Using the ONIOM hybrid method to apply equation of motion CCSD to larger systems: Benchmarking and comparison with time-dependent density functional theory, configuration interaction singles, and time-dependent Hartree–Fock

Equation of motion coupled-cluster singles and doubles (EOM-CCSD) is one of the most accurate computational methods for the description of one-electron vertical transitions. However, its O(N6) scaling, where N is the number of basis functions, often makes the study of molecules larger than 10–15 heavy atoms prohibitive. In this work we investigate how accurately less expensive methods can approximate the EOM-CCSD results. We focus on our own N-layer integrated molecular orbital molecular mechanics (ONIOM) hybrid scheme, where the system is partitioned into regions which are treated with different levels of theory. For our set of benchmark calculations, the comparison of conventional configuration interaction singles (CIS), time-dependent Hartree–Fock (TDHF), and time-dependent density functional theory (TDDFT) methods and ONIOM (with different low level methods) showed that the best accuracy-computational time combination is obtained with ONIOM(EOM:TDDFT), which has a rms of the error with respect to the conventional EOM-CCSD of 0.06 eV, compared with 0.47 eV of the conventional TDDFT

Anharmonic transitions in nearly dry L-cysteine I

Two special dynamical transitions of universal character have been recently observed in macromolecules at $T_{D}\sim 180 - 220$ K and $T^{*}\sim 100$ K. Despite their relevance, a complete understanding of the nature of these transitions and their consequences for the bio-activity of the macromolecule is still lacking. Our results and analysis concerning the temperature dependence of structural, vibrational and thermodynamical properties of the orthorhombic polymorph of the amino acid L-cysteine (at a hydration level of 3.5%) indicated that the two referred temperatures define the triggering of very simple and specific events that govern all the biochemical interactions of the biomolecule: activation of rigid rotors ($T<T^{*}$), phonon-phonon interactions with phonons of water dimer ($T^{*}<T<T_{D}$), and water rotational barriers surpassing ($T>T_{D}$).Comment: 4 pages, 4 figures, submitted to Physical Review Letter

16p11.2 600 kb Duplications confer risk for typical and atypical Rolandic epilepsy

Rolandic epilepsy (RE) is the most common idiopathic focal childhood epilepsy. Its molecular basis is largely unknown and a complex genetic etiology is assumed in the majority of affected individuals. The present study tested whether six large recurrent copy number variants at 1q21, 15q11.2, 15q13.3, 16p11.2, 16p13.11 and 22q11.2 previously associated with neurodevelopmental disorders also increase risk of RE. Our association analyses revealed a significant excess of the 600 kb genomic duplication at the 16p11.2 locus (chr16: 29.5-30.1 Mb) in 393 unrelated patients with typical (n = 339) and atypical (ARE; n = 54) RE compared with the prevalence in 65 046 European population controls (5/393 cases versus 32/65 046 controls; Fisher's exact test P = 2.83 × 10−6, odds ratio = 26.2, 95% confidence interval: 7.9-68.2). In contrast, the 16p11.2 duplication was not detected in 1738 European epilepsy patients with either temporal lobe epilepsy (n = 330) and genetic generalized epilepsies (n = 1408), suggesting a selective enrichment of the 16p11.2 duplication in idiopathic focal childhood epilepsies (Fisher's exact test P = 2.1 × 10−4). In a subsequent screen among children carrying the 16p11.2 600 kb rearrangement we identified three patients with RE-spectrum epilepsies in 117 duplication carriers (2.6%) but none in 202 carriers of the reciprocal deletion. Our results suggest that the 16p11.2 duplication represents a significant genetic risk factor for typical and atypical R