http://lod.bco-dmo.org/id/dataset/865489
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2021-11-24
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Kinetics of δ18O and Δ47 equilibration in the dissolved carbonate system revealed by time-series quantitative inorganic carbonate precipitation experiments and numerical modeling.
2021-11-30
publication
2021-11-30
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2021-11-30
publication
https://doi.org/10.26008/1912/bco-dmo.865489.1
Richard Zeebe
University of Hawai'i
principalInvestigator
Joji Uchikawa
University of Hawai'i
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Zeebe, R., Uchikawa, J. (2021) Kinetics of δ18O and Δ47 equilibration in the dissolved carbonate system revealed by time-series quantitative inorganic carbonate precipitation experiments and numerical modeling. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2021-11-30 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.865489.1 [access date]
inorganic carbonate precipitation experiments and numerical modeling Dataset Description: <p>We analyzed oxygen and clumped isotope values of inorganic BaCO<sub>3</sub> samples from Uchikawa and Zeebe (2012), which were quantitatively precipitated from NaHCO<sub>3</sub> solutions over the course of isotopic equilibration. These time-series quantitative inorganic BaCO<sub>3</sub> precipitation experiments were conducted under a normal condition at 25 °C and in the presence of varying amount of carbonic anhydrase enzyme that is known to catalyze CO<sub>2</sub> hydration and known to be possessed by a range of marine calcareous organisms.</p>
<p>Summary of new δ<sup>18</sup>O and Δ<sub>47</sub> values measured on BaCO<sub>3</sub> samples from Uchikawa and Zeebe (2012). These BaCO<sub>3</sub> samples were quantitatively precipitated from NaHCO<sub>3</sub> solutions at various times over the course of isotopic equilibration at 25 °C. Also included in the file are δ<sup>18</sup>O and Δ<sub>47</sub> values of the NaHCO<sub>3</sub> used in the experiments and original δ<sup>18</sup>O data by Uchikawa and Zeebe (2012) on the BaCO<sub>3</sub> samples and experimental NaHCO<sub>3</sub> and H<sub>2</sub>O.</p>
<p>We also developed a fully open-sourced numerical codes (ExClump38 model) that can simulate the time-course of oxygen and clumped isotope equilibration in the dissolved carbonate system as a function of temperature, pH and carbonic anhydrase concentration by extending the work of Chen et al. (2018). By extending the framework of earlier work (Chen et al., 2018), this model tracks temporal change in the abundance of singly (i.e., δ<sup>13</sup>C and δ<sup>18</sup>O) and doubly-substituted (i.e., Δ<sub>47</sub>) aqueous CO<sub>2</sub> and the sum of HCO<sub>3</sub>- and CO<sub>3</sub><sup>2-</sup> (referred to as the dissolved carbonate pool: DCP) from a given initial condition/state to the expected isotopic equilibrium in the dissolved carbonate system.</p>
<p><strong>Matlab codes for the ExClump38 model and accompanying experimental data.</strong> These data are attached to this datapackage as a supplemental file. The zipfile contains 9 different files. Descriptions of the files:</p>
<p>* ExClump38.m: A Matlab m-file for the ExClump38 model, which can simulate the progress of isotopic (δ<sup>18</sup>O and Δ<sub>47</sub>) equilibration in the dissolved carbonate system as a function of temperature, pH and carbonic anhydrase activity.</p>
<p>* IsoEquilibration.m: A Matlab m-file containing a set of differential equations to be solved in the ExClump38 model. This file needs to be downloaded with ExClump.m and stored in the same folder.</p>
<p>* Model_Constants.m: A Matlab m-file containing a set of equilibrium and kinetic rate constants as well as isotope fractionation factors used in the ExClump38 model. This file needs to be downloaded with ExClump.m and stored in the same folder.</p>
<p>* Data_Entry.m:<u> </u>A supplementary Matlab m-file for the entry of our experimental data as well as the initial condition for each experimental series for the ExClump38 model.</p>
<p>* TS2.dat: A supplementary .dat file needed for the entry of isotope data from the “TS-2” experimental series. The TS-2 experiments were conducted at T = 25 °C, pH<sub>NBS</sub> = 8.9 and in the absence of carbonic anhydrase enzyme.</p>
<p>* TS2_CAmn.dat:<u> </u>A supplementary .dat file needed for the entry of isotope data from the “TS-mnCA” experimental series. The TS-2 experiments were conducted at T = 25 °C and pH<sub>NBS</sub> = 8.9, with the addition of carbonic anhydrase enzyme to a concentration of 3.7 nM.</p>
<p>* TS2_CA2.dat: A supplementary .dat file needed for the entry of isotope data from the “TS-2CA” experimental series. The TS-2 experiments were conducted T = 25 °C and pH<sub>NBS</sub> = 8.9, with the addition of carbonic anhydrase enzyme to a concentration of 9.3 nM.</p>
<p>* TS2_CA3.dat: A supplementary .dat file needed for the entry of isotope data from the “TS-3CA” experimental series. The TS-2 experiments were conducted T = 25 °C and pH<sub>NBS</sub> = 8.9, with the addition of carbonic anhydrase enzyme to a concentration of 19 nM.</p>
<p>* SS18.dat: A supplementary .dat file needed for the entry of isotope data from similar experiments done by Staudigel and Swart (2018) at T = 25 °C.</p>
<p>All of the .dat files are organized as follows:</p>
<p>* 1st column (far left): pH<sub>NBS</sub> of the experimental NaHCO<sub>3</sub> solution.<br />
* 2nd column: Elapsed equilibration time (minutes)<br />
* 3rd column: δ<sup>13</sup>C of BaCO<sub>3</sub> samples (‰, VPDB)<br />
* 4th column: δ<sup>13</sup>C measurement uncertainty for BaCO<sub>3</sub> (1σ standard error, ‰ VPDB)<br />
* 5th column: δ<sup>18</sup>O of BaCO<sub>3</sub> samples (‰, VPDB)<br />
* 6th column: δ<sup>18</sup>O measurement uncertainty for BaCO<sub>3</sub> (1σ standard error, ‰ VSMOW)<br />
* 7th column: δ<sup>18</sup>O of experimental H<sub>2</sub>O (‰, VSMOW) from Uchikawa &amp; Zeebe (2012)<br />
* 8th column: δ<sup>18</sup>O measurement uncertainty for H<sub>2</sub>O (1σ standard error, ‰ VSMOW)<br />
* 9th column: Δ<sub>47</sub> of BaCO<sub>3</sub> samples (‰, ARF)<br />
* 10th column (far right): Δ<sub>47</sub> measurement uncertainty (1σ standard error, ‰ ARF)</p>
<p>&nbsp;</p>
<p>Related publications:</p>
<p>* Data contained original data for d18O of H2O from&nbsp; Uchikawa, J., &amp; Zeebe, R. E. (2012)<br />
* The numerical model is adopted and modified from Chen et al. (2018)<br />
* The model is also applied to (their dataset is attached as SS18): Staudige &amp; Swart (2018)</p> Methods and Sampling: <p>Carbonate samples (BaCO<sub>3</sub> and experimental NaHCO<sub>3</sub>) were digested with 104% phosphoric acid at 90 °C in a common acid bath. After purification, the CO<sub>2</sub> gases liberated from acid digestion of the samples were analyzed by a Thermo Finnigan MAT253 dual-inlet isotope ratio monitoring mass spectrometer for δ<sup>13</sup>C, δ<sup>18</sup>O and Δ<sub>47</sub> at the California Institute of Technology.</p>
<p>The codes for the ExClump38 model are developed in the Matlab computational software.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1558699 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1558699
completed
Richard Zeebe
University of Hawai'i
808-956-6473
1000 Pope Road Marine Sciences Building 504
Honolulu
HI
96822
USA
zeebe@hawaii.edu
pointOfContact
Joji Uchikawa
University of Hawai'i
100 Pope Rd.
Honolulu
HI
96822
USA
uchikawa@hawaii.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Series
Sample
pH
Time
delta_C_13_BaCO3
delta_C_13_BaCO3_std
delta_O_18_BaCO3
delta_O_18_BaCO3_std
cap_47
cap_47_std
Thermo Finnigan MAT253
theme
None, User defined
experiment id
sample identification
pH
time_elapsed
d13C
standard deviation
oxygen 16 to oxygen 18 ratio
ratio
featureType
BCO-DMO Standard Parameters
Isotope-ratio Mass Spectrometer
instrument
BCO-DMO Standard Instruments
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Experimental study of CO2 hydration in seawater: Mechanism and kinetic isotope effects
https://osprey.bco-dmo.org/project/859504
Experimental study of CO2 hydration in seawater: Mechanism and kinetic isotope effects
<p><em>NSF Award Abstract:</em><br />
The chemical reaction of carbon dioxide (CO2) with water in the marine environment is a fundamental process that creates carbonic acid (H2CO3) and all of the associated chemical ions (carbonate (CO3); hydrogen ions (H+), and bicarbonate (HCO3-)) that serve as the dominant buffer for pH in the ocean. Dehydration refers to the opposite reaction that releases CO2 gas. By entering into important reactions and serving to control pH, these species govern a wide variety of chemical and biological processes in the ocean. Surprisingly, while the important reactions that involve CO2 hydration and its resulting products have been extensively studied in the ocean, some of the fundamental mechanisms remain poorly understood and datasets are sparse. In particular, almost nothing is known about how the natural isotopes of the carbon and oxygen atoms are involved and this is critically needed to explain observed changes in chemical species and solid calcium carbonate such as that created by coral reefs. This research aims to carefully produce novel experimental data that includes critical measurements of carbon and oxygen isotopes before and after the hydration of CO2 in the ocean. Because these resulting carbonate species are used widely in many studies in the ocean sciences, particularly those examining past climates, this research will have far-reaching influences. Additionally, the results will provide new fundamental insight on exactly how the ocean will take up and respond to changing concentrations of atmospheric CO2 in a changing climate. The research will fund an early-career scientist who is dedicated to graduate and undergraduate education as well as scientific outreach to the community.</p>
<p>While hydration/dehydration of CO2 in the ocean critically influences a variety of marine chemical and biological processes, there are certain aspects of the reaction that are poorly understood. The molecular mechanism is not yet clear, as there are two possible pathways that have been proposed. Additionally, kinetic isotope effects during CO2 have not been well studied, and the data regarding this topic is inconsistent. This research aims to study the carbon and oxygen isotope fractionation, which will not only clarify the molecular mechanism of the reaction but also will add a consistent dataset on kinetic isotope effects. The main challenge in this study is separating the product, HCO3-, from CO2 before re-equilibration, but the researcher will resolve this by rapidly precipitating dissolved carbon as carbonate. Since carbonates formed from the process of hydration are considered critical indicators of water chemistry, biological processes, and the inorganic carbon cycle as a whole and are used in a wide variety of oceanographic research, particularly as paleo-proxies, this research will provide fundamental mechanistic data that will greatly advance studies reaching beyond the physical chemical measurements that will be made here.</p>
CO2 Hydration Mechanism and KIEs
largerWorkCitation
project
eng; USA
oceans
2021-11-30
University of Hawaii at Manoa
0
BCO-DMO catalogue of parameters from Kinetics of δ18O and Δ47 equilibration in the dissolved carbonate system revealed by time-series quantitative inorganic carbonate precipitation experiments and numerical modeling.
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/865600.rdf
Name: Series
Units: unitless
Description: <p>series id</p>
http://lod.bco-dmo.org/id/dataset-parameter/865601.rdf
Name: Sample
Units: unitless
Description: <p>sample id</p>
http://lod.bco-dmo.org/id/dataset-parameter/865602.rdf
Name: pH
Units: unitless
Description: <p>pH, NBS scale</p>
http://lod.bco-dmo.org/id/dataset-parameter/865603.rdf
Name: Time
Units: min (minutes)
Description: <p>Elapsed isotopic equilibration time (minutes)</p>
http://lod.bco-dmo.org/id/dataset-parameter/865604.rdf
Name: delta_C_13_BaCO3
Units: ‰ (per mil)
Description: <p>δ13CBaCO3, stable carbon isotope ratio</p>
http://lod.bco-dmo.org/id/dataset-parameter/865605.rdf
Name: delta_C_13_BaCO3_std
Units: ‰ (per mil)
Description: <p>± 1σ S.D.</p>
http://lod.bco-dmo.org/id/dataset-parameter/865606.rdf
Name: delta_O_18_BaCO3
Units: ‰ (per mil)
Description: <p>δ18OBaCO3, stable oxygen isotope ration</p>
http://lod.bco-dmo.org/id/dataset-parameter/865607.rdf
Name: delta_O_18_BaCO3_std
Units: ‰ (per mil)
Description: <p>± 1σ S.D.</p>
http://lod.bco-dmo.org/id/dataset-parameter/865608.rdf
Name: cap_47
Units: ‰ (per mil)
Description: <p>Δ47</p>
http://lod.bco-dmo.org/id/dataset-parameter/865609.rdf
Name: cap_47_std
Units: ‰ (per mil)
Description: <p>± 1σ S.D.</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
13872
https://darchive.mblwhoilibrary.org/bitstream/1912/27790/1/NaHCO3_Isotope_Data.xlsx
download
4289
https://darchive.mblwhoilibrary.org/bitstream/1912/27790/2/dataset-865489_experimental-data-and-model-code-d18o-and-d47-equilibration-kinetics__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.865489.1
download
onLine
dataset
<p>Carbonate samples (BaCO<sub>3</sub> and experimental NaHCO<sub>3</sub>) were digested with 104% phosphoric acid at 90 °C in a common acid bath. After purification, the CO<sub>2</sub> gases liberated from acid digestion of the samples were analyzed by a Thermo Finnigan MAT253 dual-inlet isotope ratio monitoring mass spectrometer for δ<sup>13</sup>C, δ<sup>18</sup>O and Δ<sub>47</sub> at the California Institute of Technology.</p>
<p>The codes for the ExClump38 model are developed in the Matlab computational software.</p>
Specified by the Principal Investigator(s)
<p>BCO-DMO processing notes:</p>
<p>* added model code and datafiles as supplemental documentation<br />
* added NACHO3 file as data file<br />
* BaCO3 file is added as main data file and viewable in the dataviewer.<br />
* adjusted data parameter names to comply with database requirements.</p>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
Thermo Finnigan MAT253
Thermo Finnigan MAT253
PI Supplied Instrument Name: Thermo Finnigan MAT253 PI Supplied Instrument Description:Thermo Finnigan MAT253 dual-inlet isotope ratio monitoring mass spectrometer. Instrument Name: Isotope-ratio Mass Spectrometer Instrument Short Name:IR Mass Spec; IRMS Instrument Description: The Isotope-ratio Mass Spectrometer is a particular type of mass spectrometer used to measure the relative abundance of isotopes in a given sample (e.g. VG Prism II Isotope Ratio Mass-Spectrometer). Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB16/