---
_id: '14603'
abstract:
- lang: eng
text: Computing the solubility of crystals in a solvent using atomistic simulations
is notoriously challenging due to the complexities and convergence issues associated
with free-energy methods, as well as the slow equilibration in direct-coexistence
simulations. This paper introduces a molecular-dynamics workflow that simplifies
and robustly computes the solubility of molecular or ionic crystals. This method
is considerably more straightforward than the state-of-the-art, as we have streamlined
and optimised each step of the process. Specifically, we calculate the chemical
potential of the crystal using the gas-phase molecule as a reference state, and
employ the S0 method to determine the concentration dependence of the chemical
potential of the solute. We use this workflow to predict the solubilities of sodium
chloride in water, urea polymorphs in water, and paracetamol polymorphs in both
water and ethanol. Our findings indicate that the predicted solubility is sensitive
to the chosen potential energy surface. Furthermore, we note that the harmonic
approximation often fails for both molecular crystals and gas molecules at or
above room temperature, and that the assumption of an ideal solution becomes less
valid for highly soluble substances.
acknowledgement: A.R. and B.C. acknowledge resources provided by the Cambridge Tier-2
system operated by the University of Cambridge Research Computing Service funded
by EPSRC Tier-2 capital Grant No. EP/P020259/1. P.Y.C. acknowledges support from
the Ernest Oppenheimer Fund and the Winton Programme for the Physics of Sustainability.
article_number: '184110'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Aleks
full_name: Reinhardt, Aleks
last_name: Reinhardt
- first_name: Pin Yu
full_name: Chew, Pin Yu
last_name: Chew
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
citation:
ama: Reinhardt A, Chew PY, Cheng B. A streamlined molecular-dynamics workflow for
computing solubilities of molecular and ionic crystals. Journal of Chemical
Physics. 2023;159(18). doi:10.1063/5.0173341
apa: Reinhardt, A., Chew, P. Y., & Cheng, B. (2023). A streamlined molecular-dynamics
workflow for computing solubilities of molecular and ionic crystals. Journal
of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0173341
chicago: Reinhardt, Aleks, Pin Yu Chew, and Bingqing Cheng. “A Streamlined Molecular-Dynamics
Workflow for Computing Solubilities of Molecular and Ionic Crystals.” Journal
of Chemical Physics. AIP Publishing, 2023. https://doi.org/10.1063/5.0173341.
ieee: A. Reinhardt, P. Y. Chew, and B. Cheng, “A streamlined molecular-dynamics
workflow for computing solubilities of molecular and ionic crystals,” Journal
of Chemical Physics, vol. 159, no. 18. AIP Publishing, 2023.
ista: Reinhardt A, Chew PY, Cheng B. 2023. A streamlined molecular-dynamics workflow
for computing solubilities of molecular and ionic crystals. Journal of Chemical
Physics. 159(18), 184110.
mla: Reinhardt, Aleks, et al. “A Streamlined Molecular-Dynamics Workflow for Computing
Solubilities of Molecular and Ionic Crystals.” Journal of Chemical Physics,
vol. 159, no. 18, 184110, AIP Publishing, 2023, doi:10.1063/5.0173341.
short: A. Reinhardt, P.Y. Chew, B. Cheng, Journal of Chemical Physics 159 (2023).
date_created: 2023-11-26T23:00:54Z
date_published: 2023-11-14T00:00:00Z
date_updated: 2023-11-28T08:39:23Z
day: '14'
ddc:
- '530'
- '540'
department:
- _id: BiCh
doi: 10.1063/5.0173341
external_id:
arxiv:
- '2308.10886'
file:
- access_level: open_access
checksum: f668ee0d07096eef81159d05bc27aabc
content_type: application/pdf
creator: dernst
date_created: 2023-11-28T08:39:06Z
date_updated: 2023-11-28T08:39:06Z
file_id: '14620'
file_name: 2023_JourChemicalPhysics_Reinhardt.pdf
file_size: 6276059
relation: main_file
success: 1
file_date_updated: 2023-11-28T08:39:06Z
has_accepted_license: '1'
intvolume: ' 159'
issue: '18'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
issn:
- 0021-9606
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
related_material:
record:
- id: '14619'
relation: research_data
status: public
scopus_import: '1'
status: public
title: A streamlined molecular-dynamics workflow for computing solubilities of molecular
and ionic crystals
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 159
year: '2023'
...
---
_id: '14604'
abstract:
- lang: eng
text: Sex chromosomes have evolved independently multiple times, but why some are
conserved for more than 100 million years whereas others turnover rapidly remains
an open question. Here, we examine the homology of sex chromosomes across nine
orders of insects, plus the outgroup springtails. We find that the X chromosome
is likely homologous across insects and springtails; the only exception is in
the Lepidoptera, which has lost the X and now has a ZZ/ZW sex-chromosome system.
These results suggest the ancestral insect X chromosome has persisted for more
than 450 million years—the oldest known sex chromosome to date. Further, we propose
that the shrinking of gene content the dipteran X chromosome has allowed for a
burst of sex-chromosome turnover that is absent from other speciose insect orders.
acknowledgement: All computational analyses were performed on the server at Institute
of Science and Technology Austria. We thank Marwan Elkrewi and Vincent Bett for
analytical advice, and Tanja Schwander and Vincent Merel for useful discussions.
We also thank Matthew Hahn for comments on an earlier version of the manuscript.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Melissa A
full_name: Toups, Melissa A
id: 4E099E4E-F248-11E8-B48F-1D18A9856A87
last_name: Toups
orcid: 0000-0002-9752-7380
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Toups MA, Vicoso B. The X chromosome of insects likely predates the origin
of class Insecta. Evolution. 2023;77(11):2504-2511. doi:10.1093/evolut/qpad169
apa: Toups, M. A., & Vicoso, B. (2023). The X chromosome of insects likely predates
the origin of class Insecta. Evolution. Oxford University Press. https://doi.org/10.1093/evolut/qpad169
chicago: Toups, Melissa A, and Beatriz Vicoso. “The X Chromosome of Insects Likely
Predates the Origin of Class Insecta.” Evolution. Oxford University Press,
2023. https://doi.org/10.1093/evolut/qpad169.
ieee: M. A. Toups and B. Vicoso, “The X chromosome of insects likely predates the
origin of class Insecta,” Evolution, vol. 77, no. 11. Oxford University
Press, pp. 2504–2511, 2023.
ista: Toups MA, Vicoso B. 2023. The X chromosome of insects likely predates the
origin of class Insecta. Evolution. 77(11), 2504–2511.
mla: Toups, Melissa A., and Beatriz Vicoso. “The X Chromosome of Insects Likely
Predates the Origin of Class Insecta.” Evolution, vol. 77, no. 11, Oxford
University Press, 2023, pp. 2504–11, doi:10.1093/evolut/qpad169.
short: M.A. Toups, B. Vicoso, Evolution 77 (2023) 2504–2511.
date_created: 2023-11-26T23:00:54Z
date_published: 2023-11-02T00:00:00Z
date_updated: 2023-11-28T08:25:28Z
day: '02'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1093/evolut/qpad169
external_id:
pmid:
- '37738212'
file:
- access_level: open_access
checksum: b66dc10edae92d38918d534e64dda77c
content_type: application/pdf
creator: dernst
date_created: 2023-11-28T08:12:15Z
date_updated: 2023-11-28T08:12:15Z
file_id: '14618'
file_name: 2023_Evolution_Toups.pdf
file_size: 1399102
relation: main_file
success: 1
file_date_updated: 2023-11-28T08:12:15Z
has_accepted_license: '1'
intvolume: ' 77'
issue: '11'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 2504-2511
pmid: 1
publication: Evolution
publication_identifier:
eissn:
- 1558-5646
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://git.ista.ac.at/bvicoso/veryoldx
record:
- id: '14616'
relation: research_data
status: public
- id: '14617'
relation: research_data
status: public
scopus_import: '1'
status: public
title: The X chromosome of insects likely predates the origin of class Insecta
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 77
year: '2023'
...
---
_id: '14616'
abstract:
- lang: eng
text: Sex chromosomes have evolved independently multiple times, but why some are
conserved for more than 100 million years whereas others turnover rapidly remains
an open question. Here, we examine the homology of sex chromosomes across nine
orders of insects, plus the outgroup springtails. We find that the X chromosome
is likely homologous across insects and springtails; the only exception is in
the Lepidoptera, which has lost the X and now has a ZZ/ZW sex chromosome system.
These results suggest the ancestral insect X chromosome has persisted for more
than 450 million years – the oldest known sex chromosome to date. Further, we
propose that the shrinking of gene content of the Dipteran X chromosome has allowed
for a burst of sex-chromosome turnover that is absent from other speciose insect
orders.
article_processing_charge: No
author:
- first_name: Melissa A
full_name: Toups, Melissa A
id: 4E099E4E-F248-11E8-B48F-1D18A9856A87
last_name: Toups
orcid: 0000-0002-9752-7380
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Toups MA, Vicoso B. The X chromosome of insects likely predates the origin
of Class Insecta. 2023. doi:10.5061/DRYAD.HX3FFBGKT
apa: Toups, M. A., & Vicoso, B. (2023). The X chromosome of insects likely predates
the origin of Class Insecta. Dryad. https://doi.org/10.5061/DRYAD.HX3FFBGKT
chicago: Toups, Melissa A, and Beatriz Vicoso. “The X Chromosome of Insects Likely
Predates the Origin of Class Insecta.” Dryad, 2023. https://doi.org/10.5061/DRYAD.HX3FFBGKT.
ieee: M. A. Toups and B. Vicoso, “The X chromosome of insects likely predates the
origin of Class Insecta.” Dryad, 2023.
ista: Toups MA, Vicoso B. 2023. The X chromosome of insects likely predates the
origin of Class Insecta, Dryad, 10.5061/DRYAD.HX3FFBGKT.
mla: Toups, Melissa A., and Beatriz Vicoso. The X Chromosome of Insects Likely
Predates the Origin of Class Insecta. Dryad, 2023, doi:10.5061/DRYAD.HX3FFBGKT.
short: M.A. Toups, B. Vicoso, (2023).
date_created: 2023-11-28T08:01:53Z
date_published: 2023-09-15T00:00:00Z
date_updated: 2023-11-28T08:17:31Z
day: '15'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.5061/DRYAD.HX3FFBGKT
has_accepted_license: '1'
license: https://creativecommons.org/publicdomain/zero/1.0/
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.hx3ffbgkt
month: '09'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '14604'
relation: used_in_publication
status: public
status: public
title: The X chromosome of insects likely predates the origin of Class Insecta
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14617'
abstract:
- lang: eng
text: Sex chromosomes have evolved independently multiple times, but why some are
conserved for more than 100 million years whereas others turnover rapidly remains
an open question. Here, we examine the homology of sex chromosomes across nine
orders of insects, plus the outgroup springtails. We find that the X chromosome
is likely homologous across insects and springtails; the only exception is in
the Lepidoptera, which has lost the X and now has a ZZ/ZW sex chromosome system.
These results suggest the ancestral insect X chromosome has persisted for more
than 450 million years – the oldest known sex chromosome to date. Further, we
propose that the shrinking of gene content of the Dipteran X chromosome has allowed
for a burst of sex-chromosome turnover that is absent from other speciose insect
orders.
article_processing_charge: No
author:
- first_name: Melissa A
full_name: Toups, Melissa A
id: 4E099E4E-F248-11E8-B48F-1D18A9856A87
last_name: Toups
orcid: 0000-0002-9752-7380
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Toups MA, Vicoso B. The X chromosome of insects likely predates the origin
of Class Insecta. 2023. doi:10.5281/ZENODO.8138705
apa: Toups, M. A., & Vicoso, B. (2023). The X chromosome of insects likely predates
the origin of Class Insecta. Zenodo. https://doi.org/10.5281/ZENODO.8138705
chicago: Toups, Melissa A, and Beatriz Vicoso. “The X Chromosome of Insects Likely
Predates the Origin of Class Insecta.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8138705.
ieee: M. A. Toups and B. Vicoso, “The X chromosome of insects likely predates the
origin of Class Insecta.” Zenodo, 2023.
ista: Toups MA, Vicoso B. 2023. The X chromosome of insects likely predates the
origin of Class Insecta, Zenodo, 10.5281/ZENODO.8138705.
mla: Toups, Melissa A., and Beatriz Vicoso. The X Chromosome of Insects Likely
Predates the Origin of Class Insecta. Zenodo, 2023, doi:10.5281/ZENODO.8138705.
short: M.A. Toups, B. Vicoso, (2023).
date_created: 2023-11-28T08:04:03Z
date_published: 2023-09-15T00:00:00Z
date_updated: 2023-11-28T08:25:28Z
day: '15'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.5281/ZENODO.8138705
has_accepted_license: '1'
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.8138705
month: '09'
oa: 1
oa_version: Published Version
other_data_license: MIT License
publisher: Zenodo
related_material:
record:
- id: '14604'
relation: used_in_publication
status: public
status: public
title: The X chromosome of insects likely predates the origin of Class Insecta
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14619'
abstract:
- lang: eng
text: Data underlying the publication "A streamlined molecular-dynamics workflow
for computing solubilities of molecular and ionic crystals" (DOI https://doi.org/10.1063/5.0173341).
article_processing_charge: No
author:
- first_name: Bingqing
full_name: Cheng, Bingqing
id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9
last_name: Cheng
orcid: 0000-0002-3584-9632
citation:
ama: 'Cheng B. BingqingCheng/solubility: V1.0. 2023. doi:10.5281/ZENODO.8398094'
apa: 'Cheng, B. (2023). BingqingCheng/solubility: V1.0. Zenodo. https://doi.org/10.5281/ZENODO.8398094'
chicago: 'Cheng, Bingqing. “BingqingCheng/Solubility: V1.0.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8398094.'
ieee: 'B. Cheng, “BingqingCheng/solubility: V1.0.” Zenodo, 2023.'
ista: 'Cheng B. 2023. BingqingCheng/solubility: V1.0, Zenodo, 10.5281/ZENODO.8398094.'
mla: 'Cheng, Bingqing. BingqingCheng/Solubility: V1.0. Zenodo, 2023, doi:10.5281/ZENODO.8398094.'
short: B. Cheng, (2023).
date_created: 2023-11-28T08:32:18Z
date_published: 2023-10-02T00:00:00Z
date_updated: 2023-11-28T08:39:22Z
day: '02'
ddc:
- '530'
department:
- _id: BiCh
doi: 10.5281/ZENODO.8398094
has_accepted_license: '1'
main_file_link:
- open_access: '1'
url: https://doi.org/10.5281/zenodo.8398094
month: '10'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
record:
- id: '14603'
relation: used_in_publication
status: public
status: public
title: 'BingqingCheng/solubility: V1.0'
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...