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.
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.
An in depth investigation of the fine structure adopted by the helical stacks of C 3 -discotics 1 incorporating three 3,3 0 -diamino-2,2 0 -bipyridine units is described. In the bulk the molecules display liquid crystalline behaviour in a temperature window of >300 K and an ordered rectangular columnar mesophase (Col ro ) with an inter-disc distance of 3.4A is assigned. X-Ray diffraction on aligned samples has also revealed a helical superstructure in the liquid crystalline state, and a rotation angle of 13-16 between consecutive discs. The proposed superstructure in the bulk phase has been further substantiated by a combination of quantum-chemical calculations and solid-state NMR spectroscopy. Dilute solution NMR spectroscopy and elaborate CD spectroscopy on aggregated samples have revealed an isodesmic growth pattern of the C 3 -discotics. From the combined results it has become evident that the fine tuning interaction responsible for the highly ordered helical architectures is not weak intermolecular hydrogen bonding, but rather rigidification, due to propeller formation after preorganisation by p-p interactions. Although all the techniques used underpin the structural features proposed, none of them individually is able to point to a unique structure. However, together the techniques give very strong evidence for a confined ship-screw arrangement in which all amidic carbonyl oxygens point in one direction.
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.
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.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
customersupport@researchsolutions.com
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
This site is protected by reCAPTCHA and the Google Privacy Policy and Terms of Service apply.
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.