Nonlinear time-resolved vibrational spectroscopy is used to compare spectral broadening of the amide I band small peptide trialanine with that N-methylacetamide, a commonly model system for bond. In contrast significantly inhomogeneously broadened. Employing classical molecular-dynamics simulations combined density-functional-theory calculations, origin inhomogeneity investigated. While both systems exhibit similar hydrogen-bonding dynamics, it found conformational dynamics causes...

Driven by recent two-dimensional infrared experiments Woutersen and Hamm, trialanine has emerged as a paradigm to study conformational dynamics of small peptide in aqueous solution. Employing the exceptional amount experimental ab initio data, this work, serves model problem perform comprehensive comparison six popular force fields, including versions AMBER, CHARMM, GROMOS, OPLS models. For all fields under consideration, 20 ns long molecular-dynamics simulations are performed, structure...

Various aspects of the ab initio-based parametrization an exciton model amide I vibrations in peptides are discussed. Adopting "glycine dipeptide" (Ac-Gly-NHCH3) as a simple building-block that describes vibrational interaction between two peptide units, we perform comprehensive quantum-chemical calculations to investigate effect and importance level theory, choice local coordinates, localization method. A solvent continuum description turns out important obtain planar CONH units when full...

An atom−atom partitioning of the electrostatic energy between unperturbed molecules is proposed on basis topology electron density. Atom−atom contributions to are computed exactly, i.e., via a novel six-dimensional integration over two atomic basins, and by means spherical tensor multipole expansion, up total interaction rank L = lA + lB 1 6. The convergence behavior topological expansion compared with that using distributed analysis (DMA) moments for set van der Waals complexes at...

An atom–atom partitioning of the (super)molecular Coulomb energy is proposed on basis topological electron density. Atom–atom contributions to molecular intra- and intermolecular are computed exactly, i.e., via a double integration over atomic basins, by means spherical tensor multipole expansion, up rank L=lA+lB+1=5. The convergence expansion able reproduce exact interaction with an accuracy 0.1–2.3 kJ/mol at L=5 for atom pairs, each belonging different molecule constituting van der Waals...

We discuss the use of super-fermion formalism to represent and solve quantum kinetic equations for electron transport problem. Starting with Lindblad master equation molecule connected two metal electrodes, we convert problem finding nonequilibrium steady state many-body non-Hermitian Liouvillian in super-Fock space. transform normal ordered form, introduce quasiparticles by a set canonical nonunitary transformations develop general theory through interacting region. The approach is applied...

The theory of atoms in molecules (AIM) defines bounded atomic fragments real space that generate transferable properties. As part a program investigates the topological partitioning electromagnetic properties based on electron density, we have calculated exact electrostatic potential (AEP) an AIM atom molecule. Second expand this terms multipole moments spherical tensors. We prove convergence expansion is faster than previously assumed, even for complicated shapes.

Amine-terminated molecules show well-behaved conductance in the scanning tunneling microscope break-junction experimental measurements. We performed density functional theory based electron transport calculations to explain nature of this phenomenon. find that amines can be adsorbed only on apex Au atom, while thiolate group attached equally well undercoordinated and clean surfaces. Our one adsorption geometry is sterically energetically possible for amine-anchored junction whereas three...

Recent experimental realization [J. Am. Chem. Soc., 127 (2005) 7328] of various dithiocarbamate self-assembly on gold surface opens the possibility for use linkers to anchor molecular wires electrodes. In this paper, we explore hypothesis computationally. We computed electron transport properties 4,4'-bipyridine (BP), 4,4'-bipyridinium-1,1'-bis(carbodithioate) (BPBC), 4-(4'-pyridyl)-peridium-1-carbodithioate (BPC) molecule junctions based density functional theory and nonequilibrium Green's...

Spontaneously formed Si–S bonds enable monolayer and single-molecule Si–molecule–Si circuits.

Bullvalene is the archetypical "shape shifting" molecule, undergoing continuous Cope rearrangements in solution at room temperature a rate of about 3 kHz. In confined spaces an scanning tunneling microscopy break junction (STMBJ) setup, isolated bisarylbullvalene molecules have recently been shown to exhibit very restricted isomerization and slower interconversion rates. The number populated bullvalene isomers displayed large variances conductivity with confinement manifest high...

The exact atomic electrostatic potential (AEP) and multipole moments are calculated using the topological partitioning of electron density. High rank (l⩽20) spherical tensor used to examine convergence properties expansion. We vary independently maximum rank, lmax, radius grid around an atom in a molecule where we measure discrepancy between AEP one obtained via root mean square values 0.1 1.6 kJ/mol for four atoms (C, N, O, S) on with ρ=0.001 a.u. lmax=4. Our calculations demonstrate that...

Abstract Nanoscale electro-mechanical systems (NEMS) displaying piezoresistance offer unique measurement opportunities at the sub-cellular level, in detectors and sensors, emerging generations of integrated electronic devices. Here, we show a single-molecule NEMS piezoresistor that operates utilising constitutional conformational isomerisation individual diaryl-bullvalene molecules can be switched 850 Hz. Observations are made using scanning tunnelling microscopy break junction (STMBJ)...

We investigate the effects of alternating voltage on nonequilibrium quantum systems with localised phonon modes. Nonequilibrium Green's functions are utilised, electron-phonon coupling being considered $GD$ approximation (self-consistent Born approximation). Using a Floquet approach, we assume periodicity dynamics. This approach allows us to influence driven electronic component occupation vibrations. It was found that signatures inelastic transport gained photon-assisted peaks. A simplistic...

We study computationally the electron transport properties of dithiocarboxylate terminated molecular junctions. Transport are computed self-consistently within density functional theory and nonequilibrium Green's functions formalism. A microscopic origin experimentally observed current amplification by anchoring groups is established. For 4,4‘-biphenyl bis(dithiocarboxylate) junction, we find that interaction lowest unoccupied orbital (LUMO) group with LUMO highest occupied (HOMO) biphenyl...

We discuss the use of tunneling electron current to control and catalyze chemical reactions. Assuming separation time scales for electronic nuclear dynamics we employ Langevin equation a reaction coordinate. The contains nonconservative current-induced forces gives nonequilibrium, effective potential energy surface current-carrying molecular systems. are computed via Keldysh nonequilibrium Green's functions. Once current-depended is defined, modeled as an escape Brownian particle from well....

The paper describes the derivation of Kohn-Sham equations for a nanowire with direct current. A value electron current enters problem as an input via subsidiary condition imposed by pointwise Lagrange multiplier. Using constrained minimization Hohenberg-Kohn energy functional, we derive set self-consistent carrying orbitals molecular wire.

We present a method to perform stability analysis of nonequilibrium fixed points appearing in self-consistent electron transport calculations. The are given by the solution stationary, nonlinear kinetic equation for single-particle density matrix. obtain matrix linearizing around and analyze real part its spectrum assess asymptotic time behavior points. derive expressions matrices within Hartree-Fock linear response adiabatic time-dependent functional theory. multiple is performed...

We present an escape rate theory for current-induced chemical reactions. use Keldysh nonequilibrium Green's functions to derive a Langevin equation the reaction coordinate. Due out of equilibrium electronic degrees freedom, friction, noise, and effective temperature in depend locally on As example, we consider dissociation diatomic molecules induced by current from scanning tunnelling microscope tip. In resonant regime, molecular involves two processes which are intricately interconnected:...

Quantum transport of electrons through a molecule is series individual electron tunneling events separated by stochastic waiting time intervals. We study the emergence temporal correlations between successive times for in vibrating molecular junction. Using master equation approach, we compute joint probability distribution two events. show that completely reset after each event if vibrations are thermally equilibrated. If treat vibrational dynamics exactly without imposing equilibration...

On the elementary level, electronic current consists of individual electron tunnelling events that are separated by random time intervals. The waiting distribution is a probability to observe transfer in detector electrode at t+τ given an was detected same earlier t. We study for quantum transport vibrating molecular junction. By treating electron-vibration interaction exactly and molecule-electrode coupling perturbatively, we obtain master equation compute times transport. details...

Molecule-electrode interfaces in molecular electronic junctions are prone to chemical reactions, structural changes, and localized heating effects caused by electric current. These can be exploited for device functionality or may degrading processes that limit performance lifetime. We develop a nonequilibrium Green's function based transport theory which the central region atoms and, more importantly, on molecule-electrode allowed move. The separation of time-scales slow nuclear motion fast...

We use a superoperator representation of the quantum kinetic equation to develop nonequilibrium perturbation theory for an inelastic electron current through dot. derive Lindblad-type embedded dot (i.e. connected Lindblad dissipators buffer zone). The is converted non-Hermitian field in Liouville-Fock space. general many-body developed and applied with electron-vibronic electron-electron interactions. Our becomes equivalent Keldysh Green's function perturbative treatment provided that zone...