Abstract
In molecular and cellular biology, dissolved ions and molecules have decisive effects on chemical and biological reactions, conformational stabilities, and functions of small to large biomolecules. Despite major efforts, the current state of understanding of the effects of specific ions, osmolytes, and bioprotecting sugars on the structure and dynamics of water H-bonding networks and proteins is not yet satisfactory. Recently, to gain deeper insight into this subject, we studied various aggregation processes of ions and molecules in high-concentration salt, osmolyte, and sugar solutions with time-resolved vibrational spectroscopy and molecular dynamics simulation methods. It turns out that ions (or solute molecules) have a strong propensity to self-assemble into large and polydisperse aggregates that affect both local and long-range water H-bonding structures. In particular, we have shown that graph-theoretical approaches can be used to elucidate morphological characteristics of large aggregates in various aqueous salt, osmolyte, and sugar solutions. When ion and molecular aggregates in such aqueous solutions are treated as graphs, a variety of graph-theoretical properties, such as graph spectrum, degree distribution, clustering coefficient, minimum path length, and graph entropy, can be directly calculated by considering an ensemble of configurations taken from molecular dynamics trajectories. Here we show percolating behavior exhibited by ion and molecular aggregates upon increase in solute concentration in high solute concentrations and discuss compelling evidence of the isomorphic relation between percolation transitions of ion and molecular aggregates and water H-bonding networks. We anticipate that the combination of graph theory and molecular dynamics simulation methods will be of exceptional use in achieving a deeper understanding of the fundamental physical chemistry of dissolution and in describing the interplay between the self-aggregation of solute molecules and the structure and dynamics of water.
| Original language | English |
|---|---|
| Pages (from-to) | 125-149 |
| Number of pages | 25 |
| Journal | Annual Review of Physical Chemistry |
| Volume | 69 |
| DOIs | |
| Publication status | Published - 2018 Apr 20 |
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Keywords
- Graph theory
- Hofmeister effect
- Ion aggregation
- Molecular dynamics simulation
- Osmolyte effect
- Percolation
- Salt solubility
- Sugar aggregation
- Vibrational spectroscopy
- Water hydrogen-bonding network
ASJC Scopus subject areas
- Physical and Theoretical Chemistry
Cite this
Graph Theory and Ion and Molecular Aggregation in Aqueous Solutions. / Choi, Jun Ho; Lee, Hochan; Choi, Hyung Ran; Cho, Minhaeng.
In: Annual Review of Physical Chemistry, Vol. 69, 20.04.2018, p. 125-149.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Graph Theory and Ion and Molecular Aggregation in Aqueous Solutions
AU - Choi, Jun Ho
AU - Lee, Hochan
AU - Choi, Hyung Ran
AU - Cho, Minhaeng
PY - 2018/4/20
Y1 - 2018/4/20
N2 - In molecular and cellular biology, dissolved ions and molecules have decisive effects on chemical and biological reactions, conformational stabilities, and functions of small to large biomolecules. Despite major efforts, the current state of understanding of the effects of specific ions, osmolytes, and bioprotecting sugars on the structure and dynamics of water H-bonding networks and proteins is not yet satisfactory. Recently, to gain deeper insight into this subject, we studied various aggregation processes of ions and molecules in high-concentration salt, osmolyte, and sugar solutions with time-resolved vibrational spectroscopy and molecular dynamics simulation methods. It turns out that ions (or solute molecules) have a strong propensity to self-assemble into large and polydisperse aggregates that affect both local and long-range water H-bonding structures. In particular, we have shown that graph-theoretical approaches can be used to elucidate morphological characteristics of large aggregates in various aqueous salt, osmolyte, and sugar solutions. When ion and molecular aggregates in such aqueous solutions are treated as graphs, a variety of graph-theoretical properties, such as graph spectrum, degree distribution, clustering coefficient, minimum path length, and graph entropy, can be directly calculated by considering an ensemble of configurations taken from molecular dynamics trajectories. Here we show percolating behavior exhibited by ion and molecular aggregates upon increase in solute concentration in high solute concentrations and discuss compelling evidence of the isomorphic relation between percolation transitions of ion and molecular aggregates and water H-bonding networks. We anticipate that the combination of graph theory and molecular dynamics simulation methods will be of exceptional use in achieving a deeper understanding of the fundamental physical chemistry of dissolution and in describing the interplay between the self-aggregation of solute molecules and the structure and dynamics of water.
AB - In molecular and cellular biology, dissolved ions and molecules have decisive effects on chemical and biological reactions, conformational stabilities, and functions of small to large biomolecules. Despite major efforts, the current state of understanding of the effects of specific ions, osmolytes, and bioprotecting sugars on the structure and dynamics of water H-bonding networks and proteins is not yet satisfactory. Recently, to gain deeper insight into this subject, we studied various aggregation processes of ions and molecules in high-concentration salt, osmolyte, and sugar solutions with time-resolved vibrational spectroscopy and molecular dynamics simulation methods. It turns out that ions (or solute molecules) have a strong propensity to self-assemble into large and polydisperse aggregates that affect both local and long-range water H-bonding structures. In particular, we have shown that graph-theoretical approaches can be used to elucidate morphological characteristics of large aggregates in various aqueous salt, osmolyte, and sugar solutions. When ion and molecular aggregates in such aqueous solutions are treated as graphs, a variety of graph-theoretical properties, such as graph spectrum, degree distribution, clustering coefficient, minimum path length, and graph entropy, can be directly calculated by considering an ensemble of configurations taken from molecular dynamics trajectories. Here we show percolating behavior exhibited by ion and molecular aggregates upon increase in solute concentration in high solute concentrations and discuss compelling evidence of the isomorphic relation between percolation transitions of ion and molecular aggregates and water H-bonding networks. We anticipate that the combination of graph theory and molecular dynamics simulation methods will be of exceptional use in achieving a deeper understanding of the fundamental physical chemistry of dissolution and in describing the interplay between the self-aggregation of solute molecules and the structure and dynamics of water.
KW - Graph theory
KW - Hofmeister effect
KW - Ion aggregation
KW - Molecular dynamics simulation
KW - Osmolyte effect
KW - Percolation
KW - Salt solubility
KW - Sugar aggregation
KW - Vibrational spectroscopy
KW - Water hydrogen-bonding network
UR - http://www.scopus.com/inward/record.url?scp=85032006654&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85032006654&partnerID=8YFLogxK
U2 - 10.1146/annurev-physchem-050317-020915
DO - 10.1146/annurev-physchem-050317-020915
M3 - Article
AN - SCOPUS:85032006654
VL - 69
SP - 125
EP - 149
JO - Annual Review of Physical Chemistry
JF - Annual Review of Physical Chemistry
SN - 0066-426X
ER -