Background. The honey bee (Apis mellifera) is the most important pollinator in agriculture worldwide. However, the number of honey bees has fallen significantly since 2006, becoming a huge ecological problem nowadays. The principal cause is CCD, or Colony Collapse Disorder, characterized by the seemingly spontaneous abandonment of hives by their workers. One of the characteristics of CCD in hon...

We present a parallel implementation of second-order Møller-Plesset perturbation theory with the resolution-of-the-identity approximation (RI-MP2). The implementation is based on a recent improved sequential implementation of RI-MP2 within the Turbomole program package and employs the message passing interface (MPI) standard for communication between distributed memory nodes. The parallel imple...

The infrared (IR) and Raman spectra of triphenylene with intensities were calculated using both density functional theory (DFT, B3LYP method) and Moller-Plesset perturbation method of second order (MP2) with ccpVDZ basis set. Spectra were compared with experimentally measured; the agreement between the observed and calculated spectra is good in case of IR spectroscopy, MP2 simulated spectra wer...

A hybrid quantum mechanical/molecular mechanical (QM/MM) potential energy function with Hartree-Fock, density functional theory (DFT), and post-HF (RIMP2, MP2, CCSD) capability has been implemented in the CHARMM and Q-Chem software packages. In addition, we have modified CHARMM and Q-Chem to take advantage of the newly introduced replica path and the nudged elastic band methods, which are power...

In arthropods, melanization plays a major role in the innate immune response to encapsulate and kill the invasive organisms. It is mediated by a serine protease cascade and is regulated by serpins. The identification of the molecular components of melanization and the regulation of those components are still unclear in Drosophila melanogaster, although some genetic research on the activation of...

Basis set pairings for dual-basis calculations are presented for the aug-cc-pVXZ (X = D, T, Q) series of basis sets. Fidelity with single-basis results is assessed at the second-order Møller-Plesset perturbation theory (MP2) level within the resolution-of-the-identity (RI) approximation, using the S22 set of noncovalent interactions and a series of electron affinities from the G3 set. Root-mean...

A satisfactory account of the van der Waals (London dispersion) forces is, in general, not possible by the Kohn-Sham method using standard local, semi-local GGA or meta-GGA density functionals. The recently proposed range-separated hybrid (RSH) approach, supplemented by second order perturbational corrections (MP2) to include long range dynamic correlation effects offers a physically consistent...

Atomic populations and localization [lambda(A)] and delocalization [delta(A,B)] indices (LIs and DIs) are calculated for a large set of molecules at the Hartree-Fock (HF), MP2, MP4(SDQ), CISD, and QCISD levels with the 6-311++G(2d,2p) basis set. The HF method and the conventional correlation methods [MP2, MP4(SDQ), CISD, and QCISD] yield distinct sets of LIs and DIs. Yet, within the four conven...

We present a derivation and efficient implementation of the formally complete analytic second derivatives for domain-based local pair natural orbital order Møller–Plesset perturbation theory (MP2) method, applicable to electric or magnetic field-response properties but not yet harmonic frequencies. also discuss occurrence avoidance numerical instability issues related singular linear equation s...