Rapid, high-capacity adsorption of iodine from aqueous environments with amide functionalized covalent organic frameworks.

The uses and production of radionuclides in nuclear energy production and medical therapy are becoming more significant in today's world. While these applications have many benefits, they can produce harmful pollutants, such as radioactive iodine, that need to be sequestered. Effective capture and storage of radioactive iodine waste remains a major challenge for nuclear energy generation and nuclear medicine. Here we report the highly efficient capture of iodine in a series of mesoporous, two-dimensional (2D) covalent organic frameworks, called COFamides, which contain amide sidechains in their pores. COFamides are capable of rapidly removing iodine from aqueous solution at concentrations as low as 50 ppm, with total capacities greater than 650 wt%. In order to explain the high affinity of the COFamide series for iodine and iodide species in water, we performed a computational analysis of the interactions between the COFamide framework and iodine guests. These studies suggest that the origin of the large iodine capacity in these materials can be explained by the presence of multiple, cooperative, non-covalent interactions between the framework and both iodine, and iodide species.

Superalkalis with Hydrogen as Central Electronegative Atom and their Possible Applications: Ab Initio and DFT Study.

Superalkalis are unusual species having ionization energies lower than that of the alkali metals. These species with various applications are of great importance in chemistry due to their low ionization energies and strong reducing property. A typical superalkali contains a central electronegative core decorated with excess metal ligands. In the quest for novel superalkalis, we have designed the superalkalis HLi2, HLiNa and HNa2 using hydrogen as central electronegative atom for the first time employing high level ab initio (CCSD(T), MP2) and density functional theory (ωB97X-D) methods. The superalkalis exhibit very low ionization energies, even lower than that of cesium. Stability of these species is verified from binding energy and dissociation energy values. The superalkalis are capable of reducing SO2, NO, CO2, CO and N2 molecules by forming stable ionic complexes and therefore can be used as catalysts for the reduction or activation of systems possessing very low electron affinities. The superalkalis form stable supersalts with tailored properties when interact with a superhalogen. They also show remarkably high non-linear optical responses, hence could have industrial applications. It is hoped that this work will enrich the superalkali family and spur further theoretical and experimental research in this direction.

Investigation of the stability of D5SIC-DNAM-incorporated DNA duplex in Taq polymerase binary system: a systematic classical MD approach.

DNA polymerases are fundamental enzymes that play a crucial role in processing DNA with high fidelity and accuracy ensuring the faithful transmission of genetic information. The recognition of unnatural base pairs (UBPs) by polymerases, enabling their replication, represents a significant and groundbreaking discovery with profound implications for genetic expansion. Romesberg et al. examined the impact of DNA containing 2,6-dimethyl-2H-isoquiniline-1-thione: D5SIC (DS) and 2-methoxy-3-methylnaphthalene: DNAM (DN) UBPs bound to T. aquaticus DNA polymerase (Taq) through crystal structure analysis. Here, we have used polarizable and nonpolarizable classical molecular dynamics (MD) simulations to investigate the structural aspects and stability of Taq in complex with a DNA duplex including a DS-DN pair in the terminal 3' and 5' positions. Our results suggest that the flexibility of UBP-incorporated DNA in the terminal position is arrested by the polymerase, thus preventing fraying and mispairing. Our investigation also reveals that the UBP remains in an intercalated conformation inside the active site, exhibiting two distinct orientations in agreement with experimental findings. Our analysis pinpoints particular residues responsible for favorable interactions with the UBP, with some relying on van der Waals interactions while other on Coulombic forces.

Investigation of dynamical flexibility of D5SIC-DNAM inside DNA duplex in aqueous solution: a systematic classical MD approach.

Incorporation of artificial 3rd base pairs (unnatural base pairs, UBPs) has emerged as a fundamental technique in pursuit of expanding the genetic alphabet. 2,6-Dimethyl-2H-isoquiniline-1-thione: D5SIC (DS) and 2-methoxy-3-methylnaphthalene: DNAM (DN), a potential unnatural base pair (UBP) developed by Romesberg and colleagues, has been shown to have remarkable capability for replication within DNA. Crystal structures of a Taq polymerase/double-stranded DNA (ds-DNA) complex containing a DS-DN pair in the 3' terminus showed a parallelly stacked geometry for the pre-insertion, and an intercalated geometry for the post-insertion structure. Unconventional orientations of DS-DN inside a DNA duplex have inspired scientists to investigate the conformational orientations and structural properties of UBP-incorporated DNA. In recent years, computational simulations have been used to investigate the geometry of DS-DN within the DNA duplex; nevertheless, unresolved questions persist owing to inconclusive findings. In this work, we investigate the structural and dynamical properties of DS and DN inside a ds-DNA strand in aqueous solution considering both short and long DNA templates using polarizable, and non-polarizable classical MD simulations. Flexible conformational change of UBP with major populations of Watson-Crick-Franklin (WCF) and three distinct non-Watson-Crick-Franklin (nWCFP1, nWCFP2, nWCFO) conformations through intra and inter-strand flipping have been observed. Our results suggest that a dynamical conformational change leads to the production of diffierent conformational distribution for the systems. Simulations with a short ds-DNA duplex suggest nWCF (P1 and O) as the predominant structures, whereas long ds-DNA duplex simulations indicate almost equal populations of WCF, nWCFP1, nWCFO. DS-DN in the terminal position is found to be more flexible with occasional mispairing and fraying. Overall, these results suggest flexibility and dynamical conformational change of the UBP as well as indicate varied conformational distribution irrespective of starting orientation of the UBP and length og DNA strand.

Dual modification to stabilize Non-IPR C72 fullerene: A new theoretical strategy.

The stabilization of non-IPR fullerenes for their isolation and characterization is an area of recent interest. In the present study, we have explored the stabilization techniques of C72 isomers via endo and exo-modifications and finally approached dual modification. A total of four isomers of C72 have been considered in this study; among them, one is IPR derivative (1), and the rest are non-IPR derivatives with one (2) and two (3 and 4) fused pentagon rings. First, we have studied the endohedral modification by encapsulating one and two La atoms in the C72 cavity. Secondly, we have exohedrally modified the C72 isomers via chlorination by adding four and eight chlorides, respectively. Our final approach is to study the dual modification, where we have implemented both endo exo-modifications together. This dual modification can be achieved in two ways: exo followed by endo and endo followed by exo. For each modification, the relative stability of every modified C72 derivative has been checked by calculating the relative energy with respect to the most stable modified analogue. To find out whether these modifications are energetically feasible or not, we have calculated the binding energy of each modified C72 isomer. The binding energy calculation reveals that the encapsulation and exo-modification techniques are good enough to stabilize the non-IPR C72 derivatives. Moreover, the effectiveness of dual modification has also been established from the enhanced binding energy compared to either endo- or exo-modification. We have also studied the NPA charges on the encapsulated La atoms for each endo- and dual-modified C72 derivative. Furthermore, the AIM study has also been perceived to find out the interaction between the La atom and the fullerene cages for both mono- and di-encapsulated fullerene derivatives and also between La-La centres for di-encapsulated derivatives. Overall, the present theoretical study will provide an idea about the stability of the modified C72 derivatives, which will help the experimentalists to design new strategies for synthesizing modified non-IPR fullerene derivatives that have vast applications in the medicinal and industrial fields.

Dehydrogenation of ammonia-borane to functionalize neutral and Li+-encapsulated C60, C70 and C36 fullerene cages: a DFT approach.

Mechanistic investigations into the functionalization of three fullerene cages, viz. C60, C70, and C36 through dehydrogenation of ammonia-borane (AB) have been conducted using Density Functional Theory (DFT). In this process of functionalization, different ring fusions, namely (6-6), (6-5) positions for C60 and C70, and an additional (5-5) for C36 fullerene have been investigated. The optimized geometries of all the complexes and transition states have been characterized using the M06-2X functional in conjunction with the 6-31G(d) basis set. The effect of Li+-encapsulation on the energetics and activation barriers of H2 attachment has also been examined. Although the process of functionalization of neutral fullerenes proceeds extensively through concerted pathways, a step-wise route has been observed for the encapsulated systems. NPA charge analysis and Wiberg bond index (WBI) have been used in order to detect the change in the nature of participating hydrogen atoms and validate the variation in the bond order of the C-C connectivity respectively upon hydrogenation. GCRD parameters have also been calculated to explicate the electronic properties of the hydrogenated products. The (6-6) hydrogenation is observed to be favoured thermodynamically and kinetically for both neutral and Li+-encapsulated C60 and C70, while (5-5) is found to be the most preferred site for C36 systems. Our theoretical exploration suggests that the covalent functionalization of the fullerene cages can be done successfully viaAB resulting in the stabilization of these systems. In short, the present work will provide a general idea about the detailed mechanism related to the functionalization of fullerene cages, which will further motivate researchers in fullerene chemistry.

Theoretical study of gas-phase detoxication of DMMP and DMPT using ammonia-borane and its analogous compound.

The detoxication of DMMP (Dimethyl methylphosphonate) and DMPT (O, S-dimethyl methylphosphonothiolate) via hydrogenation have been investigated computationally employing density functional theory (DFT). In this present study, we aim to explore the direct molecular H2 assisted as well as ammonia-borane (NH3BH3) and 3-methyl-1,2-BN-cyclopentane (denoted as cy-AB) assisted hydrogenation pathways of DMMP and DMPT in order to detoxify them. The detoxication of DMMP has been carried out by successive elimination of two -OMe groups. However, in the case of DMPT, two possibilities have been identified because of two different substituents, -OMe and -SMe. In possibility-I, the elimination of the -OMe group occurs at the beginning, followed by the -SMe group, whereas in possibility-II, the reverse order of elimination occurs for -OMe and -SMe groups. During the detoxication of DMMP using both NH3BH3 and cy-AB as the assisting reagents, the first step has been identified as the rate-determining step (RDS) in which the hydrogens attached to the N- and B-centers of NH3BH3 are transferred to the O-center of PO and P-center, respectively. In harmony with DMMP detoxication, for DMPT also, analyzing the activation barriers, it can be articulated that for both NH3BH3 and cy-AB assisted pathways, both the possibilities are equally feasible as in both the possibilities the common first step is the RDS. Therefore, our computational study is designed to explore the assisting efficiency of NH3BH3 and its cyclic analogue for detoxifying the OPCs.

Exploration of M(100)-2×1 (M=Si, Ge) surface termination through hydrogen passivation using ethane and ammonia-borane derivatives: A theoretical approach.

Termination process of Si(100)-2 × 1 as well as Ge(100)-2 × 1 reconstructed surfaces have been explored comprehensively through the dehydrogenation of ethane and ammonia-borane and their several analogues by employing density functional theory (DFT). From our study, it is evident that the termination of Si-surface via the dehydrogenation of aforementioned ethane and NH3BH3 derivatives is more feasible compared to Ge-surface. For ethane, the investigation shows that the substitution of non-participating hydrogens with +I group (electron donating) causes an enhancement in the kinetic and thermodynamic feasibility of the termination process, whereas the implementation of -I substituent (electron withdrawing) makes an adverse effect. While exploring the termination of Si- as well as Ge-surfaces through the dehydrogenation of NH3BH3 and its derivatives, it is noticed that from both the kinetic as well as thermodynamic perspectives, the termination processes are more feasible than that of ethane and its derivatives. We have further examined the detailed mechanism of each termination process by analyzing the geometrical parameters and NPA charges. From bonding evaluation, it is evident that the hydrogen abstraction from ethane by both the surfaces is symmetric in nature, where both the hydrogens show slightly positive charge. But for NH3BH3 the hydrogen abstraction process becomes asymmetric, where the boron associated hydrogen is abstracted as hydride by the electrophilic surface Si (Ge) and the hydrogen bonded with the N-centre is abstracted as proton by the nucleophilic surface Si (Ge). Overall, the present theoretical work reveals one of the efficient chemical processes for terminating Si as well as Ge(100)-2 × 1 reconstructed surfaces through the formation of non-polar SiH bonds.

Towards a comprehensive understanding of the Si(100)-2×1 surface termination through hydrogen passivation using methylamine and methanol: a theoretical approach.

Using density functional theory, we explored the termination process of Si (100)-2 × 1 reconstructed surface mechanistically through the dehydrogenation of small molecules, considering methyl amine and methanol as terminating reagents. At first, both the terminating reagents form two types of adduct through adsorption on the Si (100)-2 × 1 surface, one in chemisorption mode and the other via physisorption, from which the dehydrogenation process is initiated. By analyzing the activation barriers, it was observed that termination of the Si-surface through the dehydrogenation is kinetically almost equally feasible using either reagent. We further examined in detail the mechanism for each termination process by analyzing geometrical parameters and natural population analysis charges. From bonding evaluation, it is evident that hydrogen abstraction from adsorbates on the Si-surface is asymmetric in nature, where one hydrogen is abstracted as hydride by the electrophilic surface Si and the other hydrogen is abstracted as proton by the neucleophilic surface Si. Moreover, it was also observed that hydride transfer from adsorbate to the Si-surface occurs first followed by proton transfer. Overall, our theoretical interpretation provides a mechanistic understanding of the Si (100)-2 × 1 reconstructed surface termination by amine and alcohol that will further motivate researchers to design different types of decorated semiconductor devices. Graphical Abstract Surface termination process of Si(100)-2×1 through formation of non-polar Si-H bonds via dehydrogenation of methylamine and methanol as terminating reagents.

Identification and characterization of intramolecular γ-halo interaction in d0 complexes: a theoretical approach.

A mechanistic investigation to detect intramolecular M⋯X-C type interactions in d0 neutral and cationic complexes was carried out through a benchmark study employing different density functional methods. As γ-halogen is involved in M⋯X-C type interactions, it is denoted as a γ-halo interaction and the respective conformers are designated as halo-conformers. By analyzing the geometrical parameters of halo-conformers, it was observed that, irrespective of the nature of the metal and the halogen, the Cγ-X bond distance increases compared to the usual C-X bond, which brings the M and X centers close enough to generate a weak interaction. Generation of the M⋯X-C interaction was confirmed by performing NBO, AIM and Wiberg bond index analyses, from which the persistence of γ-halo interaction was seen to be prominent. Moreover, for each neutral and cationic complex, the values of Wiberg bond order are in good agreement with the AIM results. The effect of the metal center, as well as γ-halogen substitution, on γ-halo interaction was also studied in the present work. To justify the practical subsistence of the halo-conformers, we checked the stability of the conformers with respect to their ß-conformers by comparing the zero-point-corrected electronic energies. Therefore, the entire study was designed in such a way that it can provide evidence in support of intramolecular M⋯X-C interactions, where, instead of the C-H bond, the Cγ-X bond will interact with the central transition metal.

Mechanistic Insight into the Molecular TiO2-Mediated Gas Phase Detoxication of DMMP: A Theoretical Approach.

The detoxication of DMMP (dimethyl methylphosphonate) mediated by molecular TiO2 has been investigated computationally using density functional theory (DFT). From our previous studies, it is evident that the unimolecular detoxication of OPCs (organophosphorus compounds) is kinetically unfeasible at room temperature due to the significantly high activation barrier. Thus, the aim of our work is to find out whether molecular TiO2 can make any significant impact on the kinetic feasibility of the detoxication processes or not. Here, we have identified a total of three detoxication pathways, where in the first step the detoxication occurs through H-abstraction with the assistance of TiO2, and in the second step, the titanium complex is separated from the respective phospho-titanium complexes. The outcomes reveal that the TiO2-mediated detoxication pathways are at least 20.0 kcal/mol more favorable than their respective unimolecular pathways and that among them, the α-H-mediated isomerization is found to be the most feasible pathway. When the separation of a titanium complex is under consideration, the double H2O-assisted mechanism is found to be the favored pathway. Overall, the entire work provides a widespread idea about the efficiency of molecular TiO2-assisted detoxication of DMMP, which can be well applicable to other OPCs also.

Exploration of Unimolecular Gas-Phase Detoxication Pathways of Sarin and Soman: A Computational Study from the Perspective of Reaction Energetics and Kinetics.

A mechanistic investigation has been carried out to explore all possible gas phase unimolecular isomerization as well as decomposition pathways of toxic organophosphorus compounds (OPCs), namely, sarin (GB) and soman (GD), which are better known as nerve agents. We have identified a total of 13 detoxication pathways for sarin, where the α-H, ß-H, and γ-H take part in the H-transfer process. However, for soman, due to the presence of ω-H, three additional detoxication pathways are obtained, where the ω-H is involved in the H-transfer process. Among all the pathways, the D3 decomposition pathway, where the phosphorus oxoacid derivative and alkene are generated via the formation of a six-membered ring in the transition state, is identified as the most feasible pathway from the perspective of both activation barrier and reaction enthalpy values. Moreover, we have studied the feasibility of the isomerization and decomposition pathways by performing the reaction kinetics in the temperature range of 300 K-1000 K using the one-dimensional Rice-Ramsperger-Kassel-Marcus (RRKM) master equation. From the RRKM calculation also, D3 pathway is confirmed as the most feasible pathway for both OPCs. The rate constant values associated with the D3 pathway within the temperature range of 600 K-700 K imply that the degradation of the OPCs is possible within this temperature range via the D3 pathway, which is in good agreement with the earlier reported experimental result. It is also observed that at higher temperature range (∼900 K), the increased rate constant values of other detoxication pathways indicate that along with D3, all other pathways become more or less equally feasible. Therefore, the entire work provides a widespread idea about the kinetic as well as thermodynamic feasibility of the explored detoxication pathways of the titled OPCs.

Efficient White-Light Generation from Ionically Self-Assembled Triply-Fluorescent Organic Nanoparticles.

Low cost, simple, and environmentally friendly strategies for white-light generation which do not require rare-earth phosphors or other toxic or elementally scare species remain an essentially unmet challenge. Progress in the area of all-organic approaches is highly sought, single molecular systems remaining a particular challenge. Taking inspiration from the designer nature of ionic-liquid chemistry, we now introduce a new strategy toward white-light emission based on the facile generation of nanoparticles comprising three different fluorophores assembled in a well-defined stoichiometry purely through electrostatic interactions. The building blocks consist of the fluorophores aminopyrene, fluorescein, and rhodamine 6G which represent blue, green, and red-emitting species, respectively. Spherical nanoparticles 16(±5) nm in size were prepared which display bright white-light emission with high fluorescence quantum efficiency (26 %) and color coordinate at (0.29, 0.38) which lie in close proximity to pure white light (0.33, 0.33). It is noteworthy that this same fluorophore mixture in free solution yields only blue emission. Density functional theory calculations reveal H-bond and ground-state proton transfer mediated absolute non-parallel orientation of the constituent units which result in frustrated energy transfer, giving rise to emission from the individual centers and concomitant white-light emission.

Exploration of Binding Interactions of Cu(2+) with d-Penicillamine and its O- and Se- Analogues in Both Gas and Aqueous Phases: A Theoretical Approach.

We have theoretically explored the entire binding phenomena of d-penicillamine and its O- and Se-analogues with Cu(2+) in both gas and aqueous phases. At first, a brief conformational analysis has been performed via -XH and -COOH rotations to investigate such conformers that are suitable for binding in both bidentate as well as tridentate fashions. The stability of each bidentate and tridentate complex is determined on the basis of relative energy (ΔE) and gas phase metal ion affinity (MIA) along with the bonding analysis by using atoms in molecule theory. The effect of conformational change on the stability of the complexes is also examined thoroughly. By analyzing the MIA values, we have shown that the side chain substitution makes an impact on the binding process. To delve into the binding phenomena in aqueous phase, we have introduced both the first and second hydration sphere models. In first hydration sphere model, to realize the precise effect of water molecules we have considered stable octahedral hexa-aqua copper complex, [Cu(H2O)6](+2) and accordingly substituted water molecules depending on the bidentate or tridentate nature of the chelating agents. The influence of bulk water molecules on the energetics and geometries of the first hydrated sphere complexes have also been investigated by employing second hydration sphere model assuming physiological pH through the implementation of implicit COSMO and polarizable continuum models, respectively. In the second hydration sphere model, the zwitterionic structures of the amino acids and their side chain deprotonated forms are also included to study the binding phenomena with Cu(2+). The complete work furnishes both the binding properties and the energetics of the copper-artificial amino acid complexes in both gas and aqueous phases that will reflect a realistic overview of the entire binding phenomena.

Hydrolysis of ammonia borane and metal amidoboranes: A comparative study.

A gas phase mechanistic investigation has been carried out theoretically to explore the hydrolysis pathway of ammonia borane (NH3BH3) and metal amidoboranes (MNH2BH3, M = Li,Na). The Solvation Model based on Density (SMD) has been employed to show the effect of bulk water on the reaction mechanism. Gibbs free energy of solvation has also been computed to evaluate the stabilization of the participating systems in water medium which directly affects the barrier heights in the potential energy surface of hydrolysis reaction. To validate the experimentally observed kinetics studies, we have carried out transition state theory calculations on these hydrolysis reactions. Our result shows that the hydrolysis of both the metal amidoboranes exhibits greatly improved kinetics over the neat NH3BH3 hydrolysis which corroborates well with the experimental observation. Between the two amidoboranes, hydrolysis of LiNH2BH3 is found to be kinetically favored over that of NaNH2BH3, making it a better candidate for releasing molecular hydrogen.

Comprehensive study of methylation on the silicon (100)-2 × 1 surface: a density functional approach.

A detailed mechanistic investigation of Si-Me formation over the silicon (100)-2 × 1 surface using the Si9H12 cluster model has been performed using various reagents, based on two basic mechanisms: dissociation and substitution. The reagents CH4, CH3Cl for dissociation and CH3Li, CH3MgBr for substitution mechanism are used to explore the methylation process on the silicon surface at the M062X/6-311+G(2d, p) level of theory. The associated potential energy surfaces explored here are aimed to unveil the most favored pathway of methylation with appropriate reagents. Dissociation of methane forms a monomethylated product (D1) through an energetically unfavorable pathway. All the adsorption modes of CH3Cl over the silicon surface are also detected and analyzed. Methyl chloride dissociates to form another monomethylated product D2 and its derivative D3 in the entrance channel, while, in the next step, bridged compounds I1 (Cl-bridged) and I2 (H-bridged) are produced from them, respectively. The C-Cl dissociation leads to the formation of D2 having a lower activation barrier. With a comparably high activation barrier in the C-H dissociation, producing D3, very interestingly carbene intermediate has been detected in the reaction pathway. Detection of energetically unfavored conversions from D2 to I1 and D3 to I2 ensured that the methylation process will not be hampered through these interconversions. For substitution, HCl- and Cl2-passivated Si surfaces are taken, where chlorine is to be substituted by the methyl group of both of the methylating agents. With both substituents, HCl-passivated Si9H12 gives D1. The substitution process on Cl2-passivated Si9H12 leads to the formation of D2 in the first step and dimethylated product (S1) in the final step. In all the above substitution processes, methyl lithium proved to be the better substituent for the formations of D1, D2, and S1 on HCl- or Cl2-passivated surfaces. The present work not only demonstrated methyl lithium as one of the best methylating agents but also revealed the interrelation among the dissociative adsorption modes of CH3Cl, reported earlier, in a single potential energy surface with a remarkable detection of carbene intermediate formed in the pathway of C-H dissociation.

Towards a comprehensive understanding of the chemical vapor deposition of titanium nitride using Ti(NMe2)4: a density functional theory approach.

A gas phase mechanistic investigation of the chemical vapor deposition (CVD) of titanium nitride (TiN) from the decomposition of Ti(NMe2)4, tetrakis(dimethylamido)titanium (TDMAT) as a single source precursor as well as from the reaction of Ti(NMe2)4 with NH3, i.e., the ammonia assisted mechanism is carried out and reported herein within the framework of density functional theory. Contrary to the theoretical result reported previously for a model TDMAT, metallacycle formation and ß-H elimination pathways are found to be the major decomposition pathways responsible for the decomposition of TDMAT, and this finding is in accord with the experimental observation. Interestingly, agostic interaction is found to play a key role in promoting ß-H elimination in the decomposition of TDMAT. A new additional pathway of decomposition of TDMAT has been identified theoretically in this present study. Exploration of the complex gas phase mechanism and thereby a detailed identification of the reaction intermediates enable us in realizing the origin of incorporation of carbon contamination in TiN films produced from TDMAT alone and then how the contamination is removed in the presence of ammonia. The ammonia assisted mechanism is found to proceed through the formation of a pre-equilibrium complex. The computed barrier height of 7.3 kcal mol(-1) for the initial transamination process associated with the Ti(NMe2)4 + NH3 reaction is found to be in very good agreement with the experimental activation energy. The total rate constant ktot for the ammonia assisted mechanism is calculated to be 1.28 × 10(-51) cm(3) molecule(-1) s(-1) at 298.15 K.