Molecular dynamics simulations of beta-cyclodextrin-aziadamantane complexes in water

Force-field-based atomistic simulations of host-guest supramolecular complexes between beta-cyclodextrin and several aziadamantane derivatives have been analyzed with respect to relative orientation and interaction energies, explicitly considering solvent (water) molecules. For each case, the calculations revealed two stable orientations of the guest within the host that are different in interaction energy. Fluctuation of and correlation between characteristic properties were analyzed. Among other things, it turned out that orientation angle and inclusion depth are clearly correlated. In addition, for the unsubstituted aziadamantane, the enthalpy of complex formation was calculated and compared to experimental results.     

A sodium atom in a large water cluster: electron delocalization and infrared spectra

Ab initio molecular dynamics simulations modeling low-energy collisions of a sodium atom with a cluster with more than 30 water molecules are presented. We follow the dynamics of the atom-cluster interaction and the delocalization of the valence electron of sodium together with the changes in the electron binding energy. This electron tends to be shared by the nascent sodium cation and the water cluster. IR spectra of the sodium-water cluster are both computationally and experimentally obtained, with a good agreement between the two approaches.     

Curvature coupling dependence of membrane protein diffusion coefficients

We consider the lateral diffusion of a protein interacting with the curvature of the membrane. The interaction energy is minimized if the particle is at a membrane position with a certain curvature that agrees with the spontaneous curvature of the particle. We employ stochastic simulations that take into account both the thermal fluctuations of the membrane and the diffusive behavior of the particle. In this study, we neglect the influence of the particle on the membrane dynamics, thus the membrane dynamics agrees with that of a freely fluctuating membrane. Overall, we find that this curvature coupling substantially enhances the diffusion coefficient. We compare the ratio of the projected or measured diffusion coefficient and the free intramembrane diffusion coefficient, which is a parameter of the simulations, with analytical results that rely on several approximations. We find that the simulations always lead to a somewhat smaller diffusion coefficient than that from our analytical approach. A detailed study of the correlations of the forces acting on the particle indicates that the diffusing inclusion tries to follow favorable positions on the membrane such that forces along the trajectory are on average smaller than they would be for random particle positions.     

Optimization of augmentation functions for correlated calculations of spin-spin coupling constants and related properties

A new hierarchy of augmented basis sets optimized for the calculation of molecular properties such as indirect spin-spin coupling constants is presented. Based on the Dunning hierarchy of cc-pVXZ (X = D, T, Q, and 5) basis sets augmentation functions with tight exponents have been optimized for coupled-cluster calculations of indirect spin-spin coupling constants. The optimal exponents for these tight functions have been obtained by optimizing the sum of the absolute values of all contributions to the coupling constant. On the basis of a series of test cases (CO, HF, N(2), F(2), H(2)O, NH(3), and CH(4)) we propose a set of tight s, p, and d functions to be added to the uncontracted Dunning basis sets, and, subsequently, to recontract. The resulting ccJ-pVXZ (X = D, T, Q, and 5) basis sets demonstrate excellent cost efficiency in benchmark calculations. These new basis sets should generally be applicable for the calculation of spin-spin coupling constants and other properties that have a strong dependence on powers of 1r or even contain a delta distribution for correlated ab initio methods.     

NHC-Adducts of Cyclopentadienyl-Substituted Alanes

The mono- and bis-iodo-substituted NHC-stabilized alanes (NHC) ⋅ AlH₂I and (NHC) ⋅ AlHI₂ offer a convenient entry for further substitution reactions at aluminum. Reactions of (NHC) ⋅ AlH₂I 1 – 4 with one equivalent of NaCp afforded the adducts (NHC) ⋅ AlH₂Cp 9 – 12 (NHC=Me₂Im^Me ( 9 ), iPr₂Im^Me ( 10 ), iPr₂Im ( 11 ), Dipp₂Im ( 12 )). Alane adducts with two Cp substituents (NHC) ⋅ AlHCp₂ 13 – 16 (NHC=Me₂Im^Me ( 13 ), iPr₂Im^Me ( 14 ), iPr₂Im ( 15 ), Dipp₂Im ( 16 )) were prepared by the analogous reaction of (NHC) ⋅ AlHI₂ 5 – 8 using two equivalents of NaCp. The unusual dimeric adducts ((NHC) ⋅ AlH₂Cp ⋅ CpMgI)₂ 17 – 19 (NHC=Me₂Im^Me ( 17 ), iPr₂Im^Me ( 18 ), iPr₂Im ( 19 )) were obtained from the reaction of 1 – 3 with MgCp₂.     

Finite Element Analysis of Eigendynamics of Rolling Tires

The eigenvalue analysis of rolling tires is one part of the simulation of tire rolling noise radiation for the reduction of traffic noise. In this paper the general strategies of numerical eigenvalue analysis for nonsymmetric matrices are shown. The special effects observed on rotating bodies are discussed in details. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Modeling of Electromechanical Contact on a Microscopic Lengthscale

This paper treats the simulation of the contact mode of an atomic force microscope (AFM). The contact forces between the tip and the sample surface is calculated via the van derWaals force in a Finite Element approach, the integration of the contact force a FEM environment is discussed and numerical examples are presented. (© 2005 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)