Thirty years after the seminal contribution by Warshel and Levitt, we review the state of the art of combined quantum-mechanics/molecular-mechanics (QM/MM) methods, with a focus on biomolecular systems. We provide a detailed overview of the methodology of QM/MM calculations and their use within optimization and simulation schemes. A tabular survey of recent applications, mostly to enzymatic reactions, is given.

QM/MM Methods for Biological Systems

Calcium Silicate Hydrate from Dry to Saturated State: Structure, Dynamics and Mechanical Properties

Electronic and vibrational properties of chemically modified single-wall carbon nanotubes

Here we fabricated a novel nanocomposite HZO-201, an encapsulated nanosized hydrous zirconium oxide (HZO) within a commercial porous polystyrene anion exchanger D201, for highly efficient defluoridation of water. HZO-201 exhibited much higher preference than activated alumina and D201 toward fluoride removal when competing anions (chloride, sulfate, nitrate, and bicarbonate) coexisted at relatively high levels. Fixed column adsorption indicated that the effective treatable volume of water with HZO-201 was about 7-14 times as much as with D201 irrespective of whether synthetic solution or groundwater was the feeding solution. In addition, HZO-201 could treat >3000 BV of the acidic effluent (around 3.5 mg F(-)/L) per run at pH 3.5, compared to only ∼4 BV with D201. The exhausted HZO-201 could be regenerated by NaOH solution for repeated use without any significant capacity loss. Such attractive performance of HZO-201 resulted from its specific hybrid structure, that is, the host anion exchanger D201 favors the preconcentration of fluoride ions inside the polymer based on the Donnan principle, and the encapsulated nanosized HZO exhibits preferable sequestration of fluoride through specific interaction, as further demonstrated by XPS spectra. The influence of solution pH, competitive anions, and contact time was also examined. The results suggested that HZO-201 has a great potential in efficient defluoridation of groundwater and acidic mine drainage.

Enhanced Removal of Fluoride by Polystyrene Anion Exchanger Supported Hydrous Zirconium Oxide Nanoparticles

chemisorption of water molecules onto the silica surface, forming silanol (SiOH) groups at a concentration consistent with experimental data. Water penetration and silanol formation 7-8 A below the outermost oxygen are observed. Because of the dissociative nature of the water potential, formation of hydronium ions is allowed, and, whereas seldom observed in the simulations of bulk water, hydronium ions are formed during the reactions causing the formation of the silanols. The formation of hydronium ions has also been observed in ab initio calculations of water adsorption onto silica surfaces. The time evolution of the reactions involving hydronium ions in our MD simulations is similar to that observed in first-principles MD calculations. Hydronium ions offer a mechanism by which initially singly coordinated terminal oxygen (Si-O - ) receives a H + ion from a relatively distant chemisorbed H2O molecule via multiple H + ion transfer, creating two SiOH sites.

https://pubs.acs.org/doi/pdf/10.1021/jp8015134

Dissociative Chemisorption of Water onto Silica Surfaces and Formation of Hydronium Ions

We have performed large-scale molecular dynamics simulations of the polymerization of silicic acid in aqueous solution using the potential developed by Fueston and Garofalini [J. Phys. Chem. 1990, 94, 5351]. Seventeen simulations, with different water-to-silicon ratios and silicic acid concentrations, were each run for between 1.6 and 12.5 ns, at temperatures of 1500, 2000, and 2500 K. Water clearly acts as a catalyst in these simulations. When the water-to-silicon ratio is large, we find that the initial stages of the polymerization process are dominated by the conversion of monomers to dimers and addition of monomers to small clusters, while at longer times cluster−cluster aggregation is observed. Using data from simulations at different temperatures, the activation energies of condensation between silicic acid monomers were calculated at different water-to-silicon ratios and found to compare favorably with experimental results; an extrapolation (at constant density) of simulated reaction rates to ambie...

Molecular dynamics simulations of the polymerization of aqueous silicic acid and analysis of the effects of concentration on silica polymorph distributions, growth mechanisms, and reaction kinetics

The extraction kinetics and equilibrium concentrations of caffeine and 3-chlorogenic acid (3-CGA) in cold brew coffee were investigated by brewing four coffee samples (dark roast/medium grind, dark roast/coarse grind, medium roast/medium grind, medium roast/coarse grind) using cold and hot methods. 3-CGA and caffeine were found at higher concentrations in cold brew coffee made with medium roast coffees, rather than dark roast. The grind size did not impact 3-CGA and caffeine concentrations of cold brew samples significantly, indicating that the rate determining step in extraction for these compounds did not depend on surface area. Caffeine concentrations in cold brew coarse grind samples were substantially higher than their hot brew counterparts. 3-CGA concentrations and pH were comparable between cold and hot brews. This work suggests that the difference in acidity of cold brew coffee is likely not due to 3-CGA or caffeine concentrations considering that most acids in coffee are highly soluble and extract quickly. It was determined that caffeine and 3-CGA concentrations reached equilibrium according to first order kinetics between 6 and 7 hours in all cold brew samples instead of 10 to 24 hours outlined in typical cold brew methods.

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The Effect of Time, Roasting Temperature, and Grind Size on Caffeine and Chlorogenic Acid Concentrations in Cold Brew Coffee

Standard enthalpies of formation, ionization potentials, electron affinities, and band gaps of finite length [5,5] armchair and [9,0] zigzag single-walled carbon nanotubes (SWNTs) capped with C30 hemispheres obtained by halving the C60 fullerene have been computed at the B3LYP/6-311G* level of theory. Properties of SWNTs are found to depend strongly on the tube length and, in the case of the [9,0] zigzag species, on the relative orientation of the caps. The metallic character of an uncapped infinite length [5,5] armchair SWNT manifests itself in the oscillatory dependence of the properties of capped finite length tubes on their size. An infinite-length [9,0] zigzag SWNT is predicted to be a semiconductor rather than a metal irrespective of the presence of caps. The present results underscore the slow convergence of SWNT properties with respect to the tube length and uncover small but significant radial distortions along the long axes of SWNTs.

Electronic structures and energetics of [5,5] and [9,0] single-walled carbon nanotubes.

The acidity and antioxidant activity of cold brew coffee were investigated using light roast coffees from Brazil, two regions of Ethiopia, Columbia, Myanmar, and Mexico. The concentrations of three caffeoylquinic acid (CQA) isomers were also determined. Cold brew coffee chemistry was compared to that of hot brew coffee prepared with the same grind-to-coffee ratio. The pH values of the cold and hot brew samples were found to be comparable, ranging from 4.85 to 5.13. The hot brew coffees were found to have higher concentrations of total titratable acids, as well as higher antioxidant activity, than that of their cold brew counterparts. It was also noted that both the concentration of total titratable acids and antioxidant activity correlated poorly with total CQA concentration in hot brew coffee. This work suggests that the hot brew method tends to extract more non-deprotonated acids than the cold brew method. These acids may be responsible for the higher antioxidant activities observed in the hot brew coffee samples.

/pdf/acidity-and-antioxidant-activity-of-cold-brew-coffee-2fiznewg2k.pdf

Acidity and Antioxidant Activity of Cold Brew Coffee.

The role of roasting in cold brew coffee chemistry is poorly understood. The brewing temperature influences extraction processes and may have varying effects across the roast spectrum. To understand the relationship between brew temperature and roast temperature, hot and cold brew coffees were prepared from Arabica Columbian coffee beans roasted to light, medium, and dark levels. Chemical and physical parameters were measured to investigate the relationships among degree of roast, water temperature, and key characteristics of resulting coffees. Cold brew coffees showed differential extraction marked by decreased acidity, lower concentration of browned compounds, and fewer TDS indicating that cold water brewing extracts some compounds less effectively than hot water brewing. Compounds in coffee did exhibit sensitivity to degree of roast, with darker roasts resulting in decreased concentrations for both hot and cold brew coffees. Total antioxidant capacity (TAC) was only sensitive to degree of roast in cold brew coffees, while hot brew coffees had a constant TAC for all three roast levels. This indicates that the solid bean matrix and its chemical constituents interact with cold water differently than with hot water. Surface wetting, pore dynamics, and solubility all contribute to the extraction potential during brewing and are all functions of water temperature.

/pdf/physiochemical-characteristics-of-hot-and-cold-brew-coffee-599uptgf7v.pdf

Niny Z. Rao

Papers

Molecular dynamics simulations of the polymerization of aqueous silicic acid and analysis of the effects of concentration on silica polymorph distributions, growth mechanisms, and reaction kinetics

The Effect of Time, Roasting Temperature, and Grind Size on Caffeine and Chlorogenic Acid Concentrations in Cold Brew Coffee

Electronic structures and energetics of [5,5] and [9,0] single-walled carbon nanotubes.

Acidity and Antioxidant Activity of Cold Brew Coffee.

Physiochemical Characteristics of Hot and Cold Brew Coffee Chemistry: The Effects of Roast Level and Brewing Temperature on Compound Extraction.