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Related Concept Videos

¹H NMR Chemical Shift Equivalence: Homotopic and Heterotopic Protons01:03

¹H NMR Chemical Shift Equivalence: Homotopic and Heterotopic Protons

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Protons in identical electronic environments within a molecule are chemically equivalent and have the same chemical shift. The replacement test is a useful tool to identify chemical equivalence and predict NMR spectra. A substituent replaces each of the protons being examined and the resulting molecules are compared. If the same molecule is obtained, the protons are equivalent or homotopic. Replacement of any hydrogens in ethane by chlorine yields chloroethane because all six protons are...
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Stereoisomers

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On the basis of mirror symmetry, stereoisomers of an organic molecule can be further classified into diastereomers and enantiomers. Diastereomers are stereoisomers that are not mirror images of each other. Substituted alkenes, such as the cis and trans isomers of 2-butene, are diastereomers, as these molecules exhibit different spatial orientations of their constituent atoms, are not mirror images of each other, and do not interconvert. Here, the interconversion is suppressed due to...
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¹H NMR: Complex Splitting01:13

¹H NMR: Complex Splitting

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A proton M that is coupled to a proton X results in doublet signals for M. However, NMR-active nuclei can be simultaneously coupled to more than one nonequivalent nucleus. When M is coupled to a second proton A, such as in styrene oxide, each peak in the doublet is split into another doublet.
Splitting diagrams or splitting tree diagrams are routinely used to depict such complex couplings. While drawing splitting diagrams, the splitting with the larger coupling constant is usually applied...
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Isomerism02:43

Isomerism

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Isomers are molecules with the same molecular formula but different structural arrangements. Isomers can be further classified into constitutional isomers and stereoisomers. Constitutional isomers differ in the connectivity of their constituent atoms. For example, 2-butanol and diethyl ether are constitutional isomers, as they have the same chemical formula, C4H10O, but differ in the connectivity of the carbon and oxygen atoms. Constitutional isomers have different physical and chemical...
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¹H NMR Chemical Shift Equivalence: Enantiotopic and Diastereotopic Protons00:58

¹H NMR Chemical Shift Equivalence: Enantiotopic and Diastereotopic Protons

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Replacing each alpha-hydrogen in chloroethane by bromine (or a different functional group) yields a pair of enantiomers. Such protons are called prochiral or enantiotopic and are related by a mirror plane. Enantiotopic protons are chemically equivalent in an achiral environment. Because most proton NMR spectra are recorded using achiral solvents, enantiotopic hydrogens yield a single signal.
In chiral compounds such as 2-butanol, replacing the methylene hydrogens at C3 produces a pair of...
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Disubstituted Cyclohexanes: cis-trans Isomerism02:37

Disubstituted Cyclohexanes: cis-trans Isomerism

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Depending upon the different spatial orientation of the substituents, the disubstituted cycloalkanes exhibit two types of stereoisomers. The cis isomers have the substituents on the same side of the ring, whereas the trans isomers have the substituents on the opposite sides. These stereoisomers exhibit different physical properties and cannot be interconverted without breaking the carbon-carbon bonds.
In cyclohexane, the substituents can occupy different positions generating distinct isomers....
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Backmapping with Mapping and Isomeric Information.

Siyoung Kim1

  • 1Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637 United States.

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|December 4, 2023
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Summary
This summary is machine-generated.

A new Multiscale Simulation Tool (mstool) converts coarse-grained (CG) to all-atom (AA) molecular models. This powerful backmapping tool requires only mapping and isomeric information, simplifying complex molecular simulations.

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Area of Science:

  • Computational chemistry
  • Molecular dynamics
  • Biophysics

Background:

  • Coarse-grained (CG) simulations offer computational efficiency for large biomolecular systems.
  • Reconstructing all-atom (AA) representations from CG models is crucial for detailed analysis but often complex.
  • Existing backmapping methods can be computationally intensive or require extensive parameterization.

Purpose of the Study:

  • To introduce the Multiscale Simulation Tool (mstool), a novel and flexible software for CG to AA system backmapping.
  • To provide a user-friendly tool that requires minimal input for accurate molecular model reconstruction.
  • To demonstrate the tool's capability in handling diverse biological systems.

Main Methods:

  • The mstool employs a two-step backmapping procedure: random placement of AA atoms guided by CG mapping, followed by energy minimization.
  • Force field modifications include using cosine functions for nonbonded interactions to enhance stability.
  • Additional torsional potentials are incorporated to preserve essential isomeric properties (cis/trans, dihedral, chiral).

Main Results:

  • Successfully backmapped various CG membrane and protein structures to AA resolution.
  • Achieved a significant resolution increase (34-fold for a lipid model) without intermediate resolutions.
  • Demonstrated the tool's robustness and simplicity across different molecular systems.

Conclusions:

  • The mstool provides an efficient and accessible method for CG to AA model conversion.
  • The tool simplifies the process of obtaining high-resolution molecular details from large-scale simulations.
  • Freely available software facilitates broader application in computational molecular studies.