Spartan Computational Chemistry Software
This article is organized by China Science Software Network
Operating systems supported by Spartan include Windows (Windows XP, XP64, 32-bit and 64-bit VISTA), Macintosh (OS X 10.4 Tiger and OS X 10.5 Leopard), and Linux (RedHat Enterprise 4 and higher, SLES 9 and higher) version). Spartan can perform all computing tasks on a single machine, and also supports Client-Serve mode, which can remotely submit calculations to Linux servers over the network. Starting with Spartan, Spartan runs on a variety of platforms (Windows, Macintosh, and Linux) that provide a unified graphical interface and computing capabilities. In addition, Spartan can achieve parallel operation of multiple CPUs in a shared memory manner.
Spartan is compiled with the latest version of the Intel compiler, which improves program performance by 15-20% compared to previous releases. Spartan will include the graphical user interface and algorithms provided by Wavefunction, as well as the computing capabilities of the latest version of Q-Chem.
1, solution model
Spartan will provide the Continuum Solvation Model SS(V)PE model and the SM8 (Cramer-Truhlar) model, which will help improve the calculation accuracy of ionic compounds. At present, Spartan can calculate the energy, optimal conformation and reaction transition state of the solution system by HF and DFT methods.
2, RI-CIS (D)
Spartan's new RI-CIS(D) algorithm is used to simulate excited-state molecules. The algorithm can achieve the same computational accuracy as the CIS(D) algorithm, while the computational speed is greatly improved, and the speed is approximately 3 times faster when optimizing the structure. The speed is increased by an order of magnitude when performing energy calculations.
3. New DFT functionals
Spartan will integrate the GGA-PBE functional and the two meta-GGA functionals M05 and M06. In addition, there are a variety of exchange-related functions to choose from when performing DFT calculations, including: Slater-Dirac, Vokso-Wilk-Nusair, Perdew-Zunger, Wigner, Becke88, Gill96, Gilbert-Gill99, Lee-Yang- Parr, Perdew86, GGA91, BMK, EDF1 and EDF2.
4, nuclear magnetic spectrum
When using the B3LYP/6-31G* method to predict the chemical shift of 13C, Spartan uses a new empirical correction formula to improve the accuracy of the calculation. The absolute deviation between the theoretical predicted value and the experimental value can be controlled within 2 ppm. Make Spartan's predictions more reliable. In simulating the 1H nuclear magnetic signal, Spartan uses an empirical method to estimate the HH coupling constant and split of the triple bond, thereby obtaining a 1H nuclear magnetic spectrum and a COSY spectrum that are more similar to the actual spectrum. As long as it provides accurate molecular configuration, Spartan can predict 1H, 13C one-dimensional nuclear magnetic spectra, and 1H two-dimensional COSY and NOSY spectra.
5, generate heat
Spartan improved the T1 algorithm [20]. For neutral molecules consisting of H, C, N, O, F, S, Cl or Br, the T1 algorithm can accurately calculate the heat of formation of such molecules. The principle of T1 algorithm for predicting the heat of molecular formation is similar to that of G3 (MP2). The calculated result is only 2kJ/mol average deviation compared with G3 (MP2), but the calculation speed is several orders of magnitude higher. Using this method, Spartan is able to accurately calculate the thermodynamic properties of organic compounds with a molecular weight of around 500.
The T1 algorithm was used to predict two thousand molecules in the NIST thermochemical database [21] with a predicted average deviation of no more than 9 kJ/mol. Based on this result, the T1 algorithm was subsequently used to construct a thermodynamic database containing approximately 40,000 molecules, which not only covers the thermodynamic data of a large number of organic compounds, but also provides energy for multiple molecules in different conformations. difference.
6. Molecular conformation library
Spartan's molecular conformation library adds more content. The data in the molecular conformation library is taken from the MMFF molecular mechanics for the conformational space search. The three-dimensional structure of the molecule represents the optimal conformation of the compound molecules in the aqueous environment. The molecular conformation library is mainly used for similarity analysis, and the types of compounds covered include common drug molecules (about 500 species), Maybridge drug chemistry catalogue [22] (about 5,000 species), and biochemical small molecules [23] (about 240,000 species). .
7, SMD database (Spartan Molecular Database [24])
The Spartan Molecular Database has been developed to include approximately 150,000 compounds, each of which provides up to 10 different theoretical models: HF/3-21G, HF/6-31G*, HF/6-311++G **, EDF1/6-31G*, B3LYP/6-31G*, B3LYP/6-311G++G**, MP2/6-31G*, MP2/6-311++G**, G3 (MP2) And T1. In addition to the G3 (MP2) and T1 models, all other models contain the following data: Two-dimensional structure of molecules, optimal three-dimensional configuration optimized by MMFF method, gas phase energy, (water) solvation energy, HOMO and LUMO orbital energy , dipole moment, atomic charge of Mulliken and NBO analysis, van der Waals surface and surface electrostatic potential. In addition, about 40,000 compounds have theoretically predicted IR profiles, about 15,000 compounds with nuclear magnetic spectra, and about 1,500 compounds with UV/Vis spectra. The molecular configuration in the G3 (MP2) model is derived from the MP2/6-31G* level calculation, while the molecular configuration in the T1 model is derived from the HF/6-31G* calculations and only generates thermal data. The SMD database can be searched not only by substructures, but also by compound name, molecular weight, molecular formula or isomer.
8. Introduction of IR and NMR spectra
Spartan is able to import experimentally determined IR and NMR spectra (JCAMP format) and compare the spectra to existing theoretical predictions.
9. Transition state and SRD database (Spartan Reaction Database)
Through the automatic transition state guessing of the structural database described above, Spartan's reaction database has been expanded to include hundreds of new organic and metal organic reactions, and can be queried through substructures. The transition state structure in the Spartan reaction database includes at least one of the following models: AM1, PM3, HF/3-21G, and HF/6-31G*, each of which contains a transition state structure and corresponding frequency. analyze data. In addition, Spartan's automatic transition state guessing functionality is still available and has evolved to handle nearly 2,000 types of reactions.
10, enhanced file structure
Spartan can embed various types of data such as experimental data, text and journal documents in the original file structure. The currently supported embedded formats are: Word, PowerPoint, Excel, PDF, and JPG, PNG, TXT, etc.
11, color icon
In addition to being able to display data such as surface electrostatic potential in the calculation results, data can now be analyzed with colored stripes, which contributes to the acidity, reactivity and selectivity of different regions in the three-dimensional structure of the molecule. Differences were further analyzed.
12, electronic density profile
When using electron density simulations to show molecular shape, Spartan now offers a new way of defining surfaces, with the option of using the percentage of total electron density to show the surface shape of the molecule.
13, input and output
Spartan is capable of importing CIF files from single crystal structures and can import or export MOL2 and SDF file formats (including atomic charges).
14. Reaction heat calculation tool
The reaction heat can be calculated in Spartan by simple operation. The thermodynamic data can be defined by the user or read in the SMD database.
15, the substituent building tool
Spartan's substituent building capabilities have been enhanced to allow direct calls to standard templates for programs or user-defined chemical groups for database searches, as well as for calculating heat of reaction.
16, ChemDraw interface
Spartan can automatically convert ChemDraw's 2D structure into a 3D structure, or edit the ChemDraw formula directly in Spartan's table file.
17, enhanced list and drawing capabilities
Vector data can be stored in Spartan's table file, and graphics can be drawn with this type of data.
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