Relationship between Conformational Dynamics and Electron Transfer in a Desolvated Peptide. Part I. Structures

The structures, dynamics and energetics of the protonated, derivatized peptide DyeX-(Pro)₄-Arg⁺-Trp, where “Dye” stands for the BODIPY analogue of tetramethylrhodamine and X is a (CH₂)₅ linker, have been investigated using a combination of modeling approaches in order to provide a numerical framework to the interpretation of fluorescence quenching data in the gas phase. Molecular dynamics (MD) calculations using the new generation AMOEBA force field were carried out using a representative set of conformations, at eight temperatures ranging from 150 to 500 K. Force field parameters were derived from ab initio calculations for the Dye. Strong electrostatic, polarization and dispersion interactions combine to shape this charged peptide. These effects arise in particular from the electric field generated by the charge of the protonated arginine and from several hydrogen bonds that can be established between the Dye linker and the terminal Trp. This conclusion is based on both the analysis of all structures generated in the MD simulations and on an energy decomposition analysis at classical and quantum mechanical levels. Structural analysis of the simulations at the different temperatures reveals that the relatively rigid polyproline segment allows for the Dye and Trp indole side chain to adopt stacking conformations favorable to electron transfer, yielding support to a model in which it is electron transfer from tryptophan to the dye that drives fluorescence quenching

Finite Temperature Infrared Spectra from Polarizable Molecular Dynamics Simulations

Infrared spectra of biomolecules are obtained from molecular dynamics simulations at finite temperature using the AMOEBA force field. Diverse examples are presented such as <i>N</i>-methylacetamide and its derivatives and a helical peptide. The computed spectra from polarizable molecular dynamics are compared in each case to experimental ones at various temperatures. The role of high-level electrostatic treatment and explicit polarization, including parameters improvements, is highlighted for obtaining spectral sensitivity to the environment including hydrogen bonds and water molecules and a better understanding of the observed experimental bands

Ab Initio Extension of the AMOEBA Polarizable Force Field to Fe²⁺

We extend the AMOEBA polarizable molecular mechanics force field to the Fe²⁺ cation in its singlet, triplet, and quintet spin states. Required parameters are obtained either directly from first principles calculations or optimized so as to reproduce corresponding interaction energy components in a hexaaquo environment derived from quantum mechanical energy decomposition analyses. We assess the importance of the damping of point-dipole polarization at short distance as well as the influence of charge-transfer for metal-water interactions in hydrated Fe²⁺; this analysis informs the selection of model systems employed for parametrization. We validate our final Fe²⁺ model through comparison of molecular dynamics (MD) simulations to available experimental data for aqueous ferrous ion in its quintet electronic ground state

CO₂ Adsorption in Fe₂(dobdc): A Classical Force Field Parameterized from Quantum Mechanical Calculations

Carbon dioxide adsorption isotherms have been computed for the metal–organic framework (MOF) Fe₂(dobdc), where dobdc^4– = 2,5-dioxido-1,4-benzenedicarboxylate. A force field derived from quantum mechanical calculations has been used to model adsorption isotherms within a MOF. Restricted open-shell Møller–Plesset second-order perturbation theory (ROMP2) calculations have been performed to obtain interaction energy curves between a CO₂ molecule and a cluster model of Fe₂(dobdc). The force field parameters have been optimized to best reproduced these curves and used in Monte Carlo simulations to obtain CO₂ adsorption isotherms. The experimental loading of CO₂ adsorbed within Fe₂(dobdc) was reproduced quite accurately. This parametrization scheme could easily be utilized to predict isotherms of various guests inside this and other similar MOFs not yet synthesized

Empirical and Theoretical Insights into the Structural Features and Host–Guest Chemistry of M₈L₄ Tube Architectures

We demonstrate a general method for the construction of M₈L₄ tubular complexes via subcomponent self-assembly, starting from Cu^I or Ag^I precursors together with suitable elongated tetraamine and 2-formylpyridine subcomponents. The tubular architectures were often observed as equilibrium mixtures of diastereomers having two different point symmetries (<i>D</i>_2d or <i>D</i>₂ ⇄ <i>D</i>₄) in solution. The equilibria between diastereomers were influenced through variation in ligand length, substituents, metal ion identity, counteranion, and temperature. In the presence of dicyanoaurate­(I) and Au^I, the <i>D</i>₄-symmetric hosts were able to bind linear Au­(Au­(CN)₂)₂^– (with two different configurations) as the best-fitting guest. Substitution of dicyanoargentate­(I) for dicyanoaurate­(I) resulted in the formation of Ag­(Au­(CN)₂)₂^– as the optimal guest through transmetalation. Density functional theory was employed to elucidate the host–guest chemistries of the tubes