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MRCC is a package of ab initio and density functional quantum chemistry programs for accurate electronic structure calculations. The suite has efficient implementations of both low- and high-level correlation methods, such as second-order Møller–Plesset (MP2), random-phase approximation (RPA), second-order algebraic-diagrammatic construction [ADC(2)], coupled-cluster (CC), configuration interaction (CI), and related techniques. It has a state-of-the-art CC singles and doubles with perturbative triples [CCSD(T)] code, and its specialties, the arbitrary-order iterative and perturbative CC methods developed by automated programming tools, enable achieving convergence with regard to the level of correlation. The package also offers a collection of multi-reference CC and CI approaches. Efficient implementations of density functional theory (DFT) and more advanced combined DFT-wave function approaches are also available. Its other special features, the highly competitive linear-scaling local correlation schemes, allow for MP2, RPA, ADC(2), CCSD(T), and higher-order CC calculations for extended systems. Local correlation calculations can be considerably accelerated by multi-level approximations and DFT-embedding techniques, and an interface to molecular dynamics software is provided for quantum mechanics/molecular mechanics calculations. All components of MRCC support shared-memory parallelism, and multi-node parallelization is also available for various methods. For academic purposes, the package is available free of charge. [ABSTRACT FROM AUTHOR]

Recognition of the methylated regions of the DNA plays an important role in the epigenetic processes. We analyze the interactions between the methylated DNA and the methyl-CpG-binding proteins using two models. The first model was built from a methylated or non-methylated cytosine, a guanine and an arginine residue in the experimental arrangement. We applied the M06L density functional method with a small, polarized double-ζ basis set for the geometry optimizations, and the MP2 method with polarized triple-ζ basis set for the energy calculations. The second model was built from two methylcytosines, guanines, guanidinium groups plus an additional carboxyl group in the experimental arrangement. We applied the B3LYP method with a small, polarized double-ζ basis set for the geometry optimizations and thermal corrections. The single-point energies were obtained from dual-hybrid dRPA75 and dRPA@PBE0 calculations supplemented by a moderately large polarized triple-ζ basis set. The hydration effects were modeled by adding explicit water molecules. These calculations revealed that the hydrophobic interaction has the largest contribution to the Gibbs interaction energy and turns the arginine side chains into hydrogen bonding position. Our results show that the translation of the protein along the DNA double helix is sterically hindered by the contact of its arginine side chains with the methyl groups of the methyl cytosines. This supports a hopping mechanism for the searching movement of the protein along the DNA. [ABSTRACT FROM AUTHOR]

While most molecules and solids are spin-unpolarized, most chemically-active atoms are partly spin-polarized. As a result, the errors of the spin-dependence of a density functional are much more troublesome for atomization energies than they are for typical reaction or formation energies. This observation explains why the atomization energy errors of approximate functionals do not correlate with their other errors, and why the errors of atomization energies for a given functional can be radically reduced by fitting the energies of the atoms. We present an illustrative example from the recent nonempirical construction of the SCAN meta-generalized gradient approximation. [ABSTRACT FROM AUTHOR]

Glycoproteins play a central role in the immune response. In this study, we focus on the core of the common O-linked mucin-type glycopeptides. It has been observed that glycosylation stabilizes the protein in a stiffened, extended structure. We provide a unified picture for the conformation and stabilization of the O-glycosidic linkage using O-(2-acetylamino-2-deoxy-α- or -β- d-galacto- or -mannopyranosyl)- N-acetyl- l-serinamide model structures. We have calculated equilibrium geometries of the model structures with the B3LYP/6-31G(2 df, p) method suggested in the Gaussian-4 theory. According to the relative energies, we confirm that the GalNAc-Ser linkage is more stable than its mannose analogues. The natural preference for the α-GalNAc-Ser over the β-GalNAc-Ser anomers can be explained by entropic effects. We explored the hydrogen bonding patterns on the carbohydrate unit calculating highly accurate dRPA@PBE0.25 and dRPA75 energies and found that in some cases, the acetamido group can be fixed by hydrogen bonding from the (O3)H atom, but in most of the cases, it can rotate more freely. The torsion angles in the glycosidic linkage show that the linkage is stiffened more in the α-anomers and the most in the α-GalNAc-Ser structure because of the steric strains in the axial position and by two or three intramolecular hydrogen bonds. We also found that although, in our gas-phase model geometries, the peptide backbone prefers to be in a γ-turn, a structural water molecule can stabilize a polyproline II helix of a proline-rich sequence, a β-sheet, or more likely random coils. [ABSTRACT FROM AUTHOR]

The size limit of substituents allowingO-through-the-annulus rotation of substituted calix[4]arenes was further extended to the propargyloxy group in 24-propargyloxy-25,26,27-tris(N,N-dimethylcarbamoylmethoxy)-p-tert-butylcalix[4]arene by demonstrating its free but slow motion affording equilibrium between the partial cone and 1,2-alternate conformers. The effect of solvent and upper rim substituents R1on the conformational inversion was investigated by means of1H NMR. The rotational isomerisation of the parent (R1= H) analogue could not unambiguously be detected. The experimental results were supported by comprehensive density functional theory studies. [ABSTRACT FROM AUTHOR]

Electrolyte Cathode Discharge (ELCAD) spectrometry, a novel sensitive multielement direct analytical method for metal traces in aqueous solutions, was introduced in 1993 as a new sensing principle. Since then several works have tried to develop an operational mechanism for this exotic atmospheric glow plasma technique, however these attempts cannot be combined into a valid model description. In this review we summarize the conceptual and technical problems we found in this upcoming research field of direct sensors. The TG gas temperature and the ne electron density values published up to now for ELCAD are very confusing. These data were evaluated by three conditions. The first is the gas composition of the ELCAD plasma, since TG was determined from the emitted intensity of the N2 and OH bands. Secondly, since the ELCAD is an atmospheric glow discharge, thus, the obtained TG has to be close to the Te electron temperature. This can be used for the mutual validation of the received temperature data. Thirdly, as a consequence of the second condition, the values of TG and ne have to agree with the Engel-Brown approximation of the Saha-equation related to weakly ionized glow discharge plasmas. Application of non-adequate experimental methods and theoretical treatment leads to unreliable descriptions which cannot be used to optimize the detector performance. [ABSTRACT FROM AUTHOR]