Prediction of the pKa's of Hydrated Metal Carbonates and Bicarbonates for Mg, Ca, Mn, Fe, Co, Ni, Cu, and Zn Dications

The gas- and aqueous-phase acidities of hydrated metal dication carbonates, bicarbonates, and hydroxide complexes M(CO3)(H2O)n for n = 1 to 3, M(HCO3)2, M(HCO3)2(H2O)2, M(HCO3)(OH), and M(HCO3)(H2O)2(OH) for M = Mg, Ca, Mn, Fe, Co, Ni, Cu, and Zn were calculated at the CCSD(T)/aug-cc-pwCVDZ/cc-pwCVDZ level in the gas phase and at the B3LYP/aug-cc-pVTZ/cc-pVTZ(-PP) level with the COSMO self-consistent reaction field (SCRF) method in the aqueous phase. The composite correlated molecular orbital theory G3(MP2) and G3(MP2)B3 methods were used to predict the pKa's of the Mg structures and cis-cis carbonic acid to provide additional benchmarks. Using values scaled to experiment for H2CO3, the pKa's of bicarbonate ligands in group 2 and transition-metal complexes were compared to carbonic acid to gauge the effect of the metal complex on the bicarbonate. The group 2 metal complexes M(HCO3)2 and M(HCO3)(OH) decreased the acidity of the bicarbonate ligands, whereas their dihydrates were even less acidic. The transition-metal di-bicarbonate and bicarbonate hydroxide complexes generally made the bicarbonate more acidic especially when reduction of the metal occurs consistent with electron donation from the ligands; this is accompanied by spin transfer which typically increases in the order Mn < Fe < Co < Ni < Cu. The transition-metal dihydrates were less acidic than carbonic acid. Using values scaled to experiment for hydrated metal dications, the pKa's of water coordinated to group 2 and transition-metal complexes were generally more acidic than the hydrated metal dications, with the exception of Ca bicarbonate dihydrate, Co carbonate, Ni di-bicarbonate dihydrate, and Cu bicarbonate hydroxide di-bicarbonate.

Hydrogen chloride (HCl) at ground sites during CalNex 2010 and insight into its thermodynamic properties

Gas phase hydrogen chloride (HCl) was measured at Pasadena and San Joaquin Valley (SJV) ground sites in California during May and June 2010 as part of the CalNex study. Observed mixing ratios were on average 0.83 ppbv at Pasadena, ranging from below detection limit (0.055 ppbv) to 5.95 ppbv, and were on average 0.084 ppbv at SJV with a maximum value of 0.776 ppbv. At both sites, HCl levels were highest during midday and shared similar diurnal variations with HNO3. Coupled phase partitioning behavior was found between HCl/Cl- and HNO3/NO3 - using thermodynamic modelling and observations. Regional modeling of Cl- and HCl using CMAQ captures some of the observed relationships but underestimates measurements by a factor of 5 or more. Chloride in the 2.5-10 μm size range in Pasadena was sometimes higher than sea salt abundances, based on co-measured Na+, implying that sources other than sea salt are important. The acid-displacement of HCl/Cl- by HNO3/NO3 - (phase partitioning of semi-volatile acids) observed at the SJV site can only be explained by aqueous phase reaction despite low RH conditions and suggests the temperature dependence of HCl phase partitioning behavior was strongly impacted by the activity coefficient changes under relevant aerosol conditions (e.g., high ionic strength). Despite the influence from activity coefficients, the gas-particle system was found to be well constrained by other stronger buffers and charge balance so that HCl and Cl- concentrations were reproduced well by thermodynamic models.

Ursolic acid as a potential inhibitor of Mycobacterium tuberculosis cytochrome bc1 oxidase-a molecular modelling perspective

The escalating burden of tuberculosis disease and drastic effects of current medicine has stimulated a search for alternative drugs. A medicinal plant Warburgia salutaris has been reported to possess inhibitory properties against M. tuberculosis. In this study, we apply computational methods to investigate the probability of W. salutaris compounds as potential inhibitors of M. tuberculosis QcrB protein. We performed molecular docking, molecular dynamics simulations, radius of gyration, principal component analysis (PCA), and molecular mechanics-generalized born surface area (MM-GBSA) binding-free energy calculations in explicit solvent to achieve our objective. The results suggested that ursolic acid (UA) and ursolic acid acetate (UAA) could serve as preferred potential inhibitors of mycobacterial QcrB compared to lansoprazole sulphide (LSPZ) and telacebec (Q203)-UA and UAA have a higher binding affinity to QcrB compared to LSPZ and Q203 drugs. UA binding affinity is attributed to hydrogen bond formation with Val120, Arg364 and Arg366, and largely resonated from van der Waals forces resulting from UA interactions with hydrophobic amino acids in its vicinity. UAA binds to the porphyrin ring binding site with higher binding affinity compared to LSPZ. The binding affinity results primarily from van der Waals forces between UAA and hydrophobic residues of QcrB in the porphyrin ring binding site where UAA binds competitively. UA and UAA formed stable complexes with the protein with reduced overall residue mobility, consequently supporting the magnitude of binding affinity of the respective ligands. UAA could potentially compete with the porphyrin ring for the binding site and deprive the mycobacterial cell from oxygen, consequently disturbing mycobacterial oxygen-dependent metabolic processes. Therefore, discovery of a compound that competes with porphyrin ring for the binding site may be useful in QcrB pharmocological studies. UA proved to be a superior compound, although its estimated toxicity profile revealed UA to be hepatotoxic within acceptable parameters. Although preliminary findings of this report still warrant experimental validation, they could serve as a baseline for the development of new anti-tubercular drugs from natural resources that target QcrB.

Implicit Solvation Methods for Catalysis at Electrified Interfaces

Implicit solvation is an effective, highly coarse-grained approach in atomic-scale simulations to account for a surrounding liquid electrolyte on the level of a continuous polarizable medium. Originating in molecular chemistry with finite solutes, implicit solvation techniques are now increasingly used in the context of first-principles modeling of electrochemistry and electrocatalysis at extended (often metallic) electrodes. The prevalent ansatz to model the latter electrodes and the reactive surface chemistry at them through slabs in periodic boundary condition supercells brings its specific challenges. Foremost this concerns the difficulty of describing the entire double layer forming at the electrified solid–liquid interface (SLI) within supercell sizes tractable by commonly employed density functional theory (DFT). We review liquid solvation methodology from this specific application angle, highlighting in particular its use in the widespread ab initio thermodynamics approach to surface catalysis. Notably, implicit solvation can be employed to mimic a polarization of the electrode’s electronic density under the applied potential and the concomitant capacitive charging of the entire double layer beyond the limitations of the employed DFT supercell. Most critical for continuing advances of this effective methodology for the SLI context is the lack of pertinent (experimental or high-level theoretical) reference data needed for parametrization.

Dissociation of HCl in water nanoclusters: an energy decomposition analysis perspective

As known, small HCl-water nanoclusters display a particular dissociation behaviour, whereby at least four water molecules are required for the ionic dissociation of HCl. In this work, we examine how intermolecular interactions promote the ionic dissociation of such nanoclusters. To this end, a set of 45 HCl-water nanoclusters with up to four water molecules is introduced. Energy decomposition analysis based on absolutely localized molecular orbitals (ALMO-EDA) is employed in order to study the importance of frozen interaction, dispersion, polarization, and charge-transfer for the dissociation. The vertical ALMO-EDA scheme is applied to HCl-water clusters along a proton-transfer coordinate varying the amount of spectator water molecules. The corresponding ALMO-EDA results show a clear preference for the dissociated cluster only in the presence of four water molecules. Our analysis of adiabatic ALMO-EDA results reveals a push-pull mechanism for the destabilization of the HCl bond based on the synergy between forward and backward charge-transfer.

Density functional theory study on the initial reactions of d-Xylose and d-Xylulose dehydration to furfural

The mechanism of the initial reactions in the acid-catalytic conversion of d-xylose/d-xylulose to furfural was studied with density functional theory. The reactions included mutual transformations among d-xylose, d-xylulose and the intermediate of 1,2-enediol. The catalytic performances of several acids including H₂SO₄, HNO₃, HCl, HBr and HI, and the solvent effects of water and THF (tetrahydrofuran) were studied. A simplified kinetic model of the d-xylose/d-xylulose-to-furfural conversion in water solvent was built, with the assumption that the conversion from 1,2-enediol to furfural was the rate-limiting step and could be treated as one-step reaction. The simulation can well fit the experimental regulation, which verifies the rationality of the model simplification. The dominant reaction pathways from d-xylose/d-xylulose to furfural were deduced based on the calculated energy barriers and corresponding reaction rate constants, with different acid catalysis and reaction mediums.

First-Principles Simulations of CuCl in High-Temperature Water Vapor

Experimental data suggest that the solubility of copper in high-temperature water vapor is controlled by the formation of hydrated clusters of the form CuCl(H₂O)_n, where the average number of water molecules in the cluster generally increases with increasing density [Migdisov, A. A.; et al. Geochim. Cosmochim. Acta 2014, 129, 33-53]. However, the precise nature of these clusters is difficult to probe experimentally. Moreover, there are some discrepancies between experimental estimates of average cluster size and prior simulation work [Mei, Y. Geofluids 2018, 2018, 4279124]. We have performed first-principles Monte Carlo (MC) and molecular dynamics (MD) simulations to explore these clusters in finer detail. We find that molecular dynamics is not the most appropriate technique for studying aggregation in vapor phases, even at relatively high temperatures. Specifically, our MD simulations exhibit substantial problems in adequately sampling the equilibrium cluster size distribution. In contrast, MC simulations with specialized cluster moves are able to accurately sample the phase space of hydrogen-bonding vapors. At all densities, we find a stable, slightly distorted linear H₂O-Cu-Cl structure, which is in agreement with the earlier simulations, surrounded by a variable number of water molecules. The surrounding water molecules do not form a well-defined second solvation shell but rather a loose network of hydrogen-bonded water with molecular CuCl on the outside edge of the water cluster. We also find a broad distribution of hydration numbers, especially at higher densities. In contrast to previous simulation work but in agreement with experimental data, we find that the average hydration number substantially increases with increasing density. Moreover, the value of the hydration number depends on the choice of cluster definition.

Catalytic strategy for conversion of fructose to organic dyes, polymers, and liquid fuels

We report a process to produce a versatile platform chemical from biomass-derived fructose for organic dye, polymer, and liquid fuel industries. An aldol-condensed chemical (HAH) is synthesized as a platform chemical from fructose by catalytic reactions in acetone/water solvent with non-noble metal catalysts (e.g., HCl, NaOH). Then, selective reactions (e.g., etherification, reduction, dimerization) of the functional groups, such as enone and hydroxyl groups, in the HAH molecule enable applications in organic dyes and polyether precursors. High yields of target products, such as 5-(hydroxymethyl) furfural (HMF) (85.9% from fructose) and HAH (86.3% from HMF) are achieved by sequential dehydration and aldol-condensation with a simple purification process (>99% HAH purity). The use of non-noble metal catalysts, the high yield of each reaction, and the simple purification of the target product allow for beneficial economics of the process. Techno-economic analysis indicates that the process produces HAH at minimum selling price (MSP) of $1958/ton. The MSP of HAH product allows the economic viability of applications in organic dye and polyether markets by replacing its counterparts, such as anthraquinone ($3200-$3900/ton) and bisphenol-A ($1360-$1720/ton).

Valorization of lignocellulosic fibres of paper waste into levulinic acid using solid and aqueous Brønsted acid

This study aims to produce levulinic acid (LA) from paper towel waste in environment-friendly and economically feasible conditions, and evaluate the difference using solid and aqueous Brønsted acids. Direct dehydration of glucose to LA required sufficiently strong Brønsted acidity, where Amberlyst 36 demonstrated rapid production of approximately 30Cmol% of LA in 20min. However, the maximum yield of LA was limited by mass transfer. In contrast, the yield of LA gradually increased to over 40Cmol% in 1M H₂SO₄ at 150°C in 60min. The SEM images revealed the conversion in dilute acids under microwave at 150°C resulting in swelling structures of cellulose, which were similar to the pre-treatment process with concentrated acids. Further increase in reaction temperature to 200°C significantly shortened the reaction time from 60 to 2.5min, which saved the energy cost as revealed in preliminary cost analysis.

Acid Dissociation in HCl-Water Clusters is Temperature Dependent and Cannot be Detected Based on Dipole Moments

The dissociation of acids in aqueous environments at low temperatures in the presence of a limited amount of water is underlying a wealth of processes from atmospheric to interstellar science. For the paradigmatic case of HCl(H_{2}O)_{n} clusters, our extensive ab initio path integral simulations quantify in terms of free energy differences and barriers that n=4 water molecules are indeed required to dissociate HCl at low temperatures. Increasing the temperature, however, reverses the process and thus counteracts dissociation by fluctuation-driven recombination. The size of the electric dipole moment is shown to not correlate with the acid being in its dissociated or molecular state, thus rendering its measurement as a function of n unable to detect the dissociation transition.

Approaches for calculating solvation free energies and enthalpies demonstrated with an update of the FreeSolv database

Solvation free energies can now be calculated precisely from molecular simulations, providing a valuable test of the energy functions underlying these simulations. Here, we briefly review "alchemical" approaches for calculating the solvation free energies of small, neutral organic molecules from molecular simulations, and illustrate by applying them to calculate aqueous solvation free energies (hydration free energies). These approaches use a non-physical pathway to compute free energy differences from a simulation or set of simulations and appear to be a particularly robust and general-purpose approach for this task. We also present an update (version 0.5) to our FreeSolv database of experimental and calculated hydration free energies of neutral compounds and provide input files in formats for several simulation packages. This revision to FreeSolv provides calculated values generated with a single protocol and software version, rather than the heterogeneous protocols used in the prior version of the database. We also further update the database to provide calculated enthalpies and entropies of hydration and some experimental enthalpies and entropies, as well as electrostatic and nonpolar components of solvation free energies.

An efficient approach to ab initio Monte Carlo simulation

We present a Nested Markov chain Monte Carlo (NMC) scheme for building equilibrium averages based on accurate potentials such as density functional theory. Metropolis sampling of a reference system, defined by an inexpensive but approximate potential, was used to substantially decorrelate configurations at which the potential of interest was evaluated, thereby dramatically reducing the number needed to build ensemble averages at a given level of precision. The efficiency of this procedure was maximized on-the-fly through variation of the reference system thermodynamic state (characterized here by its inverse temperature β(0)), which was otherwise unconstrained. Local density approximation results are presented for shocked states of argon at pressures from 4 to 60 GPa, where-depending on the quality of the reference system potential-acceptance probabilities were enhanced by factors of 1.2-28 relative to unoptimized NMC. The optimization procedure compensated strongly for reference potential shortcomings, as evidenced by significantly higher speedups when using a reference potential of lower quality. The efficiency of optimized NMC is shown to be competitive with that of standard ab initio molecular dynamics in the canonical ensemble.

Predicting pKa in Implicit Solvents: Current Status and Future Directions

Computational prediction of condensed phase acidity is a topic of much interest in the field today. We introduce the methods available for predicting gas phase acidity and pKas in aqueous and non-aqueous solvents including high-level electronic structure methods, empirical linear free energy relationships (LFERs), implicit solvent methods, explicit solvent statistical free energy methods, and hybrid implicit–explicit approaches. The focus of this paper is on implicit solvent methods, and we review recent developments including new electronic structure methods, cluster-continuum schemes for calculating ionic solvation free energies, as well as address issues relating to the choice of proton solvation free energy to use with implicit solvation models, and whether thermodynamic cycles are necessary for the computation of pKas. A comparison of the scope and accuracy of implicit solvent methods with ab initio molecular dynamics free energy methods is also presented. The present status of the theory and future directions are outlined.