First principles study and database analyses of structural preferences for sodium ion (Na+) solvation and coordination

Cation-stimulated drug delivery via lipid assembly comprising macrocyclized disaccharides - A DFT study

In the attempt to create a delivery system for an alkali-cation stimulated drug release, a computational study was conducted, aiming for the evaluation of synthetic access towards glycolipid crown ethers analogs and their potential for coordination-induced changes of packing constraints for molecular assemblies. The results disfavor amide-linkages for the creation of macrocycles around the inter-glycosidic bond of a disaccharide. Conformational changes upon cation coordination of the macrocycle decrease the intersection area for easily accessible macrocycles based on lactose. This leads to shrinking intersection areas upon alkali complexation. Maltose-based analogs, on the other hand, exhibited the targeted increase of the glycolipid intersection area and, hence, may be considered as a promising resource.

Fate of Sc-Ion Interaction With Water: A Computational Study to Address Splitting Water Versus Solvating Sc Ion

An exhaustive study of Sc-ion interaction with water molecules in all its possible oxidation and spin states has been carried out to delineate the relative propensity of Sc ions toward solvation and water splitting. Potential energy surface analysis of the Sc-ion reaction with water molecules, topological analysis of bonds, and the effect of sequential solvation up to 6 water molecules have been examined. Calculated values showed good agreement with the available experimental results. Close-shell systems such as singlet mono- and tricationic Sc ions prefer to split the water molecules. In contrast, the open-shell systems such as triplet mono- and doublet dicationic Sc ions prefer to get solvated than split the water molecule. Topological analysis of electron density predicted the Sc^+/2+–water bond as a noncovalent bond while Sc³⁺–OH₂, Sc²⁺–OH, and Sc⁺–H bonds as partially covalent in nature. Energy decomposition analysis revealed that Sc ion–water interactions are driven by electrostatic energy followed by polarization energy. The current study reveals that transition metal catalysis can be one of the most effective tools to employ in water splitting, by properly tuning the electrons, spin, and ligands around the catalytic center.

Excitation of hydrated Li+ and Na+ to their dissociative states: The effect of hydrogen bond on the dissociation of LiO and NaO bonds and the comparison of the TD-DFT and SAC-CI excited dissociative states

In this work, the ground and excited dissociative potential energy curves of hydrated Li⁺ and Na⁺ ions with different structures, containing two, three, and four M-O bonds (M = Li and Na), have been calculated. The vertical energies for the excitation of the clusters to their dissociative states were calculated. The scanning of the potential surfaces was performed in the direction of two normal vibrational modes related to the symmetric and asymmetric stretching of M-O bonds. The difference in the arrangement and number of water molecules around the alkali cation made it possible to study the effect of the hydrogen bond network on the dissociation of M-O bonds. Two different methods including the time-dependent density functional theory (TD-DFT) and direct-symmetry adapted cluster-configuration interaction (direct-SAC-CI) were used for calculating the potential energy curves, separately to compare the TD-DFT method with a correlative computational method such as SAC-CI. The TD-DFT method predicted the charge transfer from water molecules to alkali cation during the dissociation of clusters in the gas phase while the electrostatic field of water blocked this charge transfer. For some clusters, it was found that the change of the theoretical method from the TD-DFT to SAC-CI creates changes in the states of fragments obtained from the dissociation and charge transfer.

Role of aquifer media in determining the fate of polycyclic aromatic hydrocarbons in the natural water and sediments along the lower Ganges river basin

Groundwater-sourced drinking water quality in South Asia, specifically India, is extremely stressed, mostly from the presence of many pervasive and geogenic pollutants. The presence and behavior of anthropogenic pollutants like polycyclic aromatic hydrocarbons (PAHs) are poorly investigated on a regional or basin-wide scale. The present study provides one of the first documentation of the presence and behavior of PAH in the aquifer sediments in the Ganges river basin. Lower and medium molecular weight PAHs, e.g., naphthalene, phenanthrene, and fluoranthene were detected in 79, 36, and 13% of samples (n = 25). The PAH level in groundwater was approximately five times lower than river water. The sorption behavior of PAHs were studied in experiments in presence/absence of organic carbon and by simulating advective transport of low to medium molecular weight PAHs, e.g., naphthalene, phenanthrene, and fluoranthene in aquifer sediments collected from agricultural, peri-urban, and urban areas. Naphthalene and phenanthrene adsorbed on quartz and kaolinite, but not on clay minerals like kaolinite. Fluoranthene adsorbed more favorably on kaolinite. Numerical modeling of the advective transport of PAHs in aquifers suggest up to 25 times faster movement of pollutants from irrigation-induced pumping, indicating the strong control of hydraulics on the spatial distribution of PAHs in subsurface.

Hydrated Sodium Ion Clusters [Na+(H2O)n (n = 1-6)]: An ab initio Study on Structures and Non-covalent Interaction

Structural, thermodynamic, and vibrational characteristics of water clusters up to six water molecules incorporating a single sodium ion [Na⁺(H₂O)_n (n = 1–6)] are calculated using a comprehensive genetic algorithm combined with density functional theory on global search, followed by high-level ab initio calculation. For n ≥ 4, the coordinated water molecules number for the global minimum of clusters is 4 and the outer water molecules connecting with coordinated water molecules by hydrogen bonds. The charge analysis reveals the electron transfer between sodium ions and water molecules, providing an insight into the variations of properties of O–H bonds in clusters. Moreover, the simulated infrared (IR) spectra with anharmonic correction are in good agreement with the experimental results. The O–H stretching vibration frequencies show redshifts comparing with a free water molecule, which is attributed to the non-covalent interactions, including the ion–water interaction, and hydrogen bonds. Our results exhibit the comprehensive geometries, energies, charge, and anharmonic vibrational properties of Na⁺(H₂O)_n (n = 1–6), and reveal a deeper insight of non-covalent interactions.

Ionic radii of hydrated sodium cation from QTAIM

The sodium cation is ubiquitous in aqueous chemistry and biological systems. Yet, in spite of numerous studies, the (average) distance between the sodium cation and its water ligands, and the corresponding ionic radii, are still controversial. Recent experimental values in solution are notably smaller than those from previous X-ray studies and ab initio molecular dynamics. Here we adopt a "bottom-up" approach of obtaining these distances from quantum chemistry calculations [full MP2 with the 6-31++G(d,p) and cc-pVTZ basis-sets] of gas-phase Na⁺(H₂O)_n clusters, as a function of the sodium coordination number (CN = 2-6). The bulk limit is obtained by the polarizable continuum model, which acts to increase the interatomic distances at small CN, but has a diminishing effect as the CN increases. This extends the CN dependence of the sodium-water distances from crystal structures (CN = 4-12) to lower CN values, revealing a switch between two power laws, having a small exponent at small CNs and a larger one at large CNs. We utilize Bader's theory of atoms in molecules to bisect the Na⁺-O distances into Na⁺ and water radii. Contrary to common wisdom, the water radius is not constant, decreasing even more than that of Na⁺ as the CN decreases. We also find that the electron density at the bond critical point increases exponentially as the sodium radius decreases.

X-Ray absorption spectra of microsolvated metal cations

Core excited states of microsolvated ions undergo substantial delocalisation whose degree strongly depends on the ion's charge.

Molecular tailoring approach: a route for ab initio treatment of large clusters

Conspectus Chemistry on the scale of molecular clusters may be dramatically different from that in the macroscopic bulk. Greater understanding of chemistry in this size regime could greatly influence fields such as materials science and atmospheric and environmental chemistry. Recent advances in experimental techniques and computational resources have led to accurate investigations of the energies and spectral properties of weakly bonded molecular clusters. These have enabled researchers to learn how the physicochemical properties evolve from individual molecules to bulk materials and to understand the growth patterns of clusters. Experimental techniques such as infrared, microwave, and photoelectron spectroscopy are the most popular and powerful tools for probing molecular clusters. In general, these experimental techniques do not directly reveal the atomistic details of the clusters but provide data from which the structural details need to be unearthed. Furthermore, the resolution of the spectral properties of energetically close cluster conformers can be prohibitively difficult. Thus, these investigations of molecular aggregates require a combination of experiments and theory. On the theoretical front, researchers have been actively engaged in quantum chemical ab initio calculations as well as simulation-based studies for the last few decades. To obtain reliable results, there is a need to use correlated methods such as Møller-Plesset second order method, coupled cluster theory, or dispersion corrected density functional theory. However, due to nonlinear scaling of these methods, optimizing the geometry of large clusters still remains a formidable quantum chemistry challenge. Fragment-based methods, such as divide-and-conquer, molecular tailoring approach (MTA), fragment molecular orbitals, and generalized energy-based fragmentation approach, provide alternatives for overcoming the scaling problem for spatially extended molecular systems. Within MTA, a large system is broken down into two or more subsystems that can be readily treated computationally. Finally, the properties of the large system are obtained by patching the corresponding properties of all the subsystems. Due to these approximations, the resulting MTA-based energies carry some error in comparison with calculations based on the full system. An approach for correcting these errors has been attempted by grafting the error at a lower basis set onto a higher basis set. Furthermore, investigating the growth patterns and nucleation processes in clusters is necessary for understanding the structural transitions and the phenomena of magic numbers in cluster chemistry. Therefore, systematic building-up or the introduction of stochastics for generating molecular assemblies is the most crucial step for studying large clusters. In this Account, we discuss the working principle of MTA for probing molecular clusters at ab initio level followed by a brief summary of an automated and electrostatics-guided algorithm for building molecular assemblies. The molecular aggregates presented here as test cases are generated based on either an electrostatic criterion or the basin hopping method. At MP2 level computation, the errors in MTA-based grafted energies are typically reduced to a submillihartree level, reflecting the potential of finding accurate energies of molecular clusters much more quickly. In summary, MTA provides a platform for effectively studying large molecular clusters at ab initio level of theory using minimal computer hardware.