Chemistry Molecular Models

0 views
Skip to first unread message

Jule Kue

unread,
Aug 5, 2024, 2:33:30 AM8/5/24
to fragtiomira
Balland 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.

Each wooden ball has a number of holes drilled into it. These correspond with the number of bonds that the atom can form with other atoms. The number of bonds that can be made depends on how many electrons an atom has, which varies depending on the element. For example, oxygen atoms can make two bonds, but hydrogen atoms can only make one.


The chemist Wilhelm August Hofmann first used coloured balls to represent the elements around 1865. John Dalton, who in the 19th century made great advances in thinking about the structure of atoms, used ball and spoke models in his lectures. Some of his models and diagrams of atoms are displayed in the Science Museum in London.


Skeletal models are similar to the ball and spoke kind; they are both classified as 'open' structures, as opposed to the 'closed' space-filling type. In skeletal models, the atoms are not shown as spheres. Instead the atoms are assumed to be at the intersection of two or more rods, which represent the bonds. The main advantage of skeletal models that is easy to measure angles and dimensions due to their open structure. The Whipple Museum has a set of Orbit skeletal models, shown in Image 2.


Space-filling models give a representation of the size and shape of the whole molecule, showing (relatively) how much space each atom occupies. Space-filling models were first designed by H. A. Stuart in 1934.


Chemistry students use space-filling models to help when visualising whether the shape of certain bulky structures will prevent them reacting with other molecules. However, space-filling models make it difficult to see how the atoms bond together and prevents seeing the structure of the whole molecule clearly. Ball and spoke representations are much better for showing this information.


This set of space-filling models in the Whipple Museum's collection was made by Griffin and George, a company that designed mass-produced models for students learning chemistry. Griffin and George's Courtauld Atomic Models set is extremely well known amongst students of the period. It was developed from the designs of Dr. G. S. Hartley of Courtaulds Ltd. in 1952 and underwent several improvements over the next fourteen years. The company Griffin and George had this name only between 1954-1957, so these sets of models can be closely dated to this time.


The models themselves are made of a rigid plastic, with a colour scheme that is different from the recommendations set out by the Institute of Physics. Instead, the colours of these models were chosen for how good they would look in black and white photographs.(1) The set comes with scale cards by Gallenkamp for estimating the size of the molecules (20mm equivalent to 0.1nm).


Models that represent how atoms pack together can be similar in type to the space-filling kind. Atoms can be packed together in several different arrangements, and models are used to represent these arrangements. In the Museum's collection are models that demonstrate hexagonal close packing and cubic close packing.


These particular models are classified as the space-filling type because they model the atoms as hard spheres that are in contact with one another. Although this is not an entirely realistic way to think about atoms, it provides a clear way of visualising the arrangement.


Molecular model kits are designed to be re-used; models can be built and then taken apart again, but chemists often make permanent models of molecular structures for demonstrations or teaching. This crystallographic model of the metal beta-manganese was made by Mr C. E. Chapman, Chief technician of the Crystallography Department, part of the Cavendish Laboratory at the University of Cambridge, in about 1952. It shows how the atoms of manganese are arranged at high temperatures.


A crystal lattice is a repeating pattern of atoms in a solid. It is an ideal representation of how atoms are bonded together and where they are situated with respect to their neighbours within the solid.


This crystal lattice model (Image 5) shows the distances between atoms of manganese and their geometrical arrangement within the crystal structure. The black wire cube represents the smallest possible cube that describes the general arrangement of atoms in the crystal lattice. It is referred to in crystallography as the unit cell.


In many metals all of the atoms are the same distance apart and surrounded by 12 other atoms (much like the arrangement of stacks of oranges in supermarkets). In manganese however, for reasons not fully understood, this is not the case. At room temperature some of the distances are shorter than others. This makes the arrangement of managese atoms in the crystal lattice more complicated than most other metals.


When metallic manganese is heated the crystal lattice undergoes changes in its structure before the metal melts. These different states are known as allotropes, and are named alpha, beta, gamma and delta to distinguish them. Between temperatures of about 700 to 1100 degrees centigrade, manganese exists in the beta state. As in the alpha state, not all the atoms are the same distance apart; but further, the atoms exist in two different geometrical arrangements (shown as red and green balls in Images 5 & 6). This does not mean that they are a different kind of atom, just that their neighbouring atoms are arranged differently.


Students of crystallography often find it difficult to understand the concepts of different geometrical sites in a crystal lattice, this problem is increased in a complicated crystal lattice such as beta-manganese. C. E. Chapman made this model especially to help a student visualise the arrangement of such sites. Models such as this are still used in teaching today.


Chemistry with molecular modelling is a chemistry-based creative-science course that is used to develop everything from new materials such as superconductors for new batteries, to new drug molecules for the pharmaceutical industry. Without it, many modern science disciplines such as materials science, molecular biology and environmental science would not be possible. Chemistry with molecular modelling embeds computermodelling techniques. Advancements in molecular modelling have led to an explosive growth in a range of applications. The modelling aspects of this course focus on modelling the structure and reactivity of molecules and solids including:


Chemistry with Molecular Modelling at Trinity This degree is designed to train our students with the creative talent and skills required for research and industry. The course provides a broad base in organic, inorganic and physical chemistry so that our graduates have a wide selection of career prospects. This degree also provides students with the unique opportunity to study the fundamentals of modern chemistry, whilst developing computer/ IT skills and applying computer-modelling techniques to explore chemical problems.


Former Trinity Chemistry graduates are working in companies such as Henkel, Pfizer, Allergan, GlaxoSmithKline and Bristol-Myers Squibb. Patent offices, government advisory and information services, food science, public analytical laboratories, schools and third level institutions also employ our chemists.


Other successful routes our graduates have taken in the past include careers in business and the financial services sectors and in management. In addition, the specially developed computational skills make graduates an attractive prospect for employers both within computing environments and in other professions. Examples of industries where people are employed directly in scientific computing/modelling include: pharmaceutical (computational drug design), chemical (developing catalysts), materials chemistry (semi-conductors/magnetic materials), financial services and meteorology.


The course is based on the Chemistry degree with core components of chemistry (inorganic, organic and physical) taken alongside special molecular-modelling modules, practical work and project work. You will be assessed by a combination of continuous assessments and examinations.


In the third and fourth years you will take core modules in chemistry with additional modules in molecular modelling to include general molecular modelling, quantum mechanics, optimisation, modelling protein structure, drug design, molecular dynamics, and modelling in solid-state materials chemistry.


Lectures are complemented by laboratory classes where you will gain experience in more sophisticated preparative chemical techniques and spectroscopic analysis. About one third of your laboratory class time will be spent in computer laboratories performing computational experiments using molecular modelling.


As a fourth-year student you will undertake a Capstone research project, typically from September to December. This may be done in Trinity or in an academic or research laboratory abroad. This is complemented by lectures covering fundamental material in organic, inorganic and physical chemistry. In addition, an extensive range of optional courses are also offered that allow each student to develop her/ his own particular interests.


The School of Chemistry has exchange agreements with a large number of universities and research institutes where students may carry out their fourth-year Capstone project, in places such as Vienna, Berlin, Bologna, Toulouse, and Utrecht, North America and Australia. A limited number of places are also available in China. The areas of research are wide-ranging, including cancer chemotherapy and DNA chemistry, device fabrication and materials processing, homogeneous catalysis, supramolecular chemistry and computational chemistry.


Students who wish to study Chemistry with Molecular Modelling apply to the TR061 Chemical Sciences stream and at the end of the second year may select Chemistry with Molecular Modelling as their specialist area for the third and fourth years.

3a8082e126
Reply all
Reply to author
Forward
0 new messages