Combining MOSCED with molecular simulation free energy calculations or electronic structure calculations to develop an efficient tool for solvent formulation and selection
暂无分享,去创建一个
Jeremy R. Phifer | Andrew S. Paluch | Courtney E. Cox | Larissa Ferreira da Silva | Gabriel Gonçalves Nogueira | Ryan T. Ley | Elizabeth J. O'Loughlin | Ana Karolyne Pereira Barbosa | Brett T. Rygelski | C. E. Cox | G. G. Nogueira | A. Barbosa | Elizabeth J. O'Loughlin | Larissa Ferreira da Silva
[1] B. Efron. The jackknife, the bootstrap, and other resampling plans , 1987 .
[2] Charles H. Bennett,et al. Efficient estimation of free energy differences from Monte Carlo data , 1976 .
[3] Andrew S. Paluch,et al. Developing a Predictive Form of MOSCED for Nonelectrolyte Solids Using Molecular Simulation: Application to Acetanilide, Acetaminophen, and Phenacetin , 2016 .
[4] E. Maginn,et al. Computing the melting point and thermodynamic stability of the orthorhombic and monoclinic crystalline polymorphs of the ionic liquid 1-n-butyl-3-methylimidazolium chloride. , 2007, The Journal of chemical physics.
[5] J. M. Haile,et al. Thermodynamics: THE BASICS , 2005 .
[6] J. Ilja Siepmann,et al. Novel Configurational-Bias Monte Carlo Method for Branched Molecules. Transferable Potentials for Phase Equilibria. 2. United-Atom Description of Branched Alkanes , 1999 .
[7] C. Cramer,et al. Self-Consistent Reaction Field Model for Aqueous and Nonaqueous Solutions Based on Accurate Polarized Partial Charges. , 2007, Journal of chemical theory and computation.
[8] R. F. Blanks,et al. Thermodynamics of Polymer Solubility in Polar and Nonpolar Systems , 1964 .
[9] Andrew S. Paluch,et al. A method for computing the solubility limit of solids: application to sodium chloride in water and alcohols. , 2010, The Journal of chemical physics.
[10] J. Ilja Siepmann,et al. Transferable Potentials for Phase Equilibria. 6. United-Atom Description for Ethers, Glycols, Ketones, and Aldehydes , 2004 .
[11] D. Ambrose,et al. Handbook of the thermodynamics of organic compounds , 1987 .
[12] C. Vega,et al. Solubility of KF and NaCl in water by molecular simulation. , 2007, The Journal of chemical physics.
[13] Sebastian Diaz-Rodriguez,et al. Predicting cyclohexane/water distribution coefficients for the SAMPL5 challenge using MOSCED and the SMD solvation model , 2016, Journal of Computer-Aided Molecular Design.
[14] Timothy C. Frank,et al. Application of MOSCED and UNIFAC to Screen Hydrophobic Solvents for Extraction of Hydrogen-Bonding Organics from Aqueous Solution , 2007 .
[15] Å. Rasmuson,et al. Thermodynamics of molecular solids in organic solvents , 2012 .
[16] J. Smith,et al. Introduction to chemical engineering thermodynamics , 1949 .
[17] W. L. Jorgensen,et al. Comparison of simple potential functions for simulating liquid water , 1983 .
[18] A. Mark,et al. Avoiding singularities and numerical instabilities in free energy calculations based on molecular simulations , 1994 .
[19] Carsten Kutzner,et al. GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. , 2008, Journal of chemical theory and computation.
[20] Jeanette G. Grasselli,et al. CRC Handbook of Data on Organic Compounds , 1985 .
[21] C. Vega,et al. Solubility of NaCl in water by molecular simulation revisited. , 2012, The Journal of chemical physics.
[22] Neeraj Rai,et al. Transferable potentials for phase equilibria. 7. Primary, secondary, and tertiary amines, nitroalkanes and nitrobenzene, nitriles, amides, pyridine, and pyrimidine. , 2005, The journal of physical chemistry. B.
[23] K. Kobe. The properties of gases and liquids , 1959 .
[24] Andrzej Parczewski,et al. Organic solvents in the pharmaceutical industry. , 2010, Acta poloniae pharmaceutica.
[25] Wei Yang,et al. The Structure, Thermodynamics and Solubility of Organic Crystals from Simulation with a Polarizable Force Field. , 2012, Journal of chemical theory and computation.
[26] T. Brinck,et al. Prediction of solubility of solid organic compounds in solvents by UNIFAC , 2002 .
[27] Michael R. Shirts,et al. Statistically optimal analysis of samples from multiple equilibrium states. , 2008, The Journal of chemical physics.
[28] Neeraj Rai,et al. Transferable potentials for phase equilibria. 10. Explicit-hydrogen description of substituted benzenes and polycyclic aromatic compounds. , 2013, The journal of physical chemistry. B.
[29] David L. Mobley,et al. Guidelines for the analysis of free energy calculations , 2015, Journal of Computer-Aided Molecular Design.
[30] Å. Rasmuson,et al. Determination of the activity of a molecular solute in saturated solution , 2008 .
[31] D. Dollimore,et al. Calculation of vapor pressure curves for hydroxy benzoic acid derivatives using thermogravimetry , 2002 .
[32] William Q. Meeker,et al. Statistical Intervals: A Guide for Practitioners and Researchers , 2017 .
[33] Jürgen Gmehling,et al. Present status and potential of group contribution methods for process development , 2009 .
[34] Charles A. Eckert,et al. Revision of MOSCED Parameters and Extension to Solid Solubility Calculations , 2005 .
[35] Athanassios Z Panagiotopoulos,et al. Mean ionic activity coefficients in aqueous NaCl solutions from molecular dynamics simulations. , 2015, The Journal of chemical physics.
[36] Katherine S. Shing,et al. Computer simulation methods for the calculation of solubility in supercritical extraction systems , 1987 .
[37] M. Lísal,et al. Molecular simulation of aqueous electrolyte solubility. 3. Alkali-halide salts and their mixtures in water and in hydrochloric acid. , 2012, The journal of physical chemistry. B.
[38] Peter A. Crafts,et al. Correlation and Prediction of Drug Molecule Solubility in Mixed Solvent Systems with the Nonrandom Two-Liquid Segment Activity Coefficient (NRTL−SAC) Model , 2006 .
[39] J. Ilja Siepmann,et al. TRANSFERABLE POTENTIALS FOR PHASE EQUILIBRIA. 3. EXPLICIT-HYDROGEN DESCRIPTION OF NORMAL ALKANES , 1999 .
[40] Alán Aspuru-Guzik,et al. Advances in molecular quantum chemistry contained in the Q-Chem 4 program package , 2014, Molecular Physics.
[41] John W. Eaton,et al. GNU Octave manual version 3: a high-level interactive language for numerical computations , 2008 .
[42] Michael R. Shirts,et al. Solvation free energies of amino acid side chain analogs for common molecular mechanics water models. , 2005, The Journal of chemical physics.
[43] Peter T. Cummings,et al. Precision and accuracy of staged free-energy perturbation methods for computing the chemical potential by molecular simulation , 1998 .
[44] Å. Rasmuson,et al. Prediction of solubility curves and melting properties of organic and pharmaceutical compounds. , 2009, European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences.
[45] J. Prausnitz,et al. Regular and related solutions : the solubility of gases, liquids, and solids , 1970 .
[46] C. Hansen,et al. The Universality of the Solubility Parameter , 1969 .
[47] Jens Abildskov,et al. Solubility and Related Properties of Large Complex Chemicals – Part 2 , 2005 .
[48] David J. C. Constable,et al. Perspective on Solvent Use in the Pharmaceutical Industry , 2007 .
[49] R. Liu. Water-insoluble drug formulation , 2000 .
[50] David L Mobley,et al. Nonlinear scaling schemes for Lennard-Jones interactions in free energy calculations. , 2007, The Journal of chemical physics.
[51] Gregory D. Hawkins,et al. Prediction of Vapor Pressures from Self-Solvation Free Energies Calculated by the SM5 Series of Universal Solvation Models , 2000 .
[52] Christophe Chipot,et al. Comprar Free Energy Calculations · Theory and Applications in Chemistry and Biology | Chipot, Christophe | 9783540736172 | Springer , 2007 .
[53] C. Cramer,et al. Universal solvation model based on solute electron density and on a continuum model of the solvent defined by the bulk dielectric constant and atomic surface tensions. , 2009, The journal of physical chemistry. B.
[54] L. Fried,et al. Monte Carlo simulations of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB): Pressure and temperature effects for the solid phase and vapor-liquid phase equilibria. , 2008, The Journal of chemical physics.
[55] Rainer Storn,et al. Differential Evolution – A Simple and Efficient Heuristic for global Optimization over Continuous Spaces , 1997, J. Glob. Optim..
[56] Laura C. Draucker,et al. Experimental Determination and Model Prediction of Solid Solubility of Multifunctional Compounds in Pure and Mixed Nonelectrolyte Solvents , 2007 .
[57] Peter M. Kasson,et al. GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit , 2013, Bioinform..
[58] Bin Chen,et al. Microscopic structure and solvation in dry and wet octanol. , 2006, The journal of physical chemistry. B.
[59] J. M. Haile,et al. Thermodynamics: THE BASICS , 2005 .
[60] P. Kollman,et al. Automatic atom type and bond type perception in molecular mechanical calculations. , 2006, Journal of molecular graphics & modelling.
[61] Andrew S. Paluch,et al. Predicting the Solubility of Solid Phenanthrene: A Combined Molecular Simulation and Group Contribution Approach , 2013 .
[62] William R. Smith,et al. Molecular simulation of aqueous electrolyte solubility. 2. Osmotic ensemble Monte Carlo methodology for free energy and solubility calculations and application to NaCl. , 2011, The journal of physical chemistry. B.
[63] Michael R. Shirts,et al. Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins , 2003 .
[64] Neeraj Rai,et al. Transferable potentials for phase equilibria. 9. Explicit hydrogen description of benzene and five-membered and six-membered heterocyclic aromatic compounds. , 2007, The journal of physical chemistry. B.
[65] R. Reid,et al. The Properties of Gases and Liquids , 1977 .
[66] David M. Eike,et al. Atomistic simulation of solid-liquid coexistence for molecular systems: application to triazole and benzene. , 2006, The Journal of chemical physics.
[67] Michael R. Shirts,et al. Equilibrium free energies from nonequilibrium measurements using maximum-likelihood methods. , 2003, Physical review letters.
[68] Holger Gohlke,et al. The Amber biomolecular simulation programs , 2005, J. Comput. Chem..
[69] J. M. Haile,et al. Thermodynamics : fundamentals for applications , 2005 .
[70] G. Ciccotti,et al. Solubility of KF in water by molecular dynamics using the Kirkwood integration method , 2002 .
[71] Gürkan Sin,et al. Group-contribution+ (GC+) based estimation of properties of pure components: Improved property estimation and uncertainty analysis , 2012 .
[72] J. S. Rowlinson,et al. Molecular Thermodynamics of Fluid-Phase Equilibria , 1969 .
[73] Junmei Wang,et al. Development and testing of a general amber force field , 2004, J. Comput. Chem..
[74] J. Ilja Siepmann,et al. Transferable Potentials for Phase Equilibria. 1. United-Atom Description of n-Alkanes , 1998 .
[75] Peter T. Cummings,et al. Quantitative comparison and optimization of methods for evaluating the chemical potential by molecular simulation , 1997 .
[76] Melanie Keller,et al. Essentials Of Computational Chemistry Theories And Models , 2016 .
[77] J. Ilja Siepmann,et al. Monte Carlo Calculations for Alcohols and Their Mixtures with Alkanes. Transferable Potentials for Phase Equilibria. 5. United-Atom Description of Primary, Secondary, and Tertiary Alcohols , 2001 .
[78] P. Kollman,et al. A well-behaved electrostatic potential-based method using charge restraints for deriving atomic char , 1993 .
[79] J. I. Siepmann,et al. Investigation of the driving forces for retention in reversed-phase liquid chromatography: Monte Carlo simulations of solute partitioning between n-hexadecane and various aqueous-organic mixtures , 2010 .
[80] Ken A Dill,et al. Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations. , 2007, Journal of chemical theory and computation.
[81] J. Ilja Siepmann,et al. Transferable Potentials for Phase Equilibria. 4. United-Atom Description of Linear and Branched Alkenes and Alkylbenzenes , 2000 .
[82] Andrew S. Paluch,et al. Calculating the Fugacity of Pure, Low Volatile Liquids via Molecular Simulation with Application to Acetanilide, Acetaminophen, and Phenacetin , 2015 .
[83] Stanley M. Walas,et al. Phase equilibria in chemical engineering , 1985 .
[84] D. Truhlar,et al. The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals , 2008 .
[85] Rafiqul Gani,et al. Thermodynamic Property Modeling for Chemical Process and Product Engineering: Some Perspectives , 2009 .
[86] Peter A. Kollman,et al. Application of the multimolecule and multiconformational RESP methodology to biopolymers: Charge derivation for DNA, RNA, and proteins , 1995, J. Comput. Chem..
[87] David A. Kofke,et al. Appropriate methods to combine forward and reverse free-energy perturbation averages , 2003 .
[88] Jeremy R. Phifer,et al. Computing MOSCED parameters of nonelectrolyte solids with electronic structure methods in SMD and SM8 continuum solvents , 2017 .
[89] Measurement and Prediction of Solubility of Paracetamol in Water−Isopropanol Solution. Part 2. Prediction , 2006 .
[90] Charles A. Eckert,et al. Prediction of limiting activity coefficients by a modified separation of cohesive energy density model and UNIFAC , 1984 .
[91] Wim F Vranken,et al. ACPYPE - AnteChamber PYthon Parser interfacE , 2012, BMC Research Notes.
[92] Donald G Truhlar,et al. Generalized Born Solvation Model SM12. , 2013, Journal of chemical theory and computation.