560 research outputs found
Ultrafast Relaxation Dynamics of the Ethylene Cation C2H4+
No full textWe present a combined experimental and computational study of the relaxation dynamics of the ethylene cation. In the experiment, we apply an extreme-ultraviolet-pump/infrared-probe scheme that permits us to resolve time scales on the order of 10 fs. The photoionization of ethylene followed by an infrared (IR) probe pulse leads to a rich structure in the fragment ion yields reflecting the fast response of the molecule and its nuclei. The temporal resolution of our setup enables us to pinpoint an upper bound of the previously defined ethylene-ethylidene isomerization time to 30 ± 3 fs. Time-dependent density functional based trajectory surface hopping simulations show that internal relaxation between the first excited states and the ground state occurs via three different conical intersections. This relaxation unfolds on femtosecond time scales and can be probed by ultrashort IR pulses. Through this probe mechanism, we demonstrate a route to optical control of the important dissociation pathways leading to separation of H or H2
Development of Site-Specific Mg2+-RNA Force Field Parameters: A Dream or Reality? Guidelines from Combined Molecular Dynamics and Quantum Mechanics Simulations
No full textThe vital contribution of Mg2+ ions to RNA biology is challenging to dissect at the experimental level. This calls for the integrative support of atomistic simulations, which at the classical level are plagued by limited accuracy. Indeed, force fields intrinsically neglect nontrivial electronic effects that Mg2+ exerts on its surrounding ligands in varying RNA coordination environments. Here, we present a combined computational study based on classical molecular dynamics (MD) and Density Functional Theory (DFT) calculations, aimed at characterizing (i) the performance of five Mg2+ force field (FF) models in RNA systems and (ii) how charge transfer and polarization affect the binding of Mg2+ ions in different coordination motifs. As a result, a total of similar to 2.5 mu s MD simulations (100/200 ns for each run) for two prototypical Mg2+-dependent ribozymes showed remarkable differences in terms of populations of inner-sphere coordination site types. Most importantly, complementary DFT calculations unveiled that differences in charge transfer and polarization among recurrent Mg2+-RNA coordination motifs are surprisingly small. In particular, the charge of the Mg2+ ions substantially remains constant through different coordination sites, suggesting that the common philosophy of developing site-specific Mg2+ ion parameters is not in line with the physical origin of the Mg2+-RNA MD simulations inaccuracies. Overall, this study constitutes a guideline for an adept use of current Mg2+ models and provides novel insights for the rational development of next-generation Mg2+ FFs to be employed for atomistic simulations of RNA.LCB
Valence and conduction band tuning in halide perovskites for solar cell applications
No full textWe performed density functional calculations aimed at identifying the atomistic and electronic structure origin of the valence and conduction band, and band gap tunability of halide perovskites ABX3 upon variations of the monovalent and bivalent cations A and B and the halide anion X. We found that the two key ingredients are the overlap between atomic orbitals of the bivalent cation and the halide anion, and the electronic charge on the metal center. In particular, lower gaps are associated with higher negative antibonding overlap of the states at the valence band maximum (VBM), and higher charge on the bivalent cation in the states at the conduction band minimum (CBM). Both VBM orbital overlap and CBM charge on the metal ion can be tuned over a wide range by changes in the chemical nature of A, B and X, as well as by variations of the crystal structure. On the basis of our results, we provide some practical rules to tune the valence band maximum, respectively the conduction band minimum, and thus the band gap in this class of materials
Scanning Reactive Pathways with Orbital Biased Molecular Dynamics
No full textTo accelerate reactive events in molecular dynamics simulations we introduce a
general bias potential scheme which depends only on the electronic degrees of freedom of the
reactive system. This electronic reaction coordinate, which is expressed in terms of a penalty
function of the one-electron orbital energies, has been applied to study different reaction pathways
of s-cis-butadiene. Three different reactive channels have been identified: the cis/trans
isomerization, the s-cis/s-trans isomerization, and the symmetry allowed cyclization. For the
latter, despite the fact that the Woodward-Hoffmann rules are guided by the butadiene frontier
orbitals, biasing only these orbitals is not enough to drive the system toward cyclization, but a
low-lying valence shell orbital needs to be included
Multiscale biomolecular simulations in the exascale era
No full textThe complexity of biological systems and processes, spanning molecular to macroscopic scales, necessitates the use of multiscale simulations to get a comprehensive understanding. Quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations are crucial for capturing processes beyond the reach of classical MD simulations. The advent of exascale computing offers unprecedented opportunities for scientific exploration, not least within life sciences, where simulations are essential to unravel intricate molecular mechanisms underlying biological processes. However, leveraging the immense computational power of exascale computing requires innovative algorithms and software designs. In this context, we discuss the current status and future prospects of multiscale biomolecular simulations on exascale supercomputers with a focus on QM/MM MD. We highlight our own efforts in developing a versatile and high-performance multiscale simulation framework with the aim of efficient utilization of state-of-the-art supercomputers. We showcase its application in uncovering complex biological mechanisms and its potential for leveraging exascale computing.</p
A Hamiltonian electrostatic coupling scheme for hybrid Car-Parrinello molecular dynamics simulations
No full textWe present a fully Hamiltonian and computationally efficient scheme to include the electrostatic effects due to the classical environment in a Car-Parrinello mixed quantum Mechanics/molecular mechanics (QM/MM) method. The polarization due to the MM atoms close to the quantum system is described by a Coulombic potential modified at short range. We show that the functional form of this potential has to be chosen carefully in order to obtain the correct interaction properties and to prevent an unphysical escape of the electronic density to the MM atoms (the so-called spill-out effect). The interaction between the QM system and the more distant MM atoms is modeled by a Hamiltonian term explicitly coupling the multipole moments of the quantum charge distribution with the classical point charges. Our approach remedies some of the well known deficiencies of current electrostatic coupling schemes in QM/MM methods, allowing molecular dynamics simulations of mixed systems within a fully consistent and energy conserving approach
Cis-trans isomerization in triply-bonded ditungsten complexes: A multitude of possible pathways
No full textWe have investigated different possible mechanisms for the cis-trans isomerization in triply bonded ditungsten complexes with stoichiometry W2Cl4(NHEt)(2)(PMe3)(2) using static density functional calculations as well as Car-Parrinello simulations. Our studies reveal an unexpected richness of possible reaction pathways that include both unimolecular and bimolecular mechanisms. Among the possible routes that have been identified are processes involving successive dissociation/reassociation of phosphine ligands, intramolecular chloride hopping, intertungsten phosphine exchange as well as numerous combinations of these basic reaction types. All pathways involve maximal activation barriers of less than 35 kcal/mol and include phosphine concentration dependent and independent routes. The energetically most favorable phosphine-dependent pathway is based on the dissociation/reassociation of phosphine ligands. This path is characterized by a maximal dissociation barrier of IS kcal/mol. The fastest alternative unimolecular route (with a maximal activation barrier of 24 kcal/mol) is based on a direct exchange of phosphine between the two metallic coordination centers. All the identified pathways, with the exception of a previously proposed internal flip mechanism that can be ruled out on energetic grounds, are competitive and may contribute in various combinations to the overall reaction rate. The identified isomerization mechanisms are fully consistent with the experimentally observed 3-state-kinetics and the dependence of the overall reaction rate on the excess concentration of phosphine which is demonstrated with a simplified kinetic model of the process
Wagging the Tail: Essential Role of Substrate Flexibility in FAAH Catalysis
No full textThe serine hydrolase, fatty acid amide hydrolase (FAAH), is responsible for the intracellular degradation of anandamide and other bioactive fatty acid ethanolamides involved in the regulation of pain, inflammation, and other pathophysiological processes. The catalytic site of FAAH is composed of multiple cavities with mixed hydrophobic and hydrophilic properties, the role of which remains incompletely understood. Anandamide is thought to enter the active site through a “membrane-access” (MA) channel and position its flexible fatty acyl chain in a highly hydrophobic “acyl chain- binding” (AB) cavity to allow for hydrolysis to occur. Using microsecond molecular dynamics (MD) simulations of FAAH embedded in a realistic membrane/water environment, we show now that anandamide may not lock itself into the AB cavity but may rather assume catalytically significant conformations required for hydrolysis by moving its flexible arachidonoyl tail between the MA and AB cavities. This process is regulated by a phenylalanine residue (Phe432) located at the boundary between the two cavities, which may act as a “dynamic paddle.” The results identify structural flexibility as a key determinant by which FAAH recognizes its primary lipid substrate.LCB
New insights into ultrafast relaxation dynamics of the ethylene cation C2H4+
No full textUltrafast relaxation dynamics of the ethylene cation are investigated with unprecedented temporal resolution. This enabled us to redefine the isomerization time to 30 fs and identify relaxation channels evolving on time scales <50 fs
Extended intermolecular interactions governing photocurrent-voltage relations in ternary organic solar cells
No full textEfficient organic solar cells are based on (electron) donor−acceptor
heterojunctions. An optically generated excited molecular state (exciton) is dissociated at
this junction, forming a charge-transfer (CT) state in an intermediate step before the
electron and hole are completely separated. The observed highly efficient dissociation of
this Coulombically bound state raises the question on the dissociation mechanism. Here,
we show that the observed high quantum yields of charge carrier generation and CT state
dissociation are due to extended (and consequently weakly bound) CT states visible in
absorption and emission spectra and first-principles calculations. Identifying a new
geminate-pair loss mechanism via donor excimers, we find that the hole on the small-
molecule donor is not localized on a single molecule and charge separation is correlated with the energetic offset between excimer and CT states. Thus, the charges upon interface charge transfer and even in the case of back-transfer and recombination are less localized than commonly assumed
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