A new electronic structure method for doublet states: configuration interaction in the space of ionized 1h and 2h1p determinants.

An implementation of gradient and energy calculations for configuration interaction variant of equation-of-motion coupled cluster with single and double substitutions for ionization potentials (EOM-IP-CCSD) is reported. The method (termed IP-CISD) treats the ground and excited doublet electronic states of an N-electron system as ionizing excitations from a closed-shell N+1-electron reference state. The method is naturally spin adapted, variational, and size intensive. The computational scaling is N(5), in contrast with the N(6) scaling of EOM-IP-CCSD. The performance and capabilities of the new approach are demonstrated by application to the uracil cation and water and benzene dimer cations by benchmarking IP-CISD against more accurate IP-CCSD. The equilibrium geometries, especially relative differences between different ionized states, are well reproduced. The average absolute errors and the standard deviations averaged for all bond lengths in all electronic states (58 values in total) are 0.014 and 0.007 A, respectively. IP-CISD systematically underestimates intramolecular distances and overestimates intermolecular ones, because of the underlying uncorrelated Hartree-Fock reference wave function. The IP-CISD excitation energies of the cations are of a semiquantitative value only, showing maximum errors of 0.35 eV relative to EOM-IP-CCSD. Trends in properties such as dipole moments, transition dipoles, and charge distributions are well reproduced by IP-CISD.

The effect of pi-stacking and H-bonding on ionization energies of a nucleobase: uracil dimer cation.

The electronic structure of the ionized pi-stacked and H-bonded uracil dimers as well as that of the monomer, is characterized by the equation-of-motion coupled-cluster method for ionization potentials (EOM-IP). Vertical ionization energies (IEs) for the 5 lowest states of the monomer and the 10 lowest states of the dimers are presented. Non-covalent interactions in the dimers reduce the lowest vertical IE by 0.34 and 0.13 eV in the pi-stacked and H-bonded dimers, respectively. The electronic spectra of the cations are also presented. The two dimer cations feature intense charge resonance bands at 0.52 and 0.11 eV, respectively. The position and intensity of the bands are sensitive to the dimer structures, for example, the geometric relaxation in the pi-stacked dimer blue-shifts the CR band by more than 1 eV and results in a threefold intensity increase. The results of the calculations are rationalized within the dimer molecular orbital - linear combination of fragment molecular orbitals (DMO-LCFMO) framework. The basis set effects and energy additivity schemes are also discussed.

Characterization of a complete cycle of acetylcholinesterase catalysis by ab initio QM/MM modeling.

The reaction mechanism of acetylcholine hydrolysis by acetylcholinesterase, including both acylation and deacylation stages from the enzyme-substrate (ES) to the enzyme-product (EP) molecular complexes, is examined by using an ab initio type quantum mechanical - molecular mechanical (QM/MM) approach. The density functional theory PBE0/aug-6-31+G* method for a fairly large quantum part trapped inside the native protein environment, and the AMBER force field parameters in the molecular mechanical part are employed in computations. All reaction steps, including the formation of the first tetrahedral intermediate (TI1), the acylenzyme (EA) complex, the second tetrahedral intermediate (TI2), and the EP complex, are modeled at the same theoretical level. In agreement with the experimental rate constants, the estimated activation energy barrier of the deacylation stage is slightly higher than that for the acylation phase. The critical role of the non-triad Glu202 amino acid residue in orienting lytic water molecule and in stabilizing the second tetrahedral intermediate at the deacylation stage of the enzymatic process is demonstrated.

Performance of the spin-flip and multireference methods for bond breaking in hydrocarbons: a benchmark study.

Benchmark results for spin-flip (SF) coupled-cluster and multireference (MR) methods for bond-breaking in hydrocarbons are presented. The nonparallelity errors (NPEs), which are defined as an absolute value of the difference between the maximum and minimum values of the errors in the potential energy along bond-breaking curves, are analyzed for (i) the entire range of nuclear distortions from equilibrium to the dissociation limit and (ii) in the intermediate range (2.5-4.5 A), which is the most relevant for kinetics modeling. For methane, the spin-flip and MR results are compared against full configuration interaction (FCI). For the entire potential energy curves, the NPEs for the SF model with single and double substitutions (SF-CCSD) are slightly less than 3 kcal/mol. Inclusion of triple excitations reduces the NPEs to 0.32 kcal/mol. The corresponding NPEs for the MR-CI are less than 1 kcal/mol, while those of multireference perturbation theory are slightly larger (1.2 kcal/mol). The NPEs in the intermediate range are smaller for all of the methods. The largest errors of 0.35 kcal/mol are observed, surprisingly, for a spin-flip approach that includes triple excitations, while MR-CI, CASPT2, and SF-CCSD curves are very close to each other and are within 0.1-0.2 kcal/mol of FCI. For a larger basis set, the difference between MR-CI and CASPT2 is about 0.2 kcal/mol, while SF-CCSD is within 0.4 kcal/mol of MR-CI. For the C-C bond breaking in ethane, the results of the SF-CCSD are within 1 kcal/mol of MR-CI for the entire curve and within 0.4 kcal/mol in the intermediate region. The corresponding NPEs for CASPT2 are 1.8 and 0.4 kcal/mol, respectively. Including the effect of triples by energy-additivity schemes is found to be insignificant for the intermediate region. For the entire range of nuclear separations, sufficiently large basis sets are required to avoid artifacts at small internuclear separations.