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Molecular modelling and computational chemistry

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DILRAJ KAUR SEHMI M PHARM 3 MOLECULAR MODELLING AND COMPUTATIONAL CHEMISTRY Molecular modelling and graphics are extremely important tools used in disciplines that require an understanding of the structure and function of molecules. The ability to visualise molecules and in turn derive important structural information from them has been a great step in science, allowing the creation of novel drugs or the better understanding of current molecules of interest. The production of a 3-D model needs input regarding the Cartesian coordinates of individual atoms in space. These are obtained from long used procedures such as X-ray crystallography, NMR spectroscopy or mathematical manipulation. For visualisation of the model generated by this information, molecular graphics is necessary so as to display the model on a computer screen. The basic input required for generation of the 3-D model will depend on what sort of data can be extracted from the molecule in question. If the compound conforms to the requirements for X-ray crystallography then the information obtained will pertain to the structure as a solid crystalline phase. NMR spectroscopy is generally carried out on molecules in solution and currently cannot provide 3-D structures for molecules larger than 25kDa. When one cannot get any experimental data theoretical approaches to calculation are available. ...read more.


corresponds to repulsion of the proton by the atomic nuclei in regions where low electron density exists and the nuclear charge is incompletely shielded. When a proton approaches a positive region of the molecule, the repulsive interaction results in an increasing positive potential energy (blue), as a proton approaches a negative region an attractive interaction results in negative potential energy (red). The more red / blue differences, the more polar the molecule. If the surface is largely white or lighter color shades, the molecule is mostly non-polar. The electrostatic surfaces of the three ACE inhibitors have similarities and differences. The similarity of all three is that they all have similar regions of positive electrostatic potential due to the common presence of a proline moiety. They all have negative electrostatic potential (red) due to presence of the electron rich carbonyl group next to nitrogen in proline and the electron rich carboxylic acid attached to one of the carbons in the proline. However since the remaining parts of the molecules are different from each other, the electrostatic potential is different. Overall, Succinyl proline appears to be more polar due to the dark shades of red and blue and less of white as compared to Captopril. ...read more.


The tertiary structure of the enzyme is formed by interaction between ?-helices and �-pleated sheets. The activity of the enzyme depends on the tertiary structure. Figure 3 shows the lisinopril molecule (dark blue) and the active sites on the enzyme (yellow). Also present is a zinc active site on the enzyme where the zinc atom on lisinopril (purple) binds on an ?-helix of the enzyme. The zinc atom is bound to the lisinopril molecule at the carboxylate where the Zn2+ binds. Figure 4 shows the structure of lisinopril aligned parallel to the helix with the zinc active site and a clearer picture of the physical docking of the molecule within the enzyme. It also gives an idea of the various interactions in play. For example, the phenol ring is in contact with a hydrophobic group branching from the helix. Conclusion The objectives of the practical were met and the uses and applications of molecular graphics and molecular modeling was also explored via first hand manipulation of ISIS Draw and Viewer Lite. The molecule properties were analyzed using X-ray crystallography and molecular mechanics through which the geometry and energy of the molecule, lisinopril was found. This led to the appreciation of the uses and growth in the field of molecular modeling though the data about molecular structure obtained from these sources does not correspond to the real world. ...read more.

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