gaussian 09 program package (Molecular Dynamics Inc)

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Molecular Dynamics Inc gaussian 09 program package
Gaussian 09 Program Package, supplied by Molecular Dynamics Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/09+program+package/gaussian+09/pm37676850-143-56-94
Average 90 stars, based on 1 article reviews

gaussian 09 program package - by Bioz Stars, 2026-10

90/100 stars

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Solvent:

Article Title: Visible-Light-Driven [2 + 2] Photocycloaddition for Constructing Dimers of N , N '-Diacyl-1,4-dihydropyrazines: Experimental and Theoretical Investigation.
Article Snippet: In this study, the visible-light-driven [2 + 2] photocycloaddition of 1,4-dihydropyrazines in solution was reported.. The N,N′-diacyl-1,4-dihydropyrazines with different substituents showed completely different reactivity under the irradiation of a 430 nm blue light-emitting diode (LED) lamp.. N,N′-Diacetyl-1,4-dihydropyrazine and N,N′-dipropionyl-1,4-dihydropyrazine were the only compounds capable of undergoing a [2 + 2] photocycloaddition reaction, yielding syn-dimers and cage-dimers (known as 3,6,9,12-tetraazatetraasteranes) with overall yields of 76 and 83%, correspondingly.

Generated:

Software:

Article Title: Hybridizing carbonate and ether at molecular scales for high-energy and high-safety lithium metal batteries
Article Snippet: .. All complexes were directly extracted from the corresponding molecular dynamics (MD) simulation results and optimized using the Gaussian 09 software package at the 3LYP/6-311++G(d) level. ..

other:

Article Title: Molecular Modeling Studies of Hapten Design and Antibody Recognition for Sensitive Detection of Vitamin K3 by Strip Biosensor.
Article Snippet: Computer-aided molecular design techniques are used to analyze vitamin K3 (VK3) and VK3-hapten.. Based on VK3-hapten, a specific monoclonal antibody (mAb) against VK3 is prepared with a sensitivity (IC50) of 0.49 ng mL −1.. The recombinant technology is used to investigate the molecular docking mechanism of mAb recognition of VK3.

Article Title: Supplementary Information: Collagen breaks at weak sacrificial bonds taming its mechanoradicals
Article Snippet: Structure design and QM visualizations GaussView 5.0.9 [1] QM calculations Gaussian 09, revision D.01 [2] MD simulations GROMACS, versions 2018 and 2020 [3] Bond rupture simulations KIMMDY [4] Visualization of molecular structures VMD [5] Data analysis Python 3.8.10, Seaborn 0.11.2 [6] PYD Pyridinoline DPD Deoxypyridinoline HLKNL Hydroxylysino-keto-norleucine deH-LNL Dehydro-lysino-norleucine DOPA Dihydroxy-phenylalanines BDE Bond dissociation energy RSE Radical stabilization energy QM Quantum mechanics or quantum mechanical DFT Density functional theory BMK Boese-Martin for Kinetics MD Molecular dynamics KIMMDY Hybrid Kinetic Monte Carlo/Molecular Dynamics Simulations MS Mass spectrometry EPR Electron paramagnetic resonance

Article Title: Reversible Control of Native GluN2B-Containing NMDA Receptors with Visible Light.
Article Snippet: The geometry of OptoNAM-3 was then optimized at the M06-2X/6-31+G(d,p) level of geometry in a PCM of water with Gaussian09 A.02.92 The RESP charges were then obtained at the HF/6-31G(d) level of geometry with Gaussian09 C.01, and acpype93 and antechamber94 were used to get the GAFF2 force field parameters for OptoNAM3.95 Finally, the force field was modified with an improved description of the azo moiety.96 Molecular dynamics (MD) simulations were performed with Gromacs97−99 with the Amber14SB force field to describe the protein atoms and ions100 and the TIP3P description of water.101 After solvation in a rhombic odecahedron box with at least 8 Å between the solute atoms and the edges of the box, the system was neutralized with 18 sodium ions.

Functional Assay:

Article Title: Multi-scale molecular dynamics simulations of enhanced energy transfer in organic molecules under strong coupling
Article Snippet: Because no experimental data is available for the Rhodamine model used here, we instead verified the validity of our model by recomputing the electronic energies along an excited-state molecular dynamics trajectory of a single Rhodamine molecule in water at higher levels of theory: • Time-dependent density functional theory (TDA-DFT)25 within the Tamm-Dancoff approx- imation26 with the CAM-B3LYP functional,27,28 in combination with the 6-31G(d) basis set;29 • Complete Active Space Self Consistent Field (CASSCF) with 12 electrons in 12 π orbitals,30 averaged over the first two states (SA2) and expanded in a cc-pVDZ basis set;31 • Extended Multi-Configuration Quasi-Degenerate Perturbation Theory to second order (xMC- QDPT2),32 based on the SA2-CASSCF(12,12)/cc-pVDZ reference. .. The TD-DFT calculations were carried out with the Gaussian09 program,33 while the CASSCF and xMCQDPT2 calculations were performed with Firefly.34 Supplementary Figure 3: Panel a: potential energies in the electronic ground (S0, continuous lines) and excited state (S1, dashed lines) as a function of time in an excited-state Molecular Dynamics (MD) trajectory of a single Rhodamine at the Configuration Interaction restricted to single excitations and the 3-21G basis set (CIS/3-21G, green) level of theory, re-evaluated at the Extended MultiConfiguration Quasi-Degenerate Perturbation Theory to second order, based on a two-state-averaged Complete Active Space Self Consistent Field reference and the correlation-consistent polarizable valence-only double-zeta basis set (xMCQDPT2//SA2-CASSCF(12,12)/cc-pVDZ, black), two-stateaveraged Complete Active Space Self Consistent Field with the correlation-consistent polarizable valence-only double-zeta basis set (SA2-CASSCF(12,12)/cc-pVDZ, red), and time-dependent density functional theory within the Tamm-Dancoff approximation for the CAM-B3LYP functional and the 6-31G(d) basis set (TDA-CAM-B3LYP/6-31G(d), blue) levels of theory. ..

Chick Chorioallantoic Membrane Assay:

Membrane:

Article Title: Shape-Selective Molecular Separations Enabled by Rigid and Interconnected Confinements Engineered in Conjugated Microporous Polymer Membranes.
Article Snippet: .. Molecular Dynamics Simulations: Quantum Chemical Calculations: The monomer, dimer, and trimer of TCTA, and the model structure of PEG1000 and single pore of TCTA membrane were optimized with M06-2X method by the Gaussian 09 package[33] with a compound basis set; the 6- 311+G(d) basis set was used for all bridgehead C and N atoms and the 6-31G(d) basis set was employed for the H and non-bridgehead C atoms. ..

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