dye resulted in lower ARS dye removal. Furthermore, the MCN could easily be regenerated and reused for up to at least five cycles with more than 70% of its original efficiency. Most importantly, the spent MCN was pyrolytically converted into N-doped magnetic carbon and used as an adsorbent for various dyes, thus establishing a waste-free adsorption process.


2021 ◽  
Author(s):  
Nandan Haloi ◽  
Archit Kumar Vasan ◽  
Emily Jane Geddes ◽  
Arjun Prasanna ◽  
Po-Chao Wen ◽  
...  

Antibiotic resistance of Gram-negative bacteria is largely attributed to the low permeability of their outer membrane (OM). Recently, we disclosed the eNTRy rules, a key lesson of which is that the introduction of a primary amine enhances OM permeation in certain contexts. To understand the molecular basis for this finding, we perform an extensive set of molecular dynamics (MD) simulations and free energy calculations comparing the permeation of aminated and amine-free antibiotic derivatives through the most abundant OM porin of E. coli, OmpF. To improve sampling of conformationally flexible drugs in MD simulations, we developed a novel, Monte Carlo and graph theory based algorithm to probe more efficiently the rotational and translational degrees of freedom visited during the permeation of the antibiotic molecule through OmpF. The resulting pathways were then used for free-energy calculations, revealing a lower barrier against the permeation of the aminated compound, substantiating its greater OM permeability. Further analysis revealed that the amine facilitates permeation by enabling the antibiotic to align its dipole to the luminal electric field of the porin and while forming favorable electrostatic interactions with specific, highly-conserved charged residues. The importance of these interactions in permeation was further validated with experimental mutagenesis and whole cell accumulation assays. Overall, this study provides insights on the importance of the primary amine for antibiotic permeation into Gram-negative pathogens that could help the design of future antibiotics. We also offer a new computational approach for calculating free-energy of processes where relevant molecular conformations cannot be efficiently captured.


2018 ◽  
Vol 74 (8) ◽  
pp. 986-990 ◽  
Author(s):  
Yimin Mao ◽  
Peter Y. Zavalij

Furan-2,5-dicarboxylic acid (FDCA) has been ranked among the top 12 bio-based building-block chemicals by the Department of Energy in the US. The molecule was first synthesized in 1876, but large-scale production has only become possible since the development of modern bio- and chemical catalysis techniques. The structures of two FDCA solvates, namely, FDCA dimethylformamide (DMF) disolvate, C6H4O5·2C3H7NO, (I), and FDCA dimethyl sulfoxide (DMSO) monosolvate, C6H4O5·C2H6OS, (II), are reported. Solvate (I) crystallizes in the orthorhombic Pbcn space group and solvate (II) crystallizes in the triclinic P\overline{1} space group. In (I), hydrogen bonds form between the carbonyl O atom in DMF and a hydroxy H atom in FDCA. Whilst in (II), the O atom in one DMSO molecule hydrogen bonds with hydroxy H atoms in two FDCA molecules. Combined with intermolecular S...O interactions, FDCA molecules form a two-dimensional network coordinated by DMSO.


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