PS_1.3 Redox Potential:

Redox (Oxidation/Reduction) Potential is a measure of a tendency, either gain or lose electrons when it is subject with a new species. A chemical reaction in which electrons are transferred from one atom (which is oxidized) to another atom (which is reduced).

The Redox Potential is a measure (in Volts) of the affinity of a substance for electrons, it is electro-negativity, compared with hydrogen (which is set at 0). Substances are more strongly electronegative than (i.e. capable of oxidizing) hydrogen have positive redox potentials. Substances are less electronegative than (i.e. capable of reducing) hydrogen have negative redox potentials.

Oxidations and Reduction always go together. They are called Redox Reactions. Oxidation means losing of electrons. Reduction means receiving (or gaining) of electrons.

Fig: Oxidation & Reduction

This figure is a favorite mnemonic to understand the Redox potential and also very descriptive and informative of this process, I hope so[1].

  What Kind of Person Are u by Spl BiNal on Scribd

PS_1.2.1 Mathematical Expression of Dihedral Angle:

The dihedral angle ($\phi$) is the angle between two planes.

First of all, we should know the General equation of Plane:

$\mathbf{Ax + By + Cz + D = 0}$ .......... (i)

Where $A, B, C, D$ are constants.

And, Equation of plane passing through points $(x_1, y_1, z_1), (x_2, y_2, z_2), (x_3, y_3, z_3)$ is,

$\begin{vmatrix}
x-x_1 & y-y_1  & z-z_1\\
x_2-x_1 & y_2-y_1 & z_2-z_1\\
x_3-x_1 & y_3-y_1 & z_3-z_1
\end{vmatrix}=0$ .......... (ii)

Or,

$\begin{vmatrix}
y_2-y_1 & z_2-z_1\\
y_3-y_1 & z_3-z_1
\end{vmatrix} (x-x_1) + \begin{vmatrix}
z_2-z_1 & x_2-x_1\\
z_3-z_1 & x_3-x_1
\end{vmatrix} (y-y_1) + \begin{vmatrix}
x_2-x_1 & y_2-y_1\\
x_3-x_1 & y_3-y_1
\end{vmatrix} (z-z_1) = 0$ 

.......... (iii)

After Solving $eq^n (iii)$, we get; 

$\left.\begin{matrix}
\left \{ (y_2-y_1)(z_3-z_1) - (z_2-z_1)(y_3-y_1)\right \}x\;+\\
\left \{ (x_3-x_1)(z_2-z_1) - (x_2-x_1)(z_3-z_1)\right \}y\;+ \\
\left \{ (x_2-x_1)(y_3-y_1) - (x_3-x_1)(y_2-y_1)\right \}z + D = 0 \;\;\;\;\;\;\;\;\;\;\;
\end{matrix}\right\}$ .......... (iv)

Where $D$ is Constant term. This $eq^n (iv)$ gives the equation of plane passing through points.

Now,

From the above references, we have to calculate the Dihedral angle between the two planes:

$a_1x + b_1y + c_1z + d_1 = 0$ ..........  (v)

$a_2x + b_2y + c_2z + d_2 = 0$ ..........   (vi)

Which have normal vectors $n_1 = (a_1, b_1, c_1)$ and $n_2 = (a_2, b_2, c_2)$ is simply given dihedral angle through the dot product of the normals.

i.e. $Cos\phi = \hat{n_1}.\hat{n_2}$   ..........  (vii)

Or, 

$Cos\phi = \frac{a_1a_2 + b_1b_2 + c_1c_2}{\sqrt{a_1^2 + b_1^2 + c_1^2}\sqrt{a_2^2 + b_2^2 + c_2^2}}$  ..........  (viii)

Note: Unit Vector - If A is a vector with magnitude A $\neq 0$), then $\hat{n} = \frac{\vec{A}}{\left | A \right |}$ is a unit vector having the same direction as $\vec{A}$.

Click here for: Basic concept on Dihederal angle.

PS_2.2 Highlights in Photosynthesis Research:

1771	: Joseph Priestley, England	: Discovers that plants can "purify" air that has been "burned out" by a candle.
1779	: Jan Ingenhousz, The  Netherlands	: Demonstrates that the plant in Priestley's experiment is dependent on light and its green parts.
1782 - 1804		: Several researchers show that carbon dioxide and water are stored as organic matter by plants.
1845	: Robert Mayer, Germany	: Points out that plants store solar energy in organic matter.
Ca 1915	: Richard Willstätter, Germany	: Suggests that chlorophyll plays an active role in plants (Nobel Prize in 1915).
Ca 1930	: Cornelis van Niel, USA	: Proposes that photosynthesis is based on oxidation-reduction reactions and that the primary reaction is a photolysis of water followed by oxygen evolution.
1932	: Robert Emerson and William Arnold, USA	: Conclude that several hundred chlorophyll molecules cooperate in photosynthesis.
1939	: Robert Hill, England	: Demonstrates that photolysis of water and carbon dioxide fixation are separate processes.
1940	: Hans Fischer, Germany	: Solves the chemical structure of chlorophyll. (Nobel Prize 1930 for his investigations of hemes and chlorophyll.)
1954	: Melvin Calvin, USA	: (Nobel Prize 1961) and coworkers unravel the reactions of carbon dioxide fixation (Nobel Prize in 1961).
1954	: Daniel Arnon, USA	: Discovers light-dependent synthesis of ATP (photophosphorylation).
1960 - 1961	: Robert Hill and Fay Bendall, England, and independently Louis  Duysens, The Netherlands	: Show how two separate photosystems cooperate in plants.
1968	: William Parson, USA	: Confirms Duysens' hypothesis (1956) that chlorophyll is oxidized in the primary reaction of photosynthesis.
1984	: Johann Deisenhofer, Robert Huber and Hartmut Michel	: The Federal Republic of Germany, solve the structure of a photosynthetic reaction center from a bacterium (Nobel Prize in 1988).
1992	: Rudolph A. Marcus	: For the  contributions to the theory of electron transfer reactions in chemical systems (Nobel Prize in 1992).

Source: Nobel Academy

PS_2.3.2 Electron Transfer Reaction - Nobel Prize:

The Nobel prize in Chemistry in 1992 was awarded to Rudolph A. Marcus - "for the contributions to the theory of electron transfer reactions in chemical systems."

The Nobel Prize in Chemistry 1992 [1]

Reaction rate is a fundamental concept in chemistry. A mixture of chemical compounds undergoes changes or chemical reactions at different rates. During the reaction, no bonds are broken, there are still small changes in structure when electrons are added or removed.
Further more, Here have to click a Press Release which held on Nobel Academy, 12 October 1992.

Here is the Nobel Lecture, held on December 8 1992:

By Rudolph A. Marcus*: ELECTRON TRANSFER REACTIONS IN CHEMISTRY: THEORY AND EXPERIMENT (pdf).

PS_2.3.1 Photosynthesis Reaction Center - Nobel Prize:

The Nobel Prize in Chemistry 1988 was awarded jointly to Johann Deisenhofer, Robert Huber and Hartmut Michel - "for the determination of the three - dimensional structure of a photosynthetic reaction centre". 

The Nobel Prize in Chemistry 1988[1]

Photosynthesis - the most important chemical reaction on earth. In the green leaves of plants solar light is converted to chemical energy, which is used as nutrition not only by the green plants themselves but also for example: by cows who eat green grass, by ourselves who eat the meat of the cow and drink its milk, and so on through the nutritional chain.

Further more, Here have to click a Press Release which held on Nobel Academy, 19 October 1988.

Here is the Nobel Lecture held on December 8, 1988:

By JOHANN DEISENHOFER* and HARTMUT MCHEL**: The Photosynthetic Reaction Center from the Purple Bacterium Rhodopseudomonas Viridis (pdf).

By ROBERT HUBER*: A Structural basis of light energy and Electron Transfer in Biology (pdf).

PS_1.2 Dihedral Angle:

"Act as if what you do makes a difference. It does."    ~ William James

A dihedral angle:  - angle between two intersecting planes.
In chemistry: - angle between planes through two sets of three atoms, having two atoms in common.
In solid Geometry: - union of a line and two half-planes that have this line as a common edge.

Look around the room we are in one stationary position. And we observe where one of the walls of the room meets the ceiling. There we see, both of these are 2-dimensional flat surfaces which makes them planes.

Notice that where this happens, an angle is formed between two planes. That angle is called a dihedral angle [1].

[Note:The dihedral angle can be defined as the angle through which plane $A$ must be rotated (about their common line of intersection) to align it with plane $B$. For precision, one should specify the angle or its supplement, since both rotations will cause the plane to coincide.]

Picture Source

Given two plane; the measure of an angle formed by intersecting the two planes with another plane orthogonal (the dot product of two vector is Zero i.e. $A.B = 0$) to the line of intersection [2].

Picture Source

The angle measure between the normal direction of the two planes is the same as the measure of dihedral angles.

So, dihedral angle can be measured by taking dot product of the normal directions and using Cosine Theorem for Dot products.

Dihedral angles are used to specify the molecular conformation. 

This is the demonstration of dihedral effect in Aircraft Flight. 

How to I calculate the Dihedral angle?

This is a calculator to calculate the dihedral angle.

Click here for: Mathematical expression of Dihedral angle.

PS_2.1 Photosynthesis

"In a green leaves of plants solar light is converted to chemical energy."

Photosynthesis is a process by which green plants and other organisms turn carbon dioxide and water into carbohydrates and oxygen, using light trapped by chlorophyll.

The word photosynthesis is made from two words: Photon and Synthesis. Photon:  Smallest unit (quantum) of light energy. Synthesis:  Production of something by combining separate things. 

Thus, Photosynthesis is a natural process by which green plants, algae and bacteria  convert carbon dioxide into organic food using solar energy.

Photosynthesis - Brief Introduction

Photosynthesis Research in the Hastings Lab

Ligand:

- a molecule that binds to another (usually large) molecule.

- a molecule, as an antibody, hormone, or drug that binds to a receptor.

- an ion or molecule (functional group) that binds to a central metal atom to form a coordination complex [1].

Residue:

- a substance whatever remains after a process such as evaporation [1].

- an atom or a group of atoms, that forms part of a molecule.

Solvent Accessible Surface Structure:

- The solvent accessible surface area is the area of the surface swept out by the center of a probe sphere rolling over a molecule (atoms are spheres of varying radii).

- is just the boundary of the union of atom balls that have their radius             increased by the probe radius (typically 1.4 Angstroms). So the accessible      area is the surface area of a union balls [1]. 

Protein Surface Structure:

PS_4.1 Research - Proposal/Thesis Format:

1. A format for Research Proposals.

2. The format for a proposal.

3. Title of the final year project.

4. Format of Project Report.

5. How to write thesis Proposal.

PS_1.1 Quinone - Brief introduction:

Ubiquinone - $10$ ($3$ letter code: $U10$);           Formula: ${C}_{59}{H}_{90}{O}_{4}$

Quinone: any member of a class of cyclic organic compounds containing two carbonyl groups ($-C = O$), either adjacent or separated by a Vinylene group ($-CH = CH-$) in a six-membered unsaturated ring. In a few quinones, the carbonyl groups are located in different rings.

      

A Quinone is a class of Organic Compounds that are formally "derived from aromatic compounds (Such as Benzene or Naphthalene) by conversion of an even number of  $- CH = groups$ into $-C(=O)- groups$ with any necessary rearrangement of double bonds" resulting in "a fully conjugated cyclic dione structure [1]."

Quinone Structure (A)

Quinone: is a biologically active molecule; electron acceptor in electron transport chains such as those in Photosynthesis (Plastoquinone, Phylloquinone) & aerobic respiration (Ubiquinone). Phylloquinone is also known as Vitamin ${K}_1$ as it is used by animals to help form certain proteins, which are involved in blood coagulation, bone formation and other process.

Surface Structure (C)

Surface Structure (B)

In this  Image (B)  &  Image (C),  we see how the $Quinone$ - the small molecules shown inside the protein structure is nicely tucked inside the active site.

The Quinone structure plays an important role in theories concerning the relationship of chemical constitution to color.

PS_4. Miscellaneous:

4.1  Research - Proposal/ Thesis Format

4.2  References - Photosynthesis Reaction Center

4.3  Journals/ Books Linklist - Website

4.4  MikTeX - TexMaker Collection

PS_1. 1AIJ - Brief introduction:

(PHOTOSYNTHETIC REACTION CENTER FROM  RHODOBACTER   SPHAEROIDES  IN THE CHARGE - NEUTRAL  $D{Q}_A{Q}_B$  STATE)

Classification: Photosynthetic Reaction Center;  

Organism: Rhodobacter Sphaeroides 

Deposited: 1997-04-18; Released: 1997-10-22

Deposited Author: Stowell, M.H.B.,  Mcphillips, T.M.,  Soltis, S.M.,  Rees, D.C.,  Abresch, E., Feher, G.

Experimental Data snapshot:

Method: X-Ray Diffraction

Resolution: $2.2 A^0$

1AIJ structural view - PyMOL

1AIJ is a 6 chain structure with sequence from Rhodobacter Sphaeroides [1]. These are represented by 3 sequence - unique entities [2].

(Rhodobacter Sphaeroides is a kind of purple bacteria; a group of bacteria that can obtain energy through photosynthesis). 

(Purple Bacteria are Proteobacteria that are Phototrophic: i.e capable of producing their own food via. Photosynthesis). 

1AIJ structural view - PyMOL

Molecule: Photosynthetic Reaction Center (L sub-unit); Chain: L, R 

Molecule: Photosynthetic Reaction Center (M sub-unit); Chain: M, S 

Molecule: Photosynthetic Reaction Center (H sub-unit); Chain: H, T

Basic information about 1AIJ

Full wwPDB X-ray structure validation Report

Photosynthetic Reaction Center - 1AIJ

PS_4.3 Journal/Books Linklist - Collection:

• MDPI - Open Access Publishing

• NCBI - National Center for Biotechnology Information

• Cell.Com - Journal Home

• Journal of Chemical Information & Modeling

• Publishing Journals, Books & Database

• IDEALS Journal Collection

• JACS - Journal of American Chemistry Society

• Science Direct - Journal

• Oxford Press - Journal

• Scolar.Com - (Anything what ever you want to search)

****************************************

Books:

- Photosynthesis Reaction Center - Johann Deisen Hofer*, James R. Norris

- The Reaction Center of Photosynthetic Bacteria Structure and Dynamics - M. Michel*, E. Beyerle (**)

- Molecular Dynamics Simulation of the primary process in the Photosynthetic Reaction Center of Rhodopseudomonas Viridis - H. Treutlein, K.Schulten, J. Deisenhafer*, H. Michel*, A. Brunger, M. Karplus

PS_3. Computational Tools - Molecular Structure:

• Swiss - PDB Viewer (Deep View)

• PyMOL - 3D Structure (Click here for Software Download or here)

        -  PyMOL Tutorial (Click here for PDF View)

• Molecular Graphics Laboratoty (MGL) - (Click here for Software Download) 

• Discovery Studio 3.5 Client - (Click here for Software Download)

• Software Application - Schrodinger Collection

PS_4.2 References - Photosynthesis Reaction Center:

• Molecular Bio-Physics - Amit Kessel Ph.D

• Bacterial Photosynthesis - Mike Jones

• Biological Chemistry Department - David Lawson

• Photosynthesis Reaction Center - Madhu Sudhan Bhusal

• Photosynthesis Reaction Center - Charles Yocum 

• WorldWide PDB - Protein Data Bank

• RCSB PDB - Protein Data Bank

• BioPhysical Society - Molecular Structure & Behavior

• Magnesium in PDB files 101d - 1atr (Part 1) // 99 - PDB files

PS_5. At last - My Work:

"The truth is rarely pure and never simple !!" ~ Unknown

“Great  Things never  came From  comfort  zones.”

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Additional References:

1. Structure of electron transfer flavoprotein - ubiquinone oxidoreductase and electron transfer to the mitochondrial ubiquinone pool (pdf)

2. Structure of the photosynthetic reaction centre from Rhodobacter sphaeroides at 2.65 •A resolution: cofactors and protein-cofactor interactions (pdf)

3. Structure of the reaction center from Rhodobacter sphaeroides R-26: The cofactors* (pdf)

» Summarized the Dissertation Work:

PS_4.4 MikTex - Texmaker Collection:

1) MikTeX - Click here for Download. 

2) TexMaker - Click here for Download. 

Instruction:

• Open MikTeX 2.9 (32/64 bit) folder and install the setup2.9.4250 

• Install Texmakerwin32. 

• Open the Texmaker file and then enjoy with the LaTeX!!  

3) Sample of LaTex Templates - Click here for Download.

4) LaTex Tutorial on You tube (for beginners).

(For more information: Click here).