Shermo: A general code for calculating molecular thermochemistry properties

doi:10.1016/j.comptc.2021.113249

Computational and Theoretical Chemistry

Volume 1200, June 2021, 113249

https://doi.org/10.1016/j.comptc.2021.113249 Get rights and content

Highlights

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Quasi-RRHO thermodynamic model is supported by Shermo.
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Very detailed components of thermodynamic data can be printed by Shermo to gain a deep insight.
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Frequency scaling factors for various components of thermodynamic data can be individually specified in Shermo.
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Variation of various thermodynamic data with respect to temperature and pressure can be easily studied.
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Conformation/configuration weights and weighted thermodynamic data can be obtained by Shermo.

Abstract

In this article, we present a stand-alone, versatile and flexible code named Shermo for calculating various thermochemistry data. This code is compatible with various mainstream quantum chemistry codes, and has many unique advantages: The output information is very clear and easy to read; thermodynamic quantities can be fully decomposed to contributions of various sources to gain a deeper insight; temperature and pressure can be conveniently scanned; two quasi-rigid-rotor harmonic oscillator (quasi-RRHO) models are supported to properly deal with contributions of low frequencies; different frequency scale factors can be simultaneously specified for calculating different thermodynamic quantities; conformation weighted thermodynamic data can be directly evaluated; the code can be easily run and embedded into shell script to automatically process large amount of systems. We hope the Shermo program will bring great convenience to quantum chemists in their daily research. The Shermo code can be freely obtained at http://sobereva.com/soft/shermo.

Graphical abstract

This article introduces our new code named Shermo, which is a general, stand-alone, very easy-to-use, flexible and powerful program for calculating various molecular thermochemistry data. Shermo greatly facilitates quantum chemistry studies of chemical substances. This code is freely available at http://sobereva.com/soft/shermo.

Introduction

Calculation of molecular thermodynamic quantities, such as enthalpy, Gibbs free energy and heat capacity, is one of the most frequently involved problems in daily quantum chemistry research. Due to its importance, almost all popular quantum chemistry packages have their own code to compute thermodynamic data. However, these codes often have various shortcomings and limitations, for example: (1) No better model beyond harmonic approximation for low frequency modes is supported (2) Frequency scale factors for different purposes cannot be separately specified at the same time (3) Data is inconvenient to recalculate at various temperatures and pressures (4) Temperature and pressure cannot be easily scanned to understand how thermodynamic data depend on them (5) Contribution to thermodynamic data from various vibrational modes cannot be individually printed to gain a deeper insight (6) Conformation weighting cannot be directly taken into account (7) Output information of some programs is complicated and thus difficult for beginners to correctly understand. Since these problems have caused great inconveniences to researchers in the field of quantum chemistry, we believe it is very valuable to develop a general, flexible and very easy-to-use code for calculating molecular thermodynamic quantities to address the aforementioned issues. Due to this consideration, a code named Shermo was recently developed by us and will be introduced in this article. Briefly speaking, Shermo is a stand-alone and versatile molecular thermodynamic calculation code based on output file of frequency analysis task of mainstream quantum chemistry programs, including Gaussian [1], ORCA [2], GAMESS-US [3], NWChem [4], as well as a popular first-principle code CP2K [5]. More programs will be supported in the future. Since Shermo makes molecular thermochemistry analysis unprecedentedly convenient, we believe this code will become a new useful member in many quantum chemists' toolbox and will be frequently employed in daily research.

In Section 2, we will describe the model employed by Shermo for calculating thermodynamic data, in Section 3 various features of Shermo will be introduced. A few application examples of using Shermo to study practical chemical problems will be given in Section 4. Finally, in Section 5 we summarize this article.

Section snippets

Calculation model in Shermo

Shermo calculates molecular thermodynamic data mostly based on rigid-rotor harmonic oscillator model under ideal gas assumption, which is also employed in thermochemistry analysis of almost all quantum chemistry codes. This model has been very detailedly documented in the appendix of Shermo manual and also briefly introduced in some books [6], [7], therefore full introduction of this model will not be presented here, only key points will be overviewed.

Shermo is able to calculate all common

Basic characteristics

Shermo is a code fully written in Fortran 90, its precompiled executable files under Windows and Linux platforms, source code files, as well as a very detailed manual can be freely downloaded at http://sobereva.com/soft/shermo. Although executable file for MacOS system is not officially provided, compiling Shermo under MacOS is very straightforward since no any dependent library is needed.

Shermo can be run easily without installation or preparation of any running environment like Python. After

Examples

In this section, we present two simple examples to briefly illustrate use and practical value of the Shermo program, more examples can be found in Shermo manual. Shermo 2.0.5, Gaussian 16. A.03 [1] and ORCA 4.2.1 [2] were utilized in the examples. Molecular structure was plotted by ChimeraX program [27].

Summary

In this article, we introduced our newly developed code named Shermo, which is designed as an unified tool for calculating molecular thermodynamic quantities. The theoretical backgrounds and basic usage of Shermo are briefly described, and practical application examples are given. This user-friendly program makes thermochemistry analysis at different temperatures and pressures as well as with various frequency scale factors significantly more convenient than before. Shermo also brings many

CRediT authorship contribution statement

Tian Lu: Conceptualization, Methodology, Software, Writing - original draft. Qinxue Chen: Validation, Writing - review & editing.

Declaration of Competing Interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

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View full text

Shermo: A general code for calculating molecular thermochemistry properties

Highlights

Abstract

Graphical abstract

Introduction

Section snippets

Calculation model in Shermo

Basic characteristics

Examples

Summary

CRediT authorship contribution statement

Declaration of Competing Interest

Comput. Phys. Commun.

J. Mol. Struct. (THEOCHEM)

Lancet. Infect. Dis

Comput. Phys. Commun.

Software update: the ORCA program system, version 4.0

WIREs Comput. Mol. Sci.

General atomic and molecular electronic structure system

J. Comput. Chem.

NWChem: scalable parallel computational chemistry

WIREs: Comput. Mol. Sci.

CP2K: An electronic structure and molecular dynamics software package - Quickstep: Efficient and accurate electronic structure calculations

J. Chem. Phys.

Essential Statistical Thermodynamics

Computational Thermochemistry: Prediction and Estimation of Molecular Thermodynamics (ACS Symposium Series 677)

Introduction to Computational Chemistry

Computational Thermochemistry: Scale Factor Databases and Scale Factors for Vibrational Frequencies Obtained from Electronic Model Chemistries

J. Chem. Theory Comput.

Frequency and Zero-Point Vibrational Energy Scale Factors for Double-Hybrid Density Functionals (and Other Selected Methods): Can Anharmonic Force Fields Be Avoided?

J. Phys. Chem. A

New Scale Factors for Harmonic Vibrational Frequencies Using the B3LYP Density Functional Method with the Triple-ζ Basis Set 6–311+G(d, p)

J. Phys. Chem. A

Scaling Factors for Obtaining Fundamental Vibrational Frequencies and Zero-Point Energies from HF/6–31G* and MP2/6–31G* Harmonic Frequencies

Isr. J. Chem.

Concerning zero-point vibrational energy corrections to electronic energies

J. Chem. Phys.

Frequency Scale Factors for Some Double-Hybrid Density Functional Theory Procedures: Accurate Thermochemical Components for High-Level Composite Protocols

J. Chem. Theory Comput.

An Evaluation of Harmonic Vibrational Frequency Scale Factors

J. Phys. Chem. A

Harmonic Vibrational Frequencies: Scaling Factors for HF, B3LYP, and MP2 Methods in Combination with Correlation Consistent Basis Sets

J. Phys. Chem. A

Harmonic Vibrational Frequencies: An Evaluation of Hartree−Fock, Møller−Plesset, Quadratic Configuration Interaction, Density Functional Theory, and Semiempirical Scale Factors

J. Phys. Chem.

Use of Solution-Phase Vibrational Frequencies in Continuum Models for the Free Energy of Solvation

J. Phys. Chem. B

Resolution of a Challenge for Solvation Modeling: Calculation of Dicarboxylic Acid Dissociation Constants Using Mixed Discrete-Continuum Solvation Models

J. Phys. Chem. Lett.