Solubility Prediction of Organic Molecules with Molecular Dynamics Simulations

被引：21

作者：

Bjelobrk, Zoran ^{[1
]}

Mendels, Dan ^{[2
]}

Karmakar, Tarak ^{[3
]}

Parrinello, Michele ^{[3
]}

Mazzotti, Marco ^{[1
]}

机构：

[1] Swiss Fed Inst Technol, Inst Energy & Proc Engn, CH-8092 Zurich, Switzerland

[2] Univ Chicago, Pritzker Sch Mol Engn, Chicago, IL 60637 USA

[3] Ist Italiano Tecnol IIT, I-16163 Genoa, GE, Italy

来源：

CRYSTAL GROWTH & DESIGN | 2021年 / 21卷 / 09期

关键词：

CRYSTAL-GROWTH; FREE-ENERGY; UREA; WATER; GROMACS; DISSOLUTION; COEXISTENCE; NUCLEATION; MODEL; NACL;

D O I：

10.1021/acs.cgd.1c00546

中图分类号：

O6 [化学];

学科分类号：

0703 ;

摘要：

We present a molecular dynamics simulation method for the computation of the solubility of organic crystals in solution. The solubility is calculated based on the equilibrium free energy difference between the solvated solute and its crystallized state at the crystal surface kink site. To efficiently sample the growth and dissolution process, we have carried out well-tempered metadynamics simulations with a collective variable that captures the slow degrees of freedom, namely, the solute diffusion to and adsorption at the kink site together with the desolvation of the kink site. Simulations were performed at different solution concentrations using constant chemical potential molecular dynamics, and the solubility was identified at the concentration at which the free energy values between the grown and dissolved kink states were equal. The effectiveness of this method is demonstrated by its success in reproducing the experimental trends of solubility of urea and naphthalene in a variety of solvents.

引用

页码：5198 / 5205

页数：8

共 50 条

[21] Direct prediction of residual dipolar couplings of small molecules in a stretched gel by stochastic molecular dynamics simulations
Frank, Andreas O.
Freudenberger, J. Christoph
Shaytan, Alexey K.
Kessler, Horst
Luy, Burkhard
MAGNETIC RESONANCE IN CHEMISTRY, 2015, 53 (03) : 213 - 217
[22] Parameterization of prototype organic small molecules suitable for OPVs and molecular dynamics simulations: the BTT and BPT cases
Garcia-Ruiz, Karl M.
Marmolejo-Valencia, Andres F.
Gonzalez-Navejas, Augusto
Dominguez, Laura
Amador-Bedolla, Carlos
JOURNAL OF MOLECULAR MODELING, 2019, 25 (05)
[23] Parameterization of prototype organic small molecules suitable for OPVs and molecular dynamics simulations: the BTT and BPT cases
Karl M. García-Ruiz
Andrés F. Marmolejo-Valencia
Augusto González-Navejas
Laura Dominguez
Carlos Amador-Bedolla
Journal of Molecular Modeling, 2019, 25
[24] Prediction of aqueous solubility of organic chemicals based on molecular structure
Nirmalakhandan, N.N.
Speece, R.E.
Environmental Science and Technology, 1988, 22 (03): : 328 - 338
[25] Prediction of aqueous solubility of organic compounds from molecular structure
Mitchell, BE
Jurs, PC
JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES, 1998, 38 (03): : 489 - 496
[26] Nanoaggregation and Solubility of Crude Oil Asphaltenes from Molecular Dynamics Simulations
Frigerio, Francesco
RECENT ADVANCES IN BIOLOGY, BIOPHYSICS, BIOENGINEERING AND COMPUTATIONAL CHEMISTRY, 2009, : 51 - 57
[27] Universal methodology to predict solubility via molecular dynamics simulations of naphthalene
Li, Lunna
Totton, Tim
Frenkel, Daan
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2018, 256
[28] Molecular Mechanism of Gas Solubility in Liquid: Constant Chemical Potential Molecular Dynamics Simulations
Ansari, Narjes
Karmakar, Tarak
Parrinello, Michele
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2020, 16 (08) : 5279 - 5286
[29] Predicting Melting Points of Organic Molecules: Applications to Aqueous Solubility Prediction Using the General Solubility Equation
McDonagh, J. L.
van Mourik, T.
Mitchell, J. B. O.
MOLECULAR INFORMATICS, 2015, 34 (11-12) : 715 - 724
[30] Transport properties of dumbbell molecules by equilibrium molecular dynamics simulations
Lee, SH
BULLETIN OF THE KOREAN CHEMICAL SOCIETY, 2004, 25 (05) : 737 - 741

← 1 2 3 4 5 →