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Related Concept Videos

Mechanistic Models: Compartment Models in Algorithms for Numerical Problem Solving01:29

Mechanistic Models: Compartment Models in Algorithms for Numerical Problem Solving

Mechanistic models play a crucial role in algorithms for numerical problem-solving, particularly in nonlinear mixed effects modeling (NMEM). These models aim to minimize specific objective functions by evaluating various parameter estimates, leading to the development of systematic algorithms. In some cases, linearization techniques approximate the model using linear equations.
In individual population analyses, different algorithms are employed, such as Cauchy's method, which uses a...
Conformations of Cycloalkanes02:29

Conformations of Cycloalkanes

Adolf von Baeyer attempted to explain the instabilities of small and large cycloalkane rings using the concept of angle strain — the strain caused by the deviation of bond angles from the ideal 109.5° tetrahedral value for sp3  hybridized carbons. However, while cyclopropane and cyclobutane are strained, as expected from their highly compressed bond angles, cyclopentane is more strained than predicted, and cyclohexane is virtually strain-free. Hence, Baeyer’s theory that was based on the...
¹H NMR of Conformationally Flexible Molecules: Temporal Resolution00:52

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

At room temperature, the chair conformer of cyclohexane undergoes rapid ring flipping between two equivalent chair conformers at a rate of approximately 105 times per second. These two chair conformers are in equilibrium. The rapid ring flipping results in the interconversion of the axial proton to an equatorial proton and an equatorial to the axial proton. Such interconversions are too rapid and cannot be detected on the NMR timescale. Hence, the NMR spectrometer cannot distinguish between the...
Chair Conformation of Cyclohexane02:02

Chair Conformation of Cyclohexane

The chair conformation is the most stable form of cyclohexane due to the absence of angle and torsional strain. The absence of angle strain is a result of cyclohexane’s bond angle being very close to the ideal tetrahedral bond angle of 109.5° in its chair conformer. Similarly, the torsional strain is also absent owing to the perfectly staggered arrangement of bonds.
The hydrogen atoms linked to carbons are arranged in two different axial and equatorial orientations to achieve this staggered...
Conformations of Cyclohexane02:11

Conformations of Cyclohexane

Cyclohexane does not exist in a planar form due to the high angle and torsional strain it would experience in the planar structure. Instead, it adopts non-planar chair and boat conformations.
The chair form is the most stable and derives its name from its resemblance to the “easy chair.” In the chair conformation, two carbon atoms are arranged out-of-plane — one above and one below, minimizing the torsional strain. In the chair form, the bond angle is very close to the ideal tetrahedral value,...
¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR01:15

¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR

The axial and equatorial protons in cyclohexane can be distinguished by performing a variable-temperature NMR experiment. In this process, except for one proton, the remaining eleven protons are replaced by deuterium. The deuterium substitution avoids the possible peak splitting caused by the spin-spin coupling between the adjacent protons. The remaining proton flips between the axial and equatorial positions.

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Updated: May 18, 2026

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
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Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

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A parallel systematic-Monte Carlo algorithm for exploring conformational space.

Yasset Perez-Riverol1, Roberto Vera, Yuliet Mazola

  • 1Department of Proteomics and Bioinformatics, Center for Genetic Engineering and Biotechnology, Havana, Cuba. yasset.perez@biocomp.cigb.edu.cu

Current Topics in Medicinal Chemistry
|October 4, 2012
PubMed
Summary
This summary is machine-generated.

This study introduces a hybrid algorithm combining systematic search and Monte Carlo methods to efficiently explore molecular conformations. The parallelized approach enhances computational speed and efficiency for simulating chemical compound flexibility.

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Area of Science:

  • Chemoinformatics
  • Computational Chemistry
  • Molecular Modeling

Background:

  • Exploring the conformational space of small molecules is computationally intensive.
  • Existing methods often require significant computational resources.
  • Understanding molecular flexibility is crucial in drug discovery and materials science.

Purpose of the Study:

  • To present a novel hybrid algorithm for efficient conformational space exploration of organic molecules.
  • To simulate an ensemble of low-energy conformations reflecting molecular flexibility.
  • To implement and evaluate a parallelized version of the algorithm.

Main Methods:

  • A hybrid approach combining systematic search and Monte Carlo methods.
  • Utilizing the Metropolis criterion for conformation acceptance/rejection.
  • Employing an in-house implementation of the MMFF94s force field for energy calculations.
  • Parallel implementation using the Message Passing Interface (MPI) paradigm.

Main Results:

  • The hybrid algorithm successfully generates an ensemble of low-energy conformations.
  • The parallelized algorithm demonstrates significant improvements in speed and efficiency.
  • The method effectively simulates the flexibility of small chemical compounds.

Conclusions:

  • The developed hybrid algorithm offers an efficient solution for exploring molecular conformational space.
  • Parallelization using MPI enhances computational performance, making it suitable for complex simulations.
  • This approach advances chemoinformatics by providing a faster and more efficient tool for molecular modeling.