Sadhana Mohan

Molecular dynamics simulation of aqueous urea solution: is urea a structure breaker?

An aqueous solution of urea is a very important mixture of biological relevance because of the definitive role of urea as protein denaturant at high concentrations. There has been an extended debate over the years on ureas influence on the structure of water. On the basis of a variety of analysis methods employed, urea has been described as a structure-breaker, a structure-maker, or as neutral toward water structure. Using molecular dynamics simulation and a nearest neighbor approach of analyzing water structure, we present here a detailed analysis of the effect of urea on water structure. By carefully choosing the nearest neighbors, allowing urea also to be a neighbor of a reference water molecule, we have conclusively shown that urea does not break the local tetrahedral structure of water even at high concentrations. A slight change in the distribution of tetrahedral order parameters as a function of urea concentration has been shown to be a result of change in the proportions of n-hydrogen-bonded water molecules. The present result thus suggests that urea is able to substitute for water in the hydrogen-bonded network nicely without breaking the tetrahedral, hydrogen-bonded structure of water.

Correlation of Structural Order, Anomalous Density, and Hydrogen Bonding Network of Liquid Water

We use extensive molecular dynamics simulations employing different state-of-the-art force fields to find a common framework for comparing structural orders and density anomalies as obtained from different water models. It is found that the average number of hydrogen bonds correlates well with various order parameters as well as the temperature of maximum densities across the different models, unifying apparently disparate results from different models and emphasizing the importance of hydrogen bonding in determining anomalous properties and the structure of water. A deeper insight into the hydrogen bond network of water reveals that the solvation shell of a water molecule can be defined by considering only those neighbors that are hydrogen-bonded to it. On the basis of this view, the origin of the appearance of a non-tetrahedral peak at a higher temperature in the distribution of tetrahedral order parameters has been explained. It is found that a neighbor that is hydrogen-bonded to the central molecule is tetrahedrally coordinated even at higher temperatures. The non-tetrahedral peak at a higher temperature arises due to the strained orientation of the neighbors that are non-hydrogen-bonded to the central molecule. With the new definition of the solvation shell, liquid water can be viewed as an instantaneously changing random hydrogen-bonded network consisting of differently coordinated hydrogen-bonded molecules with their distinct solvation shells. The variation of the composition of these hydrogen-bonded molecules against temperature accounts for the density anomaly without introducing the concept of large-scale structural polyamorphism in water.

Effects of Concentration on Like-Charge Pairing of Guanidinium Ions and on the Structure of Water: An All-Atom Molecular Dynamics Simulation Study

Like-charge ion-pair formation in an aqueous solution of guanidinium chloride (GdmCl) has two important facets. On one hand, it describes the role of the arginine (ARG) side chain in aggregation and dimer formation in proteins, and on the other hand, it lends support for the direct mechanism of protein denaturation by GdmCl. We employ all-atom molecular dynamics simulations to investigate the effect of GdmCl concentration on the like-charge ion-pair formation of guanidinium ions (Gdm(+)). From analyses of the radial distribution function (RDF) between the carbon atoms of two guanidinium moieties, the existence of both contact pairs and solvent-separated pairs has been observed. Although the peak height corresponding to the contact-pair state decreases, the number of Gdm(+) ions in the contact-pair state actually increases with increasing GdmCl concentration. We have also investigated the effect of the concentration of Gdm(+) on the structure of water. The effect of GdmCl concentration on the radial and tetrahedral structures of water is found to be negligibly small; however, GdmCl concentration has a considerable effect on the hydrogen-bonding structure of water. It is demonstrated that the presence of chloride ions, not Gdm(+), in the first solvation shell of water causes the distortion in the hydrogen-bonding network of water. In order to establish that Gdm(+) not only stacks against another Gdm(+) but also directly attacks the ARG residue of a protein or peptide, simulation of an ARG-rich peptide in 6 M aqueous solution of GdmCl has been performed. The analyses of RDFs and orientation distributions reveal that the Gdm(+) moiety of the GdmCl attacks the same moiety in the ARG side chain with a parallel stacking orientation.

Molecular engineering of functionalized crown ether resins for the isotopic enrichment of gadolinium: from computer to column chromatography

Density functional theoretical modelling was performed to design and screen suitable macrocyclic crown ether functionalized resins for the isotopic enrichment of gadolinium. Theoretical calculations predict the complexation stability order of Gd3+ ion as follows: di-cylohexano-18-crown-6 (DCH18C6) > dibenzo-18-crown-6 (DB18C6) > benzo-15-crown-5 (B15C5), which was experimentally verified. The calculated isotopic separation factor value was shown to be the highest for DB18C6. From the theoretical analysis of both the stability and isotopic separation factor, DB18C6 is predicted to be the most promising candidate for isotopic separation of gadolinium. Hence, DB18C6 was functionalized with chloromethylated polystyrene (CMPS) resin. Subsequently, CMPS-grafted DB18C6 resin was synthesized and characterized. Furthermore, isotopic enrichment of gadolinium was carried out by performing column chromatographic experiments using CMPS-DB18C6 resin. The absorption capacity of the novel CMPS-DB18C6 resin for gadolinium was found to be 1 mg g−1. The separation coefficient, e × 103, was found to be 6.3, 8.9, 3.4, and 9.7 for Gd-155/158, Gd-156/158, Gd-157/158, and Gd-155/160 isotopic pairs, respectively, and thus hold promise for future isotopic enrichment technology.

Investigation of holdup and axial dispersion of liquid phase in a catalytic exchange column using radiotracer technique

Holdup and axial dispersion of liquid phase in a catalytic exchange column were investigated by measuring residence time distributions (RTD) using a radiotracer technique. RTD experiments were independently carried out with two different types of packings i.e. hydrophobic water-repellent supported platinum catalyst and a mixture (50% (v/v)) of hydrophobic catalyst and a hydrophillic wettable packing were used in the column. Mean residence times and hold-ups of the liquid phase were estimated at different operating conditions. Axial dispersion model (ADM) and axial dispersion with exchange model (ADEM) were used to simulate the measured RTD data. Both the models were found equally suitable to describe the measured data. The degree of axial mixing was estimated in terms of Peclet number (Pe) and Bodenstein number (Bo). Based on the obtained parameters of the ADM, correlations for total liquid hold-up (HT) and axial mixing in terms of Bo were proposed for design and scale up of the full-scale catalytic exchange column.

Recovery of deuterium from hydrogen–deuterium mixture using palladium

ABSTRACT The applicability of palladium for the separation of hydrogen isotopes (hydrogen and deuterium) is evaluated systematically by generating isotherm data and conducting column experiments in a laboratory set-up. Effect of various parameters such as concentration of the isotopic mixture, particle size, eluent flow rate, etc. is studied experimentally. A fixed-bed chromatographic model is developed and validated using the experimental data. The model is further used to predict the performance of a multi-column configuration for large-scale separation. Chromatographic separation is thus found to be a promising technique to achieve the required purity and hence it may be clubbed with the existing systems (e.g. cryogenic distillation) to obtain enhanced performance.

Comparison of orders, structures and anomalies of water: A molecular dynamics simulation study

Molecular dynamics simulations of three water models and a heavy water model have been carried out over a wide range of temperatures to investigate the local orders and anomalies of water. Different local orders related to the internal arrangements of water molecules are calculated and compared. It is found that various properties and orders of water at a particular state point as obtained from different water models are different. However, a strong correlation between average number of hydrogen bonds and local structural and orientational orders of water has been observed. A key parameter that determines local orders and properties of water across state points and therefore reconciles results from different water models has been identified.

Sulphur ligand functionalized carbon nanotubes for removal of mercury from waste water – experimental and density functional theoretical study

ABSTRACT Owing to the strong interaction of mercury with sulphur, thiol(SH) and dithiocarbamate (DTC) ligands were grafted on multi-walled carbon nanotubes (MWCNTs) and were characterized by elemental analysis, SEM-EDS, FTIR, and XRD analysis. The maximum adsorption capacity of MWCNT-DTC was found to be 3.5 times higher than that of MWCNT-SH at the optimum pH of 6. The kinetics and equilibrium data revealed that the adsorption of Hg2+ follow pseudo-first-order and Langmuir isotherm model, respectively. Density functional theoretical calculation performed for the interaction of Hg2+ ion with SWCNT-DTC and SWCNT-SH corroborated the experimental output that former have greater adsorption than the later.Test- L2

Molecular Facts on the Structure and Dynamics of Electrolyte Species in Cu–Cl Cycle for Hydrogen Generation: An Insight from Molecular Dynamic Simulations

The Cu complex, which is the key chemical species in well-known Cu-Cl hybrid thermochemical cycles and also in numerous metal hydrometallurgical and sedimentary deposit processes, displays a wide variety of structural and dynamical characteristics that are further complicated by the presence of multiple oxidation states of Cu ions with different coordination chemistries, therefore they are difficult to explore from experiments alone. In this article, an attempt has been made to understand the coordination behavior of the Cu complex using MD simulations. The study provides compelling evidence of the experimentally observed multiple stoichiometries of Cu ions, i.e., 1:6:0, 1:5:1, and 1:4:2 for Cu+:H2O:Cl- and 1:6:0 for Cu2+:H2O:Cl-. The presence of the anionic Cu complex, [Cu+Cl2]-·2H2O, [Cu+Cl2]-·3H2O, [Cu2+Cl3]-·H2O, and [Cu2+Cl3]-·2H2O, was captured in the presence of excess chloride ions. Furthermore, the probability distribution profiles have been estimated to determine the most possible complex in the considered systems. The results establish structural and dynamical reformation of the Cu complex with change in the salt concentration or variation in the solvent medium in which they are dissolved. Moreover, the structure and kinetics of the Cu ions in the Cu-Cl electrolyzer have been explored over a large range of the electric field by extending the simulated systems for varied strengths of the electric fields. It has been observed that with an increase in the strength of the electric field, the water molecules lose their coordination strength with central Cu ions, which, on the other hand, results in a significant change in the structure of the captured complex. The diffusion dynamics of the ions is altered while applying the electric field, which is furthermore modified while increasing the strength of electric field beyond a critical limit. In fact, the diffusion mechanism of the ions was seen to be transformed from Brownian-like to linear motion and then to hopping diffusion with the increasing strength of the electric field. To the best of our knowledge, this is the first time when the multiple oxidation states of the Cu ion are explored using MD simulations, and the coexisting pictures of the multiple coordinations and the solvent effects have been clearly revealed. Also to date, the present article is the first one to report the insights of the structure and the dynamics of the ions in the Cu-Cl electrolyzer over a wide range of the electric field. The present studies will be very helpful in understanding the mechanism involved in numerous metal hydrometallurgical and sedimentary deposit processes and to comprehend the analogies involved in the electrode reactions of the Cu-Cl cycle for hydrogen generation.

Estimation of Tritium Release from LLCB TBM and Its Ancillary Systems and Tritium Management in Different Locations of ITER

Abstract The Indian Lead Lithium Ceramic Breeder (LLCB) Test Blanket Module (TBM) is to be installed in one half of equatorial port #2 for testing in ITER machine. Liquid Pb-Li and solid Li2TiO3 are the tritium breeder materials in LLCB TBM. Tritium permeates through structural materials in particular at higher temperatures, which is a major operational and safety concern. Therefore, tritium flows in different locations of ITER Tokamak complex have been estimated. Tritium transport from LLCB TBM and its ancillary systems into process rooms has been studied and analyzed in this work. A steady state diffusion limited permeation model neglecting surface effects has been used for the analysis. Tritium permeation to the Vacuum Vessel, Pipe Forest Area, Port Cell, Pipe Chase Area, Tokamak Cooling Water System Vault Annex (TCWS-VA) and Tritium Process Room in L-2 level has been estimated. The requirement to be fulfilled in each equatorial port cell is that the tritium concentration in the port cell during maintenance operations should be below the admissible limit for human access (regulatory maximum allowable value < 1 DAC = 3.4 × 105 Bq/m3, Derived Air concentration). The presence of the Detritiation System (DS) in the Port cell has to be taken into account.This admissible limit for human access has to be reached in a sufficiently short time (target = 12 h) after plasma shutdown. Additional release during maintenance and radiological zoning with recommended <10 µSv/h need to be considered. Management of concentration of permeated tritium in different locations considering above requirement has also been discussed in this paper.