Intermolecular Interaction Energies Research Articles

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.

Electron density-based protocol to recover the interacting quantum atoms components of intermolecular binding energy.

A new approach for obtaining interacting quantum atoms-defined components of binding energy of intermolecular interactions, which bypasses the use of standard six-dimensional integrals and two-particle reduced density matrix (2-RDM) reconstruction, is proposed. To examine this approach, three datasets calculated within the density functional theory framework using the def2-TZVP basis have been explored. The first two, containing 53 weakly bound bimolecular associates and 13 molecular clusters taken from the crystal, were used in protocol refinement, and the third one containing other 20 bimolecular and three cluster systems served as a validation reference. In addition, to verify the performance of the proposed approach on an exact 2-RDM, calculations within the coupled cluster formalism were performed for part of the first set systems using the cc-pVTZ basis set. The process of optimization of the proposed parametric model is considered, and the role of various energy contributions in the formation of non-covalent interactions is discussed with regard to the obtained trends.

Elucidation of Substituent-Responsive Reactivities via Hierarchical and Asymmetric Assemblies in Crystalline p-Quinodimethane Derivatives.

We propose a mechanism for substituent-responsive reactivities of p-quinodimethane derivatives with four ester groups through their hierarchical and asymmetric assembly modes. Four asymmetric 7,8,8-tris(methoxycarbonyl)-p-quinodimethanes with a 7-positioned ethoxycarbonyl (2a(H)), 2'-fluoroethoxycarbonyl (2b(F)), 2'-chloroethoxycarbonyl (2c(Cl)), or 2'-bromoethoxycarbonyl (2d(Br)) were synthesized and crystallized. 2a(H), 2b(F) and 2d(Br) afforded only one shape crystal, while 2c(Cl) did two polymorphic 2c(Cl)-a and 2c(Cl)-b. UV-irradiation induced topochemical polymerization for 2a(H), no reactions for 2b(F) and 2c(Cl)-a, and [6+6] photocycloaddition dimerization for 2c(Cl)-b and 2d(Br). Such substituent-responsive reactivities and crystal structures were compared with those of the known symmetric 7,7,8,8-tetrakis(alkoxycarbonyl)-p-quinodimethanes such as 7,7,8,8-tetrakis(methoxycarbonyl)- (1a(Me)-a and 1a(Me)-b), 7,7,8,8-tetrakis(ethoxycarbonyl)- (1b(Et)), and 7,7,8,8-tetrakis(bromoethoxycarbonyl)- (1c(BrEt)). The comparative study clarified that the reactivities and crystal structures are classified into four types that link to each other. This linkage is understandable when we analyze the crystal structures through the following hierarchical and asymmetric assemblies; conformers, dimers, 1D-columns, 2D-sheets, and 3D-stacked sheets (3D-crystals). This supramolecular viewpoint is supported by intermolecular interaction energies among neighbored molecules with the density functional theory (DFT) calculation. Such research enables us to elucidate the substituent-responsive reactivities of the crystals, and reminds us of the selection of the right path in a so-called "maze game".

Thermal behavior of cyclodextrin/adamantane host/guest inclusion complex in an aqueous media

Understanding the thermal behavior of cyclodextrin/adamantane (CD/Ad) host/guest inclusion complex, and the effect of CD type, i.e., α, β, and γ, on their hybridization are fundamentally attractive to find broad contemporary applications toward improving efficient drug delivery systems. In this work, β-cyclodextrin was found as the best host to capture the Ad guest with the minimum intermolecular interaction energy of −11.996 ± 0.026 kcal/mol. This behavior was due to the perfect size match of adamantane with a diameter of 6.49 Å into β-cyclodextrin. It was observed that adamantane was supported by all sides of the inner wall of β-cyclodextrin, while the guest interacted with only one side of the inner wall of γ-cyclodextrin. The results proved that rising the solution temperature has prevented the formation of a host/guest inclusion complex, at the temperature range of 330–340 K. Deep molecular view into the solubility of adamantane showed that the failure of non-bonded interactions of CD-Ad with temperature led to the entrance of water molecules into the hollow part of the β-cyclodextrin created an obstacle against the entrance of the guest. According to the interactional achievements, the electrostatic contribution of the host-water and the dispersive contribution of guest-water led to reducing the interaction energy of host–guest with the temperature. The present research offers some insight into the design of β-cyclodextrin/adamantane-based host/guest assemblies to form a thermoreversible hydrogel in an aqueous media.

A quantum chemical interaction energy dataset for accurately modeling protein-ligand interactions

Fast and accurate calculation of intermolecular interaction energies is desirable for understanding many chemical and biological processes, including the binding of small molecules to proteins. The Splinter [“Symmetry-adapted perturbation theory (SAPT0) protein-ligand interaction”] dataset has been created to facilitate the development and improvement of methods for performing such calculations. Molecular fragments representing commonly found substructures in proteins and small-molecule ligands were paired into >9000 unique dimers, assembled into numerous configurations using an approach designed to adequately cover the breadth of the dimers’ potential energy surfaces while enhancing sampling in favorable regions. ~1.5 million configurations of these dimers were randomly generated, and a structurally diverse subset of these were minimized to obtain an additional ~80 thousand local and global minima. For all >1.6 million configurations, SAPT0 calculations were performed with two basis sets to complete the dataset. It is expected that Splinter will be a useful benchmark dataset for training and testing various methods for the calculation of intermolecular interaction energies.

DFT-Quality Adsorption Simulations in Metal-Organic Frameworks Enabled by Machine Learning Potentials.

Nanoporous materials such as metal-organic frameworks (MOFs) have been extensively studied for their potential for adsorption and separation applications. In this respect, grand canonical Monte Carlo (GCMC) simulations have become a well-established tool for computational screenings of the adsorption properties of large sets of MOFs. However, their reliance on empirical force field potentials has limited the accuracy with which this tool can be applied to MOFs with challenging chemical environments such as open-metal sites. On the other hand, density-functional theory (DFT) is too computationally demanding to be routinely employed in GCMC simulations due to the excessive number of required function evaluations. Therefore, we propose in this paper a protocol for training machine learning potentials (MLPs) on a limited set of DFT intermolecular interaction energies (and forces) of CO2 in ZIF-8 and the open-metal site containing Mg-MOF-74, and use the MLPs to derive adsorption isotherms from first principles. We make use of the equivariant NequIP model which has demonstrated excellent data efficiency, and as such an error on the interaction energies below 0.2 kJ mol-1 per adsorbate in ZIF-8 was attained. Its use in GCMC simulations results in highly accurate adsorption isotherms and heats of adsorption. For Mg-MOF-74, a large dependence of the obtained results on the used dispersion correction was observed, where PBE-MBD performs the best. Lastly, to test the transferability of the MLP trained on ZIF-8, it was applied to ZIF-3, ZIF-4, and ZIF-6, which resulted in large deviations in the predicted adsorption isotherms and heats of adsorption. Only when explicitly training on data for all ZIFs, accurate adsorption properties were obtained. As the proposed methodology is widely applicable to guest adsorption in nanoporous materials, it opens up the possibility for training general-purpose MLPs to perform highly accurate investigations of guest adsorption.

Theoretical study of intermolecular interaction energy for $$\textrm{F}_{2}\cdots \textrm{F}_{2}$$ complex

Theoretical study of intermolecular interaction energy for $$\textrm{F}_{2}\cdots \textrm{F}_{2}$$ complex

A Study of Molecular Dynamic Simulation and Experimental Performance of the Eucommia Ulmoides Gum-Modified Asphalt.

In recent years, eucommia ulmoides gum (EUG), also known as gutta-percha, has been extensively researched. Molecular dynamic simulations and experiments were used together to look at how well gutta-percha and asphalt work together and how gutta-percha-modified asphalt works. To investigate the gutta-percha and asphalt blending systems, the molecular models of asphalt and various dosages of gutta-percha-modified asphalt were set up using Materials Studio (MS), and the solubility parameters, intermolecular interaction energy, diffusion coefficient, and mechanical properties (including elastic modulus, bulk modulus, and shear modulus) of each system were calculated using molecular dynamic simulations at various temperatures. The findings indicate that EUG and asphalt are compatible, and sulfurized eucommia ulmoides gum (SEUG) and asphalt are more compatible than EUG. However, SEUG-modified asphalt has better mechanical properties than EUG, and the best preparation conditions are 10 wt% doping and 1 h of 180 °C shearing. Primarily, physical modifications are required for gutta-percha-modified asphalt.

Hirshfeld surface analysis, interaction energy calculations and in silico anti-SARS-CoV-2 potentials of metal (II) 3,4-dimethoxybenzoate with nicotinamide complexes

In this study, types of the intermolecular interactions, the intermolecular interaction energies, void analysis of diaquabis(3,4-dimethoxybenzoate)bis(nicotinamide)zinc(II) dihydrate (Complex 1), diaquabis(3,4-dimethoxybenzoate)bis(nicotinamide)nickel(II) dihydrate (Complex 2), diaquabis(3,4-dimethoxybenzoate)bis(nicotinamide)cobalt(II) dihydrate (Complex 3), whose crystal structures were characterized before, were investigated with the help of the CrystalExplorer program (Version 21.5). It has been determined that H…H, H…O/O…H, H…C/C…H, H…N/N…H, C…C, C…O/O…C, O…O, and C…N/N…C interactions are intermolecular interactions that contribute to the Hirshfeld surface of the complexes. According to the results of the interaction energy analysis calculated with the help of B3LYP/6-31G(d,p), B3LYP/6-31G(d), B3LYP/3-21G, HF/6-31G(d,p), HF/6-31G(d), HF/3-21G, DFT/6-31G(d,p), DFT/6-31G(d), DFT/3-21G, MP2/6-31G(d,p), MP2/6-31G(d), MP2/3-21G basis sets, the major amount of the total energy is contributed by electrostatic and polarization energies. The interactions between Complexes 1-3 and the main protease enzyme and the spike protein of Omicron variant of the SARS-CoV-2 were investigated by Molecular docking studies. It was determined that complexes 1-3 and the main protease enzyme and the spike protein of Omicron variant of the SARS-CoV-2 interact via attractive charges, hydrogen bonding, electrostatic contacts, and hydrophobic interactions. According to the obtained results, further in vivo/in vitro studies are recommended for complex 3. The results determined as a result of interaction energy analysis and molecular docking studies show that the hydrogen bonds formed by the hydrogen bond donor/acceptor groups in the structure of the complexes are an important factor in both the stability of the crystal package and inhibition of important enzymes of SARS CoV-2.

Synthesis, crystal structure and Hirshfeld surface analysis of naphthalene-2,3-diyl bis-(3-benz-yl-oxy)benzoate.

In the title compound, C38H28O6, the dihedral angles between the naphthalene ring system and its pendant benz-yloxy rings A and B are 88.05 (7) and 80.84 (7)°, respectively. The dihedral angles between the A and B rings and their attached phenyl rings are 49.15 (8) and 80.78 (8)°, respectively. In the extended structure, the mol-ecules are linked by weak C-H⋯O and C-H⋯π hydrogen bonds, and π-π stacking inter-actions, which variously generate C(11) chains and R 2 2(12) loops as part of a three-dimensional network. The Hirshfeld surface [fingerprint contributions= H⋯H (42.3%), C⋯H/H⋯C (40.3%) and O⋯H/H⋯O (15.7%)] and inter-molecular inter-action energies are reported, with dispersion (E dis = -428.6 kJ mol-1) being the major contributor.

Complexes of HXeY with HX (Y, X = F, Cl, Br, I): Symmetry-Adapted Perturbation Theory Study and Anharmonic Vibrational Analysis

A comprehensive analysis of the intermolecular interaction energy and anharmonic vibrations of 41 structures of the HXeY⋯HX (X, Y = F, Cl, Br, I) family of noble-gas-compound complexes for all possible combinations of Y and X was conducted. New structures were identified, and their interaction energies were studied by means of symmetry-adapted perturbation theory, up to second-order corrections: this provided insight into the physical nature of the interaction in the complexes. The energy components were discussed, in connection to anharmonic frequency analysis. The results show that the induction and dispersion corrections were the main driving forces of the interaction, and that their relative contributions correlated with the complexation effects seen in the vibrational stretching modes of Xe–H and H–X. Reasonably clear patterns of interaction were found for different structures. Our findings corroborate previous findings with better methods, and provide new data. These results suggest that the entire group of the studied complexes can be labelled as “naturally blueshifting”, except for the complexes with HI.

A comparative study of structural and spectroscopic properties of three structurally similar mechanically bending organic single crystals – 2-Amino-3-nitro-5-halo (halo = Cl, Br, or I) pyridine

In recent years, scientists have been very interested in single crystals of monoaromatic compounds with mechanical softness, but they are hard to find. The present work reports a comparative study of structural, spectroscopic, and quantum chemical investigations of three structurally similar mechanically bending monoaromatic compounds, namely, 2-amino-3-nitro-5-chloro pyridine (I), 2-amino-3-nitro-5-bromo pyridine (II), and 2-amino-3-nitro-5-iodo pyridine (III). The mechanical responses of the three organic crystals studied here are very intriguing due to the similarity of their chemical structures, which only differ in the presence of halogen atoms (Cl, Br, and I) at the fifth position of the pyridine ring and are explained through examining intermolecular interaction energies from energy frameworks analysis, slip layer topology, and Hirshfeld surface analysis. The crystals of all the three feature one dimensional ribbons comprising alternating NaminoH⋯Onitro and NaminoH⋯Npyridine hydrogen bonds that form R22(12) and R22(8) dimeric rings, respectively. In (III), weak I⋯I interactions link the adjacent ribbons forming a two dimensional sheet. Layer-like structures are observed in all three crystals, with no significant interactions between the adjacent architectures (ribbons or sheets). Energy framework calculations are used for estimating the bending ability of the three compounds, with the three following the order Cl ≪ Br < I. The iterative electrostatic scheme coupled with the supermolecule approach (SM) at the DFT/CAM-B3LYP/aug-cc-pVTZ level is used to calculate the third-order nonlinear susceptibility (χ3) values in a simulated crystalline environment for the static case as well as two typical electric field frequency values, (λ = 1064 nm) and (λ = 532 nm). In addition, estimates of the topological studies (localized orbital locator and electron localization function) and reactivity characteristics (global reactivity parameters, molecular electrostatic potential, and Fukui function) are made for the compounds under investigation. Docking studies done using AutoDock software with a protein target (PDB ID: 6CM4) revealed that three compounds could be used to treat Alzheimer's disease.

Геометрические характеристики нанокапли. Ранжирование энергии капли

The equilibrium condition of a hanging axially symmetric droplet is derived for the Deryagin model, which takes into account the thickness of the wedging/molecular layer of the droplet surface. For an axisymmetric drop, the forming line of which depends on a natural parameter, a differential equation is found, the solution of which is the integrand function of the functional of the wedging energy. The solution of this differential equation is found. The functional of the wedging energy of the drop is constructed. The functional of the total energy of an axisymmetric hanging drop is refined, taking into account the second-order component of the smallness of the energy of intermolecular interaction. As a result of solving the variational problem, the equilibrium condition of a liquid droplet is obtained for the Deryagin model, which takes into account the thickness of the surface layer of the droplet. Due to the fact that the first variation of the functional of the total energy of a drop for an equilibrium drop is zero, a more accurate form of the dependence of the liquid-solid contact angle on the radius and height of the drop is obtained. The decomposition of the potential energy of the intermolecular interaction by degrees of the potential well is obtained for the Deryagin model, which takes into account the thickness of the wedging/molecular layer of the droplet surface, which is why a second-order element of smallness appeared in the decomposition by degrees of the potential well. A comparison with other models specifying the relationship of the wetting angle depending on the height of the drop is carried out.

Unusual short intramolecular N–H⋅⋅⋅H–C contact and weak intermolecular interactions in two N-(adamantan-1-yl)piperazine carbothioamides: Crystallography, quantum chemical study and in vitro urease inhibitory activity

Crystal structures of two closely related N-(adamantan-1-yl)piperazine carbothioamides have been examined in detail using the Hirshfeld surface, fingerprint analysis, PIXEL energy for molecular dimers and noncovalent interaction (NCI) plots for intermolecular interactions. Both compounds namely, ethyl 4-[(adamantan-1-yl)carbamothioyl]piperazine-1-carboxylate (1) and N-(adamantan-1-yl)-4-(2-methoxyphenyl)piperazine-1-carbothioamide (2) crystallized in the triclinic system with two crystallographically independent molecules in each case. X-ray analysis indicates that the piperazine ring in one of the molecules of 1 exhibits a boat and chair conformation in the other crystallographically independent molecule, while the corresponding ring in 2 adopts a chair conformation. An analysis of the fingerprint plots of the Hirshfeld surface provides a qualitative picture of how carboxylate and methoxyphenyl substituents contribute to stabilizing the crystal packing. Both structures show unusually short intramolecular N–H⋅⋅⋅H–C contact with some geometrical constraints in addition to intramolecular C–H⋅⋅⋅S interactions. The role of intramolecular N–H⋅⋅⋅H–C contact was established with potential energy surface scan and structural optimization. The CLP-PIXEL calculation gives the intermolecular interaction energies for the molecular dimers in these structures. Many dimers in 1 are stabilized by C–H⋅⋅⋅O/S/π interactions, while others are stabilized by short H⋅⋅⋅H contacts. Intermolecular C–H⋅⋅⋅O interactions do not occur in 2. There are, however, intermolecular C–H⋅⋅⋅S/π interactions and short H⋅⋅⋅H contacts in some dimers. We used NCI plots to identify the nature of the observed noncovalent interactions. Compared to the control inhibitor (thiourea), the title compounds have good inhibitory activity against urease in vitro. Molecular docking analysis identifies the key active site residues involved in intermolecular interactions between a small molecule and an enzyme.

Unraveling the Structural and Property Differences between Highly Similar Chiral and Racemic Crystals Composed of Analogous Molecules

The structural differences between chiral and racemic crystals of enantiomers have piqued interest, as exemplified by classical Wallach’s rule. However, the mechanical and thermal disparities between these materials have not been thoroughly investigated. This study reports the structural and mechanical differences between chiral and racemic crystals of two analogous molecules. The similarity of molecular and crystal structures between the two analogues was validated through comparison with known chiral–racemic crystal pairs. Young’s moduli of the four crystals revealed larger values for racemic crystals than their chiral counterparts, consistent with the intermolecular interaction energies projected along the loading direction. The thermal response of crystals plays a significant role in their elastic behavior, and the temperature dependence of interaction energies along the [001] direction was found to agree with the temperature dependence of lattice dynamics for all four crystals.

Morphology control by tuning electrostatic interactions for efficient polythiophene-based all-polymer solar cells

•Correlations between electrostatic force and interaction energy are established •Domain purity of the film can be modulated by tuning the donor:acceptor ESP difference •A high PCE of 15.3% is demonstrated in a PT-based all-polymer solar cell Polythiophenes are one of the most classical donors for organic solar cells, which have simple chemical structures and thus low production costs. However, their photovoltaic performance is lagging far behind the donor-acceptor-type polymers, especially when blending with polymer acceptors, where morphology control is a huge challenge. Here, we systematically study the intermolecular interaction in polythiophene:polymer acceptor (PY-IT) combinations and establish a rational relationship between chemical structure and blend miscibility. Our results suggest that the electrostatic force plays a key role in determining the donor:acceptor intermolecular interaction energy. Introducing electron-withdrawing functional groups into the backbone of P3HT can increase the electrostatic potential (ESP) and suppress the intermolecular interaction with PY-IT. Due to the proper miscibility and improved domain purity, the corresponding polymer PDCBT records a high-power conversion efficiency (PCE) of 15.3%, which is the highest value in polythiophene-based all-polymer solar cells (all-PSCs) and crucial for advancing their practical applications. Polythiophenes are one of the most classical donors for organic solar cells, which have simple chemical structures and thus low production costs. However, their photovoltaic performance is lagging far behind the donor-acceptor-type polymers, especially when blending with polymer acceptors, where morphology control is a huge challenge. Here, we systematically study the intermolecular interaction in polythiophene:polymer acceptor (PY-IT) combinations and establish a rational relationship between chemical structure and blend miscibility. Our results suggest that the electrostatic force plays a key role in determining the donor:acceptor intermolecular interaction energy. Introducing electron-withdrawing functional groups into the backbone of P3HT can increase the electrostatic potential (ESP) and suppress the intermolecular interaction with PY-IT. Due to the proper miscibility and improved domain purity, the corresponding polymer PDCBT records a high-power conversion efficiency (PCE) of 15.3%, which is the highest value in polythiophene-based all-polymer solar cells (all-PSCs) and crucial for advancing their practical applications.

Global Optimization of Dinitrogen Clusters Bound to Monolayer and Bilayer Graphene: A Swarm Intelligence Approach

Locating the global minimum of a potential energy surface is an arduous task. The complexity of the potential energy surface increases as the number of degrees of freedom of the system increases. The highly rugged nature of the potential energy surface makes the minimization of the total energy of the molecular clusters a difficult optimization problem. A solution to this conundrum is the use of metaheuristic techniques that efficiently track down the global minima through a trade-off between exploration and exploitation. Herein, we use the swarm intelligence technique, particle swarm optimization to locate the global minima geometries of N2 clusters of size 2-10, in free and adsorbed states. We have investigated the structures and energetics of bare N2 clusters, followed by N2 clusters adsorbed on graphene and intercalated between the layers in bilayer graphene. The noncovalent interactions between dinitrogen molecules are modeled using the Buckingham potential as well as the electrostatic point charge model, while those of the N2 molecules with the carbon atoms of graphene are modeled using the improved Lennard-Jones potential. The interactions of the carbon atoms belonging to different layers in a bilayer are modeled using the Lennard-Jones potential. The bare cluster geometries and intermolecular interaction energies obtained using particle swarm optimization are found to be the same as reported in the literature, validating the use of particle swarm optimization for studying molecular clusters. The N2 molecules are found to adsorb as a monolayer on top of the graphene sheet and intercalate themselves right in the middle of the two sheets of bilayer graphene. Our study establishes that particle swarm optimization is a feasible global optimization technique for performing the optimization of high-dimensional molecular clusters, both in pristine and in confined forms.

High-Order Quantum-Mechanical Analysis of Hydrogen Bonding in Hachimoji and Natural DNA Base Pairs.

High-order quantum chemistry is applied to hydrogen-bonded natural DNA nucleobase pairs [adenine:thymine (A:T) and guanine:cytosine (G:C)] and non-natural Hachimoji nucleobase pairs [isoguanine:1-methylcytosine (B:S) and 2-aminoimidazo[1,2a][1,3,5]triazin-4(1H)-one:6-amino-5-nitropyridin-2-one (P:Z)] to see how the intermolecular interaction energies and their energetic components (electrostatics, exchange-repulsion, induction/polarization, and London dispersion interactions) vary among the base pairs. We examined the Hoogsteen (HG) geometries in addition to the traditional Watson-Crick (WC) geometries. Coupled-cluster theory through perturbative triples [CCSD(T)] extrapolated to the complete basis set (CBS) limit and high-order symmetry-adapted perturbation theory (SAPT) at the SAPT2+(3)(CCD)δMP2/aug-cc-pVTZ level are used to estimate highly accurate noncovalent interaction energies. Electrostatic interactions are the most attractive component of the interaction energies, but the sum of induction/polarization and London dispersion is nearly as large, for all base pairs and geometries considered. Interestingly, the non-natural Hachimoji base pairs interact more strongly than the corresponding natural base pairs, by -21.8 (B:S) and -0.3 (P:Z) kcal mol-1 in the WC geometries, according to CCSD(T)/CBS. This is consistent with the H-bond distances being generally shorter in the non-natural base pairs. The natural base pairs are energetically more stabilized in their Hoogsteen geometries than in their WC geometries. The Hoogsteen geometry makes the A:T base pair slightly more stable, by -0.8 kcal mol-1, and it greatly stabilizes the G:C+ base pair, by -15.3 kcal mol-1. The G:C+ stabilization is mainly due to the fact that C has typically added a proton when found in Hoogsteen geometries. By contrast, Hoogsteen geometries are substantially less favorable than WC geometries for non-natural Hachimoji base pairs, by 17.3 (B:S) and 13.8 (P:Z) kcal mol-1.