Shermo：A general code for calculating molecular thermodynamic properties


Latest version：2.3.5 (Release date: 2023-Jan-21)

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!

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_2.3.5.pdf. Many examples and introduction of background knowledge of thermochemistry calculation can also be found in the manual.

Executable file: Shermo_2.3.5.zip (including executable files of Windows and Linux platforms)

Source code (in Fortran): Shermo_2.3.5_src.zip

Quickly getting start

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

中国的用户可以看此文快速入门：使用Shermo结合量子化学程序方便地计算分子的各种热力学数据

使用Shermo程序计算各种热力学数据的基本操作演示视频：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

Update History

2023-Jan-21: Updated 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. Chunjian Tan, Shaogang Wang, Huiru Yang, et al., Understanding the interaction of nucleotides with UVC light: an insight from quantum chemical calculation-based findings, Phys. Chem. Chem. Phys. (2023) https://pubs.rsc.org/en/content/articlelanding/2023/cp/d2cp05054d/
  2. Xin-bo Yang, Chen-hui Jia, Xiang-yan Miao, et al., Synthesis and characterization of potential polycyclic energetic materials using bicyclic triazole and azetidine structures as building blocks, RSC Adv., 13, 2600 (2023) https://pubs.rsc.org/en/content/articlehtml/2023/ra/d2ra06646g
  3. Yuxuan Sun, Liu Wang, Yangyang Ni, et al., 3D printing of thermosets with diverse rheological and functional applicabilities, Nat. Commun., 14, 245 (2023) https://www.nature.com/articles/s41467-023-35929-y
  4. Ji Liu, Yuan-Gu Xia, Yang-Wen Wu, et al., Microscopic mechanism for the effect of potassium on heterogeneous NO–char(N) interaction: A theoretical account, Fuel Proc. Technol., 242, 107657 (2023) https://www.sciencedirect.com/science/article/pii/S037838202300005X
  5. Zhongxu Zhu, Feng Tang, Yuqi Jin, et al., Computational study on the chain cracking mechanisms and rate constants of C2 chain hydrocarbons during pyrolysis/gasification, Journal of Fuel Chemistry and Technology (2023) http://rlhxxb.sxicc.ac.cn/cn/article/doi/10.19906/j.cnki.JFCT.2022048
  6. Nyiang Kennet Nkungli, Aymard Didier Tamafo Fouegue, Stanley Numbonui Tasheh, et al., In silico investigation of falcipain-2 inhibition by hybrid benzimidazole-thiosemicarbazone antiplasmodial agents: A molecular docking, molecular dynamics simulation, and kinetics study, Mol. Diversity (2023) https://link.springer.com/article/10.1007/s11030-022-10594-3
  7. Yue Lu, Fangyi Liang, Fanzhi Qin, et al., Tourmaline guiding the electric field and dechlorination pathway of 2,3-dichlorophenol by Desulfitobacterium hafniense, J. Environ. Sci. (2023) https://www.sciencedirect.com/science/article/abs/pii/S1001074222006489
  8. Xu Li, Shanshan Dong, Ting Fan, et al., Role of Chiral Skeleton in Chiral Phosphoric Acids Catalyzed Asymmetric Transfer Hydrogenation: A DFT Study, Catalysts, 13, 98 (2023) https://doi.org/10.3390/catal13010098
  9. Feng Tang, Zhongxu Zhu, Chunlai Xu, et al., Effects of steam and CO2 on gasification tar composition and evolution of aromatic compounds, Waste Manag., 157, 219 (2023) https://www.sciencedirect.com/science/article/abs/pii/S0956053X22006079
  10. Jianfeng Zhu, Hongwu Wang, Abing Duan, Yanqiong Wang, Mechanistic insight into the degradation of ciprofloxacin in water by hydroxyl radicals, J. Hazard. Mater. (2022) https://www.sciencedirect.com/science/article/abs/pii/S0304389422024724
  11. Dual functions of cyclo[18]carbon in desensitizing and sensing two powerful energetic molecules DNTF and ICM103, Mater. Today Commun., 34, 105206 (2023) https://www.sciencedirect.com/science/article/abs/pii/S2352492822020475
  12. Tenglong Lv, Minggao Xu, Wei He, et al., An experimental and kinetic modeling study on pyrolysis of chlorobenzene, Combust. Flame, 248, 112548 (2023) https://www.sciencedirect.com/science/article/abs/pii/S0010218022005569
  13. Quantum chemistry insight into the interactions of 1,3-diisopropoxycalix[4]arenecrown-6 with alkali metal cations: Structure, selectivity, and solvation, J. Mol. Liq., 370, 121054 (2023) https://www.sciencedirect.com/science/article/abs/pii/S0167732222025934
  14. Jingjing Li, Jinzhao Wang, Palladium-catalyzed generation of CO from formic acid for alkoxycarbonylation of internal alkenes exploits a PTSA-assisted NH-Pd mechanism: a DFT mechanistic study, Phys. Chem. Chem. Phys. (2022) https://pubs.rsc.org/en/content/articlehtml/2022/cp/d2cp04231b
  15. Yang Yu, Hao Liu, Juan Chen, Transformation and capture mechanism of selenium in sludge gasification: Modeling and density functional theory study, Fuel (2022) https://www.sciencedirect.com/science/article/abs/pii/S0016236122037930
  16. Lipeng Su, Jiankun Zhuo, Hao Liu, et al., Fragmentation modeling of gas-phase ionic liquid clusters in high-voltage electric field, Fuel, 335, 126919 (2023) https://www.sciencedirect.com/science/article/abs/pii/S0016236122037437
  17. Zhongchao Zhou, Xu Zhang, Rui Xu, et al., Atomic/molecular layer deposition mechanism of alucone organic–inorganic hybrid materials, Mater. Today Commun., 34, 105061 (2023) https://www.sciencedirect.com/science/article/abs/pii/S235249282201902X
  18. Alessandro Papa, Silvia Pasquini, Francesca Galvani, et al., Development of potent and selective FAAH inhibitors with improved drug-like properties as potential tools to treat neuroinflammatory conditions, Eur. J. Med. Chem. (2022) https://www.sciencedirect.com/science/article/abs/pii/S0223523422008546
  19. An Ning, Ling Liu, Shaobing Zhang, et al., The critical role of dimethylamine in the rapid formation of iodic acid particles in marine areas, npj Clim. Atmos. Sci., 5, 92 (2022) https://www.nature.com/articles/s41612-022-00316-9
  20. Jiabin Huang, Can Huang, Qifeng Hou, et al., A theoretical study on dissociative photoionization and photoionization cross-sections of a typical ketohydroperoxide in n-butane low-temperature oxidation, Combust. Flame (2022) https://www.sciencedirect.com/science/article/abs/pii/S0010218022004990
  21. Rui Chen, Qiuyue Li, Kai Xu, et al., Structural and spectroscopic analysis, solvent effect on the molecular properties and molecular docking of trans-2-(4-(dimethylamino) styryl)-benzothiazole, Chem. Phys. Lett. (2022) https://www.sciencedirect.com/science/article/abs/pii/S0009261422008491
  22. Qiu Zhao, Hui Zhao, Gang Wang, et al., Kinetic and mechanistic insights into the roles of protonated morpholine species and weak acidic environment in methylacrolein production catalyzed by morpholine/acid, Chem. Eng. J. (2022) https://www.sciencedirect.com/science/article/abs/pii/S1385894722058892
  23. Xiaoyun Liu, Guorui Liu, Shuting Liu, et al., Free radical mechanism of toxic organic compound formations from o-chlorophenol, J. Hazard. Mater., 443, 130367 (2023) https://www.sciencedirect.com/science/article/abs/pii/S0304389422021616
  24. Delong Ma, Song Ma, Yunfeng Li, et al., Reactivities of silane coupling agents in the silica/rubber composites: Theoretical insights into the relationships between energy barriers and electronic characteristics, J. Comput. Chem. (2022) https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.27024
  25. Chao Chen, Yves Gnanou, Xiaoshuang Feng, Borinane-based organoboron catalysts for alternating copolymerization of CO2 with cyclic ethers: improved productivity and facile recovery, Polym. Chem. (2022) https://repository.kaust.edu.sa/bitstream/handle/10754/685372/d2py01161a1.pdf
  26. Xiaofeng Yuan, Qianjin Guo, Shuhai Zhang, et al., Comprehensive study on thermal decomposition mechanism and interaction of 3-Nitro-1,2,4-Triazol-5-One/Poly-3-nitromethyl-3-methyloxetane plastic bonded explosives, J. Anal. Appl. Pyrol., 168, 105753 (2022) https://www.sciencedirect.com/science/article/abs/pii/S0165237022003230
  27. Xiaoxue Wu, Wei Shi, Yunfan Yang, et al., Multi-targeted fluorescent probes for detection of Zn(II) and Cu(II) ions based on ESIPT mechanism, 287, 122051 (2023) https://www.sciencedirect.com/science/article/abs/pii/S1386142522011994
  28. Yanwen Wang, Xiangxin Han, Zheng Gao, Xiumin Jiang, Thermal cracking of the large molecular alcohols in shale oil by experimental study and kinetic modeling, J. Anal. Appl. Pyrol., 168, 105749 (2022) https://www.sciencedirect.com/science/article/abs/pii/S0165237022003199
  29. Bahram Ghanbari, Fatemeh Ziaeifar, Ameneh Kazemi, Amir Hossein Mohammadzadeh, Comparative DFT-D3 assessment of fluorogenic supramolecular interaction of naphthalene moiety location on new dibenzodiaza-crown ether macrocycles with C60, J. Mol. Struct. (2022) https://www.sciencedirect.com/science/article/abs/pii/S0022286022019937
  30. Yu Zhu, Qiang Chen, Chaoyang Wang, et al., Side-chain engineering for high degradation performance of mandrel materials in ICF target fabrication, Phys. Chem. Chem. Phys. (2022) https://pubs.rsc.org/en/content/articlelanding/2022/cp/d2cp03324k/
  31. Liying Zheng, Jifeng Yang, Lihui Ou, et al., Theoretical investigation on the mechanisms for reactions of hydroxyl radicals with sulfamethoxazole in aqueous phase, Environ. Chem. (2022) http://hjhx.rcees.ac.cn/en/article/doi/10.7524/j.issn.0254-6108.2022071601
  32. Shuhui Zhang, Liwei Wang, Yan Zhang, et al., Effect of hydroxyl functional groups on SO2 adsorption by activated carbon, J. Environ. Chem. Eng. (2022) https://www.sciencedirect.com/science/article/abs/pii/S2213343722016001
  33. Shuang Liu, Liyan Shan, Guannan Li, B.Shane Underwood, et al., Molecular-based asphalt oxidation reaction mechanism and aging resistance optimization strategies based on quantum chemistry, Mater. Design (2022) https://www.sciencedirect.com/science/article/pii/S0264127522008474
  34. Zhe-Yuan Xu, De-Guang Liu, Cheng-Yu Yao, et al., Mechanistic Study on Palladium-Catalyzed Cycloaddition of Vinylethylene Carbonates with α,β-Unsaturated Imines, Organometallics (2022) https://pubs.acs.org/doi/abs/10.1021/acs.organomet.2c00349
  35. Suwen Wang, Zhaohui Wu, Cui Xu, et al., Triple-Phase Interface Engineering over an In2O3 Electrode to Boost Carbon Dioxide Electroreduction, ACS Appl. Mater. Interfaces (2022) https://pubs.acs.org/doi/abs/10.1021/acsami.2c13286
  36. Hang Yang, Zhi-Jiang Yang, Qi-Fan Yang, et al., Simple and high-precision DFT-QSPR prediction of enthalpy of combustion for sesquiterpenoid high-energy–density fuels, Fuel, 332, 126157 (2023) https://www.sciencedirect.com/science/article/abs/pii/S0016236122029817
  37. Ning Li, Rui Yang, Ye Tian, et al., Synthesis of durable hydrophobic fluorinated polyurethanes with exceptional cavitation erosion resistance, Tribol. Int. (2022) https://www.sciencedirect.com/science/article/abs/pii/S0301679X22005448
  38. Weijun Weng, Jia Guo, The effect of enantioselective chiral covalent organic frameworks and cysteine sacrificial donors on photocatalytic hydrogen evolution, Nat. Commun., 13, 5768 (2022) https://www.nature.com/articles/s41467-022-33501-8
  39. Jingsi Qiu, Yue Liu, Quantum chemistry calculation and experimental research on the component proportion of black disperse dye, Textile Research Journal (2022) https://journals.sagepub.com/doi/abs/10.1177/00405175221125255
  40. Wenjin Cao, Zhubin Hu, Xiaogai Peng, et al., Annihilating Actinic Photochemistry of the Pyruvate Anion by One and Two Water Molecules, J. Am. Chem. Soc. (2022) https://pubs.acs.org/doi/abs/10.1021/jacs.2c06319
  41. Shulei Liu, Ming Qin, Songsong Liu, et al., Theoretical perspective for the relationship between molecular structures and circularly polarised thermally activated delayed fluorescence properties, Mol. Phys. (2022) https://www.tandfonline.com/doi/abs/10.1080/00268976.2022.2127381
  42. Na Shan, QingQing Wang, RunYu Zhou, Study on the activation mechanism of protactinium and NH3 by density functional theory, Chem. Phys. Lett. (2022) https://www.sciencedirect.com/science/article/abs/pii/S0009261422007291
  43. Wei Wu, HengYuan Zhao, Jingchao Chen, et al., Umpolung Reactivity of Imine Ester: Visible-Light Mediated Transfer Hydrogenation of α-Aryl Imino Esters by Phenylsilane and Water, Chem. Eur. J. (2022) https://chemistry-europe.onlinelibrary.wiley.com/doi/abs/10.1002/chem.202202460
  44. Xiaomin Song, Meishan Wang, Chuanlu Yang, et al., The molecular structure, spectroscopic properties and partition functions of C3H2S isomers: An ab initio study, Comput. Theor. Chem. (2022) https://www.sciencedirect.com/science/article/abs/pii/S2210271X22002900
  45. Yao Ma, Haoliang Li, Chunsheng Xie, et al., Treatment of PBDEs from Soil-Washing Effluent by Granular-Activated Carbon: Adsorption Behavior, Influencing Factors and Density Functional Theory Calculation, Processes, 10, 1815 (2022) https://www.mdpi.com/2227-9717/10/9/1815
  46. Zhibin Qu, Fei Sun, Xinxin Pi, et al., Revealing the activity origin of oxygen-doped amorphous carbon material for SO2 catalytic oxidation: A descriptor considering dynamic electron transfer during O2 activation, Carbon (2022) https://www.sciencedirect.com/science/article/abs/pii/S0008622322006947
  47. Guifa Zhai, Senhua Chen, Hongjie Shen, et al., Bioactive Monoterpenes and Polyketides from the Ascidian-Derived Fungus Diaporthe sp. SYSU-MS4722, Mar. Drugs, 20, 553 (2022) https://www.mdpi.com/1660-3397/20/9/553
  48. Wen-Bo Sui, Ya-Qin Sun, Xiao-Li Wang, Zhi-Long Xiu, Synergistic Extraction of 1,3-Propanediol from Fermentation Broths Using Multialcohol Extractants, ACS Sustainable Chem. Eng. (2022) https://pubs.acs.org/doi/abs/10.1021/acssuschemeng.2c02853
  49. Yao Ma, Jinfan Chen, Xiaodong Du, et al., Efficient removal of polybrominated diphenyl ethers from soil washing effluent by dummy molecular imprinted adsorbents: Selectivity and mechanisms, J. Environ. Sci. (2022) https://www.sciencedirect.com/science/article/abs/pii/S1001074222004284
  50. Long Li,Yanying Zheng, A molecular switch via chemisorption of the Au6 cluster by cyclo [18] carbon: utilization of an external electric field, ChemRxiv (2022) https://chemrxiv.org/engage/chemrxiv/article-details/6309c436f07ee121c8f37e6f
  51. Feng Gao, Jing Li, Tanveer Ahmad, et al., Asymmetric synthesis of bedaquiline based on bimetallic activation and non-covalent interaction promotion strategies, Sci. China Chem. (2022) https://doi.org/10.1007/s11426-022-1387-7
  52. Siyuan Fang, Yun Hang Hu, Temperature, pressure, and adsorption‐dependent redox potentials-I. Processes of CO2 reduction to value‐added compounds, Energy Sci. Eng. (2022) https://onlinelibrary.wiley.com/doi/10.1002/ese3.1287
  53. Yuhui Yi, Jie Wang, Yingli Niu, et al., Exploring the evolution patterns of melem from thermal synthesis of melamine to graphitic carbon nitride, RSC Adv. (2022) https://pubs.rsc.org/en/content/articlelanding/2022/ra/d2ra03337b
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  56. Suocheng Chi, Yingzhe Yu, Minhua Zhang, An investigation on chain transfer to monomers and initiators, termination of radical chains and primary radicals in EVA copolymerization process based on DFT calculation and microkinetic simulation, Polymer (2022) https://www.sciencedirect.com/science/article/abs/pii/S0032386122006693
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  58. Fan Xiao, Li Yang, Ben He, et al., Experimental and theoretical study on the evolution of functional groups in cellulose char during oxidative pyrolysis, Fuel, 329, 125400 (2022) https://www.sciencedirect.com/science/article/abs/pii/S0016236122022347
  59. Wenxia Niu, Peng Li, The Complexation between Siloxane Species and Methylsiloxane: Electronic Structure, Thermodynamic, and Interaction Characteristics, ChemistrySelect (2022) https://chemistry-europe.onlinelibrary.wiley.com/doi/abs/10.1002/slct.202201761
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  73. An Ning, Ling Liu, Lin Ji, Xiuhui Zhang, Molecular-level nucleation mechanism of iodic acid and methanesulfonic acid, Atmos. Chem. Phys., 22, 6103 (2022) https://acp.copernicus.org/articles/22/6103/2022/
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