Integrating Molecular Modeling into the Inorganic Chemistry Laboratory

Montgomery, Craig D.

doi:10.1021/ed078p840

Cited by 15 publications

(17 citation statements)

References 3 publications

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“…Molecular mechanics methods are based on moving equations, established under the Isaac Newton laws, and mainly based on the Born–Oppenheimer approximation, which suggest that core and electron can be treated separately, because of the core mass is larger than the electron mass 31…”

Section: Methodsmentioning

confidence: 99%

“…based on the Born-Oppenheimer approximation, which suggest that core and electron can be treated separately, because of the core mass is larger than the electron mass. [31] The MM calculations also called as force field calculations use a number of empirically derived equations to the surface Born-Oppenheimer, whose mathematical formalism is based on a classical mechanical model of molecular structure. [32] In this method, the atoms electron and core were not explicitly included on calculations, because the classic mechanics do not describe the behavior of very small particles, as the electron and core of atoms and molecules.…”

Section: Global Interaction Energy Calculationsmentioning

confidence: 99%

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Theoretical and practical study of the cefoxitin‐Escherichia coli PBP5 complex interaction by molecular dynamics to obtain computational prototype of antimicrobial susceptibility to Gram negative bacteria

et al. 2020

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The Penicillin Binding Proteins (PBPs) are important biological target for new antibacterial drugs development. This study focused on molecular interaction between cefoxitin and the Escherichia coli PBP5 by molecular dynamics (MD) by using hybrid quantum mechanics/molecular mechanics (QM/MM) simulations approach, searching to develop a computational simulations prototype method on antimicrobial susceptibility of gram-negative bacteria against antibiotics. E. coli ATCC 8739 strain susceptibility for the drugs used in the antimicrobial susceptibility testing and selection of bioactive molecules against resistant strain. The protonation revealed a deprotonate state for His146, His151, His216 and His320 residues. The complex was stabilized after 0.6 ns of MD simulation. The global interaction means for inhibition zone diameters of E. coli ATCC8739 strain and cefoxitin was 24.33 mm no showing significant difference between computational and experimental methods. Our computational simulation method can reliably be performed as a molecular modeling prototype for gram-negative antimicrobial susceptibility testing bacteria. This article is protected by copyright. All rights reserved.

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Section: Methodsmentioning

confidence: 99%

Section: Global Interaction Energy Calculationsmentioning

confidence: 99%

Theoretical and practical study of the cefoxitin‐Escherichia coli PBP5 complex interaction by molecular dynamics to obtain computational prototype of antimicrobial susceptibility to Gram negative bacteria

et al. 2020

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“…The importance of molecular modeling in the chemistry undergraduate curriculum is increasingly recognized. , In the pharmaceutical industry, computer-aided molecular design methods are now an integral part of drug discovery projects. , Incorporation of molecular modeling into the organic, − inorganic, and physical chemistry curriculums have all been discussed. In medicinal chemistry, too, molecular modeling provides a valuable teaching aid.…”

mentioning

confidence: 99%

An Integrated Visualization and Basic Molecular Modeling Laboratory for First-Year Undergraduate Medicinal Chemistry

Hayes

2014

J. Chem. Educ.

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A 3D model visualization and basic molecular modeling laboratory suitable for first-year undergraduates studying introductory medicinal chemistry is presented. The 2 h practical is embedded within a series of lectures on drug design, target−drug interactions, enzymes, receptors, nucleic acids, and basic pharmacokinetics. Serving as a teaching aid to the lecture material, 3D models of biological macromolecules exploiting Schrodinger software and the Maestro graphical user interface (GUI) is explored to enhance student learning. A considerably positive response was received from the participants. Background and details of the laboratory are outlined, while the student handout with answers is included as Supporting Information.

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“…This poses a challenge as to how to introduce students to the world of atoms and molecular interactions so that they can understand the properties of molecules resulting from the spatial arrangement of atoms. − As didactic tools, various molecular models are applied using computer visualization. However, this requires professional programs or model sets. − There is, therefore, a need for a convenient, accessible, and inexpensive method of building molecular models. − In this communication, a simple method for preparing chemical models using plastic caps is described.…”

mentioning

confidence: 99%

Building Molecular Models Using Screw-On Bottle Caps

Siodłak

2013

J. Chem. Educ.

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Chemical models can be built using screw-on bottle caps. Two identical caps can be joined together by thermal welding to form atoms, and the resulting atoms can be joined together by welding or by hot polymer glue to form molecules. The method is easy, can be applied at every level of chemical education, and gives access to an unlimited number of models at almost no cost. It inspires hands-on activity of pupils and can be used to show the dependence between the three-dimensional structure of molecules and their chemical, physical, and biological features.

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Integrating Molecular Modeling into the Inorganic Chemistry Laboratory

Cited by 15 publications

References 3 publications

Theoretical and practical study of the cefoxitin‐Escherichia coli PBP5 complex interaction by molecular dynamics to obtain computational prototype of antimicrobial susceptibility to Gram negative bacteria

Theoretical and practical study of the cefoxitin‐Escherichia coli PBP5 complex interaction by molecular dynamics to obtain computational prototype of antimicrobial susceptibility to Gram negative bacteria

An Integrated Visualization and Basic Molecular Modeling Laboratory for First-Year Undergraduate Medicinal Chemistry

Building Molecular Models Using Screw-On Bottle Caps

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