Estimate Of Interaction Energy Research Articles

Noncovalent and Covalent O-H···O Interactions in PPh3O Cocrystals: A Correlation Study Involving QTAIM, SAPT, NBO, and IBSI Methods.

PPh3O.hemihydrate polymorphs and 11 assorted PPh3O cocrystals collectively constitute a reliable stock to pursue a systematic analysis aiming to investigate the impacts of some vital issues on the TPPO.H-bond donor aggregates. The issues highlighted herein are (i) effect of varying acidity of H-bond donors on the degeneracy of lone pairs of the H-bond acceptor (PPh3O), (ii) effectiveness of the |V(r)|/G(r) and H(r)/ρ(r) parameters as a covalency metric, (iii) 3c-4e bonding in the covalent PPh3O.nitric acid cocrystal, (iv) salient features of H-bond interaction energy and an interplay of its components, (v) an intrinsic bond strength scale for the PPh3O cocrystals, and (vi) reliable empirical relations between several bond descriptors for a quick estimation of interaction energy. To be specific about point (vi), we have propounded two promising avenues for a fast semiquantitative calculation of interaction energy from an endearing nonenergetic parameter, viz., bond length: dO-H···O → ρBCP (MAPE = 2.36%) → ESAPT0 (MAPE = 9.26%), and dO-H···O → IBSI (MAPE = 1.87%) → ESAPT0 (MAPE = 9.66%). All the aforesaid issues have been explored in detail through the QTAIM, NBO, and IBSI analyses (M06-2X-D3/def2-TZVP level), as well as by the SAPT study at the SAPT0/aug-cc-pVDZ platform. The statistically valid correlation studies can be particularly conducive for practical purposes as a transformative extension of the established facts into postulates for the unknown cocrystals.

Integrative modeling of diverse protein-peptide systems using CABS-dock.

The CABS model can be applied to a wide range of protein-protein and protein-peptide molecular modeling tasks, such as simulating folding pathways, predicting structures, docking, and analyzing the structural dynamics of molecular complexes. In this work, we use the CABS-dock tool in two diverse modeling tasks: 1) predicting the structures of amyloid protofilaments and 2) identifying cleavage sites in the peptide substrates of proteolytic enzymes. In the first case, simulations of the simultaneous docking of amyloidogenic peptides indicated that the CABS model can accurately predict the structures of amyloid protofilaments which have an in-register parallel architecture. Scoring based on a combination of symmetry criteria and estimated interaction energy values for bound monomers enables the identification of protofilament models that closely match their experimental structures for 5 out of 6 analyzed systems. For the second task, it has been shown that CABS-dock coarse-grained docking simulations can be used to identify the positions of cleavage sites in the peptide substrates of proteolytic enzymes. The cleavage site position was correctly identified for 12 out of 15 analyzed peptides. When combined with sequence-based methods, these docking simulations may lead to an efficient way of predicting cleavage sites in degraded proteins. The method also provides the atomic structures of enzyme-substrate complexes, which can give insights into enzyme-substrate interactions that are crucial for the design of new potent inhibitors.

Systematic elucidation of the second coordination sphere effect on the structure and properties of a blue copper protein, pseudoazurin

The rational structural and computational studies of a blue copper protein, pseudoazurin (PAz), and its Met16X (X = Phe, Leu, Val, Ile) variants gave clear functional meanings of the noncovalent interaction (NCI) through the second coordination sphere. The high-resolution X-ray crystal structures of Met16X PAz demonstrated that the active site geometry is significantly affected by the substitution of Met16, which is located within the NCI distance from the His81 imidazole ring at the copper active site. The computational chemistry calculations based on the crystal structure analyses confirmed that the NCI of S-π/CH-π (wild-type), π-π (Met16Phe), double CH-π (Met16Leu), and single CH-π (Met16Val and Met16Ile). The estimated interaction energies for the NCI demonstrated that the fine-tuning of the protein stability and Cu site properties form the second coordination sphere of PAz.

Molecular insights into the functionalization of Au13 nanocluster with mercaptopurine anti-cancer drug

The exploration of formation of biomolecule-nanostructures complexes is vastly fascinating and fortunes the coherent growth and fabrication of nano-materials such as nanosensors and nanocarriers. In the present study, DFT-D3 calculations were performed to explore the possible formation of a complex between mercaptopurine and Au13 cluster. After complete structural optimization of interacting molecules at various interaction ways, we found that mercaptopurine bounded strongly to the gold cluster surface through its N and S chemical sites. The estimated interaction energy (-59.505 kcal/mol) and bonding distances demonstrated that the interaction was typical for the chemisorption. The interaction nature analysis obtained by AIM theory showed that the bonding properties were determined to be primarily covalent and has also a high polar characteristic. These computational findings present appreciated information about the interaction properties of biomolecule and gold cluster and its application as nanocarrier and nanosensor.

Density Functional Theory-Based Studies Predict Carbon Nanotubes as Effective Mycolactone Inhibitors

Fullerenes, boron nitride nanotubes (BNNTs), and carbon nanotubes (CNTs) have all been extensively explored for biomedical purposes. This work describes the use of BNNTs and CNTs as mycolactone inhibitors. Density functional theory (DFT) has been used to investigate the chemical properties and interaction mechanisms of mycolactone with armchair BNNTs (5,5) and armchair CNTs (5,5). By examining the optimized structure and interaction energy, the intermolecular interactions between mycolactone and nanotubes were investigated. The findings indicate that mycolactone can be physically adsorbed on armchair CNTs in a stable condition, implying that armchair CNTs can be potential inhibitors of mycolactone. According to DOS plots and HOMO–LUMO orbital studies, the electronic characteristics of pure CNTs are not modified following mycolactone adsorption on the nanotubes. Because of mycolactone’s large π-π interactions with CNTs, the estimated interaction energies indicate that mycolactone adsorption on CNTs is preferable to that on BNNTs. CNTs can be explored as potentially excellent inhibitors of mycolactone toxins in biological systems.

Non-conventional interactions of N3 inhibitor with the main protease of SARS-CoV and SARS-CoV-2

The extensive spread of COVID-19 in every continent shows that SARS-CoV-2 virus has a higher transmission rate than SARS-CoV virus which emerged in 2002. This results in a global pandemic that is difficult to control. In this investigation, we analyze the interaction of N3 inhibitor and the main protease of SARS-CoV and SARS-CoV-2 by quantum chemistry calculations. Non-covalent interactions involved in these systems were studied using a model of 469 atoms. Density Functional Theory and Quantum Theory of Atoms in Molecules calculations lead us to the conclusion that non-conventional hydrogen bonds are important to describe attractive interactions in these complexes. The energy of these non-conventional hydrogen bonds represents more than a half of the estimated interaction energy for non-covalent contacts. This means that hydrogen bonds are crucial to correctly describe the bonds between inhibitors and the main proteases. These results could be useful for the design of new drugs, since non-covalent interactions are related to possible mechanisms of action of molecules used against these viruses.

Нанорозмірні квазібінарні евтектичні системи і їх характерні параметри

A method for accounting for the influence of the outer surface on the internal state of the electron ― ion system for nanoparticles is proposed. The estimated interaction energy of the representative elements of the components (LaB6, MeB2) is part of the composite depending on the size of the nanoplate. The characteristic parameters of the eutectic of quasi-binary boride-boride systems are calculated and analytically presented. During the transition of bulk materials to nanomaterials, the melting temperature of the eutectic decreases, and the concentration ratio of the components changes. With the help of first-principle methods the scheme of calculation of energy of interaction of representative elements of components from the first principles is developed. The dependence of the interaction energy of the representative elements on the sizes of the materials is analytically obtained. It is proved that the reduction of the size of the eutectic composite leads to a significant decrease in the melting temperature at the eutectic point, as well as to a change in the concentration ratio of the components. The obtained analytical formulas allow to estimate the change of concentration and melting temperature at the eutectic point depending on the thickness of the nanocomposite. Keywords: electron-ion system energy, pseudopotential method, nanosystem, nanoplate surface energy, concentration and melting point at the eutectic point.

Enhancing low-rank coal flotation using mixed collector of dodecane and oleic acid: Effect of droplet dispersion and its interaction with coal particle

Low-rank coal is difficult to float using oily collectors due to the rich oxygen-containing functional groups on the surface. In recent years, a variety of mixed collectors have been used to enhance the low-rank coal flotation. In this study, the effects of droplets dispersion and interaction with particles on the low-rank coal flotation using mixed collector (MC) of dodecane (D) and oleic acid (OA) were discussed. Interfacial tension experiment and Focused Beam Reflectance Measurement (FBRM) was used to analyze the oil droplets dispersion. The interaction energy estimation using EDLVO theory and the induction time measurement was performed to investigate the interaction between oil droplets and coal particles. The results showed that the addition of OA can significantly reduce the oil–water interfacial tension and shorten the time of interfacial tension equilibrium, which decreased droplets size and increased droplets counts. There was always attraction interaction between oil droplets and coal particles, and the absolute value of interaction energy and attraction force decreased in the order of D > MC > OA. The results of induction time measurement confirmed the interaction energy estimation using EDLVO theory. The flotation performance of the single reagent was greatly improved by mixed use, and OA and D showed synergistic effect. It was indicated that the effect of OA in mixed collector was to promote dispersion, that is, to reduce droplets size and increase droplets counts, rather than to improve interaction energy between oil droplets and coal particles.

Formation, breakage, and re-growth of quartz flocs generated by non-ionic high molecular weight polyacrylamide

Flotation of fine mineral particles is one of the major challenges faced by the minerals industries worldwide. Flocculation of these fine particles prior to flotation, to form separate hydrophobic and hydrophilic flocs, is one of the methods to tackle this challenge. In order to gain a better understanding of the properties of hydrophilic polymer flocs for the intended flocculation flotation, this paper reports testwork completed on the formation, breakage, and re-growth of quartz flocs when non-ionic high molecular weight polyacrylamide (PAM) was used as a flocculant under different test conditions in an alkaline environment. Focused beam reflectance measurement (FBRM) particle size analyses, coupled with sedimentation tests and optical microscope observations were performed to monitor the real-time evolution and change of quartz flocs. In addition, adsorption experiments and zeta potential measurements were carried out and used as parameters in the DLVO theory interaction energy estimation. The results of DLVO theory interaction energy estimation, settling experiments and optical microscope observations showed that the quartz particles dispersed well in slurry at pH 9. PAM had a strong flocculation ability to quartz particles, the peak values of floc size were affected by both the stirring rate and PAM concentration. In addition, the degree of floc breakage depended on the increased stirring rate and the shear time. Floc re-growth occurred to different extents according to the breakage durations and PAM dosages.

Magnetic susceptibility of pyrochlores R2Ti2O7: R = Gd, Dy, Tb

We present the study of magnetic susceptibility of pyrochlores Gd2Ti2O7, Dy2Ti2O7 and Tb2Ti2O7 which belong to frustrated magnets. The temperature dependence of the susceptibility χ(T) of powder samples was measured in the temperature range from 4.2 to 300 K and analyzed in the framework of mean field approximation taking into account both crystal field effects and anisotropy of the exchange interaction. We developed a simple approach allowing us to estimate interaction energies of magnetic ions from χ(T) dependences and data on wave functions of the crystal-field states of the ions using a minimum number of fitting parameters. We revealed a strong anisotropy of the exchange interaction in the paramagnetic state of Gd2Ti2O7 and obtained nearest-neighbor effective bond energies of the magnetic ions in Tb2Ti2O7 and Dy2Ti2O7 which are in good agreement with the temperatures of formation of the spin-ice state in these compounds.

Silver clusters tune up electronic properties of graphene nanoflakes: A comprehensive theoretical study

Graphene-silver composites show a synergic effect of both components with enhanced electronic, adsorption and catalytic properties. We present here the detailed theoretical study on geometric, thermodynamic and electronic properties of silver clusters Agn (n = 2–10) adsorbed on graphene nanoflakes as a model for silver-graphene composites. First, a benchmark study is performed on Agn…coronene complexes (n = 2, 4) by evaluating various functional against reported high level ab-initio method for the selection of best functional for further calculations. Then, density functional theory study at the best chosen level is performed to inquire how clustering of adsorbate attached with carbon surface can impact geometric, electronic and thermodynamic properties of silver-graphene composites. Furthermore, the interaction energies are corrected for dispersion and basis set superposition error in order to get more realistic estimate of interaction energies. In progression, we investigated the dependence of interaction energy upon cluster size and dimensionality. For Agn…coronene, the binding energies increase monotonically as the number of atoms in the cluster increases. However, for Agn…dodecabenzocoronene, the interaction energies show a sudden drop at Ag7…dodecabenzocoronene. The difference in behavior between Agn…dodecabenzocoronene and Agn…coronene for interaction energy is attributed to edge effect present in coronene. Furthermore, coplanar orientations of the silver clusters on polyaromatic hydrocarbons have higher interaction energies. The 2D-3D transition of the silver cluster is observed for Ag7…coronene. CDA analysis reveals that backdonation from dodecabenzocoronene to silver clusters is more dominant in Ag4–Ag7 whereas other clusters have dominant charge transfer to dodecabenzocoronene. Charge transfer analysis via constrained density functional theory (CDFT) reveals significant energy lowering from charge donor-acceptor interactions. Further energy decomposition analysis (EDA) using absolutely-localized molecular orbitals (ALMO) suggests that, while charge-transfer is important in these systems, the sum of electrostatics, Pauli repulsion, and London dispersion are far more significant as silver cluster size increases. NCI results also support the presence of van der Waals and electrostatic interactions. The hollow top is most favorite interaction sites compared to bridge top and head top binding sites over coronene lattice. The ionization potential, electron affinity, frontier molecular orbital analysis, chemical hardness, softness, chemical potential, and Fermi levels are deliberated to verify the stability and reactivity of most stable silver-graphene composites. The remarkable outcome of the current findings makes our silver-graphene composite as a potential applicant for high performance electronic and catalytic devices.

Crystal packing of a zinc(II)-azide complex with a N,N,S-tridentate thiosemicarbazone ligand: An experimental and computational study

The aim of this study was to provide a crystallographic and electronic analysis of a zinc(II)-azide complex with a N,N,S-tridentate thiosemicarbazone ligand. The characterization was performed by single-crystal X-ray diffraction, elemental analysis and FT-IR spectroscopy. This compound showed a distorted square-planar structure and its crystal structure was in the triclinic space group P1¯ with Z = 2. Based on the Hirshfeld surface analysis, the van der Waals forces, N⋅⋅⋅H hydrogen bonds and C–H⋅⋅⋅π are the main intermolecular interactions that stabilize the crystal packing assembly. In addition, the Density Functional Theory (DFT) was used to predict the electronic properties. DFT calculations estimated interaction energy of −12.6 kcal mol−1 required to form the dimer structure. Nevertheless, based on a Natural Bond Orbital (NBO) analysis, two hydrogen bonds between nitrogen atoms of the azide group and the hydrogen atom of the amine one (N–H⋅⋅⋅N) are the main interactions responsible for the stabilization of the dimer structure studied. In addition, we were also able to characterize other important intermolecular interactions as the Sulfur⋅⋅⋅Sulfur and the C–H⋅⋅⋅N formed between the azide groups and the aromatic rings performed with the Quantum Theory of Atoms in Molecules (QTAIM).

Unraveling the effect of sub-cooling temperatures on the kinetic performance of biopolymers for methane hydrate

In deep sea plays, where the driving force or sub-cooling temperature for hydrate formation is high, the commercially used kinetic hydrate inhibitors (KHIs) lose their kinetic inhibition performance, additionally they are toxic. Though, biodegradable biopolymers are deliberated as an alternative KHIs. However, the inhibition performance of biopolymers solely for methane hydrate formation at high sub-cooling temperatures has not been evaluated. In current work the kinetic inhibition performance of five biopolymers (Pectin, Sodium- Carboxymethyl cellulose (Na-CMC), Tapioca starch, Dextran and Xanthan gum) on methane hydrate formation is evaluated using isochoric constant cooling method on sapphire hydrate reactor at 95 bar and sub-cooling temperatures of 9 °C and 12 °C. Induction time, hydrate formation rate, amount of methane consumed and percentage relative inhibition power are determined and used as kinetic inhibition indicators. Present data-set reveals that biopolymers efficiently inhibit methane hydrate formation at high sub-cooling temperatures. Among all studied biopolymers Pectin and Na-CMC commendably delayed hydrate nucleation for 78 and 61min respectively. Furthermore, Tapioca starch, Pectin and Na-CMC significantly reduced hydrate formation rate, methane consumption and percentage relative inhibition power. For further analysis on molecular level Conductor like Screening Model for Real Solvents (COSMO-RS) software is used. The interaction energy estimation using COSMO-RS showed that attractive interactions between biopolymers and water molecules are leading to prolonged nucleation. Furthermore, the effect of biopolymer concentrations (0.12 wt% - 1.5 wt%) on kinetic inhibition is elaborated by establishing a relationship between induction time, air-liquid interfacial and electrokinetic properties.

Quantitative and qualitative analyses of intermolecular interactions in neutral/deprotonated aspirin@β-CD inclusion complexes: QTAIM and NBO analyses

Most of the researches in supramolecular chemistry area are focused on the conventional hydrogen bonds without taking into account unconventional intermolecular interactions. The nature and strength of the conventional and unconventional interactions in inclusion complexes formed between neutral aspirin (ASA) and its deprotonated form (ASA−) with β-cyclodextrin (β-CD) have been studied. It was conducted through combining atoms in molecules (AIM) theoretical criteria suggested by Koch and Popelier and natural bond orbital (NBO) analyses by means of dispersion-corrected density functional theory (DFT-D3) with the functional B3LYP using cc-pvdz basis set in the gas phase. We have found five intermolecular closed-shell interaction groups responsible for neutral ASA:β-CD and deprotonated ASA−:β-CD inclusion complexes stability: One is conventional O–H···O bond group. The four C–H···O, C–H···C, O–H···H–C and C–H···H–C groups are nonconventional. Also, with respect to the Koch and Popelier criteria, some of them present the properties of a hydrogen bond, while others do not. The non-covalent interaction energies are calculated using Espinosa approach. Finally, according to the AIM and NBO analyses, the topological parameters (electron density ρb and its Laplacian ∇2ρb), estimated interaction energies (Eint), and the stabilization energy E(2) of both complexes were correlated with the intermolecular bond lengths.

Interactions between Endohedral Metallofullerenes and Proteins: The Gd@C60-Lysozyme Model.

Endohedral metallofullerenes (EMFs) have great potential as radioisotope carriers for nuclear medicine and as contrast agents for X-ray and magnetic resonance imaging. EMFs have still important restrictions for their use due to low solubility in physiological environments, low biocompatibility, nonspecific cellular uptake, and a strong dependence of their peculiar properties on physiological parameters, such as pH and salt content. Conjugation of the EMFs with proteins can overcome many of these limitations. Here we investigated the thermodynamics of binding of a model EMF (Gd@C60) with a protein (lysozyme) that is known to act as a host for the empty fullerene. As a rule, even if the shape of an EMF is exactly the same as that of the related fullerene, the interactions with a protein are significantly different. The estimated interaction energy (ΔGbinding) between Gd@C60 and lysozyme is −18.7 kcal mol–1, suggesting the possibility of using proteins as supramolecular carriers for EMFs. π–π stacking, hydrophobic interactions, surfactant-like interactions, and electrostatic interactions govern the formation of the hybrid between Gd@C60 and lysozyme. The comparison of the energy contributions to the binding between C60 or Gd@C60 and lysozyme suggests that, although shape complementarity remains the driving force of the binding, the presence of electron transfer from the gadolinium atom to the carbon cage induces a charge distribution on the fullerene cage that strongly affects its interaction with the protein.

New models of electron density for electrostatic interaction energy estimation

New models of electron density for electrostatic interaction energy estimation

Spreading and orientation of silver nano-drops over a flat graphene substrate: An atomistic investigation

The spreading and orientation of silver nano-drop over the graphene substrate are important in various applications such as flexible electronic, bio-medical, electrochemical, and coating materials, etc and have been explored by molecular dynamics simulations. The tuning of interaction energy parameter between graphene and silver affects both spreading and phase transitions of silver nano-drop over the graphene substrate. At high interaction energy, silver nano-drops spread over the graphene substrate and solidified at a higher temperature compared to lower interaction energies. Silver depicts fcc with a layered hcp structure over the graphene substrate during cooling from 1500 K to 10 K. However, at the interface between graphene and silver nano-drop, silver shows the fcc{111} planner orientations. Spreading and orientation of silver nano-drop over the graphene substrate has been characterized by estimation of interaction energies, average number distributions, bond order parameters, the percentage of a crystalline atom during solidification. The results suggest that the silver nano-drop depicts the unique crystal structure with high thermal stability over the graphene substrate compared to the bulk. Therefore, it is extremely desirable material for the development of an efficient catalyst and flexible electronic circuits.

Estimation of interaction energy and contact stiffness in atomic-scale sliding on a model sodium chloride surface in ethanol

Friction force microscopy (FFM) in aqueous environments has recently proven to be a very effective method for lattice-resolution imaging of crystal surfaces. Here we demonstrate the use of ethanol for similar measurements on water-soluble materials. Lattice resolved frictional stick-slip traces of a cleaved NaCl(100) surface submerged in ethanol are compared with previous obtained FFM results in ultrahigh vacuum (UHV). We use the Prandtl-Tomlinson framework to estimate the amplitude of the corrugation potential and the contact stiffness. The surface potential amplitude scales with the applied normal loads are in good agreement with data obtained for NaCl measured under UHV conditions, but demonstrates deviations from the ideal periodic potential given by the Prandtl-Tomlinson model. An additional finding is that the use of ethanol allows us to explore higher load ranges without detectable evidence of surface wear. The contact stiffness does not vary significantly with the normal load up to 38 nN, while above it a sudden increase by almost one order of magnitude was observed. Comparing this to previous results suggests that considerable atom rearrangements may occur in the contact region, although the (100) surface structure is preserved by ethanol-assisted diffusion of Na and Cl ions.

Interaction of Elemental Mercury with a Diverse Series of π-Organic Substrates Probed by Computational Methods: Is Mercury Fixation Possible?

A multitude of electronic structure computational methods has been employed to study the intermolecular adducts formed upon the interaction of elemental mercury, Hg0, with benzene and substituted benzenes of the general formula [Hg(η6-1,3,5-C3H3R3)], where R is either an electron donor substituent, such as −NH2, −OH, −SH, −NH(COCH3), −C≡CH, −S(CH3), −C═CH2, −CH3, −N(CH3)3, and −O(CH3)3 or an electron acceptor substituent, such as −COOH, −NO2, −CHO, −CO(CH3), −CN, −SO2H, −CF3, −C(CO)(NH2), −Cl, −F, and −C(CO)Cl. In addition, a set of neutral and negatively charged octupolar molecules, with alternating electron donor and electron acceptor groups in the 1,3,5 and 2,4,6 positions of the benzene ring, have been included in this study. The estimated interaction energies of Hg0 with these systems range from −2.6 to −13.7 kcal/mol. The interplay of electrostatic, dispersion forces and covalent interaction components constitute the Hg0···π-organic substrate interactions. In the [Hg(η6-1,3,5-C3H3R3)] adducts with e...

An interaction energy driven biased sampling technique: A faster route to ionization spectra in condensed phase.

We introduce a computationally efficient approach for calculating spectroscopic properties, such as ionization energies (IEs) in the condensed phase. Discrete quantum mechanical/molecular mechanical (QM/MM) approaches for spectroscopic properties in a dynamic system, such as aqueous solution, need a large sample space to obtain converged estimates, especially for the cases where particle (electron) number is not conserved, such as IEs or electron affinities (EAs). We devise a biased sampling technique based on an approximate estimate of interaction energy between the solute and solvent, that accelerates the convergence and therefore, reduces the computational cost significantly. The approximate interaction energy also provides a good measure of the spectral width of the chromophores in the condensed phase. This technique has been tested and benchmarked for (i) phenol, (ii) HBDI anion (hydroxybenzylidene dimethyl imidazolinone), and (iii) thymine in water. © 2017 Wiley Periodicals, Inc.