Project description:Most current biomolecular simulations are based on potential energy functions that treat the electrostatic energy as a sum of pairwise Coulombic interactions between effective fixed atomic charges. This approximation, in which many-body induced polarization effects are included in an average way, is expected to be satisfactory for a wide range of systems, but less accurate for processes involving the transfer and partition of ions among heterogeneous environments. The limitations of these potential energy functions are perhaps most obvious in studies of ion permeation through membrane channels. In many cases, the pore is so narrow that the permeating ion must shed most of its surrounding water molecules and the large energetic loss due to dehydration must be compensated by coordination with protein atoms. Interactions of cations with protein backbone carbonyl oxygens, in particular, play a critical role in several important biological channels. As a first step toward meeting the challenge of developing an accurate explicit accounting for induced polarization effects, the present work combines experiments and computation to characterize the interactions of alkali and halide ions with N-methylacetamide chosen to represent the peptide bond. From solubility measurements, we extract the solvation free energies of KCl and NaCl in liquid N-methylacetamide. Polarizable models based on the Drude oscillator are then developed and compared with available experimental and ab initio data. The good agreement for a range of structural and thermodynamic properties in the gas and condensed phases suggests that the polarizable models provide an accurate representation of ion-amide interactions in biological systems.
Project description:An effort to combine theoretical analyses and protein engineering methods has been made to probe the folding mechanism of SH3 by using Energy Landscape Theory and a phi-value analysis. Particular emphasis was given to core residues and the effect of desolvation during the folding event by replacing the core valines with isosteric threonines. These mutations have the advantage of keeping the core structurally invariant while affecting core stability relative to the unfolded state. Although the valines that form the core appear spatially invariant, the folding kinetics of their threonine mutants varies, indicating their different extent of solvation in the transition-state ensemble. Theoretical studies predicted the distribution of folding kinetics of threonine mutants without previous knowledge of the measured rates. This initial success encourages further investigations of the molecular details behind these macroscopic phenomena and of the role of solvation in the folding mechanism.
Project description:Thermally activated delayed fluorescence (TADF) molecules have a theoretical 100% photoluminescence quantum yield in comparison with traditional fluorescent materials, leading to broad application in organic light-emitting diode (OLED). However, the application of TADF molecules with conjugated donor-acceptor structures in blue OLED remains a challenge due to their generally narrow energy gap between frontier molecular orbitals. Recently, a strategy has been approved in the improvement of the performance in TADF, in which void-carbon atoms between donor and acceptor fragments (donor-void-acceptor (D-v-A)) could regulate blue light emission. In this study, we first select three reported isomers followed by two proposed D-v-A TADF isomers to verify the feasibility of the void-carbon strategy through evaluation of the electronic structures in the excited state and photophysical properties. We further proposed a series of TADF molecules by replacing different donor and acceptor fragments to assess the applicability of the void-carbon strategy from the aspect of simulations in electronic structures, different properties of donor and acceptor fragments, photophysical properties, and analysis in the molecular conjugation. The results indicate that void-carbon strategy has conditional feasibility and applicability. Donor-acceptor molecular properties could be tuned through void-carbon strategy on aromatic acceptor fragments during the selection of promising candidates of TADF molecules. However, the void-carbon strategy does not work for the molecules with antiaromatic acceptor fragments, where the steric hindrance of the molecules plays a dominant role. Our work provides insightful guidance for the design of the blue-emission TADF molecules.
Project description:Aqueous Zn-ion batteries (AZIBs) have attracted increasing attention in next-generation energy storage systems due to their high safety and economic. Unfortunately, the side reactions, dendrites and hydrogen evolution effects at the zinc anode interface in aqueous electrolytes seriously hinder the application of aqueous zinc-ion batteries. Here, we report a critical solvation strategy to achieve reversible zinc electrochemistry by introducing a small polar molecule acetonitrile to form a "catcher" to arrest active molecules (bound water molecules). The stable solvation structure of [Zn(H2O)6]2+ is capable of maintaining and completely inhibiting free water molecules. When [Zn(H2O)6]2+ is partially desolvated in the Helmholtz outer layer, the separated active molecules will be arrested by the "catcher" formed by the strong hydrogen bond N-H bond, ensuring the stable desolvation of Zn2+. The Zn||Zn symmetric battery can stably cycle for 2250 h at 1 mAh cm-2, Zn||V6O13 full battery achieved a capacity retention rate of 99.2% after 10,000 cycles at 10 A g-1. This paper proposes a novel critical solvation strategy that paves the route for the construction of high-performance AZIBs.
Project description:We present a new theoretical method for rapid calculation of the solvation free energy in water by combining molecular simulation and the classical density functional theory (DFT). The DFT calculation is based on an accurate free-energy functional for water that incorporates the simulation results for long-range correlations and the fundamental measure theory for the molecular excluded-volume effects. The numerical performance of the theoretical method has been validated with simulation results and experimental data for the solvation free energies of halide (F(-), Cl(-), Br(-), and I(-)) and alkali (Li(+), Na(+), K(+), Rb(+), and Cs(+)) ions in water at ambient conditions. Because simulation is applied only to the particular thermodynamic condition of interest, the hybrid method is computationally much more efficient than conventional ways of solvation free energy calculations.
Project description:Elucidating the solvation and size effects on the reactions between water and neutral metals is crucial for understanding the microscopic mechanism of the catalytic processes but has been proven to be a challenging experimental target due to the difficulty in size selection. Here, MO4H6 and M2O6H7 (M = Sc, Y, La) complexes were synthesized using a laser-vaporization cluster source and characterized by size-specific infrared-vacuum ultraviolet spectroscopy combined with quantum chemical calculations. The MO4H6 and M2O6H7 complexes were found to have H˙M(OH)3(H2O) and M2(μ2-OH)2(η1-OH)3(η1-OH2) structures, respectively. A combination of experiments and theory revealed that the formation of H˙M(OH)3(H2O) and M2(μ2-OH)2(η1-OH)3(η1-OH2) is both thermodynamically exothermic and kinetically facile in the gas phase. The results indicated that upon the addition of water to H˙M(OH)3, the feature of the hydrogen radical is retained. In the processes from mononuclear H˙M(OH)3 to binuclear M2(μ2-OH)2(η1-OH)3(η1-OH2), the active hydrogen atom undergoes the evolution from hydrogen radical → bridging hydrogen → metal hydride → hydrogen bond, which is indicative of a reduced reactivity. The present system serves as a model for clarifying the solvation and size effects on the reactions between water and neutral rare-earth metals and offers a general paradigm for systematic studies on a broad class of the reactions between small molecules and metals at the nanoscale.
Project description:Recently, we derived experimental oscillator strengths (OSs) from well-defined UV-visible absorption spectral peaks of 100 molecules in solution. Here, we focus on a subset of transitions with the highest reliability to further benchmark the OSs from several wave function methods and density functionals. We consider multiple basis sets, transition moment gauges (length, velocity, and mixed), and solvent corrections. Most transitions in the comparison set come from conjugated molecules and have π → π* character. We use an automated algorithm to assign computed transitions to experimental bands. OSs computed using the Tamm-Dancoff approximation (TDA), CIS, or EOM-CCSD exhibited a strong gauge dependence, which is diminished in linear response theories (TD-DFT, TD-HF, and to a smaller degree LR-CCSD). OSs calculated from TD-DFT with PCM solvent models are systematically larger than apparent OSs derived from experimental spectra. For example, fcomp from hybrid functionals and PCM have mean absolute errors that are ∼10% of n·fexp, where n is a solvent refractive index factor that arises from the energy flux of the radiation field in a dielectric (solvent). Theoretical cavity field corrections considering spherical cavities do not improve the agreement between computed and experimental data. Corrections that account for the molecular shape and the direction of transition dipole moments, or that explicitly account for the effect of solvent molecules on the local field, should be more appropriate.
Project description:One of the interactions between macromolecules is the attractive forcethrough the excluded volume effect. We studied the attraction betweenthe molecules of muscle protein, actin, in the two points by using theextended scaled particle theory (XSPT). I) we verified the basic assumptionused in the XSPT that topological elements which determine the analyticalexpression of the excluded volume are almost unchanged through the scalingdown of the solute molecule in the thought experiment. Results of thecomputational geometry method (?-shape method) showed that thisassumption is valid even in the case of the actin molecule. II) wecalculated the attraction between actin monomer molecules, G-actin.Calculated differences of the values of the attraction potential of twomacromolecules between at contact and at one macromolecule apart by theXSPT is almost the same as those by the Asakura-Oosawa theory.
Project description:Ab initio CASSCF/MRCI + Q calculations have been used to investigate the electronic structure and transition properties of the alkaline earth astatine molecules SrAt and BaAt. The adiabatic potential energy curves have been computed and plotted for the low-lying electronic states in the representations 2S+1Λ+/- and Ω(±) (with and without spin-orbit coupling effect). The spectroscopic and vibrational constants have been deduced for the corresponding bound states. An analysis of the Franck-Condon factors, the Einstein Coefficients, and the branching ratios among different vibrational levels has shown that both SrAt and BaAt molecules are suitable candidates for Doppler and Sysphus laser cooling. Experimental laser cooling schemes and conditions for these two molecules have been proposed. These results may pave the way for new spectroscopic and laser cooling experiments of alkaline earth astatine molecules.
Project description:In this article, both experimental and computational methods are employed to investigate the photophysics of rhaponticin (RH). The bathochromic shift was observed in absorption and fluorescence spectra with increasing solvent polarity, which implied that the charge transition of RH involved was π → π*. The results showed that RH possess strong intramolecular charge transfer (ICT), and the most important parameter to characterize the photophysical behavior of RH is the intermolecular hydrogen bonding ability of the solvent. The hydrogen bonding effect occurred at the localized electron-acceptor oxygen at the glycoside bond. Density functional theory (DFT) and time dependent density functional theory (TDDFT) were used to obtain the most stable structure, electronic excitation energy, dipole moments and charge distribution. The result was found to be 2.23 and 3.67 D in ground state and excited state respectively. Fluorescence quenching of RH owing to the photoinduced electron transfer (PET) is facilitated in alkaline media. The pK a value of RH was 6.39, which defined RH as a highly efficient "off-on" switcher. The effect of different metal ions on the fluorescence spectra of RH was also investigated, and the fluorescence quenching of RH depended on the nature of ions. The best performance was accomplished for binding with the Fe3+ ion. The interactions of RH with the Fe3+ ion were studied by FT-IR and HPLC, and the binding parameter was calculated by the Stern-Volmer equation. The results obtained reveal the binding activity of RH can make this a candidate as a good source of new agents for thalassemic patients.