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Herboth R, Lyubartsev AP. Exploring Carbamazepine Polymorph Crystal Growth in Water by Enhanced Sampling Simulations. ACS OMEGA 2024; 9:36718-36731. [PMID: 39220538 PMCID: PMC11360048 DOI: 10.1021/acsomega.4c05458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 08/01/2024] [Accepted: 08/06/2024] [Indexed: 09/04/2024]
Abstract
In this work, the polymorphism of the active pharmaceutical ingredient carbamazepine (CBZ) was investigated by using molecular dynamics simulations with an enhanced sampling scheme. A single molecule of CBZ attaching to flat surfaces of different polymorphs was used as a model for secondary nucleation in water. A novel approach was developed to compute the free energy profile characterizing the adsorption of molecules with orientation aligned with the crystal structure of the surface. The distribution of states that showed alignment was used to rescale the adsorption free energy to include only the contribution that is consistent with crystal growth. The resulting free energy surfaces showed favorable thermodynamics for the most stable form, Form III and the second most stable form, Form I. The primary crystallization product, a dihydrate, was found to be less favorable, implying a nonclassical crystallization pathway. We suggest that a major contribution determining the energetics is the hydrophobicity of the surface. This thermodynamic ranking provides valuable information about the molecular pathways of polymorph growth and will further contribute to the understanding of the crystallization process of CBZ, which is imperative since polymorph formation can alter the physical properties of a drug significantly.
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Affiliation(s)
- Radost Herboth
- Department of Materials and
Environmental Chemistry, Stockholm University, Svante Arrhenius väg 16C, 106 91 Stockholm, Sweden
| | - Alexander P. Lyubartsev
- Department of Materials and
Environmental Chemistry, Stockholm University, Svante Arrhenius väg 16C, 106 91 Stockholm, Sweden
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2
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Raman AS, Selloni A. Insights into the structure and dynamics of K+ ions at the muscovite-water interface from machine learning potential simulations. J Chem Phys 2024; 160:244708. [PMID: 38940541 DOI: 10.1063/5.0217720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Accepted: 06/10/2024] [Indexed: 06/29/2024] Open
Abstract
The surfaces of many minerals are covered by naturally occurring cations that become partially hydrated and can be replaced by hydronium or other cations when the surface is exposed to water or an aqueous solution. These ion exchange processes are relevant to various chemical and transport phenomena, yet elucidating their microscopic details is challenging for both experiments and simulations. In this work, we make a first step in this direction by investigating the behavior of the native K+ ions at the interface between neat water and the muscovite mica (001) surface with ab-initio-based machine learning molecular dynamics and enhanced sampling simulations. Our results show that the desorption of the surface K+ ions in pure ion-free water has a significant free energy barrier irrespective of their local surface arrangement. In contrast, facile K+ diffusion between mica's ditrigonal cavities characterized by different Al/Si orderings is observed. This behavior suggests that the K+ ions may favor a dynamic disordered surface arrangement rather than complete desorption when exposed to deionized water.
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Affiliation(s)
- Abhinav S Raman
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - Annabella Selloni
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
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3
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Qi X, Pfaendtner J. High-Throughput Computational Screening of Solid-Binding Peptides. J Chem Theory Comput 2024; 20:2959-2968. [PMID: 38499981 DOI: 10.1021/acs.jctc.3c01286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Inspired by biomineralization, a naturally occurring, protein-facilitated process, solid-binding peptides (SBPs) have gained much attention for their potential to fabricate various shaped nanocrystals and hierarchical nanostructures. The advantage of SBPs over other traditionally used synthetic polymers or short ligands is their tunable interaction with the solid material surface via carefully programmed sequence and being solution-dependent simultaneously. However, designing a sequence with targeted binding affinity or selectivity often involves intensive processes such as phage display, and only a limited number of sequences can be identified. Other computational efforts have also been introduced, but the validation process remains prohibitively expensive once a suitable sequence has been identified. In this paper, we present a new model to rapidly estimate the binding free energy of any given sequence to a solid surface. We show how the overall binding of a polypeptide can be estimated from the free energy contribution of each residue based on the statistics of the thermodynamically stable structure ensemble. We validated our model using five silica-binding peptides of different binding affinities and lengths and showed that the model is accurate and robust across a wider range of chemistries and binding strengths. The computational cost of this method can be as low as 3% of the commonly used enhanced sampling scheme for similar studies and has a great potential to be used in high-throughput algorithms to obtain larger training data sets for machine learning SBP screening.
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Affiliation(s)
- Xin Qi
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03784, United States
| | - Jim Pfaendtner
- Department of Chemical & Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
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Sanz Matias A, Roncoroni F, Sundararaman S, Prendergast D. Ca-dimers, solvent layering, and dominant electrochemically active species in Ca(BH 4) 2 in THF. Nat Commun 2024; 15:1397. [PMID: 38360965 PMCID: PMC11258298 DOI: 10.1038/s41467-024-45672-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 02/01/2024] [Indexed: 02/17/2024] Open
Abstract
Divalent ions (Mg, Ca, and Zn) are being considered as competitive, safe, and earth-abundant alternatives to Li-ion electrochemistry, but present challenges for stable cycling due to undesirable interfacial phenomena. We explore the formation of electroactive species in the electrolyte Ca(BH4)2∣THF using molecular dynamics coupled with a continuum model of bulk and interfacial speciation. Free-energy analysis and unsupervised learning indicate a majority population of neutral Ca dimers and monomers with diverse molecular conformations and an order of magnitude lower concentration of the primary electroactive charged species - the monocation, CaBH[Formula: see text] - produced via disproportionation of neutral complexes. Dense layering of THF molecules within ~1 nm of the electrode surface strongly modulates local electrolyte species populations. A dramatic increase in monocation population in this interfacial zone is induced at negative bias. We see no evidence for electrochemical activity of fully-solvated Ca2+. The consequences for performance are discussed in light of this molecular-scale insight.
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Affiliation(s)
- Ana Sanz Matias
- Joint Center for Energy Storage Research, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Fabrice Roncoroni
- Joint Center for Energy Storage Research, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Siddharth Sundararaman
- Joint Center for Energy Storage Research, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - David Prendergast
- Joint Center for Energy Storage Research, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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Chakrabarti R, Verma L, Hadjiev VG, Palmer JC, Vekilov PG. The elementary reactions for incorporation into crystals. Proc Natl Acad Sci U S A 2024; 121:e2320201121. [PMID: 38315836 PMCID: PMC10873555 DOI: 10.1073/pnas.2320201121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 12/26/2023] [Indexed: 02/07/2024] Open
Abstract
The growth rates of crystals are largely dictated by the chemical reaction between solute and kinks, in which a solute molecule severs its bonds with the solvent and establishes new bonds with the kink. Details on this sequence of bond breaking and rebuilding remain poorly understood. To elucidate the reaction at the kinks we employ four solvents with distinct functionalities as reporters on the microscopic structures and their dynamics along the pathway into a kink. We combine time-resolved in situ atomic force microscopy and x-ray and optical methods with molecular dynamics simulations. We demonstrate that in all four solvents the solute, etioporphyrin I, molecules reach the steps directly from the solution; this finding identifies the measured rate constant for step growth as the rate constant of the reaction between a solute molecule and a kink. We show that the binding of a solute molecule to a kink divides into two elementary reactions. First, the incoming solute molecule sheds a fraction of its solvent shell and attaches to molecules from the kink by bonds distinct from those in its fully incorporated state. In the second step, the solute breaks these initial bonds and relocates to the kink. The strength of the preliminary bonds with the kink determines the free energy barrier for incorporation into a kink. The presence of an intermediate state, whose stability is controlled by solvents and additives, may illuminate how minor solution components guide the construction of elaborate crystal architectures in nature and the search for solution compositions that suppress undesirable or accelerate favored crystallization in industry.
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Affiliation(s)
- Rajshree Chakrabarti
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX77204-4004
| | - Lakshmanji Verma
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX77204-4004
| | - Viktor G. Hadjiev
- Texas Center for Superconductivity, University of Houston, Houston, TX77004-50024
| | - Jeremy C. Palmer
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX77204-4004
| | - Peter G. Vekilov
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX77204-4004
- Department of Chemistry, University of Houston, Houston, TX77204-5003
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Spackman PR, Walisinghe AJ, Anderson MW, Gale JD. CrystalClear: an open, modular protocol for predicting molecular crystal growth from solution. Chem Sci 2023; 14:7192-7207. [PMID: 37416706 PMCID: PMC10321482 DOI: 10.1039/d2sc06761g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 05/22/2023] [Indexed: 07/08/2023] Open
Abstract
We present a new protocol for the prediction of free energies that determine the growth of sites in molecular crystals for subsequent use in Monte Carlo simulations using tools such as CrystalGrower [Hill et al., Chemical Science, 2021, 12, 1126-1146]. Key features of the proposed approach are that it requires minimal input, namely the crystal structure and solvent only, and provides automated, rapid generation of the interaction energies. The constituent components of this protocol, namely interactions between molecules (growth units) in the crystal, solvation contributions and treatment of long-range interactions are described in detail. The power of this method is shown via prediction of crystal shapes for ibuprofen grown from ethanol, ethyl acetate, toluene and acetonitrile, adipic acid grown from water, and five polymorphs (ON, OP, Y, YT04 and R) of ROY (5-methyl-2-[(2-nitrophenyl)amino]-3-thiophenecarbonitrile), with promising results. The predicted energies may be used directly or subsequently refined against experimental data, facilitating insight into the interactions governing crystal growth, while also providing a prediction of the solubility of the material. The protocol has been implemented in standalone, open-source software made available alongside this publication.
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Affiliation(s)
- Peter R Spackman
- Curtin Institute for Computation, School of Molecular and Life Sciences, Curtin University GPO Box U1987 Perth Western Australia 6845 Australia
| | - Alvin J Walisinghe
- Curtin Institute for Computation, School of Molecular and Life Sciences, Curtin University GPO Box U1987 Perth Western Australia 6845 Australia
- Centre for Nanoporous Materials, Department of Chemistry, The University of Manchester Oxford Road Manchester M13 9PL UK
| | - Michael W Anderson
- Curtin Institute for Computation, School of Molecular and Life Sciences, Curtin University GPO Box U1987 Perth Western Australia 6845 Australia
- Centre for Nanoporous Materials, Department of Chemistry, The University of Manchester Oxford Road Manchester M13 9PL UK
| | - Julian D Gale
- Curtin Institute for Computation, School of Molecular and Life Sciences, Curtin University GPO Box U1987 Perth Western Australia 6845 Australia
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