scholarly journals Potential Energy Surfaces of Vinylogous Wolff Rearrangement: NBO Analysis and Molecular Dynamic Simulation

ChemistryOpen ◽  
2021 ◽  
Author(s):  
Hossein Taherpour Nahzomi ◽  
Faten Divsar
Keyword(s):  
Potential Energy ◽  
Molecular Dynamic Simulation ◽  
Molecular Dynamic ◽  
Dynamic Simulation ◽  
Potential Energy Surfaces ◽  
Nbo Analysis ◽  
Wolff Rearrangement ◽  
Energy Surfaces

A Comparison of Kinetostatic and Multibody Dynamics Models for Simulating Protein Structures

2007 ◽  
Author(s):  
Hai-Jun Su ◽  
Jesse Parker ◽  
Kazem Kazerounian ◽  
Horea Ilies
Keyword(s):  
Potential Energy ◽  
Molecular Dynamic Simulation ◽  
Molecular Dynamic ◽  
Dynamic Simulation ◽  
Multibody Dynamics ◽  
Energy State ◽  
Protein Structures ◽  
Rigid Bodies ◽  
Static Compliance ◽  
Protein Molecules

This paper presents an initial comparison of two approaches to energy minimization of protein molecules, namely the Molecular Dynamic Simulation and the Kineto-Static Compliance Method. Both methods are well established and are promising contenders to the seemingly insurmountable task of global optimization in the protein molecules potential energy terrain. The Molecular Dynamic Simulation takes the form of Constrained Multibody Dynamics of interconnected rigid bodies, as implemented at the Virtual Reality Application Center from Iowa State University. The Kineto-Static Compliance Method is implemented in the Protofold Computer package developed in the Mechanical Engineering Department at the University of Connecticut. The simulation results of both methods are compared through the trajectory of potential energy, the Root Mean Square Deviation (RMSD) of the alpha carbons, as well as based on visual observations. The preliminary results indicate that both techniques are very effective in converging the protein structure to a state with significantly less potential energy. At present, the converged solutions for the two methods are, however, different from each other and are very likely different from the global minimum potential energy state.

Synthesis, Characterization and TheoreticalStudies of Nand#39;-(4-methoxybenzylidene)benzenesulfonohydrazide

2021 ◽  
Vol 43 (2) ◽  
pp. 212-212
Author(s):  
H G zin Aslan and L tfiye Aydin H G zin Aslan and L tfiye Aydin
Keyword(s):  
Potential Energy ◽  
Gas Phase ◽  
Vibrational Spectra ◽  
Potential Energy Surfaces ◽  
Solid Phase ◽  
Nbo Analysis ◽  
Basis Set ◽  
Basis Sets ◽  
Stable Conformer ◽  
Energy Surfaces

Nand#39;-(4-methoxybenzylidene)benzenesulfonohydrazide was synthesized and elemental analysis was conducted; IR, Raman, 1H, and 13C NMR spectral data were recorded. The potential energy surfaces (PES) of the Nand#39;-(4-methoxybenzylidene)benzenesulfonohydrazide molecule were obtained by selected degree of torsional freedom, which varied from 0o to 360and#186; in 4and#186; increments. The conformers were optimized by using a (DFT/B3LYP/6-31G(d,p)) basis set in the gas phase. The eleven conformers in the gas phase of the obtained molecule were determined and the most stable conformer (conformer 1) was re-optimized by three different basis sets of 6-31G(d,p), 6-311G(d,p), and LanL2Dz. HOMO-LUMO analyses were performed. NBO analysis was performed to describe the around of intramolecular charge transfer. The vibrational spectra were measured in solid phase IR and detailed analysis of the vibrational spectra of conformer 1 was done; all the bands of the spectra were interpreted by the use of the potential energy distributions (PED) and the molecular electrostatic potential (MEP) was plotted.

Resolving the Quadruple Bonding Conundrum in C2 Using Insights Derived from Excited State Potential Energy Surfaces: A Molecular Orbital Perspective

2019 ◽  
Author(s):  
Ishita Bhattacharjee ◽  
Debashree Ghosh ◽  
Ankan Paul
Keyword(s):  
Excited State ◽  
Potential Energy ◽  
Molecular Orbital ◽  
High Spin ◽  
Potential Energy Surfaces ◽  
Valence Bond ◽  
Deep Minimum ◽  
State Potential ◽  
Energy Surfaces ◽  
Mo Theory

The question of quadruple bonding in C<sub>2</sub> has emerged as a hot button issue, with opinions sharply divided between the practitioners of Valence Bond (VB) and Molecular Orbital (MO) theory. Here, we have systematically studied the Potential Energy Curves (PECs) of low lying high spin sigma states of C<sub>2</sub>, N<sub>2</sub> and Be<sub>2</sub> and HC≡CH using several MO based techniques such as CASSCF, RASSCF and MRCI. The analyses of the PECs for the<sup> 2S+1</sup>Σ<sub>g/u</sub> (with 2S+1=1,3,5,7,9) states of C<sub>2</sub> and comparisons with those of relevant dimers and the respective wavefunctions were conducted. We contend that unlike in the case of N<sub>2</sub> and HC≡CH, the presence of a deep minimum in the <sup>7</sup>Σ state of C<sub>2</sub> and CN<sup>+</sup> suggest a latent quadruple bonding nature in these two dimers. Hence, we have struck a reconciliatory note between the MO and VB approaches. The evidence provided by us can be experimentally verified, thus providing the window so that the narrative can move beyond theoretical conjectures.

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