Pharmaceutical Digital Design: From Chemical Structure through Crystal Polymorph to Conceptual Crystallization Process Christopher L. Burcham, Michael F. Doherty, Baron G. Peters, Sarah L. Price, Matteo Salvalaglio, Susan M. Reutzel-Edens, Louise S. Price, Ravi Kumar Reddy Addula, Nicholas Francia, Vikram Khanna, Yongsheng Zhao Crystal Growth and Design, 2024 A workflow for the digital design of crystallization processes starting from the chemical structure of the active pharmaceutical ingredient (API) is a multistep, multidisciplinary process. A simple version would be to first predict the API crystal structure and, from it, the corresponding properties of solubility, morphology, and growth rates, assuming that the nucleation would be controlled by seeding, and then use these parameters to design the crystallization process. This is usually an oversimplification as most APIs are polymorphic, and the most stable crystal of the API alone may not have the required properties for development into a drug product. This perspective, from the experience of a Lilly Digital Design project, considers the fundamental theoretical basis of crystal structure prediction (CSP), free energy, solubility, morphology, and growth rate prediction, and the current state of nucleation simulation. This is illustrated by applying the modeling techniques to real examples, olanzapine and succinic acid. We demonstrate the promise of using ab initio computer modeling for solid form selection and process design in pharmaceutical development. We also identify open problems in the application of current computational modeling and achieving the accuracy required for immediate implementation that currently limit the applicability of the approach.
Kinetic coefficient for ice-water interface from simulated non-equilibrium relaxation at coexistence Ravi Kumar Reddy Addula, Baron Peters Journal of Chemical Physics, 2022 In the theory of solidification, the kinetic coefficient multiplies the local supercooling to give the solid–liquid interface velocity. The same coefficient should drive interface migration at the coexistence temperature in proportion to a curvature force. This work computes the ice–water kinetic coefficient from molecular simulations starting from a sinusoidal ice–water interface at the coexistence temperature. We apply this method to the basal and prismatic ice planes and compare results to previous estimates from equilibrium correlation functions and simulations at controlled supercooling.
Computing contact angles for oil-water-rock systems via thermodynamic integration Rohan Patel, Ravi Kumar Reddy Addula, Majeed Shaik, Sudeep N. Punnathanam Journal of Chemical Physics, 2022 Wettability of rock surfaces with respect to oil and water, which is characterized by the contact angle, is an important factor that determines the efficacy of enhanced oil recovery operations. Experimental determination of contact angles for oil–water–rock systems is expensive and time-consuming due to the extremely long times needed for the establishment of adsorption equilibrium at the liquid–solid interface. Hence, molecular simulations form an attractive tool for computing contact angles. In this work, we use the cleaving wall technique that was developed previously in our group [R. K. R. Addula and S. N. Punnathanam, J. Chem. Phys. 153, 154504 (2020)] to compute solid–liquid interfacial free energy, which is then combined with Young’s equation to compute the oil–water contact angle on silica surfaces. The silica surface is modeled with the INTERFACE force field that has been developed to accurately reproduce experimental data. We have considered three different surface chemistries of silica, namely, Q2, Q3, and Q4, in this study. Our calculations reveal that while the Q2 and Q3 surfaces are completely wetted by water, the Q4 surface is partially non-wetted by water. All the simulations needed for this calculation can be performed using the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) molecular package. This should facilitate wider adoption of the Young’s equation route to compute contact angles for systems comprised of complex molecules.
Molecular Theory of Nucleation from Dilute Phases: Formulation and Application to Lennard-Jones Vapor Ravi Kumar Reddy Addula, Sudeep N. Punnathanam Physical Review Letters, 2021 In this Letter, we present a molecular theory of nucleation from dilute phases such as vapors or dilute solutions. The theory can model the nonclassical two-step crystal nucleation seen in many systems. When applied to study and analyze the crystal nucleation pathways from Lennard-Jones vapor, we find that prior explanations of the two-step mechanism based on lower barrier height for liquid nuclei is incomplete. The analysis from the molecular theory reveal that a complete explanation would also require consideration of anisotropy in the diffusion constants for growth of liquid droplets vis-á-vis the crystal nuclei.
Computation of solid-fluid interfacial free energy in molecular systems using thermodynamic integration Ravi Kumar Reddy Addula, Sudeep N. Punnathanam Journal of Chemical Physics, 2020 In this article, we present two methods based on thermodynamic integration for computing solid-fluid interfacial free energy for a molecular system. As a representative system, we choose two crystal polymorphs of orcinol (5-methylbenzene-1,3-diol) as the solid phase and chloroform and nitromethane as the liquid phase. The computed values of the interfacial free energy are then used in combination with the classical nucleation theory to predict solvent induced polymorph selectivity during crystallization of orcinol from solution.
RECENT SCHOLAR PUBLICATIONS
Modeling homogeneous ice nucleation from drop-freezing experiments: impact of droplet volume dispersion and cooling rates RKR Addula, I de Almeida Ribeiro, V Molinero, B Peters Atmospheric Chemistry and Physics 24 (18), 10833-10848 , 2024 2024 Citations: 4
Pharmaceutical digital design: From chemical structure through crystal polymorph to conceptual crystallization process CL Burcham, MF Doherty, BG Peters, SL Price, M Salvalaglio, ... Crystal Growth & Design 24 (13), 5417-5438 , 2024 2024 Citations: 33
Ice nucleation from drop-freezing experiments: Impact of droplet volume dispersion and cooling rates RKR Addula, I de Almeida Ribeiro, V Molinero, B Peters EGUsphere 2024, 1 , 2024 2024 Citations: 3
A Mathematical Model to Describe the Oriented Attachment of Molecules in Crystal Growth. RKR Addula, B Peters 2022 AIChE Annual Meeting , 2022 2022
Kinetic coefficient for ice–water interface from simulated non-equilibrium relaxation at coexistence RKR Addula, B Peters The Journal of Chemical Physics 157 (17) , 2022 2022 Citations: 6
Computing contact angles for oil-water-rock systems via thermodynamic integration SNP Rohan Patel, Ravi kumar reddy Addula, Majeed Shaik Journal of chemical physics , 2022 2022 Citations: 5
Study of solvent induced polymorphism and crystal nucleation from solution RKR Addula 2021
Review of the Frenkel–Ladd technique for computing free energies of crystalline solids RK Reddy Addula, SK Veesam, SN Punnathanam Molecular Simulation 47 (10-11), 824-830 , 2021 2021 Citations: 9
Molecular Theory of Nucleation from Dilute Phases: Formulation and Application to Lennard-Jones Vapor SNP Ravi Kumar Reddy A Physical Review Letters 126 (14), 146001 , 2021 2021 Citations: 8
Computation of solid–fluid interfacial free energy in molecular systems using thermodynamic integration RKR Addula, SN Punnathanam The Journal of Chemical Physics 153 (15) , 2020 2020 Citations: 13
Calculation of excess free energy of molecular solids comprised of flexible molecules using Einstein molecule method RK Reddy A, SN Punnathanam Molecular Simulation 44 (10), 781-788 , 2018 2018 Citations: 9
MOST CITED SCHOLAR PUBLICATIONS
Pharmaceutical digital design: From chemical structure through crystal polymorph to conceptual crystallization process CL Burcham, MF Doherty, BG Peters, SL Price, M Salvalaglio, ... Crystal Growth & Design 24 (13), 5417-5438 , 2024 2024 Citations: 33
Computation of solid–fluid interfacial free energy in molecular systems using thermodynamic integration RKR Addula, SN Punnathanam The Journal of Chemical Physics 153 (15) , 2020 2020 Citations: 13
Review of the Frenkel–Ladd technique for computing free energies of crystalline solids RK Reddy Addula, SK Veesam, SN Punnathanam Molecular Simulation 47 (10-11), 824-830 , 2021 2021 Citations: 9
Calculation of excess free energy of molecular solids comprised of flexible molecules using Einstein molecule method RK Reddy A, SN Punnathanam Molecular Simulation 44 (10), 781-788 , 2018 2018 Citations: 9
Molecular Theory of Nucleation from Dilute Phases: Formulation and Application to Lennard-Jones Vapor SNP Ravi Kumar Reddy A Physical Review Letters 126 (14), 146001 , 2021 2021 Citations: 8
Kinetic coefficient for ice–water interface from simulated non-equilibrium relaxation at coexistence RKR Addula, B Peters The Journal of Chemical Physics 157 (17) , 2022 2022 Citations: 6
Computing contact angles for oil-water-rock systems via thermodynamic integration SNP Rohan Patel, Ravi kumar reddy Addula, Majeed Shaik Journal of chemical physics , 2022 2022 Citations: 5
Modeling homogeneous ice nucleation from drop-freezing experiments: impact of droplet volume dispersion and cooling rates RKR Addula, I de Almeida Ribeiro, V Molinero, B Peters Atmospheric Chemistry and Physics 24 (18), 10833-10848 , 2024 2024 Citations: 4
Ice nucleation from drop-freezing experiments: Impact of droplet volume dispersion and cooling rates RKR Addula, I de Almeida Ribeiro, V Molinero, B Peters EGUsphere 2024, 1 , 2024 2024 Citations: 3
A Mathematical Model to Describe the Oriented Attachment of Molecules in Crystal Growth. RKR Addula, B Peters 2022 AIChE Annual Meeting , 2022 2022
Study of solvent induced polymorphism and crystal nucleation from solution RKR Addula 2021