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

Statically Indeterminate Problem Solving01:16

Statically Indeterminate Problem Solving

866
Statically indeterminate problems are those where statics alone can not determine the internal forces or reactions. Consider a structure comprising two cylindrical rods made of steel and brass. These rods are joined at point B and restrained by rigid supports at points A and C. Now, the reactions at points A and C and the deflection at point B are to be determined. This rod structure is classified as statically indeterminate as the structure has more supports than are necessary for maintaining...
866
Gaussian Elimination: Problem Solving01:30

Gaussian Elimination: Problem Solving

277
Systems of linear equations in several variables are pivotal in modeling complex scenarios involving multiple unknowns and constraints. Such systems are widely used in various fields to represent relationships where several conditions must be simultaneously satisfied. Each variable in the system corresponds to an unknown quantity, while each equation imposes a linear constraint, leading to a structured approach for analyzing and solving real-world problems.A system of three equations with three...
277
One-Compartment Open Model: Wagner-Nelson and Loo Riegelman Method for ka Estimation01:24

One-Compartment Open Model: Wagner-Nelson and Loo Riegelman Method for ka Estimation

1.4K
This lesson introduces two critical methods in pharmacokinetics, the Wagner-Nelson and Loo-Riegelman methods, used for estimating the absorption rate constant (ka) for drugs administered via non-intravenous routes. The Wagner-Nelson method relates ka to the plasma concentration derived from the slope of a semilog percent unabsorbed time plot. However, it is limited to drugs with one-compartment kinetics and can be impacted by factors like gastrointestinal motility or enzymatic degradation.
On...
1.4K
Root-Locus Method01:19

Root-Locus Method

560
A cruise control system in a car is designed to maintain a specified speed automatically by adjusting the gas pedal. The system continuously measures the vehicle's speed and makes fine adjustments to the pedal to achieve this goal. The root locus method is particularly useful for understanding how the cruise control system's behavior changes under varying conditions, such as when the car goes uphill, downhill, or faces strong wind resistance.
This system can be represented by a block...
560
Woodward–Hoffmann Selection Rules and Microscopic Reversibility01:34

Woodward–Hoffmann Selection Rules and Microscopic Reversibility

4.2K
Electrocyclic reactions, cycloadditions, and sigmatropic rearrangements are concerted pericyclic reactions that proceed via a cyclic transition state. These reactions are stereospecific and regioselective. The stereochemistry of the products depends on the symmetry characteristics of the interacting orbitals and the reaction conditions. Accordingly, pericyclic reactions are classified as either symmetry-allowed or symmetry-forbidden. Woodward and Hoffmann presented the selection criteria for...
4.2K
SN2 Reaction: Stereochemistry02:23

SN2 Reaction: Stereochemistry

13.0K
In an SN2 reaction, the nucleophilic attack on the substrate and departure of the leaving group occurs simultaneously through a transition state. As the nucleophile approaches the substrate from the back-side, the configuration of the substrate carbon changes from tetrahedral to trigonal bipyramidal and then back to tetrahedral, leading to an inversion in the configuration of the product.
If the substrate is an achiral molecule at the α-carbon, the inversion of configuration is not...
13.0K

You might also read

Related Articles

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

Sort by
Same author

Weak Noncovalent Interactions in Nonequilibrium Structures: How Good Are the Dispersion Corrections?

The journal of physical chemistry letters·2026
Same author

Generalized Internal Coordinates for Creative Exploration of Interatomic Geometries.

Journal of chemical theory and computation·2025
Same author

Toward Validated Quantum Mechanical Workflows Predicting pH-Dependent Properties: Benchmarking Protocols for Conformational Sampling, Model Solvent, Basis Set, Density Functional, and Empirical Corrections.

The journal of physical chemistry. A·2025
Same author

The Pediatric Heart Center Melting Pot: Sharing Recipes for Success: Proceedings from the 8th World Congress of Pediatric Cardiology and Cardiac Surgery.

World journal for pediatric & congenital heart surgery·2024
Same author

Multiple-time scale integration method based on an interpolated potential energy surface for ab initio path integral molecular dynamics.

The Journal of chemical physics·2024
Same author

Comparison of Variational and Perturbative Spin-Orbit Coupling within Two-Component CASSCF.

The journal of physical chemistry. A·2024
Same journal

Multilevel Fragmentation and Boundary Corrections for Accurate Vibrational Spectra of Large Molecules.

Journal of chemical theory and computation·2026
Same journal

Special Topics: Developments of Theoretical and Computational Chemistry Methods in Asia.

Journal of chemical theory and computation·2026
Same journal

Predicting Excited-State Energies from Ground-State Descriptors in Thermally Fluctuating π-Conjugated Molecules.

Journal of chemical theory and computation·2026
Same journal

Many-Body Theory Predictions of Positron Binding Energies in Five-Membered Heterocycles Involving N, O, S, and NH Substituents.

Journal of chemical theory and computation·2026
Same journal

<i>opt</i>-DDAP: Optimizable Density-Derived Atomic Point Charges via Automatic Differentiation.

Journal of chemical theory and computation·2026
Same journal

A Force-Kernel Reformulation of the Extended-System Adaptive Biasing Force for Free-Energy Calculations.

Journal of chemical theory and computation·2026
See all related articles

Related Experiment Video

Updated: Mar 29, 2026

In Situ Monitoring of Diffusion of Guest Molecules in Porous Media Using Electron Paramagnetic Resonance Imaging
06:34

In Situ Monitoring of Diffusion of Guest Molecules in Porous Media Using Electron Paramagnetic Resonance Imaging

Published on: September 2, 2016

6.9K

Transition State Search Using a Guided Direct Inversion in the Iterative Subspace Method.

Joseph W May1, Jeremy D Lehner1, Michael J Frisch2

  • 1Department of Chemistry, University of Washington, Seattle, Washington 98195, United States.

Journal of Chemical Theory and Computation
|November 24, 2015
PubMed
Summary
This summary is machine-generated.

A new guided energy-represented direct inversion in the iterative subspace (gEn-DIIS) algorithm offers faster transition state optimization. This method excels in challenging chemical reaction path calculations, especially those with flat energy landscapes.

More Related Videos

Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry
12:11

Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry

Published on: April 8, 2020

8.8K
Isotopic Effect in Double Proton Transfer Process of Porphycene Investigated by Enhanced QM/MM Method
05:51

Isotopic Effect in Double Proton Transfer Process of Porphycene Investigated by Enhanced QM/MM Method

Published on: July 19, 2019

6.8K

Related Experiment Videos

Last Updated: Mar 29, 2026

In Situ Monitoring of Diffusion of Guest Molecules in Porous Media Using Electron Paramagnetic Resonance Imaging
06:34

In Situ Monitoring of Diffusion of Guest Molecules in Porous Media Using Electron Paramagnetic Resonance Imaging

Published on: September 2, 2016

6.9K
Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry
12:11

Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry

Published on: April 8, 2020

8.8K
Isotopic Effect in Double Proton Transfer Process of Porphycene Investigated by Enhanced QM/MM Method
05:51

Isotopic Effect in Double Proton Transfer Process of Porphycene Investigated by Enhanced QM/MM Method

Published on: July 19, 2019

6.8K

Area of Science:

  • Computational Chemistry
  • Chemical Physics
  • Theoretical Chemistry

Background:

  • Transition state (TS) optimization is crucial for understanding chemical reaction mechanisms.
  • Traditional methods like quasi-Newton rational function optimization (RFO) can struggle with complex potential energy surfaces.
  • Efficient algorithms are needed to accurately locate saddle points on these surfaces.

Purpose of the Study:

  • Introduce and evaluate a novel transition state optimization method, guided energy-represented direct inversion in the iterative subspace (gEn-DIIS).
  • Compare the performance of gEn-DIIS against the established RFO method.
  • Develop and assess a hybrid approach combining RFO and gEn-DIIS for improved optimization efficiency.

Main Methods:

  • Implementation of the gEn-DIIS algorithm for transition state optimization.
  • Development of a hybrid optimization strategy integrating RFO and gEn-DIIS.
  • Comparative analysis using a suite of test molecules to evaluate optimization speed and robustness.

Main Results:

  • The gEn-DIIS method demonstrates significantly faster optimization convergence compared to RFO.
  • The hybrid RFO-gEn-DIIS approach shows practical advantages across various convergence stages.
  • gEn-DIIS proves particularly effective for challenging optimizations involving flat reaction paths.

Conclusions:

  • The gEn-DIIS algorithm represents a computationally efficient advancement for transition state optimization.
  • The hybrid method offers a versatile and robust tool for exploring chemical reaction pathways.
  • This work provides a valuable alternative for computational chemists dealing with difficult saddle point searches.