Tuesday, February 10, 2015

Hiyperconjugation and its stabalizing effect and it's corrosponding Resonance Structure for stability.

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Hyperconjugation is a general stabilising interaction. It involves delocalisation of σ electrons of C—H bond of an alkyl group directly attached to an atom of unsaturated system or to an atom with an unshared p orbital. The σ electrons of C—H bond of the alkyl group enter into partial conjugation with the attached unsaturated system or with the unshared p orbital. Hyperconjugation is a permanent effect.
To understand hyperconjugation effect, let us take an example of  (ethyl cation) in which the positively charged carbon atom has an empty p orbital. One of the C-H bonds
of the methyl group can align in the plane of this empty p orbital and the electrons constituting the C-H bond in plane with this p orbital can then be delocalised into the
empty p orbital.
This type of overlap stabilises the carbocation because electron density from the adjacent σ bond helps in dispersing the
positive charge.
Hyperconjugation is also possible in alkenes and alkylarenes. Delocalisation of electrons by hyperconjugation in the case of alkene as shown in the video.
There are various ways of looking at the hyperconjugative effect. One of the way is to regard C—H bond as possessing partial ionic character due to resonance.
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Resonance and stability of benzene,Mechanism of electrophilic substitution reactions and Hyperconjugation,Carbocation,RNA,ATP and Mathematics Behind them.

Today i will start from the forces at molecular level and their stabilizing effect responsible for the existence of a particular compound or structure and also how resonance mathematically it is the oscillation of molecule between its all possible combination possible,at molecular level resonance is mainly found in compound having double bond.so what are the forces mainly responsible for stabilizing effects at molecular level and this altering physical property like boiling point,polarity etc.
These interaction includes
1)Covalent interaction  2) Resonance Interaction leading to dispersal of charge 3)Hyperconjugative interaction 3)ionic interaction 4)Hydrogen bond interaction 3)van der wall's Force interaction 4)London Dispersion interaction 5)Electromeric Effect +E Effect and -E effect. etc

Let's start from various domain of bio molecular Science and molecular science where they play vital role.
a)RNA (Ribo nucleic Acid) :RNA is similar to DNA, but with two major chemical differences. First, RNA molecules contain ribose sugars in which the number 2 carbon is bonded to a hydroxyl group. In DNA, this hydroxyl group is replaced by a hydrogen atom. Second, RNA molecules utilize uracil in place of thymine. Uracil has the same structure as thymine, except that one of its carbons lacks a methyl (—CH3) group. Transcribing the DNA message into a chemically different
molecule such as RNA allows the cell to tell which is the original information storage molecule and which is the transcript. DNA molecules are always double-stranded (except
for a few single-stranded DNA viruses)while the RNA molecules transcribed from DNA are typically single-stranded.  
The figure of  DNA and RNA can develop some  motivation here for their stability in terms of fundamental forces of interaction.
In DNA it is hydrogen bond as discussed in the previous article as depicted here
  Although there is no chemical reason why RNA cannot form double helices as DNA does, cells do not possess the enzymes necessary to assemble double strands of RNA, as they do for DNA. Using two different molecules, one single-stranded and the other double-stranded, separates the role of DNA in storing hereditary information from the role of RNA in using this information to specify protein structure.
But my question is which bio molecular interaction is responsible for the stability of single strand ,why doesn't it decompose down?
Let's analyses it in terms of figure 
DNA versus RNA. DNA forms a double helix, uses deoxyribose as the sugar in its sugar-phosphate backbone, and utilizes thymine among its nitrogenous bases. RNA, on the other hand, is usually single-stranded, uses ribose as the sugar in its sugar-phosphate backbone, and utilizes uracil in place of thymine.

Let's come to another instance where these molecular force will stabilize ATP molecule by storing Energy in bond.

 
ATP. Adenosine triphosphate (ATP) contains adenine, a fivecarbon sugar, and three phosphate groups. This molecule serves to transfer energy rather than store genetic information.
What molecular force is responsible for stability of ATP. In addition to serving as subunits of DNA and RNA, nucleotide bases play other critical roles in the life of a cell.
For example, adenine is a key component of the molecule adenosine triphosphate the energy currency of the cell. It also occurs in the molecules nicotinamide adenine dinucleotide (NAD+) and flavin adenine dinucleotide (FAD+), which carry electrons whose energy is used to make ATP. A nucleic acid is a long chain of five-carbon sugars with
an organic base protruding from each sugar. DNA is a
double-stranded helix that stores hereditary information as a specific sequence of nucleotide bases. RNA is a single-stranded molecule that transcribes this information to direct protein synthesis.

Benzene:A completely different phenomenon will come to define the stability of benzene and mathematically it is equivalent to oscillation ie benzene switching on and off between to energy equivalent term and hence the average energy of benzene decreases on an average ie it's bind dissociation enthalpy is in between double and single bond and bond length also between double and single bond.
and it's resonance can be shown as

its Equivalence is as following

We can say that the three pi bond is executing oscillation so the six pi electron is present everywhere the hexagonal ring.


  Its other energetically same structure is as following
The sum up of the above two resonance structure is equivalent to the following hybrid.



 The electron free electron density or pi electron density is increasing above and below the hexagonal benzene where each carbon is SP2 hybridized and thus trigonal planar and the unhybrid P orbital oriented perpendicular above and below the hexagonal plane total six having six electron  in this orthogonal p orbital forming pi bond leads to electron density above and below the plane.
I will come to different interactions at molecular level which will lead to stability of molecular structure or system and try to correlate them using mathematics till then wait.

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Sunday, February 8, 2015

DNA Deoxyribonucleic acid,The Structure of Nucleic Acids and DNA as massive Data storage site in human which can't be destroyed and calculus behind it's stability and Artificial information transfer from animals to humans and the end of gaining knowledge already present in human!

Deoxyribonucleic acid is a molecule that encodes the genetic instructions used in the development and functioning of all known living organisms and many viruses. DNA is a nucleic acid; alongside proteins and carbohydrates, nucleic acids compose the three major macromolecules essential for all known forms of life. Most DNA molecules consist of two biopolymer strands coiled around each other to form a double helix. The two DNA strands are known as polynucleotides since they are composed of simpler units called nucleotides. Each nucleotide is composed of a nitrogen-containing nucleobase—either guanine (G), adenine (A), thymine (T), or cytosine (C)—as well as a monosaccharide sugar called deoxyribose and a phosphate group. The nucleotides are joined to one another in a chain by covalent bonds between the sugar of one nucleotide and the phosphate of the next, resulting in an alternating sugar-phosphate backbone. According to base pairing rules (A with T and C with G), hydrogen bonds bind the nitrogenous bases of the two separate polynucleotide strands to make double-stranded DNA.
DNA is well-suited for biological information storage. The DNA backbone is resistant to cleavage, and both strands of the double-stranded structure store the same biological information. Biological information is replicated as the two strands are separated. A significant portion of DNA (more than 98% for humans) is non-coding, meaning that these sections do not serve as patterns for protein sequences.
The two strands of DNA run in opposite directions to each other and are therefore anti-parallel. Attached to each sugar is one of four types of nucleobases (informally, bases). It is the sequence of these four nucleobases along the backbone that encodes biological information. Under the genetic code, RNA strands are translated to specify the sequence of amino acids within proteins. These RNA strands are initially created using DNA strands as a template in a process called transcription.
Within cells, DNA is organized into long structures called chromosomes. During cell division these chromosomes are duplicated in the process of DNA replication, providing each cell its own complete set of chromosomes. Eukaryotic organisms (animals, plants, fungi, and protists) store most of their DNA inside the cell nucleus and some of their DNA in organelles, such as mitochondria or chloroplasts. In contrast, prokaryotes (bacteria and archaea) store their DNA only in the cytoplasm. Within the chromosomes, chromatin proteins such as histones compact and organize DNA. These compact structures guide the interactions between DNA and other proteins, helping control which parts of the DNA are transcribed.

DNA is a long polymer made from repeating units called nucleotides which is shown below.
Structure of a nucleotide. The nucleotide subunits of DNA and RNA are made up of three elements: a five-carbon sugar, an organic nitrogenous base, and a phosphate group.

Nucleic acids are long polymers of repeating subunits called nucleotides. Each nucleotide consists of three components:a five-carbon sugar (ribose in RNA and deoxyribose in DNA); a phosphate (—PO4) group; and an organic nitrogencontaining base.
When a nucleic acid polymer forms, the phosphate group of one nucleotide binds to the hydroxyl group of another, releasing water and forming a phosphodiester bond. A nucleic acid, then, is simply a chain of five-carbon sugars linked together by phosphodiester bonds with an organic base protruding from each sugar as shown in the following figure.


 The structure of a nucleic acid

Two types of organic bases occur in nucleotides. The
first type, purines, are large, double-ring molecules found in
both DNA and RNA; they are adenine (A) and guanine
(G). The second type, pyrimidines, are smaller, single-ring
molecules; they include cytosine (C, in both DNA and
RNA), thymine (T, in DNA only), and uracil (U, in RNA
only).

 The above two figure is showing you
The structure of a nucleic acid and the organic nitrogen-containing bases. In a nucleic acid, nucleotides are linked to one another
via phosphodiester bonds, with organic bases protruding from the chain.  The organic nitrogenous bases can be either purines or
pyrimidines. In DNA, thymine replaces the uracil found in RNA.

 DNA
Organisms encode the information specifying the amino acid sequences of their proteins as sequences of nucleotides
in the DNA. This method of encoding information is very similar
to that by which the sequences of letters encode information in a
sentence. While a sentence written in English consists of a combination of the 26 different letters of the alphabet
in a specific order, the code of a DNA molecule consists of different combinations of the four types of nucleotides in specific sequences such as CGCTTACG. The information encoded in DNA is used in the everyday metabolism of the organism and is passed on to the organism’s descendants. 

DNA molecules in organisms exist not as single chains folded into
complex shapes, like proteins, but rather as double chains. Two DNA polymers wind around each other like the outside and inside rails of a circular staircase. Such a winding
shape is called a helix, and a helix composed of two chains winding
about one another, as in DNA, is called a double helix. Each step of
DNA’s helical staircase is a basepair, consisting of a base in one
chain attracted by hydrogen bonds to a base opposite it on the other
chain. These hydrogen bonds hold the two chains together as a duplex The base-pairing rules are rigid: adenine can pair only with
thymine (in DNA) or with uracil (in RNA), and cytosine can pair only with guanine. The bases that participate in base-pairing are said to be complementary to each other. Additional
details of the structure of DNA and how it interacts with RNA
in the production of proteins can be found in my next blog till that wait.

 Conclusion:
1)Where the calculus is coming into picture ?Calculus deals with the concept of maxima and minima and domain of function where this max or min exist.Here the Function is H-Bond that is required to be maximized to minimizes the energy of DNA system we see that this maximization of H-Bond can only be achieved iff the two strands of Nucleotides undergo rotation about central axis generating Double Helical structure of DNA.
This H-bond maximization as the function variable along x and y axis can be represented by following figure.
 
The point is what are the two variables Along x and y axis upon which H-bond depends in other word H-bond=F(x,y).This x and y variable is required to be found as a research work.
2) Base sequence determines the information stored in the human and how we can upgrade it and can transfer the DNA information of animals in the human to learn their language and knowledge which they can't share with us .If this transfer of knowledge becomes possible we no longer need to study the already present material but we only require to imagine beyond our knowledge whose base will be the knowledge of our forefathers.
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Conservative vector field like Gravitational and Electric Field are also path independent and irrotational and we can always find scalar potential such that -Grad(potential)=Field vector.


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Conservative Gravitational Fields ,Gravitational Potential and Gradient of scalar potential.


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Gravitational Field vector due to a uniform solid Sphere with calculus and Algebra:



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Gravitational field is the distortion of Space Time 4D fabric by mass m making plane convex downward.Thus Gravitational field is the curvature on space time fabrics.


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