Reversible hydrogen bond network dynamics: molecular dynamics simulations of calix[4]arene-catenanes.

We present detailed molecular dynamics (MD) simulations of mechanically interlocked calix[4]arene-catenanes under external force. Single-molecule force spectroscopy experiments revealed that the separation of dimers with two aliphatic loops results in reversible hydrogen bond breakage through an intermediate in a triple-well potential, while the tetra-loop species separates in a one-step manner (Janke, M.; et al. Nat. Nanotechnol. 2009, 4, 225). MD simulations show that calix[4]arenes interlocked by four loops (1) display a complete restructuring of the hydrogen bond network under mechanical force. All hydrogen bonds of the closed structure open, and new ones are formed in the extended structure. For small loading rates, we found reversible rejoining of the hydrogen bond network, while the rebinding ability diminishes with increasing pulling velocity, demonstrating the feasibility of MD simulations to capture also rebinding dynamics. Calix[4]arene dimers with two longer loops (2) under external force display more intricate physics because the elongation proceeds in a two-step transition from a compact structure to an open one, in which complete dissociation into calix[4]arene monomers is only prevented by the mechanical locking of the loops. We present a detailed analysis of hydrogen bond breakage and show that the transition from the closed to the intermediate structure is very similar to the transition from the closed to the open structure in the tetra-loop case. The stability of the intermediate is explained in terms of the closed hydrogen bonds, which are only broken when the transition to the open structure is enforced.

Mechanically interlocked calix[4]arene dimers display reversible bond breakage under force.

The physics of nanoscopic systems is strongly governed by thermal fluctuations that produce significant deviations from the behaviour of large ensembles. Stretching experiments of single molecules offer a unique way to study fundamental theories of statistical mechanics, as recently shown for the unzipping of RNA hairpins. Here, we report a molecular design based on oligo calix[4]arene catenanes-calixarene dimers held together by 16 hydrogen bridges-in which loops within the molecules limit how far the calixarene nanocapsules can be separated. This mechanically locked structure tunes the energy landscape of dimers, thus permitting the reversible rupture and rejoining of the individual nanocapsules. Experimental evidence, supported by molecular dynamics simulations, reveals the presence of an intermediate state involving the concerted rupture of the 16 hydrogen bridges. Stochastic modelling using a three-well potential under external load allows reconstruction of the energy landscape.

Parallel Calculation of CCSD and CCSD(T) Analytic First and Second Derivatives.

In this paper we present a parallel adaptation of a highly efficient coupled-cluster algorithm for calculating coupled-cluster singles and doubles (CCSD) and coupled-cluster singles and doubles augmented by a perturbative treatment of triple excitations (CCSD(T)) energies, gradients, and, for the first time, analytic second derivatives. A minimal-effort strategy is outlined that leads to an amplitude-replicated, communication-minimized implementation by parallelizing the time-determining steps for CCSD and CCSD(T). The resulting algorithm is aimed at affordable cluster architectures consisting of compute nodes with sufficient memory and local disk space and that are connected by standard communication networks like Gigabit Ethernet. While this scheme has disadvantages in the limit of very large numbers of compute nodes, it proves to be an efficient way of reducing the overall computational time for large-scale coupled-cluster calculations. In this way, CCSD(T) calculations of molecular properties such as vibrational frequencies or NMR-chemical shifts for systems with more than 1000 basis functions are feasible. A thorough analysis of the time-determining steps for CCSD and CCSD(T) energies, gradients, and second derivatives is carried out. Benchmark calculations are presented, proving that the parallelization of these steps is sufficient to obtain an efficient parallel scheme. This also includes the calculation of parallel CCSD energies and gradients using unrestricted (UHF) and restricted open-shell (ROHF) Hartree-Fock references, parallel UHF-CCSD(T) energies and gradients, parallel ROHF-CCSD(T) energies as well as parallel equation-of-motion CCSD energies and gradients for closed- and open-shell references. First applications to the calculation of the NMR chemical shifts of benzene using large basis sets and to the calculation of the equilibrium geometry of ferrocene as well as energy calculations with more than 1300 basis functions demonstrate the efficiency of the implementation.

Helical packing of discotic hexaphenyl hexa-peri-hexabenzocoronenes: theory and experiment.

The arrangement of discotic hexa-peri-hexabenzocoronenes (HBCs) into columnar helical superstructures has been investigated in relation to their molecular architecture. The supramolecular structure of two hexaphenyl-substituted HBC derivatives, differing only in the chiral/achiral nature of the attached alkyl side chains, was studied by circular dichroism and temperature-dependent wide-angle X-ray diffraction on oriented filaments. A structural model in agreement with the experimental observations was developed on the basis of accompanying quantum-chemical calculations. The helical organization along the self-assembled columnar structures was induced by the steric requirements of the bulky phenyl rings near the aromatic core, i.e., by their rotation out-of-plane with respect to the aromatic core. On the other hand, a uniform handedness of the twist was generated by chiral alkyl substituents. At higher temperatures the degree of helical organization decreases due to lateral and longitudinal dynamics of the discotic molecules. Annealing at ambient conditions improved the long-range arrangement of the discs along the columnar structures. This reorganization indicated a self-healing of the plastic material which is desirable for application of discotics as active layers in electronic devices. The helical packing resulted in a considerable stability of the mesophase up to 500 degrees C, which has not been reported for a discotic so far.

Low-pressure pyrolysis of tBu2SO: synthesis and IR spectroscopic detection of HSOH.

Sulfenic acid (HSOH, 1) has been synthesized in the gas-phase by low-pressure high-temperature (1150 degrees C) pyrolysis of di-tert-butyl sulfoxide (tBu(2)SO, 2) and characterized by means of matrix isolation and gas-phase IR spectroscopy. High-level coupled-cluster (CC) calculations (CCSD(T)/cc-pVTZ and CCSD(T)/cc-pVQZ) support the first identification of the gas-phase IR spectrum of 1 and enable its spectral characterization. Five of the six vibrational fundamentals of matrix-isolated 1 have been assigned, and its rotational-resolved gas-phase IR spectrum provides additional information on the O-H and S-H stretching fundamentals. Investigations of the pyrolysis reaction by mass spectrometry, matrix isolation, and gas-phase FT-IR spectroscopy reveal that, up to 500 degrees C, 2 decomposes selectively into tert-butylsulfenic acid, (tBuSOH, 3), and 2-methylpropene. The formation of the isomeric sulfoxide (tBu(H)SO, 3 a) has been excluded. Transient 3 has been characterized by a comprehensive matrix and gas-phase vibrational IR study guided by the predicted vibrational spectrum calculated at the density functional theory (DFT) level (B3LYP/6-311+G(2d,p)). At higher temperatures, the intramolecular decomposition of 3, monitored by matrix IR spectroscopy, yields short-lived 1 along with 2-methylpropene, but also H(2)O, and most probably sulfur atoms. In addition, HSSOH (6), H(2), and S(2)O are found among the final pyrolysis products observed at 1150 degrees C in the gas phase owing to competing intra- and intermolecular decomposition routes of 3. The decomposition routes of the starting compound 2 and of the primary intermediate 3 are discussed on the basis of experimental results and a computational study performed at the B3LYP/6-311G* and second-order Møller-Plesset (MP2/6-311G* and RI-MP2/QZVPP) levels of theory.

Determining the geometry of hydrogen bonds in solids with picometer accuracy by quantum-chemical calculations and NMR spectroscopy.

The structure of multiply hydrogen-bonded systems is determined with picometer accuracy by a combined solid-state NMR and quantum-chemical approach. On the experimental side, advanced 1H-15N dipolar recoupling NMR techniques are capable of providing proton-nitrogen distances of up to about 250 pm with an accuracy level of +/-1 pm for short distances (i.e., around 100 pm) and +/-5 pm for longer ones (i.e., 180 to 250 pm). The experiments were performed under fast magic-angle spinning, which ensures sufficient dipolar decoupling and spectral resolution of the 1H resonance lines. On the quantum-chemical side, the structures of the hydrogen-bonded systems were computationally optimised, yielding complete sets of nitrogen-proton and proton-proton distances, which are essential for correctly interpreting the experimental NMR data. In this way, nitrogen-proton distances were determined with picometer accuracy, so that vibrational averaging effects on dipole-dipole couplings need to be considered. The obtained structures were finally confirmed by the complete agreement of computed and experimental 'H and '5N chemical shifts. This demonstrates that solid-state NMR and quantum-chemical methods ideally complement each other and, in a combined manner, represent a powerful approach for reliable, high-precision structure determination whenever scattering techniques are inapplicable.