Stochastic structure determination for conformationally flexible heterogenous molecular clusters: application to ionic liquids

Reactions of N2O and CO on neutral Rh10On clusters: a density functional study

Density functional theory calculations were performed to identify product, reactant and intermediate dissociative/associative structures for the oxygen abstraction and addition reactions: Rh10On + CO → Rh10On-1 + CO2, n = 1-5 and Rh10On + N2O → Rh10On+1 + N2, n = 0-4 reactions. In the case of the oxygen abstraction reactions, the energetics of the reaction path were very similar in energy regardless of the number of oxygen atoms on the Rh10On cluster, whereas for the addition of oxygen to the Rh10On cluster, the reaction was found to become significantly less exothermic with each successive addition of oxygen.

An infrared study of CO2 activation by holmium ions, Ho+ and HoO. Phys Chem Chem Phys 2022;24:22716-22723. [PMID: 36106954 DOI: 10.1039/d2cp02862j]

We report a combined experimental and computational study of carbon dioxide activation at gas-phase Ho⁺ and HoO⁺ centres. Infrared action spectra of Ho(CO₂)_n⁺ and [HoO(CO₂)_n]⁺ ion-molecule complexes have been recorded in the spectral region 1700-2400 cm^-1 and assigned by comparison with simulated spectra of energetically low-lying structures determined by density functional theory. Little by way of activation is observed in Ho(CO₂)_n⁺ complexes with CO₂ binding end-on to the Ho⁺ ion. By contrast, all [HoO(CO₂)_n]⁺ complexes n ≥ 3 show unambiguous evidence for formation of a carbonate radical anion moiety, . The signature of this structure, a new vibrational band observed around 1840 cm^-1 for n = 3, continues to red-shift monotonically with each successive CO₂ ligand binding with net charge transfer from the ligand rather than the metal centre.

Regulation nature of water-choline amino acid ionic liquid mixtures on the disaggregation behavior of starch

Fully green and renewable choline amino acid (choline glycine, [Cho][Gly]) ionic liquid (IL) was firstly explored and evaluated as a solvent for starch. By a thorough investigation of microstructure evolution of water-[Cho][Gly] (w:IL) mixtures, its regulation mechanism on disaggregation behaviors of starch was revealed and illuminated. Compared with pure water, existed hydrated free ions in w:IL-9:1 and w:IL-7:3 restrict starch-water interactions to disaggregate of starch, thus hampering gelatinization of starch. While the gelatinization temperatures decreased at w:IL-5:5 and w:IL-4:6 mixtures with a result of homogeneous starch solutions. The tight and water-separated ion pairs existed at w:IL-5:5 and w:IL-4:6 mixtures allow adequate ions to interact with starch to facilitate the disaggregation of starch. At w:IL-2:8 and w:IL-0:10 mixtures, an exothermic dissolution of starch was observed at high temperatures as a result of predominant starch-ion interactions. These results provide the possibility of using [Cho][Gly] solvent to meet various application requirements of starch.

Role of Host-Guest Interaction in Understanding Polymerisation in Metal-Organic Frameworks

Metal-organic frameworks, MOFs, offer an effective template for polymerisation of polymers with precisely controlled structures within the sub-nanometre scales. However, synthetic difficulties such as monomer infiltration, detailed understanding of polymerisation mechanisms within the MOF nanochannels and the mechanism for removing the MOF template post polymerisation have prevented wide scale implementation of polymerisation in MOFs. This is partly due to the significant lack in understanding of the energetic and atomic-scale intermolecular interactions between the monomers and the MOFs. Consequently in this study, we explore the interaction of varied concentration of styrene, and 3,4-ethylenedioxythiophene (EDOT), at the surface and in the nanochannel of Zn₂(1,4-ndc)₂ (dabco), where 1,4-ndc = 1,4-naphthalenedicarboxylate and dabco = 1,4-diazabicyclo[2.2.2]octane. Our results showed that the interactions between monomers are stronger in the nanochannels than at the surfaces of the MOF. Moreover, the MOF-monomer interactions are strongest in the nanochannels and increase with the number of monomers. However, as the number of monomers increases, the monomers turn to bind more strongly at the surface leading to a potential agglomeration of the monomers at the surface.

Density-functional tight-binding: basic concepts and applications to molecules and clusters

The scope of this article is to present an overview of the Density Functional based Tight Binding (DFTB) method and its applications. The paper introduces the basics of DFTB and its standard formulation up to second order. It also addresses methodological developments such as third order expansion, inclusion of non-covalent interactions, schemes to solve the self-interaction error, implementation of long-range short-range separation, treatment of excited states via the time-dependent DFTB scheme, inclusion of DFTB in hybrid high-level/low level schemes (DFT/DFTB or DFTB/MM), fragment decomposition of large systems, large scale potential energy landscape exploration with molecular dynamics in ground or excited states, non-adiabatic dynamics. A number of applications are reviewed, focusing on -(i)- the variety of systems that have been studied such as small molecules, large molecules and biomolecules, bare orfunctionalized clusters, supported or embedded systems, and -(ii)- properties and processes, such as vibrational spectroscopy, collisions, fragmentation, thermodynamics or non-adiabatic dynamics. Finally outlines and perspectives are given.

Silica bound co-pillar[4+1]arene as a novel supramolecular stationary phase

A novel co-pillar[4+1]arene incorporating two bromo-octyl substituents has been synthesised for the first time, using microwave irradiation in high yield (88%) in under four minutes, and bound to the surface of chromatographic silica particles. The resulting new stationary phase has been successfully utilised to separate xylene isomers via liquid chromatographic techniques.

Externally predictive quantum-mechanical models for the adsorption of aromatic organic compounds by graphene-oxide nanomaterials

Graphene oxide is most often chosen as an alternative to graphene in the applications of carbon-based nanomaterials where adsorption is the primary process. However, its adsorption properties are poorly understood. The existing reports on the adsorption mechanism of graphene oxide rely on the linear free-energy/solvation-energy relationship (LFER/LSER) models. This computational work explores the role of quantum mechanical descriptors in the adsorption of aromatic organic compounds by graphene-oxide. For this, externally predictive quantitative models based on quantum-mechanical descriptors are developed and compared with the existing LSERs for the prediction of adsorption coefficients of organic compounds at three different adsorbate concentrations. The predictivity of the models is assessed using an external prediction set of compounds not used for developing the models. Notably, the mean polarizability, but originating from the quantum mechanical exchange interactions (between electrons of parallel spin), is found to be the most significant factor in driving the adsorption on graphene oxide. The present work also proposes quantum-mechanical-LSER models based on a combination of quantum-mechanical and LSER descriptors, which are in fact found to be equally predictive as the existing LSERs. The quantum-mechanical models proposed in this work are further utilized for the prediction of adsorption coefficients of aliphatic compounds.

The Fragment Molecular Orbital Method Based on Long-Range Corrected Density-Functional Tight-Binding

The presently available linear scaling approaches to density-functional tight-binding (DFTB) based on the fragment molecular orbital (FMO) method are severely impacted by the problem of artificial charge transfer due to the self-interaction error (SIE), which hampers the simulation of zwitterionic systems such as biopolymers or ionic liquids. Here we report an extension of FMO-DFTB where we included a long-range corrected (LC) functional designed to mitigate the DFTB SIE, called the FMO-LC-DFTB method, resulting in a robust method which succeeds in simulating zwitterionic systems. Both energy and analytic gradient are developed for the gas phase and the polarizable continuum model of solvation. The scaling of FMO-LC-DFTB with system size N is shown to be almost linear, O( N^1.13-1.28), and its numerical accuracy is established for a variety of representative systems including neutral and charged polypeptides. It is shown that pair interaction energies between fragments for two mini-proteins are in excellent agreement with results from long-range corrected density functional theory. The new method was employed in long time scale (1 ns) molecular dynamics simulations of the tryptophan cage protein (PDB: 1L2Y ) in the gas phase for four different protonation states and in stochastic global minimum structure searches for 1-ethyl-3-methylimidazolium nitrate ionic liquid clusters containing up to 2300 atoms.

Accurate prediction of the structure and vibrational spectra of ionic liquid clusters with the generalized energy-based fragmentation approach: critical role of ion-pair-based fragmentation

The GEBF method with the ion-pair-based fragmentation has been developed to facilitate ab initio calculations of general ionic liquid clusters.

Quantum Chemical Methods for the Prediction of Energetic, Physical, and Spectroscopic Properties of Ionic Liquids

The accurate prediction of physicochemical properties of condensed systems is a longstanding goal of theoretical (quantum) chemistry. Ionic liquids comprising entirely of ions provide a unique challenge in this respect due to the diverse chemical nature of available ions and the complex interplay of intermolecular interactions among them, thus resulting in the wide variability of physicochemical properties, such as thermodynamic, transport, and spectroscopic properties. It is well understood that intermolecular forces are directly linked to physicochemical properties of condensed systems, and therefore, an understanding of this relationship would greatly aid in the design and synthesis of functionalized materials with tailored properties for an application at hand. This review aims to give an overview of how electronic structure properties obtained from quantum chemical methods such as interaction/binding energy and its fundamental components, dipole moment, polarizability, and orbital energies, can help shed light on the energetic, physical, and spectroscopic properties of semi-Coulomb systems such as ionic liquids. Particular emphasis is given to the prediction of their thermodynamic, transport, spectroscopic, and solubilizing properties.

Nanostructure, hydrogen bonding and rheology in choline chloride deep eutectic solvents as a function of the hydrogen bond donor

Ab initio MD and experiments are combined to reveal how the nanostructures in choline chloride deep eutectic solvents, and hence their properties, are modulated by the hydrogen bond donor structure.

Enhanced stability of the model mini-protein in amino acid ionic liquids and their aqueous solutions

Using molecular dynamics simulations, the structure of model mini-protein was thoroughly characterized in the imidazolium-based amino acid ionic liquids and their aqueous solutions. Complete substitution of water by organic cations and anions further results in hindered conformational flexibility of the mini-protein. This observation suggests that amino acid-based ionic liquids are able to defend proteins from thermally induced denaturation. We show by means of radial distributions that the mini-protein is efficiently solvated by both solvents due to a good mutual miscibility. Amino acid-based anions prevail in the first coordination sphere of positively charged sites of the mini-protein whereas water molecules prevail in the first coordination sphere of negatively charged sites of the mini-protein.

Computational approaches to understanding reaction outcomes of organic processes in ionic liquids

The utility of using a combined experimental and computational approach for understanding ionic liquid media, and their effect on reaction outcome, is highlighted through a number of case studies.

Combined friction force microscopy and quantum chemical investigation of the tribotronic response at the propylammonium nitrate–graphite interface

The energetic origins of the variation in friction with potential at the propylammonium nitrate–graphite interface are revealed using friction force microscopy (FFM) in combination with quantum chemical simulations.

Non-covalent interactions in ionic liquid ion pairs and ion pair dimers: a quantum chemical calculation analysis

Weak non-covalent interactions were studied by means of QTAIM and NCI approaches in ion pairs and ion pair dimers of 1-alkyl-3-methylimidazolium cations coupled with perfluorinated anions.

Nanostructure of [Li(G4)] TFSI and [Li(G4)] NO3solvate ionic liquids at HOPG and Au(111) electrode interfaces as a function of potential

Atomic force microscopy (AFM) force measurements have been used to study the solvate ionic liquid (IL) double layer nanostructure at highly ordered pyrolytic graphite (HOPG) and Au(111) electrode surfaces as a function of potential.

Competitive pi interactions and hydrogen bonding within imidazolium ionic liquids

In this paper we have explored the structural and energetic landscape of potential π(+)-π(+) stacked motifs, hydrogen-bonding arrangements and anion-π(+) interactions for gas-phase ion pair (IP) conformers and IP-dimers of 1,3-dimethylimidazolium chloride, [C1C1im]Cl. We classify cation-cation ring stacking as an electron deficient π(+)-π(+) interaction, and a competitive anion on-top IP motif as an anion-donor π(+)-acceptor interaction. 21 stable IP-dimers have been obtained within an energy range of 0-126 kJ mol(-1). The structures have been found to exhibit a complex interplay of structural features. We have found that low energy IP-dimers are not necessarily formed from the lowest energy IP conformers. The sampled range of IP-dimers exhibits new structural forms that cannot be recovered by examining the ion-pairs alone, moreover the IP-dimers are recovering additional key features of the local liquid structure. Including dispersion is shown to impact both the relative energy ordering and the geometry of the IPs and IP-dimers, however the impact is found to be subtle and dependent on the underlying functional.

Assessment of the Density Functional Tight Binding Method for Protic Ionic Liquids

Density functional tight binding (DFTB), which is ∼100–1000 times faster than full density functional theory (DFT), has been used to simulate the structure and properties of protic ionic liquid (IL) ions, clusters of ions and the bulk liquid. Proton affinities for a wide range of IL cations and anions determined using DFTB generally reproduce G3B3 values to within 5–10 kcal/mol. The structures and thermodynamic stabilities of n-alkyl ammonium nitrate clusters (up to 450 quantum chemical atoms) predicted with DFTB are in excellent agreement with those determined using DFT. The IL bulk structure simulated using DFTB with periodic boundary conditions is in excellent agreement with published neutron diffraction data.

3-Dimensional atomic scale structure of the ionic liquid-graphite interface elucidated by AM-AFM and quantum chemical simulations

In situ amplitude modulated atomic force microscopy (AM-AFM) and quantum chemical simulations are used to resolve the structure of the highly ordered pyrolytic graphite (HOPG)-bulk propylammonium nitrate (PAN) interface with resolution comparable with that achieved for frozen ionic liquid (IL) monolayers using STM. This is the first time that (a) molecular resolution images of bulk IL-solid interfaces have been achieved, (b) the lateral structure of the IL graphite interface has been imaged for any IL, (c) AM-AFM has elucidated molecular level structure immersed in a viscous liquid and (d) it has been demonstrated that the IL structure at solid surfaces is a consequence of both thermodynamic and kinetic effects. The lateral structure of the PAN-graphite interface is highly ordered and consists of remarkably well-defined domains of a rhomboidal superstructure composed of propylammonium cations preferentially aligned along two of the three directions in the underlying graphite lattice. The nanostructure is primarily determined by the cation. Van der Waals interactions between the propylammonium chains and the surface mean that the cation is enriched in the surface layer, and is much less mobile than the anion. The presence of a heterogeneous lateral structure at an ionic liquid-solid interface has wide ranging ramifications for ionic liquid applications, including lubrication, capacitive charge storage and electrodeposition.

The impact of anion electronic structure: similarities and differences in imidazolium based ionic liquids

In this paper the structural and energetic landscapes of ion-pair dimer conformers of 1,3-dimethylimidazolium based ionic liquids have been explored ([C1C1im][A])2, A = Cl(-), [NO3](-), [MeSO4](-), [OTf](-) and [BF4](-)). A common low-energy conformer has been selected for full electronic structure analysis. We have compared and contrasted each cluster based on the relative hydrogen bonding ability (β-value) of the anion, which varies experimentally as Cl(-) > [NO3](-) ≈ [MeSO4](-) > [OTf](-) ≈ [BF4](-). Correlations between experimental β-values, computed binding energies, charge transfer and various hydrogen bonding data have been made and outliers have been explained in terms of environmental effects present in the liquid phase. This is most evident in the structurally similar [MeSO4](-) and [OTf](-) anions that have very similar hydrogen bonding motifs, but significantly different β-values. Moreover, detailed analysis of the cluster molecular orbitals, for each anion, reveals a subtle interplay between two modes of interaction, an in-plane traditional H-bonding and inter-planar anion-π interaction. Inter-planar anion-π interactions are particularly prominent for the [NO3](-) cluster. We have rationalized how the full range of interactions could impact on the structuring of ILs at surfaces and the effect these may have on viscosity.