Article
Biochemistry & Molecular Biology
Spencer J. Sabatino, Andrew S. Paluch
Summary: In this study, blind predictions of octanol/water partition coefficients for drug-like compounds were made using molecular dynamics simulations. It was found that the predictions were sensitive to the choice of water force field, and the inclusion of water in the octanol-rich phase had a significant impact, which was also dependent on the chemical structure of the solute.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
(2021)
Article
Environmental Sciences
Wanran Li, Dezhi Chen, Shuhua Chen, Jing Zhang, Guobin Song, Yawei Shi, Ya Sun, Guanghui Ding, Willie J. G. M. Peijnenburg
Summary: In this study, generalized predictive models were developed to estimate KOA values of aromatic pollutants by considering the solvation free energy and the dimer effect. The results showed that uncorrected log KOA values underestimated experimental values and the deviation increased with increasing log KOA. The dimer effect on the apparent KOA values was found to be significant and driven by 7C -7C interactions.
Article
Engineering, Environmental
Satoshi Endo
Summary: Polyparameter linear free energy relationships (PP-LFERs) are accurate models for predicting equilibrium partition coefficients of organic chemicals. This study evaluates the applicability domain of PP-LFERs and suggests using the prediction interval as a metric to define their domain. The analysis shows that PP-LFERs calibrated with a large number of training data are robust against extrapolation error.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2022)
Article
Chemistry, Physical
Wanran Li, Guobin Song, Jing Zhang, Jianwei Song, Haonan Wang, Yawei Shi, Guanghui Ding
Summary: In this study, the thermodynamic relationship between log K-OW and solvation free energy was utilized to estimate log K-OW of PCBs. The HF/MIDI16D calculation level was found optimal for geometry optimization and energy calculation. Results showed that the Delta G(OW) model had comparable goodness-of-fit and predictive ability to other models, with a more universal application domain. The solvation free energy method shows promise in predicting K-OW.
COMPUTATIONAL AND THEORETICAL CHEMISTRY
(2021)
Article
Biochemical Research Methods
Zheming Liu, Xiangfei Sun, Yan Xu
Summary: Equilibrium passive sampling techniques using LDPE film are increasingly used to determine contaminant concentrations in water and air. This study recalibrated reliable polyparameter linear free energy relationships for LDPE-water and LDPE-air systems using carefully collected partition coefficients and solute descriptors. The recalibrated models successfully predicted a wide range of partition coefficients and clarified the partitioning mechanisms of compounds to LDPE.
JOURNAL OF CHROMATOGRAPHY A
(2023)
Article
Chemistry, Physical
Zhaoxi Sun, Abhijit Kayal, Zhihao Gong, Lei Zheng, Qiaole He
Summary: Validation of basic issues in molecular modelling of ionic liquids using fixed-charge force fields has been conducted through extensive free energy calculations, component-specific force-field refitting, and box-size dependence analysis. It is found that a combination of scaled RESP charges and GAFF2 parameter set provides an accurate and efficient option for atomistic simulations of ionic liquids derivatives.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Chemistry, Physical
Zuo-Yuan Zhang, Xiaohui Wang, Qiaole He, Zhaoxi Sun
Summary: This study develops low-cost machine-learning estimators to further explore the chemical accuracy frontier. By collecting experimental data, a dataset is created to accurately predict solvation and water-ILs biphasic partition.
JOURNAL OF MOLECULAR LIQUIDS
(2023)
Article
Chemistry, Physical
Alhadji Malloum, Jeanet Conradie
Summary: In this study, the solvation free energy of the proton in acetonitrile was calculated using the cluster continuum solvation model, with an estimated value of -1022.0 kJmol(-1) at the MP2/CBS level of theory. The results showed excellent agreement with the experimental estimate based on the tetraphenylarsonium-tetraphenylborate (TATB) approach.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Review
Chemistry, Physical
Alhadji Malloum, Jean Jules Fifen, Jeanet Conradie
Summary: This article discusses the importance of absolute solvation energies of solutes in solution and methods for evaluating these energies. The study shows that these absolute solvation energies are crucial for determining the acids proton dissociation constant of organic compounds, as well as for the development of continuum solvation models and force fields. While the absolute solvation energies of solutes cannot be determined experimentally, they can be assessed through various methods.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Chemistry, Physical
Hafiz Saqib Ali, Richard H. Henchman
Summary: The energy-entropy multiscale cell correlation (EE-MCC) method is used to calculate toluene-water log P values of 16 drug molecules in the SAMPL9 physical properties challenge. The log P values calculated by EE-MCC have a mean average error of 0.82 and standard error of the mean of 0.97 versus experiment, which is comparable with the best methods entered in SAMPL9. The main contribution to log P is from energy. Less polar drugs have more favourable energies of transfer.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Thermodynamics
Svetlana Blokhina, Angelica Sharapova, Marina Ol'khovich, German Perlovich
Summary: This study determined the solubility of the antifungal drug CLZ in different solvents and analyzed its thermodynamic properties. The results showed that CLZ has good solubility in 1-octanol and hexane, while water is a poor solvent for CLZ.
JOURNAL OF THERMAL ANALYSIS AND CALORIMETRY
(2022)
Article
Biochemistry & Molecular Biology
Sergio A. Rodriguez, Jasmine Vy Tran, Spencer J. Sabatino, Andrew S. Paluch
Summary: This study made blind predictions of the octanol/water partition coefficients and pKa for 22 drug-like compounds. The use of solution phase-optimized geometries resulted in better agreement with experimental data compared to gas-phase optimized geometries. Furthermore, the use of an explicit water molecule improved the accuracy of pKa predictions.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
(2022)
Article
Biochemistry & Molecular Biology
Shujie Fan, Hristo Nedev, Ranjit Vijayan, Bogdan I. Iorga, Oliver Beckstein
Summary: Water-octanol partition coefficients for molecules in the SAMPL7 challenge were predicted using explicit solvent classical molecular dynamics (MD) simulations. Extensive sampling is needed to produce precise predictions, and high precision does not necessarily lead to high accuracy.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
(2021)
Article
Engineering, Environmental
Tunga Salthammer, Stefan Grimme, Marcel Stahn, Uwe Hohm, Wolf-Ulrich Palm
Summary: Quantum chemical composite approach is a powerful method for calculating reliable partition coefficients, considering all physical contributions to the conformational free energy and generating structure ensembles for the two phases independently and consistently.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2022)
Article
Mathematics, Applied
Matthias Erbar, Martin Huesmann, Thomas Leble
Summary: This study proves that at every positive temperature, the infinite-volume free energy of the one-dimensional log-gas or beta-ensemble has a unique minimizer, which is the Sine-beta process derived from random matrix theory. The research relies on a quantitative displacement convexity argument at the level of point processes, and on the screening procedure introduced by Sandier-Serfaty.
COMMUNICATIONS ON PURE AND APPLIED MATHEMATICS
(2021)
Article
Chemistry, Physical
Garrett E. Long, Pratik Dhakal, Bryce N. Redeker, Andrew S. Paluch
MOLECULAR SIMULATION
(2019)
Article
Chemistry, Physical
Pratik Dhakal, Jonathan A. Ouimet, Sydnee N. Roese, Andrew S. Paluch
JOURNAL OF MOLECULAR LIQUIDS
(2019)
Article
Chemistry, Multidisciplinary
Pratik Dhakal, Anthony R. Weise, Martin C. Fritsch, Cassandra M. O'Dell, Andrew S. Paluch
Article
Biochemistry & Molecular Biology
Osmair Vital de Oliveira, Gerd B. Rocha, Andrew S. Paluch, Luciano T. Costa
Summary: In this study, molecular modeling techniques were used to identify potential drug candidates against SARS-CoV-2 by observing conformational changes and antigen exposure through molecular dynamics simulation. A total of 24 potential candidates, including traditional herbal isolates and approved drugs, were selected from a large drug database based on binding energy calculations.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Article
Engineering, Chemical
Sydnee N. Roese, Justin D. Heintz, Cole B. Uzat, Alexa J. Schmidt, Griffin Margulis, Spencer J. Sabatino, Andrew S. Paluch
Article
Biochemistry & Molecular Biology
Spencer J. Sabatino, Andrew S. Paluch
Summary: In this study, blind predictions of octanol/water partition coefficients for drug-like compounds were made using molecular dynamics simulations. It was found that the predictions were sensitive to the choice of water force field, and the inclusion of water in the octanol-rich phase had a significant impact, which was also dependent on the chemical structure of the solute.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
(2021)
Article
Biochemistry & Molecular Biology
Osmair Vital de Oliveira, Maria Cristina Andreazza Costa, Ricardo Marques da Costa, Rafael Giordano Viegas, Andrew S. Paluch, Marcia Miguel Castro Ferreira
Summary: This study identifies six potential candidates from herbal compounds to inhibit the SARS-CoV-2 main protease through virtual screening and molecular dynamics simulations. The results suggest that these compounds interact with the protease through specific residues in the binding pocket, and non-polar and polar groups with hydrogen bond acceptors play an important role in the interactions. These findings provide valuable insights for future drug design against COVID-19.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Chemistry, Physical
Haroldo C. Da Silva, Andrew S. Paluch, Luciano T. Costa, Wagner B. De Almeida
Summary: This study investigated the solubility of flavonoid rutin in various solvents and calculated the solvation free energy using quantum chemical methods. The results did not strictly follow the observed solubility trend, but the PCM model (DIS, REP, CAV) showed overall agreement with the experimental solubility profile. Experimental and theoretical discrepancies were found in certain solvents, indicating the need for further investigation.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Engineering, Chemical
Lucas Paul, Geradius Deogratias, Daniel M. Shadrack, Celestin N. Mudogo, Kelvin M. Mtei, Revocatus L. Machunda, Andrew S. Paluch, Fidele Ntie-Kang
Summary: This study investigates the physical properties of linamarin and how different solvents affect these properties. The results show that water exhibits the strongest interaction with linamarin, and DMSO is the best solvent.
Article
Engineering, Chemical
Rachel C. Ollier, Thomas Nguyen, Hrithik Agarwal, Jeremy R. Phifer, Larissa Ferreira da Silva, Gabriel Goncalves Nogueira, Ana Karolyne Pereira Barbosa, Ryan T. Ley, Elizabeth J. O'Loughlin, Brett T. Rygelski, Spencer J. Sabatino, Andrew S. Paluch
Summary: This study demonstrates a method to predict the equilibrium solubility of nonelectrolyte solids using a small number of molecular simulation free energy calculations to generate reference data.
Article
Biochemistry & Molecular Biology
Sergio A. Rodriguez, Jasmine Vy Tran, Spencer J. Sabatino, Andrew S. Paluch
Summary: This study made blind predictions of the octanol/water partition coefficients and pKa for 22 drug-like compounds. The use of solution phase-optimized geometries resulted in better agreement with experimental data compared to gas-phase optimized geometries. Furthermore, the use of an explicit water molecule improved the accuracy of pKa predictions.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
(2022)
Article
Biochemical Research Methods
Denis Mteremko, Jaffu Chilongola, Andrew S. Paluch, Musa Chacha
Summary: A drug repositioning computational approach was used to search for inhibitors of human thymidylate synthase. The drugs Imatinib, Lumacaftor and Nal-demedine were identified as likely candidates for repurposing through ensemble-based virtual screening of FDA-approved drugs. The inclusion of water forcefield in the extended AutoDock scoring function revealed the role of water in drug-receptor interactions. Further calculations based on the Molecular Mechanics Poisson-Boltzmann Surface Area method showed that these candidate drugs have good binding affinities. Molecular dynamics trajectory analysis confirmed stable structures for these drugs throughout the simulation time.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2023)
Article
Engineering, Chemical
Nick H. Wong, Pratik Dhakal, Sydnee N. Roese, Andrew S. Paluch
Summary: Tools for predicting vapor-liquid phase equilibria are crucial for separation process design. The MOSCED method, based on solubility parameters, accurately predicts the limiting activity coefficient and sheds light on intermolecular interactions. This study demonstrates MOSCED's ability to predict phase equilibria and correlates enthalpy of vaporization and vapor pressure.
Article
Biochemical Research Methods
Denis Mteremko, Jaffu Chilongola, Andrew S. Paluch, Musa Chacha
Summary: This study demonstrates the potential of compounds NEA4433 and NEA4434 as strong candidates for drug targeting human thymidylate synthase (hTS) due to their excellent binding affinity, stability, and interaction with key residues involved in hTS substrate and cofactor binding.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2023)