The activation of human epidermal growth factor receptor (hEGFR) involves a large conformational change in its soluble extracellular domains (sECD, residues 1–620), from a tethered to an extended conformation upon binding of ligands, such as EGF. It has been reported that this dynamic process is pH-dependent, that is, hEGFR can be activated by EGF at high pH to form an extended dimer but remains as an inactive monomer at low pH. In this paper, we perform all-atom molecular dynamics (MD) simulations starting from the tethered conformation of sECD:EGF complex, at pH 5.0 and 8.5, respectively. Simulation results indicate that sECD:EGF shows different dynamic properties between the two pHs, and the complex may have a higher tendency of activation at pH 8.5. Twenty residues, including 13 histidines, in sECD:EGF have different protonation states between the two pHs (calculated by the H++ server). The charge distribution at pH 8.5 is more favorable for forming an extended conformation toward the active state of sECD than that at pH 5.0. Our study may shed light on the mechanism of pH dependence of hEGFR activation.
Differing from the weakly antiaromatic B80 buckyball, the medium-sized C1–B28 and D2h–B38, as well as their mono- to tetra-anions, are highly aromatic, as indicated by the negative nucleus-independent chemical shifts (NICSs) at their cage centers. The interior cavities and high aromaticity of the B28 and B38 cages render them very promising hosts to accommodate diverse metal atoms. Accordingly, we carried out systematic density functional theory (DFT) computations on the structures, stabilities and electronic properties of metalloborofullerenes MBn (M?=?Li, Na, K, Rb, Cs, Be, Mg, Ca, Sr, Ba, Sc, Y, La and Ti; n?=?28 and 38). Among them, besides the recently reported M@B38(M?=?Sc, Y and Ti) [Lu et al. (2015) Phys Chem Chem Phys 17:20897–20902], Ti@B28 and M@B38 (M?=?Ca and La) also favor endohedral structures with large binding energies, and are suggested promising targets for experimental applications. Note that Ti@B28 is the first endohedral derivative based on the new B28 fullerene, and La@B38 features the largest metal size inside a B38 cage thus far. These endohedral derivatives, as exemplified by Ca@B38, may exhibit σ and π double aromaticity over the whole cage surface, indicating their considerable stability. In contrast, the other metals prefer to reside at the exterior cage surface, due mainly to the mismatch of their sizes with the boron cages, though the size match is not the only factor to determine their doping form. Furthermore, the infrared absorption spectra and 11B nuclear magnetic resonance spectra of the three new M@Bn complexes were computed to assist future experimental characterization.
The geometries and thermochemistry of Re2(NO)4(CO)n (n?=?4, 3, 2, 1, 0) structures isovalent with the binuclear cobalt carbonyls Co2(CO)n+4 have been examined using density functional theory. Eight low-energy Re2(NO)4(CO)4 structures, all with formal Re–Re single bonds, lie within 6 kcal mol?1 of the global minimum. These eight structures include unbridged structures as well as structures with two bridging NO groups but no structures with bridging CO groups. Similarly, five low-energy Re2(NO)4(CO)3 structures, all with formal Re=Re double bonds, lie within 6 kcal mol?1 of the global minimum. Again these five structures include unbridged structures as well as structures with one or two bridging NO groups but no structures with bridging CO groups. The Re2(NO)4(CO)n (n?=?4, 3) appear to be fluxional systems similar to the well-known Co2(CO)8 for which doubly bridged and unbridged structures have approximately the same energies. The lowest energy Re2(NO)4(CO)2 structures have formal Re=Re double bonds including a structure with a five-electron donor bridging η2-μ-NO group. Isomeric Re2(NO)4(CO)2 structures with formal Re≡Re triple bonds lie approximately ～10 kcal mol?1 above the global minimum. For the more highly unsaturated Re2(NO)4(CO) and Re2(NO)4 systems, the lowest energy structures have formal Re≡Re triple bonds of length ～2.6 Å. Higher energy Re2(NO)4(CO) structures have shorter Re–Re distances of length ～2.5 Å suggesting formal quadruple bonds.
Graphical Abstract The geometries and thermochemistry of Re2(NO)4(CO)n (n?=?4, 3, 2, 1, 0) structures isovalent with the binuclear cobalt carbonyls Co2(CO)n+4 have been examined using density functional theory. A number of energetically closely spaced Re2(NO)4(CO)4 and Re2(NO)4(CO)3 structures are found, including unbridged and NO-bridged structures but no CO-bridged structures. The Re2(NO)4(CO)n (n?=?2, 1, 0) systems provide examples of Re–Re multiple bonds of orders ranging from 2 to 4.
Metal doped ZnO nanomaterials have attracted considerable attention as a chemical sensor for toxic gases. Here, the electronic sensitivity of pristine and Sc-, Ti-, V-, Cr-, Mn-, and Fe-doped Zn12O12 nanoclusters toward CO gas is investigated using density functional theory calculations. It is found that replacing a Zn atom by a Sc or Ti atom does not change the sensitivity of cluster but doping V and Cr atoms significantly increase the sensitivity. Also, Mn, or Fe doping slightly improves the sensitivity. It is predicted that among all, the Cr-doped ZnO cluster may be the most favorable sensor for CO detection because its electrical conductivity considerably changes after the CO adsorption, thereby, generating an electrical signal. The calculated Gibbs free energy change for the adsorption of CO molecule on the Cr-doped cluster is about -51.2 kcal mol-1 at 298.15 K and 1 atm, and the HOMO-LUMO gap of the adsorbent is changed by about 117.8 %. 相似文献
With increasing computational capabilities, an ever growing amount of data is generated in computational chemistry that contains a vast amount of chemically relevant information. It is therefore imperative to create new computational tools in order to process and extract this data in a sensible way. Kudi is an open source library that aids in the extraction of chemical properties from reaction paths. The straightforward structure of Kudi makes it easy to use for users and allows for effortless implementation of new capabilities, and extension to any quantum chemistry package. A use case for Kudi is shown for the tautomerization reaction of formic acid. Kudi is available free of charge at www.github.com/stvogt/kudi相似文献
The initial reaction mechanisms for depositing ZrO2 thin films using ansa-metallocene zirconium (Cp2CMe2)ZrMe2 precursor were studied by density functional theory (DFT) calculations. The (Cp2CMe2)ZrMe2 precursor could be absorbed on the hydroxylated Si(1 0 0) surface via physisorption. Possible reaction pathways of (Cp2CMe2)ZrMe2 were proposed. For each reaction, the activation energies and reaction energies were compared, and stationary points along the reaction pathways were shown. In addition, the influence of dispersion effects on the reactions was evaluated by non-local dispersion corrected DFT calculations. 相似文献
Titanium dioxide (TiO2) is an important metal oxide that has been used in many different applications. TiO2 has also been widely employed as a model system to study basic processes and reactions in surface chemistry and heterogeneous catalysis. In this work, we investigated the (011) surface of rutile TiO2 by focusing on its reconstruction. Density functional theory calculations aided by a genetic algorithm based optimization scheme were performed to extensively sample the potential energy surfaces of reconstructed rutile TiO2 structures that obey (2?×?1) periodicity. A lot of stable surface configurations were located, including the global-minimum configuration that was proposed previously. The wide variety of surface structures determined through the calculations performed in this work provide insight into the relationship between the atomic configuration of a surface and its stability. More importantly, several analytical schemes were proposed and tested to gauge the differences and similarities among various surface structures, aiding the construction of the complete pathway for the reconstruction process. 相似文献
