Chem Sat

Particles Sketch part 2

2013-06-17T05:53:00.002-07:00

Introductory notes:

Quantum electrodynamic (QED): It is a relativistic quantum field theory of Electrodynamic (ED) and it describes how light and matter interact. It is a combination of quantum mechanics and special relativity.

*Classical electromagnetism (Classical ED) studies the electromagnetic force between electric charge and currents; Lorentz force, EM induction, Faraday's law, Lenz's law and Maxwell's equation.

Many theories have been set to describe the nature of elements interaction and the mechanism of bonding. Therefore, the globe tries very hard to conduct a real time image of the electron cloud as well as the interaction between electrons with each other and the interaction of electrons with the nucleus.

# Covalent bond aspects :

1. Bond length; there is an optimum distance between the 2 bonded atoms to ensure a stable bond.

2. Bond strength (the energy of the bond)

3. Bond angle; it secures the embodied shape of the molecule in the space to overcome the repulsive forces of the adjacent electronic clouds in the same molecule.

- There are 2 important theories for describing the covalent bonding:

A. Valence bond theory

B. Molecular orbital theory

Particles Sketch part 1

2013-04-21T13:08:00.001-07:00

Universe Building Blocks

The mathematical functions are the relationships that define a situation in terms of a set of interaction CONDITIONS. Neither the situation nor the condition can exist INDEPENDENT of each other.

In mathematics, conditions are denoted by the term DIMENSION. In science there are 4 fundamental dimensions; mass, length, temperature and time, used to describe any physical situation in the natural world. Mass, length and temperature express the static situations, while time is a dynamic dimension used to describe CHANGES that define the action. The unites of time, the seconds, is nothing more than a reference for any CHANGE. It is a relativistic point of view according to time.

Other dimensions DERIVED from these fundamental dimensions;

such as:

Force (depends on mass)

Velocity (depends on lenght and time)

Kinetic energy (depends on mass and velocity)

# Some derived dimensions depend on other derived dimensions; such as Kinetic energy.

"That's what is called derived dimension which is a derivative from the fundamental dimension; scientific analysis or mathematical analysis"

For example:

Force = Mass * Acceleration

The force on a body is a situation defined by 2 conditions (mass and acceleration). The force is the DEPENDENT dimension, while mass and acceleration are the INDEPENDENT dimensions.

F (m,a) = m . a

Calculus is about ANALYZING functions that CHANGE

Ref:

1. http://www.understandingcalculus.com/index.php

What does proportional constant mean?

It means "To How Degree or Much Of The Change" in "Y" occurs by the a certain amount of change in "X".
Y = 1/X
It means that 1 must divided by the amount of change in X.
They always use "1" because it represents the simplest relationships.
For example, E = l.n
Therefore, E is the grade of change in between the wavelength and the frequency.
> It is called constant because the grade of change itself is fixed but the value is changed by the change of the value of X-axis; independent variable.
For instance, in Angular frequency:

"π" represents the ratio between a curved line and a straight one which both of them meet at the same starting and ending points; since we all know that curved lines always longer than straight ones if they have the same limits. If we have a straight line and we want to predict the length of the mutual curved one, we must use "π" as the proportional constant.

Scope of Medicinal chemistry

2012-09-18T06:11:00.000-07:00

John L. Neumeyer

“The unprecedented increase in human life expectancy, which has

almost doubled in a hundred years, is mainly due to drugs and to

those who discovered them.”

The oldest records of the use of therapeutic plants and minerals are derived from the ancient civilizations of the Chinese, the Hindus, the Mayans of Central America, and the Mediterranean peoples of antiquity. The Emperor Shen Nung (2735 BC) compiled what may be called a pharmacopeia, including ch'ang shang, an antimalarial alkaloid, and ma huang, from which ephedrine was isolated. Chaulmoogra fruit was known to the indigenous American Indians, and the Ipecacuanha root containing emetine was used in Brazil for the treatment of dysentery and diarrhea and is still used for the treatment of amebiasis. The early explorers found that the South American Indians also chewed cocoa leaves (containing cocaine) and used mushrooms (containing tryptamine) as hal lucinogens. In ancient Greek apothecary shops could be found herbs such as opium, Squill , Hyoscyamus, and viper toxin and such metallic drugs as copper and zinc ores, iron sulfate, and cadmium oxide.

The basic studies of chemistry and physics shifted from the Greco-Roman to the Arabian alchemists between the thirteenth and sixteenth centuries. Paracelsus (1493–1541) glorified antimony and its salts in elixirs as cure-alls in the belief that chemicals could cure disease.

The nineteenth century saw a great expansion in the knowledge of chemistry, which greatly extended the herbal pharmacopeia that had previously been established. Building on the work of Lavoisier, chemists throughout Europe refined and extended the techniques of chemical analysis. The synthesis of acetic acid by Kolbe in 1845 and of methane by Berthelot in 1856 set the stage for organic chemistry.

Pharmacognosy, the science that deals with medicinal products of plant, animal, or mineral origin in their crude state, was replaced by physiological chemistry. The emphasis was shifted from finding new medicaments from the vast world of plants to finding the active ingredients that accounted for their pharmacologic properties. The isolation of morphine by Sertürner in 1803, of emetine from ipecacuanha by Pelletier in 1816, and his purification of caffeine, quinine, and colchicine in 1820 all contributed to the increased use of “pure” substances as therapeutic agents. The nineteenth century also contributed to the use of digitalis by William Withering, the English physician and botanist, for the treatment of dropsy (hydropsy or Edema). Niemann isolated cocaine in 1860 and the active ingredient, physostigmine, from the Calabar bean in1864. As a result of these discoveries and the progress made in organic chemistry,the pharmaceutical industry came into being at the end of the nineteenth century.

In twentieth century, Diseases of protozoal and spirochetal origin responded to synthetic chemotherapeutic agents. Interest in synthetic chemicals that could inhibit the rapid reproduction of pathogenic bacteria and enable the host organism to cope with invasive bacteria was dramatically increased when Domagk reported that the red dyestuff 2,4-diaminoazobenzene-4′-sulfonamide (Prontosil) dramatically cured dangerous, systemic Gram-positive bacterial infections in man and animals. The observation by Woods and Fildes in 1940 that the bacteriostatic action of sulfonamide-like drugs was antagonized by p-aminobenzoic acid was one of the early examples in which a balance of stimulatory and inhibitory properties depends on the structural analogies of chemicals. Together with the discovery of penicil lin by Fleming in 1929 and its subsequent examination by Florey and Chain in 1941, this led to a water soluble powder of much higher antibacterial potency and lower toxici ty than those of previously known synthetic chemotherapeutic agents. With the discovery of a variety of highly potent anti-infective agents, a significant change was introduced into medical practice.

The emergence of the pharmaceutical industry took place in conjunction with the advances in organic/medicinal/pharmaceutical chemistry, pharmacology, bacteriology, biochemistry, and medicine as distinct fields of science in the late nineteenth century. Current research efforts are now focused not only on discovering new, biologically active compounds using ever increasingly sophisticated technology but also on gaining a better understanding of how and where drugs exert their effects at the molecular level. One should not underestimate, however, that the discoveries in the twentieth and twenty-first centuries, and before, represent an amazing amount of insight, determination, and luck by researchers in chemistry, pharmacology, biology, and medicine. We owe gratitude and admiration to those earlier scientists who had the imagination and inspiration to develop drugs to cure so many illnesses.

Drug molecules can be viewed as a collection of functional groups, which confer specific chemical and physical properties. Functional groups determine such characteristics as ionization, solubility (polarity), reactivity, chemical stability, and in vivo metabolic stability. Furthermore, these groups are capable of forming specific bonds (primarily non-covalent bonds) with their receptors and are thus extremely important in drug activity and potency. Chemical bonding is a basic concept in medicinal chemistry and in any branch of chemistry. Nature is a group of unlimited chemical bonding possibilities. Our great brain translates a widely different chemicals and associated bonds into our known senses. These complex translation processes shape our familiar life.

An introduction to chemical bonding theories:

Valence bond theory I

Computer-aided molecular design

2012-07-18T04:03:00.001-07:00

There is nothing radically new about the techniques we use in modern molecular modelling. Classical mechanics hasn’t changed since the time of Newton, Hamilton and Lagrange, the great ideas of statistical mechanics and thermodynamics were discovered by Ludwig Boltzmann and J.Willard Gibbs amongst others and the basic concepts of quantum mechanics appeared in the 1920s, by which time J.C. Maxwell’s famous electromagnetic equations had long since been published. The chemically inspired idea that molecules can profitably be treated as a collection of balls joined together with springs can be traced back to the work of D.H. Andrews in 1930. The first serious molecular Monte Carlo simulation appeared in 1953, closely followed by B.J. Alder and T.E. Wainwright’s classic molecular dynamics study of hard discs in 1957. The Hartrees’ 1927 work on atomic structure is the concrete foundation of our everyday concept of atomic orbitals, whilst C.C.J. Roothaan’s 1951 formulation of the HF-LCAO model arguably gave us the basis for much of modern molecular quantum theory.

Scientists and engineers first got their hands on computers in the late 1960s. We have passed the point on the computer history curve where every ten years gave us an order of magnitude increase in computer power, but it is no coincidence the that growth in our understanding and application of molecular modelling has run in parallel with growth in computer power. There have been considerable advances in the field of computer simulation of molecular systems since the basic algorithms and early applications to simple liquid systems were published. The complexity and size of the systems being studied, and the number of applications which are published annually have increased enormously during the past decade. This expansion is correlated with the improvements in computer hardware and the wider availability of simulation software. Projects which were not practicable in the 1970s became feasible using supercomputers during the 1980s, and have now become routine applications on high speed workstations. Thus, we can now reserve the current supercomputers for the most sophisticated, and hopefully most realistic, modelling applications at the cutting edge of computational science. The number of computer simulation and molecular modelling studies reported in the past five years is so large that it is difficult to cover comprehensively even the subset of studies involving the behaviour of the macromolecules, such as proteins and DNA. In this area of structural molecular biology, brief annual reviews of both methodological advances and applications are now available.

The term ‘computer simulation and modelling of macromolecules’ is used to encompass a wide range of techniques. It is possible to divide these into three classes : knowledge or rule based methods, quantum mechanical methods, and classical ‘potential energy’ based techniques. These three areas are not mutually exclusive, and it may be necessary to combine quantum mechanical and classical methods to tackle particular problems, as well as to refine rule-based models using classical ‘potential energy’ methods.

Computer Aided Molecular Design (CAMD) is identified as a mature discipline. The theoretical and practical aspects of its potential and of its basic tenets are described. Applications are chosen to underline the power of various CAMD strategies. The computer-aided design of novel molecular systems has undoubtedly reached the stage of a mature discipline offering a broad range of tools available to virtually any chemist. Indeed, as various programs, known as model builders, enable chemists to readily calculate molecular geometries, it is now possible to perform structure-based design applications that give a practically unlimited range of novel systems exhibiting specific properties. To this end, recent progress in computational chemistry play an important role by leading to a realistic description of molecular shape and motion, solvent effects, binding free energies, etc. However, it is fair to say that computer-aided techniques have in most cases to be used in combination with X-ray, NMR and other experimental tools to get a complete design of novel systems. The basic concepts of computer-aided molecular design (CAMD) are generally taught in different courses such as computer science (numerical methods and graphics), physical chemistry (quantum mechanics, statistical mechanics and simulation techniques), organic chemistry (molecular mechanics and conformational analysis) and biochemistry (protein structure and molecular recognition), rather than in a specific course devoted to CAMD. A similar statement is probably also applicable to books, as the corresponding material is often spread out in various monographs presenting more general subjects.

Ref:

1. Molecular modelling for beginners / Alan Hinchliffe. — 2nd ed.

2. Computer modelling in molecular biology / ed. by Julia M. Goodfellow. -Weinheim ; New York ; Basel ; Cambridge ; Tokyo : VCH, 1995

3. Computer-Aided Molecular Design: Theory and Applications by Jean-Pierre Doucet, J. P. Doucet, Jacques Weber