PyCO2SYS v1.8: marine carbonate system calculations in Python

Oceanic dissolved inorganic carbon (TC) is the largest pool of carbon that substantially interacts with the atmosphere on human timescales. Oceanic TC is increasing through uptake of anthropogenic carbon dioxide (CO2), and seawater pH is decreasing as a consequence. Both the exchange of CO2 between the ocean and atmosphere and the pH response are governed by a set of parameters that interact through chemical equilibria, collectively known as the marine carbonate system. To investigate these processes, at least two of the marine carbonate system's parameters are typically measured – most commonly, two from TC, total alkalinity (AT), pH, and seawater CO2 fugacity (fCO2; or its partial pressure, pCO2, or its dry-air mole fraction, xCO2) – from which the remaining parameters can be calculated and the equilibrium state of seawater solved. Several software tools exist to carry out these calculations, but no fully functional and rigorously validated tool written in Python, a popular scientific programming language, was previously available. Here, we present PyCO2SYS, a Python package intended to fill this capability gap. We describe the elements of PyCO2SYS that have been inherited from the existing CO2SYS family of software and explain subsequent adjustments and improvements. For example, PyCO2SYS uses automatic differentiation to solve the marine carbonate system and calculate chemical buffer factors, ensuring that the effect of every modelled solute and reaction is accurately included in all its results. We validate PyCO2SYS with internal consistency tests and comparisons against other software, showing that PyCO2SYS produces results that are either virtually identical or different for known reasons, with the differences negligible for all practical purposes. We discuss insights that guided the development of PyCO2SYS: for example, the fact that the marine carbonate system cannot be unambiguously solved from certain pairs of parameters. Finally, we consider potential future developments to PyCO2SYS and discuss the outlook for this and other software for solving the marine carbonate system. The code for PyCO2SYS is distributed via GitHub (https://github.com/mvdh7/PyCO2SYS, last access: 23 December 2021) under the GNU General Public License v3, archived on Zenodo (Humphreys et al., 2021), and documented online (https://pyco2sys.readthedocs.io/en/latest/, last access: 23 December 2021).

THEORETICAL AND EXPERIMENTAL STUDY OF MACROMOLECULAR NANOSTRUCTURES BASED ON HEPARIN AND LANTHANOIDS

Исследование синтетических и природных материалов пригодных для создания наноносителей и их модификация обеспечит прорыв в лечении многих заболеваний. Хорошим выбором для создания наноносителей являются гликозаминогликаны (гепарин и его производные), благодаря их уникальным биологическим и физико-химическим особенностям. Формирование композиций было исследовано методом pH -метрического титрования при 37 °С на фоне 0,15 М NaCl. С использованием программы NewDALSFEK определены значимые формы и химические равновесия. В диапазоне pH от 2,7 до 5 образуется комплекс вида {[LnHep]}, где Hep - мономерное звено макромолекулы гепарина. Получены данные об устойчивости нанокомпозиций: lgβ[PrHep] = 4,27 ± 0,04, lgβ[SmHep] = 4,28 ± 0,03 , lgβ[EuHep] = 4,28 ± 0,03. Методом M06-HF в сочетании с базисным набором CSDZ+* выполнено квантово-химическое моделирование комплексов. Study of synthetic and natural materials suitable for the creation of nanocarriers and their modification will provide a breakthrough in the treatment of many diseases. Glycosaminoglycans (heparin and its derivatives) are a good choice for creating nanocarriers due to their unique biological and physicochemical properties. The complexation of Pr (III), Sm (III), Eu (III) with heparin anions was studied by potentiometric titration at 37 °C and an ionic strength of 0,15 M NaCl. Significant forms and chemical equilibria were determined using the NewDALSFEK program. In the pH range from 2,7 to 5 , a complex of the type {[LnHep]} is formed, where Hep is a monomeric unit of the heparin macromolecule. Data on the stability of nanocompositions were obtained: lgβ[PrHep] = 4,27 ±0,04, lgβ[SmHep] = 4,28±0,03, lgβ[EuHep] = 4,28±0,03. The M06-HF method in combination with the CSDZ+* basic set was used to perform quantum chemical modeling of the complexes.

Thermodynamics and Transport Properties

The fundamentals of thermodynamics are reviewed, focusing on the chemistry of high-temperature metals, oxides (slags), and salts. Thermochemical data are provided for important molten metals: the free energies of solution of alloy elements, and interaction coefficients. Standard free energies of reactions are also provided, so the reader may calculate important chemical equilibria. Example calculations are provided for the deoxidation of steel. The removal of sulfur and phosphorus are also described. The second half of the chapter considers fundamental aspects of important physical properties: viscosity, surface tension, diffusion, and thermal and electrical conductivity.

Thermochemistry of Polonium Evaporation from LBE

Polonium is formed in relatively large quantities in lead-bismuth eutectic (LBE) cooled nuclear systems. Because of its radiotoxicity and volatility, a good understanding of the chemical equilibria governing polonium release from LBE is required. In this work, a set of thermochemical data is derived for the chemical species involved in the equilibrium between a solution of polonium in LBE and its vapor in inert conditions. The data were obtained by matching thermochemical models with experimental vapor pressure measurements and ab initio results. The dilute-limit activity coefficient of dissolved polonium in LBE is estimated, as well as the solubility of solid lead polonide in LBE. The results indicate that polonium evaporates from LBE according to the experimentally determined Henry’s law, up to dissolved polonium concentrations well above that expected in LBE cooled nuclear systems.

Generalized Chemical Equilibrium Constant of Formaldehyde Oligomerization

Formaldehyde reacts with solvents that contain hydroxyl groups (R–OH) in oligomerization reactions to oxymethylene oligomers (R–(OCH2)n–OH). The chemical equilibria of these reactions have been studied in the literature for water, for the mono-alcohols methanol, ethanol, and 1-butanol, as well as for the diols ethylene glycol and 1,4-butynediol. In the present work, the collective data were analyzed. It was found that the prolongation of the oxymethylene chains by the addition of formaldehyde can be described very well with a generalized chemical equilibrium constant Kx,n≥2R–OH, which is independent of the substructure (R) of the solvent. This holds for the oligomerization reactions leading to R–(OCH2)n–OH with n ≥ 2. The chemical equilibrium constant Kx,1R–OH of the reaction of formaldehyde with the solvent R–OH depends on the solvent, but simple trends are observed. The hypotheses of the existence of a generalized chemical equilibrium constant Kx,n≥2R–OH was tested for the reactions of formaldehyde with ethanol and 1-propanol, for which neither Kx,1R–OH nor Kx,nR–OH was previously available. The corresponding equilibria were studied by 13C NMR spectroscopy and the equilibrium constants were determined. A novel method was developed and used in these studies to obtain data on Kx,1R–OH by NMR spectroscopy, which is difficult because of the low amount of molecular formaldehyde. It was found that the generalized equilibrium constant is even valid for the acid-catalyzed formation of poly(oxymethylene) dimethyl ethers (OME).

NMR of Natural Products as Potential Drugs

This review outlines methods to investigate the structure of natural products with emphasis on intramolecular hydrogen bonding, tautomerism and ionic structures using NMR techniques. The focus is on 1H chemical shifts, isotope effects on chemical shifts and diffusion ordered spectroscopy. In addition, density functional theory calculations are performed to support NMR results. The review demonstrates how hydrogen bonding may lead to specific structures and how chemical equilibria, as well as tautomeric equilibria and ionic structures, can be detected. All these features are important for biological activity and a prerequisite for correct docking experiments and future use as drugs.

PyCO2SYS v1.7: marine carbonate system calculations in Python

Oceanic dissolved inorganic carbon (TC) is the largest pool of carbon that interacts considerably with the atmosphere on human timescales. Oceanic TC is increasing through uptake of anthropogenic carbon dioxide (CO2), and seawater pH is decreasing as a consequence. Both the exchange of CO2 between ocean and atmosphere and the pH response are governed by a set of parameters that interact through chemical equilibria, collectively known as the marine carbonate system. To investigate these processes, at least two of the marine carbonate system's parameters are typically measured – most commonly, two from TC, total alkalinity (AT), pH, and seawater CO2 fugacity (fCO2; or its partial pressure, pCO2, or its dry-air mole fraction, xCO2) – from which the remaining parameters can be calculated and the equilibrium state of seawater solved. Several software tools exist to carry out these calculations, but no fully functional and rigorously validated tool was previously available for Python, a popular scientific programming language. Here, we present PyCO2SYS, a Python package intended to fill this capability gap. We describe the elements of PyCO2SYS that have been inherited from the existing CO2SYS family of software and explain subsequent adjustments and improvements. For example, PyCO2SYS uses automatic differentiation to solve the marine carbonate system and calculate chemical buffer factors, ensuring that the effect of every solute and reaction is accurately included in all its results. We validate PyCO2SYS with internal consistency tests and comparisons against other software, showing that PyCO2SYS produces results that are either virtually identical or different for known reasons, with the differences negligible for all practical purposes. We discuss new insights that arose during the development process, for example that the marine carbonate system cannot be unambiguously solved from the total alkalinity and carbonate ion parameter pair. Finally, we consider potential future developments to PyCO2SYS and discuss the outlook for this and other software for solving the marine carbonate system. The code for PyCO2SYS is distributed via GitHub (https://github.com/mvdh7/PyCO2SYS) under the GNU General Public License v3, archived on Zenodo (Humphreys et al., 2021), and documented online (https://PyCO2SYS.readthedocs.io).

Calculations of Complex Chemical Reaction Equilibria using Free Energy Minimization and Arc-Length Continuation

In the present paper, we determine the chemical equilibrium compositions for two combustion reactions involving either hydrazine or propane at fixed high pressure and temperature values using several computational approaches. Then, we compute the chemical equilibria for reacting systems under a multitude of temperature and pressure conditions and various initial system compositions. These sensitivity analyses are based on a combination of the method of Lagrangian multipliers and the arc-length continuation technique. Indeed, three industrially relevant case studies are elucidated: (1) the synthesis of ammonia using the Haber process, (2) the gasification of a typical biomass surrogate: glucose using steam and (3) the gasification of cellulose using steam. For all the above reacting systems, our results are benchmarked against their counterparts obtained either from the ubiquitous process simulator: ASPEN-Plus® or from data available in the open literature.