The Martini coarse-grained force field has been successfully used for simulating a wide range of (bio)molecular systems. Recent progress in our ability to test the model against fully atomistic force fields, however, has revealed some shortcomings. Most notable, phenylalanine and proline were too hydrophobic, and dimers formed by polar residues in apolar solvents did not bind strongly enough. Here, we reparametrize these residues either through reassignment of particle types or by introducing embedded charges. The new parameters are tested with respect to partitioning across a lipid bilayer, membrane binding of Wimley-White peptides, and dimerization free energy in solvents of different polarity. In addition, we improve some of the bonded terms in the Martini protein force field that lead to a more realistic length of α-helices and to improved numerical stability for polyalanine and glycine repeats. The new parameter set is denoted Martini version 2.2.

We report a theoretical study of the photoisomerization step in the operating cycle of a prototypical fluorene-based molecular rotary motor (1). The potential energy surfaces of the ground electronic state (S0) and the first singlet excited state (S1) are explored by semiempirical quantum-chemical calculations using the orthogonalization-corrected OM2 Hamiltonian in combination with a multireference configuration interaction (MRCI) treatment. The OM2/MRCI results for the S0 and S1 minima of the relevant 1-P and 1-M isomers and for the corresponding S0 transition state are in good agreement with higher-level calculations, both with regard to geometries and energetics. The S1 surface is characterized at the OM2/MRCI level by locating two S0-S1 minimum-energy conical intersections and nearby points on the intersection seam and by computing energy profiles for pathways toward these MECIs. Semiclassical Tully-type trajectory surface hopping (TSH) simulations with on-the-fly OM2/MRCI calculations are carried out to study the excited-state dynamics after photoexcitation to the S1 state. Fast relaxation to the ground state is observed through the conical intersection regions, predominantly through the lowest-energy one with a strongly twisted central C═C double bond and pyramidalized central carbon atom. The excited-state lifetimes for the direct and inverse photoisomerization reactions (1.40 and 1.79 ps) and the photostationary state ratio (2.7:1) from the TSH-OM2 simulations are in good agreement with the available experimental data (ca. 1.7 ps and 3:1). Excited-state lifetimes, photostationary state ratio, and dynamical details of the TSH-OM2 simulations also agree with classical molecular dynamics simulations using a reparametrized optimized potentials for liquid simulations (OPLS) all-atom force field with ad-hoc surface hops at predefined conical intersection points. The latter approach allows for a more extensive statistical sampling.

We present an algorithm to reconstruct atomistic structures from their corresponding coarse-grained (CG) representations and its implementation into the freely available molecular dynamics (MD) program package GROMACS. The central part of the algorithm is a simulated annealing MD simulation in which the CG and atomistic structures are coupled via restraints. A number of examples demonstrate the application of the reconstruction procedure to obtain low-energy atomistic structural ensembles from their CG counterparts. We reconstructed individual molecules in vacuo (NCQ tripeptide, dipalmitoylphosphatidylcholine, and cholesterol), bulk water, and a WALP transmembrane peptide embedded in a solvated lipid bilayer. The first examples serve to optimize the parameters for the reconstruction procedure, whereas the latter examples illustrate the applicability to condensed-phase biomolecular systems.

Molekularer Lichtschalter: Am Ein‐/Ausschalten der Fluoreszenz des Proteins asFP595 ist eine trans‐cis‐Isomerisierung beteiligt (siehe Schema). Quantenmechanische und klassische Simulationen erhellen die spektroskopischen Eigenschaften von asFP595 und verschaffen einen genauen Einblick in den Photoschaltmechanismus. Der trans‐cis‐Konformationswechsel löst eine Protonentransferkaskade zwischen dem Chromophor und benachbarten Aminosäuren aus.

It was proved by Hitchin that any solution of his evolution equations for a half-flat SU(3)structure on a compact six-manifold M defines an extension of M to a seven-manifold with holonomy in G 2. We give a new proof, which does not require the compactness of M . More generally, we prove that the evolution of any half-flat G-structure on a six-manifold M defines an extension of M to a Ricci-flat seven-manifold N , for any real form G of SL(3, C). If G is non-compact, then the holonomy group of N is a subgroup of the non-compact form G * 2 of G C 2 . Similar results are obtained for the extension of nearly half-flat structures by nearly parallel G 2-or G * 2 -structures, as well as for the extension of cocalibrated G2-and G * 2 -structures by parallel Spin(7)-and Spin 0 (3, 4)-structures, respectively. As an application, we obtain that any six-dimensional homogeneous manifold with an invariant half-flat structure admits a canonical extension to a seven-manifold with a parallel G 2-or G * 2 -structure. For the group H3 × H3, where H 3 is the three-dimensional Heisenberg group, we describe all left-invariant half-flat structures and develop a method to explicitly determine the resulting parallel G 2-or G * 2 -structure without integrating. In particular, we construct three eight-parameter families of metrics with holonomy equal to G 2 and G * 2 . Moreover, we obtain a strong rigidity result for the metrics induced by a half-flat structure (ω, ρ) on H 3 × H3 satisfying ω(z, z) = 0, where z denotes the centre. Finally, we describe the special geometry of the space of stable three-forms satisfying a reality condition. Considering all possible reality conditions, we find four different special Kähler manifolds and one special para-Kähler manifold.Proposition 1.1. Let V be an n-dimensional real or complex vector space. The general linear group GL(V ) has an open orbit in Λ k V * , with 0 k n/2, if and only if k 2 or if k = 3 and n = 6, 7 or 8.Proof. The representation of GL(V ) on Λ k V * is irreducible. In the complex case the result thus follows, for instance, from the classification of irreducible complex prehomogeneous vector spaces [32]. The result in the real case follows from the complex case, since the complexification of the GL(n, R)-module Λ k R n * is an irreducible GL(n, C)-module. Remark 1.2. An open orbit is unique in the complex case, since an orbit that is open in the usual topology is also Zariski-open and Zariski-dense (see [31, Proposition 2.2]). Over the reals, the number of open orbits is finite by a well-known theorem of Whitney.Proposition 1.4. Let V be an oriented real vector space of dimension n and assume that k ∈ {2, n − 2} with n even, or k ∈ {3, n − 3} with n = 6, 7 or 8. There is a GL + (V )-equivariant mappinghomogeneous of degree n/k, which assigns a volume form to a stable k-form and which vanishes on non-stable forms. Given a stable k-form ρ, the derivative of φ in ρ defines a dual (n − k)-form ρ ∈ Λ n−k V * by the property(1.1)The dual formρ is also stable and satisfiesA stable form, it...