What is Molecular Modeling

Molecular Modeling, is one of the fastest growing fields in science. It may vary from building and visualizing molecules


...to performing complex calculations on molecular systems. Below, molecular dynamics simulations are performed on a lipid-protein complex. Shown are the backbone structure of the protein, a bound fatty acid molecule within the protein, and a small shell of water surrounding the protein. The time for the simulation was 100 picoseconds. The graphs give information about the motion of the lipid inside the protein.

Why is Molecular Modeling Important?

By the time many of today`s students enter the workforce, career opportunities will have radically changed. Most if not all of the 100,000 genes in the Human Genome will have been sequenced. Using molecular modeling scientists will be better able to design new and more potent drugs against diseases such as Cancer, AIDS, and Arthritis.

Molecular modeling not only has the potential to bring new drugs to the market, but a vast array of new materials. The discovery of fullerenes, and superconducting cuprates (as well as other complex inorganic compounds), are expected to produce new materials in the optics, ceramic, semiconductor and biomaterials markets.
recent structural determination of vital photosynthetic proteins will lead the way to artificial photosynthesis.



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Why the Math in MathMol?
Numerous connections are found between mathematics and molecular modeling.


Many molecular structures have the same shape of familiar space figures. Take another look at the fullerene molecule shown above. The molecule has the same shape as an icosohedron. Notice that the faces are composed of hexagons and pentagons. The picture above shows another familiar space figure, that of the tetrahedron.



Angles are formed by the intersection of two rays (or line segments). The figure on the left shows a parallelogram with one base angle equal to 112 degrees. We measure angles formed by molecular bonds in a similar way, using three consecutive atoms to represent three points on a plane. The figure on the right shows the bond angle formed by 3 consecutive carbon atoms in a benzene ring.



Dihedral angles are formed by the intersection of two planes in space. On the left, two intersecting planes form a dihedral angle of 90 degrees. On the right, the dihedral angle shown for the hexane molecule is 59.4 degrees.



A line is a set of points described by an equation which may be written in the form y=mx+b where the constant m is the slope of the line and b represents its y intercept. As x varies y varies. In the figure above, as the temperature (T) of the system varies, the kinetic energy (E) of the molecule varies. The line describes the equation E=kT where k is the slope of the line.


The set of points which satisfy the equation y=1/x is a hyperbola. As x varies y varies inversely. As x becomes smaller y becomes larger. The movie above shows two particles of opposite charge attracted to each other. The relationship between coulombic energy and distance is an inverse relationship. The coulombic energy between the two particles varies with -1/r, where r is the distance separating their center of masses. In the movie notice that as r gets smaller, the potential energy becomes more negative.


Many geometric figures display symmetry. The equilateral triangle on the left displays rotational symmetry. Rotating the figure about about a point formed by the intersection of the three angle bisectors (the incenter of the triangle) will give the same appearance. The ammonia molecule on the right also shows symmetry. It has a 3-fold axis of symmetry. Rotating the molecule 120 degrees about its axis will give the same appearance.


 

Electrochemistry

Electrochemistry is a branch of chemistry that studies the reactions which take place at the interface of an electronic conductor (the electrode composed of a metal or a semiconductor, including graphite) and an ionic conductor (the electrolyte).

If a chemical reaction is caused by an external voltage, or if a voltage is caused by a chemical reaction, as in a battery, it is an electrochemical reaction. In general, electrochemistry deals with situations where an oxidation and a reduction reaction are separated in space. The direct charge transfer from one molecule to another is not the topic of electrochemistry.

History

16th to 18th century developments
The 16th century marked the beginning of the electrical understanding. During the 1550s the English scientist William Gilbert spent 17 years experimenting with magnetism and, to a lesser extent, electricity. For his work on magnets, Gilbert became known as the "Father of Magnetism." He discovered various methods for producing and strengthening magnets.

In 1663 the German physicist Otto von Guericke created the first electric generator, which produced static electricity by applying friction in the machine. The generator was made of a large sulfur ball cast inside a glass globe, mounted on a shaft. The ball was rotated by means of a crank and a static electric spark was produced when a pad was rubbed against the ball as it rotated. The globe could be removed and used as source for experiments with electricity.

By the mid—1700s the French chemist Charles François de Cisternay du Fay discovered two types of static electricity, and that like charges repel each other whilst unlike charges attract. Du Fay announced that electricity consisted of two fluids: "vitreous" (from the Latin for "glass"), or positive, electricity; and "resinous," or negative, electricity. This was the two-fluid theory of electricity, which was to be opposed by Benjamin Franklin`s one-fluid theory later in the century.

Late 1780s diagram of Galvani`s experiment on frog legs.Charles-Augustin de Coulomb developed the law of electrostatic attraction in 1781 as an outgrowth of his attempt to investigate the law of electrical repulsions as stated by Joseph Priestley in England.


Italian physicist Alessandro Volta showing his "battery" to French emperor Napoleon Bonaparte in early 1800s.In the late 1700s the Italian physician and anatomist Luigi Galvani marked the birth of electrochemistry by establishing a bridge between chemical reactions and electricity on his essay "De Viribus Electricitatis in Motu Musculari Commentarius" (Latin for Commentary on the Effect of Electricity on Muscular Motion) in 1791 where he proposed a "nerveo-electrical substance" on biological life forms.

On his essay Galvani concluded that animal tissue contained a here-to-fore neglected innate, vital force, which he termed "animal electricity," which activated nerves and muscles spanned by metal probes. He believed that this new force was a form of electricity in addition to the "natural" form produced by lightning or by the electric eel and torpedo ray as well as the "artificial" form produced by friction (i.e., static electricity).

Galvani`s scientific colleagues generally accepted his views, but Alessandro Volta rejected the idea of an "animal electric fluid," replying that the frog`s legs responded to differences in metal temper, composition, and bulk. Galvani refuted this by obtaining muscular action with two pieces of the same material.

19th century

In 1800, the English chemists William Nicholson (chemist) and Johann Ritter succeeded in decomposing water into hydrogen and oxygen by electrolysis. Soon thereafter Johann Ritter discovered the process of electroplating. He also observed the amount of metal deposited and the amount of oxygen produced during an electrolytic process that depended on the distance between the electrodes. By 1801 Ritter observed thermoelectric currents and anticipated the discovery of thermoelectricity by Thomas Johann Seebeck.

By the 1810s William Hyde Wollaston made improvements to the galvanic pile. Sir Humphry Davy`s work with electrolysis led to the conclusion that the production of electricity in simple electrolytic cells resulted from chemical action and that chemical combination occurred between substances of opposite charge. This work led directly to the isolation of sodium and potassium from their compounds and of the alkaline earth metals from theirs in 1808.

Hans Christian Ørsted`s discovery of the magnetic effect of electrical currents in 1820 was immediately recognized as an epoch-making advance, although he left further work on electromagnetism to others. André-Marie Ampère quickly repeated Ørsted`s experiment, and formulated them mathematically.


Professor Michael Faraday`s portrait on his book The Chemical History of a Candle.In 1821, Estonian-German physicist Thomas Johann Seebeck demonstrated the electrical potential in the juncture points of two dissimilar metals when there is a heat difference between the joints.

In 1827 the German scientist Georg Ohm expressed his law in this famous book "Die galvanische Kette, mathematisch bearbeitet" (The Galvanic Circuit Investigated Mathematically) in which he gave his complete theory of electricity.

In 1832 Michael Faraday`s experiments on Electrochemistry led him to state his two laws of electrochemistry. In 1836 John Daniell invented a primary cell in which hydrogen was eliminated in the generation of the electricity. Daniell had solved the problem of polarization. In his laboratory he had learned that alloying the amalgamated zinc of Sturgeon with mercury would produce a better voltage.


Swedish chemist Svante Arrhenius portrait circa 1880s.William Grove produced the first fuel cell in 1839. In 1846, Wilhelm Weber developed the electrodynamometer. In 1866, Georges Leclanché patented a new cell which eventually became the forerunner to the world`s first widely used battery, the zinc carbon cell.

Svante August Arrhenius published his thesis in 1884 on Recherches sur la conductibilité galvanique des électrolytes (Investigations on the galvanic conductivity of electrolytes). From his results the author concluded that electrolytes, when dissolved in water, become to varying degrees split or dissociated into electrically opposite positive and negative ions.

In 1886 Paul Héroult and Charles M. Hall developed a successful method to obtain aluminum by using the principles described by Michael Faraday.

In 1894 Friedrich Ostwald concluded important studies of the electrical conductivity and electrolytic dissociation of organic acids.


German scientist Walther Nernst portrait in 1910s.Hermann Nernst developed the theory of the electromotive force of the voltaic cell in 1888. In 1889, he showed how the characteristics of the current produced could be used to calculate the free energy change in the chemical reaction producing the current. He constructed an equation, known as Nernst Equation, which related the voltage of a cell to its properties.

In 1898 Fritz Haber showed that definite reduction products can result from electrolytic processes if the potential at the cathode is kept constant. In 1898 he explained the reduction of nitrobenzene in stages at the cathode and this became the model for other similar reduction processes.


The 20th century and recent developments

In 1909, Robert Andrews Millikan began a series of experiments to determine the electric charge carried by a single electron.

In 1923, Johannes Nicolaus Brønsted and Thomas Martin Lowry published essentially the same theory about how acids and bases behave, using an electrochemical basis.

Arne Tiselius developed the first sophisticated electrophoretic apparatus in 1937 and some years later he was awarded to the 1948 Nobel Prize for his work in protein electrophoresis.

A year later, in 1949, the International Society of Electrochemistry (ISE) was founded.

By the 1960s–1970s quantum electrochemistry was developed by Revaz Dogonadze and his pupils.




 

About Physical chemistry

Physical chemistry is the application of physics to macroscopic, microscopic, atomic and particulate phenomena in chemical systems[1]within the field of chemistry traditionally using the principles, practices and concepts of thermodynamics, quantum chemistry, statistical mechanics and kinetics.[2] It is mostly defined as a large field of chemistry, in which, several sub-concepts are applied; the inclusion of quantum mechanics is used to illustrate the application of physical chemistry to atomic and particulate chemical interaction or experimentation [1].

Physical chemistry is mostly referred to as a macromolecular doctrine, as the majority of the principles on which physical chemistry was founded composed entirely of macromolecular concepts, such as colloids. [3]

The relationships that physical chemistry tries to resolve include the effects of:

Intermolecular forces on the physical properties of materials (plasticity, tensile strength, surface tension in liquids).
Reaction kinetics on the rate of a reaction.
The identity of ions on the electrical conductivity of materials.

History :

The foundation of physical chemistry is thought to have started in 1876 by Josiah Willard Gibbs after the publishing of his paper On the Equilibrium of Heterogeneous Substances, which contained several of the cornerstones of physical chemistry, such as gibbs energy, chemical potentials, gibbs phase rule and subsequent naming and accredition of enthalpy to Heike Kamerlingh Onnes and to macromolecular processes.