Energy Minimization Calculations Research Articles

Modelling and simulations of adhesion between carbon nanotubes and surfaces

Recent experiments showed that there are very strong adhesion forces between nanotubes and surfaces. These forces are much stronger than the adhesion forces of gecko's foot hairs on substrates. Thus, nanotubes become candidates to be used in dry adhesives. Here, we present theoretical investigations on the adhesion between nanotubes and graphite surfaces. Molecular dynamics simulations and energy minimisation calculations were performed. Layer-by-layer deformations of the nanotube tips were observed. Parallel and perpendicular components of the forces were calculated for different contact angles of nanotubes. Adhesion forces are found to be maximised at 15° impact angles of nanotubes with respect to surface normal.

Computational simulations of the structure of Japan twin boundaries in quartz

The structures of Japan twin boundaries in quartz are studied through molecular dynamics simulations and energy minimization calculations. Four types of twinning are grouped under the Japan twin law, comprising 10 subtypes of geometrical configurations based on the structural handedness and composition plane. For each subtype, the twin displacement vector is determined and the structures of the twin boundaries with {11 22} or {TT22} composition plane are simulated. It is shown that six subtypes composed of two crystals with same-handed structure have the same type of SiO 4 tetrahedral linkage at twin boundaries. The twin boundary structures of these six subtypes can be further divided into two enantiomorphic structures composed of right- or left-handed quartz. The other four subtypes are composed of combinations of right- and left-handed quartz, and are structurally distinct from the same-handed group. The twin boundary energies of the same-handed group are lower than for the opposite-handed group. The Si-O bond lengths in the region of the twin boundary differ by no more than 0.05 A from those in the bulk quartz for all subtypes. The differences between the Si-O-Si angles at the twin boundaries and in the bulk exceed 20°, whereas the differences in O-Si-O angles are less than 10°. The present calculations demonstrate that SiO 4 tetrahedra at Japan twin boundaries are very stiff in comparison with inter-tetrahedral forces, consistent with previous reports for silica polymorphs, and that structural matching of twin individuals is primarily achieved through the rotation of SiO 4 tetrahedra.

Binding Mode Analysis of Bacillus subtilis Obg with Ribosomal Protein L13 through Computational Docking Study

Introduction: GTPases known as translation factor play a vital role as ribosomal subunit assembly chaperone. The bacterial Obg proteins (<TEX>$Spo{\underline{0B}}$</TEX>-associated <TEX>${\underline{G}}TP$</TEX>-binding protein) belong to the subfamily of P-loop GTPase proteins and now it is considered as one of the new target for antibacterial drug. The majority of bacterial Obgs have been commonly found to be associated with ribosome, implying that these proteins may play a fundamental role in ribosome assembly or maturation. In addition, one of the experimental evidences suggested that Bacillus subtilis Obg (BsObg) protein binds to the L13 ribosomal protein (BsL13) which is known to be one of the early assembly proteins of the 50S ribosomal subunit in Escherichia coli. In order to investigate binding mode between the BsObg and the BsL13, protein-protein docking simulation was carried out after generating 3D structure of the BsL13 structure using homology modeling method. Materials and Methods: Homology model structure of BsL13 was generated using the EcL13 crystal structure as a template. Protein-protein docking of BsObg protein with ribosomal protein BsL13 was performed by DOT, a macro-molecular docking software, in order to predict a reasonable binding mode. The solvated energy minimization calculation of the docked conformation was carried out to refine the structure. Results and Discussion: The possible binding conformation of BsL13 along with activated Obg fold in BsObg was predicted by computational docking study. The final structure is obtained from the solvated energy minimization. From the analysis, three important H-bond interactions between the Obg fold and the L13 were detected: Obg:Tyr27-L13:Glu32, Obg:Asn76-L13:Glu139, and Obg:Ala136-L13:Glu142. The interaction between the BsObg and BsL13 structures were also analyzed by electrostatic potential calculations to examine the interface surfaces. From the results, the key residues for hydrogen bonding and hydrophobic interaction between the two proteins were predicted. Conclusion and Prospects: In this study, we have focused on the binding mode of the BsObg protein with the ribosomal BsL13 protein. The interaction between the activated Obg and target protein was investigated with protein-protein docking calculations. The binding pattern can be further used as a base for structure-based drug design to find a novel antibacterial drug.

A study of the pressure-induced reversible amorphization of Xe containing-LTA zeolites by energy minimization technique

A previous computational study on dehydrated LTA zeolites [J. Gulín-González, G.B. Suffritti, Micropor. Mesopor. Mater . 69 (2004) 127] suggested the reversible amorphization of calcined LTA samples at pressures below 6 GPa, in agreement with the experimental results. However, the effect of guest molecules on the amorphization process was not evaluated in that study. In this paper, the potential reversible amorphization of Xe containing-LTA samples under high external pressures is studied via energy minimization calculations. The results of the simulations confirmed the pressure-induced amorphization of LTA zeolites at pressures about 2–4 GPa for all the studied samples. Besides, the simulations stressed the importance of the structural topology, particularly of D4R secondary units, for the recovering of the crystalline order. According to our calculations the exchangeable cations (Na + and Li +) play a crucial role in the process of amorphization. Our results suggest that the reversible amorphization is essentially independent on the presence of Xe molecules in the range of the pressures studied ( P ⩽ 6 GPa).

Development of Efficient Drug Analogs for Dutasteride through Insilico Modeling

Action of drug depends on the quantity of drug that reaches to the receptor and the degree of affinity between drug and receptor. Once drug bound to its receptor, it shows its desired effect (intrinsic activity) along with major and minor side-effects. More than 500 drugs with significant side-effects are available in market. In the present study the efforts have been made to identify new candidate compounds for dutasteride through modeled structure of two existing drug targets to improve efficacy by optimizing various parameters. Three dimensional structures of both drug targets of dutasteride were generated by MODELLER, validated by PROCHECK and ERRAT programs (90.04% of model-I and 84.647% of model-II). Energy minimization and molecular dynamics calculations were done through GROMACS using OPLS force field. RMSD calculated for both simulated model attain a constant deviation within 10,000 cycles. For analog generation, mono-substitution is preferred instead of multisubstitution. Objective and subjective both approaches were used for identification and calculation of chemical descriptors. A comparison of the calculated binding affinities for structurally similar inhibitors of dutasteride gave suitable analogs. Total 169 analogs were generated and eight are selected for comparative study. Our finding reveals that three dutasteride drug analogs (CH2NH2, -CH2OH, -CF2OH) were most suitable analogs, showing theoretically more superior results. These findings need to be further evaluations in laboratory.

The filling of flexible carbon nanotubes by molten salts

The direct filling of flexible single-walled carbon nanotubes by model molten salts are described. The simulations advance on previous work, in which the carbon nanotubes were treated as fixed atomistic entities, by considering the carbon nanotubes as fully-flexible. The molten salts are described using two potential models, which vary in the relative energetic stability of two key bulk crystal structures. Small diameter carbon nanotubes are found to favour relatively low symmetry “ladder” and “hinged” structures, which can both be considered as formed from sections of square net sheet, in contrast to cylindrical geometries favoured when filling fixed carbon tubes. The small diameter tubes are also found to favour structures based on folding square, rather than hexagonal, nets. Additional energy minimisation calculations are performed in order to understand both the formation of the less symmetric structures and the favouring of square net-based structures. The role of the flexible tubes in controlling the filling mechanisms and kinetics is discussed. Larger diameter carbon tubes are found to favour relatively disordered internal structures.

Strong physisorption site for H2 in K- and Li-doped porous carbons

Molecular hydrogen adsorption between two Li, K-doped coronene molecules (taken as local environment of carbon microporous materials) is studied by first-principles DFT-B3LYP calculations. These cluster calculations are complemented with periodic DFT-LDA/GGA calculations on extended Li- and K-doped structures. In all cases, energy minimization calculations unravel that there is a stable adsorption site for molecular hydrogen in these Li- and K-doped sp(2) carbon structures with large adsorption energies. This is the direct consequence of the significant charge transfer from the doping agents on neighboring slab carbon atoms, which allows the coupling of the molecular H(2) polarizability with the resulting substrate electric field (polarization interaction) that in turn induces the stabilization of molecular hydrogen. These calculations also give an insight on the atomic configurations of interlayer species (H(2) and LiK) as the interlayer spacing increases. It can be shown that large positional changes correlate with electronic properties of interlayer species. The confined hydrogen molecule does not show any tendency for dissociation and adopts a position in the interlayer void that is deeply related to that of doping ions.

A theoretical IR spectroscopic study based on DFT calculations for free mn-15S 2O 3 maleonitrile-dithiacrown ether compound

The theoretically possible stable conformers of free mn-15S 2O 3 maleonitrile-dithiacrown ether molecule were searched by means of a conformational study which consists of molecular dynamics and energy minimization calculations performed with MM2 force field and successive geometry optimization + frequency calculations performed first at B3LYP/3-21G and then at B3LYP/6-31G(d) levels of theory. The obtained calculation results have clearly indicated that the free molecule in electronic ground state is very flexible and accordingly has many possible stable conformers of different conformational properties at room temperature; among them, the one having a macrocyclic ring structure in which all of the ether units oriented toward the center of the ring was determined the energetically most preferable conformer. In addition, the equilibrium geometrical parameters, vibrational normal modes and associated IR spectral data of the determined most stable three conformers of the molecule were calculated at B3LYP/6-31+G(d) and B3LYP/6-31++G(d,p) levels of theory. A successful assignment of the fundamental bands observed in the recorded experimental solid phase and solution phase IR spectra of the molecule was achieved in the light of the theoretical data obtained from these DFT calculations. To fit the calculated harmonic wavenumbers to the experimental ones, two different scaling procedures, referred to as “Scaled Quantum Mechanical Force Field (SQM FF) methodology” and “Scaling wavenumbers with empirical dual scale factors”, were proceeded independently.

Orientation of H platelets under local stress in Si

Hydrogen is implanted into (001) silicon under the strain field of previously formed overpressurized helium plates. Upon thermal annealing, the hydrogen atoms precipitate into platelet structures oriented within specific {111} or {001} variant determined through the local symmetry of the strain. The behavior is understood in terms of elastic interactions and is described via energy minimization calculations, predicting the formation and distribution of each platelet orientation variant. Our results demonstrate the concept that sublocal organized arrangements of precipitates can be obtained within nanosize domains using local strain fields.

Involvement of the H3O+-Lys-164 -Gln-161-Glu-345 Charge Transfer Pathway in Proton Transport of Gastric H+,K+-ATPase

Gastric H(+),K(+)-ATPase is shown to transport 2 mol of H(+)/mol of ATP hydrolysis in isolated hog gastric vesicles. We studied whether the H(+) transport mechanism is due to charge transfer and/or transfer of hydronium ion (H(3)O(+)). From transport of [(18)O]H(2)O, 1.8 mol of water molecule/mol of ATP hydrolysis was found to be transported. We performed a molecular dynamics simulation of the three-dimensional structure model of the H(+),K(+)-ATPase alpha-subunit at E(1) conformation. It predicts the presence of a charge transfer pathway from hydronium ion in cytosolic medium to Glu-345 in cation binding site 2 (H(3)O(+)-Lys-164 -Gln-161-Glu-345). No charge transport pathway was formed in mutant Q161L, E345L, and E345D. Alternative pathways (H(3)O(+)-Gln-161-Glu-345) in mutant K164L and (H(3)O(+)-Arg-105-Gln-161-Gln-345) in mutant E345Q were formed. The H(+),K(+)-ATPase activity in these mutants reflected the presence and absence of charge transfer pathways. We also found charge transfer from sites 2 to 1 via a water wire and a charge transfer pathway (H(3)O(+)-Asn-794 -Glu-797). These results suggest that protons are charge-transferred from the cytosolic side to H(2)O in sites 2 and 1, the H(2)O comes from cytosolic medium, and H(3)O(+) in the sites are transported into lumen during the conformational transition from E(1)PtoE(2)P.

Arginine‐induced conformational change in the c‐ring/a‐subunit interface of ATP synthase

The rotational mechanism of ATP synthases requires a unique interface between the stator a subunit and the rotating c-ring to accommodate stability and smooth rotation simultaneously. The recently published c-ring crystal structure of the ATP synthase of Ilyobacter tartaricus represents the conformation in the absence of subunit a. However, in order to understand the dynamic structural processes during ion translocation, studies in the presence of subunit a are required. Here, by intersubunit Cys-Cys cross-linking, the relative topography of the interacting helical faces of subunits a and c from the I. tartaricus ATP synthase has been mapped. According to these data, the essential stator arginine (aR226) is located between the c-ring binding pocket and the cytoplasm. Furthermore, the spatially vicinal residues cT67C and cG68C in the isolated c-ring structure yielded largely asymmetric cross-linking products with aN230C of subunit a, suggesting a small, but significant conformational change of binding-site residues upon contact with subunit a. The conformational change was dependent on the positive charge of the stator arginine or the aR226H substitution. Energy-minimization calculations revealed possible modes for the interaction between the stator arginine and the c-ring. These biochemical results and structural restraints support a model in which the stator arginine operates as a pendulum, moving in and out of the binding pocket as the c-ring rotates along the interface with subunit a. This mechanism allows efficient interaction between subunit a and the c-ring and simultaneously allows almost frictionless movement against each other.

Cucurbit[7]uril host–guest complexes with small polar organic guests in aqueous solution

The host-guest stability constants for the inclusion of a series of small neutral polar organic guests in cucurbit[7]uril (CB[7]) have been determined in aqueous solution by (1)H NMR titrations. The dependence of the stability constant on the nature of the guests indicates that hydrophobic and dipole-quadrupole interactions are responsible for the binding. The complexation-induced chemical shift changes in the guest proton resonances, coupled with energy-minimization calculations, suggest that the guests are located such that their dipole moment is aligned perpendicular with the quadrupole moment of the CB[7] host. The stability constants for acetone and acetophenone decrease in the presence of Na(+) or K(+) cations as a result of cation capping of the CB[7] portals.

Sorption of different cations onto clay minerals: Modelling approach with ion exchange and surface complexation

The present article investigates the sorption of heavy metals, U(VI) and Eu(III), as an analog of An(III), on montmorillonite, illite and kaolinite suspensions in aqueous Na-electrolyte solutions by applying the Gibbs energy minimization computer code. Due to the complex nature of the sorption process, several simplifying assumptions should be made to solve the problem. The cation exchange capacity of clays, the density of the aluminol (>AlOH) and silanol (>SiOH) edge-type sites, responsible for the pH-dependent surface complexation, their acidity constants were derived from the reference data and fixed as non-adjustable parameters. The site-binding constants for all selected cations were calculated according to the direct correlations with their aqueous hydrolysis constants, and an exchange parameter K ex was accepted depending on the clay type, the valence of the exchanging cations and the solid to liquid ratio. The last parameters could be adjusted for goodness of fit in some cases. Relatively good correspondence between model sorption edges, distribution coefficients and those from experimental measurements was found; moreover, these observations are also consistent with the conceptual framework of the abundant reference data. The comparative model presented here is aimed to predict sorption uptake of cations over the whole spectrum of conditions in real systems having complex solid phase composition and water chemistries.

XRD characterization of texture and internal stress in electrodeposited copper films on Al substrates

Internal stresses and textures of electroplated copper films (t=2, 8, 15, 30, 45, and 60) electrodeposited on Al substrates were studied using X-ray diffraction techniques. Results show that the stresses in the films are tensile. The 8 to 60 μm thick films have (220) fiber texture, in good agreement with strain energy minimization calculation. Results also show that a further rotational alignment of the fiber-textured grains was developed, and small amounts of the fiber-textured grains have their (2, −2, 0) planes aligned parallel to the flow direction of the electrodeposited currents. The degree of the rotation alignment increases with film thickness. Values of stress and the degree of texture of copper films were found to be adjustable using an ultrasound technique. Internal stress and the degree of the (220) texture decrease significantly by applying an ultrasound treatment during the electrodeposition process.

Atomistic study of metal clusters supported on oxide surface

Metal clusters on oxide surface are a widely studied topic in surface science and technology. In this work, we use the ab initio based pair potentials to study the shape evolution of these clusters with their width from 3 Å to 90 Å. The clusters have a basic polyhedron shape covered by (0 0 1) and (1 1 1) faces, with four undetermined parameters. The main purpose of this work is to determine the structure parameters numerically. Here, we use a combination of energy minimization calculation, least square method and Lagrange multiplier method, and go through a series of metals including Ag, Al, Au, Pd and Rh. As a result, we find that these clusters have a truncated octahedron structure on MgO(0 0 1) surface, with a square contact face for Ag, Al and Au, and an octagon one for Pd and Rh. Also, we see that misfit dislocation appears when the cluster becomes large, first at the edge, then inside the contact area.

Effects of composition and phonon scattering mechanisms on thermal transport in MFI zeolite films

We report a systematic study that reveals the effect of composition (silicon-to-aluminum ratio) and the role of different phonon scattering processes on thermal transport in the nanoporous zeolite MFI. This is accomplished via synthesis of a series of films with graded compositions, thermal property measurements, and lattice dynamical modeling in the framework of the Boltzmann equation. MFI films with different Si/Al ratios (from infinity to 26) and constant (h0l) out-of-plane orientation were successfully synthesized by a seeded hydrothermal process. Three-omega measurements on these films allowed us to obtain comprehensive information on the thermal conductivity of MFI as a function of temperature (150–450 K) and Si/Al ratio. Detailed atomistic simulations (energy minimization and phonon dispersion calculations) were carried out for the MFI crystal structure with different Si/Al ratios and incorporated into a Boltzmann transport model along with approximate theoretical expressions for describing the rate of phonon scattering through umklapp, defect, and boundary scattering processes. The model predicts the observed thermal conductivity behavior very well across the entire range of temperature and composition investigated, with only a small number of fitting parameters of physical significance which allow us to distinguish the contributions of the different phonon scattering mechanisms. In particular, our results strongly suggest that the upper limit of thermal conductivity is defined by boundary-like scattering associated with the pore structure of the material. Below this limit, silicon substitution with aluminum allows considerable suppression of thermal conductivity by point defect scattering and a decrease in phonon velocity. These findings are important from the point of view of developing a robust platform for understanding thermal transport in complex crystalline materials with nanostructural features (such as an ordered nanopore network), which in turn serve as model systems for tuning of phonon transport properties in complex materials.

Application of FactSage thermodynamic modeling of recycled slags (Al2O3–CaO–FeO–Fe2O3–SiO2–PbO–ZnO) in the treatment of wastes from end-of-life-vehicles

Abstract The FactSage thermochemical software and databases calculates complex, multi-component, multi-phase equilibria involving simultaneously slag, metal, ceramic, and gas phases, over wide ranges of temperature, oxygen potential and pressure. The databases are automatically accessed by the software and the outputs of the Gibbs free energy minimization calculations can be presented in ways that are convenient to engineering practice, and as functions of key process variables. The new thermodynamic databases for slag and solid oxide phases in the Al2O3 – CaO – FeO – Fe2O3 – SiO2 – PbO – ZnO system have been developed by critical evaluation/optimization of all available phase equilibrium and thermodynamic data. By means of the optimization process, model parameters are found which reproduce all thermodynamic and phase equilibrium data within experimental error limits. Furthermore, the models permit extrapolation into regions of temperature and composition where data are not available. Phase equilibrium calculations have been undertaken, that are of interest in the thermal treatment of Automobile Shredder Residue (ASR) in the Al2O3 – CaO – FeO – Fe2O3 – SiO2 – PbO – ZnO system. This 7-component system represents only the major components of ASR. There are at least a dozen other important components in ASR not to mention the organic matter. The operating conditions deviate from thermodynamic equilibrium and the oxygen potential during the treatment of wastes is not well established. Consequently, the calculated diagrams are intended only to give an idea to industrial engineers about the trends in the liquidus temperature, extent of crystallization and partial pressures of volatile components as functions of temperature, composition and oxygen potential. These diagrams may also help to identify the process variables that are most important for industrial practice significantly reducing the amount of experimental work that has to be done to optimize the operations.

Homology modeling of yeast cyclin-dependent protein kinase

The important functions that CDKs perform in cell division and cell cycle regulation made central protein kinase of Saccharomyces cerevisiae CDC28 a target model for structural and functional analysis. The 3D models of CDC28 protein kinase using molecular modeling techniques will enlarge our understanding of the phosphorylation mechanism and the structural changes of mutant kinases. The structural template for S. cerevisiae CDC28 was identified from PDB (Protein Databank) using BLASTP (basic local alignment search tool for proteins). Template-target alignments were generated for homology modeling and checked manually for errors. The models were then generated using MODELLER and validated using PROCHECK followed by energy minimization and molecular dynamics calculations in AMBER force field.

Engineering aluminum binding affinity in an isolated EF-hand from troponin C: A computational site-directed mutagenesis study

Peptides with the ability to specifically bind aluminum would potentially be of great use in the fields of biochemistry and environmental chemistry. Unfortunately no such peptides are known. An aluminum-specific peptide may be used as an in vivo chelator, for metalloprotein design, for understanding metal-ion induced folding and metal-ion trafficking, and as an environmental sensor to monitor metal pollution in the environment. Plants genetically engineered to produce an aluminum binding peptide might be useful in environmental remediation in areas of high free aluminum ion concentration. In this paper, which is the theoretical complement to the experimental work, we analyzed crystallographic structures of EF-hands bound to various metals in order to determine the ligand distances and identities to compare to metal-ion size, charge, electronegativity, and coordination number and performed energy minimization calculations to identify possible mutations. We then constructed various mutant sequences in silico in an isolated EF-hand from troponin C and analyzed their binding behavior using molecular mechanics for binding to Tb 3+ as compared to Al 3+. As a result of these analyses we were able to isolate some characteristics that could lead to mutant peptides with enhanced aluminum activity that we plan to test experimentally in the future. We also performed metal-ion binding studies with the isolated EF-hand used in the computational work to examine the ability of Al 3+ and comparative metals to bind the peptide. In competition studies, the peptide demonstrated preference for Tb 3+ over Al 3+.

Excited state intramolecular proton transfer (ESIPT) in a dioxotetraamine derived schiff base and its complexation with Fe(III) and Cr(III)

The excited state intramolecular proton transfer (ESIPT) process in a symmetric Schiff base derived from dioxotetraamine and salicylaldehyde, N, N′-Bis{2-[(2-hydroxybenzylidine)amino]ethyl}malonamide (BHAEM) has been investigated experimentally by the fluorescent method and a two step proton transfer mechanism from dienol to ketoenol and then to diketo tautomer has been proposed on the basis of the theoretical evidence obtained through semi-empirical MO/CI calculations using the AM1 Hamiltonian. BHAEM on interaction with Fe(III) and Cr(III), in an aqueous medium of 0.1N ionic strength and 25 ± 1 °C forms monomeric metal complexes of the type ML and MLH −2 with both metal ions, whereas with Cr(III) it forms two more additional species, MLH and MLH −1. The stabilities of these metal complexes have been evaluated using potentiometric and spectrophotometric methods and the relative stabilities of the complexes formed with this ligand are rationalized. At low pH, the ligand coordinates to the metal ions through bis-imine nitrogen and bis-phenolate oxygen atoms but with an increase of pH, further coordination occurs through two amide nitrogen atoms of the ionized amide groups. The structures of the metal complexes were predicted from minimum strain energy calculations employing molecular mechanics using the MM3 force field and from their theoretical electronic spectra obtained through semi-empirical AM1/ZINDO method.