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Molecular Models

Molecular Models

Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.

Structure of Benzene: Molecular Orbital Model

Structure of Benzene: Molecular Orbital Model

According to the molecular orbital (MO) model, benzene has a planar structure with a regular hexagon of six sp2 hybridized carbons. As shown in Figure 1, each carbon is bonded to three other atoms with C–C–C and H–C–C bond angles of 120°. The C–H bond length is 109 pm, and the C–C bond length is 139 pm which is midway between the single bond length of sp3 hybridized carbons (154 pm) and sp2 hybridized carbons (133 pm).

Mechanistic Models: Compartment Models in Individual and Population Analysis

Mechanistic Models: Compartment Models in Individual and Population Analysis

Mechanistic models are utilized in individual analysis using single-source data, but imperfections arise due to data collection errors, preventing perfect prediction of observed data. The mathematical equation involves known values (Xi), observed concentrations (Ci), measurement errors (εi), model parameters (ϕj), and the related function (ƒi) for i number of values. Different least-squares metrics quantify differences between predicted and observed values. The ordinary least...

Predicting Molecular Geometry

Predicting Molecular Geometry

VSEPR Theory for Determination of Electron Pair Geometries

Structure-Activity Relationships and Drug Design

Structure-Activity Relationships and Drug Design

Drug design is a dynamic field that involves discovering and developing new medications based on specific biological targets. This process heavily relies on structure-activity relationships (SAR) and quantitative structure-activity relationships (QSAR) to guide the design and optimization of efficient drugs.
SAR studies the intricate relationship between a drug's chemical structure and biological activity. It focuses on understanding how modifications to a drug's structure can influence...

Structure of Benzene: Kekulé Model

Structure of Benzene: Kekulé Model

In 1865, August Kekule suggested the structure of benzene according to the structural theory of organic chemistry based on the three assertions—formula of benzene is C6H6, all the hydrogens of benzene are equivalent, and each carbon must have four bonds due to its tetravalency.
He proposed that benzene has a cyclic structure of six carbon atoms attached to one hydrogen atom each, with three alternating pi bonds.

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Related Experiment Video

Updated: Mar 24, 2026

Impact Assessment of Repeated Exposure of Organotypic 3D Bronchial and Nasal Tissue Culture Models to Whole Cigarette Smoke

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Published on: February 12, 2015

SMOG 2: A Versatile Software Package for Generating Structure-Based Models.

Jeffrey K Noel^1,2, Mariana Levi³, Mohit Raghunathan¹

¹Center for Theoretical Biological Physics, Rice University, Houston, Texas, United States of America.

Plos Computational Biology

|March 11, 2016

Summary

This summary is machine-generated.

Structure-based models (SBMs) simulate protein and RNA dynamics. SMOG 2 software facilitates SBM use with GROMACS and NAMD, enabling custom restraints and features for biomolecular simulations.

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A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Area of Science:

Biophysics
Computational Biology
Structural Biology

Background:

Coarse-grained molecular dynamics simulations effectively capture large-scale biomolecular motions.
Structure-based models (SBMs) utilize known structures to define potential energy functions for simulations.
SBMs have been applied to protein folding, RNA dynamics, and molecular machine mechanisms.

Purpose of the Study:

To introduce SMOG 2, a software package for applying SBMs in molecular dynamics simulations.
To provide a flexible computational infrastructure for custom SBM development and application.
To enable the inclusion of experimental or bioinformatics-derived restraints in SBMs.

Main Methods:

SMOG 2 processes user-defined structural information and energy definitions.
It generates input files compatible with high-performance molecular dynamics packages like GROMACS and NAMD.
The software includes XML-formatted template files for common SBMs and supports user modifications.

Main Results:

SMOG 2 facilitates the creation and execution of SBM simulations.
The package supports the integration of diverse restraints, including ligands and post-translational modifications.
It enhances the accessibility and applicability of SBMs for biomolecular research.

Conclusions:

SMOG 2 is a valuable tool for researchers studying biomolecular dynamics using SBMs.
The software simplifies the setup and customization of SBM simulations.
It expands the scope of SBM applications by allowing novel structural features and restraints.