MD Calculations Research Articles

Adsorption behavior and mechanism of acidic blue 25 dye onto cucurbit[8]uril: A spectral and DFT study

The acidic blue 25 (AB25) dye was efficiently adsorbed by CB [8]; the saturated adsorption capacity (qexp) reached 434.8mg/g and was far higher than those of previous reported adsorbents. The Langmuir and Freundich isotherms were used to fit the equilibrium data, and the results showed that the Freundlich isotherm seemed to agree better with the AB25 adsorption. The adsorption kinetics followed the pseudo-second-order model. Calculated thermodynamic parameters showed that the adsorption of AB25 onto CB [8] was a spontaneous and enthalpy-driven process. The adsorption mechanism was explored by N2 adsorption-desorption, TG, FT-IR, UV–vis as well as MD simulation and DFT calculations. TG analysis revealed that a new inclusion complex was produced, and FT-IR,UV–vis spectrum and DFT calculations verify its structure. In this inclusion complex, the AB25 dye molecule inserted into cavities of CB [8] from portal, and the sulfonate and phenyl groups stayed in the hydrophobic cavity. TDDFT calculations indicated that all excitation arisen from π→π* transition.

Spectroscopic Observation and Molecular Dynamics Simulation of Ga Surface Segregation in Liquid Pd-Ga Alloys.

Liquid binary Pd-Ga alloys with low Pd contents of 0.8, 1.8, and 4.7 at % of Pd were examined as a function of sample temperature in ultra-high vacuum by using angle-resolved XPS. Upon cooling from 750 to 400 K, a pronounced temperature-dependence of the Pd concentration in the liquid phase was observed, which was explained by the transition from the pure liquid phase to a two-phase system, consisting of a solid Ga5 Pd phase and a Pd-depleted liquid Pd-Ga alloy. In the liquid Pd-Ga alloy, Pd is always depleted from the topmost interface layer, as deduced from angle-resolved XPS at 0 and 80° emission, independent of temperature and Pd concentration. This observation is interpreted as an inhomogeneous depth distribution function of Pd, that is, the segregation of Ga to the surface of the liquid phase. The results of a DFT-based molecular dynamics simulation (MD) independently show interfacial stratification of Ga and an inhomogeneous Pd distribution along the surface normal. The evaluation of the experimental data with a rigid layer model based on the MD calculations leads to excellent agreement with the simulation.

Influence of Frozen Residues on the Exploration of the PES of Enzyme Reaction Mechanisms.

In this work, we studied one of the very widely used approximations in the prediction of an enzyme reaction mechanism with computational methods, that is, fixing residues outside a given radius surrounding the active site. This avoids the unfolding of truncated models during MD calculations, avoids the expansion of the active site in cluster model calculations (albeit here only specific atoms are frozen), and prevents drifting between local minima when adiabatic mapping with large QM/MM models is used. To test this, we have used the first step of the reaction catalyzed by HIV-1 protease, as the detrimental effects of this approximation are expected to be large here. We calculated the PES with shells of frozen residues of different radii. Models with free regions under a 6.00 Å radius showed signs of being overconstrained. The QM/MM energy barrier for the remaining models was only slightly sensitive to this approximation (average of 0.8 kcal·mol-1, maximum of 1.6 kcal·mol-1). The influence over the energy of reaction was almost negligible. This widely used approximation seems safe and robust. The resulting error is on average below 1.6 kcal·mol-1, which is small when compared with others deriving from, for example, the choice of the density functional or semiempirical MO/SCC-DFTB method, the basis set used, or even the lack of sampling or incomplete sampling.

Molecular motion regulates the activity of the Mitochondrial Serine Protease HtrA2

HtrA2 (high-temperature requirement 2) is a human mitochondrial protease that has a role in apoptosis and Parkinson’s disease. The structure of HtrA2 with an intact catalytic triad was determined, revealing a conformational change in the active site loops, involving mainly the regulatory LD loop, which resulted in burial of the catalytic serine relative to the previously reported structure of the proteolytically inactive mutant. Mutations in the loops surrounding the active site that significantly restricted their mobility, reduced proteolytic activity both in vitro and in cells, suggesting that regulation of HtrA2 activity cannot be explained by a simple transition to an activated conformational state with enhanced active site accessibility. Manipulation of solvent viscosity highlighted an unusual bi-phasic behavior of the enzymatic activity, which together with MD calculations supports the importance of motion in the regulation of the activity of HtrA2. HtrA2 is an unusually thermostable enzyme (TM=97.3 °C), a trait often associated with structural rigidity, not dynamic motion. We suggest that this thermostability functions to provide a stable scaffold for the observed loop motions, allowing them a relatively free conformational search within a rather restricted volume.

Less-Common Nanostructures: Nanobuds: A Micro-Review.

Synthesis, properties, structural peculiarities, and applications of nanobuds and related nanostructures are discussed. In addition, few relevant patents to the topic have been reviewed and cited. According to observed properties and those predicted by DFT calculations, the nanobuds are semiconducting and stable in normal conditions, can accept adatoms and molecules. They contain a relatively chemically inert carbon nanotubes and more active fullerene species and can be compatible with a variety of other materials, in particular polymers. In addition to nanobuds for SWCNTs, the nanobuds with graphene, small fullerenes or metal nanobud-like structures are also known. We have undertaken an extensive search of bibliographic databases for peer-reviewed research literature using a focused review question and inclusion/exclusion criteria. The characteristics of screened papers were described and critically compared. Thirty-six papers were included in the review, mainly from high-impact international journals. The published articles correspond to the range 2006-2016; the term "nanobuds" appeared in 2006 after their discovery. The reports included approaches of the synthesis of carbon nanobuds, their formation mechanism, in situ engineering, different modes of attachment of fullerene on carbon nanotubes, DFT and MD calculations, nanobuds containing small fullerenes and graphene nanobuds, information about related noble metal nanobuds, and applications of carbon nanobuds. The findings of this review confirm the importance of novel less-common nanostructures on the basis of carbon for fundamental science, their unusual properties and current and possible applications.

Corrosion inhibition performance of chromone-3-acrylic acid derivatives for low alloy steel with theoretical modeling and experimental aspects

Chromone-3-acrylic acid (CA) and its derivatives viz. 6-hydroxy chromone-3-acrylic acid (6-OH-CA) and 7-methoxy chromone-3-acrylic acid (7-Me-CA) were synthesized and studied for inhibition of Low Alloy Steel corrosion in 1M H2SO4 at different concentration and temperature using Gravimetric, Polarization technique, EIS, AFM, DFT and MD calculations. Mass loss, Potentiodynamic Polarization and EIS results showed that inhibition efficiency increased with gradual increments in concentration of CA compounds. Polarization study revealed that these compounds act as mixed type inhibitors and Langmuir adsorption isotherm is fitted well for adsorption. The order of inhibition efficiency is 7-Me-CA (88.00%)>CA (96.37%)>6-OH-CA (96.77%). A proposed inhibition mechanism has further been described including the support from all the experimental as well as theoretical techniques.

Molecular Dynamics Investigation of Interaction of Hydrogen Impurity with Twist Boundaries in Ni and Pd

Using MD computer simulations, the interaction of hydrogen impurity with the (100) and (111) twist boundaries in Ni and Pd is investigated. It is shown that twist boundaries can act as hydrogen traps, though less efficient compared to vacancies and edge dislocations. According to the data obtained, the energy of hydrogen bonding with the twist boundaries is not higher than 0.1 eV for both metals under study.

MD and BCA simulations of He and H bombardment of fuzz in bcc elements

We present results of MD simulations of low energy He ion bombardment of low density fuzz in bcc elements. He ions can penetrate several micrometers into sparse fuzz, which allows for a sufficient He flux through it to grow the fuzz further. He kinetic energy falls off exponentially with penetration depth. A BCA code was used to carry out the same ion bombardment on the same fuzz structures as in MD simulations, but with simpler, 10 million times faster calculations. Despite the poor theoretical basis of the BCA at low ion energies, and the use of somewhat different potentials in MD and BCA calculations, the ion penetration depths predicted by BCA are only ∼12% less than those predicted by MD. The MD-BCA differences are highly systematic and trends in the results of the two methods are very similar. We have carried out more than 200 BCA calculation runs of ion bombardment of fuzz, in which parameters in the ion bombardment process were varied. For most parameters, the results show that the ion bombardment process is quite generic. The ion species (He or H), ion mass, fuzz element (W, Ta, Mo, Fe) and fuzz element lattice parameter turned out to have a modest influence on ion penetration depths at most. An off-normal angle of incidence strongly reduces the ion penetration depth. Increasing the ion energy increases the ion penetration, but the rate by which ion energy drops off at high ion energies follows the same exponential pattern as at lower energies.

Molecular dynamics, thermodynamic, and mutational binding studies for tumor-specific LyP-1 in complex with p32

Recent studies in tumor homing peptides have shown the specificity of LyP-1 (CGNKRTRGC) to tumor lymphatics. In this present work, we evaluated the possible interactions between cyclic LyP-1 and its receptor, p32, with molecular dynamics and docking studies in order to lead the design of novel LyP-1 derivatives, which could bind to p32 more effectively and perform enhanced antitumor effect. The total binding enthalpy energies have been obtained by MM-PBSA thermodynamic computations and the favorability of p32.LyP-1 complex in water has been shown by explicit water MD computations. The last 30 ns of molecular dynamics trajectory have shown the strong interaction of LyP-1 with the inner surface chains of p32, especially with chains B and C. ALA-SCAN mutagenesis studies have indicated the considerable influence of Asn3, Lys4, Arg5, and Arg7 amino acid residues on the specific binding of LyP-1. Within the knowledge of the critical role of p32 receptor in cancer cell metabolism, this study can lead to further developments in anticancer therapy by targeting p32 with LyP-1 derivatives as active targeting moiety. This data can also be applied for the development of new drug delivery systems in which LyP-1 can be used for its targeting and anticancer properties.

Molecular Dynamics Simulation of a RNA Aptasensor.

Single-stranded RNA aptamers have emerged as novel biosensor tools. However, the immobilization procedure of the aptamer onto a surface generally induces a loss of affinity. To understand this molecular process, we conducted a complete simulation study for the Flavin mononucleotide aptamer for which experimental data are available. Several molecular dynamics simulations (MD) of the Flavin in complex with its RNA aptamer were conducted in solution, linked with six thymidines (T6) and, finally, immobilized on an hexanol-thiol-functionalized gold surface. First, we demonstrated that our MD computations were able to reproduce the experimental solution structure and to provide a meaningful estimation of the Flavin free energy of binding. We also demonstrated that the T6 linkage, by itself, does not generate a perturbation of the Flavin recognition process. From the simulation of the complete biosensor system, we observed that the aptamer stays oriented parallel to the surface at a distance around 36 Å avoiding, this way, interaction with the surface. We evidenced a structural reorganization of the Flavin aptamer binding mode related to the loss of affinity and induced by an anisotropic distribution of sodium cationic densities. This means that ionic diffusion is different between the surface and the aptamer than above this last one. We suggest that these findings might be extrapolated to other nucleic acids systems for the future design of biosensors with higher efficiency and selectivity.

スペクトル解析法による固体有機結晶の振動スペクトル計算法

We performed MD calculations on chloroform and 1,3,5-triamino-2,4,6-trinitrobebzene (TATB) and further frequency analysis under high pressure. Peaks around 3000 cm−1 of chloroform uniformly blue shifted, but ones around 3000 cm−1 of TATB were red shifted. It was concluded that whether hydrogen bonds are formed or not greatly influences the shift of the peaks of the two stretching vibrations.

Largeinformation Issues in Computational Chemistry

Advanced information have turned into a deluge immersing each zone of business, science and building disciplines. In the time of Big Data, getting qualities and bits of knowledge from a lot of information utilizing rich examination turns into a vital separating ability for intensity, achievement and administration in each field. Researchers and specialists of various areas are progressively clamoring for components to oversee and break down the enormous amounts of data now accessible keeping in mind the end goal to get new answers and concentrate from it greatest esteem. Computational displaying and reenactment is the focal innovation to several of these spaces. Subatomic Dynamics (MD) is a computational reproduction system that portrays the physical powers and developments of interfacing minute components such IoT's and particles. MD has essential applications in the fields of science, biotechnology, pharmaceutical industry, vitality, atmosphere or materials science, among others. Propelled MD calculations incorporate Molecular Mechanics (MM), as well as Quantum Mechanics (QM) approaches, raising essential huge information challenges still to be dealt with. MD reproductions play out an iterative procedure producing a lot of information in spilling. Current programming innovation is a long way from having the capacity to oversee, dissect and envision the to a great degree substantial and complex informational indexes created by critical sub-atomic procedures. This paper investigates the current enormous information constrains in the Computational Chemistry field, particularly in the MD forms. To beat these testing circumstances, this work give direction to future research incorporating propels in adaptable calculations for information investigation, dynamic inquiry innovation, information models and capacity techniques, parallel executions, I/O improvement, and intelligent visual investigation what's more, investigation of MD information.

Nucleation and the spall strength of liquid metals

This article presents calculation of the nucleation rate for liquid metals (Al, Fe, Mo) based on molecular dynamic simulation for embedded atom method (EAM) potentials. The dependence of nucleation rate on pressure and temperature could be approximated accurately in the form of classical nucleation theory taking into account surface tension dependency on pore radius σ = σ0/(1 + 2δ/r), where σ—surface tension, δ—the Tolman length. Basing on the results of the calculations, we have developed a model allowing calculating the spall strength of liquid metals under tension using such parameters as surface tension, viscosity, which could be measured experimentally. The obtained results for Mo and Al are consistent with experimental data and direct MD calculations at strain rates approx. 1010-1011 s-1.

A method of solid–solid phase equilibrium calculation by molecular dynamics

A method for evaluation of solid–solid phase equilibrium curves in molecular dynamics simulation for a given model of interatomic interaction is proposed. The method allows to calculate entropies of crystal phases and provides an accuracy comparable with that of the thermodynamic integration method by Frenkel and Ladd while it is much simpler in realization and less intense computationally. The accuracy of the proposed method was demonstrated in MD calculations of entropies for EAM potential for iron and for MEAM potential for beryllium. The bcc–hcp equilibrium curves for iron calculated for the EAM potential by the thermodynamic integration method and by the proposed one agree quite well.

NMR Structure of a Triangulenium‐Based Long‐Lived Fluorescence Probe Bound to a G‐Quadruplex

AbstractAn NMR structural study of the interaction between a small‐molecule optical probe (DAOTA‐M2) and a G‐quadruplex from the promoter region of the c‐myc oncogene revealed that they interact at 1:2 binding stoichiometry. NMR‐restrained structural calculations show that binding of DAOTA‐M2 occurs mainly through π–π stacking between the polyaromatic core of the ligand and guanine residues of the outer G‐quartets. Interestingly, the binding affinities of DAOTA‐M2 differ by a factor of two for the outer G‐quartets of the unimolecular parallel G‐quadruplex under study. Unrestrained MD calculations indicate that DAOTA‐M2 displays significant dynamic behavior when stacked on a G‐quartet plane. These studies provide molecular guidelines for the design of triangulenium derivatives that can be used as optical probes for G‐quadruplexes.

NMR Structure of a Triangulenium-Based Long-Lived Fluorescence Probe Bound to a G-Quadruplex.

An NMR structural study of the interaction between a small-molecule optical probe (DAOTA-M2) and a G-quadruplex from the promoter region of the c-myc oncogene revealed that they interact at 1:2 binding stoichiometry. NMR-restrained structural calculations show that binding of DAOTA-M2 occurs mainly through π-π stacking between the polyaromatic core of the ligand and guanine residues of the outer G-quartets. Interestingly, the binding affinities of DAOTA-M2 differ by a factor of two for the outer G-quartets of the unimolecular parallel G-quadruplex under study. Unrestrained MD calculations indicate that DAOTA-M2 displays significant dynamic behavior when stacked on a G-quartet plane. These studies provide molecular guidelines for the design of triangulenium derivatives that can be used as optical probes for G-quadruplexes.

Parallel β-Sheet Structure of Alanine Tetrapeptide in the Solid State As Studied by Solid-State NMR Spectroscopy.

The structural analysis of alanine oligopeptides is important for understanding the crystalline region in silks from spiders and wild silkworms and also the mechanism of cellular toxicity of human diseases arising from expansion in polyalanine sequences. The atomic-level structures of alanine tripeptide and tetrapeptide with antiparallel β-sheet structures (AP-Ala3 and AP-Ala4, respectively) together with alanine tripeptide with parallel β-sheet structures (P-Ala3) have been determined, but alanine tetrapeptide with a parallel β-sheet structure (P-Ala4) has not been reported yet. In this article, first, we established the preparation protocol of P-Ala4 from more stable AP-Ala4. Second, complete assignments of the (13)C, (15)N, and (1)H solid-state NMR spectra were performed with (13)C- and (15)N-labeled Ala4 samples using several solid-state NMR techniques. Then, the structural constraints were obtained, for example, the amide proton peaks of P-Ala4 in the (1)H double-quantum magic-angle spinning NMR spectrum were heavily overlapped and observed at about 7.4 ppm, which was a much higher field than that of 8.7-9.1 ppm observed for AP-Ala4, indicating that the intermolecular hydrogen-bond lengths across strands (N-H···O═C) were considerably longer for P-Ala4, that is, 2.21-2.34 Å, than those reported for AP-Ala4, that is, 1.8-1.9 Å. The structural model was proposed for P-Ala4 by NMR results and MD calculations.

Effects of vacancies on atom displacement threshold energy calculations through Molecular Dynamics Methods in BaTiO3

A primary approach for evaluating the influence of point defects like vacancies on atom displacement threshold energies values Td in BaTiO3 is attempted. For this purpose Molecular Dynamics Methods, MD, were applied based on previous Td calculations on an ideal tetragonal crystalline structure. It is an important issue in achieving more realistic simulations of radiation damage effects in BaTiO3 ceramic materials. It also involves irradiated samples under severe radiation damage effects due to high fluency expositions. In addition to the above mentioned atom displacement events supported by a single primary knock-on atom, PKA, a new mechanism was introduced. It corresponds to the simultaneous excitation of two close primary knock-on atoms in BaTiO3, which might take place under a high flux irradiation. Therefore, two different BaTiO3 Td MD calculation trials were accomplished. Firstly, single PKA excitations in a defective BaTiO3 tetragonal crystalline structure, consisting in a 2×2×2 BaTiO3 perovskite like super cell, were considered. It contains vacancies on Ba and O atomic positions under the requirements of electrical charge balance. Alternatively, double PKA excitations in a perfect BaTiO3 tetragonal unit cell were also simulated. On this basis, the corresponding primary knock-on atom (PKA) defect formation probability functions were calculated at principal crystal directions, and compared with the previous one we calculated and reported at an ideal BaTiO3 tetrahedral crystal structure. As a general result, a diminution of Td values arises in present calculations in comparison with those calculated for single PKA excitation in an ideal BaTiO3 crystal structure.

Room temperature d0 ferromagnetism in hole doped Y2O3: widening the choice of host to tailor DMS

Transition metal-free-ferromagnetism in diluted magnetic semiconductors (DMS) is of much current interest in view of the search for more efficient DMS materials for spintronics applications. Our DFT results predict for the first time, that impurities from group1A (Li+, Na+, K+) doped on Y2O3 can induce a magnetic signature with a magnetic moment around 2.0 μB per defect at hole concentrations around 1.63 × 1021 cm−3, which is one order less than the critical hole density of ZnO with ferromagnetic coupling large enough to promote room temperature ferromagnetism. The induction of room temperature ferromagnetism by hole doping with an impurity atom from group 1A, which injects two holes per defect in the system, implies that the recommendation of three holes per defect given in the literature, which puts a restriction on the choice of host material and the impurity, is not a necessary criterion for hole induced room temperature ferromagnetism. DFT simulations with the generalized gradient approximation (GGA), confirmed by the more sophisticated hybrid functional, Heyd–Scuseria–Ernzerhof (HSE06), predict that the magnetic moment is mostly contributed by O atoms surrounding the impurity atom and the magnetic moment scale up with impurity concentration which is a positive indicator for practical applications. We quantitatively and extensively demonstrate through the analysis of the density of states and ferromagnetic coupling that the Stoner criterion is satisfied by pushing the Fermi level inside the valence band to activate room temperature ferromagnetism. The stability of the structure and the persistence of ferromagnetism at room temperature were demonstrated by ab initio MD simulations and computation of Curie temperature through the mean field approximation. This study widens the choice of host oxides to tailor DMS for spintronics applications.

MD Simulations and Free Energy Calculation of Synthetic Coiled-Coil Peptides with Lipid Bilayers

Molecular dynamics simulations were performed to understand the interactions of synthetic coiled-coil peptides (the shorter versions of SNARE proteins, called “E” and “K”) with lipid bilayers composed of DOPC, DOPE, and cholesterol at different molar ratios. Potentials of mean force (PMF) were calculated using the umbrella sampling method, showing the effect of the lipid type on the binding strength between peptides and bilayers. To understand the configurations and insertion of peptides into bilayer, we analyzed the helicity and tilt angles of peptides, the distance between peptide and bilayer, lateral diffusivity of lipids, and electrostatic and hydrophobic interactions between peptides and lipids, showing that K peptides retain their helicity and more deeply insert into the bilayer than do E peptides, which helps explain the experimentally proposed “the snorkeling effect”.