Orthogonalization corrections for semiempirical methods

Weber, W.; Thiel, Walter

doi:10.1007/s002149900083

Cited by 396 publications

(255 citation statements)

References 30 publications

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“…89 It includes valence-shell orthogonalization corrections both in the one-center part 87 and in the two-center part of the core Hamiltonian. 88,90 The MOs obtained from the OM2 calculation are used as input in a subsequent GUGA-MRCI calculation. 91 Conceptually, the semiempirical OM2 MO calculation already accounts for a large fraction of dynamical correlation, so that the MRCI treatment mainly needs to recover non-dynamical correlation effects.…”

Section: E Om2/mrcimentioning

confidence: 99%

Assessment of approximate computational methods for conical intersections and branching plane vectors in organic molecules

Nikiforov

Gámez

Thiel

et al. 2014

The Journal of Chemical Physics

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136

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Quantum-chemical computational methods are benchmarked for their ability to describe conical intersections in a series of organic molecules and models of biological chromophores. Reference results for the geometries, relative energies, and branching planes of conical intersections are obtained using ab initio multireference configuration interaction with single and double excitations (MRCISD). They are compared with the results from more approximate methods, namely, the state-interaction state-averaged restricted ensemble-referenced Kohn-Sham method, spin-flip time-dependent density functional theory, and a semiempirical MRCISD approach using an orthogonalization-corrected model. It is demonstrated that these approximate methods reproduce the ab initio reference data very well, with root-mean-square deviations in the optimized geometries of the order of 0.1 Å or less and with reasonable agreement in the computed relative energies. A detailed analysis of the branching plane vectors shows that all currently applied methods yield similar nuclear displacements for escaping the strong non-adiabatic coupling region near the conical intersections. Our comparisons support the use of the tested quantum-chemical methods for modeling the photochemistry of large organic and biological systems. © 2014 AIP Publishing LLC. [http://dx

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Section: E Om2/mrcimentioning

confidence: 99%

Assessment of approximate computational methods for conical intersections and branching plane vectors in organic molecules

Nikiforov

Gámez

Thiel

et al. 2014

The Journal of Chemical Physics

Self Cite

136

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“…The structures found were then re-optimized using the semiempirical OM2 (orthogonalization model 2) method [39]. To calculate the absorption spectra, the OM2 method combined with the graphical unitary group approach (GUGA) multi-reference configuration interaction (MR-CI) [40,41] within the MNDO program [42] was used.…”

Section: Computationmentioning

confidence: 99%

UV Photodissociation of Proline-containing Peptide Ions: Insights from Molecular Dynamics

Girod

Sanader

Vojković

et al. 2014

J. Am. Soc. Mass Spectrom.

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Abstract. UV photodissociation of proline-containing peptide ions leads to unusual product ions. In this paper, we report laser-induced dissociation of a series of prolinecontaining peptides at 213 nm. We observe specific fragmentation pathways corresponding to the formation of (y-2), (a + 2) and (b + 2) fragment ions. This was not observed at 266 nm or for peptides which do not contain proline residues. In order to obtain insights into the fragmentation dynamics at 213 nm, a small peptide (RPK for arginine-proline-lysine) was studied both theoretically and experimentally. Calculations of absorption spectra and non-adiabatic molecular dynamics (MD) were made. Second and third excited singlet states, S 2 and S 3 , lie close to 213 nm. Non-adiabatic MD simulation starting from S 2 and S 3 shows that these transitions are followed by C-C and C-N bond activation close to the proline residue. After this first relaxation step, consecutive rearrangements and proton transfers are required to produce unusual (y-2), (a + 2) and (b + 2) fragment ions. These fragmentation mechanisms were confirmed by H/D exchange experiments.

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“…Finally, it is worthwhile to notice that the present work does not include the latest OMx series of semiempirical methods from Prof. Thiel's group, 7 which improve on the existing semiempirical models by the inclusion of orthogonalization corrections. Those methods have been shown to considerably improve on the peptide conformations as compared to AM1 and PM3, 110 to better reproduce the water-water interaction energies in a QM/ MM environment, 111 and have recently been expanded with a dispersion correction term similar to the one used for SCC-DFTB/d.…”

Section: Discussionmentioning

confidence: 99%

Are Current Semiempirical Methods Better Than Force Fields? A Study from the Thermodynamics Perspective

2009

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The semiempirical Hamiltonians MNDO, AM1, PM3, RM1, PDDG/MNDO, PDDG/PM3, and SCC-DFTB, when used as part of a hybrid QM/MM scheme for the simulation of biological molecules, were compared on their abilities to reproduce experimental ensemble averages at or near room temperatures for the model system alanine dipeptide in water. Free energy surfaces in the (φ, ψ) dihedral angle space, 3 J(H N ,H R ) NMR dipolar coupling constants, basin populations, and peptide-water radial distribution functions (RDF) were calculated from replica exchange simulations and compared to both experiment and fully classical force field calculations using the Amber ff99SB force field. In contrast with the computational chemist's intuitive idea that the more expensive a method the better its accuracy, the ff99SB force field results were more accurate than most of the semiempirical methods, with the exception of RM1. None of the methods, however, was able to accurately reproduce the experimental data. Analysis of the results indicate that the specific QM/MM interactions have little influence on the sampling of free energy surfaces, and the differences are well explained simply by the intrinsic properties of the various QM methods.

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Orthogonalization corrections for semiempirical methods

Cited by 396 publications

References 30 publications

Assessment of approximate computational methods for conical intersections and branching plane vectors in organic molecules

Assessment of approximate computational methods for conical intersections and branching plane vectors in organic molecules

UV Photodissociation of Proline-containing Peptide Ions: Insights from Molecular Dynamics

Are Current Semiempirical Methods Better Than Force Fields? A Study from the Thermodynamics Perspective

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