IIT Madras is a public technical and research university located in Chennai, Tamil Nadu. Founded in 1959, it is recognised as an Institute of National Importance.

IIT Madras has been ranked as the top engineering institute in India for four years in a row by the National Institutional Ranking Framework of the MHRD

It currently offers undergraduate, postgraduate and research degrees across 16 disciplines in Engineering, Sciences, Humanities and Management. About 596 faculty belonging to science and engineering departments and centres of the Institute are engaged in teaching, research and industrial consultancy.

IIT Madras

We find, through atomistic molecular dynamics simulation of native cyclodextrins (CDs) in water, that although the outer surface of a CD appears like a truncated cone, the inner cavity resembles a conical hourglass because of the inward protrusion of the glycosidic oxygens. Furthermore, the conformations of the constituent α-glucose molecules are found to differ significantly from a free monomeric α-glucose molecule. This is the first computational study that maps the conformational change to the preferential hydrogen bond donating capacity of one of the secondary hydroxyl groups of CD, in consensus with an NMR experiment. We have developed a simple and novel geometry-based technique to identify water molecules occupying the nonspherical CD cavity, and the computed water occupancies are in close agreement with the experimental and density functional theory studies. Our analysis reveals that a water molecule in CD cavity loses out about two hydrogen bonds and remains energetically frustrated but possesses higher orientational degree of freedom compared to bulk water. In the context of CD-drug complexation, these imply a nonclassical, that is, enthalpically driven hydrophobic association of a drug in CD cavity. Copyright © 2020 American Chemical Society.

Department Of Biotechnology

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Department Of Chemical Engineering

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ACS Omega

Molecular View into the Cyclodextrin Cavity: Structure and Hydration

Inter-subject variability in lung morphometry could influence the transport of any disease causing microorganism to the deep lung regions and the delivery of drug to such a targeted site. This study aims in establishing the relation between aerosol deposition and parameters determining the lung morphometry. The human respiratory system is idealized as a one-dimensional trumpet, whose cross section increases as the distance from the trachea increases. The transport of the aerosol is facilitated by the alveolar expansion, resulting in inhalation. The mass balance equation along with the complicated mechanisms of deposition including deposition by impaction, sedimentation and diffusion has been solved. The model has been validated using experimental data on total particle deposition and alveolar deposition over a range of particle sizes. The sensitivity deposition in the alveoli has been studied by performing a sensitivity analysis on the parameters determining the lung morphometry. From the sensitivity analysis it is concluded that the people with constricted distal airways are more susceptible to infection as well as can be targeted for efficient drug delivery. Thus the occurrence of secondary infection in patients with constricted lung dimensions could be explained. The sensitivity analysis also gives an important conclusion that the particles sizes which deposit in alveolar region of the lung in more concentration are the ones which are least sensitive to inter subject variability. Thus the drug which can be engineered in such particle sizes could result in maximum deposition at the targeted site. Based on the sensitivity co-efficient of deposition concentration of a particular particle size, the deviation of the given individual’s morphometry with respect to the base Weibel parameters is determined. Thus the deviation of the Weibel parameters can be used as a morphometric marker for treatment of the specific individual. © 2015 International Conference on Liquid Atomization and Spray Systems. All rights reserved.

Department of Applied Mechanics

ICLASS 2015 - 13th International Conference on Liquid Atomization and Spray Systems

Towards personalised medicine - The development of morphometric marker for alveolar deposition

Cosolvent hydrophobic preferential interactions with methane in aqueous methanol solutions are evaluated on the basis of the solute excess chemical potential derived from molecular simulations using the quasi-chemical (QC) theory generalization of the potential distribution theorem (PDT). We find that the methane–methanol preferential interaction parameter derived from QC theory quantitatively captures the favorable solvation of methane in methanol solutions in terms of important local solute–solvent (water and methanol) intermolecular interactions within a defined inner shell around the solute, and nonlocal solute interactions with solvent molecules outside this inner shell. Moreover, a unique inner shell can be defined such that the preferential interaction parameter is derived exclusively from the free energy of cavity formation in the aqueous cosolvent solution without the solute, where this cavity corresponds to the specified inner shell, and the mean interaction or binding energy of the solute with solvent molecules outside this inner shell. This inner-shell definition leads to a description of solute–cosolvent preferential interactions in which the molecular details of those interactions are derived from the effect of cosolvent on cavity statistics in the aqueous cosolvent solution alone. The finding suggests that solution thermodynamic behavior beyond steric exclusion (macromolecular crowding) contribute to the molecular mechanisms by which cosolvent preferential interactions influence protein stability and activity.

Quasi-Chemical Theory of Cosolvent Hydrophobic Preferential Interactions

We extend the application of Kirkwood - Buff (KB) solution theory integrals to calculate cosolvent preferential interaction parameters from molecular simulations by deriving from a single simulation trajectory the excess chemical potential of the solute in addition to the solute - solvent molecular distribution functions. The solute excess chemical potential is derived from the potential distribution theorem (PDT) and used to define the local solvent domain around the solute, as distinguished from bulk solution. We show that this KB/PDT characterization of preferential molecular interactions resolves the problem of convergence of the preferential interaction parameter in the bulk solution limit, and as such, gives reliable estimates of preferential interaction parameters for methanol, ethanol, glycerol, and urea in aqueous cosolvent solutions with neopentane or tetramethyl ammonium ion as the solute. Preferential interaction parameters that are also calculated on the basis of cosolvent proximal distributions around the constituent methyl groups of the two solutes with the assumption of group additivity are in good agreement with those obtained by considering the molecular solute as a whole. The results suggest that this approach can be applied to estimate site-specific cosolvent preferential interaction parameters locally on the surface of complex, macromolecular solutes, such as proteins. © 2011 American Chemical Society.

Journal of Physical Chemistry B

Cosolvent preferential molecular interactions in aqueous solutions

We compare protein–protein and protein–polymer osmotic virial coefficients measured by static light scattering for aqueous solutions of lysozyme with low-molecular-weight, hydroxy-terminated (hPEG) and methyl-terminated (mPEG) poly(ethylene glycol) at two solution conditions: pH 7.0 and 0.01 M ionic strength, and pH 6.2 and 0.8 M ionic strength. We find that adding PEG to aqueous lysozyme solutions makes a net repulsive contribution to lysozyme–lysozyme interactions, independent of ionic strength and PEG end-group hydrophobicity. PEG end-group hydrophobicity has a profound effect on the magnitude of this contribution, however, at low ionic strength where mPEG-lysozyme attractive interactions become significant. The enhanced attractions promote mPEG–lysozyme preferential interactions at the expense of lysozyme self-interactions, which leads to lysozyme–lysozyme interactions that are more repulsive in the presence of mPEG. These preferential interactions also lead to the preferential exclusion of diffusable ions locally around the protein, which results in a pronounced ionic strength dependence of mPEG-mediated lysozyme–lysozyme interactions.

Effect of PEG End-Group Hydrophobicity on Lysozyme Interactions in Solution Characterized by Light Scattering

Motivated by a quasi-chemical view of protein hydration, we define specific hydration sites on the surface of globular proteins in terms of the local water density at each site relative to bulk water density. The corresponding kinetic definition invokes the average residence time for a water molecule at each site and the average time that site remains unoccupied. Bound waters are identified by high site occupancies using either definition. In agreement with previous molecular dynamics simulation studies, we find only a weak correlation between local water densities and water residence times for hydration sites on the surface of two globular proteins, lysozyme and staphylococcal nuclease. However, a strong correlation is obtained when both the average residence and vacancy times are appropriately taken into account. In addition, two distinct kinetic regimes are observed for hydration sites with high occupancies: long residence times relative to vacancy times for a single water molecule, and short residence times with high turnover involving multiple water molecules. We also correlate water dynamics, characterized by average occupancy and vacancy times, with local heterogeneities in surface charge and surface roughness, and show that both features are necessary to obtain sites corresponding to kinetically bound waters. © 2008 by the Biophysical Society.

Biophysical Journal

Distinguishing thermodynamic and kinetic views of the preferential hydration of protein surfaces

The photocatalytic degradation of seven phenols, substituted with two of the following <a href="https://www.sciencedirect.com/topics/chemistry/chloro-group">groups: chloro</a>, methyl and nitro, was investigated using combustion-synthesized catalyst. The intermediates were analyzed and a possible pathway of degradation was proposed. The first order <a href="https://www.sciencedirect.com/topics/chemistry/degradation-rate">kinetic rate constants</a> for the degradation of various phenols were determined. The rate of photocatalytic degradation followed the order: 4-chloro,3-methyl phenol&nbsp;&gt;&nbsp;2-chloro,4-methylphenol&nbsp;&gt;&nbsp;4-chloro,2-nitrophenol&nbsp;&gt;&nbsp;4-chloro,2-methyl phenol&nbsp;&gt;&nbsp;4-chloro,3-nitrophenol&nbsp;∼&nbsp;2-chloro,4-nitrophenol&nbsp;&gt;&nbsp;4-methyl,2-nitrophenol. The overall degradation rate of 4-chloro,3-methyl phenol was nearly an order of magnitude faster than the degradation rate of 4-methyl,2-nitrophenol. Chloromethylphenols degraded faster than chloronitrophenols due to the ring deactivating characteristic of <a href="https://www.sciencedirect.com/topics/chemistry/nitro-group">nitro group</a> for <a href="https://www.sciencedirect.com/topics/chemistry/hydroxyl">hydroxyl</a> radical attack. The nature of substituent groups plays a more important role than the position of the substituent groups in determining the degradation rate of multi-substituted phenols.

Department of Electrical Engineering

Kinetics of photocatalytic degradation of phenols with multiple substituent groups

The ultrasonic degradation of two dyes, Rhodamine B (C28H31ClN2O3) and Rhodamine Blue (C28H32N2O3), were studied in the absence of catalyst and in the presence of two catalysts (combustion-synthesized anatase TiO2 and commercial Degussa P-25 TiO2. The rate of degradation of catalyzed reaction was higher than that obtained with in the absence of the catalysts. Among the catalysts, combustion-synthesized anatase TiO2 degraded the dyes faster when compared to the degradation with commercial Degussa P-25 catalyst. A Langmuir−Hinshelwood kinetic model was developed and the kinetic rate parameters were determined. The effect of other operating parameters, such as initial concentration, pH, temperature, and power intensity, was also investigated. The degradation rate increased with decreasing pH, increasing temperature, and higher intensity.

Kinetics of TiO2-Catalyzed Ultrasonic Degradation of Rhodamine Dyes

The photocatalytic degradation of nitrobenzene and substituted nitrobenzenes under UV exposure was investigated with combustion synthesized nano-TiO2 and commercial TiO2 catalyst, Degussa P-25. The experimental data indicated that the photodegradation kinetics was first order. The photocatalytic degradation rates were considerably higher when catalyzed with combustion synthesized TiO2 compared to that of Degussa P-25. The degradation rate coefficients followed the order: 1-chloro,2,4-dinitrobenzene≃4-nitrophenol&gt;2-nitrophenol&gt; 1-chloro,4-nitrobenzene&gt;3-nitrophenol&gt;2,4-dinitrophenol&gt; 1-chloro,2-nitrobenzene&gt;nitrobenzene&gt;1,3-dinitrobenzene. Plausible mechanisms and reasons for the observation of the above order are discussed. © 2005 Elsevier B.V. All rights reserved.

Journal of Photochemistry and Photobiology A: Chemistry

Photocatalytic degradation of nitrobenzenes with combustion synthesized nano-TiO2

The kinetics of photocatalytic degradation of binary mixtures of chlorophenol and nitrophenol was investigated using solution combustion synthesized nano-TiO2. The degradation rates of both organics decreased in the binary mixture compared to the individual degradation rates of the organics. This was attributed to interaction between the mother compounds, interaction between the intermediates, and competition for the active reaction site on the catalyst. A modified Langmuir−Hinshelwood kinetic model was developed, and the kinetic parameters were determined from initial rate analysis for the degradation of chlorophenol and nitrophenol. The evolution of intermediates was also investigated, and a possible pathway for degradation of chlorophenol and nitrophenol was proposed.

Kinetics of Photocatalytic Degradation of Chlorophenol, Nitrophenol, and Their Mixtures

Two new compounds, LiBi4Nb3O14 and LiBi4Ta3O14, have been synthesized by the solid-state method, using Li2CO3, Bi2O 3, and M2O5 (M = Nb, Ta) in stoichiometric quantities. These compounds crystallize in the monoclinic C2/c space group with a = 13.035(3) Å, b = 7.647(2) Å, c = 12.217(3) Å, β= 101.512(4)°, V = 1193.4(5) Å3, and Z = 4 and a = 13.016(2) Å, b = 7.583(1) Å, c = 12.226(2) Å, β= 101.477(3)°, V = 1182.6(5) Å3, and Z = 4, respectively. These are isostructural and the structure along the b axis consists of layers of [Bi 2O2]2+ units separated by layers of LiO 4 tetrahedra and NbO6 octahedra hence depicting an unusual variation in the Aurivillius phase isolated for the first time. The presence of lithium has been confirmed by 7Li NMR studies, ac impedance measurements and variable temperature 7Li NMR studies indicate oxygen ion conductivity in these materials. The UV-visible spectra suggest a band gap of 3.0 eV for LiBi4Nb3O14 and 3.5 eV for LiBi4Ta3O14, respectively, and the associated studies on degradation of dyes and phenols render these materials suitable for photocatalysis. © 2005 American Chemical Society.

Synthesis, structure, and photocatalysis in a new structural variant of the aurivillius phase: LiBi4M3O14 (M = Nb, Ta)

A nano-sized, high surface area phase pure <a href="https://www.sciencedirect.com/topics/chemical-engineering/titanium-dioxide">anatase</a> TiO2 synthesized by the solution combustion method was used to study the photocatalytic degradation of various chlorophenols and methylphenols. The photocatalytic degradation rates of o-chlorophenol, p-chlorophenol, dichlorophenol, trichlorophenol, pentachlorophenol, o- and m-methylphenol (cresol) under UV exposure were determined using the combustion synthesized TiO2 and compared with the degradation rates with commercial Degussa P-25. The chlorophenols degraded much faster than the methylphenols, which degraded faster than phenol. The photocatalytic activity of combustion synthesized TiO2 was significantly higher than that of Degussa P-25 under similar conditions. No intermediates were observed when combustion synthesized TiO2 catalyst was used for the photocatalytic degradation of the phenols, while several intermediates were observed for the same reactions catalyzed by Degussa P-25. Because some of the intermediates are toxic, combustion synthesized TiO2 may be more beneficial in environmental catalysis. The mechanisms for the photocatalytic degradation were proposed and the kinetic parameters were determined by regressing the experimental data.