The dynamics of copper intercalated molybdenum ditelluride

Layered transition metal dichalcogenides are emerging as key materials in nanoelectronics and energy applications. Predictive models to understand their growth, thermomechanical properties and interactions with metals are needed in order to accelerate their incorporation into commercial products. Interatomic potentials enable large-scale atomistic simulations at the device level, beyond the range of applications of first principle methods. We present a ReaxFF reactive force field to describe molybdenum ditelluride and its interactions with copper. We optimized the force field parameters to describe the properties of layered MoTe2 in various phases, the intercalation of Cu atoms and clusters within its van der Waals gap, including a proper description of energetics, charges and mechanical properties. The training set consists of an extensive set of first principle calculations computed from density functional theory. We use the force field to study the adhesion of a single layer MoTe2 on a Cu(111) surface and the results are in good agreement with density functional theory, even though such structures were not part of the training set. We characterized the mobility of the Cu ions intercalated into MoTe2 under the presence of an external electric fields via molecular dynamics simulations. The results show a significant increase in drift velocity for electric fields of approximately 0.4 V/A and that mobility increases with Cu ion concentration.Comment: 21 pages, 9 Figure

Ultrafast electron diffraction imaging of bond breaking in di-ionized acetylene

Visualizing chemical reactions as they occur requires atomic spatial and femtosecond temporal resolution. Here, we report imaging of the molecular structure of acetylene (C2H2) 9 femtoseconds after ionization. Using mid-infrared laser–induced electron diffraction (LIED), we obtained snapshots as a proton departs the [C2H2]2+ ion. By introducing an additional laser field, we also demonstrate control over the ultrafast dissociation process and resolve different bond dynamics for molecules oriented parallel versus perpendicular to the LIED field. These measurements are in excellent agreement with a quantum chemical description of field-dressed molecular dynamicsPostprint (author's final draft

Quantum simulations of the hydrogen molecule on ammonia clusters

2openMassimo Mella;E. CurottoMella, Massimo; E., Curott

Influence of electronic polarization on the binding of anions to a chloride-pumping rhodopsin

The functional properties of some biological ion channels and membrane transport proteins are proposed to exploit anion-hydrophobic interactions. Here, we investigate a chloride-pumping rhodopsin as an example of a membrane protein known to contain a defined anion binding site composed predominantly of hydrophobic residues. Using molecular dynamics simulations, we explore Cl- binding to this hydrophobic site and compare the dynamics arising when electronic polarization is neglected (CHARMM36 [c36] fixed-charge force field), included implicitly (via the prosECCo force field), or included explicitly (through the polarizable force field, AMOEBA). Free energy landscapes of Cl- moving out of the binding site and into bulk solution demonstrate that the inclusion of polarization results in stronger ion binding and a second metastable binding site in chloride-pumping rhodopsin. Simulations focused on this hydrophobic binding site also indicate longer binding durations and closer ion proximity when polarization is included. Furthermore, simulations reveal that Cl- within this binding site interacts with an adjacent loop to facilitate rebinding events that are not observed when polarization is neglected. These results demonstrate how the inclusion of polarization can influence the behavior of anions within protein binding sites and can yield results comparable with more accurate and computationally demanding methods

Density Functional Theory of doped superfluid liquid helium and nanodroplets

During the last decade, density function theory (DFT) in its static and dynamic time dependent forms, has emerged as a powerful tool to describe the structure and dynamics of doped liquid helium and droplets. In this review, we summarize the activity carried out in this field within the DFT framework since the publication of the previous review article on this subject [M. Barranco et al., J. Low Temp. Phys. 142, 1 (2006)]. Furthermore, a comprehensive presentation of the actual implementations of helium DFT is given, which have not been discussed in the individual articles or are scattered in the existing literature. This is an Accepted Manuscript of an article published on August 2, 2017 by Taylor & Francis Group in Int. Rev. Phys. Chem. 36, 621 (2017), available online: http://dx.doi.org/10.1080/0144235X.2017.1351672Comment: 113 pages, 42 figure

Kinetic characterization of the critical step in HIV-1 protease maturation

HIV maturation requires multiple cleavage of long polyprotein chains into functional proteins that include the viral protease itself. Initial cleavage by the protease dimer occurs from within these precursors, and yet only a single protease monomer is embedded in each polyprotein chain. Self-activation has been proposed to start from a partially dimerized protease formed from monomers of different chains binding its own N termini by self-association to the active site, but a complete structural understanding of this critical step in HIV maturation is missing. Here, we captured the critical self-association of immature HIV-1 protease to its extended amino-terminal recognition motif using large-scale molecular dynamics simulations, thus confirming the postulated intramolecular mechanism in atomic detail. We show that self-association to a catalytically viable state requires structural cooperativity of the flexible β-hairpin “flap” regions of the enzyme and that the major transition pathway is first via self-association in the semiopen/open enzyme states, followed by enzyme conformational transition into a catalytically viable closed state. Furthermore, partial N-terminal threading can play a role in self-association, whereas wide opening of the flaps in concert with self-association is not observed. We estimate the association rate constant (k(on)) to be on the order of ∼1 × 10(4) s(−1), suggesting that N-terminal self-association is not the rate-limiting step in the process. The shown mechanism also provides an interesting example of molecular conformational transitions along the association pathway

Roaming: a phase space perspective

In this review we discuss the recently described roaming mechanism for chemical reactions from the point of view of nonlinear dynamical systems in phase space. The recognition of the roaming phenomenon shows the need for further developments in our fundamental understanding of basic reaction dynamics, as is made clear by considering some questions that cut across most studies of roaming: Is the dynamics statistical? Can transition state theory be applied to estimate roaming reaction rates? What role do saddle points on the potential energy surface play in explaining the behavior of roaming trajectories? How do we construct a dividing surface that is appropriate for describing the transformation from reactants to products for roaming trajectories? How should we define the roaming region? We show that the phase space perspective on reaction dynamics provides the setting in which these questions can be properly framed and answered. We illustrate these ideas by considering photodissociation of formaldehyde. The phase-space formulation allows an unambiguous description of all possible reactive events, which also allows us to uncover the phase space mechanism that explains which trajectories roam, as opposed to evolving toward a different reactive event