Shermo：A general code for calculating molecular thermodynamic properties

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Latest version：2.4 (Release date: 2023-Jul-8)

Developer

Dr. Tian Lu (Contact: sobereva[at]sina.com. Beijing Kein Research Center for Natural Sciences, China)

If you encountered any difficulty in using Shermo, or you have found bug, or you have any suggestion on improving Shermo, please feel free to contact me!

Note: There is a nice online version of Shermo maintained by Stevan Armakovi?: https://atomistica-online-shermo.anvil.app. After uploading a file, you will quickly obtain result from the webpage. Please contact corresponding developer if you have any relevant question.

Citation

If Shermo is utilized in your work, the following paper must be cited in your article:

Tian Lu, Qinxue Chen, Shermo: A general code for calculating molecular thermodynamic properties, Comput. Theor. Chem., 1200, 113249 (2021) DOI: 10.1016/j.comptc.2021.113249

If you do not have permission to access the above paper, see preprint version DOI: 10.26434/chemrxiv.12278801, but please cite the above one.

Download

Manual: Shermo_manual_2.4.pdf. Many examples and introduction of background knowledge of thermochemistry calculation can also be found in the manual.

Executable file: Shermo_2.4.zip (including executable files of Windows and Linux platforms with manual)

Source code (in Fortran): Shermo_2.4_src.zip

Quickly getting start

Learning basic usages of Shermo in minutes (Video tutorial): https://youtu.be/qGJRt4j-5mY

中國的用戶可以看此文快速入門：使用Shermo結合量子化學程序方便地計算分子的各種熱力學數據

使用Shermo程序計算各種熱力學數據的基本操作演示視頻：https://www.bilibili.com/video/BV1EN411X7b3/

Introduction of Shermo

What is Shermo?

Shermo program is a free, general, very easy-to-use and flexible code for calculating molecular thermochemistry data based on ideal gas assumption. Although most quantum chemistry programs have their own codes used to calculate thermochemistry data after performing frequency analysis, their functionalities are very limited, and usually their outputs are inconvenient to read, especially for beginners. The aim of developing Shermo is making calculation of various basic and some advanced thermochemistry data as convenient as possible, and meantime providing deeper insight into their components.

Features of Shermo

• Output file of frequency analysis task of various quantum chemistry programs can be used as input file, including Gaussian, ORCA, GAMESS-US, NWChem and CP2K. Other programs can also utilize Shermo to compute thermochemistry data as long as they can generate the .shm file defined by Shermo.
• All common thermochemistry quantities can be calculated, including internal energy (U), enthalpy (H), entropy (S), constant volume heat capacity (C_V), constant pressure heat capacity (C_P) and partition function (q).
• Contributions of translation, rotation, vibration, electron to various thermochemistry properties are outputted in a very compact and clear format. Contribution of every vibrational mode can also be printed to understand their influences on the calculated properties.
• Temperature and pressure can be easily scanned.
• Conformation/configuration weights and weighted thermodynamic data can be obtained.
• The thermochemistry properties are calculated based on rigid-rotor harmonic oscillator (RRHO) model. In order to better deal with low frequencies, two quasi-RRHO treatments are supported: Raising lower frequencies to a specific value, interpolation between harmonic oscillator and free-rotor approximations (can be applied to both entropy and internal energy parts).
• Frequency scaling factors for ZPE, heating contribution to internal energy, entropy and heat capacity can be individually specified.
• Point group and rotational symmetry number can be automatically assigned.
• Variation of Gibbs free energy due to concentration change from current state to specific state can be taken into account.
• Shermo can not only run in interactive mode but also run in command-line mode, thus it can be easily incorporated into shell script for batch processing.
• Very easy to use. The program can be used without installation, and users do not need to prepare any running environment like Python.
  

Update History

2023-Jul-8: Version 2.4. J. Comput. Chem., 44, 1807 (2023) suggests applying interpolation between harmonic oscillator and free rotor models to both entropy and internal energy to obtain better result and more consistent theory than only applying it to entropy. Now this scheme has been implemented and can be used by setting "ilowfreq" in settings.ini to 3.

2023-May-4: Version 2.3.6. Fixed minor bugs of dealing with CP2K output file. In addition, rule has changed to: when dealing with CP2K output file, if imode=1 (use for periodic systems), point group will simply be set to C1 since determining it is meaningless in this case, while for imode=0 (used for isolated systems), point group will be determined as usual to proper account for rotation contribution.

2023-Jan-21: Version 2.3.5, now compatible with CP2K 2023.1.

2022-Oct-7: Updated Version 2.3.4, fixed a bug, which causes crashing when loading ORCA output file with "usesym" keyword.

2022-Apr-1: Updated Version 2.3.4, fixed a bug of loading modmass setting from settings.ini file.

2022-Mar-24: Updated Version 2.3.4, making it compatible with CP2K 9.1.

2022-Jan-24: Version 2.3.4. Bug fixed: When dealing with multiple systems recorded in a list file, point group is only determined for the first system rather than respectively determined for each system.

2022-Jan-9: Version 2.3.3. Bug fixed: When loading frequencies from ORCA output file, if a frequency ends with "0.00", e.g. 2580.00, then frequencies cannot be correctly loaded, leading to wrong vibrational contribution.

2021-Dec-28: Version 2.3.2. "PGlabel" parameter in settings.ini now supports four-letter point group label, such as D11h.

2021-Dec-23: Version 2.3.1. Fixed a bug: When explicitly considering electronic transition contribution by defining excitation energies in .shm file, the thermal corrections to U, H, G contributed by electronic transition are incorrect.

2021-Sep-4: Version 2.3. Variation of Gibbs free energy due to concentration change from present state to specific state can be printed and automatically added to reported Gibbs free energy. See corresponding description in Section 2.3 of manual for detail and example in Section 3.8.

In addition, Shermo now can be invoked by Molclus since version 1.9.9.6 (http://www.keinsci.com/research/molclus.html) for calculating thermodynamic data during configuration/coformation search.

2021-Jun-17: Version 2.2. New option "imode" has been added to settings.ini. When it is set to 1, then translation and rotation contributions to thermodynamic data will be ignored. This is suitable for crystal, slab and adsorbate systems.

2021-Apr-27: Version 2.1.2. Fixed a bug: Frequency analysis task of ORCA cannot be normally loaded if effective core potential is used.

2021-Apr-14: Version 2.1.1. Fixed a bug: The unit of the energy read from CP2K output file is wrong.

2021-Mar-18: Version 2.1. Source code of Shermo is now available for public download. A new section "Appendix 2: Structure and subroutines of Shermo" has been added at the end of manual to facilitate professional users to easily extend the functionality of Shermo. A video tutorial of Shermo has been presented.

2021-Feb-10: Version 2.0.8. Output file of vibrational analysis task of CP2K has been supported, see manual for detail. "PGlabel" parameter now can be specified via argument.

2021-Feb-8: Version 2.0.7. Point group now can be directly specified by "PGlabel" parameter in settings.ini. See manual for supported point group labels.

2021-Feb-4: Version 2.0.6. Fixed a bug: U, H, G are shown as NaN when temperature is set to 0.

2020-Sep-30: Version 2.0.5. Fixed a bug: Rotational symmetry number of molecules of Th point group cannot be assigned.

2020-Sep-20: Version 2.0.4.
Bug Fixed: (1) Rotation contribution is wrong for single atom system in rare cases. (2) In the printed information, the negative sign of -TS term is missing.
Section 3.8 has been added to manual to show how to use shell script to invoke Shermo to deal with a batch of files.

2020-Jul-23: Version 2.0.3. Fixed a bug: Rotation entropy in scan task is incorrect for linear molecule

2020-Jul-12: Version 2.0.2. Fixed a bug: Rotation symmetry number cannot be identified for molecule of Td point group

2020-May-20: Version 2.0.1. Fixed the bug of loading frequency scale factor for heat capacity

2020-May-14: Updated version 2.0. Now electronic energy can be directly specified via the "E" parameter, and in the conformation weighted calculation, electronic energies can be directly specified in the list file.

2020-May-12: Initial release of version 2.0

Published papers that utilized Shermo

Shermo has been utilized by more and more computational chemists in their daily research due to its unique value. The following publications have employed and cited Shermo (incomplete list):

1. Melisa Alkan, Haley K. Banovetz, Mark S. Gordon, Levi M. Stanley, Computational and Mechanistic Studies of Pd-Catalyzed Alkene Carboacylation via Ester C–O Bond Activation, ACS Catal., 13, 9766 (2023) https://pubs.acs.org/doi/abs/10.1021/acscatal.3c01405
2. Saeedreza Emamian, Majid Salami, Diels-Alder Reaction of Oxazolidine-fused Butadienes Toward Alkenes: Shedding Light on the Energetics, Selectivities, and Molecular Mechanistic Aspects by a Density Functional Theory Study, ChemistrySelect (2023) https://chemistry-europe.onlinelibrary.wiley.com/doi/abs/10.1002/slct.202300710
3. Yajie Zhang, Changjiao Shang, Chaofan Sun, Lingling Wang, Understanding prominent effects of the intramolecular hydrogen bond on the photophysical properties and antiradical abilities of six flavonoids, J. Mol. Liq., 386, 122534 (2023) https://www.sciencedirect.com/science/article/abs/pii/S0167732223013387
4. Chang Liang, Xiaopei Zhang, Weifeng Liu, et al., Thermo-responsive ion imprinted polymer on the surface of magnetic carbon nanospheres for recognizing and capturing low-concentration lithium ion, Miner. Eng., 201, 108210 (2023) https://www.sciencedirect.com/science/article/abs/pii/S0892687523002248
5. Wenyan Jia, Maoshuai Li, Mingchan Chen, et al., Mechanistic insight into epoxide methoxycarbonylation catalyzed by Co complexes, 547, 113303 (2023) https://www.sciencedirect.com/science/article/abs/pii/S2468823123003875
6. Qiyang Lin, Shuai Wang, Xin Ma, et al., O-Isobutyl-N-hydroxyethyl Thionocarbamate: Molecular Behavior and Flotation Mechanism to Chalcopyrite, Ind. Eng. Chem. Res. (2023) https://pubs.acs.org/doi/abs/10.1021/acs.iecr.3c01029
7. Tian Lu, Qinxue Chen, A simple, efficient and universal energy decomposition analysis method based on dispersion-corrected density functional theory, ChemRxiv (2023) https://doi.org/10.26434/chemrxiv-2023-n79rz
8. Feng Tang, Yong Chi, Zhong-xu Zhu, et al., Mechanisms and rate constant calculation for pyrolysis/gasification of C3 chain hydrocarbons, J. Chem. Eng. Chin. Univ. (2023) http://www.xml-data.org/GXHXGCXB/html/9e45f9d9-04d0-41d6-9786-d629dc401fc4.htm
9. Shen Li, Chao Bian, Zhong-Xin Liu, et al., Identifying the essential roles of light and sonication in dual-stimuli regulated bulk atom transfer radical polymerization by multiscale simulation, AIChE J. (2023) https://aiche.onlinelibrary.wiley.com/doi/abs/10.1002/aic.18155
10. Linshan Liu, Yang Liu, Zhuxia Zhang, Taishan Wang, Theoretical Study on a Supramolecular Dimeric Structure Constructed by Metallofullerene Y3N@C80 and Figure-of-Eight Nanoring, ACS Omega (2023) https://pubs.acs.org/doi/full/10.1021/acsomega.3c02049
11. Han Chen, Yao Jie, Hong Yan, et al., Numerical simulation and validation of reaction mechanism for the Siemens process in silicon production, J. Cryst. Growth (2023) https://www.sciencedirect.com/science/article/abs/pii/S0022024823002403
12. Xudong Zhou, Yujie Guo, Lei Shi, et al., Degradation pathways and mechanisms insight of indigo and shikonin with experiments and quantum chemical calculations, Dyes Pigments, 218, 111455 (2023) https://www.sciencedirect.com/science/article/abs/pii/S0143720823003819
13. Jinbin Lai, Ting Tang, Xiaodong Du, et al., Oxidation of 1,3-diphenylguanidine (DPG) by goethite activated persulfate: Mechanisms, products identification and reaction sites prediction, Environ. Res. (2023) https://www.sciencedirect.com/science/article/abs/pii/S001393512301112X
14. Lei Tang, Jingyu Ran, Xinyuan Bu, et al., Effect of Pd doping on CH4 oxidation mechanism over Pt clusters: A systematic DFT study, Mol. Catal., 546, 113208 (2023) https://www.sciencedirect.com/science/article/abs/pii/S2468823123002924
15. Emmanuel Israel Edache, Adamu Uzairu, Paul Andrew Mamza, et al., Methimazole and propylthiouracil Design as a Drug for Anti-Graves' Disease: Structural Studies, Hirshfeld Surface Analysis, DFT Calculations, Molecular Docking, Molecular Dynamics Simulations, and Design as a Drug for Anti-Graves' Disease, J. Mol. Struct. (2023) https://www.sciencedirect.com/science/article/abs/pii/S0022286023010074
16. Qiang Ren, Juming Liu, Zhilin Yang, Qi Yang, Boosting transformation of dissolved oxygen to superoxide radical: function of P25, Water Environ. Res. (2023) https://onlinelibrary.wiley.com/doi/abs/10.1002/wer.10898
17. Jinyun Zheng, Xinxin Liu, Wenbin Li, et al., Green Synthesis of Novel Conjugated Poly (perylene diimide) as Cathode with Stable Sodium Storage, NanoResearch (2023) https://www.sciopen.com/article_pdf/1661634992397860865.pdf
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24. Wenping Li, Jiafu Shi, Yu Chen, et al., Nano-Sized Mesoporous Hydrogen-Bonded Organic Frameworks for in situ Enzyme Immobilization, Chem. Eng. J. (2023) https://www.sciencedirect.com/science/article/abs/pii/S1385894723023409
25. Pengcheng Shi, Yingdan Zhu, Haibing Xu, et al., Insights into the carbonization mechanism of PAN-derived carbon precursor fibers and establishment of a kinetics-driven accelerated reaction template for atomistic simulation, Phys. Chem. Chem. Phys. (2023) https://pubs.rsc.org/en/content/articlelanding/2023/cp/d2cp05196f/
26. Da Sheng, Lingjun Bu, Shumin Zhu, et al., Pre-oxidation coupled with charged covalent organic framework membranes for highly efficient removal of organic chloramines precursors in algae-containing water treatment, Chemosphere, 333, 138982 (2023) https://www.sciencedirect.com/science/article/abs/pii/S0045653523012493
27. Tian Meng, Yilin Guo, Jingwei Chen, Jiaqiang E, Exploring detailed microcosmic mechanisms of sodium chloride deposition in supercritical water reactors from the aspect of solvation structure: A combination of MD and QM simulations, J. Mol. Liq., 383, 122118 (2023) https://www.sciencedirect.com/science/article/abs/pii/S0167732223009212
28. Jianzhang Gao, Jiaqi Chen, Huitao Lv, et al., Electrocatalytic and green system coupling strategy for simultaneous recovery and purification of uranium from uranium-containing wastewater, J. Environ. Manage., 342, 118151 (2023) https://www.sciencedirect.com/science/article/abs/pii/S0301479723009398
29. Pingping Sun, Devesh R Kripalani, Weijie Chi, Molecular Principles of the Excited-State Intramolecular Thiol Proton Transfers in 3-thiolflavone Derivatives, Chem. Asian J. (2023) https://onlinelibrary.wiley.com/doi/abs/10.1002/asia.202300314
    
30. Fangjing Mu, Hao Wang, Zhanhang He, et al., Theoretical Study on the Potential Existing Forms and Microwave Rotational Spectrum of Short-Chain Fatty Acids in Interstellar Space, Arxiv (2023) https://arxiv.org/ftp/arxiv/papers/2305/2305.04762.pdf
31. Zhiyou Wei, Hongguang Xu, Xiling Xu, et al., Solvation of magnesium chloride dimer in water: The case of anionic and neutral clusters, J. Chem. Phys., 158, 174311 (2023) https://doi.org/10.1063/5.0146319
32. Rui Wang, Ziqi Zhang, Jinquan Suo, et al., Metal-and Pyrolysis-Free Ionic Covalent Organic Framework Nanosheet for Efficient Oxygen Evolution Reaction, ChemRxiv (2023) https://chemrxiv.org/engage/chemrxiv/article-details/645304b627fccdb3ea73c36e
33. Bin Wang, Chunying Rong, Ming Lei, et al., Mechanistic Study and Conceptual Chemical Reactivity Analysis of Hydroboration of Carbon Dioxide Catalyzed by a Manganese(I)–PNP–Pincer Complex, Inorg. Chem. (2023) https://pubs.acs.org/doi/abs/10.1021/acs.inorgchem.3c00553
34. Baoli Zhang, Haifeng Wu, Shan Li, et al., Enzyme-Mimetic Photo-decarboxylation Based on Geometry-Dependent Supramolecular Association, ACS Catal., 13, 6763 (2023) https://pubs.acs.org/doi/abs/10.1021/acscatal.3c01669
35. Yanyan Liao, Shunmin Zhang, Xuefeng Jiang, Construction of Thioamide Peptides from Chiral Amino Acids, Angew. Chem. (2023) https://onlinelibrary.wiley.com/doi/10.1002/anie.202303625
36. Liwei Ye, Xiaoyang Liu, Kristen Beckett, et al., Catalyst Design to Address Nylon Plastics Recycling, ChemRxiv (2023) https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6448089f83fa35f8f63ce256/original/catalyst-design-to-address-nylon-plastics-recycling.pdf
37. Ziyi Wang, Weigen Chen, Tianyi Sang, et al., Fullerenol-based Toxic Fluoride Gas Sensing: A Promising Way to Monitoring Li-ion Battery Status, Surf. Interf. (2023) https://www.sciencedirect.com/science/article/abs/pii/S2468023023002638
38. Xiaodong Du, Haoliang Li, Jiahao Liang, et al., Hydrogen-Donor-Controlled Polybrominated Dibenzofuran (PBDF) Formation from Polybrominated Diphenyl Ether (PBDE) Photolysis in Solutions: Competition Mechanisms of Radical-Based Cyclization and Hydrogen Abstraction Reactions, Environ. Sci. Technol. (2023) https://pubs.acs.org/doi/abs/10.1021/acs.est.2c08003
39. Zhenpeng Zhang, Hailin Yin, Yanlei Shang, Sheng-Nian Luo, Accurate rate constants for barrierless dissociation of ethanol: VRC-VTST and SS-QRRK calculations with the cheaper DFT method, Chem. Phys. Lett. (2023) https://www.sciencedirect.com/science/article/abs/pii/S0009261423002270
40. Ke Du, Yang Wang, Infinitenes as the Most Stable Form of Cycloarenes: The Interplay among π Delocalization, Strain, and π–π Stacking, J. Am. Chem. Soc. (2023) https://doi.org/10.1021/jacs.3c01644
    
41. Xu Zhang, Zhongchao Zhou, Rui Xu, et al., Reaction mechanism of nickel sulfide atomic layer deposition using bis(N,N′-di-tert-butylacetamidinato)nickel(II) and hydrogen sulfide, Phys. Chem. Chem. Phys. (2023) https://pubs.rsc.org/en/content/articlelanding/2023/cp/d2cp05450g/
42. Kaiyu Zhang, WeiSheng Yu, Xiaolin Ge, et al., DFT insight of hydroxide degradation pathways for heterocyclic quaternary ammonium cations in anion exchange membranes, J. Membrane Sci. (2023) https://www.sciencedirect.com/science/article/abs/pii/S0376738823003289
43. Alfian Ma'arif, Ekky Haqindytia Saputra, Reza Alayi, Electricity power monitoring based on internet of things, Signal and Image Processing Letters (2023) https://simple.ascee.org/index.php/simple/article/view/48
44. Farshad Shiri, Alireza Ariafard, Factors Influencing the Chemoselectivity of Pd(OAc)2- Catalyzed Cyclization Reactions Involving 1,6-Enynes as a Substrate and PhI(OAc)2 as a Reagent, Chem. Eur. J. (2023) https://doi.org/doi.org/10.1002/chem.202300115
45. Yaoyao Li, Wei Chen, Tianyu Lei, et al., Reconstruction Suppressed Solid-Electrolyte Interphase by Functionalized Metal-Organic Framework, Energy Storage Mater. (2023) https://www.sciencedirect.com/science/article/abs/pii/S2405829723001447
46. Qi Xu, Liang Liu, Hengtong Xia, et al., Nanoarchitectonics of Co9S8/Zn0.5Cd0.5S nanocomposite for efficient photocatalytic hydrogen evolution, Coll. Surf. A, 667, 131404 (2023) https://www.sciencedirect.com/science/article/abs/pii/S0927775723004880
47. Xiaokun He, Yuan Xue, Ran Zuo, Gas-Phase reaction mechanism of InN MOVPE: A systematic DFT study, J. Cryst. Growth, 612, 127197 (2023) https://www.sciencedirect.com/science/article/pii/S0022024823001239
48. Ben He, Yun Yu, Xun Gong, et al., Mechanism of acid-catalyzed pyrolysis of levoglucosan: Formation of anhydro-disaccharides, Fuel, 345, 128242 (2023) https://www.sciencedirect.com/science/article/abs/pii/S0016236123008554
49. Jiangxue Ning, Qinyuan Qiu, Haixia Ma, Liyu Chen, Development and catalytic mechanism of ionic liquid catalysts for polyoxymethylene dimethyl ethers, Chem. Phys. Lett. (2023) https://www.sciencedirect.com/science/article/abs/pii/S0009261423001768
50. Xiaohua Yang, Xiangyang Liu, Jinhui Han, et al., Tuning Fluorination of Carbonates for Lithium-Ion Batteries: A Theoretical Study, J. Phys. Chem. B (2023) https://pubs.acs.org/doi/abs/10.1021/acs.jpcb.3c00475
51. Hualei zhang, Zheng Lin, Pinit Kidkhunthod, Jia Guo, Stable Immobilization of Nickel Ions on Covalent Organic Frameworks for Panchromatic Photocatalytic Hydrogen Evolution, Angew. Chem. (2023) https://onlinelibrary.wiley.com/doi/abs/10.1002/ange.202217527
52. Chenggen Zhang, Shuyuan Yu, Fei Wang, et al., Insights into the Three-Component Coupling Reactions of Aldehydes, Alkynes, and Amines Catalyzed by N-heterocyclic Carbene Silver: A DFT Study, Catalysts, 13, 646 (2023) https://doi.org/10.3390/catal13040646
53. Qi Cheng, Wenxin Yan, Tian Li, et al., Insights into the regioselectivity and diastereoselectivity of the Nazarov cyclization of 3-alkenyl-2-indolylmethanol with tryptophol, Org. Chem. Front. (2023) https://pubs.rsc.org/en/content/articlelanding/2023/qo/d2qo01896a/
54. Rongchuan Su, Zhenmei Huang, A Series of Singlet-Triplet InVerted TADF Fluorescent Probes with High Stability, Low Molecular Weight, and Synthesis Accessibility, Adv. Theory Simulat. (2023) https://onlinelibrary.wiley.com/doi/abs/10.1002/adts.202200863
55. Study on the pyrolysis characteristics and reaction mechanisms of WLED packaging materials, J. Anal. Appl. Pyroly., 170, 105935 (2023) https://www.sciencedirect.com/science/article/abs/pii/S0165237023000797
56. Qiang Wu, Yuansheng Wang, Yunye Liang, Simulation and quantitative characterisation of polyvinyl alcohol grafted ethylenediamine tetraacetic acid chelating material, Mater. Today Commun. (2023) https://www.sciencedirect.com/science/article/abs/pii/S2352492823004117
57. J. Lupi, M. Kelly, A. O’Shea, et al., Quantum Chemical Modelling of Hemicellulose Fast Pyrolysis: β-D-xylopyranose as a Structural Motif, ChemRxiv (2023) https://chemrxiv.org/engage/chemrxiv/article-details/6400cfeb37e01856dc082d26
58. Xinbo Yang, Nan Li, Yuchuan Li, Siping Pang, Insensitive High-Energy Density Materials Based on Azazole-Rich Rings: 1,2,4-Triazole N-Oxide Derivatives Containing Isomerized Nitro and Amino Groups, Int. J. Mol. Sci., 24, 3918 (2023) https://doi.org/10.3390/ijms24043918
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64. Shiyao Niu, Xiaoqing Wu, Qifeng Hou, et al., Theoretical Kinetic Studies on Thermal Decomposition of Glycerol Trinitrate and Trimethylolethane Trinitrate in the Gas and Liquid Phases, J. Phys. Chem. A (2023) https://pubs.acs.org/doi/abs/10.1021/acs.jpca.2c07282
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