Saikat Banerjee

Theoretical and Computational Analysis of Static and Dynamic Anomalies in Water−DMSO Binary Mixture at Low DMSO Concentrations

Experiments have repeatedly observed both thermodynamic and dynamic anomalies in aqueous binary mixtures, surprisingly at low solute concentration. Examples of such binary mixtures include water-DMSO, water-ethanol, water-tertiary butyl alcohol (TBA), and water-dioxane, to name a few. The anomalies have often been attributed to the onset of a structural transition, whose nature, however, has been left rather unclear. Here we study the origin of such anomalies using large scale computer simulations and theoretical analysis in water-DMSO binary mixture. At very low DMSO concentration (below 10%), small aggregates of DMSO are solvated by water through the formation of DMSO-(H(2)O)(2) moieties. As the concentration is increased beyond 10-12% of DMSO, spanning clusters comprising the same moieties appear in the system. Those clusters are formed and stabilized not only through H-bonding but also through the association of CH(3) groups of DMSO. We attribute the experimentally observed anomalies to a continuum percolation-like transition at DMSO concentration X(DMSO) ≈ 12-15%. The largest cluster size of CH(3)-CH(3) aggregation clearly indicates the formation of such percolating clusters. As a result, a significant slowing down is observed in the decay of associated rotational auto time correlation functions (of the S═O bond vector of DMSO and O-H bond vector of water). Markedly unusual behavior in the mean square fluctuation of total dipole moment again suggests a structural transition around the same concentration range. Furthermore, we map our findings to an interacting lattice model which substantiates the continuum percolation model as the reason for low concentration anomalies in binary mixtures where the solutes involved have both hydrophilic and hydrophobic moieties.

Enhanced Pair Hydrophobicity in the Water−Dimethylsulfoxide (DMSO) Binary Mixture at Low DMSO Concentrations

We observe a surprisingly sharp increase in the pair hydrophobicity in the water-dimethylsulfoxide (DMSO) binary mixture at small DMSO concentrations, with the mole fraction of DMSO (x(D)) in the range 0.12-0.16. The increase in pair hydrophobicity is measured by an increase in the depth of the first minimum in the potential of mean force (PMF) between two methane molecules. However, this enhanced hydrophobicity again weakens at higher DMSO concentrations. We find markedly unusual behavior of the pure binary mixture (in the same composition range) in the diffusion coefficient of DMSO and in the local composition fluctuation of water. We find that, in the said composition range, the average coordination number of the methyl groups (of distinct DMSO) varies between 2.4 and 2.6, indicating the onset of the formation of a chain-like extended connectivity in an otherwise stable tetrahedral network comprising of water and DMSO molecules. We propose that the enhanced pair hydrophobicity of the binary mixture at low DMSO concentrations is due to the participation of the two methane molecules in the local structural order and the emerging molecular associations in the water-DMSO mixture.

Structural Transformations, Composition Anomalies and a Dramatic Collapse of Linear Polymer Chains in Dilute Ethanol-Water Mixtures

Water-ethanol mixtures exhibit many interesting anomalies, such as negative excess partial molar volume of ethanol, excess sound absorption coefficient at low concentrations, and positive deviation from Raoults law for vapor pressure, to mention a few. These anomalies have been attributed to different, often contradictory origins, but a quantitative understanding is still lacking. We show by computer simulation and theoretical analyses that these anomalies arise from the sudden emergence of a bicontinuous phase that occurs at a relatively low ethanol concentration of x(eth) ≈ 0.06-0.10 (that amounts to a volume fraction of 0.17-0.26, which is a significant range!). The bicontinuous phase is formed by aggregation of ethanol molecules, resulting in a weak phase transition whose nature is elucidated. We find that the microheterogeneous structure of the mixture gives rise to a pronounced nonmonotonic composition dependence of local compressibility and nonmonotonic dependence in the peak value of the radial distribution function of ethyl groups. A multidimensional free energy surface of pair association is shown to provide a molecular explanation of the known negative excess partial volume of ethanol in terms of parallel orientation and hence better packing of the ethyl groups in the mixture due to hydrophobic interactions. The energy distribution of the ethanol molecules indicates additional energy decay channels that explain the excess sound attenuation coefficient in aqueous alcohol mixtures. We studied the dependence of the solvation of a linear polymer chain on the composition of the water-ethanol solvent. We find that there is a sudden collapse of the polymer at x(eth) ≈ 0.05-a phenomenon which we attribute to the formation of the microheterogeneous structures in the binary mixture at low ethanol concentrations. Together with recent single molecule pulling experiments, these results provide new insight into the behavior of polymer chain and foreign solutes, such as enzymes, in aqueous binary mixtures.

Anomalous behavior of linear hydrocarbon chains in water-DMSO binary mixture at low DMSO concentration.

We find that at a mole fraction 0.05 of DMSO (x(DMSO) = 0.05) in aqueous solution, a linear hydrocarbon chain of intermediate length (n=30-40) adopts the most stable collapsed conformation. In pure water, the same chain exhibits an intermittent oscillation between the collapsed and the extended coiled conformations. Even when the mole fraction of DMSO in the bulk is 0.05, the concentration of the same in the first hydration layer around the hydrocarbon of chain length 30 (n=30) is as large as 17%. Formation of such hydrophobic environment around the hydrocarbon chain may be viewed as the reason for the collapsed conformation gaining additional stability. We find a second anomalous behavior to emerge near x(DMSO)=0.15, due to a chain-like aggregation of the methyl groups of DMSO in water that lowers the relative concentration of the DMSO molecules in the hydration layer. We further find that as the concentration of DMSO is gradually increased, it progressively attains the extended coiled structure as the stable conformation. Although Flory-Huggins theory (for binary mixture solvent) fails to predict the anomaly at x(DMSO)=0.05, it seems to capture the essence of the anomaly at 0.15.

Stability of fluctuating and transient aggregates of amphiphilic solutes in aqueous binary mixtures: Studies of dimethylsulfoxide, ethanol, and tert-butyl alcohol

In aqueous binary mixtures, amphiphilic solutes such as dimethylsulfoxide (DMSO), ethanol, tert-butyl alcohol (TBA), etc., are known to form aggregates (or large clusters) at small to intermediate solute concentrations. These aggregates are transient in nature. Although the system remains homogeneous on macroscopic length and time scales, the microheterogeneous aggregation may profoundly affect the properties of the mixture in several distinct ways, particularly if the survival times of the aggregates are longer than density relaxation times of the binary liquid. Here we propose a theoretical scheme to quantify the lifetime and thus the stability of these microheterogeneous clusters, and apply the scheme to calculate the same for water-ethanol, water-DMSO, and water-TBA mixtures. We show that the lifetime of these clusters can range from less than a picosecond (ps) for ethanol clusters to few tens of ps for DMSO and TBA clusters. This helps explaining the absence of a strong composition dependent anomaly in water-ethanol mixtures but the presence of the same in water-DMSO and water-TBA mixtures.

Sensitivity of polarization fluctuations to the nature of protein-water interactions: Study of biological water in four different protein-water systems

Since the time of Kirkwood, observed deviations in magnitude of the dielectric constant of aqueous protein solution from that of neat water (∼80) and slower decay of polarization have been subjects of enormous interest, controversy, and debate. Most of the common proteins have large permanent dipole moments (often more than 100 D) that can influence structure and dynamics of even distant water molecules, thereby affecting collective polarization fluctuation of the solution, which in turn can significantly alter solutions dielectric constant. Therefore, distance dependence of polarization fluctuation can provide important insight into the nature of biological water. We explore these aspects by studying aqueous solutions of four different proteins of different characteristics and varying sizes, chicken villin headpiece subdomain (HP-36), immunoglobulin binding domain protein G (GB1), hen-egg white lysozyme (LYS), and Myoglobin (MYO). We simulate fairly large systems consisting of single protein molecule and 20000-30000 water molecules (varied according to the protein size), providing a concentration in the range of ∼2-3 mM. We find that the calculated dielectric constant of the system shows a noticeable increment in all the cases compared to that of neat water. Total dipole moment auto time correlation function of water ⟨δMW(0)δMW(t)⟩ is found to be sensitive to the nature of the protein. Surprisingly, dipole moment of the protein and total dipole moment of the water molecules are found to be only weakly coupled. Shellwise decomposition of water molecules around protein reveals higher density of first layer compared to the succeeding ones. We also calculate heuristic effective dielectric constant of successive layers and find that the layer adjacent to protein has much lower value (∼50). However, progressive layers exhibit successive increment of dielectric constant, finally reaching a value close to that of bulk 4-5 layers away. We also calculate shellwise orientational correlation function and tetrahedral order parameter to understand the local dynamics and structural re-arrangement of water. Theoretical analysis providing simple method for calculation of shellwise local dielectric constant and implication of these findings are elaborately discussed in the present work.

Syntheses, crystal structures, DNA binding, DNA cleavage, molecular docking and DFT study of Cu(II) complexes involving N2O4 donor azo Schiff base ligands

Here, we have reported three novel copper(II) complexes (1–3) involving azo Schiff base ligands. All the complexes have been well characterized using different spectroscopic tools and single crystal X-ray diffraction analysis. Structural and electronic parameters of the complexes have been justified by DFT and TDDFT computation. All the complexes showed minor groove binding to the AT-rich sequence of DNA. The binding properties of the complexes have been extensively studied, and are further supported by a molecular docking analysis. These complexes also showed H2O2-mediated DNA cleavage properties involving a hydroxyl radical. MTT assay of the complexes was performed and they were found to be cytotoxic. The intrinsic binding constants (Kb) were calculated to be 7.11 × 105 M−1, 8.36 × 105 M−1 and 10.81 × 105 M−1 for complexes 1–3, respectively. The complexes show interesting supramolecular architectures in the solid state mainly supported by π–π stacking interactions.

A robust fluorescent chemosensor for aluminium ion detection based on a Schiff base ligand with an azo arm and application in a molecular logic gate

In this present work we have reported the synthesis and structural characterisations of a N2O2 donor Schiff base chemosensor with an azo arm (H2L). Various spectroscopic tools like single crystal X-ray, NMR, UV-vis, FTIR, ESI-mass spectrometry etc. have been deployed to develop the present work. In recent years a number of azo derived chemosensors have been reported by different research groups. This is first time we are reporting the design and properties of an azo derived chemosensor (H2L) for the detection of aluminium ions in semi aqueous medium. It has been found that it selectively senses Al3+ ions in semi aqueous solution. Here, the sensing process is mainly based on a chelation enhanced fluorescence process (CHEF). It has very high selectivity over other metal ions and anions. A detailed literature survey has been carried out and compared with this work. It has an appreciably low detection limit i.e. 6.93 nM. 1H NMR titration was carried out to support the plausible complexation process. 1 : 1 stoichiometry binding between the chemosensor and Al3+ ions has been confirmed from Jobs plot. An inhibition molecular logic gate has been constructed using chemosensor (H2L), where Al3+ and EDTA act as inputs and fluorescence emission is the output. The structural and electronic parameters of the chemosensor (H2L) and complex [AL(L)]NO3 have been studied in detail using theoretical tools like DFT and TDDFT.

Orientational order as the origin of the long-range hydrophobic effect

The long range attractive force between two hydrophobic surfaces immersed in water is observed to decrease exponentially with their separation-this distance-dependence of effective force is known as the hydrophobic force law (HFL). We explore the microscopic origin of HFL by studying distance-dependent attraction between two parallel rods immersed in 2D Mercedes Benz model of water. This model is found to exhibit a well-defined HFL. Although the phenomenon is conventionally explained by density-dependent theories, we identify orientation, rather than density, as the relevant order parameter. The range of density variation is noticeably shorter than that of orientational heterogeneity. The latter is comparable to the observed distances of hydrophobic force. At large separation, attraction between the rods arises primarily from a destructive interference among the inwardly propagating oppositely oriented heterogeneity generated in water by the two rods. As the rods are brought closer, the interference increases leading to a decrease in heterogeneity and concomitant decrease in free energy of the system, giving rise to the effective attraction. We notice formation of hexagonal ice-like structures at the onset of attractive region which suggests that metastable free energy minimum may play a role in the origin of HFL.

Exploration of unconventional π–hole and C–H⋯H–C types of supramolecular interactions in a trinuclear Cd(II) and a heteronuclear Cd(II)–Ni(II) complex and experimental evidence for preferential site selection of the ligand by 3d and 4d metal ions

In this present work we report the synthesis and structural characterisation of a trinuclear cadmium(II) (1) and a di(phenoxido)-bridged dinuclear cadmium(II)–nickel(II) (2) complex derived from a bicompartmental (N2O4) Schiff base ligand, H2L. It has been observed that, in bicompartmental ligands the relatively small inner core is suitable for 3d metal ions and outer core can be occupied by different metal centers like 3d, 1s, 2s, 4d and 4f. We have experimentally established the above fact. In homotrinuclear complex 1 both inner (N2O2) and outer (O4) core has been occupied by cadmium(II) ions. Complex 1 upon reaction with NiCl2·6H2O produces heterodinuclear complex 2. Structural studies reveal that, in complex 1 terminal Cd units acquire trigonal prismatic geometry whereas the central Cd unit is eight coordinated. In case of complex 2 both nickel(II) and cadmium(II) ions are hexa-coordinated in a distorted octahedral environment. Both the complexes are studied using different spectroscopic techniques. Complexes 1 and 2 exhibit important and relatively unexplored group of supramolecular interactions like π–hole, C–H⋯π and C–H⋯H–C along with other hydrogen bonding interactions. Theoretical DFT calculations are devoted to analyze these non covalent interactions. Several computational tools like MEP surface analysis and NCI analysis are utilized to explain and illustrate such interactions.