CHNOSZ

Publications citing CHNOSZ

The linked citations are followed by a brief description of the usage of CHNOSZ. Hover over the links to show the titles.

Journal Articles (Property Calculations)

  1. Hörbrand et al. (2018) — Calculation of log10K for dissociation reactions of aqueous complexes for comparison with other databases
  2. Tarnas et al. (2018) — Henry's Law constant for H2 at temperatures and pressures in the ancient Martian crust
  3. Dahle et al. (2018) — ΔG0r at temperatures and pressures of mixing seawater and hydrothermal fluid (used to modify a thermodynamic database for The Geochemist's Workbench (GWB))
  4. Liu et al. (2018) — Equilibrium constants and activity coefficients for reactions involving aqueous tungsten species (350 °C, 100 MPa)
  5. Voigt et al. (2018) — Properties of aqueous species used in calculation of equilibrium constants for dissolution of zeolite-group minerals
  6. Li et al. (2018) — Heat capacities of aqueous ions over a temperature range of 273.15-523.15 K
  7. Wang et al. (2018) — Vapor pressure of H2O at 25 to 435 °C and 1000 bar
  8. Reed et al. (2017) — Standard Gibbs energy of methane oxidation by oxygen
  9. Zaarur et al. (2017) — Standard Gibbs energies for acetate-yielding oxidation reactions in dissimilatory sulfate reduction
  10. Möller et al. (2017) — logK of anorthite-albite ion exchange reaction (0 to 150 °C)
  11. Gao et al. (2017) — Heat capacities of Rb+, Cs+, Cl- (273.15-523.15 K)
  12. Bristow et al. (2017) — Equilibrium constants of iron oxide reactions adjusted for temperature and salinity (probably using the ionic strength setting in subcrt())
  13. Louca et al. (2016) — Standard Gibbs energies of reactions (ΔGro) in a metabolic network
  14. Li et al. (2016) — Heat capacities of aqueous ions over a temperature range of 273.15-523.15 K
  15. Urschel et al. (2016) — Energy available from reduction of elemental sulfur
  16. Canovas and Shock (2016) — CHNOSZ as a tool to explore the geobiochemistry of the citric acid cycle
  17. Pearce and Pudritz (2016) — (Standard) Gibbs free energy of formation of nucleobases and precursors (0 to 500 °C) (database limitations noted: no formamide or non-aqueous HCN)
  18. Harrold et al. (2016) — Standard-state Gibbs free energy and logarithm of the reaction quotient for oxidation of thiosulfate (S2O32-)
  19. Neveu and Desch (2015) — Molar volumes of solutes and minerals in the OBIGT database
  20. Li et al. (2015) — Heat capacities of aqueous ions over a temperature range of 273.15-523.15 K
  21. Reed et al. (2015) — Standard Gibbs energies of metabolic reactions in the deep ocean (275.15 K, 210 bar)
  22. Dahle et al. (2015) — ΔG0r at temperatures and pressures of mixing seawater and hydrothermal fluid (used to modify a thermodynamic database for GWB)
  23. Neveu et al. (2015) — Apparent molar heat capacity and volume of NaCl at subzero temperatures (-15 °C) and extrapolation down to 235 K using the IAPWS-95 equations
  24. Neveu et al. (2014) — Thermal expansivity and isothermal compressibility of water, equilibrium constants of mineral precipitation reactions (extrapolated down to 261 K), enthalpies of mineral (de)hydration reactions
  25. Reed et al. (2014) — Standard Gibbs free energy (ΔG0) for metabolic reactions in the Arabian Sea oxygen minimum zone (OMZ)
  26. Cobb et al. (2013) — Gibbs energy for species in Strecker-type synthesis of amino acids (0-350 °C; database limitations: no glycolaldehyde)
  27. De Lucia et al. (2012) — Assessment of pressure effect on mineral formation equilibrium constants (1-200 bar)
  28. Klevenz et al. (2011) — OBIGT database used to compile a database for GWB (0 to 400 °C at 500 bar)
  29. Manyá and Antal (2009) — Heat capacity of NaCl(aq), HCl(aq), and NaOH(aq) calculated using the revised HKF model (298.15 to 493.15 K)

Journal Articles (Diagrams)

  1. Cheshire et al. (2018) — Eh–pH mosaic diagrams for Fe-Cr-Ni-H2O, Fe-S-H2O, and Fe-Cr-S-Ni-H2O from 25 to 300 °C and 1 to 160 bar (added data for chromite from Ziemniak et al., 2007)
  2. Matteo et al. (2018) — logaCO2–pH diagram for Ca-H2O-CO2 at PCO2 = 10-6 to 1 bar
  3. Schindelholz et al. (2018) — Eh–pH (Pourbaix) diagram for copper in 4 molal NaCl
  4. Schaller et al. (2017) — Activity phase diagrams for the Na–Al–CO2–H2O system; uses the mosaic() function to calculate the phase boundaries considering the effect of pH on Al and CO2 speciation
  5. Neveu et al. (2017) — logfH2–T predominance diagrams for C, N, and S species (0 to 200 °C) and pH–T stability diagram for biotite
  6. Caporuscio et al. (2017) — Eh–pH diagram for Cu–S–Cl–H2O (incl. copper, cuprite, chalcocite) at 200 and 300 °C
  7. Morrison et al. (2014) — Eh–pH mineral stability diagram for the Fe–S–O–H system
  8. Petit et al. (2013) — Potential-pH diagrams for carbon species (25 and 300 °C)

Journal Articles (Other Applications)

  1. Ghaffari et al. (2018) — (Supplemental Document to this article) Filtering BLAST hits by E-value and similarity score
  2. Lowe et al. (2017) — Fitting experimental heat capacity data for aqueous adenine using the revised HKF equations (see the adenine demo)
  3. Groah et al. (2016) — Differences in taxon relative abundance
  4. Castro-Nallar et al. (2015) — Differential species abundance in asthma-associated microbial communities (unspecified functions used in CHNOSZ, maybe for processing taxonomy files?)
  5. LeBlanc et al. (2015) — Derivation of higer taxonomic classifications within the NCBI taxonomy
  6. Castro-Nallar et al. (2015) — Differential species abundance in schizophrenia-associated oropharynx microbiomes
  7. Dodsworth et al. (2013) — Derive taxonomy fom BLASTP hits
  8. Hentscher and Bach (2012) — Relation between free energy (ΔrG) and affinity (Ar)

Journal Articles (Developer as Author)

  1. Dick (2017) — Basis species comparison and logaH2O–logfO2 diagrams for proteins in cancer and cell-culture experiments (see canprot vignettes)
  2. Dick and Shock (2013) — Relative abundances of microbial phyla in metastable equilibrium, and natural communities' distance from equilibrium
  3. Dick et al. (2013) — Metastable equilibrium ratios of methylphenanthrene isomers and MPI-1 maturity index (0 to 500 °C)
  4. LaRowe and Dick (2012) — CP° and ΔGf° of crystalline proteins using group additivity (0-140 °C)
  5. Dick and Shock (2011) — Relative stabilities of proteins at different locations in a Yellowstone hot spring (logaH2–T diagrams)
  6. Dick (2009) — Eh–pH and logfO2–logaH2O diagrams and metastable equilibrium abundances as a function of logfO2 for proteins in different subcellular compartments
  7. Dick (2008) — First paper describing CHNOSZ; comparison of relative stabilities of microbial cell surface-layer proteins

Theses

  1. Law (2018) — Carbonic acid dissociation constants at temperatures of thermal features in Yellowstone National Park
  2. Schmidt (2017) — Eh–pH diagrams for C–O–H, S–O–H and Fe–O–H systems
  3. Dahlquist (2017) — Eh–pH diagram for clay minerals (smectite is absent due to limitations of the database)
  4. Wang (2017) — Equilibrium constants for reactions in a graphite-saturated C–O–H fluid
  5. Rupe (2017) — Extract data from NCBI taxonomy files
  6. O'Donnell (2016) — Equilibrium constants of gas-aqueous reactions of CO2, H2S, and NH3
  7. Zohren (2016) — Filtering BLAST hits by length, similarity score, and E-value
  8. Heia (2016) — Henry's constant (gas generation in artificial maturation of source rock)
  9. Cobb (2013) — Gibbs energy for species in Strecker-type synthesis of amino acids (0-350 °C; database limitations: no isobutyraldehyde)
  10. Hentscher (2012) — Create a database of logKr values for use in GWB

Book Chapters

  1. Di Bonito et al. (2018) — CHNOSZ as an example of appearance of thermodynamic databases in R packages
  2. Witting (2018) — Counting atoms in chemical formulas for mass spectrometry-based metabolomics
  3. Bleam (2017) — Standard Gibbs energies for mineral solubility calculations
  4. Manning et al. (2013) — CHNOSZ as a program with a data file for equation-of-state coefficients for aqueous species

Conference Abstracts

  1. Prasad and Shock (2013) — Chemical affinities for comparing relative stabilities of proteins in methanogens

Preprints

  1. Peil et al. (2018) — CHNOSZ is part of an R application developed for protein domain analysis, alignment, and visualization
  2. Hamidieh (2018) — Check validity of chemical formulas of superconducting materials
  3. Dick (2015) — logfO2–logaH2O diagrams for the morphogen Shh and induced transcription factors

Technical Reports

  1. Choens et al. (2018) — Calculation of logK for laumontite dehydration (added data from Neuhoff and Bird, 2001) and construction of log(aCa+2/aH+2) - T diagrams
  2. Caporuscio et al. (2016) — Eh–pH diagram for Cu–S–Cl–H2O
  3. Zavarin et al. (2016) — Mentions availability of IAPWS-95 equations of state for H2O (Wagner and Pruss, 2002) in CHNOSZ
  4. Jové-Colón (2015) — Activity phase diagrams: logaH2O–logaSO4-2, logaSO4-2–T, pH–T
  5. Jové-Colón et al. (2014) — Phase stability diagrams of clays and zeolites (e.g. data added for smectite); effect on diagrams of updates for Al3+, SiO2, and kaolinite
  6. Lisle (2014) — Values of ΔG° and ΔGr for biogeochemical reactions
  7. Rutqvist et al. (2013) — Activity phase diagrams for the systems Ca–Al–SO4–H2O and Ca–Al–SiO2–SO4–H2O

Patents

  1. Groah et al. (2018) — One of a few packages used for exploratory analysis and differences in taxon abundances

R Packages

  1. LipidMS (2018) — (CRAN package by M. I. Alcoriza-Balaguer and J. C. Garcia-Canaveras) Chemical formula processing for lipidomics
  2. MatchWeiz (2016) — (github package by N. Shahaf) Using makeup() and as.chemical.formula() to parse the adduct formula from the CAMERA Bioconductor package and output a chemical formula
  3. ecipex (2014) — (CRAN package by A. Ipsen) Chemical formula processing

Websites

  1. Biostars (2018) — Using parent() and sciname() to get kingdom name from NCBI taxonomy ID
  2. StackOverflow (2017) — CHNOSZ as a package for thermodynamic functions for aqueous solutions
  3. StackOverflow (2017) — Using makeup() to parse a chemical formula (see also related questions in 2016 and 2015)
  4. StackOverflow (2016) — Read a protein sequence using read.fasta()
  5. Chemistry StackExchange (2015) — Equilibrium constant of sodium oxide hydration
  6. Chemistry StackExchange (2015) — CHNOSZ as a source of thermochemical data
  7. StackOverflow (2014) — Using the EF-Tu.aln example file to demonstrate a function to read FASTA files
  8. StackOverflow (2013) — R package that could be used to create a solid-liquid-gas phase diagram() (see also the density demo)
  9. R-help (2010) — Discussion of using makeup() for formula parsing
  10. R-packages (2009) — Announcement of CHNOSZ on R-packages mailing list

Please contact Jeffrey Dick with updates or corrections.

Last updated: 2018-11-06