Molecular Interaction Energy Research Articles

Aggregation Behavior of Inorganic 2D Nanomaterials Beyond Graphene: Insights from Molecular Modeling and Modified DLVO Theory.

We report the comparative aggregation behavior of three emerging inorganic 2D nanomaterials (NMs): MoS2, WS2, and h-BN in aquatic media. Their aqueous dispersions were subjected to aggregation under varying concentrations of monovalent (NaCl) and divalent (CaCl2) electrolytes. Moreover, Suwanee River Natural Organic Matter (SRNOM) has been used to analyze the effect of natural macromolecules on 2D NM aggregation. An increase in electrolyte concentration resulted in electrical double-layer compression of the negatively charged 2D NMs, thus displaying classical Derjaguin-Landau-Verwey-Overbeek (DLVO)-type interaction. The critical coagulation concentrations (CCC) have been estimated as 37, 60, and 19 mM NaCl and 3, 7.2, and 1.3 mM CaCl2 for MoS2, WS2, and h-BN, respectively. Theoretical predictions of CCC by modified DLVO theory have been found comparable to the experimental values when dimensionality of the materials is taken into account and a molecular modeling approach was used for calculating molecular level interaction energies between individual 2D NM nanosheets. Electrostatic repulsion has been found to govern colloidal stability of MoS2 and WS2 while the van der Waals attraction has been found to govern that of h-BN. SRNOM stabilizes the 2D NMs significantly possibly by electrosteric repulsion. The presence of SRNOM completely stabilized MoS2 and WS2 at both low and high ionic strengths. While h-BN still showed appreciable aggregation in the presence of SRNOM, the aggregation rates were decreased by 2.6- and 3.7-fold at low and high ionic strengths, respectively. Overall, h-BN nanosheets will have higher aggregation potential and thus limited mobility in the natural aquatic environment when compared to MoS2 and WS2. These results can also be used to mechanistically explain fate, transport, transformation, organismal uptake, and toxicity of inorganic 2D NMs in the natural ecosystems.

Regium bonds formed by MX (M═Cu, Ag, Au; X═F, Cl, Br) with phosphine-oxide/phosphinous acid: comparisons between oxygen-shared and phosphine-shared complexes

ABSTRACTRegium bonds interaction between phosphine oxide (H3PO), the trans phosphinuous acid (T-PH2OH), the cis phosphinuous acid (C-PH2OH) and MX (M═Cu, Ag, Au; X═F, Cl, Br) complexes were investigated by means of ab initio MP2/aug-cc-pVTZ method. For phosphinuous acid and MX complexes, two types of regium bonded interaction (trans and cis complexes) are observed and the two types of structures are very easily transformed from one type to another due to a low energy barrier. The molecular interaction energies are in the order of Au > Cu > Ag, F > Cl > Br and increase with the decrease of intermolecular distance Rint. Two resonance-type structures of P:M-X (ωI) ↔ P–M:X (ωII), O:M-X (ωI) ↔ O–M:X (ωII) are recognised by the natural resonance theory (NRT) and the natural bond orbitals (NBOs) analysis. The competition between ωI ↔ ωII resonance structures mainly arises from hyperconjugation interactions, in all phosphor-shared complexes, P–M:X resonance accounts for a larger proportion which leads to the covalent characters. All of complexes have been described in terms of their electron density properties.

Enzymatic and non-enzymatic pathways of kynurenines' dimerization: the molecular factors for oxidative stress development.

Kynurenines, the products of tryptophan oxidative degradation, are involved in multiple neuropathologies, such as Huntington's chorea, Parkinson's disease, senile dementia, etc. The major cause for hydroxykynurenines's neurotoxicity is the oxidative stress induced by the reactive oxygen species (ROS), the by-products of L-3-hydroxykynurenine (L-3HOK) and 3-hydroxyanthranilic acid (3HAA) oxidative self-dimerization. 2-aminophenol (2AP), a structural precursor of L-3HOK and 3HAA, undergoes the oxidative conjugation to form 2-aminophenoxazinone. There are several modes of 2AP dimerization, including both enzymatic and non-enzymatic stages. In this study, the free energies for 2AP, L-3HOK and 3HAA dimerization stages have been calculated at B3LYP/6-311G(d,p)//6-311+(O)+G(d) level, both in the gas phase and in heptane or water solution. For the intermediates, ionization potentials and electron affinities were calculated, as well as free energy and kinetics of molecular oxygen interaction with several non-enzymatically formed dimers. H-atom donating power of the intermediates increases upon the progress of the oxidation, making possible generation of hydroperoxyl radical or hydrogen peroxide from O2 at the last stages. Among the dimerization intermediates, 2-aminophenoxazinole derivatives have the lowest ionization potential and can reduce O2 to superoxide anion. The rate for O-H homolytic bond dissociation is significantly higher than that for C-H bond in non-enzymatic quinoneimine conjugate. However, the last reaction passes irreversibly, reducing O2 to hydroperoxyl radical. The inorganic ferrous iron and the heme group of Drosophila phenoxazinone synthase significantly reduce the energy cost of 2AP H-atom abstraction by O2. We have also shown experimentally that total antioxidant capacity decreases in Drosophila mutant cardinal with L-3HOK excess relative to the wild type Canton-S, and lipid peroxidation decreases in aged cardinal. Taken together, our data supports the conception of hydroxykynurenines' dual role in neurotoxicity: serving as antioxidants themselves, blocking lipid peroxidation by H-atom donation, they also can easily generate ROS upon dimerization, leading to the oxidative stress development.

Continuous Approximation for Interaction Energy Transfer of DNA through Lipid Bilayers

In this study the interaction energies for single-stranded DNA and double-stranded DNA molecules with a lipid bilayer are investigated. The 6-12 Lennard-Jones potential and continuous approximation are used to derive analytical expressions for these interaction energies. Assuming that there is a circular gap in the lipid bilayer, we determine the relationship of the molecular interaction energy, including the circular gap radius and the perpendicular distance of the single-stranded DNA and double-stranded DNA molecules from the gap. For both single-stranded and double-stranded DNA molecules, the relationship between the minimum energy location and the hole radius b is calculated; in the case of the double-stranded DNA molecule, we assume that the helical phase angle ϕ is equal to π. By minimizing the total interaction energies, the results demonstrate that the single-stranded DNA and double-stranded DNA molecules move through a lipid bilayer when the gap radius b> 10 Å and b> 13.8 Å, respectively. The results present in this project can be leveraged to understand the interactions between cell-penetrating peptides and biomembranes, which may improve gene and drug delivery.

Prediction of Mefenamic Acid Solubility and Molecular Interaction Energies in Different Classes of Organic Solvents and Water

Determination of solubility data either through experimental- or model-based approaches becomes a necessity in the crystallization of pharmaceutical compounds. The current work predicts the mefenamic acid solubility and molecular interaction energy, namely electrostatic (H-MF), hydrogen bonding (H-HB), and van der Waals (H-vdW), in different solvents at temperatures from 298 to 323 K using the conductor-like screening model for real solvents (COSMO-RS). The solvents used were N,N-dimethylacetamide, N,N-dimethylformamide, acetone, ethyl acetate, ethanol, iso-propyl alcohol, n-hexane, n-heptane, cyclohexane, and water. The Gibbs free energy of fusion required in COSMO-RS computation was determined using differential scanning calorimetry and reference solubility method. The accuracy of methods employed in prediction of solubility were evaluated using mean squared quadratic error (MSE). The mefenamic acid solubility predicted using COSMO-RS with reference solubility method showed a small MSE value of less than 2%. The predicted solubility also follows the same trend as the experimental values and increases with temperature. The predicted H-HB energy and Gibbs free energy changes of mefenamic acid dissolution in the solvents studied highly influence the solubility data. Therefore, COSMO-RS with reference solubility method is a promising approach to predict the solubility and intermolecular interaction energy of mefenamic acid in different solvents.

Restoring Size Consistency of Approximate Functionals Constructed from the Adiabatic Connection.

Approximate exchange–correlation functionals built by modeling in a nonlinear way the adiabatic connection (AC) integrand of density functional theory have many attractive features, being virtually parameter-free and satisfying different exact properties, but they also have a fundamental flaw: they violate the size-consistency condition, crucial to evaluate interaction energies of molecular systems. We show that size consistency in the AC-based functionals can be restored in a very simple way at no extra computational cost. Results on a large set of benchmark molecular interaction energies show that functionals based on the interaction strength interpolation approximations are significantly more accurate than second-order perturbation theory.

A theoretical investigation on Cu/Ag/Au bonding in XH2P⋯MY(X = H, CH3, F, CN, NO2; M = Cu, Ag, Au; Y = F, Cl, Br, I) complexes.

Intermolecular interaction of XH2P···MY (X = H, CH3, F, CN, NO2; M = Cu, Ag, Au; Y = F, Cl, Br, I) complexes was investigated by means of an ab initio method. The molecular interaction energies are in the order Ag < Cu < Au and increased with the decrease of RP···M. Interaction energies are strengthened when electron-donating substituents X connected to XH2P, while electron-withdrawing substituents produce the opposite effect. The strongest P···M bond was found in CH3H2P···AuF with -70.95 kcal/mol, while the weakest one was found in NO2H2P···AgI with -20.45 kcal/mol. The three-center/four-electron (3c/4e) resonance-type of P:-M-:Y hyperbond was recognized by the natural resonance theory and the natural bond orbital analysis. The competition of P:M-Y ↔ P-M:Y resonance structures mainly arises from hyperconjugation interactions; the bond order of bP-M and bM-Y is in line with the conservation of the idealized relationship bP-M + bM-Y ≈ 1. In all MF-containing complexes, P-M:F resonance accounted for a larger proportion which leads to the covalent characters for partial ionicity of MF. The interaction energies of these Cu/Ag/Au complexes are basically above the characteristic values of the halogen-bond complexes and close to the observed strong hydrogen bonds in ionic hydrogen-bonded species.

Computer Simulations Reveal a Novel Blocking Mode of the hERG Ion Channel by the Antiarrhythmic Agent Clofilium.

The binding modes of many hERG ion channel blockers are well understood, but a notable exception is clofilium, a potent antiarrhythmic agent whose action relies on blocking the current mediated by hERG. From the previously hypothesized binding modes of clofilium to hERG, only two can explain most of the experimental results. In this study, computer simulations are performed in order to analyze the hypothesized binding modes and to identify the consensus one. This is accomplished by employing molecular dynamics (MD) simulations and interaction energy calculations. The results show an unexpected binding mode, in which the quaternary nitrogen is placed in the upper part of the inner cavity, interacting strongly with Ser624, while the chlorophenyl group is located in the lower part, in better agreement with previous experimental results. This novel binding position also explains the higher affinity of clofilium for the related hEag1 channel and was correlated with the possibility that potent hERG blockers interact in specific ways with the residues near the intracellular activation gate, offering a new explanation that could help predict the potency of other hERG-blocking compounds.

Power transformations improve interpolation of grids for molecular mechanics interaction energies.

A common strategy for speeding up molecular docking calculations is to precompute nonbonded interaction energies between a receptor molecule and a set of three-dimensional grids. The grids are then interpolated to compute energies for ligand atoms in many different binding poses. Here, I evaluate a smoothing strategy of taking a power transformation of grid point energies and inverse transformation of the result from trilinear interpolation. For molecular docking poses from 85 protein-ligand complexes, this smoothing procedure leads to significant accuracy improvements, including an approximately twofold reduction in the root mean square error at a grid spacing of 0.4 Å and retaining the ability to rank docking poses even at a grid spacing of 0.7 Å. © 2018 Wiley Periodicals, Inc.

Alkali Metal Ion Partitioning with Calix[4]arene-benzo-crown-6 Ionophore in Acidic Medium: Insights from Experiments, Statistical Mechanical Framework, and Molecular Dynamics Simulations.

The current work reports the experimental and predicted interfacial behavior of metal ion extraction from aqueous phase-diluent system using a newly synthesized calix-benzo-crown-6 (CBCBGA) ionophore. Conductor-like screening model for real solvents was used to predict the selectivity at infinite dilution for the metal ion complexes in both aqueous and diluent phases. The selectivity for Cs+-CBCBGA extraction was found to be higher than that of other metal ions, namely, K+, Na+, and Rb+. This was confirmed by the experimental distribution coefficients obtained in the diluents system at 3 M HNO3 along with 0.01 M CBCBGA/organic solvents. The high selectivity of Cs+-CBCBGA complex over other complexes (K+, Rb+, and Na+) in nitrobenzene was also confirmed and validated by the highest occupied molecular orbital-lowest unoccupied molecular orbital energy gap (i.e., 0.13114 > 0.12411 > 0.11719 > 0.11561 eV) and interaction energy (i.e., -68.25 > -57.11 > -55.52 > -52.37 kcal/mol). The interaction and free energies of the extraction were found to increase with the dielectric constant of the organic solvents, namely, nitrobenzene > o-nitrophenyl hexyl ether > 1-octanol > chloroform. Overall, a higher selectivity of Cs+ ion over that of other metal ions (K+, Na+, and Rb+) was obtained for the newly synthesized CBCBGA ionophore in a radioactive waste solution.

Phytosterol Recognition via Rationally Designed Molecularly Imprinted Polymers

Molecularly imprinted polymers (MIPs) prepared via a semi-covalent imprinting strategy using stigmasteryl methacrylate as a polymerisable template have been evaluated by static binding methods for their ability to selectively capture other valuable phytosterol targets, including campesterol and brassicasterol. Design criteria based on molecular modelling procedures and interaction energy calculations were employed to aid the selection of the co-monomer type, as well as the choice of co-monomer:template ratios for the formation of the pre-polymerisation complex. These novel hybrid semi-covalently imprinted polymers employed N,N′-dimethylacryl-amide (N,N′-DMAAM) as the functional co-monomer and displayed specific binding capacities in the range 5.2–5.9 mg sterol/g MIP resin. Their binding attributes and selectivities towards phytosterol compounds were significantly different to the corresponding MIPs prepared via non-covalent procedures or when compared to non-imprinted polymers. Cross-reactivity studies using stigmasterol, ergosterol, cholesterol, campesterol, and brassicasterol as single analytes revealed the importance of the A-ring C-3-β-hydroxyl group and the orientational preferences of the D-ring alkyl chain structures in their interaction in the templated cavity with the N,N′-dimethylamide functional groups of the MIP. Finally, to obtain useful quantities of both campersterol and brassicasterol for these investigations, improved synthetic routes have been developed to permit the conversion of the more abundant, lower cost stigmasterol via a reactive aldehyde intermediate to these other sterols.

Towards good correlation between fragment molecular orbital interaction energies and experimental IC50 for ligand binding: A case study of p38 MAP kinase

We describe several procedures for the preprocessing of fragment molecular orbital (FMO) calculations on p38 mitogen-activated protein (MAP) kinase and discuss the influence of the procedures on the protein–ligand interaction energies represented by inter-fragment interaction energies (IFIEs). The correlation between the summation of IFIEs for a ligand and amino acid residues of protein (IFIE-sum) and experimental affinity values (IC50) was poor when considered for the whole set of protein–ligand complexes. To improve the correlation for prediction of ligand binding affinity, we carefully classified data set by the ligand charge, the DFG-loop state (DFG-in/out loop), which is characteristic of kinase, and the scaffold of ligand. The correlation between IFIE-sums and the activity values was examined using the classified data set. As a result, it was confirmed that there was a selected data set that showed good correlation between IFIE-sum and activity value by appropriate classification. In addition, we found that the differences in protonation and hydrogen orientation caused by subtle differences in preprocessing led to a relatively large difference in IFIE values. Further, we also examined the effect of structure optimization with different force fields. It was confirmed that the difference in the force field had no significant effect on IFIE-sum. From the viewpoint of drug design using FMO calculations, various investigations on IFIE-sum in this research, such as those regarding several classifications of data set and the different procedures of structural preparation, would be expected to provide useful knowledge for improvement of prediction ability about the ligand binding affinity.

In Silico Chromatography: Modeling a New Support for Alkyl-Bonded Phases and a Solvent Phase

Chromatography is a tool to measure molecular interactions, and computational chemistry is a tool to explain molecular interactions. Therefore, reversed-phase liquid chromatography of acidic drugs using a pentyl- and an octyl-bonded silica gels was quantitatively analyzed in silico. A model pentyl- and an octyl-bonded silica gel and a methanol phases were constructed for docking with acidic drugs. Molecular interaction energy values based on van der Waals energy were obtained after docking an acidic drug into the model pentyl- or octyl-phases. Solvent effects, hydrogen bonding, and electrostatic energy values were obtained after docking an acidic drug onto the model methanol phase. Chromatographically measured log k values were correlated with the sum of van der Waals, hydrogen bonding, and electrostatic energy values. The correlation coefficient between the log k values measured using the pentyl-bonded silica gel phase and the molecular interaction energy values was 0.95 (n = 20); that between the log k values measured using the octyl-bonded silica gel and the molecular interaction energy values was 0.95 (n = 20).

Quantitative Explanation of Retention Mechanisms of Hydrophobic and Hydrophilic-Interaction Liquid Chromatography-Inductive Effect of Alkyl Chain

The basic retention mechanisms of reversed-phase and hydrophilic-interaction liquid chromatography (HILIC) were quantitatively analyzed using simple molecular mechanics (MM) calculations. The model bonded phases were composed of an alkyl chain bonded to siloxane-like molecules. The head of the alkyl chain was a hydroxyl group, used to study retention mechanisms of HILIC. The standard analytes were benzoic acid, aniline, benzene, water, and acetonitrile. The molecular interaction (MI) energy values of the van der Waals (VW) force were predominant for the reversed-phase chromatography, and those of hydrogen bonding (HB) were predominant for HILIC. Up to 5 units of methylene affected the MI.

Exploring potent ligand for proteins: insights from knowledge-based scoring functions and molecular interaction energies

Two different scoring functions, Hirshfeld fingerprint-based scoring (HFBS) and molecular operating environment (MOE), and the kernel energy method (KEM) along with counterpoise (CP)-corrected approach were used to estimate the binding energies of protein–ligand complexes and tested against a series of inhibitors of human aldose reductase enzyme. The new scoring function, HFBS, is based on Hirshfeld fingerprints, which are 2D histogram plots of the distances from the molecular Hirshfeld surface to the nearest atomic nuclei inside versus outside the surface and are highly sensitive to the immediate environment of the molecule. The Hirshfeld surface plotted over the ligand molecule helped to visualize the contacts with the active site residues and solvents, which were then taken into account for interaction energy calculations. Application of KEM-assisted CP-corrected approach facilitated an efficient way of calculating interaction energies in protein complex systems. Interaction energies calculated using MP2/6-31G(d) level of theory allowed us to rank the ligands by potency. We find that both the KEM-assisted CP-corrected interaction energies and the scoring functions used here predict comparable rankings for the strength of binding of the series of ligands as docked to the active site of the protein, which are also in good agreement with the experimental binding affinities in this case.

Structural, Relative Stable, and Electronic Properties of PbnSnn (n = 2–12) Clusters were Investigated Using Density Functional Theory

The structural, relative stable and electronic properties of PbnSnn (n = 2–12) alloy clusters were systematically studied using density functional theory. The isomers of PbnSnn alloy clusters were generated and determined by ab initio molecular dynamics. By comparing the calculated parameters of Pb2 dimer and Sn2 dimers with the parameters from experiments, our calculations are reasonable. With the lowest-energy structures for PbnSnn clusters, the average binding energies, fragmentation energies, second- order energy differences, vertical ionization potentials, vertical electron affinities, HOMO–LUMO gaps, and density of states were calculated and analyzed. The results indicate that the Sn atoms have a tendency to bond together, the average binding energies tend to be stable up to n = 8, Pb8Sn8 cluster is a good candidate to calculate the molecular interaction energy parameter in Wilson equation, the clusters become less chemical stable and show an insulator-to-metallic transition, 3, 6, 8 and 11 are magic numbers of PbnSnn (n = 2–12) clusters, the charges always transfer from Sn atoms to Pb atoms in PbnSnn clusters except for Pb10Sn10 cluster, and density of states of PbnSnn clusters becoming continuous and shifting toward negative with the increasing size n.

Molecular Aggregation in Binary Mixtures of Pyrrolidine, N-Methylpyrrolidine, Piperidine, and N-Methylpiperidine with Water: Thermodynamic, SANS, and Theoretical Studies.

Piperidine and N-methylpiperidine hydrates aggregate in liquid aqueous solutions due to hydrogen bonds between hydration water molecules. No such effects occur in the mixtures of the amines with methanol, that supports the idea of active role of water solvent in the aggregation. However, the question of contributions in thermodynamic functions due to specific interactions, van der Waals forces, and the size and shape of the molecules remains open. In the present study, limiting partial molar enthalpies of solution of pyrrolidine, N-methylpyrrolidine, piperidine, and N-methylpiperidine in water and methanol and vice versa were measured and compared with those assessed from theoretically calculated molecular interaction energies using a simple "chemical reaction" model. Nearly quantitative agreement of the enthalpies was achieved for the systems studied, except the amines in water. The latter required an empirical hydrophobic hydration term to be considered. The hydrogen bonds formation and breaking which accompany the mixtures formation leads to considerable excess volumes, while the size of the solute molecules is manifested rather in the compressibility of aqueous solutions. SANS evidenced that aqueous solutions are microheterogeneous on the nanometer-order length scale. The propensity to promote phase separation increases in the order: N-methylpiperidine < N-methylpyrrolidine < piperidine < pyrrolidine.

The enhancing effect of a cation-π interaction on the cooperativity of halogen bonds: A computational study

In this work, we investigate the effect of a cation-π interaction on the cooperativity of X⋯N halogen bonds in PhX⋯NCX⋯NH3 complexes, where Ph=phenyl and X=Cl, Br, I. Molecular geometries and interaction energies of the resulting complexes are studied at the MP2/aug-cc-pVDZ(-PP) computational level. The mechanism of the cooperativity between halogen bonds is analyzed using parameters derived from the noncovalent index, quantum theory of atoms in molecules and natural bond orbital methodologies. It is found that the divalent cations (Be2+, Mg2+) have a larger influence on the cooperativity of halogen bonds than monovalent ones (Li+, Na+). The formation of a cation-π interaction leads to strengthening of the halogen bonds, hence increases their cooperativity.

A computational study of interplay between hydride bonding and cation–π interactions: H-Mg-H···X···Y triads (X = Li+, Na+, Y = C2H2, C2H4, C6H6) as model systems

ABSTRACTIn the present study, H-Mg-H···X···Y (X = Li+, Na+ and Y = C2H2, C2H4, C6H6) triads have been investigated at MP2/6-311++G(2d,2p) computational level to characterise cooperative effects between hydride bonding and cation–π interactions. Molecular geometries, binding energies, cooperative energies and many-body interaction energies were evaluated. The diminutive energy values in triads with Li+ are larger than respective values in triads with Na+. The electronic properties of the complexes are analysed using parameters derived from the quantum theory of atoms in molecules methodology.

The role of 5-arylalkylamino- and 5-piperazino- moieties on the 7-aminopyrazolo[4,3-d]pyrimidine core in affecting adenosine A1 and A2A receptor affinity and selectivity profiles

New 7-amino-2-phenylpyrazolo[4,3-d]pyrimidine derivatives, substituted at the 5-position with aryl(alkyl)amino- and 4-substituted-piperazin-1-yl- moieties, were synthesized with the aim of targeting human (h) adenosine A1 and/or A2A receptor subtypes. On the whole, the novel derivatives 1–24 shared scarce or no affinities for the off-target hA2B and hA3 ARs. The 5-(4-hydroxyphenethylamino)- derivative 12 showed both good affinity (Ki = 150 nM) and the best selectivity for the hA2A AR while the 5-benzylamino-substituted 5 displayed the best combined hA2A (Ki = 123 nM) and A1 AR affinity (Ki = 25 nM). The 5-phenethylamino moiety (compound 6) achieved nanomolar affinity (Ki = 11 nM) and good selectivity for the hA1 AR. The 5-(N4-substituted-piperazin-1-yl) derivatives 15–24 bind the hA1 AR subtype with affinities falling in the high nanomolar range. A structure-based molecular modeling study was conducted to rationalize the experimental binding data from a molecular point of view using both molecular docking studies and Interaction Energy Fingerprints (IEFs) analysis.