1
|
Risal S, Singh N, Yao Y, Sun L, Risal S, Zhu W. Accelerating Elastic Property Prediction in Fe-C Alloys through Coupling of Molecular Dynamics and Machine Learning. MATERIALS (BASEL, SWITZERLAND) 2024; 17:601. [PMID: 38591477 PMCID: PMC10856267 DOI: 10.3390/ma17030601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/18/2024] [Accepted: 01/24/2024] [Indexed: 04/10/2024]
Abstract
The scarcity of high-quality data presents a major challenge to the prediction of material properties using machine learning (ML) models. Obtaining material property data from experiments is economically cost-prohibitive, if not impossible. In this work, we address this challenge by generating an extensive material property dataset comprising thousands of data points pertaining to the elastic properties of Fe-C alloys. The data were generated using molecular dynamic (MD) calculations utilizing reference-free Modified embedded atom method (RF-MEAM) interatomic potential. This potential was developed by fitting atomic structure-dependent energies, forces, and stress tensors evaluated at ground state and finite temperatures using ab-initio. Various ML algorithms were subsequently trained and deployed to predict elastic properties. In addition to individual algorithms, super learner (SL), an ensemble ML technique, was incorporated to refine predictions further. The input parameters comprised the alloy's composition, crystal structure, interstitial sites, lattice parameters, and temperature. The target properties were the bulk modulus and shear modulus. Two distinct prediction approaches were undertaken: employing individual models for each property prediction and simultaneously predicting both properties using a single integrated model, enabling a comparative analysis. The efficiency of these models was assessed through rigorous evaluation using a range of accuracy metrics. This work showcases the synergistic power of MD simulations and ML techniques for accelerating the prediction of elastic properties in alloys.
Collapse
Affiliation(s)
- Sandesh Risal
- Department of Mechanical Engineering, University of Houston, Houston, TX 77204, USA; (S.R.); (L.S.)
| | - Navdeep Singh
- Department of Mechanical Engineering, School of Engineering and Computer Science, University of the Pacific, Stockton, CA 95211, USA
| | - Yan Yao
- Materials Science and Engineering Program, University of Houston, Houston, TX 77204, USA; (Y.Y.); (S.R.)
- Department of Electrical and Computer Engineering, University of Houston, Houston, TX 77204, USA
| | - Li Sun
- Department of Mechanical Engineering, University of Houston, Houston, TX 77204, USA; (S.R.); (L.S.)
| | - Samprash Risal
- Materials Science and Engineering Program, University of Houston, Houston, TX 77204, USA; (Y.Y.); (S.R.)
| | - Weihang Zhu
- Department of Mechanical Engineering, University of Houston, Houston, TX 77204, USA; (S.R.); (L.S.)
- Department of Engineering Technology, University of Houston, Houston, TX 77204, USA
| |
Collapse
|
2
|
Berselli A, Benfenati F, Maragliano L, Alberini G. Multiscale modelling of claudin-based assemblies: a magnifying glass for novel structures of biological interfaces. Comput Struct Biotechnol J 2022; 20:5984-6010. [DOI: 10.1016/j.csbj.2022.10.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 10/24/2022] [Accepted: 10/24/2022] [Indexed: 11/03/2022] Open
|
3
|
Morishita T. Time-dependent principal component analysis: A unified approach to high-dimensional data reduction using adiabatic dynamics. J Chem Phys 2021; 155:134114. [PMID: 34624975 DOI: 10.1063/5.0061874] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Systematic reduction of the dimensionality is highly demanded in making a comprehensive interpretation of experimental and simulation data. Principal component analysis (PCA) is a widely used technique for reducing the dimensionality of molecular dynamics (MD) trajectories, which assists our understanding of MD simulation data. Here, we propose an approach that incorporates time dependence in the PCA algorithm. In the standard PCA, the eigenvectors obtained by diagonalizing the covariance matrix are time independent. In contrast, they are functions of time in our new approach, and their time evolution is implemented in the framework of Car-Parrinello or Born-Oppenheimer type adiabatic dynamics. Thanks to the time dependence, each of the step-by-step structural changes or intermittent collective fluctuations is clearly identified, which are often keys to provoking a drastic structural transformation but are easily masked in the standard PCA. The time dependence also allows for reoptimization of the principal components (PCs) according to the structural development, which can be exploited for enhanced sampling in MD simulations. The present approach is applied to phase transitions of a water model and conformational changes of a coarse-grained protein model. In the former, collective dynamics associated with the dihedral-motion in the tetrahedral network structure is found to play a key role in crystallization. In the latter, various conformations of the protein model were successfully sampled by enhancing structural fluctuation along the periodically optimized PC. Both applications clearly demonstrate the virtue of the new approach, which we refer to as time-dependent PCA.
Collapse
Affiliation(s)
- Tetsuya Morishita
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), Central 2, 1-1-1 Umezono, Tsukuba 305-8568, Japan and Mathematics for Advanced Materials Open Innovation Laboratory (MathAM-OIL), National Institute of Advanced Industrial Science and Technology (AIST), c/o AIMR, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| |
Collapse
|
4
|
Fujisaki H. Multiscale aspects of molecular motions: From molecular vibrations, conformational changes of biomolecules to cellular dynamics. J NIPPON MED SCH 2021; 89:9-15. [PMID: 34526452 DOI: 10.1272/jnms.jnms.2022_89-116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Molecular aspects of living systems are important because it is the most basic aspects of life as exemplified in biochemistry and structural biology. Since molecules move due to interactive forces between atoms, physics plays an important role to understand the dynamic phenomena of living systems. Here we review our multiscale approaches for computationally treating different levels of molecular motions: vibrational dynamics of molecules, conformational change of biomolecules, and cellular dynamics using statistical-mechanics-based models.
Collapse
Affiliation(s)
- Hiroshi Fujisaki
- Department of Physics, Nippon Medical School.,AMED-CREST, Japan Agency for Medical Research and Development
| |
Collapse
|
5
|
Pitard I, Malliavin TE. Structural Biology and Molecular Modeling to Analyze the Entry of Bacterial Toxins and Virulence Factors into Host Cells. Toxins (Basel) 2019; 11:toxins11060369. [PMID: 31238550 PMCID: PMC6628625 DOI: 10.3390/toxins11060369] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 06/17/2019] [Accepted: 06/18/2019] [Indexed: 12/26/2022] Open
Abstract
Understanding the functions and mechanisms of biological systems is an outstanding challenge. One way to overcome it is to combine together several approaches such as molecular modeling and experimental structural biology techniques. Indeed, the interplay between structural and dynamical properties of the system is crucial to unravel the function of molecular machinery’s. In this review, we focus on how molecular simulations along with structural information can aid in interpreting biological data. Here, we examine two different cases: (i) the endosomal translocation toxins (diphtheria, tetanus, botulinum toxins) and (ii) the activation of adenylyl cyclase inside the cytoplasm (edema factor, CyA, ExoY).
Collapse
Affiliation(s)
- Irène Pitard
- Unité de Bioinformatique Structurale, Institut Pasteur and CNRS UMR3528, 75015 Paris, France.
- Centre de Bioinformatique, Biostatistique et Biologie Intégrative, Institut Pasteur and CNRS USR3756, 75015 Paris, France.
- Sorbonne Université, Collège Doctoral, Ecole Doctorale Complexité du Vivant, 75005 Paris, France.
| | - Thérèse E Malliavin
- Unité de Bioinformatique Structurale, Institut Pasteur and CNRS UMR3528, 75015 Paris, France.
- Centre de Bioinformatique, Biostatistique et Biologie Intégrative, Institut Pasteur and CNRS USR3756, 75015 Paris, France.
| |
Collapse
|
6
|
Pharmacological and molecular dynamics analyses of differences in inhibitor binding to human and nematode PDE4: Implications for management of parasitic nematodes. PLoS One 2019; 14:e0214554. [PMID: 30917179 PMCID: PMC6436744 DOI: 10.1371/journal.pone.0214554] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Accepted: 03/14/2019] [Indexed: 11/19/2022] Open
Abstract
Novel chemical controls are needed that selectively target human, animal, and plant parasitic nematodes with reduced adverse effects on the host or the environment. We hypothesize that the phosphodiesterase (PDE) enzyme family represents a potential target for development of novel nematicides and anthelmintics. To test this, we identified six PDE families present in the nematode phylum that are orthologous to six of the eleven human PDE families. We characterized the binding interactions of family-selective PDE inhibitors with human and C. elegans PDE4 in conjunction with molecular dynamics (MD) simulations to evaluate differences in binding interactions of these inhibitors within the PDE4 catalytic domain. We observed that roflumilast (human PDE4-selective inhibitor) and zardaverine (selective for human PDE3 and PDE4) were 159- and 77-fold less potent, respectively, in inhibiting C. elegans PDE4. The pan-specific PDE inhibitor isobutyl methyl xanthine (IBMX) had similar affinity for nematode and human PDE4. Of 32 residues within 5 Å of the ligand binding site, five revealed significant differences in non-bonded interaction energies (van der Waals and electrostatic interaction energies) that could account for the differential binding affinities of roflumilast and zardaverine. One site (Phe506 in the human PDE4D3 amino acid sequence corresponding to Tyr253 in C. elegans PDE4) is predicted to alter the binding conformation of roflumilast and zardaverine (but not IBMX) into a less energetically favorable state for the nematode enzyme. The pharmacological differences in sensitivity to PDE4 inhibitors in conjunction with differences in the amino acids comprising the inhibitor binding sites of human and C. elegans PDE4 catalytic domains together support the feasibility of designing the next generation of anthelmintics/nematicides that could selectively bind to nematode PDEs.
Collapse
|
7
|
Isokinetic approach in logarithmic mean-force dynamics for on-the-fly free energy reconstruction. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.07.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|
8
|
Mohammadi M, Vashisth H. Pathways and Thermodynamics of Oxygen Diffusion in [FeFe]-Hydrogenase. J Phys Chem B 2017; 121:10007-10017. [DOI: 10.1021/acs.jpcb.7b06489] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Mohammadjavad Mohammadi
- Department of Chemical Engineering, University of New Hampshire, Durham 03824, New Hampshire, United States
| | - Harish Vashisth
- Department of Chemical Engineering, University of New Hampshire, Durham 03824, New Hampshire, United States
| |
Collapse
|
9
|
Verma R, Mitchell-Koch K. In Silico Studies of Small Molecule Interactions with Enzymes Reveal Aspects of Catalytic Function. Catalysts 2017; 7:212. [PMID: 30464857 PMCID: PMC6241538 DOI: 10.3390/catal7070212] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Small molecules, such as solvent, substrate, and cofactor molecules, are key players in enzyme catalysis. Computational methods are powerful tools for exploring the dynamics and thermodynamics of these small molecules as they participate in or contribute to enzymatic processes. In-depth knowledge of how small molecule interactions and dynamics influence protein conformational dynamics and function is critical for progress in the field of enzyme catalysis. Although numerous computational studies have focused on enzyme-substrate complexes to gain insight into catalytic mechanisms, transition states and reaction rates, the dynamics of solvents, substrates, and cofactors are generally less well studied. Also, solvent dynamics within the biomolecular solvation layer play an important part in enzyme catalysis, but a full understanding of its role is hampered by its complexity. Moreover, passive substrate transport has been identified in certain enzymes, and the underlying principles of molecular recognition are an area of active investigation. Enzymes are highly dynamic entities that undergo different conformational changes, which range from side chain rearrangement of a residue to larger-scale conformational dynamics involving domains. These events may happen nearby or far away from the catalytic site, and may occur on different time scales, yet many are related to biological and catalytic function. Computational studies, primarily molecular dynamics (MD) simulations, provide atomistic-level insight and site-specific information on small molecule interactions, and their role in conformational pre-reorganization and dynamics in enzyme catalysis. The review is focused on MD simulation studies of small molecule interactions and dynamics to characterize and comprehend protein dynamics and function in catalyzed reactions. Experimental and theoretical methods available to complement and expand insight from MD simulations are discussed briefly.
Collapse
Affiliation(s)
- Rajni Verma
- Department of Chemistry, McKinley Hall, Wichita State University, 1845 Fairmount, Wichita, KS 67260-0051, USA
| | - Katie Mitchell-Koch
- Department of Chemistry, McKinley Hall, Wichita State University, 1845 Fairmount, Wichita, KS 67260-0051, USA
| |
Collapse
|
10
|
Molecular Modeling of the Catalytic Domain of CyaA Deepened the Knowledge of Its Functional Dynamics. Toxins (Basel) 2017; 9:toxins9070199. [PMID: 28672846 PMCID: PMC5535146 DOI: 10.3390/toxins9070199] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Revised: 06/21/2017] [Accepted: 06/22/2017] [Indexed: 12/16/2022] Open
Abstract
Although CyaA has been studied for over three decades and revealed itself to be a very good prototype for developing various biotechnological applications, only a little is known about its functional dynamics and about the conformational landscape of this protein. Molecular dynamics simulations helped to clarify the view on these points in the following way. First, the model of interaction between AC and calmodulin (CaM) has evolved from an interaction centered on the surface between C-CaM hydrophobic patch and the α helix H of AC, to a more balanced view, in which the C-terminal tail of AC along with the C-CaM Calcium loops play an important role. This role has been confirmed by the reduction of the affinity of AC for calmodulin in the presence of R338, D360 and N347 mutations. In addition, enhanced sampling studies have permitted to propose a representation of the conformational space for the isolated AC. It remains to refine this representation using structural low resolution information measured on the inactive state of AC. Finally, due to a virtual screening study on another adenyl cyclase from Bacillus anthracis, weak inhibitors of AC have been discovered.
Collapse
|
11
|
Morishita T, Yonezawa Y, Ito AM. Free Energy Reconstruction from Logarithmic Mean-Force Dynamics Using Multiple Nonequilibrium Trajectories. J Chem Theory Comput 2017; 13:3106-3119. [DOI: 10.1021/acs.jctc.7b00252] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Tetsuya Morishita
- Research
Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba 305-8568, Japan
- Mathematics
for Advanced Materials Open Innovation Laboratory (MathAM-OIL), National
Institute of Advanced Industrial Science and Technology (AIST), c/o
AIMR, Tohoku University, 2-1-1 Katahira, Aoba-ku,
Sendai 980-8577, Japan
| | - Yasushige Yonezawa
- High
Pressure Protein Research Center, Institute of Advanced Technology, Kindai University, 930 Nishimitani, Kinokawa, Wakayama 649-6493, Japan
| | - Atsushi M. Ito
- National Institute of Fusion Science, 322-6 Oroshi-cho, Toki 509-5292, Japan
- The Graduate University for Advanced Studies, 322-6 Oroshi-cho, Toki 509-5292, Japan
| |
Collapse
|
12
|
Persico M, Di Dato A, Orteca N, Cimino P, Novellino E, Fattorusso C. Use of Integrated Computational Approaches in the Search for New Therapeutic Agents. Mol Inform 2016; 35:309-25. [DOI: 10.1002/minf.201501028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 06/21/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Marco Persico
- Department of Pharmacy, University of Naples “Federico II”; Via D. Montesano 49 80131 Napoli Italy
- Italian Malaria Network - Centro Interuniversitario di Ricerche Sulla Malaria (CIRM); Department of Experimental Medicine and Biochemical Sciences; Via Del Giochetto 06126 Perugia Italy
| | - Antonio Di Dato
- Department of Pharmacy, University of Naples “Federico II”; Via D. Montesano 49 80131 Napoli Italy
- Italian Malaria Network - Centro Interuniversitario di Ricerche Sulla Malaria (CIRM); Department of Experimental Medicine and Biochemical Sciences; Via Del Giochetto 06126 Perugia Italy
| | - Nausicaa Orteca
- Department of Pharmacy, University of Naples “Federico II”; Via D. Montesano 49 80131 Napoli Italy
- Italian Malaria Network - Centro Interuniversitario di Ricerche Sulla Malaria (CIRM); Department of Experimental Medicine and Biochemical Sciences; Via Del Giochetto 06126 Perugia Italy
| | - Paola Cimino
- Department of Pharmacy; University of Salerno; Via Giovanni Paolo II 132 84084 Fisciano, Salerno Italy
| | - Ettore Novellino
- Department of Pharmacy, University of Naples “Federico II”; Via D. Montesano 49 80131 Napoli Italy
| | - Caterina Fattorusso
- Department of Pharmacy, University of Naples “Federico II”; Via D. Montesano 49 80131 Napoli Italy
- Italian Malaria Network - Centro Interuniversitario di Ricerche Sulla Malaria (CIRM); Department of Experimental Medicine and Biochemical Sciences; Via Del Giochetto 06126 Perugia Italy
| |
Collapse
|
13
|
Perkett MR, Mirijanian DT, Hagan MF. The allosteric switching mechanism in bacteriophage MS2. J Chem Phys 2016; 145:035101. [PMID: 27448905 PMCID: PMC4947040 DOI: 10.1063/1.4955187] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 06/07/2016] [Indexed: 01/16/2023] Open
Abstract
We use all-atom simulations to elucidate the mechanisms underlying conformational switching and allostery within the coat protein of the bacteriophage MS2. Assembly of most icosahedral virus capsids requires that the capsid protein adopts different conformations at precise locations within the capsid. It has been shown that a 19 nucleotide stem loop (TR) from the MS2 genome acts as an allosteric effector, guiding conformational switching of the coat protein during capsid assembly. Since the principal conformational changes occur far from the TR binding site, it is important to understand the molecular mechanism underlying this allosteric communication. To this end, we use all-atom simulations with explicit water combined with a path sampling technique to sample the MS2 coat protein conformational transition, in the presence and absence of TR-binding. The calculations find that TR binding strongly alters the transition free energy profile, leading to a switch in the favored conformation. We discuss changes in molecular interactions responsible for this shift. We then identify networks of amino acids with correlated motions to reveal the mechanism by which effects of TR binding span the protein. We find that TR binding strongly affects residues located at the 5-fold and quasi-sixfold interfaces in the assembled capsid, suggesting a mechanism by which the TR binding could direct formation of the native capsid geometry. The analysis predicts amino acids whose substitution by mutagenesis could alter populations of the conformational substates or their transition rates.
Collapse
Affiliation(s)
- Matthew R Perkett
- Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02474, USA
| | - Dina T Mirijanian
- Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02474, USA
| | - Michael F Hagan
- Martin Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02474, USA
| |
Collapse
|
14
|
|
15
|
Mahanti M, Bhakat S, Nilsson UJ, Söderhjelm P. Flap Dynamics in Aspartic Proteases: A Computational Perspective. Chem Biol Drug Des 2016; 88:159-77. [PMID: 26872937 DOI: 10.1111/cbdd.12745] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Recent advances in biochemistry and drug design have placed proteases as one of the critical target groups for developing novel small-molecule inhibitors. Among all proteases, aspartic proteases have gained significant attention due to their role in HIV/AIDS, malaria, Alzheimer's disease, etc. The binding cleft is covered by one or two β-hairpins (flaps) which need to be opened before a ligand can bind. After binding, the flaps close to retain the ligand in the active site. Development of computational tools has improved our understanding of flap dynamics and its role in ligand recognition. In the past decade, several computational approaches, for example molecular dynamics (MD) simulations, coarse-grained simulations, replica-exchange molecular dynamics (REMD) and metadynamics, have been used to understand flap dynamics and conformational motions associated with flap movements. This review is intended to summarize the computational progress towards understanding the flap dynamics of proteases and to be a reference for future studies in this field.
Collapse
Affiliation(s)
- Mukul Mahanti
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, PO Box 124, SE-221 00, Lund, Sweden
| | - Soumendranath Bhakat
- Division of Biophysical Chemistry, Department of Chemistry, Lund University, PO Box 124, SE-22100, Lund, Sweden
| | - Ulf J Nilsson
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, PO Box 124, SE-221 00, Lund, Sweden
| | - Pär Söderhjelm
- Division of Biophysical Chemistry, Department of Chemistry, Lund University, PO Box 124, SE-22100, Lund, Sweden
| |
Collapse
|
16
|
Rudzinski JF, Kremer K, Bereau T. Communication: Consistent interpretation of molecular simulation kinetics using Markov state models biased with external information. J Chem Phys 2016; 144:051102. [DOI: 10.1063/1.4941455] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Affiliation(s)
| | - Kurt Kremer
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - Tristan Bereau
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| |
Collapse
|
17
|
Moors SLC, Brigou B, Hertsen D, Pinter B, Geerlings P, Van Speybroeck V, Catak S, De Proft F. Influence of Solvation and Dynamics on the Mechanism and Kinetics of Nucleophilic Aromatic Substitution Reactions in Liquid Ammonia. J Org Chem 2016; 81:1635-44. [PMID: 26800020 DOI: 10.1021/acs.joc.5b02794] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The role of the solvent and the influence of dynamics on the kinetics and mechanism of the SNAr reaction of several halonitrobenzenes in liquid ammonia, using both static calculations and dynamic ab initio molecular dynamics simulations, are investigated. A combination of metadynamics and committor analysis methods reveals how this reaction can change from a concerted, one-step mechanism in gas phase to a stepwise pathway, involving a metastable Meisenheimer complex, in liquid ammonia. This clearly establishes, among others, the important role of the solvent and highlights the fact that accurately treating solvation is of crucial importance to correctly unravel the reaction mechanism. It is indeed shown that H-bond formation of the reacting NH3 with the solvent drastically reduces the barrier of NH3 addition. The halide elimination step, however, is greatly facilitated by proton transfer from the reacting NH3 to the solvent. Furthermore, the free energy surface strongly depends on the halide substituent and the number of electron-withdrawing nitro substituents.
Collapse
Affiliation(s)
- Samuel L C Moors
- Eenheid Algemene Chemie (ALGC), Vrije Universiteit Brussel (VUB) , Pleinlaan 2, 1050 Elsene, Brussels, Belgium
| | - Ben Brigou
- Eenheid Algemene Chemie (ALGC), Vrije Universiteit Brussel (VUB) , Pleinlaan 2, 1050 Elsene, Brussels, Belgium
| | - Dietmar Hertsen
- Center for Molecular Modeling (CMM), Ghent University , Technologiepark 903, 9052 Zwijnaarde, Belgium
| | - Balazs Pinter
- Eenheid Algemene Chemie (ALGC), Vrije Universiteit Brussel (VUB) , Pleinlaan 2, 1050 Elsene, Brussels, Belgium
| | - Paul Geerlings
- Eenheid Algemene Chemie (ALGC), Vrije Universiteit Brussel (VUB) , Pleinlaan 2, 1050 Elsene, Brussels, Belgium
| | - Veronique Van Speybroeck
- Center for Molecular Modeling (CMM), Ghent University , Technologiepark 903, 9052 Zwijnaarde, Belgium
| | - Saron Catak
- Department of Chemistry, Bogazici University , Bebek 34342, Istanbul, Turkey
| | - Frank De Proft
- Eenheid Algemene Chemie (ALGC), Vrije Universiteit Brussel (VUB) , Pleinlaan 2, 1050 Elsene, Brussels, Belgium
| |
Collapse
|