Inorganic-organic hybrid Cu-dipyridyl semiconducting polymers based on the redox-active cluster [SFe3(CO)9]2-: filling the gap in iron carbonyl chalcogenide polymers.

The construction of sulfur-incorporated cluster-based coordination polymers was limited and underexplored due to the lack of efficient synthetic routes. Herein, we report facile mechanochemical ways toward a new series of SFe3(CO)9-based dipyridyl-Cu polymers by three-component reactions of [Et4N]2[SFe3(CO)9] ([Et4N]2[1]) and [Cu(MeCN)4][BF4] with conjugated or conjugation-interrupted dipyridyl ligands, 1,2-bis(4-pyridyl)ethylene (bpee), 1,2-bis(4-pyridyl)ethane (bpea), 4,4'-dipyridyl (dpy), or 1,3-bis(4-pyridyl)propane (bpp), respectively. X-ray analysis showed that bpee-containing 2D polymers demonstrated unique SFe3(CO)9 cluster-armed and cluster-one-armed coordination modes via the hypervalent µ5-S atom. These S-Fe-Cu polymers could undergo flexible structural transformations with the change of cluster bonding modes by grinding with stoichiometric amounts of dipyridyls or 1/[Cu(MeCN)4]+. They exhibited semiconducting behaviors with low energy gaps of 1.55-1.79 eV and good electrical conductivities of 3.26 × 10-8-1.48 × 10-6 S cm-1, tuned by the SFe3(CO)9 cluster bonding modes accompanied by secondary interactions in the solid state. The electron transport efficiency of these polymers was further elucidated by solid-state packing, X-ray photoelectron spectroscopy (XPS), X-ray absorption near-edge spectroscopy (XANES), density of states (DOS), and crystal orbital Hamilton population (COHP) analysis. Finally, the solid-state electrochemistry of these polymers demonstrated redox-active behaviors with cathodically-shifted patterns compared to that of [Et4N]2[1], showing that their efficient electron communication was effectively enhanced by introducing 1 and dipyridyls as hybrid ligands into Cu+-containing networks.

Exploring the most stable aptamer/target molecule complex by the stochastic tunnelling-basin hopping-discrete molecular dynamics method.

The stochastic tunnelling-basin hopping-discrete molecular dynamics (STUN-BH-DMD) method was applied to the search for the most stable biomolecular complexes in water by using the MARTINI coarse-grained (CG) model. The epithelial cell adhesion molecule (EpCAM, PDB code: 4MZV) was used as an EpCAM adaptor for an EpA (AptEpA) benchmark target molecule. The effects of two adsorption positions on the EpCAM were analysed, and it is found that the AptEpA adsorption configuration located within the EpCAM pocket-like structure is more stable and the energy barrier is lower due to the interaction with water. By the root mean square deviation (RMSD), the configuration of EpCAM in water is more conservative when the AptEpA binds to EpCAM by attaching to the pocket space of the EpCAM dimer. For AptEpA, the root mean square fluctuation (RMSF) analysis result indicates Nucleobase 1 and Nucleobase 2 display higher flexibility during the CGMD simulation. Finally, from the binding energy contour maps and histogram plots of EpCAM and each AptEpA nucleobase, it is clear that the binding energy adsorbed to the pocket-like structure is more continuous than that energy not adsorbed to the pocket-like structure. This study has proposed a new numerical process for applying the STUN-BH-DMD with the CG model, which can reduce computational details and directly find a more stable AptEpA/EpCAM complex in water.

The Mechanical Behaviors of Polyethylene/Silver Nanoparticle Composites: an Insight from Molecular Dynamics study.

This research uses molecular dynamics simulation (MD) to study the mechanical properties of pristine polyethylene (PE) and its composites which include silver nanoparticles (PE/AgNPs) at two AgNP weight fractions of 1.05 wt% and 3.10 wt%. The stress-strain distribution of the tensile process shows that the embedded AgNPs can significantly improve the Young's modulus and tensile strength of the pristine PE, due to improvements in the local density and strength of the PE near the AgNP surface in the range of 12 Å. Regarding the effect of temperature on the mechanical properties of pristine PE and PE/AgNP composites, the Young's modulus and the strength of the pristine PE and PE/AgNP composites decreased significantly at 350 K and 450 K, respectively, consistent with predicted melting temperature of pristine PE, which lies at around 360 K. At such temperatures as these, PE material has stronger ductility and a higher mobility of AgNPs in the PE matrix than those at 300 K. With the increase of tensile strain, AgNPs tend to be close, and the fracture of PE leads to a similarity between both the Young's modulus and ultimate strength found for the pristine PE and those found for the PE/AgNP composites at 350 K and 450 K, respectively.

Observing the three-dimensional terephthalic acid supramolecular growth mechanism on a stearic acid buffer layer by molecular simulation methods.

The terephthalic acid (TPA) supramolecular growth mechanisms on the stearic acid (STA) buffer layer, such as the phase separation and layer-by-layer (LBL) mechanisms, were considered by molecular simulations. The electrostatic surface potential (ESP) charges obtained by the semi-empirical ab initio package VAMP with PM6 were used with the Dreiding force field. The stochastic tunneling-basin hopping-discrete molecular dynamics method (STUN-BH-DMD) was first used to construct the most stable STA buffer layers (STA100, STA120, and STA140) on graphene. At STA100 and STA120, the STA molecule stacking along their long axis is the major mechanism to obtain the stable STA buffer layer. At STA140, the hydrogen bond network between the terminal COOH groups of STA molecules makes the STA buffer layer the most stable, leading to a higher disintegration temperature among all STA coverages. In the early growth of the TPA supramolecule, TPA molecules were first adsorbed by the holes between STA piles. At STA100 and STA120, the subsequent TPA molecules were adsorbed by the TPA molecules within the holes, leading to the phase separation growth. At STA140, the TPA supramolecule tends to grow by the LBL mechanism.

Computational investigation of NH3 adsorption and dehydrogenation on a W-modified Fe(111) surface.

Hydrogen gas will play an important role in the future since it could be a replacement for gasoline, heating oil, natural gas, and other fuels. In previous reports ammonia (NH3), which has a high hydrogen content, provides a promising mode for the transferring and storing of hydrogen for its on-site generation. Therefore, the dehydrogenation of NH3 on a metal surface has been studied widely in the last few decades. In our study, we employed monolayer tungsten metal to modify the Fe(111) surface, denoted as W@Fe(111), and calculated the adsorption and dehydrogenation behaviors of NH3 on W@Fe(111) surface via first-principles calculations based on density functional theory (DFT). The three adsorption sites of the surface, top (T), 3-fold-shallow (S), and 3-fold-deep (D) were considered. The most stable structure of the NHx (x = 0-3) species on the surface of W@Fe(111) have been predicted. The calculated activation energies for NHx (x = 1-3) dehydrogenations are 19.29 kcal mol(-1) (for H2N-H bond activation), 29.17 kcal mol(-1) (for HN-H bond activation) and 27.94 kcal mol(-1) (for N-H bond activation), and the entire process is exothermic by 33.05 kcal mol(-1). To gain detailed knowledge of the catalytic processes of the NH3 molecule on the W@Fe(111) surface, the physical insights between the adsorbate/substrate interaction and interface morphology were subjected to a detailed electronic analysis.

Reaction mechanisms and kinetics of the iminovinylidene radical with NO: ab initio study.

The nitric oxide (NO) is a notorious compound for polluting environment. Recent year, removing nitric oxide from the atmosphere becomes a focus of the investigation. In our work, we study the iminovinylidene (HNCC) radical reacted with NO molecule. The mechanism and kinetic for reaction of the HNCC radical with the NO molecule is investigated via considering the possible channels of the N and O atoms of NO attacking the N and C atoms of the HNCC based on the high level ab initio molecular orbital calculations in conjunction with variational TST and RRKM calculations. The species involved have been optimized at the B3LYP/6-311++G(3df,2p) level and their single-point energies are refined by the CCSD(T)/aug-cc-PVQZ//B3LYP/6-311++G(3df,2p) method. The calculated potential energy surfaces indicated that energetically the most favorable channel for the HNCC + NO reaction was predicted to be the formation of HNC+CNO (P8) product via the addition reaction of the C atom of HNCC radical and the N atom of NO with the head to head orientation. To rationalize the scenario of the calculated results, we also employ the Fukui functions and HSAB theory to seek for a possible explanation. In addition, the reaction rate constants were calculated using VariFlex code, and the results show that the total rate coefficient, ktotal, at Ar pressure 760 Torr can be represented with an equation: ktotal = 6.433 × 10(-11) T (0.100) exp(0.275 kcal mol(-1)/RT) at T = 298-3000 K, in units of cm(3) molecule(-1) s(-1).

Ab initio chemical kinetics for H + NCN: prediction of NCN heat of formation and reaction product branching via doublet and quartet surfaces.

The reaction of NCN with H atoms has been investigated by ab initio MO and RRKM theory calculations. The mechanisms for formation of major products on the doublet and quartet potential energy surfaces have been predicted at the CCSD(T) level of theory with the complete basis set limit. In addition, the heat of formation for NCN predicted at this rigorous level and those from five isogyric reactions are in close agreement with the best value based on the isodesmic process, (3)CCO + N2 = (3)NCN + CO, 109.4 kcal/mol, which lies within the two existing experimental values. The rate constants for the three possible reaction channels, H + NCN → CH + N2 (k(P1)), HCN + (4)N (k(QP1)), and HNC + (4)N (k(QP2)), have been calculated in the temperature range 298-3000 K. The results show that k(P1) is significantly higher than k(QP1) and k(QP2) and that the total rate constant agrees well with available experimental values in the whole temperature range studied. The kinetics of the reverse CH + N2 reaction has also been revisited at the CCSD(T)/CBS level; the predicted total rate constants at 760 Torr Ar pressure can be represented by kr = 4.01 × 10(-15) T(0.90) exp(-17.42 kcal mol(-1)/RT) cm(3) molecule(-1) s(-1) at T = 800-4000 K. The result agrees closely with the most recent experimental data and the best theoretical result of Harding et al. (J. Phys. Chem. A 2008, 112, 522) as well as that of Moskaleva and Lin (Proc. Combust. Inst. 2000, 28, 2393) evaluated with a steady-state approximation after a coding error correction made in this study.

Density function theory study on adsorption and dissociation of H2O on Pd nanowire.

The adsorption and dissociation of H2O in Pd nanowire have been investigated by the density functional theory (DFT) studies. First, we construct Pd nanowire by basin-hopping method and use DFT calculation to find the ground state of Pd nanowire, and put the H2O molecular on different adsorption sites and the H2O molecule is found to preferentially absorb on a Top (T) site. The H2O molecule lies parallel to the Pd nanowire surface, while the O atom is bound at a Top site. We also calculate the partial density of state (PDOS) and election density difference. In addition, our calculated results demonstrate that the bonding between H2O and Pd nanowire is contributed by d orbitals of Pd nanowire and p orbitals of O atom. The nudged elastic band (NEB) method is applied to locate transition states and minimum energy pathways (MEP), and we discuss the dissociation behavior of the side-on H2O molecules on the top site of hexagonal and tetragonal planes, respectively.

The deformation mechanism of Ni-Ta bulk metallic glasses after tensile: molecular dynamics study.

The mechanical properties of Ni-Ta crystallizationand binary bulk metallic glasses (BMG) were investigated for this study at the nanoscale. First, the Ta9Ni3 crystals are formed by space group, and structures with different ratios (Ta1Ni1, BTa8Ni4, BTa9Ni3, BTa7Ni5) were put into unit cell randomly. The optimizations of BMG structures are performed by Density functional theory (DFT) calculation to find the stable amorphous structures and corresponding energy. The FMM is utilized to obtain the suitable parameters of tight-binding potential bystable amorphous structures and corresponding energies. Finally, we employ molecular dynamics (MD) simulation to study mechanical properties of Ni/Ta crystallization and BMG, such as atomistic stress-strain, plastic and elastic deformation, and elastic modulus.

Density function theory study of the adsorption and dissociation of carbon monoxide on tungsten nanoparticles.

The adsorption and dissociation properties of carbon monoxide (CO) molecule on tungsten W(n) (n = 10-15) nanoparticles have been investigated by density-functional theory (DFT) calculations. The lowest-energy structures for W(n) (n = 10-15) nanoparticles are found by the basin-hopping method and big-bang method with the modified tight-binding many-body potential. We calculated the corresponding adsorption energies, C-O bond lengths and dissociation barriers for adsorption of CO on nanoparticles. The electronic properties of CO on nanoparticles are studied by the analysis of density of state and charge density. The characteristic of CO on W(n) nanoparticles are also compared with that of W bulk.

The dynamics behavior of Rh nanoclusters on boron nitride sheet.

The configurations and corresponding adsorption energies of Rh(n) (n = 4-13) nanoclusters on the boron nitride sheet are investigated by density functional theory (DFT). We use the force-matching method (FMM) to modify parameters of Morse and Tersoff potential functions. To elucidate the dynamical behaviors of Rh nanoclusters on the boron nitride sheet, molecular dynamics (MD) is applied with modified Morse potential function parameter. Finally, the square displacement (SD) is utilized the dynamics behavior of different size Rh nanoclusters at different temperatures.

A density functional theory study on the structure stability of silica nanoclusters.

The studies of silica nanoclusters are of substantial interest for large potential in applications as diverse as photonics/optics, microelectronics and catalysis. In this study, we used the basing-hopping method with Buckingham potential to get the stable structures of silica nanoclusters ((SiO2)(n) = 1-13). The global minimum geometry of silica nanoclusters were determined by density functional theory calculation. We investigated the energy gap, binding energy and second order energy difference of nanoclusters to determine their structural stability with different sizes. We also calculate the second-order energy difference, binding energy to determine the magic number.

Mechanism and kinetics for ammonium dinitramide (ADN) sublimation: a first-principles study.

The mechanism for sublimation of NH(4)N(NO(2))(2) (ADN) has been investigated quantum-mechanically with generalized gradient approximation plane-wave density functional theory calculations; the solid surface is represented by a slab model and the periodic boundary conditions are applied. The calculated lattice constants for the bulk ADN, which were found to consist of NH(4)(+)[ON(O)NNO(2)](-) units, instead of NH(4)(+)[N(NO(2))(2)](-), agree quite well with experimental values. Results show that three steps are involved in the sublimation/decomposition of ADN. The first step is the relaxation of the surface layer with 1.6 kcal/mol energy per NH(4)ON(O)NNO(2) unit; the second step is the sublimation of the surface layer to form a molecular [NH(3)]-[HON(O)NNO(2)] complex with a 29.4 kcal/mol sublimation energy, consistent with the experimental observation of Korobeinichev et al. (10) The last step is the dissociation of the [H(3)N]-[HON(O)NNO(2)] complex to give NH(3) and HON(O)NNO(2) with the dissociation energy of 13.9 kcal/mol. Direct formation of NO(2) (g) from solid ADN costs a much higher energy, 58.3 kcal/mol. Our calculated total sublimation enthalpy for ADN(s) → NH(3)(g) + HON(O)NNO(2)) (g), 44.9 kcal/mol via three steps, is in good agreement with the value, 42.1 kcal/mol predicted for the one-step sublimation process in this work and the value 44.0 kcal/mol computed by Politzer et al. (11) using experimental thermochemical data. The sublimation rate constant for the rate-controlling step 2 can be represented as k(sub) = 2.18 × 10(12) exp (-30.5 kcal/mol/RT) s(-1), which agrees well with available experimental data within the temperature range studied. The high pressure limit decomposition rate constant for the molecular complex H(3)N···HON(O)NNO(2) can be expressed by k(dec) = 3.18 × 10(13) exp (-15.09 kcal/mol/RT) s(-1). In addition, water molecules were found to increase the sublimation enthalpy of ADN, contrary to that found in the ammonium perchlorate system, in which water molecules were shown to reduce pronouncedly the enthalpy of sublimation.

Computational study on reaction mechanisms and kinetics of RNCN (R = H, F, Cl, Br, CH3) radicals with NO.

We carried out a computational study of radical reactions of RNCN (R = H, F, Cl, Br, CH(3)) + NO to investigate how the substitution can influence their corresponding energy barriers and rate coefficients. The preferable reactive sites of RNCN radicals with various substituents are calculated by employing the Fukui functions and hard-and-soft acid-and-base theory, which were generally proved to be successful in the prediction and interpretation of regioselectivity in various types of electrophilic and nucleophilic reactions. Our calculated results clearly show that if the substituted RNCN radical has electron-donating substituent (for R = CH(3)), its corresponding barrier heights for transition states will be substantially decreased. The possible explanations of the observed increase and/or decrease in the energy barriers for the varied substituted RNCN radicals are also analyzed in this article.

Quantum chemical prediction of pathways and rate constants for reaction of cyanomethylene radical with NO.

High-level ab initio calculations have been performed to study the mechanism and kinetics of the reaction of the cyanomethylene radical (HCCN) with the NO. The species involved have been optimized at the B3LYP/6-311++G(3df,2p) level, and their corresponding single-point energies are improved by the CCSD(T)/aug-cc-PVQZ//B3LYP/6-311++G(3df,2p) approach. From the calculated potential energy surface, we have predicted the favorable pathways for the formation of several isomers of a HCCN-NO complex. Barrierless formation of HCN + NCO (P1) is also possible. Formation of HCNO + CN (P3) is endoergic but may become significant at high temperatures. To rationalize the scenario of our calculated results, we also employ the Fukui functions and hard-and-soft acid-and-base (HSAB) theory to seek possible clues. The predicted total rate coefficient, k(total), at He pressure 760 Torr can be represented with the equation k(total) = 1.40 × 10(-7) T(-2.01) exp(3.15 kcal mol(-1)/RT) at T = 298-3000 K in units of cm(3) molecule(-1) s(-1). The predicted total rate coefficients at some available conditions (He pressures of 6, 18, and 30 Torr in the temperature of 298 K) are in reasonable agreement with experimental observation. In addition, the rate constants for key individual product channels are provided in different temperature and pressure conditions.

Adsorption and dissociation of the O2 on W(111) surface: a density functional theory study.

The adsorption and dissociation of O2 molecules on W(111) surface have been studied at the density functional theory (DFT) level in conjunction with the projector augmented wave (PAW) method. All passable dissociation reaction paths of O2 molecule on W(111) surface are considered. The nudged elastic band (NEB) method is applied to locate transition states, and minimum energy pathways (MEP). We find that there is an existing of little barriers for the dissociations reaction of O2 molecule. Ab initio molecular dynamics simulation is also preformed to study the adsorption and dissociation mechanism of O2 molecules on the W(111) surface. Our results indicate that O2 molecule will be dissociated by inclined deposition at temperature of 10 K, but can stable adsorb on top site by normal deposition. The change of bond length and adsorption energy in process of dissociation of O2 molecules on the W(111) surface are also calculated. The O2 coverage effect is also discussed in this paper.

Computational study on reaction mechanisms and kinetics of diazocarbene radical reaction with NO.

The mechanisms of the reaction of the diazocarbene radical (CNN) with the NO have been investigated by ab initio molecular orbital in conjunction with variational TST and RRKM calculations. The potential energy surface (PES) was calculated by the high-level CCSD(T)/aug-cc-PVQZ//B3LYP/6-311++G(3df,2p) method. From the calculated potential energy surface, we have predicted that the formation of N(2)O + CN (P5) is most favorable, and the calculated energies of reaction intermediates and transition structures along this path are all below the starting reference point. The predicted total rate constants, k(total), at a 760 Torr Ar pressure can be represented by the equations: k(total) = 2.47 x 10(-17)T(1.20) exp(1.60 kcal mol(-1)/RT) at T = 300-650 K and 2.49 x 10(-19)T(1.82) exp(2.29 kcal mol(-1)/RT) at T = 660-3000 K cm(3) molecule(-1) s(-1). The calculated results also indicate that the branching ratio for R(P5) in the temperature range 300-3000 K has the largest value. In addition, the rate constants for key individual product channels are provided in different temperature and pressure conditions. To rationalize the scenario of the calculated results, we also employ the Fukui functions and HSAB theory to seek for the possible explanation.

Theoretical study on reaction mechanisms and kinetics of cyanomidyl radical with NO.

The mechanisms and kinetics of the reaction of the cyanomidyl radical (HNCN) with the NO have been investigated by the high-level ab initio molecular orbital method in conjunction with VTST and RRKM theory. The species involved have been optimized at the B3LYP/6-311++G(3df,2p) level and their single-point energies are refined by the CCSD(T)/aug-cc-PVQZ//B3LYP/6-311++G(3df,2p) method. Our calculated results indicate that the favorable pathways for the formation of several isomers of an HNCN-NO complex. Formations of HNC + N(2)O (P1) and HNCO + N(2) (P2) are also possible, although these two pathways involve little activation energy. Employing the Fukui functions and HSAB theory, we are able to rationalize the scenario of the calculated outcome. The predicted total rate constants, k(total), at a 760 Torr Ar pressure can be represented by the equations k(total) = 4.39 x 10(8) T(-7.30) exp(-1.76 kcal mol(-1)/RT) at T = 298-1000 K and 1.01 x 10(-32) T(5.32) exp(11.27 kcal mol(-1)/RT) at T = 1050-3000 K, respectively, in units of cm(3) molecule(-1) s(-1). In addition, the rate constants for key individual product channels are provided in a table for different temperature and pressure conditions. These results are recommended for combustion modeling applications.

Theoretical study on adsorption and dissociation of NO2 molecule on Fe(111) surface.

We applied periodic density-functional theory (DFT) to investigate the adsorption and dissociation of NO(2) on a Fe(111) surface. The most favorable adsorption configuration of NO(2)/Fe(111) is the FeNO(2)(S-mu(3)-N,O,O') configuration with NO(2) at the 3-fold-shallow site of the surface, which has an adsorption energy -64.59 kcal/mol. Of two geometries of NO(2)/Fe(111) for the stepwise NO(2) deoxygenation, one is the most stable structure, FeNO(2)(S-mu(3)-N,O,O'), with activation barriers 10.38 and 19.36 kcal/mol to break the first (ON-O bond activation) and second (N-O bond activation) nitrogen-oxygen bonds, respectively; another configuration FeNO(2)(B-mu(2)-N,O) has a smaller energy barrier (3.88 kcal/mol) to break the first ON-O bond. All these findings show that NO(2) can readily decompose on the Fe(111) surface. The rate constants for the two aforementioned processes were also predicted by VTST and RRKM theory, and the predicted total rate constants, k(total) (in units of cm(3) molecule(-1) s(-1)), can be represented by the equations k(total) = 5.61 x 10(-5)T(-2.060) exp(-0.639 kcal mol(-1)/RT) at T = 100-1000 K. To acquire insight into the great catalytic activity of the Fe(111) surface for the decomposition of NO(2), the nature of the interaction between the adsorbate and the substrate is subjected to a detailed electronic analysis.

Role of hydroxyl groups in the NH(x) (x = 1-3) adsorption on the TiO2 anatase (101) surface determined by a first-principles study.

A spin-polarized density functional theory calculation was carried out to study the adsorption of NH(x) species (x = 1-3) on a TiO2 anatase (101) surface with and without hydroxyl groups by using first-principles calculations. It was found that the present hydroxyl group has the effect of significantly enhancing the adsorption of monodentate adsorbates H2N-Ti(a) compared to that on a bare surface. The nature of the interaction between the adsorbate (NH(x)) and the hydroxylated or bare surface was analyzed by the Mulliken charge and density of states (DOS) calculations. This facilitation of NH2 is caused by the donation of coadsorbed H filling the nonbonding orbital of NH2, resulting in an electron gain in NH2 from the bonding. In addition, the upper valence band, which originally consisted of the mixing of O 2p and Ti 3d orbitals, has been broadened by the two adjacent H 1s and NH2 sigma(y)(b) orbitals joined to the bottom of the original TiO2 valence band. The results are important to understand the OH effect in heterogeneous catalysis.