Shermo：A general code for calculating molecular thermodynamic properties

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Latest version：2.3 (Release date: 2021-Sep-3)

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, please cite it in your paper as follows:

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 on ChemRxiv (but please cite the above one): DOI: 10.26434/chemrxiv.12278801

Download

Manual: Shermo_manual_2.3.pdf. Many examples and introduction of background knowledge of thermochemistry calculation can also be found in the manual.

Executable file: Shermo_2.3.zip (including executable files of Windows and Linux platforms)

Source code (in Fortran): Shermo_2.3_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

• 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, Grimme's entropy interpolation between harmonic and free-rotor approximations.
• 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.
  

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:

1. Lifeng Jia, Yufang Liu, The effects of electron-withdrawing and electron-donating groups on the photophysical properties and ESIPT of salicylideneaniline, Spectrochim. Acta A, 242, 118719 (2020)
2. Zhi-You Wei, Li-Jiang Yang, Hong-Guang Xu, Hydration processes of barium chloride: Size-selected anion photoelectron spectroscopy and theoretical calculations of BaCl2-water clusters, J. Chem. Phys., 153, 134301 (2020)
3. Kaifeng Wang, Qiao Wu, Yuxia Liu, et al., Theoretical Insights into Ester-Directed Reactions between Propiolates with 1,2-Benzisoxazoles by Au(I) Catalyst: [4 + 2]-Annulation versus Michael-Type Products, Organometallics, 39, 4061 (2020)
4. Emmanuel I. Ubana, Hitler Louis, Obieze C. Enudi, et al., DFT Study of the Structural, Electronic, Bonding Nature, NBO Analysis, and Thermodynamic Properties of Halogenated (F, Cl, Br) and Heteroatom (O, N, S) doped Cyclopropane, ResearchSquare (2021) https://assets.researchsquare.com/files/rs-136338/v1_stamped.pdf
5. Jia Wei, Yuanzuo Li, Peng Song, et al., Effect of Polymerization on the Charge-Transfer Mechanism in the One (Two)-Photon Absorption Process of D–A-Type Triphenylamine Derivatives, J. Phys. Chem. A (2021) https://pubs.acs.org/doi/10.1021/acs.jpca.0c09309
6. Jiandong Guo, Wu Yang, Dongju Zhang, et al., Mechanistic Insights into Formation of All-Carbon Quaternary Centers via Scandium-Catalyzed C–H Alkylation of Imidazoles with 1,1-Disubstituted Alkenes, J. Org. Chem. (2021) https://pubs.acs.org/doi/abs/10.1021/acs.joc.0c03054
7. Xueying Liu, Yanyan Liu, Xueliang Wang, et al., Study on the Molecular Structure and Chemical Properties of the Polyoxypregnane Derivatives 11α-O-2-methylbutyryl-12β-O-tigloyl Tenacigenin B and 11α,12β-O-ditigloyl Tenacigenin B by Combining Experimental and Theoretical Methods, J. Mol. Struct. (2021) https://www.sciencedirect.com/science/article/abs/pii/S002228602100483X
8. Zhiyi Wu, Simon Newstead, Philip C. Biggin, The KDEL trafficking receptor exploits pH to tune the strength of an unusual short hydrogen bond, Sci. Rep. (2020) https://www.nature.com/articles/s41598-020-73906-3
9. Yifan Feng, Haiyan Zhu, Qiyan Zhang, et al., Theoretical study on the two novel planar-type all-nitrogen N44− anions: Structures, stability, reaction rate and their stable mechanisms via protonation, Chem. Phys. Lett., 711, 138519 (2021) https://www.sciencedirect.com/science/article/abs/pii/S0009261421002025
10. Zhi-You Wei, Li-Jiang Yang, Shi-Yan Gong, et al., Comparison of the Microsolvation of CaX2 (X = F, Cl, Br, I) in Water: Size-Selected Anion Photoelectron Spectroscopy and Theoretical Calculations, J. Phys. Chem. A (2021) https://pubs.acs.org/doi/abs/10.1021/acs.jpca.1c00573
11. Haoran Sun, Jiajia Wang, Bo Zhen, et al., Polycyclic polyprenylated acylphloroglucinol derivatives from Hypericum pseudohenryi, Phytochem., 187, 112761 (2021) https://www.sciencedirect.com/science/article/abs/pii/S0031942221001102
12. Yaning Zhang, Rui Zhang, Luo Wu, et al., Solubilities, Structures, and Speciations of Bimetallic Composite Ionic Liquids: X-ray Absorption Fine Structure and Density Functional Theory Calculations, Ind. Eng. Chem. Res. (2021) https://pubs.acs.org/doi/abs/10.1021/acs.iecr.0c06196
13. Qi Zou, Zhuhao Huo, Haiyang Shao, et al., Degradation of pyrazinamide in aqueous solution by electron beam irradiation: kinetics, influence factors and mechanism study, J. Radioanal. Nucl. Ch. (2021) https://link.springer.com/article/10.1007/s10967-021-07757-1
14. Xin Jiang, Zhenming Zhang, Diqiang Luo, et al., Structural Stability and Thermodynamic Properties of(Y2O3)n(n=1-15) Clusters Based on Density Functional Theory, Authorea (2021) https://d197for5662m48.cloudfront.net/documents/publicationstatus/63683/preprint_pdf/f92739a64cb8eeb8c8e116534d1d81a2.p
15. Yanyun Zhao, Xueli Cheng, Nie Kun, et al., Structures, relative stability, bond dissociation energies, and stabilization energies of alkynes and imines from a homodesmotic reaction, Comput. Theor. Chem. (2021) https://www.sciencedirect.com/science/article/abs/pii/S2210271X21001870
16. Sonia Taamalli, Michal Pitoňák, Theodore S. Dibble, et al., Theoretical Study of the Monohydration of Mercury Compounds of Atmospheric Interest, J. Phys. Chem. A (2021) https://pubs.acs.org/doi/abs/10.1021/acs.jpca.1c02772
17. Tianyun Jin, Pinglin Li, Cili Wang, et al., Two new spongian diterpene derivatives from the aquaculture sponge Spongia officinalis Linnaeus, 1759, Nat. Prod. Res. (2021) https://www.tandfonline.com/doi/abs/10.1080/14786419.2021.1961137
18. An Ning, Ling Liu, Lin Ji, Xiuhui Zhang, Molecular-level evidence for marine aerosol nucleation of iodic acid and methanesulfonic acid, Preprints (2021) https://acp.copernicus.org/preprints/acp-2021-595/acp-2021-595.pdf
19. Hao-Ran Sun, Jia-Jia Wang, Bo Zhen, et al., Hypseudohenrins I-K: three new polycyclic polyprenylated acylphloroglucinol derivatives from Hypericum pseudohenryi, J. Asian Nat. Prod. Res., 23, 536 (2021) https://doi.org/10.1080/10286020.2021.1906232.
20. Bingru Wang, Long Lin, Shuhang Ren, Weize Wu, Specific Heat Capacity of Non-Functional and Functional Ionic Liquids during the Absorption of SO2, Ind. Eng. Chem. Res. (2021) https://pubs.acs.org/doi/abs/10.1021/acs.iecr.1c02327
21. Chaoren Shen, Kaiwu Dong, Zhihong Wei, Xinxin Tian, In silicoinvestigationof ligand-regulatedpalladium-catalysed formic acid dehydrative decomposition under acidic conditions, ChemRxiv (2021) https://chemrxiv.org/engage/chemrxiv/article-details/614c43ac87a02dd57c458aa4
22. Saiqin Meng, Xiaolong Fu, Zhejun Wang, et al., Study on the reaction mechanism of CH2O + NO2 transformed by PbO/SnO in double-base propellants through theoretical calculation and experiment, Combust. Flame, 236, 111768 (2022) https://www.sciencedirect.com/science/article/abs/pii/S0010218021005113
23. Ruipeng Li, Yuepeng Wang, Yanfei Zhao, et al., Hydrogen-Bonding-Mediated Selective Hydrogenation of Aromatic Ketones over Pd/C in Ionic Liquids at Room Temperature, ACS Sustainable Chem. Eng. (2021) https://pubs.acs.org/doi/abs/10.1021/acssuschemeng.1c04876
24. Yongfeng Liu, Long Wang, Guijun Bi, et al., Analysis of the combustion mechanism of diesel surrogate fuel under CO2/O2 atmosphere, Fuel, 309, 122223 (2022) https://www.sciencedirect.com/science/article/pii/S0016236121020986

Update History

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