We present a method to analyze biased molecular-dynamics and Monte Carlo simulations, also known as umbrella sampling. In the limiting case of a strong bias, this method is equivalent to thermodynamic integration. It employs only quantities with easily controllable equilibration and greatly reduces the statistical errors compared to the standard weighted histogram analysis method. We show the success of our approach for two examples, one analytic function, and one biological system.
Single molecules are sent and received over relatively large distances on precisely defined tracks across a flat metal surface.Single molecules are sent and received over relatively large distances on precisely defined tracks across a flat metal surface.
Molecular dynamics simulation is a prominent way of analyzing the dynamicproperties of a system. The molecular dynamics simulation of diffusion, animportant transport property, of dilute solution of cysteine in SPCE water atfive different temperatures (288 K, 293 K, 303 K, 313 K, 323 K) under thepressure of 1 bar is studied using GROMACS. OPLS AA force field parameters areused throughout the simulation. The system under study consists of 3 cysteinemolecules (mole fraction 0.003) as solute and 1039 water molecules (molefraction 0.997) as solvent. The radial distribution functions (RDFs) for fivedifferent combinations of atoms of solvent-solvent and solute solvent moleculesare studied for structural analysis. At least two or more distinct peaks areobserved in RDFs plots implying that there are interactions between atoms ofsolvent solvent and solute solvent at least up to two co ordination shells. Theself diffusion coefficients of solute and solvent are determined exploitingmean square displacement (MSD) in Einsteins equation. The self diffusioncoefficients are used to calculate the binary diffusion coefficients by meansof Darkens relation. The calculated values of self diffusion and binarydiffusion coefficients are compared with available experimental values and theyagreed within 12 percent. The temperature dependency of diffusions aredemonstrated via Arrhenius plots and with the help of these plots activationenergies for diffusions are calculated which agreed with experimental resultswithin 13 percent.
This review summarizes the state of research regarding reversible Li-ion metal electrodes, advocates for the use of limited lithium, and provides a roadmap for industrial progress towards 100 US$kWh^-1
Computational simulation of peptide adsorption at the aqueous gold interface is key to advancing the development of many applications based on gold nanoparticles, ranging from nanomedical devices to smart biomimetic materials. Here, we present a force field, GolPCHARMM, designed to capture peptide adsorption at both the aqueous Au(111) and Au(100) interfaces. The force field,compatible with the bio-organic force field CHARMM, is parametrized using a combination of experimental and firstprinciples data. Like its predecessor, GolP (Iori, F.; et al. J. Comput. Chem. 2009, 30, 1465), this force field contains terms to describe the dynamic polarization of gold atoms, chemisorbing species, and the interaction between sp2 hybridized carbon atoms and gold. A systematic study of small molecule adsorption at both surfaces using the vdW-DF functional (Dion, M.; et al. Phys. Rev. Lett. 2004, 92, 246401−1. Thonhauser, T.; et al. Phys. Rev. B 2007, 76, 125112) is carried out to fit and test force field parameters and also, for the first time, gives unique insights into facet selectivity of gold binding in vacuo. Energetic and spatial trends observed in our DFT calculations are reproduced by the force field under the same conditions. Finally, we use the new force field to calculate adsorption energies, under aqueous conditions, for a representative set of amino acids. These data are found to agree with experimental findings.
Pavol Jusko, Aude Simon, Shreyak Banhatti, Sandra Brünken, Christine Joblin
Published: Sep 2018
Disentangling the isomeric structure of C7H7+ is a longstanding experimentalissue. We report here the full mid-infrared vibrational spectrum of C7H7+tagged with Ne obtained with infrared-predissociation spectroscopy at 10 K.Saturation depletion measurements were used to assign the contribution ofbenzylium and tropylium isomers and demonstrate that no other isomer isinvolved. Recorded spectral features compare well with density functionaltheory calculations. This opens perspectives for a better understanding andcontrol of the formation paths leading to either tropylium or benzylium ions.
Nanoplasmonics has been used to enhance molecular spectroscopic signals, withexquisite spatial resolution down to the sub-molecular scale. By means of arigorous, state-of-the-art multiscale model based on a quantum chemicaldescription, here we show that optimally tuned tip-shaped metal nanoparticlescan selectively excite localized regions of typically coherent systems,eventually narrowing down to probing one single pigment. The well-known majorlight-harvesting complex LH2 of purple bacteria has been investigated becauseof its unique properties, as it presents both high and weak delocalizationamong subclusters of pigments. This finding opens the way to the directspectroscopic investigation of quantum-based processes, such as the quantumdiffusion of the excitation among the chromophores, and their externalmanipulation