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Archive for August, 2006

M. Sc. Projects - Kerala University, March 2006

Posted by admin on 28th August 2006

These are the abstracts of the Project presentations made by Chemistry students from University of Kerala for their M. Sc. All these students completed their project work using the web-enabled services provided by Computational Chemistry Portal at IIITM-K under Prof. M. S. Gopinathan and Dr. T. K. Manoj Kumar of IIITM-K.

1. VIBRATIONAL FREQUENCY CALCULATIONS OF PYRONES

by Shibitha Thampy, Dept. of Chemistrym S. N. College, Kollam

Density functional(B3LYP) calculations using aug-cc-pvdz have been made to estimate the vibrational frequencies of 2-pyrone and 4-pyrone in gas phase. The results obtained were compared with the experimental values. Molecular calculations were performed with the GAMESS program. In gas phase model, the molecular behaviour is such that there is no interaction with other molecules. The expansion of the basis set aug-cc-pvdz is augmented correlation-consistent-polarizatio-valence double zeta.

2. DENSITY FUNCTIONAL THEORY CALCULATIONS ON DICHLORO BIS (THIOUREA) ZINC (II) COMPLEX

by Salinichitra L. R., M. G. College, Trivandrum

The work involved the optimization of the geometry of the complex [Zn(tu)2 Cl2]. The structural parameters viz., bond lengths and bond angles were computed and compared with the experimental values of the X-ray diffraction data. The bond lengths and bond angles obtained by computation in general agree with the experimental values. The estimation of atomic charges and calculation of the dipole moment of the molecule are also given. The IR frequencies and intensities of the complex are also predicted. Further explanatory studies are required to compare the predicted values with the experimental values.

3. STRUCTURE OF 2-PYRONE AND 4-PYRONE IN GAS PHASE

By Aneesha, S., S. N. Collge, Kollam

In the present study the molecular structure of 2-pyrone and 4-pyrones in the gas phase have been estimated using density functional calculations. In the gas phase it is assumed that the molecules exists without any interaction with neighboring molecules.

GAMESS(General Atomic and Molecular Electronic Structure System), a high level abinitio package was used. The geometries of the molecules in the gas phase were optimized with Lee, Yang and Parr’s correlational functional(B3LYP). The calculations were done using aug-cc-pVDZ basis sets. The bond lengths and bond angles of the optimized geometries of 2-pyrone and 4-pyrones were estimated. These results were then compared with experimental results reported earlier.


4. COMPUTATIONAL STUDY OF STRUCTURAL MODIFICATION OF PYRONES IN AQUEOUS PHASE

By Jyothilekshmi L. B.; S. N. College, Kollam

In the present study the molecular electronic structure of 2-pyrone and 4-pyrone in the aqueous phase have been estimated using density functional calculations. The calculations were carried using water as solvent. The quantum chemistry package used was GAMESS(General Atomic and Molecular Electronic Structure System), which is an abinitio and semi empirical program. The geometries of the molecules in the aqueous phase were optimized by using Becke’s three-parameter exchange with Lee, Yang and Parr’s correlational functional B3LYP. The basis set used for all calculations was aug-cc-pVDZ. The geometry optimization of the structures in the aqueous phase were performed by self-consistent reaction fiels-polarisation continuum method (SCRF-PCM).

5. ELECTRON AFFINTY AND NMR STUDIES OF PYRONES- A THEORETICAL STUDY

By Veena, S. B.; S. N. Collge, Kollam

Density functional(B3LYP) calculations using aug-cc-pvdz have been made to estimate the electron affinity of 4-pyrone and 2-pyrone and nuclear magnetic shielding tensors.. GAMESS program was used to perform molecular calculations. In gas phase model, the molecular behaviour is such that there is no interaction with other molecules.

The Powerpoint presentations taken for seminar are also attached:

Aneesha

Jyothilekshmi

Veena

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ChemRefer - Open Access Scholar Search

Posted by admin on 22nd August 2006

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need some help!

Posted by satheeshchandran on 20th August 2006

can any one explain the following

boltzmann eqation

the Boltzmann equation tells us just what we want to know: the fraction of all the atoms of a given sort which are in level n=1, or n=2, or whichever we choose. The simplest form provides a ratio of the number of atoms in two particular levels:

Note the two terms on the right-hand side. The first term includes factors describing the degeneracy of each energy level. In a hydrogen atom, there are g = 2 ways that an atom can exist at the n=1 energy level, and g = 8 ways that an atom can arrange itself at the n=2 energy level. Calculating degeneracies for hydrogen is easy, and you can look up the values for more complex atoms.

I wants to know how that value of g=8 ways arrangement when n=2 energy level.

If you answer this, will be very helpful for me ………

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Research Article : A simple time delay model for eukaryotic cell cycle

Posted by admin on 10th August 2006

A simple time delay model for eukaryotic cell cycle

J. Srividhyaa and M.S. Gopinathanb

aIndiana University School of Informatics, Indiana University, Bloomington, IN 47406, USA
bIndian Institute of Information Technology and Management Kerala, Thiruvananthapuram, Kerala 695581, India

Received 7 March 2005; revised 19 December 2005; accepted 28 December 2005. Available online 13 February 2006.

Abstract

We propose a seven variable model with time delay in one of the variables for the cell cycle in higher eukaryotes. The model consists of four important phosphorylation–dephosphorylation (P–D) cycles that govern the cell cycle, namely Pre-MPF-MPF, Cdc25P-Cdc25, Wee1P-Wee1 and APCP-APC. Other variables are cyclin, free cyclin dependent kinase (Cdk) and mass. The mass acts as a G2/M checkpoint and the checkpoint is represented by a saddle node loop bifurcation.

The key feature of the model is that a time lag has been introduced in the activation of anaphase promoting complex (APC) by maturation promoting factor (MPF). This is effected by treating MPF as a time-delayed variable in the activation step of APC. The time lag acts as a spindle checkpoint. Absence of time delay induces a bistability in our model. Time delay also brings about variability in G1 phase timings. The model also reproduces the mutant phenotype experiments on wee1 cells.

Stochasticity has been introduced in the model to simulate the dependence of the cycle time on cell birth length. Mutant phenotypes in the stochastic model reproduce the experimental observations better than the deterministic model.

Keywords: Cell division cycle; P–D cycles; Positive feedback; Time delay; G1/S and G2/M transitions; Bistability

Original Abstract :

http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WMD-4J84T45-1&_coverDate=08%2F07%2F2006&_alid=433602423&_rdoc=1&_fmt=&_orig=search&_qd=1&_cdi=6932&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=4d0f55b7080acb1fe7ee3c0368eb9d98

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Research Article : Redox chemistry of 8-azaadenine: a pulse radiolysis study

Posted by admin on 10th August 2006

Research Article

Redox chemistry of 8-azaadenine: a pulse radiolysis study

G. Pramod 1, H. Mohan 2, P. Manoj 1, T. K. Manojkumar 1, V. M. Manoj 1, J. P. Mittal 2, C. T. Aravindakumar 1 *
1School of Chemical Sciences, Mahatma Gandhi University, Kottayam, Kerala, India
2Radiation Chemistry and Chemical Dynamics Division, Bhabha Atomic Research Centre, Mumbai, India
email: C. T. Aravindakumar (CT-Aravindakumar@rocketmail.com)

*Correspondence to C. T. Aravindakumar, School of Chemical Sciences, Mahatma Gandhi University, Priyadarshini Hills, P.O. Kottayam 686560, Kerala, India.

setDOI(”ADOI=10.1002/poc.1100″)Funded by:

Board of Research in Nuclear Sciences (BRNS), Mumbai

Keywords
8-Azaadenine • redox chemistry • free radicals • radiation chemical • pulse radiolysis • OH-adducts • N-centered radicals • C-centered radicals
Abstract
Aza derivatives of purines and pyrimidines are important class of compounds, which are known for their cytotoxic, antimicrobial, and mutagenic activities. The redox chemistry of 8-azaadenine (8AA) has been investigated using pulse radiolysis technique. The oxidation reactions were studied using hydroxyl radical (.OH), oxide radical anion (O.- and sulfate radical anion (SO4.-), and the reduction reactions were studied using hydrated electron (e) and hydrogen radical (H.). In the reaction of .OH, a bimolecular rate constant of 3.8 × 108 dm3 mol-1 s-1 was determined at pH 6.0. The transient spectrum obtained for the reaction of .OH at pH 6 has an absorption maximum around 340 nm and is assigned to the formation of 8AA-4OH.. The charge population density was calculated theoretically (using Gaussian 98) and it showed that the fourth carbon atom (C(4)) is the most probable site for the attack of .OH. The oxidizing nature of this radical is demonstrated by its reaction with N,N,N,N-tetramethyl-p-phenylenediamine (TMPD). The existence of this species is further supported by theoretical calculations where the absorption maximum of this radical is calculated as 338 nm. The yield of 8AA-4OH. is estimated as around 85%. At pH 10.2, the transient spectrum with maxima at 300 and 350 nm is attributed to the dehydrated 8AA-4OH., which is an N-centered radical of the type 8AA-N(9).. In the reaction of O.- (pH 14) a transient spectrum with similar features is observed. Therefore this is also assigned to 8AA-N(9).. A bimolecular rate constant for this reaction is determined as 4.2 × 108 dm3 mol-1 s-1. In the reaction of SO4.- at pH 6, the transient spectrum having max at 320 nm is attributed to the formation of a neutral radical of 8AA (8AA-N(6).), which is formed by the deprotonation of the initially formed radical cation. But at pH 10.2, the spectrum is found to be similar to the one observed in the reaction of O.- and hence it is assigned to the formation of the nitrogen-centered radical 8AA-N(9).. In the reaction of e, a second-order rate constant of 1.8 × 1010 dm3 mol-1 s-1 is determined at pH 6 and the transient absorption spectrum with max at 330 nm is assigned to the protonated electron adduct of 8AA (8AA(NH.)). The reducing nature of this intermediate is confirmed by the formation of methyl viologen radical cation (MV.+) from its reaction with MV2+. The transient intermediate in the case of the reaction of H. is proposed as 8AA-C2(H)N(3). at pH 1.Copyright © 2006 John Wiley & Sons, Ltd.Original Article Abstract : http://www3.interscience.wiley.com/cgi-bin/abstract/112695316/ABSTRACT


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