Intermolecular interaction network in liquid acetone

Ionic liquids (ILs) hold great promise in many fields including energy storage and generation, mechanical, pharmaceutical, synthetic and separation applications to name just a few. For any given application, the desired physical properties of the ideal IL may differ substantially from others and no widely applicable patterns or trends to facilitate intuitive design. The origins of physical properties lie in the characteristics of the intermolecular energetics, which consist of a complex interplay between electrostatic and dispersion forces. This thesis investigates and develops computational methodologies for calculating a reliable description of the intermolecular interactions for this challenging class of solvents and electrolytes of the future. The electrostatic approximation used in classical molecular dynamics (MD) where atomic partial charges are assigned was investigated in terms of methods based on density matrix partitioning, and the restrained electrostatic potentials (RESP) approaches. It was found that the “geodesic” atomic partial charge scheme, part of the RESP family, produced the most accurate charges. This was measured in terms of (a) charge convergence with increasing basis set size; (b) charge invariance with changes to the coordinate system; (c) insensitivity to minor structural changes on the resulting charges; (d) adequate capture of charge transfer effects; and (e) the preservation of symmetric of charges in symmetric molecules. Although charges can vary dramatically depending on the scheme used, the careful use of atomic partial charge schemes may still produce reliable forcefields, or at least serve as a rapid diagnostic tool to quantify electrostatic interactions and charge transfer. In moving towards unbiased a priori descriptions of IL intermolecular interactions, second-order Moller-Plesset perturbation theory (MP2) was used with the linear-scaling fragment molecular orbital (FMO) framework to assess the extent to which dispersion forces play a role in the intermolecular energetics. ILs of increasing size were examined such that the many-body effects may be captured. The dispersion energy contribution formed up to 20% of the total interaction energy. Furthermore, the interaction energy as produced by FMO was within 1 kJ mol−1 of the full-wavefunction MP2 interaction energy when three-body effects were included. As the dispersion interaction is purely a quantum mechanical phenomenon, correlated quantum mechanical methods, such as MP2 or coupled-cluster approaches, are required to provide an unbiased account of these effects. Ab initio methods such as MP2 and CCSD(T) scale formally as N⁵ an N⁷, respectively, with chemical system size. While the FMO approach provides a marked improvement in efficiency, the counterpoise (CP) approach to correcting the basis set superposition error (BSSE) is not amenable to fragmented approaches and requires each ion in the cluster to be calculated in the basis set of the entire system. In order to remove this bottleneck, the spin-component scaled second-order Moller Plesset perturbation theory (SCS-MP2) methodology was refined by fitting 174 non-CP corrected interaction energies at the MP2/cc-pVTZ level of theory to CP corrected CCSD(T)/CBS benchmark energies. This has resulted in an implicit BSSE correction that may be used within the highly efficient FMO framework, and is shown to yield results on par with or exceeding the accuracy of MP2/cc-pVQZ for clusters of two and four ion pairs (IPs). This new approach as been termed SCS-IL-MP2. An alternative dispersion corrected density functional theory (DFT) approach, DFT- D3, was assessed and refined in view of producing accurate interaction energies at the same CCSD(T)/CBS quality. The same test set of 174 ILs was used to fit the SCS-IL-MP2 approach was used to refit the DFT-D3 approach for both the Hartree-Fock (HF) wavefunction and the PBE and BLYP density functionals (DFs). In most cases, the selection of the DF and associated DFT-D version 3 (DFT-D3) parameters differed negligibly with all reaching within 1 to 2 kJ mol−1 per IP. HF-D3 parameters, on the other hand, showed a substantial improvement, particularly when used with the Becke-Johnson (BJ) damping function. Refitted HF-D3 and the BJ damping function was able to consistently provide interaction energy errors below 5 kJ mol−1 per IP. It would be worthwhile further investigating the application of the refined HF-D3 in its ability to produce reliable energies and geometries over a more diverse set of ILs. Both the SCS-IL-MP2 and new DFT-D3 approaches may be applied to the highly scal- able FMO framework. These form the core elements of the quantum chemistry toolbox for the study and understanding of the physicochemical properties of ILs that have so far been only superficially characterised by electronic structure theory. From this starting point, a rigorous and unbiased a priori understanding of the intermolecular interactions and resulting physicochemical properties may be predicted by means of efficient ab initio molecular dynamics (AIMD) techniques.

Preparation, physicochemical characterization and computational studies of Plectranthus ornatus codd essential oil/β-cyclodextrin inclusion complex

146In today's world, the prevention of metallic corrosion is a very challenging job and would therefore be a mammoth task considering the enormous role of metals and their alloys in several industrial applications. To prevent solution state metallic corrosion suitable amount of organic molecules as inhibitor is widely used as additives to the corrosive solution. Among the organic inhibitors, different N, O, S donor Schiff base molecules are considerably used due to their low-cost starting precursor material, easy to follow synthetic route, and environmental friendly nature. Traditionally, scientists have identified new and prospective corrosion inhibitors either by the modifying the structure of the existing inhibitors or by following up the hardcore wet chemical synthetic routes, which in many instances have become laborious, expensive, time consuming and unable to reveal their microcosmic inhibition process. To overcome these shortfalls, in modern age, newly explored avenues like hardware and software advancements have opened up the door for powerful and worthy use of theoretical chemistry in corrosion inhibitory research domain following low-cost and timesaving processes. The use of computational chemistry in designing and development of organic corrosion inhibitors has been greatly enhanced due to the development of density functional theory (DFT). DFT is a modern tool that is capable enough to mostly predict accurately the relative order of inhibition efficiencies of concerned corrosion inhibitors, based on their molecular and electronic structure and reactivity indices. Furthermore, nucleophilic and electrophilic sites of the inhibitor molecules have also been determined from the analysis values of the DFT-based Fukui indices. Along with DFT, molecular dynamic (MD) simulation has also emerged as an important tool for investigating complex systems that actually need to be faced and experienced during corrosion prevention studies. MD simulation reasonably predicts the actual interfacial configuration of the surface adsorbed inhibitor molecules. Several parameters related to inhibition measurements like interaction energy and binding energy between the inhibitor molecule and metallic surfaces can also be calculated from MD simulation. From the obtained interaction energy and binding energy values it is possible to tell that which inhibitor molecule have superior adsorption ability on the metallic surfaces.

Density functional theory assessed molecular insights into asphaltene interactions within silica and calcium carbonate surface with deep eutectic solvents

In this study, we present a combined analysis procedure between atomistic molecular dynamics (MD) simulations and network topology to obtain more understanding on the evolutionary consequences on protein stability and substrate binding of the main protease enzyme of SARS-CoV2. Communicability matrices of the protein residue networks (PRNs) were extracted from MD trajectories of both Mpro enzymes in complex with the nsp8/9 peptide substrate to compare the local communicability within both proteases that would affect the enzyme function, along with biophysical details on global protein conformation, flexibility, and contribution of amino acid side chains to both intramolecular and intermolecular interactions. The analysis displayed the significance of the mutated residue 46 with the highest communicability gain to the binding pocket closure. Interestingly, the mutated residue 134 with the highest communicability loss corresponded to a local structural disruption of the adjacent peptide loop. The enhanced flexibility of the disrupted loop connecting to the catalytic residue Cys145 introduced an extra binding mode that brought the substrate in proximity and could facilitate the reaction. This understanding might provide further help in the drug development strategy against SARS-CoV2 and prove the capability of the combined techniques of MD simulations and network topology analysis as a "reverse" protein engineering tool.

The structures and intermolecular forces between sodium ion (Na+) encapsulated in single walled carbon nanotube M+@SWCNT have been investigated by density function theory (DFT) calculations to elucidate the nature of the interaction between Na+ and SWCNT. Influence of Na+ encapsulated on electronic properties of SWCNT such as Mulliken charges, bond lengths and HOMO and LUMO energies are computed. For getting more details about the interaction between Na+ and SWCNT their interaction energy was calculated that was equal to −232.77 kJ/mol. In addition, molecular dynamic (MD) simulation has performed to determine the diffusion process of the Na+ cation on the SWCNT.

Interactions between fullerene C24 and a frequently used supplement for sport activities, ephedrine (EPH), have been studied in detail by a combination of density functional theory (DFT), time dependent DFT (TD-DFT) calculations, the symmetry-adapted perturbation theory (SAPT) approach and molecular dynamics (MD) simulations. Information about interaction energies and non-covalent interactions formed between C24 and EPH have been obtained by DFT calculations. TD-DFT calculations have been used in order to obtain UV/vis spectra and to check whether the presence of the EPH molecule produces significant changes in the spectrum. The SAPT approach has been employed in order to decompose the interaction energy into components and therefore to better understand the physical origins of interaction between C24 and EPH. Last, but not least, MD simulations have been used in order to track the influence of temperature on the interactions between C24 and EPH.

Vibrational spectra, electronic absorption, nonlinear optical properties, evaluation of bonding, chemical reactivity and thermodynamic properties of ethyl 4-(1-(2-(hydrazinecarbonothioyl)hydrazono)ethyl)-3,5-dimethyl-1H-pyrrole-2-carboxylate molecule by ab initio HF and density functional methods

Dimer interaction energies have been well studied in computational chemistry, but they can offer an incomplete understanding of molecular binding depending on the system. In the current study, we present a dataset of focal-point coupled-cluster interaction and deformation energies (summing to binding energies, De) of 28 organic molecular dimers. We use these highly accurate energies to evaluate ten density functional approximations for their accuracy. The best performing method (with a double-ζ basis set), B97M-D3BJ, is then used to calculate the binding energies of 104 organic dimers, and we analyze the influence of the nature and strength of interaction on deformation energies. Deformation energies can be as large as 50% of the dimer interaction energy, especially when hydrogen bonding is present. In most cases, two or more hydrogen bonds present in a dimer correspond to an interaction energy of -10 to -25kcal mol-1, allowing a deformation energy above 1kcal mol-1 (and up to 9.5kcal mol-1). A lack of hydrogen bonding usually restricts the deformation energy to below 1kcal mol-1 due to the weaker interaction energy.

Research on novel co-crystals has long been a focal point in the field of high-energy material modification. In the present exploration, density functional theory (DFT) and molecular dynamics (MD) simulations were employed to investigate the properties of pentaerythritol tetranitrate (PETN)/3,4-dinitrofurazanofurazan (DNTF) mixtures across a molar fraction interval of 9:1 to 1:9. This study incorporated a comprehensive analysis of multiple key characteristics, encompassing the surface electrostatic potential of molecules, atomic interaction lines, binding energy values, trigger bond lengths, cohesive energy density, together with the mechanical behaviors of the designated assembly. Additionally, the detonation characteristics of pure PETN, pure DNTF, and the PETN/DNTF system were predicted using the EXPLO-5 software in conjunction with the nitrogen equivalent coefficient (NEC) method. The outcomes of the study uncovered significant divergences in the surface electrostatic potential of PETN versus DNTF molecules. These disparities indicate that intermolecular interactions across different molecular species are stronger than the interactions within homogeneous molecular groups, which in turn points to the viability of co-crystal synthesis between PETN and DNTF. A peak value of binding energy was ascertained at a molar ratio of 3:7, indicating the highest likelihood of co-crystal formation at this composition. The primary driving forces for co-crystallization were identified as electrostatic forces and van der Waals forces. The as-obtained co-crystal explosive demonstrated modest sensitivity and intermediate mechanical behavior. In a similar vein, the detonation behavior of the co-crystal at a molar ratio of 3:7 fell between that of pure PETN and pure DNTF, positioning it as a novel type of insensitive high-energy material. Materials Studio software was utilized to forecast the characteristics of PETN/DNTF co-crystals with varying molar ratios and crystal planes via molecular dynamics (MD) simulations. The MD simulations were performed with a time step of 1 femtosecond (fs) and a total simulation duration of 2ns (ns). An isothermal-isobaric (NPT) ensemble was employed for the 2ns MD simulations. The COMPASS force field was adopted, with the temperature set at 295 Kelvin (K). For the prediction of detonation characteristics, the EXPLO-5 software was combined with the nitrogen equivalent coefficient (NEC) method.

In the chemistry of metallic complexes, two important concepts have been used to rationalize the recognition and selectivity of a host by a guest: preorganization and complementarity. Both of these concepts stem from geometrical features. Less explored in the literature has been the interactional complementarity, where mainly the electronic factors in the intermolecular forces are involved. Because the charge transfer between a species rich in electrons (ligand) and another deficient in them (cation) is one of the main intermolecular factors that control the binding energies in metallic complexes, for such systems, we propose a simple model based on density functional theory. We define an interactional energy in which the geometrical energy changes are subtracted from the binding energies and just the electronic factors are taken into account. The model is tested for the complexation between bidentate and cyclic ligands and Ca, Pb, and Hg metal dications. The charge-transfer energy described by our model fits nicely with the interactional energy. Thus, when the geometrical changes do not contribute in a significant way to the complexation energy, the interactional energy is dominated by charge-transfer effects.

An extreme dependence of the softening temperature of polycomplexes of p-phenylenediamine and low-molecular-weight polycondensation products of boric acid on the ratio thereof is revealed. The stoichiometric ratio of the BA/p-PDA complex is 75/25 wt %, which corresponds to a molar ratio of BA trimer/p-PDA = 1: 1. At a higher content of the amine, the softening temperature of the polycomplex decreases sharply, from 250 to 60°C, which is explained by the complexation of boric acid with the amine, a factor that prevents its dehydration. The energies of the intermolecular interaction between the components of the complex in a vacuum are calculated, and quantum-chemical calculations of the energy of interaction between the components of the complex are performed. The resulting products exhibit paramagnetic and fluorescent properties.

Hydration mechanisms of smithsonite from DFT-D calculations and MD simulations

The performance provided by graphene (Gr) and graphene oxide (GO) additives can be improved by achieving strong adhesion and uniform dispersion in the epoxy resin matrix. In this study, molecular modeling and simulation of DGEBA/DETA based epoxy nanocomposites containing Gr and GO additives were performed. Density functional theory and molecular dynamics simulations were used to investigate interfacial interaction energies and Young's Modulus. Improvement in the interaction energies was studied by controlling the epoxy:hardener ratio, type and the number of oxygen-containing functional groups on the GO, the mass percentage of Gr/GO filler in the epoxy matrix, size and dispersion of GO in the cell. It was demonstrated that functional groups with up to 10 % oxygen content in GO significantly increase interfacial interaction energy for large size Gr/GO. Increasing DETA type amine ratio in the preparation of epoxy polymers increases the interaction energy for high oxygen content while decreasing the interaction energy for low oxygen content in GO for small size GO with edge functional groups. The performance of material dramatically decreased even at high DETA hardener and high GO mass percentages when the aggregation factor of Gr/GO was included in simulations that explain lower Gr/GO percentages in the experimental studies.

Different geometries of nitromethane dimer and nitromethane trimer have been fully optimized employing the density functional theory B3LYP method and the 6-31++G** basis set. Three-body interaction energy has been obtained with the ab initio supermolecular approach at the levels of MP2/6-31++G**//B3LYP/6-31++G** and MP2/aug-cc-pVDZ//B3LYP/6-31++G**. The internal rotation of methyl group induced by intermolecular interaction has been observed theoretically. For the optimized structures of nitromethane dimer, the strength of C--H...O--N H-bond ranges from -9.0 to -12.4 kJ mol(-1) at the MP2/aug-cc-pVDZ//B3LYP/6-31++G** level, and the B3LYP method underestimates the interaction strength compared with the MP2 method, while MP2/6-31++G**//B3LYP/6-31++G** calculated DeltaE(C) is within 2.5 kJ mol(-1) of the corresponding value at the MP4(SDTQ)/6-31G**//B3LYP/6-31++G** level. The analytic atom-atom intermolecular potential has been successfully regressed by using the MP2/6-31++G**//B3LYP/6-31++G** calculated interaction energies of nitromethane dimer. For the optimized structures of nitromethane trimer the three-body interaction energies occupy small percentage of corresponding total binding energies, but become important for the compressed nitromethane explosive. In addition, it has been discovered that the three-body interaction energy in the cyclic nitromethane trimer is more and more negative as intermolecular distances decrease from 2.2 to 1.7 A.