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Silarski M, Dziedzic-Kocurek K, Drużbicki K, Reterski R, Grabowski P, Krzystyniak M. Non-invasive detection of hazardous materials with a thermal-to-epithermal neutron station: a feasibility study towards practical application. Sci Rep 2024; 14:18584. [PMID: 39127754 DOI: 10.1038/s41598-024-69290-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Accepted: 08/01/2024] [Indexed: 08/12/2024] Open
Abstract
The growing scale of the devastation that even a single terrorist attack can cause requires more effective methods for the detection of hazardous materials. In particular, there are no solutions for effectively monitoring threats at sea, both for the off-shore infrastructure and ports. Currently, state-of-the-art detection methods determine the density distribution and the shapes of tested subjects but only allow for a limited degree of substance identification. This work aims to present a feasibility study of the possible usage of several methods available on the thermal-to-epithermal neutron station, VESUVIO, at the ISIS neutron and muon spallation source, UK, for the detection of hazardous materials. To this end, we present the results of a series of experiments performed concurrently employing neutron transmission and Compton scattering using melamine, a commonly used explosive surrogate, in order to determine its signal characteristics and limits of detection and quantitation. The experiments are supported by first-principles modelling, providing detailed scrutiny of the material structure and the nuclear dynamics behind the neutron scattering observables.
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Affiliation(s)
- Michał Silarski
- M. Smoluchowski Institute of Physics of the Jagiellonian University, Łojasiewicza 11, 30-348, Cracow, Poland
| | - Katarzyna Dziedzic-Kocurek
- M. Smoluchowski Institute of Physics of the Jagiellonian University, Łojasiewicza 11, 30-348, Cracow, Poland
| | - Kacper Drużbicki
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Lodz, Poland
| | - Radosław Reterski
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Cracow, Poland
| | - Patryk Grabowski
- M. Smoluchowski Institute of Physics of the Jagiellonian University, Łojasiewicza 11, 30-348, Cracow, Poland
| | - Matthew Krzystyniak
- ISIS Neutron and Muon Source, STFC Rutherford Appleton Laboratory, Oxford, OX11 0QX, UK.
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2
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Arandhara M, Ramesh SG. Nuclear quantum effects in gas-phase ethylene glycol. Phys Chem Chem Phys 2024; 26:19529-19542. [PMID: 38979630 DOI: 10.1039/d4cp00700j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Path integral molecular simulations are used to explore the nuclear quantum effects (NQEs) on the structure, dihedral landscape and infrared spectrum of ethylene glycol. The simulations are carried out on a new reaction surface Hamiltonian-based model potential energy surface, with special focus on the role of the OCCO and HOCC dihedrals. In contrast with classical simulations, we analyse how the intramolecular interactions between the OH groups change due to zero-point effects as well as temperature. These are found to be weak. The NQEs on the free energy profile along the OCCO dihedral are analysed, where notable effects are seen at low temperatures and found to be correlated with the radii of gyration of the atoms. Finally, the power spectrum of the molecule from path integral simulations is compared with the experimental infrared spectrum, yielding a good agreement of band positions.
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Affiliation(s)
- Mrinal Arandhara
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India.
| | - Sai G Ramesh
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India.
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3
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Ghanavati R, Escobosa AC, Manz TA. An automated protocol to construct flexibility parameters for classical forcefields: applications to metal-organic frameworks. RSC Adv 2024; 14:22714-22762. [PMID: 39035129 PMCID: PMC11258866 DOI: 10.1039/d4ra01859a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 06/18/2024] [Indexed: 07/23/2024] Open
Abstract
In this work, forcefield flexibility parameters were constructed and validated for more than 100 metal-organic frameworks (MOFs). We used atom typing to identify bond types, angle types, and dihedral types associated with bond stretches, angle bends, dihedral torsions, and other flexibility interactions. Our work used Manz's angle-bending and dihedral-torsion model potentials. For a crystal structure containing N atoms in its unit cell, the number of independent flexibility interactions is 3(N atoms - 1). Because the number of bonds, angles, and dihedrals is normally much larger than 3(N atoms - 1), these internal coordinates are redundant. To reduce (but not eliminate) this redundancy, our protocol prunes dihedral types in a way that preserves symmetry equivalency. Next, each dihedral type is classified as non-rotatable, hindered, rotatable, or linear. We introduce a smart selection method that identifies which particular torsion modes are important for each rotatable dihedral type. Then, we computed the force constants for all flexibility interactions together via LASSO regression (i.e., regularized linear least-squares fitting) of the training dataset. LASSO automatically identifies and removes unimportant forcefield interactions. For each MOF, the reference dataset was quantum-mechanically-computed in VASP via DFT with dispersion and included: (i) finite-displacement calculations along every independent atom translation mode, (ii) geometries randomly sampled via ab initio molecular dynamics (AIMD), (iii) the optimized ground-state geometry using experimental lattice parameters, and (iv) rigid torsion scans for each rotatable dihedral type. After training, the flexibility model was validated across geometries that were not part of the training dataset. For each MOF, we computed the goodness of fit (R-squared value) and the root-mean-squared error (RMSE) separately for the training and validation datasets. We compared flexibility models with and without bond-bond cross terms. Even without cross terms, the model yielded R-squared values of 0.910 (avg across all MOFs) ± 0.018 (st. dev.) for atom-in-material forces in the validation datasets. Our SAVESTEPS protocol should find widespread applications to parameterize flexible forcefields for material datasets. We performed molecular dynamics simulations using these flexibility parameters to compute heat capacities and thermal expansion coefficients for two MOFs.
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Affiliation(s)
- Reza Ghanavati
- Chemical & Materials Engineering, New Mexico State University Las Cruces NM 88001 USA
| | - Alma C Escobosa
- Chemical & Materials Engineering, New Mexico State University Las Cruces NM 88001 USA
| | - Thomas A Manz
- Chemical & Materials Engineering, New Mexico State University Las Cruces NM 88001 USA
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4
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Chakraborty R, Talbot JJ, Shen H, Yabuuchi Y, Carsch KM, Jiang HZH, Furukawa H, Long JR, Head-Gordon M. Quantum chemical modeling of hydrogen binding in metal-organic frameworks: validation, insight, predictions and challenges. Phys Chem Chem Phys 2024; 26:6490-6511. [PMID: 38324335 DOI: 10.1039/d3cp05540j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
A detailed chemical understanding of H2 interactions with binding sites in the nanoporous crystalline structure of metal-organic frameworks (MOFs) can lay a sound basis for the design of new sorbent materials. Computational quantum chemical calculations can aid in this quest. To set the stage, we review general thermodynamic considerations that control the usable storage capacity of a sorbent. We then discuss cluster modeling of H2 ligation at MOF binding sites using state-of-the-art density functional theory (DFT) calculations, and how the binding can be understood using energy decomposition analysis (EDA). Employing these tools, we illustrate the connections between the character of the MOF binding site and the associated adsorption thermodynamics using four experimentally characterized MOFs, highlighting the role of open metal sites (OMSs) in accessing binding strengths relevant to room temperature storage. The sorbents are MOF-5, with no open metal sites, Ni2(m-dobdc), containing Lewis acidic Ni(II) sites, Cu(I)-MFU-4l, containing π basic Cu(I) sites and V2Cl2.8(btdd), also containing π-basic V(II) sites. We next explore the potential for binding multiple H2 molecules at a single metal site, with thermodynamics useful for storage at ambient temperature; a materials design goal which has not yet been experimentally demonstrated. Computations on Ca2+ or Mg2+ bound to catecholate or Ca2+ bound to porphyrin show the potential for binding up to 4 H2; there is precedent for the inclusion of both catecholate and porphyrin motifs in MOFs. Turning to transition metals, we discuss the prediction that two H2 molecules can bind at V(II)-MFU-4l, a material that has been synthesized with solvent coordinated to the V(II) site. Additional calculations demonstrate binding three equivalents of hydrogen per OMS in Sc(I) or Ti(I)-exchanged MFU-4l. Overall, the results suggest promising prospects for experimentally realizing higher capacity hydrogen storage MOFs, if nontrivial synthetic and desolvation challenges can be overcome. Coupled with the unbounded chemical diversity of MOFs, there is ample scope for additional exploration and discovery.
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Affiliation(s)
- Romit Chakraborty
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Chemistry, University of California, Berkeley, CA 94720, USA.
| | - Justin J Talbot
- Department of Chemistry, University of California, Berkeley, CA 94720, USA.
| | - Hengyuan Shen
- Department of Chemistry, University of California, Berkeley, CA 94720, USA.
| | - Yuto Yabuuchi
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Chemistry, University of California, Berkeley, CA 94720, USA.
| | - Kurtis M Carsch
- Department of Chemistry, University of California, Berkeley, CA 94720, USA.
| | - Henry Z H Jiang
- Department of Chemistry, University of California, Berkeley, CA 94720, USA.
| | - Hiroyasu Furukawa
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Chemistry, University of California, Berkeley, CA 94720, USA.
| | - Jeffrey R Long
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Chemistry, University of California, Berkeley, CA 94720, USA.
- Department of Chemical and Biomedical Engineering, University of California, Berkeley, CA 94720, USA
| | - Martin Head-Gordon
- Department of Chemistry, University of California, Berkeley, CA 94720, USA.
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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5
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Arandhara M, Ramesh SG. Nuclear quantum effects in gas-phase 2-fluoroethanol. Phys Chem Chem Phys 2024; 26:6885-6902. [PMID: 38333949 DOI: 10.1039/d3cp05657k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
Torsional motions along the FCCO and HOCC dihedrals lead to the five unique conformations of 2-fluoroethanol, of which the conformer that is gauche along both dihedrals has the lowest energy. In this work, we explore how nuclear quantum effects (NQEs) manifest in the structural parameters of the lowest energy conformer, in the intramolecular free energy landscape along the FCCO and HOCC dihedrals, and also in the infrared spectrum of the title molecule, through the use of path integral simulations. We have first developed a full dimensional potential energy surface using the reaction surface Hamiltonian framework. On this potential, we have carried out path integral molecular dynamics simulations at several temperatures starting from the minimum energy well to explore structural influences of NQEs including geometrical markers of the interaction between the OH and F groups. From the computed free energy landscapes, significant reduction of the torsional barrier is found at low temperature near the cis region of the dihedrals, which can be understood through the trends in the radii of gyration of the atomic ring polymers. We find that the inclusion of NQEs in the computation of infrared spectrum is important to obtain good agreement with the experimental band positions.
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Affiliation(s)
- Mrinal Arandhara
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India.
| | - Sai G Ramesh
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India.
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6
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Listyarini R, Gamper J, Hofer TS. Storage and Diffusion of Carbon Dioxide in the Metal Organic Framework MOF-5─A Semi-empirical Molecular Dynamics Study. J Phys Chem B 2023; 127:9378-9389. [PMID: 37857343 PMCID: PMC10627117 DOI: 10.1021/acs.jpcb.3c04155] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 09/22/2023] [Indexed: 10/21/2023]
Abstract
Metal-organic frameworks (MOFs) have attracted increasing attention due to their high porosity for exceptional gas storage applications. MOF-5 belongs to the family of isoreticular MOFs (IRMOFs) and consists of Zn4O6+ clusters linked by 1,4-benzenedicarboxylate. Due to the large number of atoms in the unit cell, molecular dynamics simulation based on density functional theory has proved to be too demanding, while force field models are often inadequate to model complex host-guest interactions. To overcome this limitation, an alternative semi-empirical approach using a set of approximations and extensive parametrization of interactions called density functional tight binding (DFTB) was applied in this work to study CO2 in the MOF-5 host. Calculations of pristine MOF-5 yield very good agreement with experimental data in terms of X-ray diffraction patterns as well as mechanical properties, such as the negative thermal expansion coefficient and the bulk modulus. In addition, different loadings of CO2 were introduced, and the associated self-diffusion coefficients and activation energies were investigated. The results show very good agreement with those of other experimental and theoretical investigations. This study provides detailed insights into the capability of semi-empirical DFTB-based molecular dynamics simulations of these challenging guest@host systems. Based on the comparison of the guest-guest pair distributions observed inside the MOF host and the corresponding gas-phase reference, a liquid-like structure of CO2 can be deduced upon storage in the host material.
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Affiliation(s)
- Risnita
Vicky Listyarini
- Theoretical
Chemistry Division, Institute of General, Inorganic and Theoretical
Chemistry, University of Innsbruck, Innrain 80-82A, A-6020 Innsbruck, Austria
- Chemistry
Education Study Program, Sanata Dharma University, Yogyakarta 55282, Indonesia
| | - Jakob Gamper
- Theoretical
Chemistry Division, Institute of General, Inorganic and Theoretical
Chemistry, University of Innsbruck, Innrain 80-82A, A-6020 Innsbruck, Austria
| | - Thomas S. Hofer
- Theoretical
Chemistry Division, Institute of General, Inorganic and Theoretical
Chemistry, University of Innsbruck, Innrain 80-82A, A-6020 Innsbruck, Austria
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7
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Wieser S, Kamencek T, Schmid R, Bedoya-Martínez N, Zojer E. Exploring the Impact of the Linker Length on Heat Transport in Metal–Organic Frameworks. NANOMATERIALS 2022; 12:nano12132142. [PMID: 35807978 PMCID: PMC9268455 DOI: 10.3390/nano12132142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/09/2022] [Accepted: 06/13/2022] [Indexed: 12/04/2022]
Abstract
Metal–organic frameworks (MOFs) are a highly versatile group of porous materials suitable for a broad range of applications, which often crucially depend on the MOFs’ heat transport properties. Nevertheless, detailed relationships between the chemical structure of MOFs and their thermal conductivities are still largely missing. To lay the foundations for developing such relationships, we performed non-equilibrium molecular dynamics simulations to analyze heat transport in a selected set of materials. In particular, we focus on the impact of organic linkers, the inorganic nodes and the interfaces between them. To obtain reliable data, great care was taken to generate and thoroughly benchmark system-specific force fields building on ab-initio-based reference data. To systematically separate the different factors arising from the complex structures of MOF, we also studied a series of suitably designed model systems. Notably, besides the expected trend that longer linkers lead to a reduction in thermal conductivity due to an increase in porosity, they also cause an increase in the interface resistance between the different building blocks of the MOFs. This is relevant insofar as the interface resistance dominates the total thermal resistance of the MOF. Employing suitably designed model systems, it can be shown that this dominance of the interface resistance is not the consequence of the specific, potentially weak, chemical interactions between nodes and linkers. Rather, it is inherent to the framework structures of the MOFs. These findings improve our understanding of heat transport in MOFs and will help in tailoring the thermal conductivities of MOFs for specific applications.
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Affiliation(s)
- Sandro Wieser
- Institute of Solid State Physics, NAWI Graz, Graz University of Technology, 8010 Graz, Austria; (S.W.); (T.K.)
| | - Tomas Kamencek
- Institute of Solid State Physics, NAWI Graz, Graz University of Technology, 8010 Graz, Austria; (S.W.); (T.K.)
- Institute of Physical and Theoretical Chemistry, NAWI Graz, Graz University of Technology, 8010 Graz, Austria
| | - Rochus Schmid
- Computational Materials Chemistry Group, Faculty of Chemistry and Biochemistry, Ruhr-University Bochum, 44801 Bochum, Germany;
| | | | - Egbert Zojer
- Institute of Solid State Physics, NAWI Graz, Graz University of Technology, 8010 Graz, Austria; (S.W.); (T.K.)
- Correspondence:
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8
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Simulation of Nuclear Quantum Effects in Condensed Matter Systems via Quantum Baths. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12094756] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
This paper reviews methods that aim at simulating nuclear quantum effects (NQEs) using generalized thermal baths. Generalized (or quantum) baths simulate statistical quantum features, and in particular zero-point energy effects, through non-Markovian stochastic dynamics. They make use of generalized Langevin Equations (GLEs), in which the quantum Bose–Einstein energy distribution is enforced by tuning the random and friction forces, while the system degrees of freedom remain classical. Although these baths have been formally justified only for harmonic oscillators, they perform well for several systems, while keeping the cost of the simulations comparable to the classical ones. We review the formal properties and main characteristics of classical and quantum GLEs, in relation with the fluctuation–dissipation theorems. Then, we describe the quantum thermostat and quantum thermal bath, the two generalized baths currently most used, providing several examples of applications for condensed matter systems, including the calculation of vibrational spectra. The most important drawback of these methods, zero-point energy leakage, is discussed in detail with the help of model systems, and a recently proposed scheme to monitor and mitigate or eliminate it—the adaptive quantum thermal bath—is summarised. This approach considerably extends the domain of application of generalized baths, leading, for instance, to the successful simulation of liquid water, where a subtle interplay of NQEs is at play. The paper concludes by overviewing further development opportunities and open challenges of generalized baths.
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9
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Kamencek T, Schrode B, Resel R, Ricco R, Zojer E. Understanding the Origin of the Particularly Small and Anisotropic Thermal Expansion of MOF‐74. ADVANCED THEORY AND SIMULATIONS 2022. [DOI: 10.1002/adts.202200031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Tomas Kamencek
- Institute of Solid State Physics Graz University of Technology NAWI Graz Petersgasse 16 Graz 8010 Austria
- Institute of Physical and Theoretical Chemistry Graz University of Technology NAWI Graz Stremayrgasse 9 Graz 8010 Austria
| | | | - Roland Resel
- Institute of Solid State Physics Graz University of Technology NAWI Graz Petersgasse 16 Graz 8010 Austria
| | - Raffaele Ricco
- Institute of Physical and Theoretical Chemistry Graz University of Technology NAWI Graz Stremayrgasse 9 Graz 8010 Austria
- School of Engineering and Technology Asian Institute of Technology 58 Moo 9 Khlong Luang Pathum Thani 12120 Thailand
| | - Egbert Zojer
- Institute of Solid State Physics Graz University of Technology NAWI Graz Petersgasse 16 Graz 8010 Austria
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10
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Xu X, Chen Z, Yang Y. Molecular Dynamics with Constrained Nuclear Electronic Orbital Density Functional Theory: Accurate Vibrational Spectra from Efficient Incorporation of Nuclear Quantum Effects. J Am Chem Soc 2022; 144:4039-4046. [PMID: 35196860 DOI: 10.1021/jacs.1c12932] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nuclear quantum effects play a crucial role in many chemical and biological systems involving hydrogen atoms yet are difficult to include in practical molecular simulations. In this paper, we combine our recently developed methods of constrained nuclear-electronic orbital density functional theory (cNEO-DFT) and constrained minimized energy surface molecular dynamics (CMES-MD) to create a new method for accurately and efficiently describing nuclear quantum effects in molecular simulations. By use of this new method, dubbed cNEO-MD, the vibrational spectra of a set of small molecules are calculated and compared with those from conventional ab initio molecular dynamics (AIMD) as well as from experiments. With the same formal scaling, cNEO-MD greatly outperforms AIMD in describing the vibrational modes with significant hydrogen motion characters, demonstrating the promise of cNEO-MD for simulating chemical and biological systems with significant nuclear quantum effects.
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Affiliation(s)
- Xi Xu
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin─Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Zehua Chen
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin─Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Yang Yang
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin─Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
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11
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Lee S, Wang G, Ji N, Zhang M, Wang D, Sun L, Meng W, Zheng Y, Li Y, Wu Y. Synthesis, characterizations and kinetics of MOF‐5 as herbicide vehicle and its controlled release in PVA/ST biodegradable composite membranes. Z Anorg Allg Chem 2021. [DOI: 10.1002/zaac.202100252] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Shaoxiang Lee
- College of Environment and Safety Engineering Qingdao University of Science and Technology No.53, Zhengzhou Road Qingdao 266042 People's Republic of China
- Shandong Engineering Research Center for Marine Environment Corrosion and Safety Protection Qingdao University of Science and Technology Qingdao 266042 People's Republic of China
- Shandong Engineering Technology Research Center for Advanced Coating Qingdao University of Science and Technology Qingdao 266042 People's Republic of China
| | - Guohui Wang
- College of Environment and Safety Engineering Qingdao University of Science and Technology No.53, Zhengzhou Road Qingdao 266042 People's Republic of China
- Shandong Engineering Research Center for Marine Environment Corrosion and Safety Protection Qingdao University of Science and Technology Qingdao 266042 People's Republic of China
- Shandong Engineering Technology Research Center for Advanced Coating Qingdao University of Science and Technology Qingdao 266042 People's Republic of China
| | - Nana Ji
- Shandong Engineering Research Center for Marine Environment Corrosion and Safety Protection Qingdao University of Science and Technology Qingdao 266042 People's Republic of China
| | - Meng Zhang
- College of Environment and Safety Engineering Qingdao University of Science and Technology No.53, Zhengzhou Road Qingdao 266042 People's Republic of China
- Shandong Engineering Research Center for Marine Environment Corrosion and Safety Protection Qingdao University of Science and Technology Qingdao 266042 People's Republic of China
- Shandong Engineering Technology Research Center for Advanced Coating Qingdao University of Science and Technology Qingdao 266042 People's Republic of China
| | - Dong Wang
- College of Environment and Safety Engineering Qingdao University of Science and Technology No.53, Zhengzhou Road Qingdao 266042 People's Republic of China
- Shandong Engineering Research Center for Marine Environment Corrosion and Safety Protection Qingdao University of Science and Technology Qingdao 266042 People's Republic of China
- Shandong Engineering Technology Research Center for Advanced Coating Qingdao University of Science and Technology Qingdao 266042 People's Republic of China
| | - Lishui Sun
- College of Environment and Safety Engineering Qingdao University of Science and Technology No.53, Zhengzhou Road Qingdao 266042 People's Republic of China
- Shandong Engineering Research Center for Marine Environment Corrosion and Safety Protection Qingdao University of Science and Technology Qingdao 266042 People's Republic of China
- Shandong Engineering Technology Research Center for Advanced Coating Qingdao University of Science and Technology Qingdao 266042 People's Republic of China
| | - Wenqiao Meng
- College of Environment and Safety Engineering Qingdao University of Science and Technology No.53, Zhengzhou Road Qingdao 266042 People's Republic of China
- Shandong Engineering Research Center for Marine Environment Corrosion and Safety Protection Qingdao University of Science and Technology Qingdao 266042 People's Republic of China
- Shandong Engineering Technology Research Center for Advanced Coating Qingdao University of Science and Technology Qingdao 266042 People's Republic of China
| | - Yuqi Zheng
- College of Environment and Safety Engineering Qingdao University of Science and Technology No.53, Zhengzhou Road Qingdao 266042 People's Republic of China
- Shandong Engineering Research Center for Marine Environment Corrosion and Safety Protection Qingdao University of Science and Technology Qingdao 266042 People's Republic of China
- Shandong Engineering Technology Research Center for Advanced Coating Qingdao University of Science and Technology Qingdao 266042 People's Republic of China
| | - Yanxin Li
- College of Environment and Safety Engineering Qingdao University of Science and Technology No.53, Zhengzhou Road Qingdao 266042 People's Republic of China
- Shandong Engineering Research Center for Marine Environment Corrosion and Safety Protection Qingdao University of Science and Technology Qingdao 266042 People's Republic of China
- Shandong Engineering Technology Research Center for Advanced Coating Qingdao University of Science and Technology Qingdao 266042 People's Republic of China
| | - Yuting Wu
- College of Chemistry and Molecular Engineering Qingdao University of Science and Technology Qingdao 266042 People's Republic of China
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12
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Bidault X, Chaudhuri S. Improved predictions of thermomechanical properties of molecular crystals from energy and dispersion corrected DFT. J Chem Phys 2021; 154:164105. [PMID: 33940806 DOI: 10.1063/5.0041511] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Thermal stability and pressure-dependent changes are key to molecular crystals and their properties. The determination of their thermal properties from ab initio methods is, however, a challenging task. While the low-frequency phonon spectrum related to intermolecular vibrations remains difficult to describe, the Quasi-Harmonic Approximation (QHA) also induces for molecular crystals a significant volume deviation, which makes their thermal behavior ill-determined. To overcome these difficulties, we consider a pragmatic energy correction (EC) that has long been used for atomic crystals, and we presently report the first ever use for molecular crystals. Applying the QHA in dispersion-corrected density functional theory (DFT-D) calculations with an ab initio parameterized EC, the resulting model can simultaneously and accurately derive thermal and mechanical properties of high-explosive molecular crystals. When compared to experiments, the mean absolute percent error of previous DFT-based thermomechanical models is 12% for mechanical and 31% for thermal properties. Our model performs significantly better and reduces these uncertainties to 4.1% and 9.8%, respectively. In particular, the agreement between our model and experiments for the thermal properties is three times better. This significant improvement greatly benefits the determination of thermomechanical properties such as the Grüneisen parameter and the shock properties. The method has been successfully applied to molecular crystals showing a large diversity of weak intermolecular interactions (β-1,3,5,7-tetranitro-1,3,5,7-tetrazoctane (HMX), α-1,1-diamino-2,2-dinitroethylene (FOX-7), Triaminotrinitrobenzene (TATB), ε-Hexanitrohexaazaisowurtzitane (CL20), and Pentaerythritol tetranitrate (PETN)-I). Due to its accuracy and transferability, our model is expected to work for a large class of computationally designed molecular crystals and co-crystals, providing a basis for a predictive framework.
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Affiliation(s)
- X Bidault
- Department of Civil, Materials and Environmental Engineering, University of Illinois at Chicago, Chicago, Illinois 60607, USA
| | - S Chaudhuri
- Department of Civil, Materials and Environmental Engineering, University of Illinois at Chicago, Chicago, Illinois 60607, USA
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13
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Lamaire A, Wieme J, Hoffman AEJ, Van Speybroeck V. Atomistic insight in the flexibility and heat transport properties of the stimuli-responsive metal–organic framework MIL-53(Al) for water-adsorption applications using molecular simulations. Faraday Discuss 2021; 225:301-323. [DOI: 10.1039/d0fd00025f] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Insight into the heat transport and water-adsorption properties of the flexible MIL-53(Al) is obtained using advanced molecular dynamics simulations.
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Affiliation(s)
- Aran Lamaire
- Center for Molecular Modeling
- Ghent University
- 9052 Zwijnaarde
- Belgium
| | - Jelle Wieme
- Center for Molecular Modeling
- Ghent University
- 9052 Zwijnaarde
- Belgium
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14
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Polynski MV, Sapova MD, Ananikov VP. Understanding the solubilization of Ca acetylide with a new computational model for ionic pairs. Chem Sci 2020; 11:13102-13112. [PMID: 34094492 PMCID: PMC8163204 DOI: 10.1039/d0sc04752j] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 10/07/2020] [Indexed: 01/05/2023] Open
Abstract
The unique reactivity of the acetylenic unit in DMSO gives rise to ubiquitous synthetic methods. We theoretically consider CaC2 solubility and protolysis in DMSO and formulate a strategy for CaC2 activation in solution-phase chemical transformations. For this, we use a new strategy for the modeling of ionic compounds in strongly coordinating solvents combining Born-Oppenheimer molecular dynamics with the DFTB3-D3(BJ) Hamiltonian and static DFT computations at the PBE0-D3(BJ)/pob-TZVP-gCP level. We modeled the thermodynamics of CaC2 protolysis under ambient conditions, taking into account its known heterogeneity and considering three polymorphs of CaC2. We give a theoretical basis for the existence of the elusive intermediate HC[triple bond, length as m-dash]C-Ca-OH and show that CaC2 insolubility in DMSO is of thermodynamic nature. We confirm the unique role of water and specific properties of DMSO in CaC2 activation and explain how the activation is realized. The proposed strategy for the utilization of CaC2 in sustainable organic synthesis is outlined.
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Affiliation(s)
- Mikhail V Polynski
- Saint Petersburg State University Universitetsky Prospect 26 Saint Petersburg 198504 Russia
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences Leninsky Prospect 47 Moscow 119991 Russia
| | - Mariia D Sapova
- Saint Petersburg State University Universitetsky Prospect 26 Saint Petersburg 198504 Russia
| | - Valentine P Ananikov
- Saint Petersburg State University Universitetsky Prospect 26 Saint Petersburg 198504 Russia
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences Leninsky Prospect 47 Moscow 119991 Russia
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15
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Wieme J, Vandenbrande S, Lamaire A, Kapil V, Vanduyfhuys L, Van Speybroeck V. Thermal Engineering of Metal-Organic Frameworks for Adsorption Applications: A Molecular Simulation Perspective. ACS APPLIED MATERIALS & INTERFACES 2019; 11:38697-38707. [PMID: 31556593 PMCID: PMC6818952 DOI: 10.1021/acsami.9b12533] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 09/26/2019] [Indexed: 05/29/2023]
Abstract
Thermal engineering of metal-organic frameworks for adsorption-based applications is very topical in view of their industrial potential, in particular, since heat management and thermal stability have been identified as important obstacles. Hence, a fundamental understanding of the structural and chemical features underpinning their intrinsic thermal properties is highly sought-after. Herein, we investigate the nanoscale behavior of a diverse set of frameworks using molecular simulation techniques and critically compare properties such as thermal conductivity, heat capacity, and thermal expansion with other classes of materials. Furthermore, we propose a hypothetical thermodynamic cycle to estimate the temperature rise associated with adsorption for the most important greenhouse and energy-related gases (CO2 and CH4). This macroscopic response on the heat of adsorption connects the intrinsic thermal properties with the adsorption properties and allows us to evaluate their importance.
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Affiliation(s)
- Jelle Wieme
- Center for Molecular
Modeling, Ghent University, Tech Lane Ghent Science Park Campus
A, Technologiepark 46, 9052 Zwijnaarde, Belgium
| | - Steven Vandenbrande
- Center for Molecular
Modeling, Ghent University, Tech Lane Ghent Science Park Campus
A, Technologiepark 46, 9052 Zwijnaarde, Belgium
| | - Aran Lamaire
- Center for Molecular
Modeling, Ghent University, Tech Lane Ghent Science Park Campus
A, Technologiepark 46, 9052 Zwijnaarde, Belgium
| | - Venkat Kapil
- Laboratory
of Computational Science and Modelling, Institute of Materials, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Louis Vanduyfhuys
- Center for Molecular
Modeling, Ghent University, Tech Lane Ghent Science Park Campus
A, Technologiepark 46, 9052 Zwijnaarde, Belgium
| | - Veronique Van Speybroeck
- Center for Molecular
Modeling, Ghent University, Tech Lane Ghent Science Park Campus
A, Technologiepark 46, 9052 Zwijnaarde, Belgium
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16
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Kapil V, Engel E, Rossi M, Ceriotti M. Assessment of Approximate Methods for Anharmonic Free Energies. J Chem Theory Comput 2019; 15:5845-5857. [DOI: 10.1021/acs.jctc.9b00596] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Venkat Kapil
- Laboratory of Computational Science and Modeling, Institut des Matériaux, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Edgar Engel
- Laboratory of Computational Science and Modeling, Institut des Matériaux, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Mariana Rossi
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany
| | - Michele Ceriotti
- Laboratory of Computational Science and Modeling, Institut des Matériaux, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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17
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Kapil V, Wieme J, Vandenbrande S, Lamaire A, Van Speybroeck V, Ceriotti M. Modeling the Structural and Thermal Properties of Loaded Metal–Organic Frameworks. An Interplay of Quantum and Anharmonic Fluctuations. J Chem Theory Comput 2019; 15:3237-3249. [DOI: 10.1021/acs.jctc.8b01297] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Venkat Kapil
- Laboratory of Computational Science and Modelling, Institute of Materials, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Jelle Wieme
- Center for Molecular Modeling, Ghent University, Tech Lane Ghent Science Park Campus A, Technologiepark 46, 9052 Zwijnaarde, Belgium
| | - Steven Vandenbrande
- Center for Molecular Modeling, Ghent University, Tech Lane Ghent Science Park Campus A, Technologiepark 46, 9052 Zwijnaarde, Belgium
| | - Aran Lamaire
- Center for Molecular Modeling, Ghent University, Tech Lane Ghent Science Park Campus A, Technologiepark 46, 9052 Zwijnaarde, Belgium
| | - Veronique Van Speybroeck
- Center for Molecular Modeling, Ghent University, Tech Lane Ghent Science Park Campus A, Technologiepark 46, 9052 Zwijnaarde, Belgium
| | - Michele Ceriotti
- Laboratory of Computational Science and Modelling, Institute of Materials, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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