Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Fischer Projections02:18

Fischer Projections

13.0K
Learning to draw Fischer projections of molecules and understanding their relevance plays a crucial role in the visual depiction of organic molecules. A Fischer projection is a two-dimensional projection on a planar surface to simplify the three-dimensional wedge–dash representation of molecules. This is especially helpful in the case of molecules with multiple chiral centers that can be difficult to draw. Here, all the bonds of interest are represented as horizontal or vertical lines.
13.0K
Crystal Field Theory - Octahedral Complexes02:58

Crystal Field Theory - Octahedral Complexes

26.1K
Crystal Field Theory
To explain the observed behavior of transition metal complexes (such as colors), a model involving electrostatic interactions between the electrons from the ligands and the electrons in the unhybridized d orbitals of the central metal atom has been developed. This electrostatic model is crystal field theory (CFT). It helps to understand, interpret, and predict the colors, magnetic behavior, and some structures of coordination compounds of transition metals.
CFT focuses on...
26.1K
Hückel's Rule Diagram of π MOs: Frost Circle01:08

Hückel's Rule Diagram of π MOs: Frost Circle

4.2K
The Frost circle or the inscribed polygon method is a graphical method for determining the relative energies of π molecular orbitals (MOs) for planar, fully conjugated, and monocyclic compounds. This method was first described by A. A. Frost and Boris Musulin in 1953.
A Frost circle is constructed by drawing a polygon whose number of edges is equal to the number of carbons of the given cyclic system, with one of the vertices pointing down. Then, a circle is drawn enclosing the polygon so...
4.2K
Molecular Geometry and Dipole Moments02:36

Molecular Geometry and Dipole Moments

12.6K
The VSEPR theory can be used to determine the electron pair geometries and molecular structures as follows:
12.6K
Aromatic Hydrocarbon Cations: Structural Overview01:18

Aromatic Hydrocarbon Cations: Structural Overview

2.7K
Cycloheptatriene is a neutral monocyclic unsaturated hydrocarbon that consists of an odd number of carbon atoms and an intervening sp3 carbon in the ring. The three double bonds in the ring correspond to 6 π electrons, which is a Huckel number, and therefore satisfies the criteria of 4n + 2 π electrons. However, the intervening sp3 carbon disrupts the continuous overlap of p orbitals. As a result, cycloheptatriene is not aromatic.
Removing one hydrogen from the intervening CH2 group...
2.7K
Crystal Field Theory - Tetrahedral and Square Planar Complexes02:46

Crystal Field Theory - Tetrahedral and Square Planar Complexes

41.4K
Tetrahedral Complexes
Crystal field theory (CFT) is applicable to molecules in geometries other than octahedral. In octahedral complexes, the lobes of the dx2−y2 and dz2 orbitals point directly at the ligands. For tetrahedral complexes, the d orbitals remain in place, but with only four ligands located between the axes. None of the orbitals points directly at the tetrahedral ligands. However, the dx2−y2 and dz2 orbitals (along the Cartesian axes) overlap with the ligands less than the dxy,...
41.4K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

On the origins and variation of nucleotide skews of archaeal genomes.

Frontiers in microbiology·2026
Same author

The Nucleic Acids Circular Dichroism and Fourier Transform Databases NACDDB and NAIRDB: New Tools for RNA Structural Analysis.

Methods in molecular biology (Clifton, N.J.)·2026
Same author

Application of Fourier Transform Infrared Spectroscopy for Structural Analysis of RNAs.

Methods in molecular biology (Clifton, N.J.)·2026
Same author

Genome-wide ribonucleotide detection in Archaea.

Nucleic acids research·2025
Same author

Ultrafast photooxidation of semireduced flavin in fatty acid photodecarboxylase.

Science advances·2025
Same author

Editorial: The metabolic pathways of archaea.

Frontiers in microbiology·2025
Same journal

PES2MP: A Python Application for Automating Collisional Dynamics of Linear Rigid-Rotors.

Journal of computational chemistry·2026
Same journal

The Anionic States of Ubiquinone Characterized by Second-Order Approximate Coupled-Cluster Theory.

Journal of computational chemistry·2026
Same journal

Hydrogen Bond Energy Estimation in Large Molecular Clusters via the Method of Synergistic Cyclic Cooperativity: A Software Update H-BEE 2.0.

Journal of computational chemistry·2026
Same journal

The Intricate Mechanism of Nitric Oxide Synthase.

Journal of computational chemistry·2026
Same journal

A Molecular "Thermometer" for Measuring Effective Non-Local Exchange.

Journal of computational chemistry·2026
Same journal

Insights to Orientation Dependence of Molecular Conduction Modeled by High-Level Quantum Embedding.

Journal of computational chemistry·2026
See all related articles

Related Experiment Video

Updated: Jun 4, 2025

Author Spotlight: Advancing Cell Membrane Biophysics - Exploring Interactions and Challenges Through Experimental and Computational Approaches
07:31

Author Spotlight: Advancing Cell Membrane Biophysics - Exploring Interactions and Challenges Through Experimental and Computational Approaches

Published on: September 1, 2023

2.1K

Additive CHARMM Force Field for Pterins and Folates.

Elsa Balduzzi1, Wenlu Yin1, Jean-Christophe Lambry1

  • 1Laboratoire d'Optique et Biosciences (CNRS UMR7645, INSERM U1182), Ecole Polytechnique, Institut polytechnique de Paris, Palaiseau, France.

Journal of Computational Chemistry
|December 22, 2024
PubMed
Summary
This summary is machine-generated.

This study developed new molecular mechanics parameters for folates, crucial for one-carbon metabolism. The optimized CHARMM36 force field model accurately simulates folate-protein interactions in various redox states.

Keywords:
CGenFFCHARMMfolic acidforce fieldmolecular dynamicspterintetrahydrobiopterintetrahydrofolate

More Related Videos

Vibrational Spectra of a N719-Chromophore/Titania Interface from Empirical-Potential Molecular-Dynamics Simulation, Solvated by a Room Temperature Ionic Liquid
08:54

Vibrational Spectra of a N719-Chromophore/Titania Interface from Empirical-Potential Molecular-Dynamics Simulation, Solvated by a Room Temperature Ionic Liquid

Published on: January 25, 2020

5.6K
Author Spotlight: In Silico Creation and Impact of Carbonylated Amino Acids on Protein Structure and Function
05:57

Author Spotlight: In Silico Creation and Impact of Carbonylated Amino Acids on Protein Structure and Function

Published on: April 26, 2024

317

Related Experiment Videos

Last Updated: Jun 4, 2025

Author Spotlight: Advancing Cell Membrane Biophysics - Exploring Interactions and Challenges Through Experimental and Computational Approaches
07:31

Author Spotlight: Advancing Cell Membrane Biophysics - Exploring Interactions and Challenges Through Experimental and Computational Approaches

Published on: September 1, 2023

2.1K
Vibrational Spectra of a N719-Chromophore/Titania Interface from Empirical-Potential Molecular-Dynamics Simulation, Solvated by a Room Temperature Ionic Liquid
08:54

Vibrational Spectra of a N719-Chromophore/Titania Interface from Empirical-Potential Molecular-Dynamics Simulation, Solvated by a Room Temperature Ionic Liquid

Published on: January 25, 2020

5.6K
Author Spotlight: In Silico Creation and Impact of Carbonylated Amino Acids on Protein Structure and Function
05:57

Author Spotlight: In Silico Creation and Impact of Carbonylated Amino Acids on Protein Structure and Function

Published on: April 26, 2024

317

Area of Science:

  • Biochemistry and Molecular Biology
  • Computational Chemistry
  • Structural Biology

Background:

  • Folates are essential cofactors in one-carbon metabolism, supporting critical physiological processes like biosynthesis and epigenetic maintenance.
  • The pterin ring structure of folates allows for redox reactions and multiple protonation states, complicating molecular modeling.
  • Accurate molecular mechanics (MM) parameters are needed for simulating folate behavior in biological systems.

Purpose of the Study:

  • To derive and validate molecular mechanics (MM) parameters for pterins and biologically relevant folates within the CHARMM36 force field.
  • To develop parameters for multiple redox states (oxidized, dihydrofolate, tetrahydrofolate) and protonation states of 18 different folates.
  • To enhance the accuracy of computational modeling for folate-protein interactions.

Main Methods:

  • Utilized the CHARMM force field parametrization protocol to derive partial charges and bonded terms.
  • Employed quantum mechanics calculations targeting monohydrate interactions, electrostatic potential, and dipole moment for charge derivation.
  • Performed 1D and 2D potential energy surface scans to parameterize bond, angle, and dihedral terms, including in-ring torsions.

Main Results:

  • Successfully parameterized 18 folates across various redox and protonation states for the CHARMM36 force field.
  • Demonstrated significantly improved performance of the optimized folate model in simulations of protein-folate complexes compared to initial parameters.
  • The new model accurately reproduced structural properties of folate-protein interactions.

Conclusions:

  • The developed molecular mechanics model provides accurate parameters for simulating folates in diverse redox states.
  • This model represents a valuable tool for computational studies involving folates and folate derivatives.
  • The optimized parameters will advance research in one-carbon metabolism and related biological processes.