Terms Of Interaction Energies Research Articles

Molecular dynamics simulation of rupture in glassy polymer bridges within filler aggregates

We present a series of nonequilibrium molecular dynamics simulations, investigating the rupture mechanisms in glassy polymer films confined between two solid surfaces. Such systems provide a useful model for the strong nonlinear reinforcement of rubber by colloidal filler particles. Depending on the degree of confinement three qualitatively different rupture modes have been found, which originate from the interplay of internal (polymer-polymer) and external (polymer-wall) interactions. In very thin films we observe the formation and stretching of many single-chain bridges between the confining surfaces. Progressing to thicker samples we observe fewer bridges, consisting of bundled polymer chains, and eventually just one large bridge in thick specimens. The yield stress and the elongational modulus of the polymer films have been calculated from the stress-strain curves at various temperatures and confinements and their behavior has been analyzed in terms of polymer-polymer and polymer-surface interaction energies. The thinnest films (5 monomer diameters) are always glassy in our simulations, while the others display a glass transition temperature around 0.50-0.55 (in units ε(0)/k(B) of the Lennard-Jones interaction energy), depending on their thickness. This range of values, which has been determined using both the nonequilibrium tensile simulations and equilibrium diffusion data, agrees with the transition temperature previously found by shear simulations [Baljon and Robbins, Science 271, 482 (1996)].

Solubility Behavior of Lornoxicam in Binary Solvents of Pharmaceutical Interest

The solubility behavior of lornoxicam was studied in binary solvent systems. Solutions containing an excess of drug were shaken for 72 h at 25 °C, filtered and analyzed. To understand the solute–solvent interactions, ideal, Hildebrand–Scatchard and extended Hildebrand solubility approaches were used. The ideal solubility of lornoxicam was calculated from the enthalpy of fusion. The molar enthalpy of fusion was obtained from DSC studies. The experimental mole fraction solubility deviated from the ideal mole fraction solubility, indicating self-association of solute, or solvent, or both in solution. The solubility behavior failed to satisfy the Hildebrand–Scatchard equations. The solubilities of lornoxicam were back calculated with an interaction energy term ‘W’ and a rational activity coefficient term ‘(log10 γ 2)/A’. These parameters were regressed against a polynomial function of δ 1, the solubility parameter of the solvent mixture. The solubility behavior of lornoxicam obeyed the extended Hildebrand equation. The solubility parameter of lornoxicam δ 2 was found to be 27 MPa1/2.

Tuning the dipole-directed assembly of core-shell nickel-coated gold nanorods

We present the dipole-directed assembly of nickel-coated gold nanorods into nanorings and nanowires. We used two different coating methods to synthesise these core-shell superstructures. Surprisingly, the two coating methods lead to very different kinds of dipole directed assembly. We show that the resultant dipole assembly is very sensitive to the reaction conditions and can be tuned to obtain core-shell nanochains, nanorings, and nanowires. In addition to the presented experimental work, cluster moving Monte Carlo simulations of a system of core-shell nanorods were carried out. These simulations are based on a small number of magnetic interaction energy terms and do not explicitly deal with steric interactions or van der Waals forces. The simulation results are in line with the obtained experimental results, confirming that the magnetic self-assembly of core-shell nanorods can be described by means of a relatively simple model

A Comparison of Pair Potential for Some Polar and Non-Polar Mesogenic Molecules

Asymmetry of pair potential plays a crucial role in the formation of mesophases in molecular systems. Variation of such asymmetry is closely related to the constituents of the molecules as well as their positions. To investigate the asymmetry as well as its effect on molecular behavior, a few polar biphenyl and non-polar 2,5 disubstituted pyridine derivatives have been chosen. The intermolecular interaction energy between a pair of molecules has been calculated with the help of a standard method as prescribed by Claverie (Claverie, P. (1978). Elaborations of approximate formulas for interactions between large molecules: Applications in organic chemistry. In: B. Pullman (Eds.), Inter Molecular Interactions from Diatomic to Biopolymers, J. Wiley & Sons Ltd.: Hoboken, NJ, 217–226.). Molecular geometry of all the selected systems was fully optimized without any constraint, and the net atomic charge and the dipole moment on each atomic center was calculated using the Gaussian03 program with density functional B3LYP method using 6-31G** as the basis set. The dispersion and the short range repulsion energy terms have been calculated using semiempirical Kitaigorodskii's “6-exp” formula. An attempt has been made to explain the phase sequences on the basis of the ratios of various interaction energy terms. Supplemental materials are available for this article. Go to the publisher's online edition of Molecular Crystals and Liquid Crystals to view the free supplemental file.

Purification of Artemisinin from Artemisia annua Extract by Sorption on Different Ligand Loaded Polymeric Adsorbents Designed by Molecular Simulation

A reactive sorption method has been devised for the purification of artemisinin from Artemisia annua extract using a polymeric adsorbent loaded with specific ligands. These ligands were designed by molecular simulation to selectively adsorb artemisinin. The specific interactions of artemisinin with different polymeric adsorbents in organic solvents of varying polarity were further quantified in terms of interaction energy, atomic charges, and vibrational spectral analysis. Solvation studies indicate use of methanol for adsorption while ethyl acetate for desorption of artemisinin. Batch equilibrium and dynamic adsorption-desorption studies were conducted to establish optimum parameters for the purification process. A weakly basic polymeric adsorbent with tertiary amino groups was chosen for artemisinic acid. After adsorption the final purity of artemisinin increases up to 90%.

Comparative Binding Energy (COMBINE) Analysis Supports a Proposal for the Binding Mode of Epothilones to β‐Tubulin

The conformational preferences of epothilone A (EPA) and a 12,13-cyclopropyl C12-epimerized analogue were explored in aqueous solution using molecular dynamics simulations. The simulated conformers that provided an optimal fit in the paclitaxel binding site of mammalian β-tubulin were then selected. The resulting modeled complexes were simulated before and after refinement of the M-loop to improve the fitting and assess ligand stability within the binding pocket. The tubulin-bound conformation of EPA was found to be unlike a previously reported solution obtained through mixed crystallographic/NMR/modeling studies. However, our conformation was in agreement with an NMR-based proposal although the exact binding pose within the site was different. Molecular models were built for the complexes of 14 epothilone derivatives with β-tubulin. A projection to latent structures regression method succeeded in providing a good prediction of the experimentally measured binding enthalpies for the whole set of ligands by assigning weights to a selection of interaction energy terms. These receptor-based, quantitative structure-activity relationships support the proposed binding mode, help confirm and interpret previously acquired experimental data, shed additional light on the effect of several β-tubulin mutations on ligand binding, and can potentially direct further experimental studies.

Pt L2,3 - Edge X-ray absorption spectroscopy investigation of zerovalent [Pt(PPh3)2(η2-L)] {L = C2H4, C60 and C2(CN)4} compounds

X-ray absorption spectra at the Pt L2,3-edges have been measured for three [Pt(PPh3)2(η2-L)] {L = C2H4, C60 and C2(CN)4} compounds. The spectral features are effective for measuring the π*-acid strength of ligands (L) coordinated to the Pt(PPh3)2 fragment. The energies of the dπ-orbitals are quantitatively determined using the difference between the edge jumping and the edge maximum shifts of the L2,3-white lines in the second derivatives of the spectra. The dπ-orbital energies follow the order [Pt(PPh3)2(η2-C2H4)] < [Pt(PPh3)2(η2-C60)] < [Pt(PPh3)2{η2-C2(CN)4}]. These dπ-orbital energies are in good agreement with the changes in the bound olefinic carbon bond lengths and the 31P NMR chemical shifts of the coordinated phosphines. Furthermore, the experimental values are in good agreement with available dπ-orbital interaction energy terms calculated using density functional theory for model [Pt(PH3)2(η2-L)] compounds.

In silico screening of indinavir-based compounds targeting proteolytic activity in HIV PR: binding pocket fit approach

The intense research on small molecule inhibitors of Human immunodeficiency virus (HIV)-protease (PR) has produced a diverse class of chemical scaffolds which includes clinically available HIV PR inhibitors (PRI). Till now, these inhibitors are insignificant for targeting proteolytic activity and few drug molecules on alterations can enhance the inhibition of PR enzyme. Here, we developed a method for screening of new hits from Cambridge structural database, based on binding mode of indinavir interaction participating atoms. Knowledge-based ligand screening technique approximately informs that new hits are also having same binding mode-like indinavir interaction patterns. Considering the importance of ligand fitting in binding pocket, we developed induced-fit models for each compound and we obtained accurate energy values in terms of binding and interaction energy. We found that newly search molecules are interacting better than known drug—indinavir and these new compounds are comparatively having better drug-like property. Finally, we demonstrated that pocket specific docking, energy utilization, interactions, and ADME for screened compounds are showing new hit compounds of indinavir are better HIV PRI and these new compounds can also show better activity in in vivo and in vitro conditions.

A statistical mechanical approach to protein aggregation

We develop a theory of aggregation using statistical mechanical methods. An example of a complicated aggregation system with several levels of structures is peptide/protein self-assembly. The problem of protein aggregation is important for the understanding and treatment of neurodegenerative diseases and also for the development of bio-macromolecules as new materials. We write the effective Hamiltonian in terms of interaction energies between protein monomers, protein and solvent, as well as between protein filaments. The grand partition function can be expressed in terms of a Zimm-Bragg-like transfer matrix, which is calculated exactly and all thermodynamic properties can be obtained. We start with two-state and three-state descriptions of protein monomers using Potts models that can be generalized to include q-states, for which the exactly solvable feature of the model remains. We focus on n × N lattice systems, corresponding to the ordered structures observed in some real fibrils. We have obtained results on nucleation processes and phase diagrams, in which a protein property such as the sheet content of aggregates is expressed as a function of the number of proteins on the lattice and inter-protein or interfacial interaction energies. We have applied our methods to Aβ(1-40) and Curli fibrils and obtained results in good agreement with experiments.

Molecular Dynamics Simulation of Au-TiO&lt;sub&gt;2&lt;/sub&gt; Catalysts: Deposition of Gold Nanoclusters on Rutile (110) Surface

In this work, molecular dynamics simulation was used to investigate the deposition process of a gold nanocluster on rutile TiO2(110) surface. The effects of surface defects (i.e., point, step, and groove) were examined in terms of interaction energy, morphology and structure. It was found that the gold nanocluster can be strongly attracted to rutile TiO2(110) surface. Moreover, a higher degree of defect results in a stronger attractive interaction between gold nanocluster and TiO2(110) surface. The simulated results also indicated that the stability of gold nanoclusters can be effectively controlled by adding citrate ions, which could lead to a high catalytic activity of gold/metal oxide catalysts.

Reassessment of Hammett σ as an effective parameter representing intermolecular interaction energy—links between traditional and modern QSAR approaches

The Hammett σ constant has for a long time been known to be one of most important linear free-energy related parameters that correlate with biological activity. It is a conventionally used electronic parameter in studies of enzymatic quantitative structure-activity relationships (QSAR). However, it is not necessarily obvious why σ represents variations in the free-energy change associated with the complex formation between a congeneric series of ligands with their target protein. So far, several powerful molecular calculations, such as the ab initio fragment molecular orbital (FMO) one, that are directly applicable to ligand-protein complexes have emerged. In this study, we comprehensively reevaluate experimentally derived parameter σ confirming it represents intermolecular interaction energy terms, by applying molecular orbital (MO) calculations to a simple ligand-protein complex model. The current results provide a rational and quantitative basis for bridging the gap between the traditional QSAR approach and 'the modern QSAR one', which involves the molecular calculations to evaluate the overall free-energy change for complex formation.

Erratum: Mixed quantum-classical dynamics of an amide-I vibrational excitation in a proteinα-helix [Phys. Rev. B82, 174308 (2010)

In the GROMACS code modifications, instead of the nanometer unit for the distance that is standard in GROMACS, a unit of 1 A was previously assumed. This led to dipole-dipole interactions between amide I vibrations at different sites and the interaction energies of the amide I vibration with the protein hydrogen bonds being overestimated, respectively, by three orders and by one order of magnitude. In addition, the quantum mechanical force terms were overestimated because, through the same error, the sites defined as hydrogen-bonded in the protein were not properly identified. Because the influence of the quantum vibration on the conformation of the polypeptide is less pronouncedwhen these errors are corrected, the simulation times are increased to 10 ps. Moreover, each of the 20 simulation runs, obtained by varying the seed of the random number generator for the initial velocities, was repeated ten times in order to sample different quantumMonte Carlo paths and to yield better statistical estimates. Thus, the results presented here, for each value of χ , represent averages over 200 simulation trajectories. Two other changes are made in the current modified GROMACS code. The first of these makes sure that the interaction energy term varies continuously with the length of the hydrogen bond, even when the hydrogen bond breaks. This term is calculated as

Antigen–antibody interactions of influenza virus hemagglutinin revealed by the fragment molecular orbital calculation

Effective interactions between amino acid residues in antigen–antibody complex of influenza virus hemagglutinin (HA) protein can be evaluated in terms of the inter-fragment interaction energy (IFIE) analysis with the fragment molecular orbital (FMO) method, in which each fragment contains the side chain of corresponding amino acid residue. We have carried out the FMO-MP2 (second-order Moeller–Plesset) calculation for the complex of HA antigen and Fab antibody of influenza virus H3N2 A/Aichi/2/68 and obtained the IFIE values between each amino acid residue in HA and the whole antibody as the sums over the residues contained in the latter. Combining this IFIE data with experimental data for hemadsorption activity of HA mutants, we succeeded in theoretically explaining the mutations in HA observed after the emergence of influenza virus H3N2 A/Aichi/2/68 in an earlier study, except for those of THR83. In the present study, we employ an alternative way of fragment division in the FMO calculation at the carbonyl C site of the peptide bond instead of the Cα site used in the previous work, which provides revised IFIE values consistent with all the historical mutation data in the antigenic region E of HA including the case of THR83 in the present prediction scheme for probable mutations in HA.

Large Changes of Static Electric Properties Induced by Hydrogen Bonding: An ab Initio Study of Linear HCN Oligomers

We report the partitioning of the interaction-induced static electronic dipole (hyper)polarizabilities for linear hydrogen cyanide complexes into contributions arising from various interaction energy terms. We analyzed the nonadditivities of the studied properties and used these data to predict the electric properties of an infinite chain. The interaction-induced static electric dipole properties and their nonadditivities were analyzed using an approach based on numerical differentiation of the interaction energy components estimated in an external electric field. These were obtained using the hybrid variational-perturbational interaction energy decomposition scheme, augmented with coupled-cluster calculations, with singles, doubles, and noniterative triples. Our results indicate that the interaction-induced dipole moments and polarizabilities are primarily electrostatic in nature; however, the composition of the interaction hyperpolarizabilities is much more complex. The overlap effects substantially quench the contributions due to electrostatic interactions, and therefore, the major components are due to the induction and exchange-induction terms, as well as the intramolecular electron-correlation corrections. A particularly intriguing observation is that the interaction first hyperpolarizability in the studied systems not only is much larger than the corresponding sum of monomer properties, but also has the opposite sign. We show that this effect can be viewed as a direct consequence of hydrogen-bonding interactions that lead to a decrease of the hyperpolarizability of the proton acceptor and an increase of the hyperpolarizability of the proton donor. In the case of the first hyperpolarizability, we also observed the largest nonadditivity of interaction properties (nearly 17%) which further enhances the effects of pairwise interactions.

Two models of Smad4 and Hoxa9 Complex are Proposed: Structural and Interactional Perspective

Transforming growth factor-beta superfamily growth factors (TGF-β) regulate a diverse range of cellular functions, including proliferation, differentiation, extracellular matrix secretion and cell adhesion. TGF-β is also one of the most abundant of the known growth factors. Osteopontin (OPN), the major non-collagenous bone matrix protein is a secreted, arginine-glycine-aspertate containing phosphorylated glycoprotein. Analysis of the OPN promoter sequence reveals both Hoxc8 and Hoxa9 (mouse homeotic gene) recognize and utilize the same consensus TAAT motif in the binding sequence to mediate the repression. Hoxa9 functions as a strong transcriptional repressor, similar to Hoxc-8 (X. Shi, X. Yang, D. Chen, Z. Chang, and X. Cao, J Biol Chem 274, 13711-13717, 1999). The DNA-binding protein Hoxa9 interacts with Smad4 (X. Shi, S. Bai, L. Li and X, and Cao X, J Biol Chem 276, 850-855, 2001), but not with Smad3 (which binds to OPN promoter), and the interaction between Smad4 and Hoxa9 results in the transcriptional activation of OPN in response to TGF- stimulation. In this paper we have proposed two possible model structures of Hoxa9 and Smad4 complex. These have been modeled based on homology modeling and a new method has been used to model the flexible loop part. Manual docking has been used to achieve the final model involving the Hoxa9 -Smad4 complex which tallies with the experimental results. We have mutated some selective important residues and looked at their effect in terms of interaction energy in complex formation in both the models.

Theoretical Study of Hydration Effects on the Selectivity of 18-Crown-6 Between K + and Na +

A combination of molecular dynamics (MD) and density functional theory (DFT) calculations were used to study the hydration structures of K + and Na + ions under the confinement of 18-crown-6 in order to identify the role of water in the selectivity of 18-crown-6 towards K +. The radial distribution functions, coordination numbers, orientation structures and interaction energies were analyzed to investigate the hydration of K + and Na + in 18-crown-6/cation complexes. All calculations of K + and Na + in bulk water were also conducted for comparison. The simulation results show that the orientation distributions of the water molecules in the first coordination shell of K + are more sensitive to the confinement of 18-crown-6 than those of Na +. It is more favorable to confine a K + in 18-crown-6 than a Na + in terms of interaction energy. Good agreement is obtained between MD results and DFT results.

DFT interpretation of 1,3-dipolar cycloaddition reaction of C,N-diphenyl nitrone to methyl crotonate in terms of reactivity indices, interaction energy and activation parameters

The cycloaddition reaction between C,N-diphenyl nitrone and an unsymmetrically disubstituted olefin, methyl crotonate has been studied in terms of several theoretical approaches at DFT/B3LYP/6-31G(d) level of theory. The electronic populations have been computed from natural orbital based charges using natural population analysis and electrostatic potential driven atomic charges using Merz–Kollman and Chirlian–Francl algorithm. The regioselectivity has been predicted on the basis of DFT based reactivity indices. Calculations of the interaction energy have been performed during the study. The interaction energy is partitioned in two terms; one resulting from the chemical potential equalization principle at constant external potential and the other step (the reshuffling of charge distribution) resulting from the maximum hardness principle at constant chemical potential. The transition states corresponding to the feasible stereoisomeric pathways along the regioisomeric reaction channels have been successfully located. Trends in the selectivities are predicted in terms of energy, enthalpy and free energy changes. An analysis of Pauling’s bond order, Wiberg bond index and atom–atom overlap-weighted NAO bond order values has been done to get a balanced measure of the extent of bond formation or bond breaking. The cycloaddition is favored along the meta reaction channel affording the endo adduct as the major diastereoisomer in agreement with the experimental results.

A closed form for the electrostatic interaction between two rod-like charged objects

We have calculated the electrostatic interaction between two rod-like charged objects with arbitraryorientations in three dimensions. We obtained a closed-form formula expressing the interactionenergy in terms of the separation distance between the centers of the two rod-like objects,r, their lengths(denoted by 2l1 and 2l2) and their relative orientations (indicated byθ andϕ). When the objectshave the same length (2l1 = 2l2 = l), for particular values of separations, i.e. forr ≤ 0.8l, two types of minimum appear in the interaction energy with respect toθ. By employing the closed-form formula and introducing a scaled temperaturet, we have also studied the thermodynamic properties of a 1D system of rod-like chargedobjects. For different separation distances, the dependence of the specific heatof the system to the scaled temperature has been studied. It is found that, forr < 0.8l, the specific heat has a maximum.

Adsorbate–substrate interaction between chlorodifluoromethane and titanium dioxide: Infrared spectroscopy and density functional theory studies

Infrared spectra of chlorodifluoromethane (CHClF 2) adsorbed on titanium dioxide (TiO 2) at room temperature have been investigated for the first time. From the comparison between the adsorption characteristics and the gas-phase spectra it can be deduced that the molecule interacts with the surface Lewis acid site (Ti 4+) mainly through the Cl atom even if also the adsorption with one F atom is also observed. Moreover, the spectra show the presence of H-bonds between the CH group and the surface Lewis basic site (OH − or O 2−). In order to obtain more information on the molecule orientation and the variation of the structural parameters, a DFT-B3LYP study has been carried out considering the anatase (1 0 1) surface and evaluating the adsorption energetics in terms of interaction, distortion and binding energies. The obtained geometries confirm that both the acid–base interactions through Cl or F atoms are possible and suggest the formation of one H-bond between the CH group of the molecule and the Lewis basic site of the surface. The calculated vibrational frequencies of the adsorbed molecule have been found to be in reasonable agreement with the experimental data.

A molecule on the surface or inside a spherical nanoparticle: the computation of the interaction energy in terms of the dielectric continuum model

The electrostatic interaction energy between a charged or polar molecule and a spherical polarizable nanoparticle is studied within the advanced dielectric continuum model proposed previously. The molecule can be located either inside or outside the nanoparticle or in the vicinity of its boundary surface. The nanoparticle and its environment are considered as a polarizable medium and described in terms of a nonuniform dielectric continuum approximation with a position-dependent dielectric permittivity function $$ \varepsilon (r) $$ , where r is the position vector. A special construction of this function accounts for the proper treatment of sophisticated boundary effects. Test computations are performed for a number of sample molecules.