Spartan 10

Manufactured by Wavefunction

Sourced in United States

Spartan'10 is a computational chemistry software package that provides a comprehensive suite of tools for molecular modeling and simulation. The core function of Spartan'10 is to assist in the analysis and prediction of molecular properties and behavior through the use of various quantum chemical methods and computational algorithms.

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Lab products found in correlation

Gaussview 06, by Wavefunction (2 mentions) Ptc 423s 15, by Jasco (1 mentions) J 815 spectrometer, by Jasco (1 mentions) Tools 1, by AutoDock (1 mentions) Tools, by AutoDock (1 mentions) Vina 4, by AutoDock (1 mentions) Pymol molecular graphics system version 1, by Schrödinger (1 mentions)

Spelling variants of this product

Spartan '10 Version 1.1.0 (4 citations) Spartan 10 V.1.1.0 (4 citations) Spartan 10 for Windows (3 citations)

33 protocols using spartan 10

Conformational Analysis and Quantum Chemical Calculations of Diterpenes

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The molecules were submitted to the default systematic conformational analysis procedure, available in the SPARTAN’10 software package (Wavefunction Inc., Irvine, CA, USA, 2000), using molecular mechanics and the MMFF force field and the most stable conformers were used for further calculations.
In order to evaluate the stereoelectronic properties, all structures were submitted to a full geometry optimization process using the Recife Model 1 (RM1) semi-empirical method, and finally the stereoelectronic properties were calculated with Hartree-Fock method using the basis set 6-311G* available in SPARTAN’10. Then, we calculated the electronic properties including Highest Occupied Molecular Orbital (HOMO) and Lowest Unoccupied Molecular Orbital (LUMO) energy, density maps, orbital coefficients distribution, molecular dipole moment and molecular electrostatic potential maps (MEP) of each compound.
Further, major ionized microspecies, water solubility, and number of hydrogen bond acceptors and donors were carried out with Chem Axon Calculator server (Copyright © 1998–2017 ChemAxon Ltd., Budapest, Hungary). All these structural features and calculated properties were used to correlate with the thrombin catalytic activity of these three diterpenes described in the literature by Moura et al., 2014 [2 (link)].

Pereira R.C., Lourenço A.L., Terra L., Abreu P.A., Laneuville Teixeira V, & Castro H.C. (2017). Marine Diterpenes: Molecular Modeling of Thrombin Inhibitors with Potential Biotechnological Application as an Antithrombotic. Marine Drugs, 15(3), 79.

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Conformational Analysis and CD Spectra

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Merck molecular force field and density functional theory (DFT) calculations were run with Spartan'10 (Wavefunction, Irvine, CA, USA 2010), with standard parameters and convergence criteria. Time-dependent DFT (TDDFT) calculations were run with Gaussian'09 (Gaussian, Wallingford, CT, USA), 14 with grids and convergence criteria. Conformational searches were run with the Monte Carlo algorithm implemented in Spartan'10 using Merck molecular force field. All structures thus obtained were optimized with DFT method using first B3LYP functional and 6-31G(d) basis set, and then the same functional with 6-311+G(d,p) basis set. 15 The above procedure afforded four minima, of which only the first two had sizable Boltzmann population (40.5%) at 300 K. TDDFT calculations were run using various functionals (B3LYP, CAM-B3LYP, PBE0, M06) and basis sets (TZVP, aug-TZVP). 15 The CAM-B3LYP/TZVP combination was employed for the final calculations, including 40 excited states (roots), and using the Polarizable Continuum solvent Model in its Integral Equation Formalism (IEF-PCM) for acetonitrile. 15 CD spectra were generated by applying a Gaussian band shape with 0.3 eV exponential half-width, from dipole-length rotational strengths. The difference with dipole-velocity values was checked to be minimal for all relevant transitions.

Cimmino A., Pescitelli G., Berestetskiy A., Dalinova A., Krivorotov D., Tuzi A, & Evidente A. (2016). Biological evaluation and determination of the absolute configuration of chloromonilicin, a strong antimicrobial metabolite isolated from Alternaria sonchi. The Journal of antibiotics, 69(1).

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HIV Protease Docking and Refinement

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The docking runs were carried out on the reference pdb structure 3NU3, complex of wild type HIV protease with amprenavir. The ligand and water molecules were removed from the structure, while hydrogens and charges were added with MGLTools. The inhibitors molecules were prepared and optimized with the MMFF forcefield as implemented in Spartan 10 (Wave Function Inc.). The size of the docking grid was 65 x 50 x 40 Ǻ, comprising the whole protein. MD refinement of the complexes was carried out at 300 °K in the NTV ensemble with 500 ps runs.

Tramutola F., Armentano M.F., Berti F., Chiummiento L., Lupattelli P., D'Orsi R., Miglionico R., Milella L., Bisaccia F, & Funicello M. (2019). New heteroaryl carbamates: Synthesis and biological screening in vitro and in mammalian cells of wild-type and mutant HIV-protease inhibitors. Bioorganic & medicinal chemistry, 27(9).

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Chiral Compound Optical Activity Analysis

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The optical activity of chiral compounds was determined using a Perkin-Elmer 241 MS polarimeter.
The electronic circular dichroism (ECD) spectra of compounds (+)-1 and (+)-3 were recorded on a JASCO J-815 spectrometer equipped with a JASCO PTC-423S/15 temperature controller at 20 °C. Each compound was measured using a scanning speed of 50 nm/min. Each measurement was repeated five times, and the five replicates were averaged. Applying the same parameters, the solvent background was recorded and subtracted from the sample measurement.
For the simulation of compound 1 and 3, a conformational analysis was first performed (Spartan’10; Wavefunction, Inc., Irvine, CA, USA, 2009), followed by geometry refinement at DFT level. Even though both compounds are fairly rigid, several conformers in the range of 4.5 kcal/mol above the energetically lowest conformer were identified from the respective set of the conformer distribution. After calculation of the electronic excitations using time-dependent DFT and Boltzmann weighting, the ECD spectra were simulated and compared to the experimental spectra (see supporting information for computational details). All quantum mechanical calculations were performed with Gaussian 16 (Frisch et al. 2019 ), while the spectra comparison was conducted using SpecDis (Bruhn et al 2017 ).

Kiefer A., Arnholdt M., Grimm V., Geske L., Groß J., Vierengel N., Opatz T, & Erkel G. (2023). Structure elucidation and biological activities of perylenequinones from an Alternaria species. Mycotoxin Research, 39(3), 303-316.

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Quantum Computation for Compound Analysis

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The quantum mechanical computation of the compounds was performed by Spartan 10' (Wavefunction Inc., version 1.1.0, 2011, Irvine, CA, USA) software package. Their geometries were initially refined by the mechanical MMFF94 method and further optimized by the semi-empirical PM6 method. The final reoptimization and computation of the compounds were performed by DFT-B3LYP functional with 6-31+G (d) basis set. The geometries of the compounds were globally optimized without symmetry constraints and their stationary points were confirmed by vibrational frequency analysis. The electron affinity (EA) of the compounds was assessed as the Gibbs' energy difference between their optimized neutral and anion free radical states (at 298.15 K). The cDFT-based global reactivity indices of the compounds were calculated applying their LUMO and HOMO eigenvalues, and their regional electrophilic reactivity was assessed in terms of the electrophilic Fukui function (f⁺) values by using the single-point FMO approach (Contreras et al., 1999[16 ]) employing the PYTHON scripting language.

Peciukaityte-Alksne M., Šarlauskas J., Miseviciene L., Maroziene A., Cenas N., Krikštopaitis K., Staniulyte Z, & Anusevicius Ž. (2017). Flavoenzyme-mediated reduction reactions and antitumor activity of nitrogen-containing tetracyclic ortho-quinone compounds and their nitrated derivatives. EXCLI Journal, 16, 663-678.

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Conformational Analysis and ECD Spectra of Compounds

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Preliminary conformational analyses of 1 and 2 were performed with Merck Molecular Force Field (MMFF) by Spartan 10 (Wavefunction, Irvine, CA, USA). The two lowest energy conformers of 1 and 2 were geometrically optimized with the B3LYP/6-31G(d,p) level of density functional theory (DFT) in methanol using Gaussian 16 (Expanding the limits of computational chemistry, Wallingford, CT, USA). The computer-assisted ECD calculation was carried out with the B3LYP/6-31G(d,p) level of time-dependent density functional theory (TDDFT). The calculated ECD spectra of 1 and 2 were obtained via visualization of SpecDis version 1.71 (SpecDis, Berlin, Germany) in combination with the calculated ECD spectra of each conformer on the basis of Boltzmann distribution theory and their relative Gibbs free energy.

Lee J., Lee J., Kim G.J., Yang I., Wang W., Nam J.W., Choi H., Nam S.J, & Kang H. (2019). Mycousfurans A and B, Antibacterial Usnic Acid Congeners from the Fungus Mycosphaerella sp., Isolated from a Marine Sediment. Marine Drugs, 17(7), 422.

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Computational Modeling of Samoamide A

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Computational molecular modeling of the energy minimized structure of samoamide A (1) was performed using Spartan’10 (Wavefunction, Inc., Irvine, CA, USA). The resultant molecular coordinates were imported into the Molecular Operating Environment software (MOE; Chemical Computing Group, Montreal, Quebec, Canada) for conformation searching using default settings and energy calculation using OPLS-AA force fields to generate a small 29 molecule conformer library. MOE was also used to import the PDB crystallographic structure of human DPP4 (PDB code 4N8D), to determine tentative interaction sites using the site finder method (Receptor Atoms). The induced fit method was used to dock the conformer library with the 4N8D structure, annotate surface maps (VDW method), and highlight specific ligand-receptor interactions using standard protocols. All computational calculations were completed using an HP Elitebook 850 G1 laptop (Hewlett Packard, Palo Alto, CA, USA) running 64-bit Windows 7 OS, containing 8 GB ram, and with an Intel i7-4600U CPU @ 2.1 GHz.

Naman C.B., Rattan R., Nikoulina S.E., Lee J., Miller B.W., Moss N.A., Armstrong L., Boudreau P.D., Debonsi H.M., Valeriote F.A., Dorrestein P.C, & Gerwick W.H. (2017). Integrating Molecular Networking and Biological Assays to Target the Isolation of a Cytotoxic Cyclic Octapeptide, Samoamide A, from an American Samoan Marine Cyanobacterium. Journal of natural products, 80(3), 625-633.

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Molecular Modeling of Carbohydrazide Derivatives

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Molecular modeling was performed using SPARTAN´10 software (Wavefunction Inc. Irvine, CA, 2000) . Three dimensional molecular structure of the carbohydrazide derivatives (4a, 4b and 4c) (non-ionized state according with the predominant molecular population in the physiological environment) and benznidazole (ionized state) were prepared and submitted to the calculations simulating the vacuum without any geometric constraint (Bello et al. 2011) . Values of LogP and volume of the compounds were obtained using the ChemAxon software available at http://www.chemicalize.org, as well as the predominant molecular states of the compounds in the physiological environment (Funk and Krise 2012, Bello et al. 2015) .
Conformational analysis for the selection of the lowest energy conformer was performed by the molecular mechanics method using force field MMFF (Merck Molecular Force Field) (Halgren 1996) . Thereafter, conformers were subjected to geometry optimization using the semi-empirical method RM1 (Rocha et al. 2006 ). The conformer with the lowest energy was subjected to single point calculation by the quantum mechanics Hartree-Fock method, with 6-31G* basis set. Subsequently, in order to observe the stereoelectronics displacement caused by substituents at C-6 of 1H-pyrazolo[3,4-b] pyridine system, the Electrostatic Potential Maps (EPM) and dipole moment were calculated.

Salvador R.R., Bello M.L., Barreto I.R., Vera M.A., Muri E.M., Albuquerque S, & Dias L.R. (2016). New carbohydrazide derivatives of 1H-pyrazolo[3,4-b]pyridine and trypanocidal activity. Anais da Academia Brasileira de Ciencias, 88(4).

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Conformational Analysis of Enantiomers

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Conformational analysis of the enantiomers of 1–5 established by ROESY analyses were carried out via Monte Carlo searching with the MMFF94s molecular mechanics force field using the Spartan 10 software (Wavefunction Inc., Irvine, CA, USA). Compounds 1–5 gave 3, 5, 4, 4, 3 geometries, respectively, which possessed relative energies within 10 kcal/mol. These geometries were optimized by DFT at the B3LYP/6-31G (d) level (methanol as the solvent) with the Gaussian 09 program (Gaussian Inc., Wallingford, CT, USA). The B3LYP/6-31G(d)-optimized conformers were then optimized at the wB97XD/DGDZVP level (methanol as the solvent). ECD computations for all wB97XD/DGDZVP-optimized conformers were carried out at the CAM-B3LYP/DGDZVP level (methanol as the solvent). Boltzmann statistics were performed for ECD simulations with a standard deviation of σ 0.3 eV. Then, the ECD spectra were simulated by the Gaussum 2.25 program [32 (link)] and generated according to the Boltzmann distribution theory and their relative Gibbs free energy (ΔG).

Jin J., Yang X., Liu T., Xiao H., Wang G., Zhou M., Liu F., Zhang Y., Liu D., Chen M., Cheng W., Yang D, & Ma M. (2018). Fluostatins M–Q Featuring a 6-5-6-6 Ring Skeleton and High Oxidized A-Rings from Marine Streptomyces sp. PKU-MA00045. Marine Drugs, 16(3), 87.

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Quantum Chemical Modeling of Nucleoside Analogs

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Spartan10 (Wavefunction) was used for all ab initio calculations. Model systems of S-sugar or N-sugar 2’-methoxy and 2’-methylseleno uracil nucleosides were built in Spartan and minimized to a DFT RB3LYP / HF6-31G(d) level as follows: MMFF → HF 3-21 → HF 6-31G(d) → DFT RB3LYP / HF 6-31G(d). Single point energy calculations at the same DFT level were then performed on the minimized structures. All minimizations and single point energy calculations were conducted using the SM8 solvation model for water and subsequently replicated in vacuum (Marenich, Olson, Kelly, Cramer, & Truhlar, 2007 (link)).

Thompson R.A., Spring A.M., Sheng J., Huang Z, & Germann M.W. (2014). The Importance of Fitting In: Conformational Preference of Selenium 2’ Modifications in Nucleosides and Helical Structures. Journal of biomolecular structure & dynamics, 33(2), 289-297.

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