1
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Jiao S, Li J, Qin X, Wan L, Hu W, Yang J. Complex-Valued K-Means Clustering of Interpolative Separable Density Fitting Algorithm for Large-Scale Hybrid Functional Enabled Ab Initio Molecular Dynamics Simulations within Plane Waves. J Phys Chem A 2024. [PMID: 38430107 DOI: 10.1021/acs.jpca.3c07172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2024]
Abstract
K-means clustering, as a classic unsupervised machine learning algorithm, is the key step to select the interpolation sampling points in interpolative separable density fitting (ISDF) decomposition for hybrid functional electronic structure calculations. Real-valued K-means clustering for accelerating the ISDF decomposition has been demonstrated for large-scale hybrid functional enabled ab initio molecular dynamics (hybrid AIMD) simulations within plane-wave basis sets where the Kohn-Sham orbitals are real-valued. However, it is unclear whether such K-means clustering works for complex-valued Kohn-Sham orbitals. Here, we propose an improved weight function defined as the sum of the square modulus of complex-valued Kohn-Sham orbitals in K-means clustering for hybrid AIMD simulations. Numerical results demonstrate that the K-means algorithm with a new weight function yields smoother and more delocalized interpolation sampling points, resulting in smoother energy potential, smaller energy drift, and longer time steps for hybrid AIMD simulations compared to the previous weight function used in the real-valued K-means algorithm. In particular, we find that this improved algorithm can obtain more accurate oxygen-oxygen radial distribution functions in liquid water molecules and a more accurate power spectrum in crystal silicon dioxide compared to the previous K-means algorithm. Finally, we describe a massively parallel implementation of this ISDF decomposition to accelerate large-scale complex-valued hybrid AIMD simulations containing thousands of atoms (2,744 atoms), which can scale up to 5,504 CPU cores on modern supercomputers.
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Affiliation(s)
- Shizhe Jiao
- Hefei National Research Center for Physical Sciences at the Microscale, and Anhui Center for Applied Mathematics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Jielan Li
- Hefei National Research Center for Physical Sciences at the Microscale, and Anhui Center for Applied Mathematics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Xinming Qin
- Hefei National Research Center for Physical Sciences at the Microscale, and Anhui Center for Applied Mathematics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Lingyun Wan
- Hefei National Research Center for Physical Sciences at the Microscale, and Anhui Center for Applied Mathematics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Wei Hu
- Hefei National Research Center for Physical Sciences at the Microscale, and Anhui Center for Applied Mathematics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Jinlong Yang
- Key Laboratory of Precision and Intelligent Chemistry, and Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
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2
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Zhou X, Huang Z, He X. Diffusion Monte Carlo method for barrier heights of multiple proton exchanges and complexation energies in small water, ammonia, and hydrogen fluoride clusters. J Chem Phys 2024; 160:054103. [PMID: 38310472 DOI: 10.1063/5.0182164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 01/09/2024] [Indexed: 02/05/2024] Open
Abstract
Proton exchange reactions are of key importance in many processes in water. However, it is nontrivial to achieve reliable barrier heights for multiple proton exchanges and complexation energies in hydrogen-bonded systems theoretically. Performance of the fixed-node diffusion quantum Monte Carlo (FN-DMC) with the single-Slater-Jastrow trial wavefunction on total energies, barrier heights of multiple proton exchanges, and complexation energies of small water, ammonia, and hydrogen fluoride clusters is investigated in this study. Effects of basis sets and those of locality approximation (LA), T-move approximation (T-move), and determinant localization approximation (DLA) schemes in dealing with the nonlocal part of pseudopotentials on FN-DMC results are evaluated. According to our results, diffuse basis functions are important in achieving reliable barrier heights and complexation energies with FN-DMC, although the cardinal number of the basis set is more important than diffuse basis functions on total energies of these systems. Our results also show that the time step bias with DLA and LA is smaller than T-move; however, the time step bias of DMC energies with respect to time steps using the T-move is roughly linear up to 0.06 a.u., while this is not the case with LA and DLA. Barrier heights and complexation energies with FN-DMC using these three schemes are always within chemical accuracy. Taking into account the fact that T-move and DLA are typically more stable than LA, FN-DMC calculations with the T-move or DLA scheme and basis sets containing diffuse basis functions are suggested for barrier heights of multiple proton exchanges and complexation energies of hydrogen-bonded clusters.
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Affiliation(s)
- Xiaojun Zhou
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, People's Republic of China
- School of Physics & Information Science, Shaanxi University of Science and Technology, Xi'an 710021, People's Republic of China
| | - Zhiru Huang
- Institute of Atomic and Molecular Physics, Key Laboratory of High Energy Density Physics and Technology, Ministry of Education, Sichuan University, Chengdu, People's Republic of China
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, People's Republic of China
- Chongqing Key Laboratory of Precision Optics, Chongqing Institute of East China Normal University, Chongqing 401120, People's Republic of China
- New York University-East China Normal University Center for Computational Chemistry, New York University Shanghai, Shanghai 200062, People's Republic of China
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Akoonjee A, Lanrewaju AA, Balogun FO, Makunga NP, Sabiu S. Waste to Medicine: Evidence from Computational Studies on the Modulatory Role of Corn Silk on the Therapeutic Targets Implicated in Type 2 Diabetes Mellitus. BIOLOGY 2023; 12:1509. [PMID: 38132335 PMCID: PMC10740667 DOI: 10.3390/biology12121509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 12/02/2023] [Accepted: 12/05/2023] [Indexed: 12/23/2023]
Abstract
Type 2 diabetes mellitus (T2DM) is characterized by insulin resistance and/or defective insulin production in the human body. Although the antidiabetic action of corn silk (CS) is well-established, the understanding of the mechanism of action (MoA) behind this potential is lacking. Hence, this study aimed to elucidate the MoA in different samples (raw and three extracts: aqueous, hydro-ethanolic, and ethanolic) as a therapeutic agent for the management of T2DM using metabolomic profiling and computational techniques. Ultra-performance liquid chromatography-mass spectrometry (UP-LCMS), in silico techniques, and density functional theory were used for compound identification and to predict the MoA. A total of 110 out of the 128 identified secondary metabolites passed the Lipinski's rule of five. The Kyoto Encyclopaedia of Genes and Genomes pathway enrichment analysis revealed the cAMP pathway as the hub signaling pathway, in which ADORA1, HCAR2, and GABBR1 were identified as the key target genes implicated in the pathway. Since gallicynoic acid (-48.74 kcal/mol), dodecanedioc acid (-34.53 kcal/mol), and tetradecanedioc acid (-36.80 kcal/mol) interacted well with ADORA1, HCAR2, and GABBR1, respectively, and are thermodynamically stable in their formed compatible complexes, according to the post-molecular dynamics simulation results, they are suggested as potential drug candidates for T2DM therapy via the maintenance of normal glucose homeostasis and pancreatic β-cell function.
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Affiliation(s)
- Ayesha Akoonjee
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, Durban 4000, South Africa; (A.A.); (A.A.L.); (F.O.B.)
| | - Adedayo Ayodeji Lanrewaju
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, Durban 4000, South Africa; (A.A.); (A.A.L.); (F.O.B.)
| | - Fatai Oladunni Balogun
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, Durban 4000, South Africa; (A.A.); (A.A.L.); (F.O.B.)
| | - Nokwanda Pearl Makunga
- Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch 7602, South Africa;
| | - Saheed Sabiu
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, Durban 4000, South Africa; (A.A.); (A.A.L.); (F.O.B.)
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4
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Arismendi-Arrieta DJ, Sen A, Eriksson A, Broqvist P, Kullgren J, Hermansson K. H2O2(s) and H2O2·2H2O(s) crystals compared with ices: DFT functional assessment and D3 analysis. J Chem Phys 2023; 159:194701. [PMID: 37966002 DOI: 10.1063/5.0145203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 07/27/2023] [Indexed: 11/16/2023] Open
Abstract
The H2O and H2O2 molecules resemble each other in a multitude of ways as has been noted in the literature. Here, we present density functional theory (DFT) calculations for the H2O2(s) and H2O2·2H2O(s) crystals and make selected comparisons with ice polymorphs. The performance of a number of dispersion-corrected density functionals-both self-consistent and a posteriori ones-are assessed, and we give special attention to the D3 correction and its effects. The D3 correction to the lattice energies is large: for H2O2(s) the D3 correction constitutes about 25% of the lattice energy using PBE, much more for RPBE, much less for SCAN, and it primarily arises from non-H-bonded interactions out to about 5 Å.The large D3 corrections to the lattice energies are likely a consequence of several effects: correction for missing dispersion interaction, the ability of D3 to capture and correct various other kinds of limitations built into the underlying DFT functionals, and finally some degree of cell-contraction-induced polarization enhancement. We find that the overall best-performing functionals of the twelve examined are optPBEvdW and RPBE-D3. Comparisons with DFT assessments for ices in the literature show that where the same methods have been used, the assessments largely agree.
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Affiliation(s)
| | - Anik Sen
- Department of Chemistry-Ångström, Uppsala University, P.O. Box 530, S-75121 Uppsala, Sweden
| | - Anders Eriksson
- Department of Chemistry-Ångström, Uppsala University, P.O. Box 530, S-75121 Uppsala, Sweden
| | - Peter Broqvist
- Department of Chemistry-Ångström, Uppsala University, P.O. Box 530, S-75121 Uppsala, Sweden
| | - Jolla Kullgren
- Department of Chemistry-Ångström, Uppsala University, P.O. Box 530, S-75121 Uppsala, Sweden
| | - Kersti Hermansson
- Department of Chemistry-Ångström, Uppsala University, P.O. Box 530, S-75121 Uppsala, Sweden
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5
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Wang R, He Z, Cao Y, Wang H, Luo X, Feng W, Chen Z, Wang T, Zhang H. Impact of crystalline structure on the digestibility of amylopectin-based starch-lipid complexes. Int J Biol Macromol 2023; 242:125191. [PMID: 37270130 DOI: 10.1016/j.ijbiomac.2023.125191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 04/24/2023] [Accepted: 05/31/2023] [Indexed: 06/05/2023]
Abstract
In this study, chain-elongated waxy corn starch (mWCS) was complexed with lauric acid (LA) to produce starch-lipid complexes (mWCS@LA) with a mixture of B- and V-type crystalline structures. Results from in vitro digestion showed that mWCS@LA had higher digestibility than mWCS, and the logarithm of slope plots of mWCS@LA revealed a two-stage digestion pattern, with digestion rate of the first stage (k1 = 0.038 min-1) being much higher than that of the following stage (k2 = 0.0116 min-1). The complexation between the long branch chains of mWCS and LA formed amylopectin-based V-type crystallites that were rapidly hydrolyzed during the first stage. The digesta isolated from the second stage of digestion had a B-type crystallinity of 52.6 %, and starch chains with degree of polymerization of 24-28 mainly contributed to the formation of the B-type crystalline structure. The results from the present study reveal that the B-type crystallites were more resistant to amylolytic hydrolysis than the amylopectin-based V-type crystallites.
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Affiliation(s)
- Ren Wang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Zhishu He
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Yijun Cao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Hongyu Wang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Xiaohu Luo
- College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315211, Zhejiang, People's Republic of China
| | - Wei Feng
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Zhengxing Chen
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Tao Wang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Hao Zhang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China.
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6
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Song S, Vuckovic S, Kim Y, Yu H, Sim E, Burke K. Extending density functional theory with near chemical accuracy beyond pure water. Nat Commun 2023; 14:799. [PMID: 36781855 PMCID: PMC9925738 DOI: 10.1038/s41467-023-36094-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 01/13/2023] [Indexed: 02/15/2023] Open
Abstract
Density functional simulations of condensed phase water are typically inaccurate, due to the inaccuracies of approximate functionals. A recent breakthrough showed that the SCAN approximation can yield chemical accuracy for pure water in all its phases, but only when its density is corrected. This is a crucial step toward first-principles biosimulations. However, weak dispersion forces are ubiquitous and play a key role in noncovalent interactions among biomolecules, but are not included in the new approach. Moreover, naïve inclusion of dispersion in HF-SCAN ruins its high accuracy for pure water. Here we show that systematic application of the principles of density-corrected DFT yields a functional (HF-r2SCAN-DC4) which recovers and not only improves over HF-SCAN for pure water, but also captures vital noncovalent interactions in biomolecules, making it suitable for simulations of solutions.
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Affiliation(s)
- Suhwan Song
- grid.15444.300000 0004 0470 5454Department of Chemistry, Yonsei University, 50 Yonsei-ro Seodaemun-gu, Seoul, 03722 Korea ,grid.266093.80000 0001 0668 7243Department of Chemistry, University of California, Irvine, CA 92697 USA
| | - Stefan Vuckovic
- grid.472716.10000 0004 1758 7362Institute for Microelectronics and Microsystems (CNR-IMM), Via Monteroni, Campus Unisalento, 73100 Lecce, Italy ,grid.12380.380000 0004 1754 9227Departments of Chemistry & Pharmaceutical Sciences and Amsterdam Institute of Molecular and Life Sciences (AIMMS), Faculty of Science, Vrije Universiteit, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands
| | - Youngsam Kim
- grid.15444.300000 0004 0470 5454Department of Chemistry, Yonsei University, 50 Yonsei-ro Seodaemun-gu, Seoul, 03722 Korea
| | - Hayoung Yu
- grid.15444.300000 0004 0470 5454Department of Chemistry, Yonsei University, 50 Yonsei-ro Seodaemun-gu, Seoul, 03722 Korea
| | - Eunji Sim
- Department of Chemistry, Yonsei University, 50 Yonsei-ro Seodaemun-gu, Seoul, 03722, Korea.
| | - Kieron Burke
- grid.266093.80000 0001 0668 7243Department of Chemistry, University of California, Irvine, CA 92697 USA ,grid.266093.80000 0001 0668 7243Departments of Physics & Astronomy, University of California, Irvine, CA 92697 USA
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7
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Nanayakkara S, Tao Y, Kraka E. Capturing Individual Hydrogen Bond Strengths in Ices via Periodic Local Vibrational Mode Theory: Beyond the Lattice Energy Picture. J Chem Theory Comput 2021; 18:562-579. [PMID: 34928619 DOI: 10.1021/acs.jctc.1c00357] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Local stretching force constants derived from periodic local vibrational modes at the vdW-DF2 density functional level have been employed to quantify the intrinsic hydrogen bond strength of 16 ice polymorphs, ices Ih, II, III, IV, V, VI, VII, VIII, IX, XI, XII, XIII, XIV, XV, XVII, and XIX, that are stable under ambient to elevated pressures. Based on this characterization on 1820 hydrogen bonds, relationships between local stretching force constants and structural parameters such as hydrogen bond length and angle were identified. Moreover, different bond strength distributions, from uniform to inhomogeneous, were observed for the 16 ices and could be explained in relation to different local structural elements within ices, that is, rings, that consist of different hydrogen bond types. In addition, criteria for the classification of hydrogen bonds as strong, intermediate, and weak were introduced. The latter was used to explore a different dimension of the water-ice phase diagram. These findings will provide important guidelines for assessing the credibility of new ice structures.
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Affiliation(s)
- Sadisha Nanayakkara
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
| | - Yunwen Tao
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
| | - Elfi Kraka
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
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8
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Binns J, Hermann A, Peña-Alvarez M, Donnelly ME, Wang M, Kawaguchi SI, Gregoryanz E, Howie RT, Dalladay-Simpson P. Superionicity, disorder, and bandgap closure in dense hydrogen chloride. SCIENCE ADVANCES 2021; 7:eabi9507. [PMID: 34516915 PMCID: PMC8442878 DOI: 10.1126/sciadv.abi9507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 07/21/2021] [Indexed: 06/13/2023]
Abstract
Hydrogen bond networks play a crucial role in biomolecules and molecular materials such as ices. How these networks react to pressure directs their properties at extreme conditions. We have studied one of the simplest hydrogen bond formers, hydrogen chloride, from crystallization to metallization, covering a pressure range of more than 2.5 million atmospheres. Following hydrogen bond symmetrization, we identify a previously unknown phase by the appearance of new Raman modes and changes to x-ray diffraction patterns that contradict previous predictions. On further compression, a broad Raman band supersedes the well-defined excitations of phase V, despite retaining a crystalline chlorine substructure. We propose that this mode has its origin in proton (H+) mobility and disorder. Above 100 GPa, the optical bandgap closes linearly with extrapolated metallization at 240(10) GPa. Our findings suggest that proton dynamics can drive changes in these networks even at very high densities.
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Affiliation(s)
- Jack Binns
- Center for High Pressure Science & Technology Advanced Research, 1690 Cailun Rd, Pudong, Shanghai 201203, China
| | - Andreas Hermann
- School of Physics and Centre for Science at Extreme Conditions, University of Edinburgh, Edinburgh EH9 3JZ, UK
| | - Miriam Peña-Alvarez
- School of Physics and Centre for Science at Extreme Conditions, University of Edinburgh, Edinburgh EH9 3JZ, UK
| | - Mary-Ellen Donnelly
- Center for High Pressure Science & Technology Advanced Research, 1690 Cailun Rd, Pudong, Shanghai 201203, China
| | - Mengnan Wang
- Center for High Pressure Science & Technology Advanced Research, 1690 Cailun Rd, Pudong, Shanghai 201203, China
| | | | - Eugene Gregoryanz
- Center for High Pressure Science & Technology Advanced Research, 1690 Cailun Rd, Pudong, Shanghai 201203, China
- School of Physics and Centre for Science at Extreme Conditions, University of Edinburgh, Edinburgh EH9 3JZ, UK
- Key Laboratory of Materials Physics, Institute of Solid State Physics, Chinese Academy of Sciences, Hefei, China
| | - Ross T. Howie
- Center for High Pressure Science & Technology Advanced Research, 1690 Cailun Rd, Pudong, Shanghai 201203, China
| | - Philip Dalladay-Simpson
- Center for High Pressure Science & Technology Advanced Research, 1690 Cailun Rd, Pudong, Shanghai 201203, China
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9
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Chedid J, Jocelyn N, Eshuis H. Energies, structures, and harmonic frequencies of small water clusters from the direct random phase approximation. J Chem Phys 2021; 155:084303. [PMID: 34470345 DOI: 10.1063/5.0059343] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The binding energies, structures, and vibrational frequencies of water clusters up to 20 molecules are computed at the direct random phase approximation (RPA) level of theory and compared to theoretical benchmarks. Binding energies of the WATER27 set, which includes neutral and positively and negatively charged clusters, are predicted to be too low in the complete basis set limit by an average of 7 kcal/mol (9%) and are worse than the results from the best density functional theory methods or from the Møller-Plesset theory. The RPA shows significant basis set size dependence for binding energies. The order of the relative energies of the water hexamer and dodecamer isomers is predicted correctly by the RPA. The mean absolute deviation for angles and distances for neutral clusters up to the water hexamer are 0.2° and 0.6 pm, respectively, using quintuple-ζ basis sets. The relative energetic order of the hexamer isomers is preserved upon optimization. Vibrational frequencies for these systems are underestimated by several tens of wavenumbers for large basis sets, and deviations increase with the basis set size. Overall, the direct RPA method yields accurate structural parameters but systematically underestimates binding energies and shows strong basis set size dependence.
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Affiliation(s)
- Julianna Chedid
- Department of Chemistry and Biochemistry, Montclair State University, Montclair, New Jersey 07043, USA
| | - Nedjie Jocelyn
- Department of Chemistry and Biochemistry, Montclair State University, Montclair, New Jersey 07043, USA
| | - Henk Eshuis
- Department of Chemistry and Biochemistry, Montclair State University, Montclair, New Jersey 07043, USA
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10
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Interactions between large molecules pose a puzzle for reference quantum mechanical methods. Nat Commun 2021; 12:3927. [PMID: 34168142 PMCID: PMC8225865 DOI: 10.1038/s41467-021-24119-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 06/02/2021] [Indexed: 02/05/2023] Open
Abstract
Quantum-mechanical methods are used for understanding molecular interactions throughout the natural sciences. Quantum diffusion Monte Carlo (DMC) and coupled cluster with single, double, and perturbative triple excitations [CCSD(T)] are state-of-the-art trusted wavefunction methods that have been shown to yield accurate interaction energies for small organic molecules. These methods provide valuable reference information for widely-used semi-empirical and machine learning potentials, especially where experimental information is scarce. However, agreement for systems beyond small molecules is a crucial remaining milestone for cementing the benchmark accuracy of these methods. We show that CCSD(T) and DMC interaction energies are not consistent for a set of polarizable supramolecules. Whilst there is agreement for some of the complexes, in a few key systems disagreements of up to 8 kcal mol-1 remain. These findings thus indicate that more caution is required when aiming at reproducible non-covalent interactions between extended molecules.
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11
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Conway LJ, Brown K, Loveday JS, Hermann A. Ammonium fluoride's analogy to ice: Possibilities and limitations. J Chem Phys 2021; 154:204501. [PMID: 34241159 DOI: 10.1063/5.0048516] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Ammonium fluoride, NH4F, is often seen as an analog to ice, with several of its solid phases closely resembling known ice phases. While its ionic and hydrogen-ordered nature puts topological constraints on the ice-like network structures it can form, it is not clear what consequences these constraints have for NH4F compound formation and evolution. Here, we explore computationally the reach and eventual limits of the ice analogy for ammonium fluoride. By combining data mining of known and hypothetical ice networks with crystal structure prediction and density functional calculations, we explore the high-pressure phase diagram of NH4F and host-guest compounds of its hydrides. Pure NH4F departs from ice-like behavior above 80 GPa with the emergence of close-packed ionic structures. The predicted stability of NH4F hydrides shows that NH4F can act as a host to small guest species, albeit in a topologically severely constraint configuration space. Finally, we explore the binary NH3-HF chemical space, where we find candidate structures for several unsolved polyfluoride phases; among them is the chemical analog to H2O2 dihydrate.
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Affiliation(s)
- L J Conway
- SUPA, School of Physics and Astronomy and Centre for Science at Extreme Conditions, The University of Edinburgh, Edinburgh EH9 3FD, United Kingdom
| | - K Brown
- SUPA, School of Physics and Astronomy and Centre for Science at Extreme Conditions, The University of Edinburgh, Edinburgh EH9 3FD, United Kingdom
| | - J S Loveday
- SUPA, School of Physics and Astronomy and Centre for Science at Extreme Conditions, The University of Edinburgh, Edinburgh EH9 3FD, United Kingdom
| | - A Hermann
- SUPA, School of Physics and Astronomy and Centre for Science at Extreme Conditions, The University of Edinburgh, Edinburgh EH9 3FD, United Kingdom
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12
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Jana S, Patra A, Śmiga S, Constantin LA, Samal P. Insights from the density functional performance of water and water–solid interactions: SCAN in relation to other meta-GGAs. J Chem Phys 2020; 153:214116. [DOI: 10.1063/5.0028821] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Subrata Jana
- School of Physical Sciences, National Institute of Science Education and Research, HBNI, Bhubaneswar 752050, India
| | - Abhilash Patra
- School of Physical Sciences, National Institute of Science Education and Research, HBNI, Bhubaneswar 752050, India
| | - Szymon Śmiga
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100 Toruń, Poland
| | - Lucian A. Constantin
- Istituto di Nanoscienze, Consiglio Nazionale delle Ricerche CNR-NANO, 41125 Modena, Italy
| | - Prasanjit Samal
- School of Physical Sciences, National Institute of Science Education and Research, HBNI, Bhubaneswar 752050, India
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13
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Xiao R, Huang L, Han Y, Liu J, Li J. Ab initio phase transition prediction for ices XV/XIV/VIII at high pressures and low temperatures. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.138015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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14
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Liquid water contains the building blocks of diverse ice phases. Nat Commun 2020; 11:5757. [PMID: 33188195 PMCID: PMC7666157 DOI: 10.1038/s41467-020-19606-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 10/23/2020] [Indexed: 11/24/2022] Open
Abstract
Water molecules can arrange into a liquid with complex hydrogen-bond networks and at least 17 experimentally confirmed ice phases with enormous structural diversity. It remains a puzzle how or whether this multitude of arrangements in different phases of water are related. Here we investigate the structural similarities between liquid water and a comprehensive set of 54 ice phases in simulations, by directly comparing their local environments using general atomic descriptors, and also by demonstrating that a machine-learning potential trained on liquid water alone can predict the densities, lattice energies, and vibrational properties of the ices. The finding that the local environments characterising the different ice phases are found in water sheds light on the phase behavior of water, and rationalizes the transferability of water models between different phases. Molecular understanding of water is challenging due to the structural complexity of liquid water and the large number of ice phases. Here the authors use a machine-learning potential trained on liquid water to demonstrate the structural similarity of liquid water and that of 54 real and hypothetical ice phases.
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15
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Akter S, Yamamoto Y, Diaz CM, Jackson KA, Zope RR, Baruah T. Study of self-interaction errors in density functional predictions of dipole polarizabilities and ionization energies of water clusters using Perdew–Zunger and locally scaled self-interaction corrected methods. J Chem Phys 2020; 153:164304. [DOI: 10.1063/5.0025601] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Sharmin Akter
- Computational Science Program, The University of Texas at El Paso, El Paso, Texas 79968, USA
| | - Yoh Yamamoto
- Department of Physics, University of Texas at El Paso, El Paso, Texas 79968, USA
| | - Carlos M. Diaz
- Computational Science Program, The University of Texas at El Paso, El Paso, Texas 79968, USA
| | - Koblar A. Jackson
- Physics Department and Science of Advanced Materials Program, Central Michigan University, Mt. Pleasant, Michigan 48859, USA
| | - Rajendra R. Zope
- Department of Physics, University of Texas at El Paso, El Paso, Texas 79968, USA
| | - Tunna Baruah
- Department of Physics, University of Texas at El Paso, El Paso, Texas 79968, USA
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16
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17
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Guo J, Zhou L, Zen A, Michaelides A, Wu X, Wang E, Xu L, Chen J. Hydration of NH_{4}^{+} in Water: Bifurcated Hydrogen Bonding Structures and Fast Rotational Dynamics. PHYSICAL REVIEW LETTERS 2020; 125:106001. [PMID: 32955332 DOI: 10.1103/physrevlett.125.106001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 08/04/2020] [Indexed: 05/08/2023]
Abstract
Understanding the hydration and diffusion of ions in water at the molecular level is a topic of widespread importance. The ammonium ion (NH_{4}^{+}) is an exemplar system that has received attention for decades because of its complex hydration structure and relevance in industry. Here we report a study of the hydration and the rotational diffusion of NH_{4}^{+} in water using ab initio molecular dynamics simulations and quantum Monte Carlo calculations. We find that the hydration structure of NH_{4}^{+} features bifurcated hydrogen bonds, which leads to a rotational mechanism involving the simultaneous switching of a pair of bifurcated hydrogen bonds. The proposed hydration structure and rotational mechanism are supported by existing experimental measurements, and they also help to rationalize the measured fast rotation of NH_{4}^{+} in water. This study highlights how subtle changes in the electronic structure of hydrogen bonds impacts the hydration structure, which consequently affects the dynamics of ions and molecules in hydrogen bonded systems.
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Affiliation(s)
- Jianqing Guo
- International Center for Quantum Materials, Peking University, Beijing 100871, People's Republic of China
- School of Physics, Peking University, Beijing 100871, People's Republic of China
| | - Liying Zhou
- International Center for Quantum Materials, Peking University, Beijing 100871, People's Republic of China
- School of Physics, Peking University, Beijing 100871, People's Republic of China
| | - Andrea Zen
- Department of Physics and Astronomy, Thomas Young Centre and London Centre for Nanotechnology University College London, Gower Street, London WC1E 6BT, United Kingdom
- Department of Earth Sciences, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Angelos Michaelides
- Department of Physics and Astronomy, Thomas Young Centre and London Centre for Nanotechnology University College London, Gower Street, London WC1E 6BT, United Kingdom
- Max Planck Institute for Solid State Research, Stuttgart 70569, Germany
| | - Xifan Wu
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - Enge Wang
- International Center for Quantum Materials, Peking University, Beijing 100871, People's Republic of China
- School of Physics, Peking University, Beijing 100871, People's Republic of China
- Collaborative Innovation Center of Quantum Matter, Beijing 100871, People's Republic of China
- Songshan Lake Materials Lab, Institute of Physics, Chinese Academy of Sciences, Guangdong 523808, People's Republic of China
- School of Physics, Liaoning University, Shenyang 110136, People's Republic of China
| | - Limei Xu
- International Center for Quantum Materials, Peking University, Beijing 100871, People's Republic of China
- School of Physics, Peking University, Beijing 100871, People's Republic of China
- Collaborative Innovation Center of Quantum Matter, Beijing 100871, People's Republic of China
| | - Ji Chen
- School of Physics, Peking University, Beijing 100871, People's Republic of China
- Max Planck Institute for Solid State Research, Stuttgart 70569, Germany
- Collaborative Innovation Center of Quantum Matter, Beijing 100871, People's Republic of China
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18
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Pruteanu CG, Naden Robinson V, Ansari N, Hassanali A, Scandolo S, Loveday JS. Squeezing Oil into Water under Pressure: Inverting the Hydrophobic Effect. J Phys Chem Lett 2020; 11:4826-4833. [PMID: 32496780 PMCID: PMC7467747 DOI: 10.1021/acs.jpclett.0c01410] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 06/04/2020] [Indexed: 06/11/2023]
Abstract
The molecular structure of dense homogeneous fluid water-methane mixtures has been determined for the first time using high-pressure neutron-scattering techniques at 1.7 and 2.2 GPa. A mixed state with a fully H-bonded water network is revealed. The hydration shell of the methane molecules is, however, revealed to be pressure-dependent with an increase in the water coordination between 1.7 and 2.2 GPa. In parallel, ab initio molecular dynamics simulations have been performed to provide insight into the microscopic mechanisms associated with the phenomenon of mixing. These calculations reproduce the observed phase change from phase separation to mixing with increasing pressure. The calculations also reproduce the experimentally observed structural properties. Unexpectedly, the simulations show mixing is accompanied by a subtle enhancement of the polarization of methane. Our results highlight the key role played by fine electronic effects on miscibility and the need to readjust our fundamental understanding of hydrophobicity to account for these.
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Affiliation(s)
- Ciprian G. Pruteanu
- Department
of Physics and Astronomy, University College
London, Gower Street, London WC1E
6BT, United Kingdom
| | - Victor Naden Robinson
- The
“Abdus Salam” International Centre for Theoretical Physics, I-34151 Trieste, Italy
| | - Narjes Ansari
- The
“Abdus Salam” International Centre for Theoretical Physics, I-34151 Trieste, Italy
| | - Ali Hassanali
- The
“Abdus Salam” International Centre for Theoretical Physics, I-34151 Trieste, Italy
| | - Sandro Scandolo
- The
“Abdus Salam” International Centre for Theoretical Physics, I-34151 Trieste, Italy
| | - John S. Loveday
- SUPA,
School of Physics and Astronomy and Centre for Science at Extreme
Conditions, The University of Edinburgh, Edinburgh EH9 3JZ, United Kingdom
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19
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Self-interaction error overbinds water clusters but cancels in structural energy differences. Proc Natl Acad Sci U S A 2020; 117:11283-11288. [PMID: 32393631 DOI: 10.1073/pnas.1921258117] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
We gauge the importance of self-interaction errors in density functional approximations (DFAs) for the case of water clusters. To this end, we used the Fermi-Löwdin orbital self-interaction correction method (FLOSIC) to calculate the binding energy of clusters of up to eight water molecules. Three representative DFAs of the local, generalized gradient, and metageneralized gradient families [i.e., local density approximation (LDA), Perdew-Burke-Ernzerhof (PBE), and strongly constrained and appropriately normed (SCAN)] were used. We find that the overbinding of the water clusters in these approximations is not a density-driven error. We show that, while removing self-interaction error does not alter the energetic ordering of the different water isomers with respect to the uncorrected DFAs, the resulting binding energies are corrected toward accurate reference values from higher-level calculations. In particular, self-interaction-corrected SCAN not only retains the correct energetic ordering for water hexamers but also reduces the mean error in the hexamer binding energies to less than 14 meV/[Formula: see text] from about 42 meV/[Formula: see text] for SCAN. By decomposing the total binding energy into many-body components, we find that large errors in the two-body interaction in SCAN are significantly reduced by self-interaction corrections. Higher-order many-body errors are small in both SCAN and self-interaction-corrected SCAN. These results indicate that orbital-by-orbital removal of self-interaction combined with a proper DFA can lead to improved descriptions of water complexes.
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20
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Mei S, Guo Y, Lin X, Dong H, Sun LD, Li K, Yan CH. Experimental and Simulation Insights into Local Structure and Luminescence Evolution in Eu 3+-Doped Nanocrystals under High Pressure. J Phys Chem Lett 2020; 11:3515-3520. [PMID: 32293899 DOI: 10.1021/acs.jpclett.0c00895] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Tremendous effort has been devoted to tailoring structure-correlated properties, especially for the luminescence of lanthanide nanocrystals (NCs). High pressure has been demonstrated as a decent way to tune the performance of lanthanide NCs; however, little attention has been paid to the local structure evolution accompanied by extreme compression and its effect on luminescence. Here, we tailor the local structure around lanthanide ions with pressure in β-NaGdF4 NCs, in which Eu3+ ions were doped as optical probes for local structure for the sensitive electric dipole transition. As the pressure increases, the intensity ratio of the 5D0 → 7F2 to 5D0 → 7F1 transition decreases monotonically from 2.04 to 0.81, implying a higher local symmetry around Eu3+ ions from compression. In situ X-ray diffraction demonstrates that the sample maintains the hexagonal structure up to 33.5 GPa, and density functional theory calculations reveal the tendency of the local structure to vary under high pressure.
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Affiliation(s)
- Sheng Mei
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Rare Earth Materials Chemistry and Applications, PKU-HKU Joint Laboratory in Rare Earth Materials and Bioinorganic Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yu Guo
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Rare Earth Materials Chemistry and Applications, PKU-HKU Joint Laboratory in Rare Earth Materials and Bioinorganic Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xiaohuan Lin
- Center for High Pressure Science and Technology Advanced Research, Beijing 100094, China
| | - Hao Dong
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Rare Earth Materials Chemistry and Applications, PKU-HKU Joint Laboratory in Rare Earth Materials and Bioinorganic Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Ling-Dong Sun
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Rare Earth Materials Chemistry and Applications, PKU-HKU Joint Laboratory in Rare Earth Materials and Bioinorganic Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Kuo Li
- Center for High Pressure Science and Technology Advanced Research, Beijing 100094, China
| | - Chun-Hua Yan
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Rare Earth Materials Chemistry and Applications, PKU-HKU Joint Laboratory in Rare Earth Materials and Bioinorganic Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
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21
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Santos Rego J, de Koning M. Density-functional theory prediction of the elastic constants of ice Ih. J Chem Phys 2020; 152:084502. [DOI: 10.1063/1.5142710] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Jéssica Santos Rego
- Instituto de Física Gleb Wataghin, Universidade Estadual de Campinas, UNICAMP, Campinas, 13083-859, São Paulo, Brazil
| | - Maurice de Koning
- Instituto de Física Gleb Wataghin, Universidade Estadual de Campinas, UNICAMP, Campinas, 13083-859, São Paulo, Brazil
- Center for Computing in Engineering and Sciences, Universidade Estadual de Campinas, UNICAMP, Campinas, 13083-861 São Paulo, Brazil
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22
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Xu J, Liu J, Liu J, Hu W, He X, Li J. Phase Transition of Ice at High Pressures and Low Temperatures. Molecules 2020; 25:molecules25030486. [PMID: 31979295 PMCID: PMC7037513 DOI: 10.3390/molecules25030486] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 01/08/2020] [Accepted: 01/21/2020] [Indexed: 11/21/2022] Open
Abstract
The behavior of ice under extreme conditions undergoes the change of intermolecular binding patterns and leads to the structural phase transitions, which are needed for modeling the convection and internal structure of the giant planets and moons of the solar system as well as H2O-rich exoplanets. Such extreme conditions limit the structural explorations in laboratory but open a door for the theoretical study. The ice phases IX and XIII are located in the high pressure and low temperature region of the phase diagram. However, to the best of our knowledge, the phase transition boundary between these two phases is still not clear. In this work, based on the second-order Møller–Plesset perturbation (MP2) theory, we theoretically investigate the ice phases IX and XIII and predict their structures, vibrational spectra and Gibbs free energies at various extreme conditions, and for the first time confirm that the phase transition from ice IX to XIII can occur around 0.30 GPa and 154 K. The proposed work, taking into account the many-body electrostatic effect and the dispersion interactions from the first principles, opens up the possibility of completing the ice phase diagram and provides an efficient method to explore new phases of molecular crystals.
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Affiliation(s)
- Jinjin Xu
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China;
- National Key Laboratory of Science and Technology on Micro/Nano Fabrication, Key laboratory for Thin Film and Microfabrication of the Ministry of Education, Department of Micro/Nano-electronics, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jinfeng Liu
- State Key Laboratory of Natural Medicines, Department of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China;
| | - Jinyun Liu
- Key Laboratory of Functional Molecular Solids of the Ministry of Education, Anhui Laboratory of Molecule-Based Materials, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, China
- Correspondence: (J.L.); (X.H.); (J.L.)
| | - Wenxin Hu
- The Computer Center, School of Computer Science and Software Engineering, East China Normal University, Shanghai 200062, China;
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China;
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
- Correspondence: (J.L.); (X.H.); (J.L.)
| | - Jinjin Li
- National Key Laboratory of Science and Technology on Micro/Nano Fabrication, Key laboratory for Thin Film and Microfabrication of the Ministry of Education, Department of Micro/Nano-electronics, Shanghai Jiao Tong University, Shanghai 200240, China
- Key Laboratory of Functional Molecular Solids of the Ministry of Education, Anhui Laboratory of Molecule-Based Materials, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, China
- Correspondence: (J.L.); (X.H.); (J.L.)
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23
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Jana S, Constantin LA, Samal P. Accurate Water Properties from an Efficient ab Initio Method. J Chem Theory Comput 2020; 16:974-987. [DOI: 10.1021/acs.jctc.9b01018] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Subrata Jana
- School of Physical Sciences, National Institute of Science Education and Research, HBNI, Bhubaneswar 752050, India
| | - Lucian A. Constantin
- Center for Biomolecular Nanotechnologies @UNILE, Istituto Italiano di Tecnologia, Via Barsanti, I-73010 Arnesano, Italy
| | - Prasanjit Samal
- School of Physical Sciences, National Institute of Science Education and Research, HBNI, Bhubaneswar 752050, India
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24
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Sakti AW, Nishimura Y, Nakai H. Recent advances in quantum‐mechanical molecular dynamics simulations of proton transfer mechanism in various water‐based environments. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2020. [DOI: 10.1002/wcms.1419] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Aditya W. Sakti
- Element Strategy Initiative for Catalysts and Batteries (ESICB) Kyoto University Kyoto Japan
| | - Yoshifumi Nishimura
- Waseda Research Institute for Science and Engineering (WISE) Waseda University Tokyo Japan
| | - Hiromi Nakai
- Element Strategy Initiative for Catalysts and Batteries (ESICB) Kyoto University Kyoto Japan
- Waseda Research Institute for Science and Engineering (WISE) Waseda University Tokyo Japan
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering Waseda University Tokyo Japan
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25
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Yong X, Burnham CJ, English NJ, Tse JS. Classical and path-integral molecular-dynamics study on liquid water and ice melting using non-empirical TTM2.1-F model. Mol Phys 2019. [DOI: 10.1080/00268976.2019.1652774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Xue Yong
- Department of Physics and Engineering Physics, University of Saskatchewan, Saskatoon, Canada
| | - Christian J. Burnham
- School of Chemical and Bioprocess Engineering, University College Dublin, Dublin, Ireland
| | - Niall J. English
- School of Chemical and Bioprocess Engineering, University College Dublin, Dublin, Ireland
| | - John S. Tse
- Department of Physics and Engineering Physics, University of Saskatchewan, Saskatoon, Canada
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26
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Rasti S, Meyer J. Importance of zero-point energy for crystalline ice phases: A comparison of force fields and density functional theory. J Chem Phys 2019; 150:234504. [DOI: 10.1063/1.5097021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Soroush Rasti
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Jörg Meyer
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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27
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Song X, Yin K, Wang Y, Hermann A, Liu H, Lv J, Li Q, Chen C, Ma Y. Exotic Hydrogen Bonding in Compressed Ammonia Hydrides. J Phys Chem Lett 2019; 10:2761-2766. [PMID: 31067056 DOI: 10.1021/acs.jpclett.9b00973] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Hydrogen-rich compounds attract significant fundamental and practical interest for their ability to accommodate diverse hydrogen bonding patterns and their promise as superior energy storage materials. Here, we report on an intriguing discovery of exotic hydrogen bonding in compressed ammonia hydrides and identify two novel ionic phases in an unusual stoichiometry NH7. The first is a hexagonal R3̅ m phase containing NH3-H+-NH3, H-, and H2 structural units stabilized above 25 GPa. The exotic NH3-H+-NH3 unit comprises two NH3 molecules bound to a proton donated from a H2 molecule. Above 60 GPa, the structure transforms to a tetragonal P41212 phase comprising NH4+, H-, and H2 units. At elevated temperatures, fascinating superionic phases of NH7 with part-solid and part-liquid structural forms are identified. The present findings advance fundamental knowledge about ammonia hydrides at high pressure with broad implications for studying planetary interiors and superior hydrogen storage materials.
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Affiliation(s)
- Xianqi Song
- State Key Laboratory of Superhard Materials, Key Laboratory of Automobile Materials of MOE, Department of Materials Science, and Innovation Center for Computational Physics Methods and Software , Jilin University , Changchun 130012 , China
| | - Ketao Yin
- State Key Laboratory of Superhard Materials, Key Laboratory of Automobile Materials of MOE, Department of Materials Science, and Innovation Center for Computational Physics Methods and Software , Jilin University , Changchun 130012 , China
| | - Yanchao Wang
- State Key Laboratory of Superhard Materials, Key Laboratory of Automobile Materials of MOE, Department of Materials Science, and Innovation Center for Computational Physics Methods and Software , Jilin University , Changchun 130012 , China
| | - Andreas Hermann
- Centre for Science at Extreme Conditions and SUPA, School of Physics and Astronomy , The University of Edinburgh , Edinburgh EH9 3FD , United Kingdom
| | - Hanyu Liu
- State Key Laboratory of Superhard Materials, Key Laboratory of Automobile Materials of MOE, Department of Materials Science, and Innovation Center for Computational Physics Methods and Software , Jilin University , Changchun 130012 , China
| | - Jian Lv
- State Key Laboratory of Superhard Materials, Key Laboratory of Automobile Materials of MOE, Department of Materials Science, and Innovation Center for Computational Physics Methods and Software , Jilin University , Changchun 130012 , China
| | - Quan Li
- State Key Laboratory of Superhard Materials, Key Laboratory of Automobile Materials of MOE, Department of Materials Science, and Innovation Center for Computational Physics Methods and Software , Jilin University , Changchun 130012 , China
- International Center of Future Science , Jilin University , Changchun 130012 , China
| | - Changfeng Chen
- Department of Physics and Astronomy , University of Nevada , Las Vegas , Nevada 89154 , United States
| | - Yanming Ma
- State Key Laboratory of Superhard Materials, Key Laboratory of Automobile Materials of MOE, Department of Materials Science, and Innovation Center for Computational Physics Methods and Software , Jilin University , Changchun 130012 , China
- International Center of Future Science , Jilin University , Changchun 130012 , China
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28
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Affiliation(s)
- Jian-wei Cao
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Feng-yi Li
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wen-sha Xia
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wen-sheng Bian
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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29
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Zurek E, Bi T. High-temperature superconductivity in alkaline and rare earth polyhydrides at high pressure: A theoretical perspective. J Chem Phys 2019; 150:050901. [DOI: 10.1063/1.5079225] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Eva Zurek
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260-3000, USA
| | - Tiange Bi
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260-3000, USA
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30
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Košata J, Merkl P, Teeratchanan P, Hermann A. Stability of Hydrogen Hydrates from Second-Order Møller-Plesset Perturbation Theory. J Phys Chem Lett 2018; 9:5624-5629. [PMID: 30179509 DOI: 10.1021/acs.jpclett.8b02274] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The formation of gas hydrates and clathrates critically depends on the interaction between the host water network and the guest gas species. Density functional calculations can struggle to quantitatively capture these dispersion-type interactions. Here, we report wave function-based calculations on hydrogen hydrates that combine periodic Hartree-Fock with a localized treatment of electronic correlation. We show that local second-order Møller-Plesset perturbation theory (LMP2) reproduces the stability of the different filled-ice-like hydrates in excellent agreement with experimental data. In contrast to various dispersion-corrected density functional theory implementations, LMP2 correctly identifies the pressures needed to stabilize the C0, C1, and C2 hydrates and does not find a spurious region of stability for an ice-Ih-based dihydrate. Our results suggest that LMP2 or similar approaches can provide quantitative insights into the mechanisms of formation and eventual decomposition of molecular host-guest compounds.
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Affiliation(s)
- Jan Košata
- Centre for Science at Extreme Conditions and SUPA, School of Physics and Astronomy , The University of Edinburgh , Edinburgh EH9 3FD , United Kingdom
| | - Padryk Merkl
- Centre for Science at Extreme Conditions and SUPA, School of Physics and Astronomy , The University of Edinburgh , Edinburgh EH9 3FD , United Kingdom
| | - Pattanasak Teeratchanan
- Centre for Science at Extreme Conditions and SUPA, School of Physics and Astronomy , The University of Edinburgh , Edinburgh EH9 3FD , United Kingdom
| | - Andreas Hermann
- Centre for Science at Extreme Conditions and SUPA, School of Physics and Astronomy , The University of Edinburgh , Edinburgh EH9 3FD , United Kingdom
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31
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Lao KU, Herbert JM. A Simple Correction for Nonadditive Dispersion within Extended Symmetry-Adapted Perturbation Theory (XSAPT). J Chem Theory Comput 2018; 14:5128-5142. [DOI: 10.1021/acs.jctc.8b00527] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ka Un Lao
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - John M. Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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32
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Kuhs WF, Hansen TC, Falenty A. Filling Ices with Helium and the Formation of Helium Clathrate Hydrate. J Phys Chem Lett 2018; 9:3194-3198. [PMID: 29809013 DOI: 10.1021/acs.jpclett.8b01423] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We have formed the long-sought He-clathrate. This was achieved by refilling helium into ice XVI, opening a new synthesis route for exotic forms of clathrate hydrates. The process was followed by neutron diffraction; structures and cage fillings were established. The stabilizing attractive van der Waals interactions are enhanced by multiple cage fillings with theoretically up to four helium atoms per large cage and up to one per small cage; He-clathrate hydrates can be considered as a solid-state equivalent of the clustering of small apolar entities dissolved in the liquid state of water. Unlike most other guests, helium easily enters and leaves the water cages at temperatures well below 100 K, hampering applications as a gas storage material. Despite the weak dispersive interactions, the inclusion of helium has a very significant effect on lattice constants; this is also established for helium inclusion in ice Ih and suggests that lattice parameters are arguably the most sensitive measure to gauge dispersive water-gas interactions.
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Affiliation(s)
- Werner F Kuhs
- GZG Abt. Kristallographie , Universität Göttingen , Goldschmidtstr. 1 , 37077 Göttingen , Germany
| | - Thomas C Hansen
- Institut Laue-Langevin (ILL) , 71 avenue des Martyrs , 38000 Grenoble , France
| | - Andrzej Falenty
- GZG Abt. Kristallographie , Universität Göttingen , Goldschmidtstr. 1 , 37077 Göttingen , Germany
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33
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Gonzalez JM, Nguyen-Cong K, Steele BA, Oleynik II. Novel phases and superconductivity of tin sulfide compounds. J Chem Phys 2018; 148:194701. [DOI: 10.1063/1.5018434] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Joseph M. Gonzalez
- Department of Physics, University of South Florida, Tampa, Florida 33620, USA
| | - Kien Nguyen-Cong
- Department of Physics, University of South Florida, Tampa, Florida 33620, USA
| | - Brad A. Steele
- Department of Physics, University of South Florida, Tampa, Florida 33620, USA
| | - Ivan I. Oleynik
- Department of Physics, University of South Florida, Tampa, Florida 33620, USA
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34
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Zheng L, Chen M, Sun Z, Ko HY, Santra B, Dhuvad P, Wu X. Structural, electronic, and dynamical properties of liquid water by ab initio molecular dynamics based on SCAN functional within the canonical ensemble. J Chem Phys 2018; 148:164505. [DOI: 10.1063/1.5023611] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Lixin Zheng
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - Mohan Chen
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - Zhaoru Sun
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - Hsin-Yu Ko
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - Biswajit Santra
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - Pratikkumar Dhuvad
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - Xifan Wu
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, USA
- Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, USA
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35
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Abstract
Computational approaches based on the fundamental laws of quantum mechanics are now integral to almost all materials design initiatives in academia and industry. If computational materials science is genuinely going to deliver on its promises, then an electronic structure method with consistently high accuracy is urgently needed. We show that, thanks to recent algorithmic advances and the strategy developed in our manuscript, quantum Monte Carlo yields extremely accurate predictions for the lattice energies of materials at a surprisingly modest computational cost. It is thus no longer a technique that requires a world-leading computational facility to obtain meaningful results. While we focus on molecular crystals, the significance of our findings extends to all classes of materials. Computer simulation plays a central role in modern-day materials science. The utility of a given computational approach depends largely on the balance it provides between accuracy and computational cost. Molecular crystals are a class of materials of great technological importance which are challenging for even the most sophisticated ab initio electronic structure theories to accurately describe. This is partly because they are held together by a balance of weak intermolecular forces but also because the primitive cells of molecular crystals are often substantially larger than those of atomic solids. Here, we demonstrate that diffusion quantum Monte Carlo (DMC) delivers subchemical accuracy for a diverse set of molecular crystals at a surprisingly moderate computational cost. As such, we anticipate that DMC can play an important role in understanding and predicting the properties of a large number of molecular crystals, including those built from relatively large molecules which are far beyond reach of other high-accuracy methods.
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36
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Usvyat D, Maschio L, Schütz M. Periodic and fragment models based on the local correlation approach. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2018. [DOI: 10.1002/wcms.1357] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Denis Usvyat
- Institut für ChemieHumboldt‐Universität zu BerlinBerlinGermany
| | - Lorenzo Maschio
- Dipartimento di Chimica and NIS (Nanostructured Interfaces and Surfaces) CentreUniversità di TorinoTorinoItaly
| | - Martin Schütz
- Institut für ChemieHumboldt‐Universität zu BerlinBerlinGermany
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37
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High pressure, a protocol to identify the weak dihydrogen bonds: experimental evidence of C–H···H–B interaction. Sci China Chem 2017. [DOI: 10.1007/s11426-017-9152-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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38
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Lin C, Yong X, Tse JS, Smith JS, Sinogeikin SV, Kenney-Benson C, Shen G. Kinetically Controlled Two-Step Amorphization and Amorphous-Amorphous Transition in Ice. PHYSICAL REVIEW LETTERS 2017; 119:135701. [PMID: 29341714 DOI: 10.1103/physrevlett.119.135701] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Indexed: 05/09/2023]
Abstract
We report the results of in situ structural characterization of the amorphization of crystalline ice Ih under compression and the relaxation of high-density amorphous (HDA) ice under decompression at temperatures between 96 and 160 K by synchrotron x-ray diffraction. The results show that ice Ih transforms to an intermediate crystalline phase at 100 K prior to complete amorphization, which is supported by molecular dynamics calculations. The phase transition pathways show clear temperature dependence: direct amorphization without an intermediate phase is observed at 133 K, while at 145 K a direct Ih-to-IX transformation is observed; decompression of HDA shows a transition to low-density amorphous ice at 96 K and ∼1 Pa, to ice Ic at 135 K and to ice IX at 145 K. These observations show that the amorphization of compressed ice Ih and the recrystallization of decompressed HDA are strongly dependent on temperature and controlled by kinetic barriers. Pressure-induced amorphous ice is an intermediate state in the phase transition from the connected H-bond water network in low pressure ices to the independent and interpenetrating H-bond network of high-pressure ices.
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Affiliation(s)
- Chuanlong Lin
- HPCAT, Geophysical Laboratory, Carnegie Institution of Washington, Argonne, Illinois 60439, USA
| | - Xue Yong
- Department of Physics and Engineering Physics, University of Saskatchewan, Saskatoon, S7N 5E2 Canada
| | - John S Tse
- Department of Physics and Engineering Physics, University of Saskatchewan, Saskatoon, S7N 5E2 Canada
| | - Jesse S Smith
- HPCAT, Geophysical Laboratory, Carnegie Institution of Washington, Argonne, Illinois 60439, USA
| | - Stanislav V Sinogeikin
- HPCAT, Geophysical Laboratory, Carnegie Institution of Washington, Argonne, Illinois 60439, USA
| | - Curtis Kenney-Benson
- HPCAT, Geophysical Laboratory, Carnegie Institution of Washington, Argonne, Illinois 60439, USA
| | - Guoyin Shen
- HPCAT, Geophysical Laboratory, Carnegie Institution of Washington, Argonne, Illinois 60439, USA
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39
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Al-Hamdani YS, Rossi M, Alfè D, Tsatsoulis T, Ramberger B, Brandenburg JG, Zen A, Kresse G, Grüneis A, Tkatchenko A, Michaelides A. Properties of the water to boron nitride interaction: From zero to two dimensions with benchmark accuracy. J Chem Phys 2017; 147:044710. [DOI: 10.1063/1.4985878] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Yasmine S. Al-Hamdani
- Thomas Young Centre and London Centre for Nanotechnology, 17–19 Gordon Street, London WC1H 0AH, United Kingdom
- Physics and Materials Science Research Unit, University of Luxembourg, L-1511 Luxembourg, Luxembourg
| | - Mariana Rossi
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany
| | - Dario Alfè
- Thomas Young Centre and London Centre for Nanotechnology, 17–19 Gordon Street, London WC1H 0AH, United Kingdom
- Department of Earth Sciences, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Theodoros Tsatsoulis
- Max Planck Institute for Solid State Research, Heisenbergstraße 1, D-70569 Stuttgart, Germany
| | - Benjamin Ramberger
- University of Vienna, Faculty of Physics and Center for Computational Materials Sciences, Sensengasse 8/12, 1090 Wien, Austria
| | - Jan Gerit Brandenburg
- Thomas Young Centre and London Centre for Nanotechnology, 17–19 Gordon Street, London WC1H 0AH, United Kingdom
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AH, United Kingdom
| | - Andrea Zen
- Thomas Young Centre and London Centre for Nanotechnology, 17–19 Gordon Street, London WC1H 0AH, United Kingdom
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Georg Kresse
- University of Vienna, Faculty of Physics and Center for Computational Materials Sciences, Sensengasse 8/12, 1090 Wien, Austria
| | - Andreas Grüneis
- Max Planck Institute for Solid State Research, Heisenbergstraße 1, D-70569 Stuttgart, Germany
| | - Alexandre Tkatchenko
- Physics and Materials Science Research Unit, University of Luxembourg, L-1511 Luxembourg, Luxembourg
| | - Angelos Michaelides
- Thomas Young Centre and London Centre for Nanotechnology, 17–19 Gordon Street, London WC1H 0AH, United Kingdom
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
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40
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Dubecký M. Noncovalent Interactions by Fixed-Node Diffusion Monte Carlo: Convergence of Nodes and Energy Differences vs Gaussian Basis-Set Size. J Chem Theory Comput 2017; 13:3626-3635. [DOI: 10.1021/acs.jctc.7b00537] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Matúš Dubecký
- Department of Physics, Faculty of Science, University of Ostrava, 30. dubna 22, 701
03 Ostrava, Czech Republic
- ATRI, Faculty of Materials
Science and Technology, Slovak University of Technology, Paulínska
16, 917 24 Trnava, Slovakia
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41
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Yang X, Rees RJ, Conway W, Puxty G, Yang Q, Winkler DA. Computational Modeling and Simulation of CO2 Capture by Aqueous Amines. Chem Rev 2017; 117:9524-9593. [PMID: 28517929 DOI: 10.1021/acs.chemrev.6b00662] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Xin Yang
- CSIRO Manufacturing, Bayview Avenue, Clayton 3169, Australia
- College
of Chemistry, Key Lab of Green Chemistry and Technology in Ministry
of Education, Sichuan University, Chengdu 610064, People’s Republic of China
| | - Robert J. Rees
- Data61
- CSIRO, Door 34 Goods
Shed, Village Street, Docklands VIC 3008, Australia
| | | | | | - Qi Yang
- CSIRO Manufacturing, Bayview Avenue, Clayton 3169, Australia
| | - David A. Winkler
- CSIRO Manufacturing, Bayview Avenue, Clayton 3169, Australia
- Monash Institute of Pharmaceutical Sciences, 392 Royal Parade, Parkville 3052, Australia
- Latrobe Institute for Molecular Science, Bundoora 3046, Australia
- School
of
Chemical and Physical Science, Flinders University, Bedford Park 5042, Australia
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42
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Mo Y, Tian G, Car R, Staroverov VN, Scuseria GE, Tao J. Performance of a nonempirical density functional on molecules and hydrogen-bonded complexes. J Chem Phys 2017; 145:234306. [PMID: 28010100 DOI: 10.1063/1.4971853] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Recently, Tao and Mo derived a meta-generalized gradient approximation functional based on a model exchange-correlation hole. In this work, the performance of this functional is assessed on standard test sets, using the 6-311++G(3df,3pd) basis set. These test sets include 223 G3/99 enthalpies of formation, 99 atomization energies, 76 barrier heights, 58 electron affinities, 8 proton affinities, 96 bond lengths, 82 harmonic vibrational frequencies, 10 hydrogen-bonded molecular complexes, and 22 atomic excitation energies. Our calculations show that the Tao-Mo functional can achieve high accuracy for most properties considered, relative to the local spin-density approximation, Perdew-Burke-Ernzerhof, and Tao-Perdew-Staroverov-Scuseria functionals. In particular, it yields the best accuracy for proton affinities, harmonic vibrational frequencies, hydrogen-bond dissociation energies and bond lengths, and atomic excitation energies.
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Affiliation(s)
- Yuxiang Mo
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - Guocai Tian
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - Roberto Car
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - Viktor N Staroverov
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | | | - Jianmin Tao
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, USA
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43
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Pham CH, Reddy SK, Chen K, Knight C, Paesani F. Many-Body Interactions in Ice. J Chem Theory Comput 2017; 13:1778-1784. [DOI: 10.1021/acs.jctc.6b01248] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- C. Huy Pham
- Department
of Chemistry and Biochemistry, University of California−San Diego, La Jolla, California 92093, United States
| | - Sandeep K. Reddy
- Department
of Chemistry and Biochemistry, University of California−San Diego, La Jolla, California 92093, United States
| | - Karl Chen
- Department
of Chemistry and Biochemistry, University of California−San Diego, La Jolla, California 92093, United States
| | - Chris Knight
- Leadership
Computing Facility, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, United States
| | - Francesco Paesani
- Department
of Chemistry and Biochemistry, University of California−San Diego, La Jolla, California 92093, United States
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44
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Mo Y, Tian G, Tao J. Performance of a nonempirical exchange functional from density matrix expansion: comparative study with different correlations. Phys Chem Chem Phys 2017; 19:21707-21713. [DOI: 10.1039/c6cp08761b] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Recently, Tao and Mo proposed a meta-generalized gradient approximation for the exchange–correlation energy with remarkable accuracy for molecules, solids, and surfaces.
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Affiliation(s)
- Yuxiang Mo
- Department of Physics
- Temple University
- Philadelphia
- USA
| | - Guocai Tian
- Department of Physics
- Temple University
- Philadelphia
- USA
- State Key Laboratory of Complex Nonferrous Metal Resources Clean Utilization
| | - Jianmin Tao
- Department of Physics
- Temple University
- Philadelphia
- USA
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45
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Azadi S, Ackland GJ. The role of van der Waals and exchange interactions in high-pressure solid hydrogen. Phys Chem Chem Phys 2017; 19:21829-21839. [DOI: 10.1039/c7cp03729e] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Our study of the van der Waals interactions in solid molecular hydrogen structures indicates two candidates for phase III.
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Affiliation(s)
- Sam Azadi
- Royal School of Mines and the Thomas Young Centre
- Imperial College London
- SW7 2AZ London
- UK
- School of Physics and Centre for Science at Extreme Conditions
| | - Graeme J. Ackland
- School of Physics and Centre for Science at Extreme Conditions
- University of Edinburgh
- Edinburgh EH9 3JZ
- UK
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46
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Hansen MH, Nilsson A, Rossmeisl J. Modelling pH and potential in dynamic structures of the water/Pt(111) interface on the atomic scale. Phys Chem Chem Phys 2017; 19:23505-23514. [DOI: 10.1039/c7cp03576d] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Modelling liquid structures averages of water in the interface with Pt(111) as grand canonical averages, that are functions of pH and electrode potential, using work functions as the absolute potential scale.
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Affiliation(s)
- Martin Hangaard Hansen
- Nano Science Center
- Department of Chemistry
- University of Copenhagen
- 2100 Copenhagen
- Denmark
| | - Anders Nilsson
- Department of Physics
- AlbaNova University Center
- Stockholm University
- S-10691 Stockholm
- Sweden
| | - Jan Rossmeisl
- Nano Science Center
- Department of Chemistry
- University of Copenhagen
- 2100 Copenhagen
- Denmark
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47
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Novko D, Tremblay JC, Blanco-Rey M. On the tautomerisation of porphycene on copper (111): Finding the subtle balance between van der Waals interactions and hybridisation. J Chem Phys 2016; 145:244701. [DOI: 10.1063/1.4972213] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Dino Novko
- Donostia International Physics Center (DIPC), Paseo Manuel de Lardizabal 4, 20018 Donostia-San Sebastián, Spain
| | - Jean Christophe Tremblay
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 3, D-14195 Berlin, Germany
| | - María Blanco-Rey
- Donostia International Physics Center (DIPC), Paseo Manuel de Lardizabal 4, 20018 Donostia-San Sebastián, Spain
- Departamento de Física de Materiales, Facultad de Químicas UPV/EHU, Apartado 1072, 20018 Donostia-San Sebastián, Spain
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48
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Powell AD, Dawes R. Calculating potential energy curves with fixed-node diffusion Monte Carlo: CO and N2. J Chem Phys 2016; 145:224308. [DOI: 10.1063/1.4971378] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Andrew D. Powell
- Department of Chemistry, Missouri University of Science and Technology, Rolla, Missouri 65409, USA
| | - Richard Dawes
- Department of Chemistry, Missouri University of Science and Technology, Rolla, Missouri 65409, USA
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49
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50
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Zen A, Roch LM, Cox SJ, Hu XL, Sorella S, Alfè D, Michaelides A. Toward Accurate Adsorption Energetics on Clay Surfaces. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2016; 120:26402-26413. [PMID: 27917256 PMCID: PMC5126707 DOI: 10.1021/acs.jpcc.6b09559] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 10/31/2016] [Indexed: 05/31/2023]
Abstract
Clay minerals are ubiquitous in nature, and the manner in which they interact with their surroundings has important industrial and environmental implications. Consequently, a molecular-level understanding of the adsorption of molecules on clay surfaces is crucial. In this regard computer simulations play an important role, yet the accuracy of widely used empirical force fields (FF) and density functional theory (DFT) exchange-correlation functionals is often unclear in adsorption systems dominated by weak interactions. Herein we present results from quantum Monte Carlo (QMC) for water and methanol adsorption on the prototypical clay kaolinite. To the best of our knowledge, this is the first time QMC has been used to investigate adsorption at a complex, natural surface such as a clay. As well as being valuable in their own right, the QMC benchmarks obtained provide reference data against which the performance of cheaper DFT methods can be tested. Indeed using various DFT exchange-correlation functionals yields a very broad range of adsorption energies, and it is unclear a priori which evaluation is better. QMC reveals that in the systems considered here it is essential to account for van der Waals (vdW) dispersion forces since this alters both the absolute and relative adsorption energies of water and methanol. We show, via FF simulations, that incorrect relative energies can lead to significant changes in the interfacial densities of water and methanol solutions at the kaolinite interface. Despite the clear improvements offered by the vdW-corrected and the vdW-inclusive functionals, absolute adsorption energies are often overestimated, suggesting that the treatment of vdW forces in DFT is not yet a solved problem.
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Affiliation(s)
- Andrea Zen
- Thomas
Young Centre and London Centre for Nanotechnology, 17−19 Gordon Street, London WC1H 0AH, United
Kingdom
- Department
of Physics and Astronomy, University College
London, Gower Street, London WC1E 6BT, United Kingdom
| | - Loïc M. Roch
- Thomas
Young Centre and London Centre for Nanotechnology, 17−19 Gordon Street, London WC1H 0AH, United
Kingdom
- Department
of Physics and Astronomy, University College
London, Gower Street, London WC1E 6BT, United Kingdom
| | - Stephen J. Cox
- Thomas
Young Centre and London Centre for Nanotechnology, 17−19 Gordon Street, London WC1H 0AH, United
Kingdom
- Department
of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Xiao Liang Hu
- Thomas
Young Centre and London Centre for Nanotechnology, 17−19 Gordon Street, London WC1H 0AH, United
Kingdom
- Department
of Physics and Astronomy, University College
London, Gower Street, London WC1E 6BT, United Kingdom
| | - Sandro Sorella
- SISSA−International
School for Advanced Studies, Via Bonomea 26, 34136 Trieste, Italy
- INFM
Democritos National Simulation Center, 34151 Trieste, Italy
| | - Dario Alfè
- Thomas
Young Centre and London Centre for Nanotechnology, 17−19 Gordon Street, London WC1H 0AH, United
Kingdom
- Department
of Earth Sciences, University College London, Gower Street, London WC1E 6BT, United
Kingdom
| | - Angelos Michaelides
- Thomas
Young Centre and London Centre for Nanotechnology, 17−19 Gordon Street, London WC1H 0AH, United
Kingdom
- Department
of Physics and Astronomy, University College
London, Gower Street, London WC1E 6BT, United Kingdom
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