1
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Huet L, Devergne T, Magrino T, Saitta AM. A New Route to the Prebiotic Synthesis of Glycine via Ab Initio-Based Machine Learning Calculations. J Phys Chem Lett 2024; 15:8697-8705. [PMID: 39159425 DOI: 10.1021/acs.jpclett.4c01954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/21/2024]
Abstract
In this work, we study the synthesis of glycine, the simplest amino acid, using ab initio molecular dynamics and enhanced sampling techniques to explore and quantify novel potential pathways. Our protocol integrates state-of-the-art machine learning approaches, allowing us to sample relevant chemical spaces more efficiently. We discover a novel "oxyglycolate path", distinct from the "standard" Strecker mechanism, identify new intermediates, and provide a full thermodynamic characterization of all reaction steps. This alternative pathway aligns better with meteoritic and experimental observations, paving the way for further investigations. Integrating quantum accuracy and machine learning in prebiotic chemistry represents a methodological milestone advancing the exploration of life's prebiotic origins.
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Affiliation(s)
- Léon Huet
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Sorbonne Université Muséum National d'Histoire Naturelle CNRS, UMR7590, Paris 75005, France
| | - Timothée Devergne
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Sorbonne Université Muséum National d'Histoire Naturelle CNRS, UMR7590, Paris 75005, France
- Atomistic Simulations, Italian Institute of Technology, 16142 Genoa, Italy
- Computational Statistics and Machine Learning, Italian Institute of Technology, 16142 Genoa, Italy
| | - Théo Magrino
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Sorbonne Université Muséum National d'Histoire Naturelle CNRS, UMR7590, Paris 75005, France
| | - A Marco Saitta
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Sorbonne Université Muséum National d'Histoire Naturelle CNRS, UMR7590, Paris 75005, France
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2
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Huet L, Magrino T, Pietrucci F, Saitta AM. Correction to "Step by Step Strecker Amino Acid Synthesis from Ab Initio Prebiotic Chemistry". J Phys Chem Lett 2024; 15:8477-8480. [PMID: 39133817 DOI: 10.1021/acs.jpclett.4c01503] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
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3
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Pyzer-Knapp EO, Curioni A. Advancing biomolecular simulation through exascale HPC, AI and quantum computing. Curr Opin Struct Biol 2024; 87:102826. [PMID: 38733863 DOI: 10.1016/j.sbi.2024.102826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 04/11/2024] [Accepted: 04/11/2024] [Indexed: 05/13/2024]
Abstract
Biomolecular simulation can act as both a digital microscope and a crystal ball; offering the potential for a deeper understanding of experimental observations whilst also presenting a forward-looking avenue for the in silico design and evaluation of hitherto unsynthesized compounds. Indeed, as the intricacy of our scientific inquiries has grown, so too has the computational prowess we seek to deploy in our pursuit of answers. As we enter the Exascale era, this mini-review surveys the computational landscape from both the point of view of the development of new and ever more powerful systems, and the simulations that are run on them. Moreover, as we stand on the cusp of a transformative phase in computational biology, this article offers a contemplative glance into the future, speculating on the profound implications of artificial intelligence and quantum computing for large-scale biomolecular simulations.
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4
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Villard J, Bircher MP, Rothlisberger U. Plane Waves Versus Correlation-Consistent Basis Sets: A Comparison of MP2 Non-Covalent Interaction Energies in the Complete Basis Set Limit. J Chem Theory Comput 2023; 19:9211-9227. [PMID: 38048449 PMCID: PMC10753812 DOI: 10.1021/acs.jctc.3c00952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/24/2023] [Accepted: 11/02/2023] [Indexed: 12/06/2023]
Abstract
Second-order Møller-Plesset perturbation theory (MP2) is the most expedient wave function-based method for considering electron correlation in quantum chemical calculations and, as such, provides a cost-effective framework to assess the effects of basis sets on correlation energies, for which the complete basis set (CBS) limit can commonly only be obtained via extrapolation techniques. Software packages providing MP2 energies are commonly based on atom-centered bases with innate issues related to possible basis set superposition errors (BSSE), especially in the case of weakly bonded systems. Here, we present noncovalent interaction energies in the CBS limit, free of BSSE, for 20 dimer systems of the S22 data set obtained via a highly parallelized MP2 implementation in the plane-wave pseudopotential molecular dynamics package CPMD. The specificities related to plane waves for accurate and efficient calculations of gas-phase energies are discussed, and results are compared to the localized (aug-)cc-pV[D,T,Q,5]Z correlation-consistent bases as well as their extrapolated CBS estimates. We find that the BSSE-corrected aug-cc-pV5Z basis can provide MP2 energies highly consistent with the CBS plane wave values with a minimum mean absolute deviation of ∼0.05 kcal/mol without the application of any extrapolation scheme. In addition, we tested the performance of 13 different extrapolation schemes and found that the X-3 expression applied to the (aug-)cc-pVXZ bases provides the smallest deviations against CBS plane wave values if the extrapolation sequence is composed of points D and T, while ( X + 1 2 ) - 4 performs slightly better for TQ and Q5 extrapolations. Also, we propose A ( X - 1 2 ) - 3 + B ( X + 1 2 ) - 4 as a reliable alternative to extrapolate total energies from the DTQ, TQ5, or DTQ5 data points. In spite of the general good agreement between the values obtained from the two types of basis sets, it is noticed that differences between plane waves and (aug-)cc-pVXZ basis sets, extrapolated or not, tend to increase with the number of electrons, thus raising the question of whether these discrepancies could indeed limit the attainable accuracy for localized bases in the limit of large systems.
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Affiliation(s)
- Justin Villard
- Laboratory
of Computational Chemistry and Biochemistry, Institute of Chemical
Sciences and Engineering, École Polytechnique
Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Martin P. Bircher
- Computational
and Soft Matter Physics, Universität
Wien, A-1090 Wien, Austria
| | - Ursula Rothlisberger
- Laboratory
of Computational Chemistry and Biochemistry, Institute of Chemical
Sciences and Engineering, École Polytechnique
Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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5
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Kar R, Mandal S, Thakkur V, Meyer B, Nair NN. Speeding-up Hybrid Functional-Based Ab Initio Molecular Dynamics Using Multiple Time-stepping and Resonance-Free Thermostat. J Chem Theory Comput 2023; 19:8351-8364. [PMID: 37933121 DOI: 10.1021/acs.jctc.3c00964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Ab initio molecular dynamics (AIMD) based on density functional theory (DFT) has become a workhorse for studying the structure, dynamics, and reactions in condensed matter systems. Currently, AIMD simulations are primarily carried out at the level of generalized gradient approximation (GGA), which is at the second rung of DFT functionals in terms of accuracy. Hybrid DFT functionals, which form the fourth rung in the accuracy ladder, are not commonly used in AIMD simulations as the computational cost involved is 100 times or higher. To facilitate AIMD simulations with hybrid functionals, we propose here an approach using multiple time stepping with adaptively compressed exchange operator and resonance-free thermostat, that could speed up the calculations by ∼30 times or more for systems with a few hundred of atoms. We demonstrate that by achieving this significant speed up and making the compute time of hybrid functional-based AIMD simulations at par with that of GGA functionals, we are able to study several complex condensed matter systems and model chemical reactions in solution with hybrid functionals that were earlier unthinkable to be performed.
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Affiliation(s)
- Ritama Kar
- Department of Chemistry, Indian Institute of Technology Kanpur (IITK), Kanpur 208016, India
| | - Sagarmoy Mandal
- Interdisciplinary Center for Molecular Materials and Computer Chemistry Center, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Nägelsbachstr. 25, Erlangen 91052, Germany
- Erlangen National High Performance Computing Center (NHR@FAU), Friedrich-Alexander-Universität Erlangen-Nürnberg, Martensstr. 1, Erlangen 91058, Germany
| | - Vaishali Thakkur
- Department of Chemistry, Indian Institute of Technology Kanpur (IITK), Kanpur 208016, India
| | - Bernd Meyer
- Interdisciplinary Center for Molecular Materials and Computer Chemistry Center, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Nägelsbachstr. 25, Erlangen 91052, Germany
- Erlangen National High Performance Computing Center (NHR@FAU), Friedrich-Alexander-Universität Erlangen-Nürnberg, Martensstr. 1, Erlangen 91058, Germany
| | - Nisanth N Nair
- Department of Chemistry, Indian Institute of Technology Kanpur (IITK), Kanpur 208016, India
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6
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Nakai H, Kobayashi M, Yoshikawa T, Seino J, Ikabata Y, Nishimura Y. Divide-and-Conquer Linear-Scaling Quantum Chemical Computations. J Phys Chem A 2023; 127:589-618. [PMID: 36630608 DOI: 10.1021/acs.jpca.2c06965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Fragmentation and embedding schemes are of great importance when applying quantum-chemical calculations to more complex and attractive targets. The divide-and-conquer (DC)-based quantum-chemical model is a fragmentation scheme that can be connected to embedding schemes. This feature article explains several DC-based schemes developed by the authors over the last two decades, which was inspired by the pioneering study of DC self-consistent field (SCF) method by Yang and Lee (J. Chem. Phys. 1995, 103, 5674-5678). First, the theoretical aspects of the DC-based SCF, electron correlation, excited-state, and nuclear orbital methods are described, followed by the two-component relativistic theory, quantum-mechanical molecular dynamics simulation, and the introduction of three programs, including DC-based schemes. Illustrative applications confirmed the accuracy and feasibility of the DC-based schemes.
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Affiliation(s)
- Hiromi Nakai
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo169-8555, Japan.,Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo169-8555, Japan
| | - Masato Kobayashi
- Department of Chemistry, Faculty of Science, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo, Hokkaido060-0810, Japan.,Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21 Nishi 10, Kita-ku, Sapporo, Hokkaido001-0021, Japan
| | - Takeshi Yoshikawa
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba274-8510, Japan
| | - Junji Seino
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo169-8555, Japan.,Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo169-8555, Japan
| | - Yasuhiro Ikabata
- Information and Media Center, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi441-8580, Japan.,Department of Computer Science and Engineering, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi441-8580, Japan
| | - Yoshifumi Nishimura
- Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo169-8555, Japan
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7
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Magrino T, Huet L, Saitta AM, Pietrucci F. Critical Assessment of Data-Driven versus Heuristic Reaction Coordinates in Solution Chemistry. J Phys Chem A 2022; 126:8887-8900. [DOI: 10.1021/acs.jpca.2c07640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Théo Magrino
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Sorbonne Université, Muséum National d’Histoire Naturelle, CNRS UMR 7590, Paris 75005, France
| | - Léon Huet
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Sorbonne Université, Muséum National d’Histoire Naturelle, CNRS UMR 7590, Paris 75005, France
| | - A. Marco Saitta
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Sorbonne Université, Muséum National d’Histoire Naturelle, CNRS UMR 7590, Paris 75005, France
| | - Fabio Pietrucci
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Sorbonne Université, Muséum National d’Histoire Naturelle, CNRS UMR 7590, Paris 75005, France
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8
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Ghanghas R, Vasudevan S. Geometries of hydrogen bonds in water-ethanol mixtures from ab initio molecular dynamics simulations. Phys Chem Chem Phys 2022; 24:23570-23577. [PMID: 36129380 DOI: 10.1039/d2cp01238c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We outline a simple procedure to determine the geometry of hydrogen bonds between different molecular species in binary mixtures from ab initio molecular dynamics (AIMD) trajectories. Here we determine the geometry of the hydrogen bonds arising from intermolecular OH⋯O interactions between different H-bonded pairs, water-water, ethanol-ethanol and water-ethanol in water-alcohol mixtures at different compositions by plotting the intermolecular non-bonded OH⋯O and O⋯O distances, and the ∠HO⋯O (θ) angles for each of the possible pairs in the ensemble. Two regions separate out in each of the scatter-plots; the one with short OH⋯O and O⋯O intermolecular distances and almost linear ∠HO⋯O angles may be identified as the region where the intermolecular OH⋯O geometry would be favorable for hydrogen bonding. Using the different geometric criteria for each of the three possible H-bonded pairs we estimate the average number of water and ethanol molecules that are hydrogen bonded to a water molecule, and to an ethanol molecule, respectively, at different mole fractions of the mixture. We validate the results from values of the chemical shift of the two OH resonances (water and ethanol) in the proton NMR spectra of the mixtures at different concentrations as these values are known to be sensitive to the local chemical environment of the resonating nuclei.
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Affiliation(s)
- Ritu Ghanghas
- Department of Inorganic and Physical Chemistry, IISc, Bangalore, India.
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9
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Mandal S, Kar R, Klöffel T, Meyer B, Nair NN. Improving the scaling and performance of multiple time stepping-based molecular dynamics with hybrid density functionals. J Comput Chem 2022; 43:588-597. [PMID: 35147988 DOI: 10.1002/jcc.26816] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 01/07/2022] [Accepted: 01/18/2022] [Indexed: 12/18/2022]
Abstract
Density functionals at the level of the generalized gradient approximation (GGA) and a plane-wave basis set are widely used today to perform ab initio molecular dynamics (AIMD) simulations. Going up in the ladder of accuracy of density functionals from GGA (second rung) to hybrid density functionals (fourth rung) is much desired pertaining to the accuracy of the latter in describing structure, dynamics, and energetics of molecular and condensed matter systems. On the other hand, hybrid density functional based AIMD simulations are about two orders of magnitude slower than GGA based AIMD for systems containing ~100 atoms using ~100 compute cores. Two methods, namely MTACE and s-MTACE, based on a multiple time step integrator and adaptively compressed exchange operator formalism are able to provide a speed-up of about 7-9 in performing hybrid density functional based AIMD. In this work, we report an implementation of these methods using a task-group based parallelization within the CPMD program package, with the intention to take advantage of the large number of compute cores available on modern high-performance computing platforms. We present here the boost in performance achieved through this algorithm. This work also identifies the computational bottleneck in the s-MTACE method and proposes a way to overcome it.
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Affiliation(s)
- Sagarmoy Mandal
- Department of Chemistry, Indian Institute of Technology Kanpur (IITK), Kanpur, India.,Interdisciplinary Center for Molecular Materials and Computer Chemistry Center, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany.,Erlangen National High Performance Computing Center (NHR@FAU), Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Ritama Kar
- Department of Chemistry, Indian Institute of Technology Kanpur (IITK), Kanpur, India
| | - Tobias Klöffel
- Interdisciplinary Center for Molecular Materials and Computer Chemistry Center, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany.,Erlangen National High Performance Computing Center (NHR@FAU), Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Bernd Meyer
- Interdisciplinary Center for Molecular Materials and Computer Chemistry Center, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany.,Erlangen National High Performance Computing Center (NHR@FAU), Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Nisanth N Nair
- Department of Chemistry, Indian Institute of Technology Kanpur (IITK), Kanpur, India
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10
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Taherivardanjani S, Elfgen R, Reckien W, Suarez E, Perlt E, Kirchner B. Benchmarking the Computational Costs and Quality of Vibrational Spectra from Ab Initio Simulations. ADVANCED THEORY AND SIMULATIONS 2021. [DOI: 10.1002/adts.202100293] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Shima Taherivardanjani
- Mulliken Center for Theoretical Chemistry Institute for Physical and Theoretical Chemistry Beringstr. 4 Bonn D‐53115 Germany
| | - Roman Elfgen
- Mulliken Center for Theoretical Chemistry Institute for Physical and Theoretical Chemistry Beringstr. 4 Bonn D‐53115 Germany
| | - Werner Reckien
- Mulliken Center for Theoretical Chemistry Institute for Physical and Theoretical Chemistry Beringstr. 4 Bonn D‐53115 Germany
| | - Estela Suarez
- Institute for Advanced Simulation Jülich Supercomputing Centre, Forschungszentrum Jülich GmbH Wilhelm‐Johnen‐Straße Jülich D‐52425 Germany
| | - Eva Perlt
- Otto Schott Institute of Materials Research Faculty of Physics and Astronomy Friedrich‐Schiller‐Universität Jena Löbdergraben 32 Jena D‐07743 Germany
| | - Barbara Kirchner
- Mulliken Center for Theoretical Chemistry Institute for Physical and Theoretical Chemistry Beringstr. 4 Bonn D‐53115 Germany
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11
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Partovi-Azar P, Sebastiani D. Minimal Optimized Effective Potentials for Density Functional Theory Studies on Excited-State Proton Dissociation. MICROMACHINES 2021; 12:mi12060679. [PMID: 34200610 PMCID: PMC8226891 DOI: 10.3390/mi12060679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/03/2021] [Accepted: 06/09/2021] [Indexed: 11/17/2022]
Abstract
Recently, a new method [P. Partovi-Azar and D. Sebastiani, J. Chem. Phys. 152, 064101 (2020)] was proposed to increase the efficiency of proton transfer energy calculations in density functional theory by using the T1 state with additional optimized effective potentials instead of calculations at S1. In this work, we focus on proton transfer from six prototypical photoacids to neighboring water molecules and show that the reference proton dissociation curves obtained at S1 states using time-dependent density functional theory can be reproduced with a reasonable accuracy by performing T1 calculations at density functional theory level with only one additional effective potential for the acidic hydrogens. We also find that the extra effective potentials for the acidic hydrogens neither change the nature of the T1 state nor the structural properties of solvent molecules upon transfer from the acids. The presented method is not only beneficial for theoretical studies on excited state proton transfer, but we believe that it would also be useful for studying other excited state photochemical reactions.
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12
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Magrino T, Pietrucci F, Saitta AM. Step by Step Strecker Amino Acid Synthesis from Ab Initio Prebiotic Chemistry. J Phys Chem Lett 2021; 12:2630-2637. [PMID: 33719462 DOI: 10.1021/acs.jpclett.1c00194] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The amino acids synthesis from elementary precursors in abiotic conditions is traditionally described according to the Strecker reaction, thoroughly invoked to justify the observation of amino acids in extraterrestrial samples and their emergence in the primordial Earth. To this day, however, a quantitative microscopic description of the mechanism, thermodynamics, and kinetics of the multistep Strecker reaction is still lacking. In the present work we tackle this study by adopting a state-of-the-art ab initio computational approach, combining an efficient scheme of exploration of the relevant chemical networks with a rigorous determination of the underlying free energy and transition states. We determine the step-by-step chemical pathway from "Strecker precursors" to glycine in solution and calculate the corresponding full free energy landscape. Our results agree well with the scarce available experimental data and complete them, thus providing the first end-to-end study of this complex reaction, a crucial bottleneck for the emergence of life.
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Affiliation(s)
- Théo Magrino
- IMPMC, UMR 7590, Sorbonne Université, MNHN, CNRS, 75005 Paris, France
| | - Fabio Pietrucci
- IMPMC, UMR 7590, Sorbonne Université, MNHN, CNRS, 75005 Paris, France
| | - A Marco Saitta
- IMPMC, UMR 7590, Sorbonne Université, MNHN, CNRS, 75005 Paris, France
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13
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Bolnykh V, Rothlisberger U, Carloni P. Biomolecular Simulation: A Perspective from High Performance Computing. Isr J Chem 2020. [DOI: 10.1002/ijch.202000022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Viacheslav Bolnykh
- Laboratory of Computational Chemistry and BiochemistryÉcole Polytechnique Fédérale de Lausanne Switzerland
| | - Ursula Rothlisberger
- Laboratory of Computational Chemistry and BiochemistryÉcole Polytechnique Fédérale de Lausanne Switzerland
| | - Paolo Carloni
- Institute for Neuroscience and Medicine and Institute for Advanced Simulations (IAS-5/INM-9) “Computational Biomedicine”, JARA-Institute INM-11 “Molecular Neuroscience and Neuroimaging”Forschungszentrum Jülich Germany
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14
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Partovi-Azar P, Sebastiani D. Optimized effective potentials to increase the accuracy of approximate proton transfer energy calculations in the excited state. J Chem Phys 2020; 152:064101. [PMID: 32061215 DOI: 10.1063/1.5140262] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Many fundamental chemical reactions are triggered by electronic excitations. Here, we propose and benchmark a novel approximate first-principles molecular dynamics simulation idea for increasing the computational efficiency of density functional theory-based calculations of the excited states. We focus on obtaining proton transfer energy at the S1 excited state through actual density functional theory calculations at the T1 state with additional optimized effective potentials. The potentials are optimized as such to reproduce the excited-state energy surface obtained using time-dependent density functional theory, but can be generalized to other more accurate quantum chemical methods. We believe that the presented method is not only suitable for studies on excited-state proton transfer and ion mobility in general systems but can also be extended to investigate more involved processes, such as photo-induced isomerization.
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Affiliation(s)
- Pouya Partovi-Azar
- Institute of Chemistry, Martin-Luther-University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
| | - Daniel Sebastiani
- Institute of Chemistry, Martin-Luther-University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
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15
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Bolnykh V, Olsen JMH, Meloni S, Bircher MP, Ippoliti E, Carloni P, Rothlisberger U. Extreme Scalability of DFT-Based QM/MM MD Simulations Using MiMiC. J Chem Theory Comput 2019; 15:5601-5613. [PMID: 31498615 DOI: 10.1021/acs.jctc.9b00424] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a highly scalable DFT-based QM/MM implementation developed within MiMiC, a recently introduced multiscale modeling framework that uses a loose-coupling strategy in conjunction with a multiple-program multiple-data (MPMD) approach. The computation of electrostatic QM/MM interactions is parallelized exploiting both distributed- and shared-memory strategies. Here, we use the efficient CPMD and GROMACS programs as QM and MM engines, respectively. The scalability is demonstrated through large-scale benchmark simulations of realistic biomolecular systems employing non-hybrid and hybrid GGA exchange-correlation functionals. We show that the loose-coupling strategy adopted in MiMiC, with its inherent high flexibility, does not carry any significant computational overhead compared to a tight-coupling scheme. Furthermore, we demonstrate that the adopted parallelization strategy enables scaling up to 13,000 CPU cores with efficiency above 70%, thus making DFT-based QM/MM MD simulations using hybrid functionals at the nanosecond scale accessible.
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Affiliation(s)
- Viacheslav Bolnykh
- Department of Physics , RWTH Aachen University , 52056 Aachen , Germany.,CaSToRC , The Cyprus Institute , 2121 Aglantzia, Nicosia , Cyprus.,Institute for Advanced Simulation (IAS-5) and Institute of Neuroscience and Medicine (INM-9) , Forschungszentrum Jülich , 52425 Jülich , Germany
| | - Jógvan Magnus Haugaard Olsen
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry , UiT The Arctic University of Norway , N-9037 Tromsø , Norway
| | - Simone Meloni
- Dipartimento di Scienze Chimiche e Farmaceutiche (DipSCF) , Università degli Studi di Ferrara (Unife) , Via Luigi Borsari 46 , I-44121 Ferrara , Italy
| | - Martin P Bircher
- Laboratory of Computational Chemistry and Biochemistry , École Polytechnique Fédérale de Lausanne , CH-1015 Lausanne , Switzerland
| | - Emiliano Ippoliti
- Institute for Advanced Simulation (IAS-5) and Institute of Neuroscience and Medicine (INM-9) , Forschungszentrum Jülich , 52425 Jülich , Germany
| | - Paolo Carloni
- Department of Physics , RWTH Aachen University , 52056 Aachen , Germany.,Institute for Advanced Simulation (IAS-5) and Institute of Neuroscience and Medicine (INM-9) , Forschungszentrum Jülich , 52425 Jülich , Germany.,Institute for Neuroscience and Medicine (INM-11) , Forschungszentrum Jülich , 52425 Jülich , Germany
| | - Ursula Rothlisberger
- Laboratory of Computational Chemistry and Biochemistry , École Polytechnique Fédérale de Lausanne , CH-1015 Lausanne , Switzerland
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16
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Marion A, Gokcan H, Monard G. Semi-Empirical Born-Oppenheimer Molecular Dynamics (SEBOMD) within the Amber Biomolecular Package. J Chem Inf Model 2019; 59:206-214. [PMID: 30433776 DOI: 10.1021/acs.jcim.8b00605] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Semi-empirical quantum methods from the neglect of differential diatomic overlap (NDDO) family such as MNDO, AM1, or PM3 are fast albeit approximate quantum methods. By combining them with linear scaling methods like the divide & conquer (D&C) method, it is possible to quickly evaluate the energy of systems containing hundreds to thousands of atoms. We here present our implementation in the Amber biomolecular package of a SEBOMD module that provides a way to run semi-empirical Born-Oppenheimer molecular dynamics. At each step of a SEBOMD, a fully converged self-consistent field (SCF) calculation is performed to obtain the semiempirical quantum potential energy of a molecular system encaged or not in periodic boundary conditions. We describe the implementation and the features of our SEBOMD implementation. We show the requirements to conserve the total energy in NVE simulations, and how to accelerate SCF convergence through density matrix extrapolation. Specific ways of handling periodic boundary conditions using mechanical embedding or electrostatic embedding through a tailored quantum Ewald summation is developed. The parallel performance of SEBOMD simulations using the D&C scheme are presented for liquid water systems of various sizes, and a comparison between the traditional full diagonalization scheme and the D&C approach for the reproduction of the structure of liquid water illustrates the potentiality of SEBOMD to simulate molecular systems containing several hundreds of atoms for hundreds of picoseconds with a quantum mechanical potential in a reasonable amount of CPU time.
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Affiliation(s)
- Antoine Marion
- Université de Lorraine, CNRS, LPCT , F-54000 Nancy , France.,Department of Chemistry , Middle East Technical University , 06800 , Ankara , Turkey
| | - Hatice Gokcan
- Université de Lorraine, CNRS, LPCT , F-54000 Nancy , France.,Department of Chemistry , University of North Texas , Denton , Texas 76201 , United States
| | - Gerald Monard
- Université de Lorraine, CNRS, LPCT , F-54000 Nancy , France
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17
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Tahchieva DN, Bakowies D, Ramakrishnan R, von Lilienfeld OA. Torsional Potentials of Glyoxal, Oxalyl Halides, and Their Thiocarbonyl Derivatives: Challenges for Popular Density Functional Approximations. J Chem Theory Comput 2018; 14:4806-4817. [PMID: 30011363 DOI: 10.1021/acs.jctc.8b00174] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The reliability of popular density functionals was studied for the description of torsional profiles of 36 molecules: glyoxal, oxalyl halides, and their thiocarbonyl derivatives. HF and 18 functionals of varying complexity, from local density to range-separated hybrid approximations and double-hybrid, have been considered and benchmarked against CCSD(T)-level rotational profiles. For molecules containing heavy halogens, most functionals fail to reproduce barrier heights accurately and a number of functionals introduce spurious minima. Dispersion corrections show no improvement. Calibrated torsion-corrected atom-centered potentials rectify the shortcomings of PBE and also improve on σ-hole based intermolecular binding in dimers and crystals.
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Affiliation(s)
- Diana N Tahchieva
- Institute of Physical Chemistry and National Center for Computational Design and Discovery of Novel Materials (MARVEL), Department of Chemistry , University of Basel , Klingelbergstrasse 80 , CH-4056 Basel , Switzerland
| | - Dirk Bakowies
- Institute of Physical Chemistry and National Center for Computational Design and Discovery of Novel Materials (MARVEL), Department of Chemistry , University of Basel , Klingelbergstrasse 80 , CH-4056 Basel , Switzerland
| | - Raghunathan Ramakrishnan
- Institute of Physical Chemistry and National Center for Computational Design and Discovery of Novel Materials (MARVEL), Department of Chemistry , University of Basel , Klingelbergstrasse 80 , CH-4056 Basel , Switzerland
| | - O Anatole von Lilienfeld
- Institute of Physical Chemistry and National Center for Computational Design and Discovery of Novel Materials (MARVEL), Department of Chemistry , University of Basel , Klingelbergstrasse 80 , CH-4056 Basel , Switzerland
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18
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Realistic Simulation of Organometallic Reactivity in Solution by Means of First-Principles Molecular Dynamics. STRUCTURE AND BONDING 2015. [DOI: 10.1007/430_2015_183] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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19
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Wang F, Dai Y, Zhao J, Li Q. Uniaxial tension-induced fracture in gold nanowires with the dependence on size and atomic vacancies. Phys Chem Chem Phys 2014; 16:24716-26. [DOI: 10.1039/c4cp03556a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The size effect dominates the rupture of gold nanowires, which is also related to atomic vacancies in a single-layer crystalline plane.
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Affiliation(s)
- Fenying Wang
- School of Chemistry
- Material Science and Engineering
- Nanchang University
- Nanchang 330031, P. R. China
| | - Yanfeng Dai
- School of Chemistry
- Material Science and Engineering
- Nanchang University
- Nanchang 330031, P. R. China
| | - Jianwei Zhao
- State Key Laboratory of Analytical Chemistry for Life Science
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210008, P. R. China
| | - Qianjin Li
- State Key Laboratory of Analytical Chemistry for Life Science
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210008, P. R. China
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20
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Curchod BFE, Rothlisberger U, Tavernelli I. Trajectory-Based Nonadiabatic Dynamics with Time-Dependent Density Functional Theory. Chemphyschem 2013; 14:1314-40. [DOI: 10.1002/cphc.201200941] [Citation(s) in RCA: 153] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Indexed: 11/11/2022]
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21
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Sparta M, Shirvanyants D, Ding F, Dokholyan NV, Alexandrova AN. Hybrid dynamics simulation engine for metalloproteins. Biophys J 2013; 103:767-76. [PMID: 22947938 DOI: 10.1016/j.bpj.2012.06.024] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Revised: 06/08/2012] [Accepted: 06/18/2012] [Indexed: 11/15/2022] Open
Abstract
Quality computational description of metalloproteins is a great challenge due to the vast span of time- and lengthscales characteristic of their existence. We present an efficient new method that allows for robust characterization of metalloproteins. It combines quantum mechanical (QM) description of the metal-containing active site, and extensive dynamics of the protein captured by discrete molecular dynamics (DMD) (QM/DMD). DMD samples the entire protein, including the backbone, and most of the active site, except for the immediate coordination region of the metal. QM operates on the part of the protein of electronic and chemical significance, which may include tens to hundreds of atoms. The breathing quantum-classical boundary provides a continuous mutual feedback between the two machineries. We test QM/DMD using the Fe-containing electron transporter protein, rubredoxin, and its three mutants as a model. QM/DMD can provide a reliable balanced description of metalloproteins' structure, dynamics, and electronic structure in a reasonable amount of time. As an illustration of QM/DMD capabilities, we then predict the structure of the Ca(2+) form of the enzyme catechol O-methyl transferase, which, unlike the native Mg(2+) form, is catalytically inactive. The Mg(2+) site is ochtahedral, but the Ca(2+) is 7-coordinate and features the misalignment of the reacting parts of the system. The change is facilitated by the backbone adjustment. QM/DMD is ideal and fast for providing this level of structural insight.
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Affiliation(s)
- Manuel Sparta
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, USA
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22
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Knight C, Voth GA. Coarse-graining away electronic structure: a rigorous route to accurate condensed phase interaction potentials. Mol Phys 2012. [DOI: 10.1080/00268976.2012.668621] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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23
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Bowler DR, Miyazaki T. O(N) methods in electronic structure calculations. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2012; 75:036503. [PMID: 22790422 DOI: 10.1088/0034-4885/75/3/036503] [Citation(s) in RCA: 210] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Linear-scaling methods, or O(N) methods, have computational and memory requirements which scale linearly with the number of atoms in the system, N, in contrast to standard approaches which scale with the cube of the number of atoms. These methods, which rely on the short-ranged nature of electronic structure, will allow accurate, ab initio simulations of systems of unprecedented size. The theory behind the locality of electronic structure is described and related to physical properties of systems to be modelled, along with a survey of recent developments in real-space methods which are important for efficient use of high-performance computers. The linear-scaling methods proposed to date can be divided into seven different areas, and the applicability, efficiency and advantages of the methods proposed in these areas are then discussed. The applications of linear-scaling methods, as well as the implementations available as computer programs, are considered. Finally, the prospects for and the challenges facing linear-scaling methods are discussed.
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Affiliation(s)
- D R Bowler
- London Centre for Nanotechnology, UCL, 17-19 Gordon St, London WC1H 0AH, UK.
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24
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Brabec J, Pittner J, van Dam HJJ, Aprà E, Kowalski K. Parallel Implementation of Multireference Coupled-Cluster Theories Based on the Reference-Level Parallelism. J Chem Theory Comput 2012; 8:487-97. [DOI: 10.1021/ct200809m] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jiří Brabec
- J. Heyrovský Institute
of Physical Chemistry, Academy of Sciences of the Czech Republic,
CZ-18223 Prague 8, Czech Republic
| | - Jiří Pittner
- J. Heyrovský Institute
of Physical Chemistry, Academy of Sciences of the Czech Republic,
CZ-18223 Prague 8, Czech Republic
| | - Hubertus J. J. van Dam
- William R. Wiley Environmental
Molecular Science Laboratory, Battelle, Pacific Northwest National
Laboratory, K8-91, P.O. Box 999, Richland, Washington 99352, United
States
| | - Edoardo Aprà
- William R. Wiley Environmental
Molecular Science Laboratory, Battelle, Pacific Northwest National
Laboratory, K8-91, P.O. Box 999, Richland, Washington 99352, United
States
| | - Karol Kowalski
- William R. Wiley Environmental
Molecular Science Laboratory, Battelle, Pacific Northwest National
Laboratory, K8-91, P.O. Box 999, Richland, Washington 99352, United
States
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25
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Hutter J. Car-Parrinello molecular dynamics. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.90] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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26
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Echenique P, Cavasotto CN, De Marco M, Garca-Risueño P, Alonso JL. An exact expression to calculate the derivatives of position-dependent observables in molecular simulations with flexible constraints. PLoS One 2011; 6:e24563. [PMID: 21931757 PMCID: PMC3171457 DOI: 10.1371/journal.pone.0024563] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Accepted: 08/15/2011] [Indexed: 11/18/2022] Open
Abstract
In this work, we introduce an algorithm to compute the derivatives of physical observables along the constrained subspace when flexible constraints are imposed on the system (i.e., constraints in which the constrained coordinates are fixed to configuration-dependent values). The presented scheme is exact, it does not contain any tunable parameter, and it only requires the calculation and inversion of a sub-block of the Hessian matrix of second derivatives of the function through which the constraints are defined. We also present a practical application to the case in which the sought observables are the Euclidean coordinates of complex molecular systems, and the function whose minimization defines the flexible constraints is the potential energy. Finally, and in order to validate the method, which, as far as we are aware, is the first of its kind in the literature, we compare it to the natural and straightforward finite-differences approach in a toy system and in three molecules of biological relevance: methanol, N-methyl-acetamide and a tri-glycine peptide.
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Affiliation(s)
- Pablo Echenique
- Instituto de Química Física Rocasolano, Consejo Superior de Investigaciones Científicas, Madrid, Spain.
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27
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Schiffmann C, Sebastiani D. Artificial Bee Colony Optimization of Capping Potentials for Hybrid Quantum Mechanical/Molecular Mechanical Calculations. J Chem Theory Comput 2011; 7:1307-15. [DOI: 10.1021/ct1007108] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Christoph Schiffmann
- Physics Department, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Daniel Sebastiani
- Physics Department, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
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28
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Wang F, Gao Y, Zhu T, Zhao J. Shock-induced breaking in the gold nanowire with the influence of defects and strain rates. NANOSCALE 2011; 3:1624-1631. [PMID: 21350764 DOI: 10.1039/c0nr00797h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Defects in metallic nanowires have raised concerns about the applied reliability of the nanowires in nanoelectromechanical systems. In this paper, molecular dynamics simulations are used to study the deformation and breaking failure of the [100] single-crystal gold nanowires containing defects at different strain rates. The statistical breaking position distributions of the nanowires show mechanical shocks play a critical role in the deformation of nanowires at different strain rates, and deformation mechanism of the nanowire containing defects is based on a competition between shocks and defects in the deformation process of the nanowire. At low strain rate of 1.0% ps(-1), defect ratio of 2% has changed the deformation mechanism because micro-atomic fluctuation is in an equilibrium state. However, owing to strong symmetric shocks, the sensitivity of defects is not obvious before a defect ratio of 25% at high strain rate of 5.0% ps(-1).
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Affiliation(s)
- Fenying Wang
- Key Laboratory of Analytical Chemistry for Life Sciences, Ministry of Education, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210008, PR China
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29
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Izgorodina EI. Towards large-scale, fully ab initio calculations of ionic liquids. Phys Chem Chem Phys 2011; 13:4189-207. [PMID: 21283896 DOI: 10.1039/c0cp02315a] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Ionic liquids have attracted a substantial amount of interest as replacement of traditional electrolytes in high efficiency electrochemical devices for generation and storage of energy due to their superior physical and chemical properties, especially low volatility and high electrochemical stability. For enhanced performance of the electrochemical devices ionic liquids are required to be highly conductive and low viscous. Long-range Coulomb and short-range dispersion interactions between ions affect physical and chemical properties of ionic liquids in a very complex way, thus preventing direct correlations to the chemical structure. Considering a vast combination of available cations and anions that can be used to synthesize ionic liquids, development of predictive theoretical approaches that allow for accurate tailoring of their physical properties has become crucial to further enhance the performance of electrochemical devices such as lithium batteries, fuel and solar cells. This perspective article gives a thorough overview of current theoretical approaches applied for studying thermodynamic (melting point and enthalpy of vapourisation) and transport (conductivity and viscosity) properties of ionic liquids, emphasizing their reliability and limitations. Strategies for improving predictive power and versatility of existing theoretical approaches are also outlined.
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30
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Wegner M, Dudenko D, Sebastiani D, Palmans ARA, de Greef TFA, Graf R, Spiess HW. The impact of the amide connectivity on the assembly and dynamics of benzene-1,3,5-tricarboxamides in the solid state. Chem Sci 2011. [DOI: 10.1039/c1sc00280e] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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31
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Kirchner B, di Dio PJ, Hutter J. Real-world predictions from ab initio molecular dynamics simulations. Top Curr Chem (Cham) 2011; 307:109-53. [PMID: 21842358 DOI: 10.1007/128_2011_195] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
In this review we present the techniques of ab initio molecular dynamics simulation improved to its current stage where the analysis of existing processes and the prediction of further chemical features and real-world processes are feasible. For this reason we describe the relevant developments in ab initio molecular dynamics leading to this stage. Among them, parallel implementations, different basis set functions, density functionals, and van der Waals corrections are reported. The chemical features accessible through AIMD are discussed. These are IR, NMR, as well as EXAFS spectra, sampling methods like metadynamics and others, Wannier functions, dipole moments of molecules in condensed phase, and many other properties. Electrochemical reactions investigated by ab initio molecular dynamics methods in solution, on surfaces as well as complex interfaces, are also presented.
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Affiliation(s)
- Barbara Kirchner
- Wilhelm-Ostwald Institute of Physical and Theoretical Chemistry, University of Leipzig, Linnéstr. 2, 04103 Leipzig, Germany.
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32
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Banyai DR, Murakhtina T, Sebastiani D. NMR chemical shifts as a tool to analyze first principles molecular dynamics simulations in condensed phases: the case of liquid water. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2010; 48 Suppl 1:S56-S60. [PMID: 21104763 DOI: 10.1002/mrc.2620] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
We present (1)H NMR chemical shift calculations of liquid water based on first principles molecular dynamics simulations under periodic boundary conditions. We focus on the impact of computational parameters on the structural and spectroscopic data, which is an important question for understanding how sensitive the computed (1)H NMR resonances are upon variation of the simulation setup. In particular, we discuss the influence of the exchange-correlation functional and the size of the basis set, the choice for the fictitious electronic mass and the use of pseudopotentials for the nuclear magnetic resonance (NMR) calculation on one hand and the underlying Car-Parrinello-type molecular dynamics simulations on the other hand. Our findings show that the direct effect of these parameters on (1)H shifts is not big, whereas the indirect dependence via the structural data is more important. The (1)H NMR chemical shifts clearly reflect the induced structural changes, illustrating once again the sensitivity of (1)H NMR observables on small changes in the local chemical structure of complex hydrogen-bonded liquids.
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Affiliation(s)
- Douglas R Banyai
- Physics Department, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931-1295, USA
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33
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Ong SW, Tok ES, Kang HC. Vibrational frequencies in Car-Parrinello molecular dynamics. Phys Chem Chem Phys 2010; 12:14960-6. [PMID: 20949201 DOI: 10.1039/c0cp00411a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Car-Parrinello molecular dynamics (CPMD) are widely used to investigate the dynamical properties of molecular systems. An important issue in such applications is the dependence of dynamical quantities such as molecular vibrational frequencies upon the fictitious orbital mass μ. Although it is known that the correct Born-Oppenheimer dynamics are recovered at zero μ, it is not clear how these dynamical quantities are to be rigorously extracted from CPMD calculations. Our work addresses this issue for vibrational frequencies. We show that when the system is sufficiently close to the ground state the calculated ionic vibrational frequencies are ω(M) = ω(0M)[1 -C(μ/M)] for small μ/M, where ω(0M) is the Born-Oppenheimer ionic frequency, M the ionic mass, and C a constant that depends upon the ion-orbital coupling force constants. Our analysis also provides a quantitative understanding of the orbital oscillation amplitudes, leading to a relationship between the adiabaticity of a system and the ion-orbital coupling constants. In particular, we show that there is a significant systematic dependence of calculated vibrational frequencies upon how close the CPMD trajectory is to the Born-Oppenheimer surface. We verify our analytical results with numerical simulations for N(2), Sn(2), and H/Si(100)-(2×1).
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Affiliation(s)
- Sheau Wei Ong
- Department of Chemistry, National University of Singapore, Singapore
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34
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Shang H, Li Z, Yang J. Implementation of Exact Exchange with Numerical Atomic Orbitals. J Phys Chem A 2009; 114:1039-43. [DOI: 10.1021/jp908836z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Honghui Shang
- Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Zhenyu Li
- Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Jinlong Yang
- Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, Anhui 230026, China
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Giannozzi P, Baroni S, Bonini N, Calandra M, Car R, Cavazzoni C, Ceresoli D, Chiarotti GL, Cococcioni M, Dabo I, Dal Corso A, de Gironcoli S, Fabris S, Fratesi G, Gebauer R, Gerstmann U, Gougoussis C, Kokalj A, Lazzeri M, Martin-Samos L, Marzari N, Mauri F, Mazzarello R, Paolini S, Pasquarello A, Paulatto L, Sbraccia C, Scandolo S, Sclauzero G, Seitsonen AP, Smogunov A, Umari P, Wentzcovitch RM. QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2009; 21:395502. [PMID: 21832390 DOI: 10.1088/0953-8984/21/39/395502] [Citation(s) in RCA: 5848] [Impact Index Per Article: 389.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
QUANTUM ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling, based on density-functional theory, plane waves, and pseudopotentials (norm-conserving, ultrasoft, and projector-augmented wave). The acronym ESPRESSO stands for opEn Source Package for Research in Electronic Structure, Simulation, and Optimization. It is freely available to researchers around the world under the terms of the GNU General Public License. QUANTUM ESPRESSO builds upon newly-restructured electronic-structure codes that have been developed and tested by some of the original authors of novel electronic-structure algorithms and applied in the last twenty years by some of the leading materials modeling groups worldwide. Innovation and efficiency are still its main focus, with special attention paid to massively parallel architectures, and a great effort being devoted to user friendliness. QUANTUM ESPRESSO is evolving towards a distribution of independent and interoperable codes in the spirit of an open-source project, where researchers active in the field of electronic-structure calculations are encouraged to participate in the project by contributing their own codes or by implementing their own ideas into existing codes.
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Affiliation(s)
- Paolo Giannozzi
- CNR-INFM Democritos National Simulation Center, 34100 Trieste, Italy. Dipartimento di Fisica, Università degli Studi di Udine, via delle Scienze 208, 33100 Udine, Italy
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36
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Hansen MR, Graf R, Sekharan S, Sebastiani D. Columnar packing motifs of functionalized perylene derivatives: local molecular order despite long-range disorder. J Am Chem Soc 2009; 131:5251-6. [PMID: 19301900 DOI: 10.1021/ja8095703] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We elucidate local packing motifs and dynamical order parameters in a perylene tetracarboxydiimide derivative (C(8,7)-PDI), one of the most promising candidates for rationally designed, self-assembling, and self-healing molecular wires. Spectroscopic fingerprints obtained from solid-state NMR spectroscopy are interpreted by means of first-principles calculations and molecular dynamics simulations. The interplay of steric repulsion, H bonding, and pi-pi packing effects leads to a specific relative molecular pitch angle of approximately 35 +/- 10 degrees between successive molecules in the stack. Dynamical order parameters, determined from NMR sideband patterns as a measure of molecular motion, yield values of S approximately = 1.0 in the core of the columnar stack, corresponding to an almost frozen molecular dynamics at ambient temperature. This rigidity is compatible with characteristic intermolecular distances obtained from dipolar couplings between specific hydrogens via double-quantum NMR experiments and further supported by ab initio calculations.
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Affiliation(s)
- Michael Ryan Hansen
- Max-Planck-Institut für Polymerforschung, Ackermannweg 10, 55128 Mainz, Germany
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37
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Morrone JA, Lin L, Car R. Tunneling and delocalization effects in hydrogen bonded systems: A study in position and momentum space. J Chem Phys 2009; 130:204511. [DOI: 10.1063/1.3142828] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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38
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Komin S, Sebastiani D. Optimization of Capping Potentials for Spectroscopic Parameters in Hybrid Quantum Mechanical/Mechanical Modeling Calculations. J Chem Theory Comput 2009; 5:1490-8. [DOI: 10.1021/ct800525u] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sittipong Komin
- Max-Planck-Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Daniel Sebastiani
- Max-Planck-Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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39
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Hess NJ, Schenter GK, Hartman MR, Daemen LL, Proffen T, Kathmann SM, Mundy CJ, Hartl M, Heldebrant DJ, Stowe AC, Autrey T. Neutron Powder Diffraction and Molecular Simulation Study of the Structural Evolution of Ammonia Borane from 15 to 340 K. J Phys Chem A 2009; 113:5723-35. [DOI: 10.1021/jp900839c] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nancy J. Hess
- Pacific Northwest National Laboratory, Richland, Washington 99352, University of Michigan, Ann Arbor, Michigan 48109, and Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - Gregory K. Schenter
- Pacific Northwest National Laboratory, Richland, Washington 99352, University of Michigan, Ann Arbor, Michigan 48109, and Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - Michael R. Hartman
- Pacific Northwest National Laboratory, Richland, Washington 99352, University of Michigan, Ann Arbor, Michigan 48109, and Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - Luc L. Daemen
- Pacific Northwest National Laboratory, Richland, Washington 99352, University of Michigan, Ann Arbor, Michigan 48109, and Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - Thomas Proffen
- Pacific Northwest National Laboratory, Richland, Washington 99352, University of Michigan, Ann Arbor, Michigan 48109, and Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - Shawn M. Kathmann
- Pacific Northwest National Laboratory, Richland, Washington 99352, University of Michigan, Ann Arbor, Michigan 48109, and Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - Christopher J. Mundy
- Pacific Northwest National Laboratory, Richland, Washington 99352, University of Michigan, Ann Arbor, Michigan 48109, and Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - Monika Hartl
- Pacific Northwest National Laboratory, Richland, Washington 99352, University of Michigan, Ann Arbor, Michigan 48109, and Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - David J. Heldebrant
- Pacific Northwest National Laboratory, Richland, Washington 99352, University of Michigan, Ann Arbor, Michigan 48109, and Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - Ashley C. Stowe
- Pacific Northwest National Laboratory, Richland, Washington 99352, University of Michigan, Ann Arbor, Michigan 48109, and Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - Tom Autrey
- Pacific Northwest National Laboratory, Richland, Washington 99352, University of Michigan, Ann Arbor, Michigan 48109, and Los Alamos National Laboratory, Los Alamos, New Mexico 87545
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40
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Alkauskas A, Broqvist P, Devynck F, Pasquarello A. Band offsets at semiconductor-oxide interfaces from hybrid density-functional calculations. PHYSICAL REVIEW LETTERS 2008; 101:106802. [PMID: 18851241 DOI: 10.1103/physrevlett.101.106802] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2008] [Indexed: 05/20/2023]
Abstract
Band offsets at semiconductor-oxide interfaces are determined through a scheme based on hybrid density functionals, which incorporate a fraction alpha of Hartree-Fock exchange. For each bulk component, the fraction alpha is tuned to reproduce the experimental band gap, and the conduction and valence band edges are then located with respect to a reference level. The lineup of the bulk reference levels is determined through an interface calculation, and shown to be almost independent of the fraction alpha. Application of this scheme to the Si-SiO2, SiC-SiO2, and Si-HfO2 interfaces yields excellent agreement with experiment.
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Affiliation(s)
- Audrius Alkauskas
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Institute of Theoretical Physics, CH-1015 Lausanne, Switzerland
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41
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Abstract
A path-integral Car-Parrinello molecular dynamics simulation of liquid water and ice is performed. It is found that the inclusion of nuclear quantum effects systematically improves the agreement of first-principles simulations of liquid water with experiment. In addition, the proton momentum distribution is computed utilizing a recently developed open path-integral molecular dynamics methodology. It is shown that these results are in good agreement with experimental data.
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Affiliation(s)
- Joseph A Morrone
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
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42
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Mundy CJ, Curioni A, Goldman N, Will Kuo IF, Reed EJ, Fried LE, Ianuzzi M. Ultrafast transformation of graphite to diamond: An ab initio study of graphite under shock compression. J Chem Phys 2008; 128:184701. [DOI: 10.1063/1.2913201] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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43
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Sebastiani D, Kudin KN. Electronic response properties of carbon nanotubes in magnetic fields. ACS NANO 2008; 2:661-668. [PMID: 19206596 DOI: 10.1021/nn700147w] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Magnetic linear response properties for achiral and chiral carbon nanotubes were investigated with first-principles electronic structure methods. We have computed the magnetic shielding inside and outside the tubes originating from electronic current densities induced by the application of an external magnetic field. This electronic response of the nanotubes was analyzed for external magnetic fields both parallel and perpendicular to the tube axis. The magnetic screening would be experienced by guest molecules inside the tubes, measurable by NMR spectroscopy on isotopically labeled samples. Special attention is given to chiral nanotubes, in which longitudinal fields induce a non-zero longitudinal current density and thus tangential magnetic fields outside the tubes.
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Affiliation(s)
- Daniel Sebastiani
- Max-Planck-Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany.
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44
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Bulo RE, Jacob CR, Visscher L. NMR Solvent Shifts of Acetonitrile from Frozen Density Embedding Calculations. J Phys Chem A 2008; 112:2640-7. [DOI: 10.1021/jp710609m] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rosa E. Bulo
- Faculty of Sciences, Department of Theoretical Chemistry, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Christoph R. Jacob
- Faculty of Sciences, Department of Theoretical Chemistry, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Lucas Visscher
- Faculty of Sciences, Department of Theoretical Chemistry, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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45
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Röhrig UF, Sebastiani D. NMR Chemical Shifts of the Rhodopsin Chromophore in the Dark State and in Bathorhodopsin: A Hybrid QM/MM Molecular Dynamics Study. J Phys Chem B 2008; 112:1267-74. [DOI: 10.1021/jp075662q] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ute F. Röhrig
- Ludwig Institute for Cancer Research and Swiss Institute of Bioinformatics, Molecular Modeling Group, Genopode Building CH-1015 Lausanne, Switzerland, and Max-Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Daniel Sebastiani
- Ludwig Institute for Cancer Research and Swiss Institute of Bioinformatics, Molecular Modeling Group, Genopode Building CH-1015 Lausanne, Switzerland, and Max-Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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46
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Lee YJ, Murakhtina T, Sebastiani D, Spiess HW. 2H Solid-State NMR of Mobile Protons: It Is Not Always the Simple Way. J Am Chem Soc 2007; 129:12406-7. [PMID: 17887682 DOI: 10.1021/ja0754857] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Young Joo Lee
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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47
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Marx D. Proton transfer 200 years after von Grotthuss: insights from ab initio simulations. Chemphyschem 2007; 7:1848-70. [PMID: 16929553 DOI: 10.1002/cphc.200600128] [Citation(s) in RCA: 612] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
In the last decade, ab initio simulations and especially Car-Parrinello molecular dynamics have significantly contributed to the improvement of our understanding of both the physical and chemical properties of water, ice, and hydrogen-bonded systems in general. At the heart of this family of in silico techniques lies the crucial idea of computing the many-body interactions by solving the electronic structure problem "on the fly" as the simulation proceeds, which circumvents the need for pre-parameterized potential models. In particular, the field of proton transfer in hydrogen-bonded networks greatly benefits from these technical advances. Here, several systems of seemingly quite different nature and of increasing complexity, such as Grotthuss diffusion in water, excited-state proton-transfer in solution, phase transitions in ice, and protonated water networks in the membrane protein bacteriorhodopsin, are discussed in the realms of a unifying viewpoint.
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Affiliation(s)
- Dominik Marx
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
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48
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Pavone M, Cimino P, Crescenzi O, Sillanpää A, Barone V. Interplay of Intrinsic, Environmental, and Dynamic Effects in Tuning the EPR Parameters of Nitroxides: Further Insights from an Integrated Computational Approach. J Phys Chem B 2007; 111:8928-39. [PMID: 17608525 DOI: 10.1021/jp0727805] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The role of stereoelectronic, environmental, and short-time dynamic effects in tuning the hyperfine and gyromagnetic tensors of a prototypical nitroxide spin probe has been investigated by an integrated computational approach based on extended Lagrangian molecular dynamics and discrete-continuum solvent models. Trajectories were generated in two protic solvents as well as in the gas phase for reference; structural analysis of the dynamics, and comparison with optimized solute-solvent clusters, allowed for the identification of the prevailing solute-solvent hydrogen-bonding patterns and helped to define the strategy for the computation of magnetic parameters. This was performed in a separate step, on a large number of frames, by a high-level DFT approach coupling the PBE0 hybrid functional with a tailored basis set and with proper account of specific and bulk solvent effects. Remarkable changes in solvation networks are found on going from aqueous to methanol solution, thus providing a rationalization of indirect experimentally available evidence. The computed magnetic parameters are in satisfactory agreement with the available measured values and allow for an unbiased evaluation of the role of different effects in tuning the overall EPR observables. Apart from their intrinsic interest, our results pave the route toward the development of tunable detection protocols based on specific spectroscopic signatures.
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Affiliation(s)
- Michele Pavone
- Dipartimento di Chimica and INSTM, Università di Napoli Federico II Complesso Universitario di Monte S. Angelo, Via Cintia, I-80126 Napoli, Italy
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49
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Thar J, Hovorka R, Kirchner B. Basis Set Superposition Error along the Free-Energy Surface of the Water Dimer. J Chem Theory Comput 2007; 3:1510-7. [DOI: 10.1021/ct600259x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jens Thar
- Lehrstuhl für Theoretische Chemie, Wilhelm-Ostwald Institut für Physikalische und Theoretische Chemie, Universität Leipzig, Linnestrasse 2, D-04103 Leipzig, Germany, and Organische Chemie, Kekulé Institut für Organische Chemie und Biochemie, Universität Bonn, Gerhard-Domagk-Strasse 1, D-53121 Bonn, Germany
| | - Rainer Hovorka
- Lehrstuhl für Theoretische Chemie, Wilhelm-Ostwald Institut für Physikalische und Theoretische Chemie, Universität Leipzig, Linnestrasse 2, D-04103 Leipzig, Germany, and Organische Chemie, Kekulé Institut für Organische Chemie und Biochemie, Universität Bonn, Gerhard-Domagk-Strasse 1, D-53121 Bonn, Germany
| | - Barbara Kirchner
- Lehrstuhl für Theoretische Chemie, Wilhelm-Ostwald Institut für Physikalische und Theoretische Chemie, Universität Leipzig, Linnestrasse 2, D-04103 Leipzig, Germany, and Organische Chemie, Kekulé Institut für Organische Chemie und Biochemie, Universität Bonn, Gerhard-Domagk-Strasse 1, D-53121 Bonn, Germany
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50
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Komin S, Gossens C, Tavernelli I, Rothlisberger U, Sebastiani D. NMR Solvent Shifts of Adenine in Aqueous Solution from Hybrid QM/MM Molecular Dynamics Simulations. J Phys Chem B 2007; 111:5225-32. [PMID: 17458990 DOI: 10.1021/jp067263l] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present first principles calculations of the NMR solvent shift of adenine in aqueous solution. The calculations are based on snapshots sampled from a molecular dynamics simulation, which were obtained via a hybrid quantum-mechanical/mechanical modeling approach, using an all-atom force field (TIP3P). We find that the solvation via the strongly fluctuating hydrogen bond network of water leads to nontrivial changes in the NMR spectra of the solutes regarding the ordering of the resonance lines. Although there are still sizable deviations from experiment, the overall agreement is satisfactory for the 1H and 15N NMR shifts. Our work is another step toward a realistic first-principles prediction of NMR chemical shifts in complex chemical environments.
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Affiliation(s)
- Sittipong Komin
- Max-Planck-Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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