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Newman Projections

Newman Projections

Different notations are used to represent the three-dimensional structure of molecules on two-dimensional surfaces. One of the most commonly used representations is the dash-wedge formula. The dashed wedges, solid wedges, and the plane lines indicate the groups situated behind the plane, coming out of the plane, and in the plane, respectively.
The organic molecules rotate across the single bonds leading to numerous temporary three-dimensional structures of varying energy known as...

Fischer Projections

Fischer Projections

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. While...

Molecular Geometry and Dipole Moments

Molecular Geometry and Dipole Moments

The VSEPR theory can be used to determine the electron pair geometries and molecular structures as follows:

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

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...

Predicting Molecular Geometry

Predicting Molecular Geometry

VSEPR Theory for Determination of Electron Pair Geometries

Conformations of Cyclohexane

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...

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ParametrizANI: Fast and Accessible Dihedral Parametrization for Small Molecules.

Pablo R Arantes¹, Souvik Sinha¹, Giulia Palermo^1,2

¹Department of Bioengineering, University of California Riverside, Riverside, California 92521, United States.

Journal of Chemical Information and Modeling

|October 9, 2025

Summary

ParametrizANI is a new tool for accurate dihedral parametrization of small molecules using force fields. It leverages deep learning models for high-precision molecular property prediction, democratizing research.

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Modeling an Enzyme Active Site using Molecular Visualization Freeware

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Published on: December 25, 2021

Area of Science:

Computational Chemistry
Molecular Modeling
Drug Discovery

Background:

Accurate parametrization of small molecules is crucial for molecular studies.
Existing methods may have limitations in precision and accessibility.

Purpose of the Study:

Introduce ParametrizANI, a novel tool for dihedral parametrization.
Provide a research-friendly environment for accurate small molecule parametrization.
Democratize access to DFT-level accuracy in parametrization.

Main Methods:

Developed ParametrizANI, a PyTorch-based tool utilizing TorchANI.
Employed GAFF and OpenFF force fields for parametrization protocols.
Utilized ANI (ANAKIN-ME) deep learning models for high-accuracy predictions.

Main Results:

ParametrizANI enables detailed protocols for dihedral parametrization.
TorchANI serves as a benchmark for precision in parametrization.
Achieved DFT-level accuracy in dihedral parametrization for small molecules.

Conclusions:

ParametrizANI significantly advances small molecule parametrization capabilities.
The tool democratizes access to high-accuracy molecular modeling.
Opens new avenues in molecular dynamics and computational chemistry research.