QSLE-v1.0: A New Software Package for the Calculation of Coupled Quantum-Classical Dynamics in Condensed Phases Based on a Stochastic Approach.

Recently, a stochastic version of the quantum-classical Liouville equation has been proposed [Campeggio, J.; Cortivo, R.; Zerbetto, M.

Analysis of Velocity Autocorrelation Functions from Molecular Dynamics Simulations of a Small Peptide by the Generalized Langevin Equation with a Power-Law Kernel.

Internal motions play an essential role in the biological functions of proteins and have been the subject of numerous theoretical and spectroscopic studies. Such complex environments are associated with anomalous diffusion where, in contrast to the classical Brownian motion, the relevant correlation functions have power law decays with time. In this work, we investigate the presence of long memory stochastic processes through the analysis of atomic velocity autocorrelation functions.

Intrinsic Flexibility beyond the Highly Ordered DNA Tetrahedron: An Integrative Spectroscopic and Molecular Dynamics Approach.

Since the introduction of DNA-based architectures, in the past decade, DNA tetrahedrons have aroused great interest. Applications of such nanostructures require structural control, especially in the perspective of their possible functionalities. In this work, an integrated approach for structural characterization of a tetrahedron structure is proposed with a focus on the fundamental biophysical aspects driving the assembly process.

A multiscale approach to coupled nuclear and electronic dynamics. II. Exact and approximated evaluation of nonradiative transition rates.

This work follows a companion article, which will be referred to as Paper I [Campeggio et al., J. Chem.

A multiscale approach to coupled nuclear and electronic dynamics. I. Quantum-stochastic Liouville equation in natural internal coordinates.

Multiscale methods are powerful tools to describe large and complex systems. They are based on a hierarchical partitioning of the degrees of freedom (d.o.

The roto-conformational diffusion tensor as a tool to interpret molecular flexibility.

Stochastic modeling approaches can be used to rationalize complex molecular dynamical behaviours in solution, helping to interpret the coupling mechanisms among internal and external degrees of freedom, providing insight into reaction mechanisms and extracting structural and dynamical data from spectroscopic observables. However, the definition of comprehensive models is usually limited by (i) the difficulty in defining - without resorting to phenomenological assumptions - a representative reduced ensemble of molecular coordinates able to capture essential dynamical properties and (ii) the complexity of numerical or approximate treatments of the resulting equations. In this paper, we address the first of these two issues.

Microsecond MD Simulations of the Plexin-B1 RBD: N-H Probability Density as Descriptor of Structural Dynamics, Dimerization-Related Conformational Entropy, and Transient Dimer Asymmetry.

Amide-bond equilibrium probability density, = exp(-) (, local potential), and associated conformational entropy, = -∫ (ln ) ─ln ∫d, are derived for the Rho GTPase binding domain of Plexin-B1 (RBD) as monomer and dimer from 1 μs MD simulations. The objective is to elucidate the effect of dimerization on the dynamic structure of the RBD. Dispersed (peaked) functions indicate "flexibility" ("rigidity"; the respective concepts are used below in this context).

Microsecond MD Simulations of the Plexin-B1 RBD: 2. N-H Probability Densities and Conformational Entropy in Ligand-Free, Rac1-Bound, and Dimer RBD.

Orientational probability densities, = exp(-) (, local potential), of bond-vectors in proteins provide information on structural flexibility. The related conformational entropy, = -∫(ln )dΩ - ln ∫dΩ, provides the entropic contribution to the free energy of the physical/biological process studied. We have developed a new method for deriving and from MD simulations, using the N-H bond as probe.

Ethanol electro-oxidation reaction on the Pd(111) surface in alkaline media: insights from quantum and molecular mechanics.

The ethanol electro-oxidation catalyzed by Pd in an alkaline environment involves several intermediate reaction steps promoted by the hydroxyl radical, OH. In this work, we report on the dynamical paths of the first step of this oxidation reaction, namely the hydrogen atom abstraction CHCHOH + OH → CHCHOH + HO, occurring at the Pd(111) surface and address the thermodynamic stability of the adsorbed reactants by means of quantum and molecular mechanics calculations, with special focus on the effect of the solvent. We have found that the impact of the solvent is significant for both ethanol and OH, contributing to a decrease in their adsorption free energies by a few dozen kcal mol with respect to the adsorption energy under vacuum.

Parameter free evaluation of S2 reaction rates for halide substitution in halomethane.

We estimate the kinetic constants of a series of archetypal S2 reactions, , the nucleophilic substitutions of halides in halomethane. A parameter free, multiscale approach recently developed [Campeggio , , 2020, , 3455] is employed. The protocol relies on quantum mechanical calculations for the description of the energy profile along the intrinsic reaction coordinate, which is then mapped onto a reaction coordinate conveniently built for the reactive process.

Stochastic Modelling of C NMR Spin Relaxation Experiments in Oligosaccharides.

A framework for the stochastic description of relaxation processes in flexible macromolecules including dissipative effects has been recently introduced, starting from an atomistic view, describing the joint relaxation of internal coordinates and global degrees of freedom, and depending on parameters recoverable from classic force fields (energetics) and medium modelling at the continuum level (friction tensors). The new approach provides a rational context for the interpretation of magnetic resonance relaxation experiments. In its simplest formulation, the semi-flexible Brownian (SFB) model has been until now shown to reproduce correctly correlation functions and spectral densities related to orientational properties obtained by direct molecular dynamics simulations of peptides.

Conformational Entropy from Mobile Bond Vectors in Proteins: A Viewpoint that Unifies NMR Relaxation Theory and Molecular Dynamics Simulation Approaches.

A new method for determining conformational entropy in proteins is reported. Proteins prevail as conformational ensembles, ∝ exp(-). By selecting a bond vector (e.

Multiscale modeling of reaction rates: application to archetypal S2 nucleophilic substitutions.

We propose an approach to the evaluation of kinetic rates of elementary chemical reactions within Kramers' theory based on the definition of the reaction coordinate as a linear combination of natural, pseudo Z-matrix, internal coordinates of the system. The element of novelty is the possibility to evaluate the friction along the reaction coordinate, within a hydrodynamic framework developed recently [J. Campeggio et al.

Glycosidic linkage flexibility: The ψ torsion angle has a bimodal distribution in α-L-Rhap-(1→2)-α-L-Rhap-OMe as deduced from C NMR spin relaxation.

The molecular dynamics (MD) computer simulation technique is powerful for the investigation of conformational equilibrium properties of biomolecules. In particular, free energy surfaces of the torsion angles (those degrees of freedom from which the geometry mostly depends) allow one to access conformational states, as well as kinetic information, i.e.

Local Ordering at the N-H Sites of the Rho GTPase Binding Domain of Plexin-B1: Impact of Dimerization.

We have developed a new molecular dynamics (MD) based method for describing analytically local potentials at mobile N-H sites in proteins. Here we apply it to the monomer and dimer of the Rho GTPase binding domain (RBD) of the transmembrane receptor plexin-B1 to gain insight into dimerization, which can compete with Rho GTPase binding. In our method, the local potential is given by linear combinations, , of the real combinations of the Wigner rotation matrix elements, , with = 1-4 and appropriate symmetry.

Mesoporous Carbon with Different Density of Thiophenic-Like Functional Groups and Their Effect on Oxygen Reduction.

The metal-support interactions between sulfur-doped carbon supports (SMCs) and Pt nanoparticles (NPs) were investigated, aiming at verifying how sulfur functional groups can improve the electrocatalytic performance of Pt NPs towards the oxygen reduction reaction (ORR). SMCs were synthetized, tailoring the density of sulfur functional groups, and Pt NPs were deposited by thermal reduction of Pt(acac) . The extent of the metal-support interaction was proved by X-ray photoelectron spectroscopy (XPS) analysis, which revealed a strong electronic interaction, proportional to the density of sulfur defects, whereas XRD spectra provided evidence of higher strain in Pt NPs loaded on SMC.

Stochastic modeling of macromolecules in solution. I. Relaxation processes.

A framework for the stochastic description of relaxation processes in flexible macromolecules, including dissipative effects, is introduced from an atomistic point of view. Projection-operator techniques are employed to obtain multidimensional Fokker-Planck operators governing the relaxation of internal coordinates and global degrees of freedom and depending upon parameters fully recoverable from classic force fields (energetics) and continuum models (friction tensors). A hierarchy of approaches of different complexity is proposed in this unified context, aimed primarily at the interpretation of magnetic resonance relaxation experiments.

Stochastic modeling of macromolecules in solution. II. Spectral densities.

In Paper I [Polimeno et al., J. Chem.

Local Ordering at Mobile Sites in Proteins: Combining Perspectives from NMR Relaxation and Molecular Dynamics.

We report on progress toward improving NMR relaxation analysis in proteins in terms of the slowly relaxing local structure (SRLS) approach by developing a method that combines SRLS with molecular dynamics (MD) simulations. N-H bonds from the Rho GTPase binding domain of plexin-B1 are used as test case. We focus on the locally restricting/ordering potential of mean force (POMF), u(θ,φ), at the N-H site (θ and φ specify the orientation of the N-H bond in the protein).

DiTe2: Calculating the diffusion tensor for flexible molecules.

We report on an extended hydrodynamic modeling of the friction tensorial properties of flexible molecules including all types of natural, Z-Matrix like, internal coordinates. We implement the new methodology by extending and updating the software DiTe [Barone et al. J.

Evaluating rotation diffusion properties of molecules from short trajectories.

We show that under proper assumptions it is possible to estimate with good precision the principal values of the rotational diffusion tensor of proteins from the analysis of short (up to 2-3 ns) molecular dynamics trajectories. We apply this analysis to a few model cases: three polyalanine peptides (2, 5, and 10 aminoacids), the fragment B3 of protein G (GB3), the bovine pancreatic trypsin inhibitor (BPTI), the hen egg-white lysozyme (LYS), the B1 domain of plexin (PB1), and thrombin. The protocol is based on the analysis of the global angular momentum autocorrelation functions, complementing the standard approach based on rotational autocorrelation functions, which requires much longer trajectories.

Differential Dynamics at Glycosidic Linkages of an Oligosaccharide as Revealed by C NMR Spin Relaxation and Stochastic Modeling.

Among biomolecules, carbohydrates are unique in that not only can linkages be formed through different positions, but the structures may also be branched. The trisaccharide β-d-Glcp-(1→3)[β-d-Glcp-(1→2)]-α-d-Manp-OMe represents a model of a branched vicinally disubstituted structure. A C site-specific isotopologue, with labeling in each of the two terminal glucosyl residues, enabled the acquisition of high-quality C NMR relaxation parameters, T and T, and heteronuclear NOE, with standard deviations of ≤0.

Spectroscopic Insights into Carbon Dot Systems.

The controversial nature of the fluorescent properties of carbon dots (CDs), ascribed either to surface states or to small molecules adsorbed onto the carbon nanostructures, is an unresolved issue. To date, an accurate picture of CDs and an exhaustive structure-property correlation are still lacking. Using two unconventional spectroscopic techniques, fluorescence correlation spectroscopy (FCS) and time-resolved electron paramagnetic resonance (TREPR), we contribute to fill this gap.

Integrated Computational Approach to the Electron Paramagnetic Resonance Characterization of Rigid 3-Helical Peptides with TOAC Nitroxide Spin Labels.

We address the interpretation, via an integrated computational approach, of the experimental continuous-wave electron paramagnetic resonance (cw-EPR) spectra of a complete set of conformationally highly restricted, stable 3-helical peptides from hexa- to nonamers, each bis-labeled with nitroxide radical-containing TOAC (4-amino-1-oxyl-2,2,6,6-tetramethylpiperidine-4-carboxylic acid) residues. The usefulness of TOAC for this type of analysis has been shown already to be due to its cyclic piperidine side chain, which is rigidly connected to the peptide backbone α-carbon. The TOAC α-amino acids are separated by two, three, four, and five intervening residues.

N-H-Related Conformational Entropy Changes Entailed By Plexin-B1 RBD Dimerization: Combined Molecular Dynamics/NMR Relaxation Approach.

We report on a new method for determining function-related conformational entropy changes in proteins. Plexin-B1 RBD dimerization serves as example, and internally mobile N-H bonds serve as probes. S (entropy in units of kT) is given by -∫(PlnP)dΩ, where P = exp(-u) is the probability density for probe orientation, and u the local potential.