Reverse Mapping of Coarse Grained Polyglutamine Conformations from PRIME20 Sampling.

An inverse coarse-graining protocol is presented for generating and validating atomistic structures of large (bio-) molecules from conformations obtained via a coarse-grained sampling method. Specifically, the protocol is implemented and tested based on the (coarse-grained) PRIME20 protein model (P20/SAMC), and the resulting all-atom conformations are simulated using conventional biomolecular force fields. The phase space sampling at the coarse-grained level is performed with a stochastical approximation Monte Carlo approach. The method is applied to a series of polypeptides, specifically dimers of polyglutamine with varying chain length in aqueous solution. The majority (>70 %) of the conformations obtained from the coarse-grained peptide model can successfully be mapped back to atomistic structures that remain conformationally stable during 10 ns of molecular dynamics simulations. This work can be seen as the first step towards the overarching goal of improving our understanding of protein aggregation phenomena through simulation methods.

Coexistence of Cationic and Anionic Phosphate Moieties in Solids: Unusual but Not Impossible.

Phosphoric acid is commonly known either as a neutral molecule or as an anion (phosphate). We theoretically confirm by ab initio molecular dynamics simulations (AIMD) that a cationic form H4PO4+ coexists with the anionic form H2PO4- in the same salt. This paradoxical situation is achieved by partial substitution of Cs+ by H4PO4+ in CsH2PO4. Thus, HnPO4 acts simultaneously as both the positive and the negative ion of the salt. We analyze the dynamical protonation pattern within the unusual hydrogen bond network that is established between the ions. Our AIMD simulations show that a conventional assignment of protonation states of the phosphate groups is not meaningful. Instead, a better description of the protonation situation is achieved by an efficiently fractional assignment of the strongly hydrogen-bonded protons to both its nearest and next-nearest oxygen neighbors.

Acute Bite Angle POP- and PSP-Type Ligands and Their Trinuclear Copper(I) Complexes: Synthesis and Photo-Luminescence Properties.

In the current work, the rational synthesis of trinuclear copper complexes, incorporating acute bite angle POP- and PSP-type ligands, is reported. The in situ formation of POP (Ph2P-O-PPh2) or PSP (Ph2P-S-PPh2) ligands in the presence of a copper(I) precursor gave access to various trinuclear copper complexes of the form [Cu3(µ3-Hal)2(µ-PXP)3]PF6 [X = O; Hal = Cl (1), Br (2), I (3) and X = S; Hal = Cl (5), Br (6), I (7)]. Related iodide-containing complexes and clusters, such as [Cu4(µ3-I)4(Ph2PI)4] (4) and [Cu3(µ3-I)2(µ-I)(µ-PSP)2] (8), could also be obtained via the variation of the reaction stoichiometry. The investigation of the photo-optical properties by photo-luminescence spectroscopy has demonstrated that the phosphorescence in the visible region can be switched off through the mere change of the heteroatom in the ligand backbone (POP vs PSP ligand scaffold). Theoretical studies have been conducted to complement the experimental photo-optical data with detailed insights into the occurring electronic transitions. Consequently, this systematic study paves the way for tuning the photo-optical properties of transition metal complexes in a more rational way.

ab-Initio Study of Hydrogen Bond Networks in 1,2,3-Triazole Phases.

The research in storage and conversion of energy is an everlasting process. The use of fuel cells is very tempting but up to now there are still several conceptual challenges to overcome. Especially, the requirement of liquid water causes difficulties due to the temperature limit. Therefore, imidazoles and triazoles are increasingly investigated in a manifold of experimental and theoretical publications as they are both very promising in overcoming this problem. Recently, triazoles were found to be superior to imidazoles in proton conduction. An ab-initio molecular dynamics simulation of pure triazole phases for investigating the behavior of both tautomer species of the triazole molecule has never been done. In this work, we investigate the structural and dynamical properties of two different solid phases and the liquid phase at two different temperatures. We are able to show how the distinct tautomers contribute to the mechanism of proton conduction, to compute dynamical properties of the four systems and to suggest a mechanism of reorientation in solid phase.

Exploring non-equilibrium molecular dynamics of mobile protons in the solid acid CsH2PO4 at the micrometer and microsecond scale.

We explicitly compute the non-equilibrium molecular dynamics of protons in the solid acid CsH2PO4 on the micrometer length scale via a multiscale Markov model: The molecular dynamics/matrix propagation (MDM) method. Within the MDM approach, the proton dynamics information of an entire molecular dynamics simulation can be condensed into a single M × M matrix (M is the number of oxygen atoms in the simulated system). Due to this drastic reduction in the complexity, we demonstrate how to increase the length and time scales in order to enable the simulation of inhomogeneities of CsH2PO4 systems at the nanometer scale. We incorporate explicit correlation of protonation dynamics with the protonation state of the neighboring proton sites and illustrate that this modification conserves the Markov character of the MDM method. We show that atomistic features such as the mean square displacement and the diffusion coefficient of the protons can be computed quantitatively from the matrix representation. Furthermore, we demonstrate the application potential of the scheme by computing the explicit dynamics of a non-equilibrium process in an 8 µm CsH2PO4 system during 5 ms.

Dynamical matrix propagator scheme for large-scale proton dynamics simulations.

We derive a matrix formalism for the simulation of long range proton dynamics for extended systems and timescales. On the basis of an ab initio molecular dynamics simulation, we construct a Markov chain, which allows us to store the entire proton dynamics in an M × M transition matrix (where M is the number of oxygen atoms). In this article, we start from common topology features of the hydrogen bond network of good proton conductors and utilize them as constituent constraints of our dynamic model. We present a thorough mathematical derivation of our approach and verify its uniqueness and correct asymptotic behavior. We propagate the proton distribution by means of transition matrices, which contain kinetic data from both ultra-short (sub-ps) and intermediate (ps) timescales. This concept allows us to keep the most relevant features from the microscopic level while effectively reaching larger time and length scales. We demonstrate the applicability of the transition matrices for the description of proton conduction trends in proton exchange membrane materials.

Effect of anion reorientation on proton mobility in the solid acids family CsHyXO4 (X = S, P, Se, y = 1, 2) from ab initio molecular dynamics simulations.

The high temperature phases of the solid acids CsHSeO4, CsHSO4 and CsH2PO4 show extraordinary high proton conductivities, while the low temperature phases do not conduct protons at all. We systematically investigate proton dynamics in the low and high temperature phases of these compounds by means of ab initio molecular dynamics simulations in order to develop a general picture of the proton transfer mechanism. For all of these compounds, proton conduction follows a Grotthuss mechanism via a combined proton transfer and subsequent structural reorientation of the environment. We demonstrate that the drastically reduced conductivity of the low temperature phases is caused by a highly ordered, rigid hydrogen bond network, while efficient long range proton transfer in the high temperature phases is enabled by the interplay of high proton transfer rates and frequent anion reorientation. Furthermore, we present a simple descriptor for the quantitative prediction of the diffusion coefficient within the solid acids family. As a side result, we show that the rate of the most elementary proton hopping reaction depends on the heavy-atom configuration of the nearest atoms in a ubiquitous manner, and is in turn almost independent from the global nature of the compound, i.e. whether it is organic or inorganic, ordered or disordered.

Efficient representation of the linear density-density response function.

We present a thorough derivation of the mathematical foundations of the representation of the molecular linear electronic density-density response function in terms of a computationally highly efficient moment expansion. Our new representation avoids the necessities of computing and storing numerous eigenfunctions of the response kernel by means of a considerable dimensionality reduction about from 103 to 101 . As the scheme is applicable to any compact, self-adjoint, and positive definite linear operator, we present a general formulation, which can be transferred to other applications with little effort. We also present an explicit application, which illustrates the actual procedure for applying the moment expansion of the linear density-density response function to a water molecule that is subject to a varying external perturbation potential. © 2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.

Proton mobility in aqueous systems: combining ab initio accuracy with millisecond timescales.

We present a multiscale simulation of proton transport in liquid water, combining ab initio molecular dynamics simulations with force-field ensemble averaging and kinetic Monte-Carlo simulations. This unique Ansatz allows for ab initio accuracy incorporating the femtosecond dielectric relaxation dynamics of the aqueous hydrogen bonding network, and bridges the time-scale gap towards the explicit simulation of millisecond diffusion dynamics.

Generalization of the electronic susceptibility for arbitrary molecular geometries.

We generalize the explicit representation of the electronic susceptibility χ[R](r, r') for arbitrary molecular geometries R. The electronic susceptibility is a response function that yields the response of the molecular electronic charge density at linear order to an arbitrary external perturbation. We address the dependence of this response function on the molecular geometry. The explicit representation of the molecular geometry dependence is achieved by means of a Taylor expansion in the nuclear coordinates. Our approach relies on a recently developed low-rank representation of the response function χ[R](r, r') which allows a highly condensed storage of the expansion and an efficient application within dynamical chemical environments. We illustrate the performance and accuracy of our scheme by computing the vibrationally induced variations of the response function of a water molecule and its resulting Raman spectrum.