Pair Interaction Energies Research Articles

Thermodynamically Motivated Criterion of Hydrogen Bonds in Water Simulations

A computer simulation study of a system containing 33666 SPC/E water molecules at the atmospheric pressure and room temperature is carried out. A thermodynamically motivated geometric criterion of the hydrogen bond is developed based on statistical regularities of joint distributions of oxygen-oxygen, oxygen-hydrogen distances, and the interaction energies of molecular pairs corresponding to these distances. Using this criterion makes it possible to substantially increase the selectivity of the algorithms for identifying hydrogen bonds during computer simulation.

High-frequency dielectric study on the hydrogen bonding interaction on aqueous Cyanoacetamide

The Complex permittivity spectra ε∗(ω) of the mixtures of Cyanoacetamide (CYN) and water in the composition of different mole fractions were achieved in the frequency domain of 10 MHz to 50 GHz at temperatures 25, 20, 15, 10 and 5 °C using Time Domain Reflectometry (TDR) method. The observed values of dielectric spectra can be well defined with the Cole-Davidson relaxation model. The dielectric functions like static dielectric constant (ε0), relaxation time (τ) and Cole Davidson distribution parameter (β) were obtained and also used to determine and discuss the theoretical parameters such as effective Kirkwood Correlation factor (geff), excess dielectric constant ε0E and excess inverse relaxation time ((1/τ)E) to provide information on dipolar alignment and molecular rotation within the solution. Thermodynamic properties such as the free energy of activation (ΔF), the entropy of activation (ΔS∗) and the enthalpy of activation (ΔH∗) were obtained. The free energy of activation is found to be independent of temperature and the average value of free energy is calculated as, 14.28 kJ mol−1. The enthalpy of activation shows the endothermic nature of the reaction. FT-IR results were compared with the Molecular Dynamics (MD) simulation study confirms the formation of the heterogeneous hydrogen-bond network in the solution. The Average Water bridge residual time period and pair interaction energy between the unlike molecules have been determined, also it is confirmed that the higher value of excess permittivity indicates the maximum probability of Hydrogen-bond formation within the system.

Interaction between a Single-Stranded DNA and a Binding Protein Viewed by the Fragment Molecular Orbital Method

Abstract The interaction between a single-stranded DNA (ssDNA) and a binding protein (Sulfolobus solfataricus ssDNA binding protein, SSB) were investigated by the ab initio fragment molecular orbital (FMO) method in explicit solvent. The calculated overall energy change upon complexation suggested that the ssDNA/SSB association is not strong. Nonetheless, more detailed analysis of interfragment interaction energy (IFIE) and pair interaction energy decomposition analysis (PIEDA) indicated that the ssDNA/SSB association is based upon a minute balance of various contributions of local structural parts of the molecules. The most stabilizing contribution was that by the electrostatic interaction between the sugar–phosphate backbone of ssDNA and charged side chains of SSB, and the second was that by the stacking interaction between bases of ssDNA and aromatic side chains of SSB. Thus, though the overall association energy change was small, the local interactions were suggested to contribute to the association.

The Heat of Sublimation of Small Cluster Systems

Within the framework of the cluster model of the structure of disordered condensed media, using the pair potential of Mie interaction with the effective depth of the potential well, the relation was obtained for calculating the heat of sublimation of small cluster systems containing up to 500 particles. It is shown that the heat of sublimation of small clusters, referred to the energy of pair interaction between particles, is a universal function of the number of particles in the cluster system, which can be mathematically represented as the square of the hyperbolic tangent. The proposed model makes it possible to estimate the potential energy of the global minimum of the cluster system.

Universal Mechanism of Viscoplastic Deformation of Metallic Materials Far from Thermodynamics Equilibrium

The article gives results of structure formation in metallic materials after different types of deformation: tungsten after rolling, nickel after thermal cycling and nickel single crystal after rolling, aluminum single crystal after cyclic tension and aluminum alloys (D16, 2024-T3) after impulsive load. We used optical and electron microscopy methods for investigation of deformation structure formation and molecular dynamics method for computer modeling of the processes of plastic deformation (LAMMPS software). The following quantitative parameters were calculated during the simulation: energy of pair interaction, temperature, total cumulative pressure, stress tensor and pressure tensor. The study shows that the plastic flow of metallic materials with any initial structure at certain loading stage can be carried out by homogeneous mass transfer through channels with a liquid-like structure, from which follows that the dislocation mechanism of plastic deformation of crystals has a limited field of application. The main role has a synergistic structure formation in the conditions of distance from thermodynamic equilibrium. The relaxation processes proceed intensively after and during the process of destruction. The results of modeling have shown the possibility of forming channels of hydrodynamic flow without the participation of defects in the initial material.

Synthesis and crystal structures of new phosphoric triamides: study of intermolecular interactions by semi-empirical calculations and Hirshfeld surface analysis

In the present paper, crystal structures and Hirshfeld surface analyses of two new phosphoric triamides [2,3,6-F3–C6H2C(O)NH]P(O)(X)2 (X=N(CH3)C6H11 and N(C2H5)2) and an improved model of [OH8C4N]3P(O) are investigated. Moreover, the semi-classical density sums (PIXEL) method, which enables the calculation of interaction energies for molecule–molecule pairs, and AIM calculations were used to evaluate intermolecular forces in the studied compounds. The previously reported structure [2,6-F2-C6H3C(O)NH]P(O)[NHC(CH3)3]2 with a [C(O)NH]P(O)[NH(C)]2 segment, which is different than the [C(O)NH]P(O)[N(C)(C)]2 segment in structures [2,3,6-F3–C6H2C(O)NH]P(O)(X)2, is compared to those of the newly determined structures. The Hirshfeld surface method shows that the crystal cohesions of structures [2,3,6-F3–C6H2C(O)NH]P(O)(X)2 are established via H···H, O···H/H···O, C···H/H···C, and F···H/H···F contacts, while for [OH8C4N]3P(O), H···H and O···H/H···O are the dominant contacts. From PIXEL and AIM calculations and the decomposition of the interaction energies for different molecular pairs, it is shown that the donor and acceptor capability of the atoms involved in an interaction introduces the nature and strength of that interaction. The more acidic NCP–H unit in the C(O)NHP(O) segment (compared to the NP–H unit in the P(O)[NH(C)]2 segment) and the higher H-atom acceptor group P=O (compared to C=O) in the studied structures form the strongest NCP–H···O=P intermolecular hydrogen bond.

Comparative study of photodynamic activity of methylene blue in the presence of salicylic acid and curcumin phenolic compounds on human breast cancer.

Curcumin and salicylic acid are both phenolic compounds and they can both affect cancer treatment efficacy. In this study, the effects of methylene blue-curcumin (CU-MB) and methylene blue-salicylic acid (SA-MB) ion pair complexes on MDA-MB-231 human breast cancer cells are studied. According to the thermodynamic parameters, the stability of curcumin and salicylic acid complexes ion pair complexes was compared. The free energy of ion pair interactions was calculated based on binding constants. A comparison of the free energies of the complexes (CU-MB: ∆G°b1 = - 21.11kJ/mol and ∆G°b2 = - 8.37kJ/mol, SA-MB: ∆G°b1 = - 12.92kJ/mol and ∆G°b2 = - 9.02kJ/mol) indicates that the interaction of methylene blue in first binding interaction with curcumin is greater than that of methylene blue with salicylic acid. Electrostatic interactions are the main forces in the binding of both compounds to methylene blue. All forces are inter-molecular physical interactions. The results of cellular experiments show that ion pairing has enhanced the reduction of cell viability. By increasing molecular stability and prevention of dimerization of methylene blue, the cell killing potential of methylene blue increases and it subsequently causes enhancement of photodynamic efficacy.

Molecular dynamics simulation of the interface between sulfur mustard and graphene

Using molecular dynamics simulations, the interface between sulfur mustard (SM) which is one of the most toxic chemical warfare agents, and single layer graphene (G) was investigated for the first time to find a new class of adsorbents. Various analyses have been done in order to atomistically understand the adsorption mechanism. Results show that: (1) A solid-like SM layer of 6 Å thick is formed near G, and its density approximates to 2.5 times as large as that of the bulk SM; (2) Adsorption is occurred in three layers, and due to two distinct orientations of SM relative to G surface, i.e. parallel and tilted, there are fine structures within first layer; (3) Study of surface self-diffusion shows that the diffusion coefficient of SM molecules on G surface is half of the diffusion coefficient of SM molecules in the bulk. Furthermore, the diffusion coefficient of SM molecules with parallel orientation is half of the diffusion coefficient of tilted SM molecules and the lifetime of parallel orientation in the first adsorption layer is about three times more than that of tilted; (4) Pair interaction energy calculation between SM and G revealed that the adsorption energy of parallel SM molecules (−11.875 kCal/mol) is greater than that of the tilted SM molecules (−6.125 kCal/mol) and parallel orientation is the favorable orientation for adsorption. SM-SM pair interaction energy analysis also revealed that SM-SM pairs near G are more associated than SM-SM pairs in the bulk of SM. In summary, our results clearly show that G can be a good candidate for adsorption of SM and similar toxic chemical warfare agents.

Empirical corrections and pair interaction energies in the fragment molecular orbital method

The energy and analytic gradient are developed for FMO combined with the Hartree-Fock method augmented with three empirical corrections (HF-3c). The auxiliary basis set approach to FMO is extended to perform pair interaction energy decomposition analysis. The FMO accuracy is evaluated for several typical systems including 3 proteins. Pair interaction energies computed with different approaches in FMO are compared for a water cluster and protein-ligand complexes.

Paraffin solubility curves of diesel fuels from thermodynamic model adjusted through experimental DSC thermograms

DSC and wax solubility curves were measured for two diesel fuel samples. Compositional profiles were also measured for the solubility curve points. The paraffin distributions of the samples were determined and the non-paraffinic components were lumped into pseudocomponents. The liquid phase was modeled using the Peng-Robinson equation of state with the classical van der Waals mixing rule. For the solid phase, the modified UNIQUAC model was employed. The models were fitted to the DSC data by tuning only four multipliers acting on the molecular weights, boiling and critical temperatures of the pseudocomponents as well as on the paraffins’ pair interaction energies from the UNIQUAC model. Then the model is used to predict wax appearance temperature, amount and composition of solid deposit as a function of temperature during cooling. Excellent results were obtained for the two samples analyzed. This way, the methodology developed is able to predict adequately the formation of solid paraffin from diesel fuels.

Pair interaction energies and local structures of titanium and nickel atom-pairs in β-Sn type silicon

Pair interaction energies (PIEs) of Ti-Ti, Ti-Ni and Ni-Ni pairs and optimized local structures around these pairs in β-Sn type Si are studied by first principles calculation to elucidate typical local structures of transition-metal (TM) atoms in Si-rich amorphous silicides or alloys. In the calculations, TM pairs are located at substitutional sites along a long axis of cuboid Si432(TM2Si430) supercell (6×3×6 unit cells of β-Sn type Si) to calculate interatomic distance dependences of PIEs up to 6 Å-distance (up to the 12th nearest neighboring (NN) distance). We find that interatomic distances of Ti-Ti and Ti-Ni pairs with largely negative PIEs agree with those in Si-rich ordered silicides such as TiSi2 and Ti4Ni4Si7, and that the optimized local structures around Ti-Ti and Ti-Ni pairs commonly have Si-hexagons, which typically appear in early-TM silicides, and thus expected to be observed in the amorphous Si-rich silicides or alloys. On the contrary, Ni-Ni pair in β-Sn type Si indicates no significant feature in PIE profile or in local structures. Properties of Ni-Ni or Ni-Si bonding in Si-rich silicides may be governed by sp3-like Si lattices.

Cluster approach to the prediction of thermodynamic and transport properties of ionic liquids.

The prediction of physicochemical properties of ionic liquids such as conductivity and melting point would substantially aid the targeted design of ionic liquids for specific applications ranging from solvents for extraction of valuable chemicals to biowaste to electrolytes in alternative energy devices. The previously published study connecting the interaction energies of single ion pairs (1 IP) of ionic liquids to their thermodynamic and transport properties has been extended to larger systems consisting of two ion pairs (2 IPs), in which many-body and same-ion interactions are included. Routinely used cations, of the imidazolium and pyrrolidinium families, were selected in the study coupled with chloride, tetrafluoroborate, and dicyanamide. Their two ion pair clusters were subjected to extensive configuration screening to establish most stable structures. Interaction energies of these clusters were calculated at the spin-ratio scaled MP2 (SRS-MP2) level for the correlation interaction energy, and a newly developed scaled Hartree-Fock method for the rest of energetic contributions to interaction energy. A full geometry screening for each cation-anion combination resulted in 192 unique structures, whose stability was assessed using two criteria-widely used interaction energy and total electronic energy. Furthermore, the ratio of interaction energy to its dispersion component was correlated with experimentally observed melting points in 64 energetically favourable structures. These systems were also used to test the correlation of the dispersion contribution to interaction energy with measured conductivity.

Pair Interaction Energy Decomposition Analysis for Density Functional Theory and Density-Functional Tight-Binding with an Evaluation of Energy Fluctuations in Molecular Dynamics.

Pair interaction energy decomposition analysis in the fragment molecular orbital (FMO) method is extended to treat density functional theory (DFT) and density-functional tight-binding (DFTB). Fluctuations of energy contributions are obtained from molecular dynamics simulations. Interactions at the DFT and DFTB levels are compared to the values obtained with Hartree-Fock, second-order Møller-Plesset (MP2), and coupled cluster methods. Hydrogen bonding in water clusters is analyzed. 200 ps NVT molecular dynamics simulations are performed with FMO for two ligands bound to the Trp-cage miniprotein (PDB 1L2Y ); the fluctuations of fragment energies and interactions are analyzed.

Specific Interactions of Protein-Protein Interaction between Human Programmed Death 1 (PD-1) and its Ligand 1 (PD-L1) with AB Initio Fragment Molecular Orbital Method

Immunologic checkpoint pathways, including Programmed Death 1 and its ligands, are crucial in mediating self-tolerance and preventing autoimmunity, so they protect tissues from self-damage. It is now clear that significant numbers of cancers manipulate the signal pathways to evade immune surveillance and efficacy of the blockade of immune checkpoints in cancer therapy was validated in preclinical studies targeting programmed death 1. Several therapies, including small molecules, to interfere interactions between PD-1 and PD-L1 have been developed. Nevertheless, this is obstructed by the imperfect structure information about these proteins, even after the crystal structures were solved. Here, we applied ab initio fragment molecular orbital method to wild-type PD-1/PD-L1 complex at MP2/6-31G∗ level with PCM. Furthermore, we also applied the FMO method to two complexes of small molecule inhibitors targeting PD-L1 at MP2/6-31G∗∗ level with PCM. Based on calculated pair interaction energies (PIEs), we revealed key interactions and quantified the strength of the interactions with Pair Interaction Energy Decomposition Analysis (PIEDA) and a visual representation of 3D scatter plot of PIEs, a so-called 3D SOP. As a result, we investigated specific interactions in previously reported three hot spots on a basis of the FMO results. This approach provides an effectual tool to understand the protein-protein interactions at the quantum mechanical level.

The effects of temperature, alkyl chain length, and anion type on thermophysical properties of the imidazolium based amino acid ionic liquids

The viscosity, surface tension, and density as well as molar volume and expansion coefficient of imidazolium based amino acid ionic liquids (AAILs) including alaninate ([ALA]−), glycinate ([GLY]−), glutamate ([GLU]−), serinate ([SER]−), and valinate ([VAL]−) anions were investigated at the extended temperature until 373.15K. Thermophysical as well as electronic properties were taken into account in order to explore the effect of alkyl chain length and anion on these properties. The results indicated that the interaction between ion pairs has a great effect on the properties; the strong interaction caused the higher viscosity and surface tension. The effect of temperature and alkyl chain length as well as anion type on the physicochemical properties was also studied. Raising the temperature resulted in a downward trend on the density, viscosity, and surface tension of all systems. In addition, the hypothetical critical temperatures of the AAILs were estimated making use of the Eötvos and Guggenheim equations. It was shown that the critical temperature decreases with alkyl chain length and its change depends on the ion pair interaction energy density and density of electronic chemical potential. The results of prediction critical temperatures of AAILs using surface tension data revealed that [EMIM][GLY] had the highest critical temperature due to its strongest ion pair interaction and stability and lower alkyl chain length in cation. Moreover, the anion charge density shows a straight correlation with interaction energy density that is in according with the stability of the ion pairs. Investigating viscosity as a transport property demonstrates that the lowest viscosity is observed for AAILs involving [GLY]− anion that is described by high flexibility of the anion. Finally, the change in volume of AAILs is small as the temperature increases confirming AAILs as solvent do not expand much which explains their good solvent characteristics.

Theoretical Analysis of Activity Cliffs among Benzofuranone-Class Pim1 Inhibitors Using the Fragment Molecular Orbital Method with Molecular Mechanics Poisson-Boltzmann Surface Area (FMO+MM-PBSA) Approach.

Significant activity changes due to small structural changes (i.e., activity cliffs) of serine/threonine kinase Pim1 inhibitors were studied theoretically using the fragment molecular orbital method with molecular mechanics Poisson-Boltzmann surface area (FMO+MM-PBSA) approach. This methodology enables quantum-chemical calculations for large biomolecules with solvation. In the course of drug discovery targeting Pim1, six benzofuranone-class inhibitors were found to differ only in the position of the indole-ring nitrogen atom. By comparing the various qualities of complex structures based on X-ray, classical molecular mechanics (MM)-optimized, and quantum/molecular mechanics (QM/MM)-optimized structures, we found that the QM/MM-optimized structures provided the best correlation (R2 = 0.85) between pIC50 and the calculated FMO+MM-PBSA binding energy. Combining the classical solvation energy with the QM binding energy was important to increase the correlation. In addition, decomposition of the interaction energy into various physicochemical components by pair interaction energy decomposition analysis suggested that CH-π and electrostatic interactions mainly caused the activity differences.

Quantum chemical analysis of electronic structure and bonding aspects of choline based ionic liquids

The gas phase quantum chemical calculation using M06-2X/6-31+G(d,p) level was carried out to understand the electronic structure and weak interactions of choline based ionic liquids (CILs; Cations: choline &N,N-dimethylaminoethanol (DMAE). Anions: Cl−, HSO4− & H2PO4−). Based on the MESP analysis, 24 different conformers were generated by arranging anions around cations in “chemically intuitive” locations where the proximity of multiple interaction pattern occurs. Investigation of optimized geometries of CILs illustrates that the presence of folded conformation in choline cation increases the stability of the most stable R1 conformers through strong O/NH⋯O hydrogen bonding interactions. Computed interaction energies of ionic pairs were correlated well with the multiple interaction patterns existing in the ionic pairs. Based on the computed interaction energies, the stability order of CILs is as follows: CS<CC<CP<NP<NS<NC. The higher stability of NC ion pair is mainly due to the presence of both strong NH⋯O and OH⋯O hydrogen bonding interactions and higher proximity of folded conformation. The cooperative behavior of CILs is analyzed through the magnitude of red shifting and nature of IR intensity of vibrational bands. The Bader's QTAIM and NCI-RDG analyses were utilized to quantify the nature of non-covalent interactions present in CILs. Our NBO analysis clearly explained the presence of nO/Cl−→σ*OH interactions in the most stable CIL ion pairs and good correlation is obtained between the hydrogen bond lengths and the stabilization energies. Overall, the present study sheds light on the importance of choosing appropriate anion and cation in preparing task-specific nature of CILs to achieve the desired physicochemical properties.

Ionization and Conformational Equilibria of Citric Acid: Delocalized Proton Binding in Solution.

The microspeciation of citric acid is studied by analyzing NMR titration data. When the site binding (SB) model, which assumes fully localized proton binding to the carboxylic groups, is used to obtain microscopic energy parameters (dissociation constants, pair and triplet interaction energies between charged carboxylate groups), contradictory results are obtained. The resulting macroscopic constants are in very good agreement with the values reported in the literature using potentiometry. However, the found pair interaction energy between the terminal carboxylates and the triplet interaction energy are physically meaningless. To solve this apparent contradiction, we consider the possibility of delocalized proton binding, so that the proton can be exchanged at high velocity in the NMR time scale through short, strong, low-barrier (SSLB) hydrogen bonds. With this aim, ab initio MP2 calculations using the SMD polarizable continuum model for the solvent were performed and the fully roto-microspeciation elucidated. First, fully localized proton binding was assumed, and the resulting microstate probabilities are in reasonable agreement with those reported in previous works that use selective blocking of the carboxylic groups. They are, however, in clear disagreement with the microstate probabilities derived from the NMR titration data, which predict, within a very narrow confidence interval, a unique microspecies for the symmetric di-ionized form. Moreover, counterintuitively, the interaction between terminal charged groups is much larger than that between central and terminal groups. As a consequence, we have explored the possibility of delocalized proton binding by calculating the energy of intermediate proton positions between two carbolxylic groups. The results reveal that the exchange of the proton through the hydrogen bonds is in some cases produced without energetic barrier. This effect is specially relevant in the di-ionized form, with all the most stable conformations forming a SSLB, which together would constitute the only microstate detected by NMR. An alternative reaction scheme for the ionization process, based on proton delocalization, is proposed.

A detailed exploration of intermolecular interactions in 4-(4-dimethylaminobenzylideneamino)-N-(5-methyl-3-isoxazolyl)benzenesulfonamide and related Schiff bases: Crystal structure, spectral studies, DFT methods, Pixel energies and Hirshfeld surface analysis

The Schiff base of the title has been synthesized and its crystal structure determined by single-crystal X-ray diffraction. The compound was characterized by IR, Raman, 1H NMR, 13C NMR and electronic absorption spectra. DFT calculations provide the quantum chemical basis for the observed molecular conformation. A study of intermolecular interactions of the title compound is compared with seven other closely related structures and reveals that molecules in most of the compounds are linked by a cooperative effect of strong and weak hydrogen bonds, CH…π, and π…π stacking interactions, and also lp…π contacts. Lattice energy calculations indicate that the dispersion component is the major contribution, with the coulombic term playing a significant role in the total energy. Interaction energies for molecular pairs involving NH···N bonds indicate a dominant contribution to packing stabilization coming from coulomb component. Hirshfeld surfaces and 2D–fingerprint plots allowed us to visualize different intermolecular contacts and its relative contributions to total surface in each compound. The analysis of electrostatic potential (ESP) maps correlates well with the computed energies providing evidences on the dominant electrostatic nature of NH···N and NH···O interactions.

Enthalpies of binary mixtures containing limonene + aliphatic alcohols at 298.15 K

Enthalpies of mixing for binary mixtures containing R-limonene and various concentrations of each of alcohols (methanol, propanol, butanol, pentanol, and hexanol) were measured at 298.15 K and compared with reported values for limonene/ethanol binary mixtures. All the systems exhibited positive values over the entire range of mole fractions. The sequence of enthalpies of mixing did not show a simple dependence on the size of the aliphatic groups of the alcohols. The experimental results were compared with the values obtained from the UNIFAC, COSMO-RS, and regular solution theories. The interaction energies of limonene + alcohols were determined by ab initio calculation (MP2/6-311++G(d,p)) in alcohols and compared with the experimental results. In addition, pair interaction energies were decomposed for molecular interactions within the Hartree–Fock approximation by the Morokuma method.