Intermolecular Interaction Energies Research Articles

Reliable Dimerization Energies for Modeling of Supramolecular Junctions.

Accurate estimates of intermolecular interaction energy, ΔE, are crucial for modeling the properties of organic electronic materials and many other systems. For a diverse set of 50 dimers comprising up to 50 atoms (Set50-50, with 7 of its members being models of single-stacking junctions), benchmark ΔE data were compiled. They were obtained by the focal-point strategy, which involves computations using the canonical variant of the coupled cluster theory with singles, doubles, and perturbative triples [CCSD(T)] performed while applying a large basis set, along with extrapolations of the respective energy components to the complete basis set (CBS) limit. The resulting ΔE data were used to gauge the performance for the Set50-50 of several density-functional theory (DFT)-based approaches, and of one of the localized variants of the CCSD(T) method. This evaluation revealed that (1) the proposed "silver standard" approach, which employs the localized CCSD(T) method and CBS extrapolations, can be expected to provide accuracy better than two kJ/mol for absolute values of ΔE, and (2) from among the DFT techniques, computationally by far the cheapest approach (termed "ωB97X-3c/vDZP" by its authors) performed remarkably well. These findings are directly applicable in cost-effective yet reliable searches of the potential energy surfaces of noncovalent complexes.

Kinetic Monte Carlo simulation of selective area growth of mix deposited organic molecules

The selective area growth approach (namely the self-assembly of molecules on pre-patterned surfaces) that takes into account the properties of organic molecular materials and traditional lithography techniques, is expected to play a significant role in manufacturing organic micro-nano patterns for photoelectric and full-color display. The manufacture of organic devices with tunable multicolor patterned films depends on the control of nucleation distribution of two or more organic molecules by using a selective area growth approach, particularly through the application of mixed deposition growth that can enhance the nucleation efficiency of multicolor thin films. However, till now the issue of mixed deposition growth of two kinds of organic molecules has been rarely reported, owing to the complexity in experimental operation. In this work, the selective area growth of mixed deposition of two kinds of molecules is studied by molecular kinetic Monte Carlo approach in order to find the experimental conditions for separating two kinds of molecular growth. In the simulation, the interaction energy between the two molecules is adjusted and controlled to study its influence on the separately selective area growth of the two molecules. The results show that when the intermolecular interaction energy is weak, the planar molecules and the non-planar molecules exhibit completely different growth behaviors. The most of non-planar molecules gather at the top of the electrode in an island mode, while planar molecules mainly accumulate in a layer-by-layer mode on the sides of the electrode. On the contrary, when the intermolecular interaction energy is strong, the number of non-planar particles on the tops decreases and a large number of planar particles appear. Moreover, on the sides of the electrode, the doping nucleation of planar molecules and non-planar molecules also exists, resulting in the failure of molecular phase separation growth. It proves that the intermolecular interaction energy can affect separately area-selective growth of various organic molecules. Therefore, when several different kinds of molecules are mixed and deposited, relatively pure crystalline monochromatic films can be obtained at the top and on the sides of the electrode, respectively, by appropriately adjusting the intermolecular interaction energy, which can further facilitate the application of multi-color organic micro-nano pattern in display and other fields.

A many-body energy decomposition analysis (MB-EDA) scheme based on a target state optimization self-consistent field (TSO-SCF) method.

In this paper, we combine an energy decomposition analysis (EDA) scheme with many-body expansion (MBE) to develop a MB-EDA method to study the cooperative and anti-cooperative effects in molecular cluster systems. Based on the target state optimization self-consistent field (TSO-SCF) method, the intermolecular interaction energy can be decomposed into five chemically meaningful terms, i.e., electrostatic, exchange, polarization, charge transfer and dispersion interaction energies. MB-EDA can decompose each of these terms in MBE. This MB-EDA has been applied to 3 different cluster systems: water clusters, ionic liquid clusters, and acetonitrile-methane clusters. This reveals that electrostatic, exchange, and dispersion interactions are highly pairwise additive in all systems. In water and ionic liquid clusters, the many-body effects are significant in both polarization and charge transfer interactions, but are cooperative and anti-cooperative, respectively. For acetonitrile-methane clusters, which do not involve hydrogen bonds or charge-charge Coulombic interactions, the many-body effects are quite small. The chemical origins of different many-body effects are deeply analyzed. The MB-EDA method has been implemented in Qbics (https://qbics.info) and can be a useful tool for understanding the many-body behavior in molecular aggregates at the quantum chemical level of theory.

Unveiling the therapeutic potential of BAP from crystallographic analysis to protein docking and anticancer assessment in MCF-7 human breast cancer cells

The 4-aminoantipyrine derivatives comprising both N- and O-donor modes generate novel coordination assemblies which tend to exhibit anti-tumor activities. Crystallographic study of 1,5-Dimethyl-4- [(2-oxo-1,2-diphenyl ethylidene) amino]-2-phenyl-1,2-dihydro-3H-pyrazol-3-one (BAP) is reported. Hirshfeld surface analysis is employed to analyze molecular electrostatic potential, inter-molecular interaction energies, and H-bonded framework. To investigate the adaptability and specificity of BAP with different protein interactions, we ran molecular docking simulations using a single ligand and many different protein targets. In this docking study, BAP crystal was selected due to its importance in cancer research, and with the different protein targets 1TNF, 2TUN, 1TNR, 5TSW, 6GK0, 6IUL, 6 K04 and 6 K05 are included. TNF-alpha, a cytokine essential for the immune system and inflammatory reactions, is generated by activated immune cells and is crucial for preventing infections and controlling cell proliferation. TNF inhibitors have improved the treatment of various ailments. TNF-alpha dysregulation is a major area of study in immunology and immunotherapy. Dihydroorotate dehydrogenase, mitochondrial enzyme, and Natterin-like proteins are also important in epigenetics and drug development. BET family proteins, including BRD2, are crucial in disease connections, cell cycle control, and gene regulation. The Swiss ADME method, which assesses medication similarity, strongly implies that the BAP may be a potential option for the treatment of breast cancer. After screening chemical libraries, BAP was shown to be an antagonist of this protein–protein interaction. In this study, the yellow tetrazolium salt (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) evaluation on MCF-7 human breast cancer cells to investigate the feasible anticancer characteristics and cytotoxicity of the BAP complex.

Self-assembled Supramolecular Frameworks and Interaction Energy Studies of Acridine and Dihydroxynaphthalene based Cocrystals

Three cocrystals of acridine with 2,7-dihydroxynaphthalene (Ia and Ib) in two different polymorphs and 1,5-dihydroxynaphthalene (II) have been synthesized and characterized by single crystal x-ray diffraction method. Two polymorphs of acridine,2,7-dihydroxynaphthalene cocrystal crystallizes in same sapcegroup P-1 with different unit-cell parameters. In (Ia) the O‒H group form a syn-anti conformation whereas in (Ib) the O‒H group form an anti-anti conformation leads to the polymorphic structure of acridine, 2,7-dihydroxynaphthalene. This study reveals that the influence of π…π and C‒H…π interactions in the formation of one-, two-, and three-dimensional supramolecular frameworks when the classical hydrogen bonds such as O‒H…N and C‒H…O are limited to discrete motifs. The acridine molecules form continuous π…π stacking in the crystal structure of (Ia) and discrete π…π stacking in the crystal structure of (Ib) and (II). The conformational flexibility of the substituted hydroxy group has an influence in the supramolecular frameworks of the three-dimensional crystal structure. The intermolecular interaction energy calculation between the molecular pairs has been carried out to study the strength of the interaction and its dependence on the geometrical parameters.

Ammonium carboxylate salts: the additivity of intermolecular interaction energies in charged organic compounds

The supramolecular organization of organic salts has been widely researched, revealing recurring patterns in crystalline lattices that describe their supramolecular properties.

The crystal structure of hexaphenylbenzene under high hydrostatic pressure

High-pressure single-crystal X-ray diffraction, intermolecular interaction energy calculations, and density functional theory are used to examine the structure and emission properties of hexaphenylbenzene during hydrostatic compression to 4.14 GPa.

Novel supramolecular co-crystal of 8-hydroxyquinoline with acetone-(2,4-dinitrophenyl)hydrazone: One pot synthesis, structural characterization, Hirshfeld surface and energy framework analysis, computational investigation and molecular docking study

Inspired by Betti reaction, a novel co-crystal of 8-hydroxyquinoline with acetone-(2,4-dinitrophenyl) hydrazone (I) was isolated in a one-pot 3 component assembly by reacting 8-hydroxyquinoline (8-HQ) with 2,4-dinitrohydrazine (DNPH) and formaldehyde. The crystal structure of (I) was characterized by single crystal X-ray diffraction analysis which shows that the hydrogen bonding and π-π stacking are the main driving forces for the co-crystal building. The topology of the intermolecular interaction energies in the crystal packing was analyzed and exposed using 3D energy framework analysis. The calculations of the studied molecule at the B3LYP levels in the 3-21g, 6-31g and 6-31++g** basis sets were made using the Gaussian package program. Theoretical calculations were executed to develop optimized geometry, frontier molecular orbital analysis and the NLO properties of the considered molecule, Furthermore, Molecular docking calculations were made. Afterwards, the interactions occurring in the docking calculation against the anti-oxidant protein (ID: 1HD2, 3NRZ, 4Z8D) were examined in detail with Schrödinger maestro.

Optical clearing of human skin: Molecular modeling and in vivo OCT study.

The results of in vivo immersion optical clearing of human skin under the action of two different optical clearing agents (OCAs), such as an aqueous sucrose solution and a radiographic contrast agent Omnipaque™ 300 (iohexol), were obtained with the use of optical coherence tomography (OCT) method. The rate of reduction of light scattering coefficient, obtained through an averaged A-scan of the OCT image in the region of dermis within the depths from 350 to 700 μm, were determined to evaluate the efficiency of optical clearing (EOC). The correlations between the EOC and the energy of intermolecular interaction of OCAs with a fragment of collagen peptide have been established as a result of molecular modeling by quantum chemistry methods HF/STO3G/DFT/B3LYP/6-311G(d) of a number of OCAs (glycerol, iohexol, sucrose, ribose, fructose, glucose) with mimetic peptide of collagen (GPH)3 .

Low Molecular Weight Supramolecular Allobetuline-, Cyclohexanol-, or Undecanol-Appended 1,2,3-Triazole-Based Gelators: Synthesis and Molecular Dynamics Simulation Study

AbstractThree novel isomeric supramolecular allobetuline-appended 1,2,3-triazole-based potential gelators and two model compounds with cyclohexanol or undecanol fragments in the structure instead of the triterpenoid platform were synthesized. Their ability to form gels in different solvents was studied experimentally and computationally by molecular dynamics simulations and quantum chemical calculations. We found that the gelling ability of such compounds is driven by the binding energy of intermolecular tail substituent interactions. The less significant factor is the molecule unfolding in a solvent, providing that the gelling substance is actually soluble. Preferred unfolded conformations were identified by classical molecular dynamics simulation and suggested the most prospective 1,2,3-triazole-based potential gelators.

Approximating Electrostatic Potential of Molecules with Point Charges Mimicking the Electron Pairs

The electrostatic component used in the traditional force fields significantly impacts their accuracy in modelling the noncovalent interactions peculiar to biomolecular systems, including hydrogen bonding. In this contribution, we present a physical model for approximating the electrostatic potential of a molecule (MEP) based on the first-principle decomposition of its charge density distribution into the localized components. In contrast to conventional schemes, which typically use atom-centered charges to approximate MEP, the proposed approach locates such charges in the positions selected so as to mimic the anisotropy of the electron density distributions related to the electron pairs of atoms or covalent bonds. This peculiarity leads to a more accurate representation of the overall electrostatic potential, as verified by applying the proposed model to approximate the electrostatic component of the intermolecular interaction energy in 145 noncovalently bound molecular complexes from GMTKN55 database. This benchmark showed the root-mean-square difference between the true and approximated values of the electrostatic component of 2.7 kcal/mol, which is 2.2 times lower as compared to the traditional RESP charges method used as a baseline.

Interaction of sulfasalazine with outer surface of boron-nitride nanotube as a drug carrier in aqueous solution: insights from quantum mechanics and Monte Carlo simulation

The improvement of the solubility of sulfasalazine in physiological media was the major aim of this study. Accordingly, BNNT inspected as a notable candidate for the carriage of this drug in aqueous media. For this purpose, four possible interactions of two tautomer of sulfasalazine with (9,0) boron-nitride nanotube were considered in aqueous media. The compounds were optimized in gas phase using density functional calculations. Solvation free energies and association free energies of the optimized structures were then studied by Monte Carlo simulation and perturbation method in water environment. Outcomes of quantum mechanical calculations presented that interaction of keto form of sulfasalazine produce the most stable complexes with boron-nitride nanotube in gas phase. Simulation results revealed that electrostatic interactions play a vital role in the intermolecular interaction energies after binding of drug and nanotube in aqueous solution. Results of association free energy calculations indicated that complexes of both two sulfasalazine tautomers (keto and enol) and nanotube were stable in solution. Computed solvation free energies in water showed that the interaction with boron-nitride nanotube significantly improved the solubility of sulfasalazine, which could improve its in vivo bioavailability.

Extractive distillation for separation of isopropanol-n-propanol-water ternary system: Mechanism analysis and process design

In the process of producing isopropanol (IPA) by direct hydration of propylene, a mixture of IPA, n-propanol (NPA) and H2O is formed. In order to obtain high purity IPA and NPA, extractive distillation technology can be used to separate these three components. In this paper, Based on the COSMO-RS model, 1-ethyl-3-methylimidazolium dicyandiamide ([EMIM][DCA]) was selected as the extractant for extractive distillation in ionic liquids. The extractive distillation process for the separation of IPA-NPA-H2O system with ethylene glycol (EG) or [EMIM][DCA] as extractant was designed and optimized by multi-objective genetic algorithm. Process simulation results show that the process using [EMIM][DCA] can reduce total annual cost by 44.635% and total gas emission by 29.873% compared with the traditional organic solvent EG as extractant. These results show that [EMIM][DCA] is a good extractant, which can reduce the gas emission and energy consumption of the distillation process. In addition, we further explored the separation mechanism of the system at the molecular level by analyzing the σ-curve and the intermolecular interaction energy.

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

Deep Eutectic Solvents (DES) have gained recent attention as asphaltene solvents due to their low cost and eco-friendliness. However, identifying the intermolecular behavior of asphaltene with different DESs using experimental methods is costly and time-consuming. Therefore, this study investigates the intermolecular interactions and electronic properties of DESs with model asphaltene in the presence of sandstone (SiO2) and carbonate (CaCO3) surfaces using Density Functional Theory (DFT) calculations. The study focuses on understanding the binding energies, interaction energies, band gap, and intermolecular mechanism between SiO2 surface, asphaltene, and DESs (SiO2-Asp-DESs systems) and CaCO3 surface, asphaltene, and DESs (CaCO3-Asp-DESs systems). The investigation yields valuable insights into the interactions, stability, and affinity of the asphaltene and DES in the overall system, enhancing understanding of asphaltene behavior in solvent environments. The study shows that DES containing choline chloride as a hydrogen bond acceptor (HBA) outperforms in the presence of both surfaces (SiO2 and CaCO3) with asphaltene. For the SiO2-Asp-DES system, which contains DES as choline chloride and ethylene glycol, a higher intermolecular interaction energy of − 747.174 kJ/mol is observed. In contrast, for the CaCO3-Asp-DES system, DES as choline chloride and glycerol show higher intermolecular interaction energy of − 259.154 kJ/mol. Variations in interaction and binding energies for the systems further show that the effectiveness of DES with asphaltene varies depending on the type of surface (SiO2/CaCO3). As for the overall reactivity, CaCO3-Asp-DESs systems show comparatively less reactivity than SiO2-Asp-DESs systems that show smaller band gaps.

Solubility prediction and intermolecular interaction energies of four explosives in the studied solvents at different temperatures

ABSTRACT Solubility prediction and intermolecular interaction of four explosives (1,3,5-Trinitroperhydro-1,3,5-triazine,ε‑2,4,6,8,10,12-Hexanitro-2,4,6,8,10,12-hexaazaiso-wurtzitane, 3-Nitro-1,2,4-triazolin-5-one，3,4-dinitro-1 H-pyrazole) are researched by the Conductor-like Screening Model – Realistic solvents (COSMO-RS). The results show that the study of σ-surface and σ-profile can qualitatively analyze the potential mechanism of the dissolution behavior of four explosives in the studied solvents. COSMO-RS can accurately predict the solubility of four explosives in the studied solvents, but some of the predicted solubility is different from the experimental solubility, and the deviation between the predicted solubility and the experimental solubility was analyzed. The molecular interaction energy between explosive molecules and solvent partially reveals the internal mechanism of the dissolution of explosives, however, the solvation of the four explosives is a complex process that requires the synthesis of various molecular interactions. This has a great effect on the study of solvation of explosives, and it is of great significance for solvent screening of other explosives molecules.

Thermodynamic and molecular simulation analysis of molecular interactions between methyl 2–hydroxyisobutyrate + water or n–alkanol (C1–C2) mixtures

Methyl 2–hydroxyisobutyrate (HBM) is essential as a photoresist thinner in semiconductor fabrication. In this study, we examined the density and viscosity of HBM combined with water or alkanol (C1–C2) at a pressure of 0.1 MPa and temperatures ranging from 288.15 K to 323.15 K. Based on experimental data, we calculated the excess molar volume, as well as apparent, partial, and excess partial molar volumes, and deviations in viscosity. These derived thermodynamic properties were then modeled using the Redlich-Kister (RK) polynomial equation. The VmE values of HBM + water mixtures are more negative compared to HBM + alkanol mixtures because of the stronger H–bonding interactions in HBM–water than in HBM–alkanol. With increasing temperature, the VmEbecome more negative, whereas the Δη values lower with a temperature rise. The values for excess molar volume and deviation in viscosity were analyzed through a graph theoretical method. Additionally, the excess free energy of activation was determined from the viscosity data. FTIR spectral analysis validated the findings related to intermolecular interactions and the graph theoretical method. Lastly, molecular dynamics simulations shed light on the intermolecular interaction energies and their differences in the studied binary systems.

Combining Force Fields and Neural Networks for an Accurate Representation of Chemically Diverse Molecular Interactions.

A key goal of molecular modeling is the accurate reproduction of the true quantum mechanical potential energy of arbitrary molecular ensembles with a tractable classical approximation. The challenges are that analytical expressions found in general purpose force fields struggle to faithfully represent the intermolecular quantum potential energy surface at close distances and in strong interaction regimes; that the more accurate neural network approximations do not capture crucial physics concepts, e.g., nonadditive inductive contributions and application of electric fields; and that the ultra-accurate narrowly targeted models have difficulty generalizing to the entire chemical space. We therefore designed a hybrid wide-coverage intermolecular interaction model consisting of an analytically polarizable force field combined with a short-range neural network correction for the total intermolecular interaction energy. Here, we describe the methodology and apply the model to accurately determine the properties of water, the free energy of solvation of neutral and charged molecules, and the binding free energy of ligands to proteins. The correction is subtyped for distinct chemical species to match the underlying force field, to segment and reduce the amount of quantum training data, and to increase accuracy and computational speed. For the systems considered, the hybrid ab initio parametrized Hamiltonian reproduces the two-body dimer quantum mechanics (QM) energies to within 0.03 kcal/mol and the nonadditive many-molecule contributions to within 2%. Simulations of molecular systems using this interaction model run at speeds of several nanoseconds per day.

Hydration Mechanism and Its Effect on the Solubility of Aripiprazole.

The propose is to investigate the reasons for the insolubility of Form III in water and to explore the mechanism of the hydration process of Form III. The conformational and cohesive energies of Form III and Form H1 were calculated using Gaussian 16 and Crystal Explorer 17. Gaussian 16 and Multiwfn 3.8 was used to calculate the molecular surface electrostatic potential of Form III and Form H1 and to calculate the energies of the stronger intermolecular interactions in the crystal structure. The behaviors of Form III in water were simulated using Gromacs 2020.6. Finally, the hydration process from Form III to Form H1 was monitored in situ using Raman spectroscopy. The conformational energies of Form III and H1 are almost the same. The cohesion energy of Form H1 is much larger than that of Form III because both number of hydrogen bonds and van der Waals interactions are higher in the Form H1. During the simulation, the supercell of APZ form a supramolecular cluster. Several molecules manually dismantled from the cluster spontaneously combine to form new molecular clusters. Both increases in temperature and external energy input accelerate the hydration process. More hydrogen bonds and strong van der Waals interactions in Form H1 lead to a greater stability. The overall decrease in polarity and the strong binding effect on APZ molecule clusters due to intermolecular interactions lead to the water insolubility of Form III. The hydration process from Form III to Form H1 follows a novel, dandelion sowing-like hydration mechanism.

A general approximation method for accurate evaluation of the intermolecular potential parameters by using density functional theory

In this work, a new approach is developed and presented for determining the intermolecular potential parameters from intermolecular interaction energy data obtained using the Density Functional Theory (DFT) method over a different basis set. The proposed method in this work is especially useful for the evaluation of all intermolecular potential parameters of arbitrary atoms and molecules. The method developed in this study can be used for evaluating some thermodynamic properties of molecules. In general, this approach has great advantages for the determination of all types of potential parameters of atoms and molecules. As an application, the Lennard-Jones (12-6) and Morse potential parameters of the Ga(CH3)3 molecule have been determined first by using the basis set with density functional method (DFT/B3LYP) method over the 6-31G basis set. The speed of sound, heat capacities, and second virial coefficient over the Lennard-Jones (L-J) (12-6) potential of Ga(CH3)3 have been calculated. The results obtained for the speed of sound and heat capacities of Ga(CH3)3 are compared with theoretical and experimental data. The results indicate that our data are in good agreement with data from the literature.

Exploring the inhibitory effect of H2O on CO2/CH4 adsorption in coal: Insights from experimental and simulation approaches

To investigate the inhibitory effect of H2O on the adsorption of CH4/CO2 in coal, the anthracite was selected for physical adsorption experiments on CH4/CO2 gases in this study. Combined with Materials Studio software, the effect of moisture on the isothermal adsorption characteristics of CH4/CO2 in coal was investigated by using density functional theory and giant canonical Monte Carlo simulation. The intermolecular interaction energies were obtained, as well as the effects of electrostatic potentials, adsorption sites, and hydrogen bonding of oxygen-containing functional groups. The results show that: ①According to the CH4/CO2 isothermal adsorption experiments, it was found that moisture significantly inhibited the adsorption of CH4/CO2 by coal. For CH4, the relationship between adsorption constants a/b and moisture content can be expressed by the equations y = 43.447-3.348x and y = 3.225-0.751x. For CO2, adsorption constant a follows a power function relationship with moisture content, expressed as y = 29.114x-0.063, while adsorption constant b is represented by the polynomial fitting equation y = 1.672+0.508x+0.083x2. ② The findings have revealed correlations between the moisture influence coefficient and moisture content. The exponential functional equation η = exp(-0.188ω) was found to be more accurate for coal adsorbing CH4, whereas the linear functional equation η = 1/(1 + 0.243ω) was considered more appropriate for CO2. ③ The van der Waals and electrostatic energies between coal and CH4/CO2 decreased with an increase in moisture content, whereas the van der Waals and electrostatic energies between coal and H2O increased. ④ The orders of hydrogen bond formation ability between CH4/CO2 and functional groups were as follows: –CHO > –COOH > –OH > –CH3 and –OH > –COOH > –CHO > –CH3. The ability of H2O to form hydrogen bonds with –COOH, –OH, –CHO, and –CH3 is as follows: –COOH > –OH > –CHO> –CH3. This study provides a theoretical basis for the integrated use of hydraulic fracturing techniques and coalbed gas injection and replacement.