Open Access Repository of Indian Theses

R, KARTHIKEYAN

Abstract
Development of Value Added Products from Keratins and their Applications in Stingray Fish Leathers
	Development of value added products from waste materials has become a matter of increasing concern in developing countries, since this constitutes the source of economic returns. Treatment and conversion of by-products into value added products would help not only to strengthen the economy of country but also to protect the environment from pollution and to improve the socio-economic status of the people by creating employment. Keratin is abundantly available as a byproduct from poultry, slaughterhouse, tanning and fur processing industry. Chicken feathers, cattle and buffalo horns, tannery hair are the abundantly available sources of keratin which could be successfully converted into high value products on a large scale. Some successful attempts have been previously made to covert the keratinous waste into keratin hydrolysate for application in tanning and retanning process.  The existing keratin hydrolysate prepared by alkali hydrolysis for retanning and tanning purpose imparts colour to the leather, which is not desirable and moreover the product is used as an auxiliary along with conventional chrome tanning and retanning process and does not have antimicrobial and tanning potency.  In the present investigation, an attempt has been made to conduct studies on the development high value added products from horn meal and chicken feathers and a detailed study has been conducted for their application in tanning and retanning.
	Horn meal hydrolysate prepared from raw horns of cattle and buffaloes by hydrothermal process is a mixture of water soluble and low molecular weight peptides with average particle size of 3.84 µm.  The horn meal hydrolysate mixed with chromium(III) salt has been used as a high exhaust chrome tanning agent. A detailed tanning study has been conducted with pickled goat skins and the exhaustion of chromium in the tanning bath was found to be above 90%. Further a study has been conducted to introduce Cr(III) into the keratin thereby providing a chromium–keratin complex that would overcome the existing problems in the conventional basic chromium sulphate.  Cr(III) has been introduced into the keratin by treating the chicken feathers in a solution containing acidified dichromate.  Dichromate at low pH is a very strong oxidising agent and is capable of oxidising disulphide bonds in chicken feathers thereby Cr(VI) has been reduced to Cr(III) without using any conventional reducing agents such as molasses or SO2. The FT-IR spectroscopy of chromium–keratin complex confirms the oxidation of cystine disulphide bonds on the basis of their distinctive, strong sulfur-oxygen vibrations.  MALDI-TOF mass spectrometry analysis reveals that chromium–keratin complex contains species of varying molar masses ranges from 102 to 617Da. Computer aided colour analysis reveals that chromium–keratin complex is somewhat greener and the overall colour difference between chromium–keratin complex and commercial BCS is very less (7.029) indicating that the new tanning material does not impart any inconvenient colour to the resulting leather. The leathers produced from the chromium–keratin complex were comparable in all the properties to the leathers from commercial BCS as evidenced from the DSC analysis, visual assessment, physical testing data and scanning electron microscopic studies.
	Keratin-silica based retanning agent (KH-Si) has been prepared from chicken feathers to overcome the existing problems in the conventional keratin hydrolysate (KH) used as a retanning agent. Sodium silicate lye was used to convert the chicken feathers into value added product suitable for retanning applications with added properties like antimicrobial character and retanning action. A comparative retanning study has been conducted between KH and KH-Si using wet blue goat skins. Compared with KH, the physical properties, organoleptic properties and general appearance of the crust leathers retanned with KH–Si was found to be better.  Both KH and KH-Si have also been characterized using FT-IR, TGA, MALDI-TOF mass spectrometry, powder XRD, EDAX-SEM, Agar-well diffusion method, HPLC and computer aided color measurement. 
	Apart from testing the newly prepared tanning and retanning agents  with goat skins, a special study has also been conducted on stingray skins because we have another problem associated with fish skins which are the byproducts of fish processing industry. The important byproducts of meat industry viz. hides and skins are commonly converted into leather. Similarly, fish skins are a by-product of the fish processing industry that can also be successfully processed into leather. Stingrays are existing in enormous numbers in the Indian seas and India is one of the world’s leading stingrays fishing nation. But in India, conversion of stingray fish skin into leather is unfamiliar and most of the stingray skins are exported to foreign countries in the form of dried fish and some of the skins are wasted by the local vendors. To create awareness and to highlight stingray skin processing, studies have been conducted to develop technologies for the preparation of leathers from stingray skins.  
	A modified chrome tanning system has been developed for the preparation of soft leathers from stingray fish skins. Initially the calcium content in the raw stingray skin has been determined by atomic absorption spectroscopy. To minimize the calcium content, the delimed pelts were treated with hydrochloric acid and the pickling process was repeated twice with intermediate ageing. The pickled pelts were then treated with fatliquor along with chromium-keratin complex. SEM-EDX investigations have been made on stingray denticles to reveal the mineral and structural characteristics. Comparison skins were also processed by conventional chrome and vegetable tanning methods and the study reveals that fibre splitting during pickling and fatliquoring during tanning in the modified chrome tanning experiment result in soft leather as evidenced by histological studies and scanning electron microscopic analysis. 
	Further a lime and sulphide free method for the preparation of leathers from stingray skins has been developed using Sodium Lauryl Sulphate (SLS). SLS has been used to remove the pigments adhered with the stingray skin, as well as to open up the hard fibre structure. SLS also plays an important role in the disruption of fibre bundles of stingray skin thereby extracting the proteoglycans. This result is confirmed by histological analysis, scanning electron microscope analysis and FT-IR analysis. In addition, special footwear termed as massage footwear has been prepared from stingray leathers where the stingray leather was used as insole/insock material to stimulate the reflex points present in the foot. Foot scan analysis confirms that stingray insoles do not offer any adverse effect or discomfort, fairly it provides massage action to the person wearing the footwear.




English

Development of Value Added Products from Keratins and their Applications in Stingray Fish Leathers

Ghosh, Ranjana

PAGE  




Synopsis 


SYNOPSIS

The thesis entitled “Towards the synthesis of camptothecin analogues and development of new methodologies” has been divided in to three chapters.
Chapter-I: This chapter deals with an introduction to cancer, including some of potent anticancer biogenetically novel alkaloid, marine macrolides and the approaches cited in the literature total synthesis of camptothecin analogues, including the total syntheses.
	Chapter-II: This chapter deals with towards the synthesis of camptothecin analogues.
Chapter-III: This chapter describes the development of new methodologies pertaining to the application of microwave radiation in organic synthesis. Including one-pot synthesis of -aminophosphonates, aynthesis of aryl hydrazides and stereoselective synthesis of aryl- substituted (E)-and (Z)-allyl iodides and bromides.
Section-A: This section describes montmorillonite clay-catalyzed one-pot synthesis of -aminophosphonates. 
Section-B: This section describes the InCl3-SiO2 catalyzed electrophilic amination of Arenes: as a facile and rapid route aryl hydrazides.
Section-C: This section describes the montmorillonite clay-catalyzed stereoselective synthesis of aryl- substituted (E)-and (Z)-allyl iodides and bromides. 
CHAPTER-I: An introduction to cancer including some potent anticancer biogenetically novel alkaloid, marine macrolides and the approaches cited, including the total synthesis camptothecin.




CHAPTER-II: 

Synthesis of camptothecin analogues

In continuation of our programme on the synthesis of biologically active antitumor agents, we under took a demanding programme on the total synthesis of camptothecin analogues. 
Camptothecin has a unique bifunctional (4-1-hydroxy) 6 membered lactone ring that is labile to alkali and alkaline reagents. Structure Activity Relationship (SAR) studies revealed that the 6-memberedlactone ring is essential for bio-activity. In view of these observations, we reasoned that isosteric replacement of 6-memberd ketone 2 might be an useful molecule with higher activity and also provide additional information pertaining to SAR. 







By a retrosynthetically analysis compound 2 can be cleaved into two major fragments tricyclic amine 3 and a chlorolactone 4 (Scheme 1).
The primary object was to prepare N-carboethoxy-3-keto pyrrolidine 16 in large quantities from inexpensive and readily available starting materials. (Scheme 2).















Glycine 12 on treatment with 2 eq of aq 4N. NaOH and ethylchloroformate 13 gave N-carboethoxy glycine 14 in 90% yield. The compound 14 on treatment at room temperature with methanol in presence of BF3. OEt2 furnished N-carboethoxy methylglycinate 10. Compound 10 and ethylacrylate 11 underwent tandem N-alkylation and Dieckmann cyclization to afford 15 Refluxing with 6N aq HCl yielded the key intermediate N-carboethoxy-3-keto pyrrolide 16 in 20% yield. The compound 5.was obtained pure from 2-nitrobenzaldehyde 18 by a reduction process with FeSO4 in presence of ferrous sulphate and ammonium hydroxide in 70 % yield. The compound 16 failed to an reaction with 5 under a variety of reaction. The compound 16 with 5 and PTSA were mixed and then heated at 190oc for 5 min under nitrogen atmosphere. 








Therefore an alternative method ABC ring system from commercially available dimethyl acetylene dicarboxylate 6 was developed as outlined in (Scheme 3).










Further treatment of 6 with 5 in the presence of 3-4 drops of H2SO4 in MeOH at 65oC for 6 h. gave 19. in 60% yield as a solid. Reduction of compound 19 with LAH THF at 0oC - r.t for 12 hr yielded diol 20. Compound 20 as treatment with MsCl in the presence of Et3N in DCM at 0oC under nitrogen atmosphere afforded compound 21, which was unstable to column chromatography. Immediately therefore treatment with liq. NH3 in MeOH (6:4) afforded compound 3 in 27% yield. 
Synthesis of chlorolactone 4:
Furfuryl alcohol was treated with propargyl bromide in presence of aq. NaOH and tetra butylammonium hydrogensulfate (PTC) to give the alkylated terminal alkyne 22 in 70% yield. The alkynyl group in Compound 22 on treatment with potassium tert-butoxide in tert-butanol at 83oC, underwent isomerization to on allene followed by an intramolecular Diels-Alder reaction and base induced ring opening to afforded uneventfully the cyclised compound 23. The double bond in compound 23 was reducted using hydrazine hydrate and hydrogen peroxide in EtOH at –10OC  to obtained compound 24. Protection of the secondary hydroxy group of compound 24 as its benzyl ether using NaH yieded compound 25 in 70% yield. 
The next objective was the conversion of furan ring to a hydroxy butenolide system. This was achieved by treatment of compound 25 with rosebengal, diisopropylethylamine under oxygen atmosphere in DCM at –78oC to yield the went photo Diels-Alder product which underwent opening of peroxy ring to give the compound 26 in 87% yield. Compound 4 on treatment with thionylchloride and cat. Amount of DMF (Vilsmeyer conditions) in CHCl3 at room temperature afforded 4 as the sole product in 80% yield (Scheme4).










  





Condensation of pyrroloquinoline (23) with chloro lactone (4):
	The coupling reaction in between pyrroloquinoline 3 and chloro lactone 4 was achieved by using pyridine anhydrous acetonitrile to afford aldehyde 27 which was further treated with sodiumacetate and acetic anhydride to furnish the benzyl ether 28 in a 25% overall yield. (Scheme 5).  
The compound 28 was deprotected with 5% Pd-C under hydrogen atmosphere to give the alcohol 29 in 80% yield. 








 The alcohol 29 was oxidized with IBX in dry DMSO and DCM to deliver the keto compound 30 in 93% yield. The keto 30 was selectively alkylated at 4th position on treatment with ethyliodide using K2CO3 and a phase transfer catalyst in acetone to give compound 31. Compound 31 it was reduced by using NaBH4 in methanol at 0oC to give the single isomer alcohol 32. The compound 32 was converted to the mesylated 33 with MsCl and triethylamine in DCM. The compound 33 was transformed into the alkene 34 by refluxing in CHCl3 in the presence of Et3N. Dihydroxylation of 34 with OsO4 / NMO in acetone/ water gave the diol 35. The diol 35 was treated with PDC or DMP in dry DCM at room temperature under nitrogen atmosphere. I did not get the target molecule 2 and i tried to alternative oxidation methods IBX, DMP, Jones oxidation failed to under above reaction conditions (Scheme 6).



























CHAPTER-III
Microwave assisted organic reactions
The rapid heating of foodstuffs in microwave ovens is routinely used by a significant proportion of mankind. However people have recognized other potential applications for this method of heating and scientists engaged in a number of disciplines have applied the rapid heating associated with microwave technology to a number of useful processes. The technique has also found use in range of decomposition processes including hydrolysis of proteins and peptides. Application to inorganic and solid state synthesis has also been shown to have significant advantages. The purpose of this review is to highlight the applications of microwave radiation to organic reactions, organic synthesis is an area, which can benefit significantly from this technology
Section-A: Montmorillonite clay-catalyzed one-pot synthesis of -aminophosphonates
 -aminophosphonates are an important class of biologically active compounds and their synthesis has received an increasing amount of interest because of their structural analogy to -amino acids. -Aminophosphonates act as peptide mimics, enzyme inhibitors, antibiotics and pharmacology agents. Generally, they are prepared by the addition of phosphorus nucleophiles to imines in the presence of either a base or an acid. Lewis acids such as SnCl4, BF3. OEt2, ZnCl2, and MgBr2 have been used for this transformation. However, these reactions cannot be carried out in a one-pot operation with a carbonyl compound, amine and diethyl phosphite, because the amine and water that exist during imine formation can decompose or deactivate the Lewis acids. In order to circumvent some of these problems in one-pot procedures lanthanide triflates and indium triochloride have been used as catalysts. Clay catalysts make the reaction processes convenient, more economic, and environmentally benign and act as both Bronsted and Lewis acids in their natural and ion-exchanged forms. A novel and highly efficient procedure for the synthesis of -amino phosphonates using an inexpensive and reusable catalyst, montmorillonite KSF under microwave irradiation has been developed (Scheme 7). 




Thus reaction of benzaldehyde, benzylamine and diethyl phosphite in the presence of KSF clay resulted in the formation of -amino phosphonate in 90% yield after 3 minutes irradiation under microwave. Similarly various aldehydes and amines were reacted with diethyl phosphite to afford the corresponding -amino phosphonates in high yields. The reactions proceeded smoothly under solvent-free conditions and was completed within 3-5 min of reaction time. Both aromatic and aliphatic aldehydes provided excellent yield of products (80-92%) in a short reaction time whereas ketones gave phosphonates in good yields (65-80%) after a longer irradiation time (6-8 min) several aromatic, ,-unsaturated, heterocyclic and aliphatic aldehydes worked well to give the phosphonates in high yields (Table 1).
 







































Section-B: InCl3-SiO2 catalyzed electrophilic amination of arenes: a facile and rapid synthesis of aryl hydrazides
As a continuation of studies on surface mediated solid state reactions coupled with microwave irradiation, an efficient and rapid method for the synthesis of aryl hydrazides through the electrophilic amination of electron rich arenes with diethyl azodicarboxylate using indium trichloride supported on SiO2 in solvent-free conditions was developed.



Aryl hydrazides were formed in high yields in short reaction time when the reactants were admixed with InCl3-SiO2 in Erlenmeyer flask and exposed to microwave irradiation at 450 W using BPL, BMO-7—T focused microwave oven (Scheme 8). The reactions were clean and completed in 2-6 min with high regioselectivtiy. The less reactive substrates like anisole, naphthalene, 3,4-dimethoxybromobenzene, 1,4-dimethoxybenzene and xylene smoothly underwent electrophilic amination to afford corresponding hydrazides in good yields under microwave irradiation. The electrophilic amination reaction of arenes with diethyl azodicarboxylate in the presence of BF3.OEt2 or CF3SO3H, or TFA resulted in a complex mixture of products and also the amination was much slower using LiClO4 as a catalyst compared to reactions carried out in the presence of indium trichloride-SiO2 under microwave irradiation. The reaction rates and yields were dramatically enhanced by microwave irradiation. This is due to the absorption of microwave energy by the polar media as well as polar reactants, which generates heat energy as required to promote the amination reaction. The reaction is highly regioselective affording high yields of products in a short reaction time.
The present study has unequivocally confirmed that the conventional heating in 1,2-dichloroethane and longer reaction times (8-22 h) required for the amination of arenes are improved using microwave irradiation, which is becoming an alternate and substitute heating source. For example, the treatment of 1,2-dimethoxybenzene with diethyl azodiocarboxylate in the presence of indium triochloride-SiO2 (3 wt equiv of arene) under microwave irradiation at 450 watts for 3 min gave the corresponding hydrazide in 88% yield after filtration through a small silica gel column, whereas under conventional heating conditions, the hydrazide was obtained in 75% yield after 10 h of heating in 1,2-dichlroethane (Table-2). Invariably, the products obtained by microwave irradiation were purified with more ease. The hydrazides thus obtained were easily converted to their corresponding anilines by reduction with zinc dust in acetic acid. 






























































Section-C: Montmorillonite clay-catalyzed stereoselective synthesis of aryl- substituted (E)-and (Z)-allyl iodides and bromides
The Baylis-Hillman reaction continues to attract organic chemists as it constructs a novel cabon-carbon bond between the -position of activated alkenes and carbon electrophiles leading to the formation of synthetically attractive and useful class of molecules with chemospecific functional groups. 
Several methods have been developed for the direct conversion of 3-hydroxy-2-methylene alkanoates to 2-(halomethyl) alk-2-enoates, including those using HBr-H2SO4, NBS-Me2S, PBr3, MsCl-Et3N and CuBr2-silica gel. Recently, the synthesis of 2-(halomethyl) alk-2-enoates has been reported from the acetyl derivative of Baylis-Hillman adducts using MgBr2-THF and AlCl3-CH2Cl2. however, there is no report of the synthesis of allyl iodides from Baylis-Hillman adducts. 
In continuation of studies on the applications of clays for various transformations, the remarkable catalytic activity of montmorillonite clay for the synthesis of 2-(iodo or bromomethyl) aryl-2-enoates from 3-hydroxy-2-methylene alkanoates (Scheme 9). In addition, microwave irradiation, which has become a powerful tool for the rapid synthesis of a variety of organic compounds, is used to enhance the rates of reaction. 




The treatment of Baylis-Hillman adducts, derived from acrylate esters, such as 3-hydroxy-2-methylene alkanoates with clay-supported NaI and NaBr under microwave irradiation led to the formation of the corresponding (Z)-allyl iodides and bromides in high yields (Table 3). The irradiation was carried out a 450W using a BPL, BMO-700T domestic microwave oven. The reaction temperature reached 110oC after 3 min pulsed irradiation (1 min on with 20 s off interval) at constant power. The same reaction, under thermal conditions, at 110oC took 5-8 h to afford yields comparable with those that are obtained by microwave irradiation. The reactions of Baylis-Hillman adducts derived from acrylonitrile, that is 3-hydroxy-2-methylene alkanenitriles with NaI and NaBr in the presence of KSF clay, produced the corresponding (E)- amd (Z)-allyl iodides and bromides in high yields (Scheme 10 and table 3).






	
































































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Evaluating Resource Potential of Gas-Hydrates using Effective Medium Theory from Geophysical Data

SHAMIM, MD. TABREZ ANWAR

A knowledge-based approach to protein structure prediction

Pallela, Ramjee

Abstract
Ab initio (HF, MP2, and CCSD(T)) and DFT (B3LYP) calculations were done in modeling the cation (H+, Li+, Na+, K+, Ca+2, Mg+2, NH4+ and NMe4+) interaction with aromatic side chain motifs of four amino acids viz. phenylalanine, tyrosine, tryptophan and histidine. As the metal ion approaches the -framework of the model systems, they form strongly bound cation- complexes, where the metal ion is symmetrically disposed with respect to all ring atoms. In contrast, proton prefers to bind covalently to one of the ring carbons. The NH4+ and NMe4+ ions have shown NH interaction and CH… interaction with the aromatic motifs. The interaction energies of NH… and CH… complexes are higher than hydrogen bonding interactions and thus the orientation of aromatic side chains in protein is effected in the presence of ammonium ions. However, the regioselectivity of metal ion complexation is controlled by the affinity of the site of attack. In the imidazole unit of histidine the ring nitrogen has much higher metal ion (as well as proton) affinity compared to the -face, facilitating the in-plane complexation of the metal ions. The interaction energies increase in the order of 1-M < 2-M < 3-M < 4-M < 5-M, for all the metal ion considered.  Similarly, the complexation energies with the model systems decrease in the following order: Mg+2 > Ca+2 > Li+ > Na+  > K+  NH4+ > NMe4+.  The energy decomposition analysis performed by block localized wavefunction – energy decomposition (BLW-ED) method indicates that the interaction of these  systems with metal cations is characterized by contributions from polarization energy, electrostatic energy and charge-transfer energy, with the contribution of the first being dominant. Charge transfer energies contribute in significant proportions, in fact more than the electrostatic energy contribution in many cases. The polarization energy contribution is superior to others (60-80%), followed by charge transfer (20-30%) in case of the proton affinities of the aromatic complexes at various sites, The results obtained in this analysis are in contrast with the earlier energy decomposition schemes, as the contribution of charge transfer is competing with the electrostatic contribution. The variation of the bond lengths and the extent of charge transfer upon complexation correlate well with the computed interaction energies.
The cooperativity of the two significant non-covalent interactions viz. cation interactions is demonstrated quantum mechanically, and with the aid of database analyses. It is observed that, subtle  interactions become substantial in the presence of a metal ion, and the cooperativity results in mutual stabilization. Quantum chemistry calculations have revealed that the  - interactions, which are traditionally considered as subtle, with a range of 2-4 kcal/mol, will be substantial, ranging up to 17-18 kcal/mol in the presence of a metal ion. The metal ions have higher affinity towards a  dimer compared to a single -moiety. This is further substantiated with the large occurrence of M- motifs in both CSD and PDB.  In the course of action, the possible interactions between cation and the -moiety of the aromatic residues present in all the proteins of Protein Data Bank (PDB) are evaluated and stored as a publicly available web-based database cation-aromatic database (CAD). All the metal ions and protonated basic amino acid residues are considered as cations. The motifs are defined on the basis of distance between the cation and the centroid of the aromatic ring.  Of these pairs, those having the cation within a cylinder with the arene ring as a base are identified. This geometric criterion enables the identification of strong cation- interactions. CAD is freely accessible via the Internet at http://203.199.182.73/gnsmmg/databases/cad/. 

The present chapter addresses the apparent disparity in the structural parameters of the X-ray structures and theoretical models of cation-π complexes in biological and chemical recognition. Hydrated metal ion (Li+, Na+, K+, Mg+2, Ca+2) complexes with benzene (cation-π) are considered as model systems to perform quantum mechanical calculations in evaluating the geometrical parameters and interaction energies of these complexes. The computations disclose that there is a variation in the structural parameters as well as in the interaction energies of these complexes with the multiple additions of water molecules. The distance between the cation and the π-system increases with the addition of water molecules, delineating the influence of solvent or the neighborhood atoms on the structural parameters of cation-π systems present in crystal structures.
The chapter describes a comprehensive database named, Protein Ligand Interaction Database (PLID), created with 6,295 ligands bound to proteins extracted from the Protein Data Bank (PDB). This is by far the most comprehensive database of physico-chemical properties, quantum mechanical descriptors and the residues present in the active site of proteins. Datamining analysis performed using decision tree, random forest and neural network techniques on the binding pockets reveals that the binding preference of a given ligand to a set of proteins is guided by certain combinations of amino acid residues present at the binding site. Further, it is found that the function of enzymes can also be correlated to the binding site residues. It is a publicly available web-based database at http://203.199.182.73/gnsmmg/databases/plid/.



Isolation and Characterization of Native Collagens from Marine Demosponges

Singh, Suruchi

iAbstract 
A number of studies on conducting polymers relating to their synthesis, 
characterization, morphology and applications in various fields have been reported in 
literature. In spite of these interesting developments, there is a scope to improve the 
properties of conducting polymers and their applications. 
In the present thesis, an attempt has been made in the following aspects:                
(i) Synthesis and characterization of polyaniline salts, complexes, composite as 
well as novel optically active polyaniline by aqueous and emulsion polymerization 
pathway, and evaluation of polyaniline as recyclable polymer based solid catalysts for 
various organic transformations.  
(ii) Evaluation of polyaniline-maleicacid-dodecylhydrogensulfate salt-coated 
ceramic material as gas sensor material for various toxic gases such as NH3, CO2, SO2 & 
H2S. 
(iii) Preparation, characterization of polyaniline 3D nanofiber networks using 
sulfonated-p-cresol as novel dopant by inverted emulsion polymerization method and 
evaluation as gas sensor material for ammonia gas sensor. 
(iv) Preparation, characterization of nanostructured (dendrite) polyaniline-
polystyrene film and evaluation as ammonia sensor.  
(v) Synthesis and characterization of nanoporous polyaniline salt using ternary 
surfactant as novel soft template.  
This thesis is divided into five chapters. 
ii
Chapter 1: Introduction  
 
In this chapter a review of intrinsically conducting polymers (ICPs) with 
emphasis on conducting polymers is presented. Conducting polymers have emerged as an 
important class of electronic materials because of their potential applications as catalyst, 
electrochromic displays and microelectronic devices etc. A large number of conducting 
polymers such as polyacetylene, polypyrrole, polythiophene and polyaniline have been 
synthesized and characterized in recent years. Among these conducting polymers, 
polyaniline has been considered as an extremely interesting and unusual member of 
polymers having the delocalized π electrons. Conducting polyaniline is basically poly 
(paraphenylene amineimine) in which its oxidation state can be varied from the fully 
oxidized (pernigraniline) to fully reduced (leucoemeraldine) states. The most stable 
emeraldine state is 50% oxidized form of polyaniline (Figure 1).   
A number of studies on conducting polyaniline relating to their structure, 
morphology, electrochromic and solid-state properties have been reported in literature. 
The literature provides an account of various routes adopted in the synthesis of 
conducting polyaniline for its potential applications. Extensive research is being carried 
out on conducting polyaniline throughout the world. However, synthesis of commercially 
valuable conducting polyaniline material is still a challenging research. In this regard, we 
have synthesized and characterized various conducting polyaniline materials by simple 
routes. Organic transformations were carried out using polyaniline salts, complexes, 
composite and optically active polyaniline as reusable polymer based catalyst. Sensor 
studies for various toxic gases (NH3, CO2, SO2 & H2S) were carried out using polyaniline 
materials in the form of bead, pellet and film.  
iii
Figure 1: Different states of polyaniline. 
 
N
H
N
H
N
H
N
H
n
n
N
H
N
H
N N
N
n
N N N
a)
b)
Completely reduced polyaniline
c)
Half-oxidized polyaniline
Fully oxidized polyaniline
n
N
H
N
H
N N
Oxidized form
d)
Reduced form
y 1-y
 
 
iv
Chapter 2: Characterization techniques and materials 
 
The various techniques adopted to characterize the polyaniline salts, complexes, 
composite, film, optically active polyaniline base and organic compounds are briefly 
discussed in this chapter. The preparation of samples for analysis and materials for 
synthesis are also described. 
Chapter 3: Organic transformations by polyaniline catalysts 
 
This work deals with the synthesis of polyaniline salts, complexes, composite as 
well as novel optically active polyaniline by aqueous and emulsion polymerization 
pathway, their characterization and evaluation of polyaniline as recyclable polymer based 
solid catalysts for various organic transformations.  
3A: Polyaniline salts, complexes and composite as polymer based solid acid                      
       catalyst 
 
 In this work, polyaniline salts, complexes and composite were investigated as 
polymer based solid acid catalysts for various organic transformations such as protection 
(Yields: 85-98%) and deprotection of aldehydes (90-96%), synthesis of bisindoles                  
(38-99%) and condensation reaction for the synthesis of coumarins (92%).  
3B: Chiral polyaniline base catalyst 
An optically active polyaniline [Poly(2-anilinomethylpyrrolidine)] was 
synthesized, characterized by circular dichroism, UV-Vis, FT-IR as well as NMR 
analysis and used as an organo polymeric base catalyst for Aldol reaction (20-73%).                            
The effect of the nature of the catalyst, amount of catalyst, mole ratio of reactants, 
time, solvents and temperature of reaction were studied to establish the optimum reaction 
conditions. The reusability of the polyaniline based solid acid & base catalysts were 
checked by employing the recovered catalyst in the reactions. The synthesized 
vpolyaniline based catalysts were successfully evaluated as solid acid or base catalyst with 
desired features such as easy preparation, easy recovery, simple work-up procedure, 
higher yield, less time, reusable and eco-friendly nature. 
Chapter 4: Polyaniline as sensor materials for toxic gases  
 
4A: Sensing properties of polyaniline-maleicacid-dodecylhydrogensulfate salt to  
       the toxic gases 
 
This chapter deals with the results of novel polyaniline-maleicacid-
dodecylhydrogensulfate salt coated ceramic material as gas sensor, capable of operating 
at room temperature for toxic gases (Chapter-4A). The change in resistance of 
polyaniline materials for NH3, CO2, SO2 & H2S gases at different concentrations (10, 
100, 1000 & 10000 ppm level) was monitored for sensor characteristics. The stability of 
the polyaniline material under continuous exposure of different gases was also studied. 
This novel gas sensor material has desirable features such as excellent sensing ability, 
stability, low cost, fast regeneration time (~1-2 min), operable at room temperature with 
simple experimental set up.  
4B: Polyaniline-3D nanofiber network synthesized by inverted emulsion  
       polymerization route: Sensor material for ammonia gas 
 
   This work deals with the synthesis and characterization of polyaniline-3D 
nanofiber network via inverted emulsion polymerization pathway using sulfonated-p-
cresol (SPC) as novel dopant, benzoyl peroxide (BPO) as oxidant and sodium lauryl 
sulfate (SLS) as surfactant (Chapter-4B). The synthesized polyaniline salt in 3D 
nanofiber networks having an average diameter 40-160 nm and reasonable conductivity 
(0.1 S/cm), were obtained in high yields (134 %) with the use of [SPC]/[An] ratio 3, 
[SLS]/[SPC] ratio 0.1 and benzoyl peroxide [BPO] (0.12 M) under stirring condition at a 
vi
temperature of 40°C for 24 hrs. This polyaniline in 3D nanofiber salt was well 
characterized by SEM, infrared, electronic absorption spectroscopy, X-ray diffraction and 
elemental analysis.   
The synthesized polyaniline nanofibers has been evaluated as sensor material for 
ammonia gas with advantages such as less response time, fast reproducibility, operable at 
room temperature with simple experimental set up.  
4C: Synthesis of polyaniline-polystyrene (PPSt) film by solution blending  
       technique: Sensing properties for ammonia gas 
 
In this work, PPSt films were prepared by solution blending with increasing 
amount of polyaniline, i.e. 3.7 (1 mL), 7.2 (2 mL) and 10.4 (3 mL) wt%. PPSt film was 
well characterized by resistance measurements, SEM, infrared spectroscopy, TGA and 
UTM techniques (Chapter-4C). Scanning electron microscopy (SEM) of the PPSt film 
prepared using 10.4 wt% polyaniline solution showed a nanostructured (dendrite) 
morphology. The prepared nanostructured film was tested for its efficacy as sensors to 
ammonia gas by monitoring the changes in resistance. The PPSt film had several 
advantages such as high reproducibility, low response time and ability to be operate at 
room temperature with simple experimental set up.  
4D:  Synthesis of nanoporous conducting polyaniline using ternary surfactant 
This work deals with the preparation of novel nanoporous polyaniline using 
ternary surfactant [a mixture of CTAB (cationic), SLS (anionic) and F-68 (nonionic 
surfactants)] as a soft template by aqueous polymerization method (Chapter-4D). The 
influence of synthesis conditions such as time of polymerization, temperature of the 
reaction, acids, oxidizing agents and reaction condition (stirring/static condition) etc., on 
the properties of porous polyaniline (PANI) were investigated. The synthesized PANI 
vii
was well characterized by SEM, TEM, FT-IR and X-ray diffraction analysis. Nanoporous 
PANI in good yield (84 wt % with respect to aniline used) and reasonable conductivity 
(10-2 S/cm) with 100 nm range was obtained under the following reaction conditions: 
sodium persulfate-1.19g, R-CSA-2.32g, constant stirring for 4 hrs at 0-5°C. Sensor 
studies on the porous PANI material revealed that this material does not show sensitivity 
to toxic gases. 
Finally, as an extension of our research work, we have synthesized and characterized 
the following materials:  
¾ A stable polypyrrole salt by inverted emulsion polymerization pathway using 
benzoyl peroxide as novel oxidizing agent, p-toluene sulfonic acid as dopant and 
sodium lauryl sulfate as surfactant.  
¾ Nano and microspheres of novel poly(aniline-formaldehyde) under static 
condition by a simple mixing process using a mixture of metal chlorides 
(FeCl3+AlCl3).  
Chapter 5: Summary   
The results of the thesis work are summarized in this chapter.  


Interactive Effects of UV-B and Soil Mineral Nutrient Status on Selected Vegetable Crops

Bharati, Kumar Avinash

Studies on enumeration and potentials of medicinal plants used in ethnoveterinary system of Sikkim (Himalayas)

BHARGAVA, VINAY K.

Assessing the potential role of Coleoptera (Insecta) as bioindicators in Simbalbara Wildlife Sanctuary, Himachal Pradesh

C.M., Santosh Kumar

Synopsis
The Arunachal Pradesh state in India is epidemic for malaria, caused by P.vivax and P.falciparum. Despite the implementation of several control strategies, the outbreak of malaria in the state is mainly due to lack of proper information regarding the disease. Hence, we completed a database to help implement appropriate control strategy for the public health officials in Arunachal Pradesh.

 Despite of all the efforts under NMEP, malaria continues to pose a serious threat. Hence, there is a need for an alternate technology for efficient targeting of malaria in this region. Here, we present application of Self-Organizing maps (SOM), a powerful data mining technique for prioritization of control operations.

Malaria continues to pose a serious threat to public health in North- Eastern states of India. Arunachal Pradesh is highly endemic for Malaria predominately with Plasmodium falciparium infections. Despite continuous efforts by government, a desirable level of control has not been achieved. The present study describes the application of self organizing maps (Kohonen maps), a data mining tool for prioritization of malaria endemic zones in this region. 60 PHCs (Public Health Centers) were randomly selected from Arunachal Pradesh and 6 malariometric parameters via Annual Blood Examination rate (ABER), Annual Parasite Incidence (API), Slide Positivity Rate (SPR), Annual Falciparum Incidence (AFI) and Slide Falciparum Rate (SFR) were considered which reflected the intensity of malaria transmission in this region. Self Organizing Maps yielded 9 clusters based on neighborhood distance, which reflects about zones based on status of intensity of malaria epidemiology. Such maps would make it possible to target control measures at high-risk areas and greatly increase the cost efficiency of malaria control programmes.

Malaria remains the leading cause of deaths attributable to a communicable disease globally, with an unprecedented death toll of over 2 million per year. The reemergence of drug-resistant Plasmodium falciparum, the most fatal human malarial parasite, has focused attention on Shikimate pathway, as it may provide the urgently required novel drug targets owing to lack of homologs of enzymes involved in the this pathway in humans. Chorismate Synthase, the key enzyme of Shikimate pathway, catalyzes the conversion of 5-enolpyruvylshikimate 3-phosphate to Chorismate via a 1, 4-trans elimination of phosphate. The strict requirement for a reduced flavin mononucleotide and the anti 1, 4 elimination are both unusual aspects which make CS reaction unique among flavin-dependent enzymes, representing an important target for the chemotherapeutic agents development. The protein sequence of Chorismate Synthase containing 527 residues was obtained from NCBI. The enzyme was characterized using in silico tools. The secondary and tertiary (3D) structure of the enzyme was predicted using CS from other species and validated by various structural quality validation tools. Results of the current study will provide a deep insight about the structure and function of Chorismate Synthase and aid in rational drug designing.





Functional Analysis of M. tuberculosis Chaperones.

S, Manjula

Abstract/Synopsis
              Following the pioneering work of Lee Esaki and Tsu in 1970 on the
study of two dimensional semiconducting heterostructures like Quantum Well,
superlattices etc., and the developments in the ultrathin film growth techniques
using Molecular Beam Epitaxy, Metal Organic Vapour Phase Epitaxy, the topic
of Low Dimensional Semiconducting Systems(LDSS) like Quantum Well,
Quantum Well Wire and Quantum Dot has developed rapidly both from the
point of view of basic Physics and of applications. Consequence of the one –
dimensional, two – dimensional and three dimensional size quantization, a
genuine quantum mechanical effect, the degrees of freedom is frozen and the
carriers in such LDSS effectively behave as if their motion were two
dimensional, one dimensional and zero dimensional, a feature which alters a
number of physical properties. Also a wide variety of quantum heterostructure
devices have come into vogue because of the dramatic development in
Semiconductor materials and technology. In the present thesis, some aspects of
LDSS like the influence of external perturbations like temperature and pressure
on the ground state as well as some low lying excited states, diamagnetic
susceptibility of a donor in ground state as well as in the low lying excited
states, the effect of external pressure on diamagnetic susceptibility and Metal –
Insulator transition have been investigated and are presented in six chapters
(from chapter 2 to chapter 7).


The temperature dependent binding energy of some low lying excited states for a compositional Quantum Well have been calculated for various impurity locations by extending the investigation of Elabsy.4 It has been observed that the temperature plays an important role in the binding energy of low lying excited states also.Bottom of Form
Top of Form

Bottom of Form



The effect of Γ-X crossover due to the external hydrostatic pressure on the ground state donor binding energy as well as for some low lying excited states for a Quantum well has been investigated by considering the non-parabolicity of the conduction band and pressure dependent spatial dielectric screening. It is observed that the effect of Γ-X crossover is predominant for ground state than for low lying excited states


The binding energies of a hydrogenic donor both in the parabolic and non-parabolic conduction band model within the effective mass approximation have been computed for the low-dimensional semiconducting systems (LDSS) like quantum well, quantum well wire and quantum dot taking GaAs/AlxGa1−xAs systems as an example. It is observed that the effect of non-parabolicity is not effective when the system goes to lower dimensionality. The diamagnetic susceptibility of a hydrogenic donor impurity has also been computed in these LDSS in the infinite barrier model. Since no theoretical or experimental works on the diamagnetic susceptibility of LDSS are available in the literature, as a realistic case the diamagnetic susceptibility has been computed in the finite barrier model (x=0.3) for a quantum well and the results are discussed in the light of semiconductor–metal transition.


We present the calculation of diamagnetic susceptibility (χdia) of a hydrogenic donor in GaAs/AlxGa1−xAs quantum well for various compositions of Al and for different impurity locations within the well. The effect of Γ–X band crossing due to hydrostatic pressure on χdia is also investigated taking into account the non-parabolicity of the conduction band.



Application of Membranes and Enzymes in Processing Vegetable Oils

R., SARAVANAN

		Abstract


Abstract

The thesis entitled “Design, Synthesis and Conformational Studies of β-, γ-, β/γ-Peptides Derived From C-Linked Carbo-β/γ-Amino Acids” is divided into two chapters.
Chapter I: Molecular Dynamic Simulation Studies on -Peptides Derived From C-Linked Carbo--Amino Acids

This section is dealt with the Molecular Dynamics simulation studies of new class of C-linked carbo -peptides, using distance information from the ROSEY experiments and coupling constants. 
Computer simulation techniques became very important tools for understanding the physical basis of the structure and function of biological macromolecules. In particular, Molecular Dynamics (MD) simulations1-3 can provide the ultimate detail concerning individual particle motions as a function of time. Thus, they can be used to address specific questions about the properties of a model system, often more easily than experiments on actual systems. Of course, experiments play an essential role in validating the simulation methodology: comparisons of simulation and experimental data serve to test the accuracy of the calculated results and to provide criteria for improving the technique. Recent experimental advances allowed an increasingly accurate description of short time protein dynamics, that is more accessible to atomically detailed computer simulations and therefore open the way for more meaningful comparison to experiments.
MD simulations of new class of C-linked carbo -peptides, using distance information derived from the ROSEY experiments by the use of CVFF force field (Consistent Valence Force Field), enables the resolution of seeming inconsistencies in the experimental data. In our design on the synthesis of peptides, we have used the concept of “alternating chirality” with the epimeric C-linked carbo--amino acids 1 and 2 as the controlling point in defining stable helices in the C-linked carbo--peptides 3-9 (Figure 1).



MD simulations were performed on the above peptides using NMR experimental data by the use of CVFF force field with Discover in Insight-II program4 on Silicon Graphics Work station. Each peptide 1ns (nanosecond) long simulations at 300 K were performed and the structures sampled were compared to primary experimental data such as proton-proton NOE intensities and 3J-coupling constants. These structure calculations for the peptides using observed NOE restraints and dihedrals have resulted in a closely related family of right-handed 12/10-helical conformations.
Peptides 3-5 formed right-handed mixed 10/12-helix and backbone NOE distances NH(i)/NH(i+1) qualify a 10-membered hydrogen bond (H-bond) between NH(1)-CO(2), NH(3)-C=O(4) in 3, NH(1)-CO(2), NH(3)-C=O(4), NH(5)-C=O(6) in 4 (Figure 2), NH(1)-CO(2), NH(3)-C=O(4), NH(5)-C=O(6) and NH(7)-C=O(8) in 5, whereas CH(i)/NH(i+2) and CH(i)/CH(pro-R) (i+2) qualify a 12-membered H-bond involving CO(1)-NH(4) in 3, CO(1)-NH(4), CO(3)-NH(6) in 4, CO(1)-NH(4), CO(3)-NH(6) and CO(5)-NH(8)  in 5. 
Figure 2 depicts bundle of 20 minimum energy structures of 4. In the Figure 2A the sugars have been replaced with methyl groups after the MD calculations. For clarity, but for the amide proton, all other protons have been removed from these structures. Clearly, this -peptide folds into a 10/12-mixed helix with hydrogen bonds from NH(i) to C=O residue of (i+1), displaying a 10-membered H-bonding, and C=O of residue (i-3) to NH residue (i), displaying a 12-membered H-bonding.
				
A					B
Figure 2: MD Pictures (A) Side view of 4; (B) top view of 4 from C-terminus

Peptides 6-9 (Figure 1) formed right-handed mixed 12/10-helix and backbone NOEs CH(i)/NH(i+2) and CH(i)/CH(pro-R) (i+2) qualify a 12-membered H-bond involving CO(Boc)-NH(3) in 6, CO(Boc)-NH(3) in 7, CO(Boc)-NH(3), CO(2)-NH(5) in 8, and CO(Boc)-NH(3), CO(2)-NH(5), CO(4)-NH(7)  in 9, whereas NH(i)/NH(i+1) NOEs qualify a 10-membered H-bond between NH(2)-CO(3) in 6, NH(2)-CO(3) in 7, NH(2)-CO(3), NH(4)-CO(5) in 8, NH(2)-CO(3), NH(4)-CO(5), NH(6)-CO(7) in 9.
In all this simulated structures, the expected hydrogen bonds were observed. In all these conformers the dihedral angle of N-C-C-C for both (S)-3-Caa and (R)-3-Caa are in gauche form ( = 60), a pre-requisite for a helical structure in -peptides. In peptides 3-5, backbone to side chain dihedral angles of all the residues H-C-C4-H () is 180, but for the second residue dihedral angle is ~ 60, whereas in peptides 6-9, first residues of  is ~ 60. (R)-3-Caa, with (R)-configuration at C, always takes part in 12-membered H-bonding, while C-C4 bond is positioned perpendicular to the helix axis, which stabilizes the helix. (S)-3-Caa, with (S)-configuration at C, always takes part in 10-membered H-bonding, C-C4 bond is positioned in along the helix axis, which creates 1.5 kcal destabilization. Even though small steric constraints are there, still the design based on alternating chirality resulted in mixed helices, with unique single robust conformations in as short as tri- and tetrapeptides.
As discussed above residue in the right-handed mixed helices, contribution of steric repulsion by (S)-3-Caa in the concept of ‘alternating chirality’, made them to be inferior in energy to Seebach’s mixed helices.5,6 In order to overcome the steric limitations, though are very low and not disrupting the helical formation, we continued to work on mixed -peptides containing 3-Caa (1) or (2) and -hGly. Introducing -hGly unit, which don’t have substitution on either 2 or 3 carbons may result into random structures on one hand, and on the other hand -hGly, homologue of Glycine, may provide more conformational freedom by replacing alternatingly 3-Caa (1) or (2). 



MD simulations were performed on the mixed -peptides 10-15 (Figure 3 and Figure 4) using NMR experimental data by the use of Tripos force field in SYBYL program7-9 on Silicon Graphics Work station. These peptides were placed at the center of a periodic truncated octahedron box. The minimum distance from any peptide atom to the box wall was chosen in this initial configuration as 14 Å. This box was filled with chloroform solvent molecules such that the distance between (non-hydrogen) solvent and solute atoms was bigger than 0.23 nm. These peptides were performed 500 ps long simulations using at constant temperature (300 K) and pressure (1 atm).
Structure calculations for the peptides 10 and 11 (Figure 3) have resulted in a closely related family of right-handed 12/10-helical conformations, whereas, 12 and 13, (Figure 4) with N-terminus -hGly gave right-handed 10/12-helix. Peptide 14 (Figure 4) was observed in left-handed mixed 12/10-helical conformation, while 15, with -hGly at N-terminus has shown left-handed 10/12-helical conformation. Figure 5 shows the left-handed 12/10-helix and right-handed 12/10-helix with hydrogen bonding.



In these mixed peptides, inspite of the availability of appreciable conformational freedom due to insertion of -hGly, mixed helices take intrinsically the most favored structures with amide of -hGly participating in 10-membered H-bonds and amide of 1 and 2 taking part in 12-membered H-bonds. The conformational preferences of 1 and 2 drive -hGly to participate in robust 12/10… and 10/12… helical structures. 
Chapter II: Design, Synthesis and Conformational Studies of - and /-Peptides Derived From C-Linked Carbo-- and -Amino Acids 

Section A.	Synthesis of Novel C-linked Carbo--Amino Acids: Design, Synthesis and Conformational Studies of Oligomers with Dipeptide Repeats of C-linked Carbo-4-Amino Acids and -Aminobutyric Acid

This section is dealt with the synthesis and conformational studies of new class of C-linked carbo -peptides. 
The design of nonnatural oligomers that form diversified secondary structures is an active area of research. An extensive search of the -peptide class of foldamers has provided several new secondary structures, while the -peptides, despite the possibility of having and traversing a larger conformational space, have received less attention. Based on our earlier findings on mixed -peptides,10 and Gellman’s previous predictions11 for -aminobutyric acid derivatives, about nearest neighbor hydrogen bonds using IR techniques, we envisaged that mixed -peptides might adopt novel interesting secondary structures. Hence, the requisite monomeric -Caas 16 and 17 were synthesized, wherein methylene group would be incorporated between -CH2 and CO of -Caa, resulting a new class of monomer, C-linked carbo -amino acid (-Caa). This extra CH2 group creates well-defined backbone conformations and more stable structures compared to the natural peptides stated by Seebach et al.12 Arndt-Eistert homologation method was used on -amino acids for the preparation of enantiomerically pure -amino acid derivatives (Scheme 1). 
	
Monomers 16 and 17 (Scheme 1) were independently coupled with -aminobutyric acid (GABA) alternatingly by conventional peptide coupling methods to afford peptides 18, 19 and 20, 21 (Figure 6) respectively. 
The conformations of -peptides can be analyzed in terms of the main chain backbone torsional angles, which are assigned the angles , , 1, 2 and . Folded helical conformations of -peptides require a gauche conformation about the 1 and 2, torsion angles defined by the C3-C4 and C2-C3 bonds respectively. According to theoretical calculations the two central torsion angles 1 and 2 only in 60 and 180 arrangements forming more stable folded helical structures.

Peptides 18 and 19 (Figure 6) have shown left-handed helical structure whereas 20 and 21 (Figure 6) did not show any helical signatures. Because of the energy difference between two different epimeric monomers, peptides 20 and 21 may not switch into form any kind of helical structures.
	
Restrained MD simulations were performed on peptides 18 and 19 using distance constrains, which were derived from the ROSEY experiments by using a two-spin approximation, to generate a structure for these peptides that is consistent with NMR experimental data. These studies confirmed the presence of a left-handed 9-helical structure. Figure 7 depicts a superimposition of 15 lowest energy structures for 18 and 19. For clarity, all the protons have been removed and sugar units were replaced by methyl groups after the MD calculations.

         
   				
Figure 7: Stereo-view of superimposed 15 minimum energy structures: (A) tetra-     peptide 18 and (B) hexapeptide 19

Helix formation is often discussed solely on the basis of energy data, according to energy calculations by Hofmann et al.13 Thus, in the present study on the peptides 20-21 derived from (R)--Caa, the unfavoured substitution pattern might be responsible for the disruption of helix formation. Thus, the theoretical studies on -peptides throw some light on why the peptides 20 and 21 differed in helix formation based on the energy consideration. This is also further explained by mass spectral fragmentation.14 
The CID (collision induced dissociation) mass spectra of [M-H]- ions of diastereomeric isomers 16 and 17 displayed difference in the fragment ion abundances. A theoretical study on the relative stabilities of these negative ions using simulated annealing dynamic studies in SYBYL 6.7 program on Silicon Graphics O2 workstation was carried out to explain the pattern of difference in the fragmentation. 
The CD spectra of tetra- and hexapeptides 18 and 19 suggest the adoption of a distinctive secondary structure. It has shown maxima at about 200 nm, zero crossing at 208 nm and minima at about 215 nm. 	
For the first time a new class of -amino acids, viz. C-linked-carbo--amino acid, (S)--Caa and (R)--Caa are prepared. The -peptides derived from (S)--Caa/GABA resulted in identification of left-handed 9-helix for first time, as a new helical structure in the domain of ‘foldamers’. On the other hand, the -peptides made from (R)--Caa have not shown the presence of any secondary structures. Thus, both the theoretical studies by Hoffman and mass spectral studies on the -Caas, amply indicate that the steric configuration that is not present in (S)--Caa is responsible for the formation of a stable 9-helix. 

Section B.	Design, Synthesis and Conformational Studies of New Class of /- Hybrid Peptides Containing C-Linked Carbo--Amino Acids and -Amino Acids 

This section is dealt with the synthesis and conformational studies of new class of C-linked carbo /-hybrid peptides. 
Based on Hofmann’s theoretical calculations15 and our earlier findings on /-hybrid peptides,16 with heterodimer motif derived from (S)--Caa and L-Ala repeats generating unprecedented right-handed 11/9-mixed helices, despite having a different backbone geometry, we envisaged that hybrid /-peptides might adopt interesting novel secondary structures.
New class of C-linked carbo /-hybrid peptides 22-24 (Figure 8) were prepared from the corresponding -Caas (1 and 2) and -Caas (16 and 17) in solution by using EDCI and HOBt as coupling reagents.

From our earlier studies on the -Caa derived peptides and the mass spectral fragmentation of the -Caa derived dipeptides, it was amply evident that the carbohydrate side chain and the stereochemistry at the amine bearing stereocentre, indeed control conformations in the derived peptides. The rigidity differences in the (S)- and (R)-epimeric -Caa residues play a crucial role in defining the helical conformations. In /-peptides 22-24, with carbohydrate side chains having (S)- stereo center in both -Caa and -Caa, have shown to fold into stable secondary structures in solution. These tetra-22, penta-23 and hexapeptides 24 have shown unprecedented left-handed 11/13-mixed helix. 
Using the NMR data, restrained MD simulations were performed to further confirm the presence of the 11/13-mixed helix. Figure 9 shows 20 lowest energy superimposed structures of 22 and 23. The RMSD of the backbone and the heavy atoms for 22 (Figure 9A) are 0.41 and 0.61 Å, whereas for 23 (Figure 9B) the corresponding values are 0.49 and 0.92 Å respectively. The average values of the dihedral angles (excluding the C- and N-termini) in 22 are:   142±4,   66±2,   -10±4;   121±2, 1  -81±2, 2  58±2 and   -101±3, while for 23 are:   145±5,   68±3 and   -8±6;   123±3, 1  -84±3, 2  63±4 and   -106±4. These values agree with those for the higher energy 11/13III-helix reported by Hofmann et al.15 
    








		

Figure 9: Stereo-view of (A): peptide 22 and (B): peptide 23 (sugars are replaced with methyl groups after calculations)

In the /-hybrid peptides, side chains at the β-residues Cγ-C4 (of sugar ring) bond is placed along the helix axis, whereas those in the γ-residues take an equitorial orientation and has a pitch of ~ 5.9 Å, with ~ 2.7 residues/turn and a ~ 2.2 Å rise/residue. 
Thus, the synthesis and conformational analysis of /-hybrid peptides 22-24 have shown a new class of 11/13-mixed helix for the first time. Further, our new design gives the first experimental proof to Hofmann’s recent predictions of the secondary structures in /-peptides. 
C-linked carbo /-hybrid peptides 25-31 (Figure 10) were prepared from the corresponding -Caas (1 and 2) and -Caas (16 and 17) in solution by using EDCI and HOBt as coupling reagents. 

1H NMR spectra of the peptides 25-27 (Figure 10) have shown good dispersion of all backbone proton resonances and low-field resonation of amide protons (> 7 ppm) in CDCl3 indicating that the presence of a stable secondary structure. CD spectra of these peptides though depicted maxima at 201 nm, which differs from the peptides starting with (S)--Caa and (S)--Caa dipeptide repeating units, we could not confirm helical patterns in 25-27 due to non availability of sufficient data from NMR data. The /-peptides 28-31 (Figure 10) derived by the design of alternating chirality, thus have not shown any secondary structures. 
Likewise, /-peptides 32-33 (Figure 11) containing alternating (S)--Caa and -hGly have also not shown any kind of structures. The unfavoured substitution pattern might be responsible for disruption. 


References:
1.	Bruccoleri, R. E.; Karplus, M. Biopolymers. 1990, 29, 1847.	
2.	Perez, J. J.; Villar, H. O.; Loew, G. H. J. Comput. Aided. Mol. Des. 1992, 6, 175.
3.	Cassels, F. J.; Hughes, C. V.; Nauss, J. L. J. Indust. Micro. 1995, 15, 176.
4.	Discover, Version 2.98, Biosym Molecular Simulations, San Diego, CA, 1995.
5.	Gademann, K.; Hane, A.; Rupeing, M.; Jaun, B.; Seebach, D. Angew. Chem. Intl. Ed. 2003, 42, 1534.
6.	Seebach, D.; Gademann, K.; Schreiber, J. V.; Matthews, J. C.; Hintermann, T.; Jaun, B.Helv. Chim. Acta., 1997, 80, 2033.
7.	Peter, C.; Daura, X.; van Gunstern, W. F. J. Am. Chem. Soc., 2000, 122, 7461.
8.	Kerrigan, J. E.; “Sybyl Dynamics Tutorial”, Molecular Dynamics Study of Funnel Web SpiderToxin Using Sybyl (Tripos).
9.	Berendsen, H. J. C.; Postma, J. P. M.; van Gunstern, W. F.; DiNola, A.; Haak, J. R. J.  Chem. Phys. 1984, 81, 3684.
10.	Sharma, G. V. M., Ravinder Reddy, K.; Ravi Sankar, A.; Jayaprakash, P.; Radha Krishna, P.; Jagannadh, B.; Kunwar, A. C. Angew. Chem., Int. Ed. Engl. 2004, 43, 3961.
11.	Dado, G. P.; Gellman, S. H. J. Am. Chem. Soc. 1994, 116, 1054.
12.	Hintermann, T.; Gademann, K.; Jaun, B.; Seebach, D. Helv. Chim. Acta 1998, 81, 983.
13.	Hofmann H. –J.; Baldauf, C.; Gunther, R. Biopolymers 2005, 80, 675.
14.	Reddy, P. N.; Swamy, N. S.; Srinivas, R.; Sharma, G. V. M.; Jayaprakash, P.; Jadav, V. B.; Nagendar, P. J. Mass Spectrom. 2006, 41, 1105.
15.	Baldauf, C.; Gunther, R.; Hofmann, H. -J. J. Org. Chem. 2006, 71, 1200.
16.	Sharma, G. V. M.; Nagendar, P.; Jayaprakash, P.; Krishna, P. R.; Ramakrishna, K. V. S.; Kunwar, A. C. Angew. Chem., Int. Ed. 2005, 44, 5878.
















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Figure 5: (A) Left-handed 12/10-helix for 14 and (B) Right-handed 12/10-helix for 11

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Molecular characterization of the bovine major histocompatibility complex DRB3 (BoLA-DRB3) alleles and its association with mastitis in crossbred cattle

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