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...

A fast stochastic method for calculating the second order Møller-Plesset (MP2) correction to the correlation energy of large systems of electrons is presented. The approach is based on reducing the exact summation over occupied and unoccupied states to a time-dependent trace formula amenable to stochastic sampling. We demonstrate the abilities of the method to treat systems with thousands of el...

The central nervous system (CNS) represents an excellent model system for examining how a multitude of unique cell fates are specified. We find that asymmetric localization of the numb protein autonomously controls a binary cell fate decision in the Drosophila CNS. The simplest lineage in the Drosophila CNS is that of the MP2 precursor: it divides unequally to generate the dMP2 and vMP2 neurons...

The melanization reaction is used as an immune mechanism in arthropods to encapsulate and kill microbial pathogens. In Drosophila, the serpin Spn27A regulates melanization apparently by inhibiting the protease that activates phenoloxidase, the key enzyme in melanin synthesis. Here, we have described the genetic characterization of two immune inducible serine proteases, MP1 and MP2, which act in...

We predict structures and energies of water clusters containing up to 19 waters with X3LYP, an extended hybrid density functional designed to describe noncovalently bound systems as accurately as covalent systems. Our work establishes X3LYP as the most practical ab initio method today for calculating accurate water cluster structures and energies. We compare X3LYP/aug-cc-pVTZ energies to the mo...

The conformations of a series of organophosphine oxides, OP(CH3)2R, where R = methyl, ethyl, isopropyl, tert-butyl, vinyl, and phenyl, are predicted using the MP2/cc-pVTZ level of theory. Comparison of potential energy surfaces for rotation about P-C bonds with crystal structure data reveals a strong correlation between predicted location and energetics of minima and histograms of dihedral angl...

BACKGROUND Cyanoform is long known as one of the strongest acid. Cyanoform is only stable below -40 °C. The issue of the stability and tautomeric equilibria of cyanoform (CF) are investigated at the DFT and MP2 levels of theory. The present work presents a detailed study of structural tautomer interconversion in three different media, namely, in the gas phase, in a solvent continuum, and in a m...

The results of harmonic and anharmonic frequency calculations on a guanine-cytosine complex with an enolic structure (a tautomeric form with cytosine in the enol form and with a hydrogen at the 7-position on guanine) are presented and compared to gas-phase IR-UV double resonance spectral data. Harmonic frequencies were obtained at the RI-MP2/cc-pVDZ, RI-MP2/TZVPP, and semiempirical PM3 levels o...

      In this study, the interaction between NO2+ cation and Hen (n = 1-7) clusters is investigated by means of ab initio calculations at MP2/aug-cc-pVTZ and QCISD/aug-cc-pVTZ computational levels. The first and second solvation shells were obtained while N atom of NO2+ interacts with five and two He atoms, respectively. Stabilizat...

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...