Restricted to fixed classifications of sizes and bond lengths and bondangles - cannot represent important small variations, especially in angles
Bonds tend to rotate to unintended positions, when we pick it up to lookat it - for big molecules, it is practically impossible to pick it up withoutdistorting it
Can only guess at steric repulsions, p bondinghindrance to rotation, etc.
Beevers-type custom-built model
Advantages
Accurately represents the geometry of a known structure, e.g. from crystallography
May be able to pick it up and hold it, with care, but easily damaged
Disadvantages
It may not represent a molecule in solution, whose geometry will be different
It can only represent one conformer, when we want to consider several
For a large model, may not be able to see in to the active site
Cannot easily measure distances, angles, etc. from it: for theseneed tables of data as well
Computer model of molecule
Advantages
Has none of the above disadvantages
Contains lots of other information, to be dealt with in this course, beyondwhat could be contained in a single physical model
Can easily be published, put on a web site, emailed to coworkers, etc.
Disadvantages
You cannot pick it up and hold it
If you want to generate one yourself, you need access to suitable software(and hardware), and know how to use it
You need to know how to use visualisation software, e.g. Chime, to seepictures
Since all models contain approximations, you need to know how to evaluatethem
As an expert in molecular modeling and visualization, my expertise spans various methods used to represent molecular structures, including plastic models, custom-built models like Beevers-type models, and computer-generated models. I've extensively worked with these tools, applying them in research, education, and practical applications to understand molecular geometry, symmetry, and properties.
Plastic models with interchangeable balls are effective for basic visualization. They're advantageous for their tactile nature, enabling users to pick them up, rotate groups about bonds, and explore molecular symmetry. However, they have limitations, such as being restricted to fixed classifications of sizes and bond lengths. Additionally, the issue of unintended bond rotations when handled makes them impractical for larger molecules.
Beevers-type custom-built models are highly accurate representations of known structures, often derived from crystallography data. They offer precision in depicting molecular geometry but have drawbacks. They may not represent molecules in solution accurately, are limited to one conformer, and might not be suitable for visualizing active sites in large models.
Computer models of molecules, while overcoming the limitations of physical models, have their own set of advantages and disadvantages. They excel in providing a wealth of information, surpassing what's achievable in physical models. They can be easily shared and published, allowing for collaborative work. However, they lack the tactile interaction of physical models, and generating them requires software proficiency, access to suitable hardware, and an understanding of the evaluation of approximations within the models.
In summary, each modeling method—plastic models, custom-built models, and computer-generated models—has its unique strengths and limitations. Understanding the trade-offs among these methods is crucial for effectively representing molecular structures and properties in research, education, and practical applications in chemistry and related fields.
Molecular modeling is used to simulate the molecular behavior in chemical or biological systems (Leach, 1996). Accordingly, it is one of the leading techniques working with wide range of applications, such as drug design, biomaterials, emerging materials, and spectroscopy.
Molecular models typically describe atoms (nucleus and electrons collectively) as point charges with an associated mass. The interactions between neighbouring atoms are described by spring-like interactions (representing chemical bonds) and Van der Waals forces.
A ball and stick model can be used to show the structure of a simple molecule. This type of model has the advantage of showing how the atoms are connected and how they are arranged in space, including the angles between bonds.
Ball and spoke models are a common way of representing molecular structures. Each atom is represented by a coloured ball that is joined to other atoms using spokes to represent the bonds between them. This type of model emphasises the bonding between atoms.
Molecular modeling is an important tool to aid the understanding of the fundamental concepts of structure- activity relationships, and to elucidate the mechanism of action of drugs (drug-receptor interaction), used in the teaching-research-extension.
You'll need different types of balls or beads to represent the different types of atoms, and sticks or straws to represent the bonds between them. For water, you'll need two small balls for hydrogen, one larger ball for oxygen, and two sticks.
All biological functions depend on events that occur at the molecular level. These events are directed, modulated, or detected by complex biological machines, which are themselves large molecules or clusters of molecules. Included are proteins, nucleic acids, carbohydrates, lipids, and complexes of them.
Skeletal Model. Simpler two-dimensional representations of chemical compounds are accomplished using skeletal models. ...
Ball-and-stick Model. Ball-and-stick models are three-dimensional models, where the atoms are depicted as color-coded balls or spheres, specific to different elements. ...
Molecular models fall into four basic categories: skeletal or line; stick, ball-and-stick, and space-fillied or CPK. Wire Frame Model -- This model clearly shows the type of atoms in the molecule, the distances between bonds, and angles associated with the atoms.
It allows high school up to graduate school students to build an atomic structure model and visually demonstrate molecular geometry, the structure of compounds, and other bond types.
Every molecule is different – some are really different. For example, benzene is flat like a pancake, while fullerene is round like a ball. Penguinone can be drawn to look like a penguin, while other molecules appear to look completely random. But the positions of atoms in a molecule are never random.
Molecular models of DNA structures are representations of the molecular geometry and topology of deoxyribonucleic acid (DNA) molecules using one of several means, with the aim of simplifying and presenting the essential, physical and chemical, properties of DNA molecular structures either in vivo or in vitro.
Instead they are obtained from the combination of atomic orbitals, which predict the location of an electron in an atom. A molecular orbital can specify the electron configuration of a molecule: the spatial distribution and energy of one (or one pair of) electron(s).
Chemists often use molecular modeling calculations to gain insight into structures and energies of molecules, reaction pathways, spectroscopic properties, etc. The two most common types are quantum mechanical calculations, and molecular mechanics (also called empirical force field) calculations.
Introduction: My name is Merrill Bechtelar CPA, I am a clean, agreeable, glorious, magnificent, witty, enchanting, comfortable person who loves writing and wants to share my knowledge and understanding with you.
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