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David R, Tuñón I, Laage D. Competing Reaction Mechanisms of Peptide Bond Formation in Water Revealed by Deep Potential Molecular Dynamics and Path Sampling. J Am Chem Soc 2024; 146:14213-14224. [PMID: 38739765 DOI: 10.1021/jacs.4c03445] [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: 05/16/2024]
Abstract
The formation of an amide bond is an essential step in the synthesis of materials and drugs, and in the assembly of amino acids to form peptides. The mechanism of this reaction has been studied extensively, in particular to understand how it can be catalyzed, but a representation capable of explaining all the experimental data is still lacking. Numerical simulation should provide the necessary molecular description, but the solvent involvement poses a number of challenges. Here, we combine the efficiency and accuracy of neural network potential-based reactive molecular dynamics with the extensive and unbiased exploration of reaction pathways provided by transition path sampling. Using microsecond-scale simulations at the density functional theory level, we show that this method reveals the presence of two competing distinct mechanisms for peptide bond formation between alanine esters in aqueous solution. We describe how both reaction pathways, via a general base catalysis mechanism and via direct cleavage of the tetrahedral intermediate respectively, change with pH. This result contrasts with the conventional mechanism involving a single pathway in which only the barrier heights are affected by pH. We show that this new proposal involving two competing mechanisms is consistent with the experimental data, and we discuss the implications for peptide bond formation under prebiotic conditions and in the ribosome. Our work shows that integrating deep potential molecular dynamics with path sampling provides a powerful approach for exploring complex chemical mechanisms.
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Affiliation(s)
- Rolf David
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Iñaki Tuñón
- Departamento de Química Física, Universitat de Valencia, Burjassot, 46100 Valencia, Spain
| | - Damien Laage
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
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Karalis K, Zahn D, Prasianakis NI, Niceno B, Churakov SV. Deciphering the molecular mechanism of water boiling at heterogeneous interfaces. Sci Rep 2021; 11:19858. [PMID: 34615926 PMCID: PMC8494797 DOI: 10.1038/s41598-021-99229-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 09/17/2021] [Indexed: 11/23/2022] Open
Abstract
Water boiling control evolution of natural geothermal systems is widely exploited in industrial processes due to the unique non-linear thermophysical behavior. Even though the properties of water both in the liquid and gas state have been extensively studied experimentally and by numerical simulations, there is still a fundamental knowledge gap in understanding the mechanism of the heterogeneous nucleate boiling controlling evaporation and condensation. In this study, the molecular mechanism of bubble nucleation at the hydrophilic and hydrophobic solid-water interface was determined by performing unbiased molecular dynamics simulations using the transition path sampling scheme. Analyzing the liquid to vapor transition path, the initiation of small void cavities (vapor bubbles nuclei) and their subsequent merging mechanism, leading to successively growing vacuum domains (vapor phase), has been elucidated. The molecular mechanism and the boiling nucleation sites' location are strongly dependent on the solid surface hydrophobicity and hydrophilicity. Then simulations reveal the impact of the surface functionality on the adsorbed thin water molecules film structuring and the location of high probability nucleation sites. Our findings provide molecular-scale insights into the computational aided design of new novel materials for more efficient heat removal and rationalizing the damage mechanisms.
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Affiliation(s)
| | - Dirk Zahn
- Lehrstuhl für Theoretische Chemie/Computer Chemie Centrum, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Nikolaos I Prasianakis
- Laboratory for Waste Management (LES), Paul Scherrer Institute, 5232, Villigen, Switzerland
| | - Bojan Niceno
- Laboratory of Scientific Computing and Modelling (LSM), Paul Scherrer Institute, 5232, Villigen, Switzerland
| | - Sergey V Churakov
- Institute of Geological Sciences, University of Bern, 3012, Bern, Switzerland.
- Laboratory for Waste Management (LES), Paul Scherrer Institute, 5232, Villigen, Switzerland.
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Zahn D. Thermodynamics and Kinetics of Prenucleation Clusters, Classical and Non-Classical Nucleation. Chemphyschem 2015; 16:2069-75. [PMID: 25914369 PMCID: PMC4529657 DOI: 10.1002/cphc.201500231] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Indexed: 11/17/2022]
Abstract
Recent observations of prenucleation species and multi-stage crystal nucleation processes challenge the long-established view on the thermodynamics of crystal formation. Here, we review and generalize extensions to classical nucleation theory. Going beyond the conventional implementation as has been used for more than a century now, nucleation inhibitors, precursor clusters and non-classical nucleation processes are rationalized as well by analogous concepts based on competing interface and bulk energy terms. This is illustrated by recent examples of species formed prior to/instead of crystal nucleation and multi-step nucleation processes. Much of the discussed insights were obtained from molecular simulation using advanced sampling techniques, briefly summarized herein for both nucleation-controlled and diffusion-controlled aggregate formation.
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Affiliation(s)
- Dirk Zahn
- Lehrstuhl für Theoretische Chemie/Computer Chemie Centrum, Friedrich-Alexander Universität Erlangen-Nürnberg, Nägelsbachstraße 25, 91052 Erlangen (Germany).
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Liu J, Cao XM, Hu P. Density functional theory study on the activation of molecular oxygen on a stepped gold surface in an aqueous environment: a new approach for simulating reactions in solution. Phys Chem Chem Phys 2014; 16:4176-85. [PMID: 24452136 DOI: 10.1039/c3cp54384f] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The activation of oxygen molecules is an important issue in the gold-catalyzed partial oxidation of alcohols in aqueous solution. The complexity of the solution arising from a large number of solvent molecules makes it difficult to study the reaction in the system. In this work, O2 activation on an Au catalyst is investigated using an effective approach to estimate the reaction barriers in the presence of solvent. Our calculations show that O2 can be activated, undergoing OOH* in the presence of water molecules. The OOH* can readily be formed on Au(211) via four possible pathways with almost equivalent free energy barriers at the aqueous-solid interface: the direct or indirect activation of O2 by surface hydrogen or the hydrolysis of O2 following a Langmuir-Hinshelwood mechanism or an Eley-Rideal mechanism. Among them, the Eley-Rideal mechanism may be slightly more favorable due to the restriction of the low coverage of surface H on Au(211) in the other mechanisms. The results shed light on the importance of water molecules on the activation of oxygen in gold-catalyzed systems. Solvent is found to facilitate the oxygen activation process mainly by offering extra electrons and stabilizing the transition states. A correlation between the energy barrier and the negative charge of the reaction center is found. The activation barrier is substantially reduced by the aqueous environment, in which the first solvation shell plays the most important role in the barrier reduction. Our approach may be useful for estimating the reaction barriers in aqueous systems.
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Affiliation(s)
- Jialong Liu
- State Key Laboratory of Chemical Engineering, Center for Computational Chemistry and Research Institute of Industrial Catalysis, East China University of Science & Technology, Shanghai 200237, China.
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Akimov AV, Muckerman JT, Prezhdo OV. Nonadiabatic Dynamics of Positive Charge during Photocatalytic Water Splitting on GaN(10-10) Surface: Charge Localization Governs Splitting Efficiency. J Am Chem Soc 2013; 135:8682-91. [DOI: 10.1021/ja4029395] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Alexey V. Akimov
- Department of Chemistry, University of Rochester, Rochester, New York 14627,
United States
- Chemistry
Department, Brookhaven National Laboratory, Upton, New York 11973,
United States
| | - James T. Muckerman
- Chemistry
Department, Brookhaven National Laboratory, Upton, New York 11973,
United States
| | - Oleg V. Prezhdo
- Department of Chemistry, University of Rochester, Rochester, New York 14627,
United States
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Zahn D. Tackling time-reversibility in transition path sampling molecular dynamics simulations. MOLECULAR SIMULATION 2012. [DOI: 10.1080/08927022.2011.614241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Anwar J, Zahn D. Atomistisches Verständnis der Keimbildung und des Kristallwachstums durch molekulare Simulationen. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201000463] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Anwar J, Zahn D. Uncovering molecular processes in crystal nucleation and growth by using molecular simulation. Angew Chem Int Ed Engl 2011; 50:1996-2013. [PMID: 21271625 DOI: 10.1002/anie.201000463] [Citation(s) in RCA: 151] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2010] [Indexed: 11/11/2022]
Abstract
Exploring nucleation processes by molecular simulation provides a mechanistic understanding at the atomic level and also enables kinetic and thermodynamic quantities to be estimated. However, whilst the potential for modeling crystal nucleation and growth processes is immense, there are specific technical challenges to modeling. In general, rare events, such as nucleation cannot be simulated using a direct "brute force" molecular dynamics approach. The limited time and length scales that are accessible by conventional molecular dynamics simulations have inspired a number of advances to tackle problems that were considered outside the scope of molecular simulation. While general insights and features could be explored from efficient generic models, new methods paved the way to realistic crystal nucleation scenarios. The association of single ions in solvent environments, the mechanisms of motif formation, ripening reactions, and the self-organization of nanocrystals can now be investigated at the molecular level. The analysis of interactions with growth-controlling additives gives a new understanding of functionalized nanocrystals and the precipitation of composite materials.
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Affiliation(s)
- Jamshed Anwar
- Computational Biophysics Laboratory, Institute of Pharmaceutical Innovation, University of Bradford, Bradford, BD7 1DP, UK.
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Peters B. Recent advances in transition path sampling: accurate reaction coordinates, likelihood maximisation and diffusive barrier-crossing dynamics. MOLECULAR SIMULATION 2010. [DOI: 10.1080/08927020903536382] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Rowley CN, Woo TK. New shooting algorithms for transition path sampling: Centering moves and varied-perturbation sizes for improved sampling. J Chem Phys 2009; 131:234102. [DOI: 10.1063/1.3274203] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Frenzel J, Seifert G, Zahn D. Surface Effects in the Pressure-Induced Structural Transformation of a ZnO Nanorod. Z Anorg Allg Chem 2009. [DOI: 10.1002/zaac.200900260] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Zahn D. Minimum energy pathways of brittle and ductile deformation/fracture processes. J Chem Phys 2008; 128:184707. [DOI: 10.1063/1.2918280] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Hu J, Ma A, Dinner AR. Bias annealing: a method for obtaining transition paths de novo. J Chem Phys 2007; 125:114101. [PMID: 16999460 DOI: 10.1063/1.2335640] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Computational studies of dynamics in complex systems require means for generating reactive trajectories with minimum knowledge about the processes of interest. Here, we introduce a method for generating transition paths when an existing one is not already available. Starting from biased paths obtained from steered molecular dynamics, we use a Monte Carlo procedure in the space of whole trajectories to shift gradually to sampling an ensemble of unbiased paths. Application to basin-to-basin hopping in a two-dimensional model system and nucleotide-flipping by a DNA repair protein demonstrates that the method can efficiently yield unbiased reactive trajectories even when the initial steered dynamics differ significantly. The relation of the method to others and the physical basis for its success are discussed.
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Affiliation(s)
- Jie Hu
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
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Fernandez-Ramos A, Miller JA, Klippenstein SJ, Truhlar DG. Modeling the kinetics of bimolecular reactions. Chem Rev 2007; 106:4518-84. [PMID: 17091928 DOI: 10.1021/cr050205w] [Citation(s) in RCA: 393] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Antonio Fernandez-Ramos
- Departamento de Quimica Fisica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
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Rowley CN, Woo TK. Generation of initial trajectories for transition path sampling of chemical reactions with ab initio molecular dynamics. J Chem Phys 2007; 126:024110. [PMID: 17228946 DOI: 10.1063/1.2424712] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Transition path sampling is an innovative method for focusing a molecular dynamics simulation on a reactive event. Although transition path sampling methods can generate an ensemble of reactive trajectories, an initial reactive trajectory must be generated by some other means. In this paper, the authors have evaluated three methods for generating initial reactive trajectories for transition path sampling with ab initio molecular dynamics. The authors have tested each of these methods on a set of chemical reactions involving the breaking and making of covalent bonds: the 1,2-hydrogen elimination in the borane-ammonia adduct, a tautomerization, and the Claisen rearrangement. The first method is to initiate trajectories from the potential energy transition state, which was effective for all reactions in the test set. Assigning atomic velocities found using normal mode analysis greatly improved the success of this method. The second method uses a high temperature molecular dynamics simulation and then iteratively reduces the total energy of the simulation until a low temperature reactive trajectory is found. This was effective in generating a low temperature trajectory from an initial trajectory run at 3000 K of the tautomerization reaction, although it failed for the other two. The third uses an orbital based bias potential to find a reactive trajectory and uses this trajectory to initiate an unbiased trajectory. The authors found that a highest occupied molecular orbital-lowest unoccupied molecular orbital bias could be used to find a reactive trajectory for the Claisen rearrangement, although it failed for the other two reactions. These techniques will help make it practical to use transition path sampling to study chemical reaction mechanisms that involve bond breaking and forming.
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Affiliation(s)
- Christopher N Rowley
- Centre for Catalysis Research and Innovation, Department of Chemistry, University of Ottawa, 10 Marie-Curie, Ottawa, Ontario, K1N 6N5, Canada
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