Macromodel 9

Manufactured by Schrödinger

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MacroModel 9.1 is a software tool for computational chemistry and molecular modeling. It is designed for the simulation and analysis of molecular structures and properties. MacroModel 9.1 provides a comprehensive set of algorithms and tools for performing molecular mechanics calculations, conformational searches, and other related tasks.

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Lab products found in correlation

Maestro, by Schrödinger (3 mentions) Matlab 2013a, by MathWorks (1 mentions) Vina 1, by AutoDock (1 mentions)

11 protocols using macromodel 9

Quantum Chemical Study of Guanidinium Hydrates

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Low-energy structures were identified using conformational searches consisting of 1000 individual steps using Macromodel 9.1 (Schrödinger Inc., Portland, OR, U.S.A.) using the OPLS2005 force field. A single search was done for small clusters, whereas up to five conformational searches starting with different initial structures were done for the larger clusters. Between two and five low-energy structures were reoptimized at the B3LYP/6-31++G** level of theory, followed by a harmonic frequency analysis. The water binding energy of H₂O to Gdm(H₂O)⁺ was obtained from various low-energy isomeric structures of Gdm(H₂O)₂⁺, correcting for the basis set superposition error using the counterpoise method. Q-Chem 4.0 (Q-Chem, Inc., Pittsburgh, PA, U.S.A.)^{51 (link)} was used for all quantum chemical computations. Relative Gibbs free energies as a function of temperature were determined from the rotational constants, unscaled harmonic frequencies and electronic ground state energies using an in-house Matlab 2013a (The MathWorks, Natick, MA, U.S.A.) routine.

Heiles S., Cooper R.J., DiTucci M.J, & Williams E.R. (2015). Hydration of guanidinium depends on its local environment †Electronic supplementary information (ESI) available: Full citation for , experimental details and reproducibility of the IRPD measurements, comparison between experimental IRPD spectra with harmonic IR spectra of energetic low lying isomers for [Gdm(H2O)n]+, n = 6–9, structures of the energetic low lying isomers of [Gdm(H2O)n]+, n = 6–9, and representative structures of [Gdm(H2O)n]+, [Na(H2O)n]+, [TMA(H2O)n]+, with n = 20 and 40. Quantitative comparison of the spectra for Gdm+, Na+ and TMA+ with n = 20–100 in the HB stretching region. See DOI: 10.1039/c5sc00618j Click here for additional data file.. Chemical Science, 6(6), 3420-3429.

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Conformational Analysis and ECD Simulation

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3D structures of isolated compounds were drawn in Maestro (Schrödinger. LLC, New York, NY, USA) and subjected to conformational analysis using MacroModel 9.1 (Schrödinger. LLC, New York, NY, USA) and OPLS-3 as a force field in H₂O. Geometrical optimization and energy calculations of conformers occurring in the energy window of 5 kcal mol⁻¹ were performed by implementing DFT/6-31G(d) in the gas phase for compound 29 or DFT/6-31G(d,p)/IEFPCM/methanol for compound 26 and 29. Subsequently, ECD spectra of optimized compounds were simulated by using TD-DFT/B3LYP/6-31G(d,p)/IEFPCM/methanol (compound 15) or TD-DFT/cam-B3LYP/6-31G(d,p)/IEFPCM/methanol (compound 26 and 29). ECD spectra obtained (with a half-band of 0.2–0.3 eV) were Boltzmann-averaged, and a UV correction of +10 to +25 nm was applied to compare them with experimental spectra obtained in methanol.

Pecio Ł., Alilou M., Kozachok S., Erdogan Orhan I., Eren G., Senol Deniz F.S., Stuppner H, & Oleszek W. (2019). Yuccalechins A–C from the Yucca schidigera Roezl ex Ortgies Bark: Elucidation of the Relative and Absolute Configurations of Three New Spirobiflavonoids and Their Cholinesterase Inhibitory Activities. Molecules, 24(22), 4162.

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Conformational Analysis of E/Z Isomers

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Conformational analyses for E/Z isomer of 1, 2, and 3 were performed with MacroModel 9.1 software (Schrödinger LLC, New York) using the Optimized Potential for Liquid Simulations 3 (OPLS3) force field in H₂O. Conformers occurring within a 1.0 kcal/mol energy window from the global minimum were chosen for geometrical optimization and energy calculation using DFT/cam-B3LYP/6-31G** was conducted in MeOH using the SCRF method, with the CPCM model with the Gaussian 09 program [11 ]. The vibrational analysis was done at the same level to confirm minima. The ECD spectra calculated using TD-DFT/cam-B3LYP/6-31G** in MeOH. The ECD curves were constructed based on rotatory strength dipole velocity (R_vel), and dipole length (R_len) were calculated with a half-band of 0.25 eV using SpecDis v1.61 [12 (link)].

Saldanha L.L., Quintiliano Delgado A., Marcourt L., de Paula Camaforte N.A., Ponce Vareda P.M., Nejad Ebrahimi S., Vilegas W., Dokkedal A.L., Queiroz E.F., Wolfender J.L, & Bosqueiro J.R. (2021). Hypoglycemic active principles from the leaves of Bauhinia holophylla: Comprehensive phytochemical characterization and in vivo activity profile. PLoS ONE, 16(9), e0258016.

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Conformational Analysis and ECD Spectra Simulation

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3D structures of isolated compounds were drawn in Maestro (Schrödinger. LLC, New York, NY, USA) and subjected to conformational analysis using MacroModel 9.1 (Schrödinger. LLC and OPLS-3 as force field in water by implementation of Monte Carlo method. Geometrical optimization and energy calculation of conformers occurring in an energy window of 2 Kcal·mol⁻¹ were done by implementation of DFT/wb97xd/6-31+g(d,p)/SMD in water phase by using Gaussian 16 (Revision A.03, Gaussian, Wallingford, CT, USA 2016). In case of compound 11, the same method used without diffusion parameter. Subsequently, ECD spectra of optimized compounds were simulated by using TD-DFT/M062x/6-31+G(d,p)/SMD/water. Obtained ECD spectra (with half-band of 0.25–0.3 eV and UV shift of 8–20 nm were Boltzmann averaged and scaled spectra compared with experimental spectra obtained in water.

Orfanoudaki M., Hartmann A., Alilou M., Gelbrich T., Planchenault P., Derbré S., Schinkovitz A., Richomme P., Hensel A, & Ganzera M. (2019). Absolute Configuration of Mycosporine-Like Amino Acids, Their Wound Healing Properties and In Vitro Anti-Aging Effects. Marine Drugs, 18(1), 35.

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Conformational Analysis and NMR Shift Calculations

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Intended compounds were subjected to conformational analysis by MacroModel 9.1 (Schrödinger. LLC, New York, NY, USA) using an OPLS-3 force field in H₂O. Geometrical optimization of using DFT/6-31G(d) in the gas phase (compound 29) or DFT/6-31G(d,p)/IEFPCM/methanol (compound 15 and 26) in Gaussian 16 was performed [89 ]. Subsequently, they were submitted to NMR chemical shift calculations using the gauge-independent atomic orbitals (GIAOs) method in rmpw1pw91/6-311G+(d,p)/IEFPCM/methanol. The shift tensors obtained were further adjusted to chemical shifts by using TMS proton and carbon chemical shifts, which were calculated using the same method. All chemical shifts were Boltzmann-averaged, and unscaled chemical shifts were used for the DP4+ probability calculation based on the method and the interactive Excel sheet published by Grimblat et al. [51 (link)]

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Conformational Analysis of Compounds

Cited 1 time

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3D structures of isolated compounds were drawn in Maestro (Schrödinger. LLC, New York, NY, USA) and subjected to conformational analysis using MacroModel 9.1 (Schrödinger. LLC) and OPLS-3 as a force field in water by the implementation of the Monte Carlo method. For the geometrical optimization and energy calculation of conformers occurring in an energy window of 2 Kcal·mol⁻¹, the same methods as those in our previous publication on MAAs were utilized [30 (link)]. Briefly, geometry optimizations were conducted at DFT/wb97xd/6−31 + g(d,p) in the gas phase, followed by the calculation of ECD spectra at the TD--DFT/wb97xd/6−31 + g(d,p) level using SMD (Solvation Model Density) in water, using Gaussian 16 (Revision A.03, Gaussian, Wallingford, CT, USA 2016). The obtained ECD spectra (with a half-band of 0.25–0.3 eV and a UV shift of 8–20 nm) were Boltzmann-averaged and scaled spectra compared with the experimental spectra obtained in water.

Orfanoudaki M., Alilou M., Hartmann A., Mayr J., Karsten U., Nguyen-Ngoc H, & Ganzera M. (2023). Isolation and Structure Elucidation of Novel Mycosporine-like Amino Acids from the Two Intertidal Red Macroalgae Bostrychia scorpioides and Catenella caespitosa. Marine Drugs, 21(10), 543.

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Conformational Analysis and ECD Spectra

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The 3D structure of selected compounds was subjected to Macro-Model 9.1 (Schrödinger. LLC, USA) to perform conformational analysis (parameters: MMFF force field; gas phase; maximum iterations: 10,000; maximum number of steps: 10,000). Conformers occurring in an energy window of 5 kcal/mol were subjected to geometry optimization and energy calculation using first DFT/B3LYP/6-31G (d) in the gas phase and then DFT/B3LYP/6-31G+(d,p)/CPCM in acetonitrile with Gaussian 16 (Frisch et al., 2016) . No imaginary frequencies were observed for the optimized structures. Calculation of excitation energy (nm), rotatory strength, dipole velocity (R vel ) and dipole length (R len ) were performed by TD-DFT/cam-B3LYP/6-31G+(d,p)/CPCM (acetonitrile) for 1-3 and 8, and TD-DFT/B3LYP/6-31G+(d,p)/CPCM (acetonitrile) for 4 and 5. ECD curves were extracted by SpecDis v.1.7 software with a half-band of 0.2-0.3 eV (Bruhn et al., 2017) . The Boltzmann-averaged ECD spectra were shifted ±25 nm in the UV range, and then compared with the experimental results.

Nguyen-Ngoc H., Alilou M., Derbré S., Blanchard P., Pham G.N., Nghiem D.T., Richomme P., Stuppner H, & Ganzera M. (2022). Chemical constituents of Antidesma bunius aerial parts and the anti-AGEs activity of selected compounds. Phytochemistry, 202.

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EV71 Protease Structure Preparation

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The EV71 protease X-ray structure (PDB accession no. 3SJO) was prepared with the Protein Preparation Wizard in Maestro 9.3 (Schrödinger, USA) using standard settings. This included the addition of hydrogen atoms, bond assignments, removal of water molecules >7 Å from the ligand, protonation state assignment, optimization of the hydrogen bond network and restrained minimization using the OPLS2005 force field14 . The co-crystallized, covalently-bound inhibitor was used as a template for modelling the conformation and orientation for all inhibitors listed in this paper. The inhibitor-protein complex was finally energy-minimized using Macromodel 9.9 (Schrödinger, USA). All residues >9 Å from the ligand were constrained before the complex was subjected to 500 steps of Conjugate Gradient energy minimization using the OPLS2005 force field15 and GB/SA continuum solvation method16 . Model visualization was done using Maestro v 9.3.

Tan Y.W., Ang M.J., Lau Q.Y., Poulsen A., Ng F.M., Then S.W., Peng J., Hill J., Hong W.J., Chia C.S, & Chu J.J. (2016). Antiviral activities of peptide-based covalent inhibitors of the Enterovirus 71 3C protease. Scientific Reports, 6, 33663.

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Computational Docking of Compound 1

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Computational docking studies were based on docking of 1 into the active site cavities using AutoDock Vina 1.1.1 [28] (link) followed by conformational searching for optimal orientations from docking to more rigorously explore the active site using Schrodinger MacroModel 9.9 [29] . For L. leichmannii NDT, PDB structure 1F8Y [9] (link) with bound 5-methyl-2′-deoxypseudouridine (5-Me-dψUrd; 2.4 Å resolution) was used as a template, and for E. coli PNP, the template was PDB structure 1PK9 [10] (link) with bound 2-fluoroadenosine (1.9 Å resolution). Phosphate and protonated Asp 204 were retained during the calculation. Compound 1 in its neutral form was subjected to the MacroModel 9.5.212 [30] minimization using OPLS 2005 (Optimized Potentials for Liquid Simulations) force field with water solvation treatment and a convergence threshold gradient of 0.01 [31] (link). Ligand diameter midpoint was set to a box of 6×6×6 Å encompassing the active site for receptor grid generation. No ligand constraints were set.

Ye W., Paul D., Gao L., Seckute J., Sangaiah R., Jayaraj K., Zhang Z., Kaminski P.A., Ealick S.E., Gold A, & Ball L.M. (2014). Ethenoguanines Undergo Glycosylation by Nucleoside 2′-Deoxyribosyltransferases at Non-Natural Sites. PLoS ONE, 9(12), e115082.

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Conformational Search and ECD Calculation

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Torsional sampling (MCMM) conformational searches using MMFF94S force field were carried out by the means of conformational search module in Macro model 9.9.223 software (Schrodinger, http://www.schrodinger.com/MacroModel), applying an energy window of 21 kJ/mol (5.02 kcal/mol) for saving structures. The dominant conformers with over 1% Boltzmann population were used for re-optimization and the following TDDFT-ECD calculation. The re-optimizations and the TDDFT-ECD calculations were performed with Gaussian 09 (Gaussian, http://www.Gaussian.com) at the same B3LYP/6-311G(d,p) level with the IEFPCM solvent model for acetonitrile. Finally, the SpecDis 1.62 software (Bruhn et al. 2013 (link)) was used to obtain the calculated ECD spectrum and visualize the results.

Li S.W., Yu D.D., Su M.Z., Yao L.G., Wang H., Liu X, & Guo Y.W. (2023). Ocellatuspyrones A‒G, new antibacterial polypropionates from the Chinese mollusk Placobranchus ocellatus. Marine Life Science & Technology, 5(3), 373-386.

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