[CHNOSZ-commits] r124 - in pkg/CHNOSZ: . inst vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Jan 31 16:07:37 CET 2017
Author: jedick
Date: 2017-01-31 16:07:36 +0100 (Tue, 31 Jan 2017)
New Revision: 124
Added:
pkg/CHNOSZ/vignettes/vig.css
Modified:
pkg/CHNOSZ/DESCRIPTION
pkg/CHNOSZ/inst/NEWS
pkg/CHNOSZ/vignettes/EOSregress.Rmd
pkg/CHNOSZ/vignettes/vig.bib
Log:
reduce size of EOSregress.html
Modified: pkg/CHNOSZ/DESCRIPTION
===================================================================
--- pkg/CHNOSZ/DESCRIPTION 2017-01-28 08:29:14 UTC (rev 123)
+++ pkg/CHNOSZ/DESCRIPTION 2017-01-31 15:07:36 UTC (rev 124)
@@ -1,6 +1,6 @@
-Date: 2017-01-28
+Date: 2017-01-29
Package: CHNOSZ
-Version: 1.0.8-13
+Version: 1.0.8-14
Title: Chemical Thermodynamics and Activity Diagrams
Author: Jeffrey Dick
Maintainer: Jeffrey Dick <j3ffdick at gmail.com>
Modified: pkg/CHNOSZ/inst/NEWS
===================================================================
--- pkg/CHNOSZ/inst/NEWS 2017-01-28 08:29:14 UTC (rev 123)
+++ pkg/CHNOSZ/inst/NEWS 2017-01-31 15:07:36 UTC (rev 124)
@@ -1,4 +1,4 @@
-CHANGES IN CHNOSZ 1.0.8-13 (2017-01-28)
+CHANGES IN CHNOSZ 1.0.8-14 (2017-01-29)
---------------------------------------
- Add "AA" as a keyword for preset species in basis() (cysteine,
Modified: pkg/CHNOSZ/vignettes/EOSregress.Rmd
===================================================================
--- pkg/CHNOSZ/vignettes/EOSregress.Rmd 2017-01-28 08:29:14 UTC (rev 123)
+++ pkg/CHNOSZ/vignettes/EOSregress.Rmd 2017-01-31 15:07:36 UTC (rev 124)
@@ -4,7 +4,9 @@
author: "Jeffrey M. Dick"
date: "`r Sys.Date()`"
output:
- tufte::tufte_html: default
+ tufte::tufte_html:
+ tufte_features: ["background", "italics"]
+ css: "vig.css"
tufte::tufte_handout:
citation_package: natbib
latex_engine: xelatex
Modified: pkg/CHNOSZ/vignettes/vig.bib
===================================================================
--- pkg/CHNOSZ/vignettes/vig.bib 2017-01-28 08:29:14 UTC (rev 123)
+++ pkg/CHNOSZ/vignettes/vig.bib 2017-01-31 15:07:36 UTC (rev 124)
@@ -1,624 +1,575 @@
-% This file was created with JabRef 2.11b4.
-% Encoding: ISO8859_1
+% Encoding: UTF-8
-
@Article{AD01,
- Title = {{E}lectrochemistry of copper in aqueous glycine solutions},
- Author = {Aksu, Serdar and Doyle, Fiona M.},
- Journal = {Journal of the Electrochemical Society},
- Year = {2001},
- Number = {1},
- Pages = {B51--B57},
- Volume = {148},
- Abstract = {Potential-pH equilibria and potentiodynamic polarization studies were used to examine the electrochemical behavior of copper in aqueous glycine solutions. Potential-pH diagrams for the copper-water-glycine system were derived at different total copper \{Cu-T\} and glycine \{L-T\} activities. The diagrams show that glycine significantly extended the solubility range of copper. Polarization experiments were conducted in deaerated and aerated aqueous solutions of 10(-2) M glycine with 10(-5) M cupric nitrate and 10(-1) M glycine with 10(-4) M cupric nitrate at pH values between 9 and 12. The results of these experiments are discussed in terms of the relevant potential-pH diagrams. Good correlations were observed. (C) 2000 The Electrochemical Society. All rights reserved.},
- Doi = {10.1149/1.1344532},
+ author = {Aksu, Serdar and Doyle, Fiona M.},
+ journal = {Journal of the Electrochemical Society},
+ title = {{E}lectrochemistry of copper in aqueous glycine solutions},
+ year = {2001},
+ volume = {148},
+ number = {1},
+ pages = {B51--B57},
+ doi = {10.1149/1.1344532},
}
@Article{AH97a,
- Title = {{G}roup additivity equations of state for calculating the standard molal thermodynamic properties of aqueous organic species at elevated temperatures and pressures},
- Author = {Amend, Jan P. and Helgeson, Harold C.},
- Journal = {Geochimica et Cosmochimica Acta},
- Year = {1997},
- Pages = {11 -- 46},
- Volume = {61},
- Abstract = {Group additivity equations of state for aqueous organic molecules have been generated by combining the revised Helgeson-Kirkham-Flowers (HKF) equations of state (Shock and Helgeson, 1988, 1990; Tanger and Helgeson, 1988; Shock et al., 1989, 1992) with experimental values of the standard molal properties of aqueous alkanes, alkanols, alkylbenzenes, carboxylic acids, amides, and amines. Equations of state parameters for the groups represented by -cn2 , -CH3, -CHCH3-, -C6H5, -CH2OH, -COOH, -CONH2, and -CH2NH2 were determined by regression of the experimental data. This procedure permits calculation of the standard molal thermodynamic properties of these groups at elevated tempera-tures and pressures. Although curves representing the apparent standard molal Gibbs free energies ( A G °) and enthalpies ( A H °) of formation, and the standard molal entropies (S °) of the groups as a function of temperature and pressure are respectively similar for each of them, the temperature dependence of the standard molal heat capacities (C~) and volumes (V°) of a number of the groups are quite different from one another. For example, the standard molal heat capacities of the hydrocarbon groups minimize with increasing temperature, but those of -CHEOH and -CH2NH2 maximize. Computed values of AG °, A H °, S °, C~, V °, and the equations of state parameters for the various groups were used together with group additivity relations to generate corresponding values of these properties for aqueous n-alkanes, 2-methylalkanes, n-alkylbenzenes, n-alkanols, n-carboxylic acids, n-amides, and n-amines at temperatures -< 250°C and pressures - 1 kbar. The validity and generality of the equations of state are supported by the fact that predicted equilibrium constants for liquid n-alkane solubility reactions in water compare favorably with experimental values reported in the literature for temperatures as high as 200°C. Furthermore, equilibrium constants for aqueous ethane coexisting with ethene at 325 and 350°C at 350 bars predicted from the equations of state are in close agreement with independently determined experimental values reported by Seewald (1994). The standard molal thermodynamic properties and equations of state parameters reported below provide the means to characterize the thermodynamic behavior of a wide variety of aqueous organic species involved in hydrothermal reactions at elevated temperatures and pressures.},
- Doi = {10.1016/S0016-7037(96)00306-7},
+ author = {Amend, Jan P. and Helgeson, Harold C.},
+ journal = {Geochimica et Cosmochimica Acta},
+ title = {{G}roup additivity equations of state for calculating the standard molal thermodynamic properties of aqueous organic species at elevated temperatures and pressures},
+ year = {1997},
+ volume = {61},
+ pages = {11 -- 46},
+ doi = {10.1016/S0016-7037(96)00306-7},
}
@Book{And05,
- Title = {{T}hermodynamics of {N}atural {S}ystems},
- Author = {Anderson, G. M.},
- Publisher = {Cambridge University Press},
- Year = {2005},
- Address = {Cambridge},
- Edition = {2nd},
- Abstract = {The fugacity was introduced by G.N. Lewis in 1901, and became widely used after the appearance of Thermodynamics, a very influential textbook by Lewis and Randall in 1923. Lewis describes the need for such a function in terms of an analogy with temperature in the attainment of equilibrium between phases. Just as equilibrium requires that heat must flow such that temperature is the same in all parts of the system, so matter must flow such that chemical potentials are also equalized. He referred to the flow of matter from one phase to another as an ?escaping tendency,? such as a liquid escaping to the gas form to achieve an equilibrium vapor pressure. He pointed out that in fact vapor pressure is equilibrated between phases under many conditions (and in fact is the basis for the isopiestic method of activity determinations, §5.8.4), and could serve as a good measure of escaping tendency if it behaved always as an ideal gas.},
- Pages = {648},
- Url = {http://www.worldcat.org/oclc/474880901}
+ author = {Anderson, G. M.},
+ publisher = {Cambridge University Press},
+ title = {{T}hermodynamics of {N}atural {S}ystems},
+ year = {2005},
+ address = {Cambridge},
+ edition = {2nd},
+ pages = {648},
+ url = {http://www.worldcat.org/oclc/474880901},
}
@Article{AA02,
- Title = {{T}he human plasma proteome - {H}istory, character, and diagnostic prospects},
- Author = {Anderson, N. Leigh and Anderson, Norman G.},
- Journal = {Molecular \& Cellular Proteomics},
- Year = {2002},
- Number = {11},
- Pages = {845--867},
- Volume = {1},
- Abstract = {The human plasma proteome holds the promise of a revolution in disease diagnosis and therapeutic monitoring provided that major challenges in proteomics and related disciplines can be addressed. Plasma is not only the primary clinical specimen but also represents the largest and deepest version of the human proteome present in any sample: in addition to the classical "plasma proteins," it contains all tissue proteins (as leakage markers) plus very numerous distinct immunoglobulin sequences, and it has an extraordinary dynamic range in that more than 10 orders of magnitude in concentration separate albumin and the rarest proteins now measured clinically. Although the restricted dynamic range of conventional proteomic technology (two-dimensional gels and mass spectrometry) has limited its contribution to the list of 289 proteins (tabulated here) that have been reported in plasma to date, very recent advances in multidimensional survey techniques promise at least double this number in the near future. Abundant scientific evidence, from proteomics and other disciplines, suggests that among these are proteins whose abundances and structures change in ways indicative of many, if not most, human diseases. Nevertheless, only a handful of proteins are currently used in routine clinical diagnosis, and the rate of introduction of new protein tests approved by the United States Food and Drug Administration (FDA) has paradoxically declined over the last decade to less than one new protein diagnostic marker per year. We speculate on the reasons behind this large discrepancy between the expectations arising from proteomics and the realities of clinical diagnostics and suggest approaches by which protein-disease associations may be more effectively translated into diagnostic tools in the future.},
- Doi = {10.1074/mcp.R200007-MCP200},
- Sn = {1535-9476},
+ author = {Anderson, N. Leigh and Anderson, Norman G.},
+ journal = {Molecular \& Cellular Proteomics},
+ title = {{T}he human plasma proteome - {H}istory, character, and diagnostic prospects},
+ year = {2002},
+ volume = {1},
+ number = {11},
+ pages = {845--867},
+ doi = {10.1074/mcp.R200007-MCP200},
+ sn = {1535-9476},
}
@Article{AA03,
- Title = {{T}he human plasma proteome: {H}istory, character, and diagnostic prospects (vol 1, pg 845, 2002)},
- Author = {Anderson, N. L. and Anderson, N. G.},
- Journal = {Molecular \& Cellular Proteomics},
- Year = {2003},
- Number = {1},
- Pages = {50--50},
- Volume = {2},
- Doi = {10.1074/mcp.A300001-MCP200},
- Sn = {1535-9476},
+ author = {Anderson, N. L. and Anderson, N. G.},
+ journal = {Molecular \& Cellular Proteomics},
+ title = {{T}he human plasma proteome: {H}istory, character, and diagnostic prospects (vol 1, pg 845, 2002)},
+ year = {2003},
+ volume = {2},
+ number = {1},
+ pages = {50--50},
+ doi = {10.1074/mcp.A300001-MCP200},
+ sn = {1535-9476},
}
@Article{AWP+09,
- Title = {{T}he {GAAS} {M}etagenomic {T}ool and {I}ts {E}stimations of {V}iral and {M}icrobial {A}verage {G}enome {S}ize in {F}our {M}ajor {B}iomes},
- Author = {Angly, Florent E. and Willner, Dana and Prieto-Dav\'o, Alejandra and Edwards, Robert A. and Schmieder, Robert and Vega-Thurber, Rebecca and Antonopoulos, Dionysios A. and Barott, Katie and Cottrell, Matthew T. and Desnues, Christelle and Dinsdale, Elizabeth A. and Furlan, Mike and Haynes, Matthew and Henn, Matthew R. and Hu, Yongfei and Kirchman, David L. and McDole, Tracey and McPherson, John D. and Meyer, Folker and Miller, R. Michael and Mundt, Egbert and Naviaux, Robert K. and Rodriguez-Mueller, Beltran and Stevens, Rick and Wegley, Linda and Zhang, Lixin and Zhu, Baoli and Rohwer, Forest},
- Journal = {PLoS Computational Biology},
- Year = {2009},
- Number = {12},
- Pages = {e1000593},
- Volume = {5},
- Abstract = {Metagenomic studies characterize both the composition and diversity of uncultured viral and microbial communities. BLAST-based comparisons have typically been used for such analyses; however, sampling biases, high percentages of unknown sequences, and the use of arbitrary thresholds to find significant similarities can decrease the accuracy and validity of estimates. Here, we present Genome relative Abundance and Average Size (GAAS), a complete software package that provides improved estimates of community composition and average genome length for metagenomes in both textual and graphical formats. GAAS implements a novel methodology to control for sampling bias via length normalization, to adjust for multiple BLAST similarities by similarity weighting, and to select significant similarities using relative alignment lengths. In benchmark tests, the GAAS method was robust to both high percentages of unknown sequences and to variations in metagenomic sequence read lengths. Re-analysis of the Sargasso Sea virome using GAAS indicated that standard methodologies for metagenomic analysis may dramatically underestimate the abundance and importance of organisms with small genomes in environmental systems. Using GAAS, we conducted a meta-analysis of microbial and viral average genome lengths in over 150 metagenomes from four biomes to determine whether genome lengths vary consistently between and within biomes, and between microbial and viral communities from the same environment. Significant differences between biomes and within aquatic sub-biomes (oceans, hypersaline systems, freshwater, and microbialites) suggested that average genome length is a fundamental property of environments driven by factors at the sub-biome level. The behavior of paired viral and microbial metagenomes from the same environment indicated that microbial and viral average genome sizes are independent of each other, but indicative of community responses to stressors and environmental conditions.},
- Doi = {10.1371/journal.pcbi.1000593},
- ISSN = {1553-734X},
+ author = {Angly, Florent E. and Willner, Dana and Prieto-Dav\'o, Alejandra and Edwards, Robert A. and Schmieder, Robert and Vega-Thurber, Rebecca and Antonopoulos, Dionysios A. and Barott, Katie and Cottrell, Matthew T. and Desnues, Christelle and Dinsdale, Elizabeth A. and Furlan, Mike and Haynes, Matthew and Henn, Matthew R. and Hu, Yongfei and Kirchman, David L. and McDole, Tracey and McPherson, John D. and Meyer, Folker and Miller, R. Michael and Mundt, Egbert and Naviaux, Robert K. and Rodriguez-Mueller, Beltran and Stevens, Rick and Wegley, Linda and Zhang, Lixin and Zhu, Baoli and Rohwer, Forest},
+ journal = {PLoS Computational Biology},
+ title = {{T}he {GAAS} {M}etagenomic {T}ool and {I}ts {E}stimations of {V}iral and {M}icrobial {A}verage {G}enome {S}ize in {F}our {M}ajor {B}iomes},
+ year = {2009},
+ volume = {5},
+ number = {12},
+ pages = {e1000593},
+ doi = {10.1371/journal.pcbi.1000593},
+ issn = {1553-734X},
}
@Article{BKM60,
- Title = {{L}imits of the natural environment in terms of p{H} and oxidation-reduction potentials},
- Author = {Baas Becking, L. G. M. and Kaplan, I. R. and Moore, D.},
- Journal = {Journal of Geology},
- Year = {1960},
- Number = {3},
- Pages = {243--284},
- Volume = {68},
- Abstract = {The electron and the proton content (measured as electrode potential [Eh] and pH) of an environment characterize this environment in many ways. In this paper the electrode potential and the pH are used as empirical parameters rather than as electrochemical data capable of thermodynamic interpretation. From published and unpublished work by the authors and from the literature, more than 6,200 pairs of characteristics were gathered, covering most types of the aqueous environment as well as the potential milieu of the chief actors in these environments: algae and bacteria. It appears that the Eh-pH limits of biological systems and of the naturally occurring aqueous environment almost coincide. This would indicate that there are few, if any, sterile terrestrial environments caused by limiting Eh-pH characteristics. As it seems unlikely that environments will be found outside the limits outlined in this paper, physico-chemical speculations on the sedimentary environment should be limited by this outline. Substances which do not occur (sulfuric acid, sulfide ion) should not be used in the electrochemical characterization of the environment. The biogenic master reaction in the environment, changing one or both characteristics (Eh-pH), is reductive photosynthesis by algae and by colored bacteria. A photosynthetic mass may raise the pH of a water to 9.4; and in the absence of bivalent cations, to 12.6. The intensity of sulfate reduction depends upon the sulfate content of the water and on the available hydrogen, in both organic and inorganic form. The iron concentration is also important, as iron is the principal acceptor of the H2S formed. The highly reactive, black iron sulfides may be partly oxidized with the formation of the more stable pyrite and marcasite. The reduction of iron from ferric to ferrous state takes place even in surface soil. Denitrification, another biologically important reduction, may be of lesser geochemical influence. Oxidative reactions comprise, apart from nitrification, chiefly the oxidation of H2S and SH- to sulfur, thiosulfate, sulfite, hydrosulfite, sulfate, and hydrosulfate and the oxidation of ferrous and manganous compounds. In contrast with the reductions, these oxidations are only in part biological. The oxidation of pyrite may give rise to extremely low pH values. Heterotrophic oxidation (respiration) results in the conversion of organic matter into CO2 and H2O. Acid formation in peat bogs is caused largely by cation exchange on plant cell walls, chiefly, but not exclusively, on Sphagnum. In sediments the reaction between iron phosphate complexes and H2S may liberate the acid H2P04- ion. 10. Certain environments are restricted, others cover almost the maximal area outlined in this paper. A progressive increase in the environmental range, arranged in a series, follows: rain water, mine water, peat bogs, sea water, rivers and lakes, marine sediments, and evaporites, while the geothermal environment shows the maximal area. The potential milieu of the green bacteria is highly restricted. Less restricted is the environment of the iron bacteria, followed by sulfate-reducing bacteria, purple bacteria, and denitrifying bacteria. Thio-bacteria have a very wide potential milieu, and algae are found literally everywhere. The Eh-pH characteristics are determined chiefly by photosynthesis, by respiration and by oxido-reductive changes in the iron and sulfur systems.},
- Url = {http://www.jstor.org/stable/30059218}
+ author = {Baas Becking, L. G. M. and Kaplan, I. R. and Moore, D.},
+ journal = {Journal of Geology},
+ title = {{L}imits of the natural environment in terms of p{H} and oxidation-reduction potentials},
+ year = {1960},
+ volume = {68},
+ number = {3},
+ pages = {243--284},
+ url = {http://www.jstor.org/stable/30059218}
}
@Book{BPJ85,
- Title = {{S}tandard {P}otentials in {A}queous {S}olution},
- Author = {Bard, A. J. and Parsons, R. and Jordan, J.},
- Publisher = {M. Dekker},
- Year = {1985},
- Address = {New York},
- Url = {http://www.worldcat.org/oclc/12106344}
+ author = {Bard, A. J. and Parsons, R. and Jordan, J.},
+ publisher = {M. Dekker},
+ title = {{S}tandard {P}otentials in {A}queous {S}olution},
+ year = {1985},
+ address = {New York},
+ url = {http://www.worldcat.org/oclc/12106344}
}
@Article{BB58,
- Title = {{A}dditivity rules for the estimation of molecular properties. {T}hermodynamic properties},
- Author = {Benson, Sidney W. and Buss, Jerry H.},
- Journal = {Journal of Chemical Physics},
- Year = {1958},
- Pages = {546 -- 572},
- Volume = {29},
- Abstract = {A general limiting law is proposed which can be used to systematize the various laws of additivity of molecularproperties. This can be stated asfollows: Ii I! is a molecularproperty, then for the disproportionation reaction: RNR+SNSz:;>2RNS, A<I1*> as ! the separation between R and S becomes large compared to their dimensions. It is shown that the zero-orderapproximation is equivalent to the law of additivity of atomic properties, the first-order approximation to the law oi additivity of bond properties, the second-orderapproximation to the law of additivity of group properties, and so forth. It is shown that for Cpand5° idealgases!, the additivity oi atomic properties works to about 3:2 cal/mole-°K, while the additivity of bond properties is usually good to about ;l;1 cal/mole-°K. The latter alsoestimates AH;° to about :l:3 kcal/ mole. T he group additivity relation is generally obeyed to within :l:O.5cal/mole-K for C Pand S° and about $0.6 kcalf mole for AH;°. Tablesare presentedfor each of the partial properties at 25°C. The agreements found for the various additivity rules is examined from a molecular point of view and certain extensions and limitations indicated. The application and utility of the rules in estimation of thermodynamic properties is discussed. The estimation of bond dissociation energies is possible with the additivity rules as are the thermodynamic properties of free radicals. An application of the rules to species NR2 and NS2 show that R and S may be ordered according to their general bond-weakening or bond-strengthening properties. For systems where N is C2H4 it is shown that the first and second bond dissociation energies for RC2H4R is very likely a constant=59.5 kcal, the excitation energy of C2H4.},
- Doi = {10.1063/1.1744539},
- Size = {27 p.},
+ author = {Benson, Sidney W. and Buss, Jerry H.},
+ journal = {Journal of Chemical Physics},
+ title = {{A}dditivity rules for the estimation of molecular properties. {T}hermodynamic properties},
+ year = {1958},
+ volume = {29},
+ pages = {546 -- 572},
+ doi = {10.1063/1.1744539},
+ size = {27 p.},
}
@Article{BBA+03,
- Title = {{T}he {SWISS}-{PROT} protein knowledgebase and its supplement {T}r{EMBL} in 2003},
- Author = {Boeckmann, Brigitte and Bairoch, Amos and Apweiler, Rolf and Blatter, Marie-Claude and Estreicher, Anne and Gasteiger, Elisabeth and Martin, Maria J. and Michoud, Karine and O'Donovan, Claire and Phan, Isabelle and Pilbout, Sandrine and Schneider, Michel},
- Journal = {Nucleic Acids Research},
- Year = {2003},
- Number = {1},
- Pages = {365 -- 370},
- Volume = {31},
- Abstract = {The SWISS-PROT protein knowledgebase (http: / / www. expasy. org/ sprot/ and http: / / www. ebi. ac. uk/ swissprot/) connects amino acid sequences with the current knowledge in the Life Sciences. Each protein entry provides an interdisciplinary overview of relevant information by bringing together experimental results, computed features and sometimes even contradictory conclusions. Detailed expertise that goes beyond the scope of SWISS-PROT is made available via direct links to specialised databases. SWISS-PROT provides annotated entries for all species, but concentrates on the annotation of entries from human ( the HPI project) and other model organisms to ensure the presence of high quality annotation for representative members of all protein families. Part of the annotation can be transferred to other family members, as is already done for microbes by the High-quality Automated and Manual Annotation of microbial Proteomes (HAMAP) project. Protein families and groups of proteins are regularly reviewed to keep up with current scientific findings. Complementarily, TrEMBL strives to comprise all protein sequences that are not yet represented in SWISS-PROT, by incorporating a perpetually increasing level of mostly automated annotation. Researchers are welcome to contribute their knowledge to the scientific community by submitting relevant findings to SWISS-PROT at swiss-prot at expasy.org.},
- Doi = {10.1093/nar/gkg095},
- Size = {6 p.},
+ author = {Boeckmann, Brigitte and Bairoch, Amos and Apweiler, Rolf and Blatter, Marie-Claude and Estreicher, Anne and Gasteiger, Elisabeth and Martin, Maria J. and Michoud, Karine and O'Donovan, Claire and Phan, Isabelle and Pilbout, Sandrine and Schneider, Michel},
+ journal = {Nucleic Acids Research},
+ title = {{T}he {SWISS}-{PROT} protein knowledgebase and its supplement {T}r{EMBL} in 2003},
+ year = {2003},
+ volume = {31},
+ number = {1},
+ pages = {365 -- 370},
+ doi = {10.1093/nar/gkg095},
+ size = {6 p.},
}
@Book{BJH84,
- Title = {{E}quilibrium {A}ctivity {D}iagrams for {C}oexisting {M}inerals and {A}queous {S}olutions at {P}ressures and {T}emperatures to 5 kb and 600$^\circ${C}},
- Author = {Bowers, Teresa S. and Jackson, Kenneth J. and Helgeson, Harold C.},
- Publisher = {Springer-Verlag},
- Year = {1984},
- Address = {Heidelberg},
- Abstract = {This book represents a revision and expansion of an earlier set of diagrams for temperatures from 25 to 300 C along the equilibrium vapor-liquid curve for H20 (Helgeson, Brown, and Leeper, 1969). The activity diagrams summarized in the following pages were generated over a six year period from 1977 to 1983 in the Laboratory of Theoretical Geochemistry (otherwise known as Prediction Central) at the University of California, Berkeley. They represent the culmination of research efforts to generate a comprehensive and internally consistent set of thermodynamic data and equations for minerals, gases, and aqueous solutions at high pressures and temperatures.},
- Pages = {397},
- Url = {http://www.worldcat.org/oclc/11133620}
+ author = {Bowers, Teresa S. and Jackson, Kenneth J. and Helgeson, Harold C.},
+ publisher = {Springer-Verlag},
+ title = {{E}quilibrium {A}ctivity {D}iagrams for {C}oexisting {M}inerals and {A}queous {S}olutions at {P}ressures and {T}emperatures to 5 kb and 600$^\circ${C}},
+ year = {1984},
+ address = {Heidelberg},
+ pages = {397},
+ url = {http://www.worldcat.org/oclc/11133620},
}
@Article{CGM+81,
- Title = {{G}roup contributions to the thermodynamic properties of non-ionic organic solutes in dilute aqueous solution},
- Author = {Cabani, Sergio and Gianni, Paolo and Mollica, Vincenzo and Lepori, Luciano},
- Journal = {Journal of Solution Chemistry},
- Year = {1981},
- Pages = {563 -- 595},
- Volume = {10},
- Abstract = {The thermodynamic properties DeltaGh0,DeltaHh0, and DeltaCp,h0 associated with the transfer of non-ionic organic compounds from gas to dilute aqueous solution and the limiting partial molar properties Cp0,2 and V20 of these compounds in water are described through a simple scheme of group contributions. A distinction is made between groups made only of carbon and hydrogen, and functional groups i.e. groups containing at least one atom different from carbon and hydrogen. Each group is assigned a contribution, for each property, through a least squares procedure which utilizes only molecules containing at most one functional group. Finally, for compounds containing more than one functional group, correction parameters are evaluated as the differences between the experimental values and those calculated by means of the group contributions. The different behavior of hydrophilic compared with hydrophobic groups is discussed for the various properties. A rationale for the correction parameters, i.e. for the effects of the interactions among hydrophilic groups on the thermodynamic properties, is attempted.},
- Doi = {10.1007/BF00646936},
+ author = {Cabani, Sergio and Gianni, Paolo and Mollica, Vincenzo and Lepori, Luciano},
+ journal = {Journal of Solution Chemistry},
+ title = {{G}roup contributions to the thermodynamic properties of non-ionic organic solutes in dilute aqueous solution},
+ year = {1981},
+ volume = {10},
+ pages = {563 -- 595},
+ doi = {10.1007/BF00646936},
}
@Article{DLE64,
- Title = {{T}hermodynamic {E}quilibria {I}n {P}rebiological {A}tmospheres},
- Author = {Dayhoff, M. O. and Lippincott, E. R. and Eck, R. V.},
- Journal = {Science},
- Year = {1964},
- Number = {3650},
- Pages = {1461--1464},
- Volume = {146},
- Abstract = {The concentrations of a large number of compounds of biological interest which would be present in the atmosphere at thermodynamic equilibrium were computed under many combinations of temperature, pressure, and elemental composition. These computations revealed a possible mechanism for the abiological formation of asphaltic tar and an oxidative threshold at which all but the simplest compounds disappear.},
- Doi = {10.1126/science.146.3650.1461},
- Sn = {0036-8075},
- Z8 = {0},
- Z9 = {60},
- Zb = {13}
+ author = {Dayhoff, M. O. and Lippincott, E. R. and Eck, R. V.},
+ journal = {Science},
+ title = {{T}hermodynamic {E}quilibria {I}n {P}rebiological {A}tmospheres},
+ year = {1964},
+ volume = {146},
+ number = {3650},
+ pages = {1461--1464},
+ doi = {10.1126/science.146.3650.1461},
+ sn = {0036-8075},
+ z8 = {0},
+ z9 = {60},
+ zb = {13}
}
@TechReport{DLEN67,
- Title = {{T}hermodynamic {E}quilibrium in {P}rebiological {A}tmospheres of {C}, {H}, {O}, {N}, {P}, {S}, and {C}l},
- Author = {Dayhoff, M. O. and Lippincott, E. R. and Eck, R. V. and Nagarajan, G.},
- Institution = {National Aeronautics and Space Administration},
- Year = {1967},
- Address = {Washington, D. C.},
- Number = {SP-3040},
- Type = {Report},
[TRUNCATED]
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