Vanadate complex spectroscopy at the RNase A active site

Krauß, M.; Wladkowski, Brian D.

doi:10.1002/(sici)1097-461x(1998)69:1<11::aid-qua3>3.0.co;2-#

Cited by 13 publications

(4 citation statements)

References 27 publications

(1 reference statement)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Due to its cost-effective formulation, EFP has found numerous applications in chemistry, such as studying solvent effects for which it was originally formulated. − ,− Other applications include solvent-induced shifts in the electronic spectra of uracil, spectroscopy of enzyme active sites, , noncovalent π–π and hydrogen-bonding interactions in DNA strands using (nucleobase oligomers), hydrogen bonding, and other noncovalently bound systems. ,, EFP has been applied to reliably study a broad range of intermolecular complexes. For example, EFP relative energies of hydrogen-bonded complexes in (MeOH/H 2 O) n clusters, for n = 2, ..., 8 were in good agreement with MP2 .…”

Section: Introductionmentioning

confidence: 99%

Comparison of the Effective Fragment Potential Method with Symmetry-Adapted Perturbation Theory in the Calculation of Intermolecular Energies for Ionic Liquids

Tan

Izgorodina

2016

J. Chem. Theory Comput.

View full text Add to dashboard Cite

The effective fragment potential (EFP) method that decomposes the interaction energy as a sum of the five fundamental forces-electrostatic, exchange-repulsion, polarization, dispersion, and charge transfer-was applied to a large test set of ionic liquid ion pairs and compared against the state-of-the-art method, Symmetry-Adapted Perturbation Theory (SAPT). The ion pairs include imidazolium and pyrrolidinium cations combined with anions that are routinely used in the field of ionic liquids. The aug-cc-pVDZ, aug-cc-pVTZ, and 6-311++G(d,p) basis sets were used for EFP, while SAPT2+3/aug-cc-pVDZ provided the benchmark energies. Differences between the two methods were found to be large, and strongly dependent on the anion type. For the aug-cc-pVTZ basis set, which produced the least errors, average relative errors were between 2.3% and 18.4% for pyrrolidinium ion pairs and between 2.1% and 27.7% for imidazolium ion pairs for each individual energetic component (excluding charge transfer), as well as the total interaction energy. Charge transfer gave the largest relative errors: 56% and 63% on average for pyrrolidinium- and imidazolium-based ion pairs, respectively. Scaling of the EFP components against SAPT2+3 showed improvement for polarization (induction) and dispersion terms, thus indicating potential for the development of cost-effective alternatives for intermolecular induction and dispersion potentials for ionic liquids.

show abstract

Section: Introductionmentioning

confidence: 99%

Comparison of the Effective Fragment Potential Method with Symmetry-Adapted Perturbation Theory in the Calculation of Intermolecular Energies for Ionic Liquids

Tan

Izgorodina

2016

J. Chem. Theory Comput.

View full text Add to dashboard Cite

show abstract

“…The effective fragment potential ͑EFP͒ method 3 is a discrete solvation approach that was designed to treat chemical reactions in solution. 3,4͑a͒,4͑b͒ However, the EFP method has also been used to study solvent clusters, 5͑a͒,5͑b͒ solvent effects on excited states of biomolecules, 6 neutral-zwitterion equilibrium in amino acids, 9͑a͒,9͑b͒ treatment of the covalent bond in proteins, 7,8 and recently it was interfaced with a continuum method ͑PCM͒. 9 The original method ͑referred as EFP1/HF͒ was designed specifically for the solvent water at the Hartree-Fock ͑HF͒ level of theory.…”

Section: Introductionmentioning

confidence: 99%

Density functional theory based effective fragment potential method

Adamovic

Freitag

Gordon

2003

The Journal of Chemical Physics

126

147

View full text Add to dashboard Cite

The effective fragment potential (EFP) method, is a discrete method for the treatment of solvent effects, originally formulated using Hartree-Fock (HF) theory. Here, a density functional theory(DFT) based implementation of the EFP method is presented for water as a solvent. In developing the DFT based EFP method for water, all molecular properties (multipole moments, polarizabilitytensors, screening parameters, and fitting parameters for the exchange repulsion potential) are recalculated and optimized, using the B3LYP functional. Initial tests for water dimer, small water clusters, and the glycine-water system show good agreement with ab initioand DFT calculations. Several computed properties exhibit marked improvement relative to the Hartree-Fock based method, presumably because the DFT based method includes some dynamic electron correlation through the corresponding functional. KeywordsDensity functional theory, Solvents, Ab initio calculations, Discrete systems, Electron correlation calculations Disciplines Chemistry CommentsThe following article appeared in Journal of Chemical Physics 118 (2003) The effective fragment potential ͑EFP͒ method, is a discrete method for the treatment of solvent effects, originally formulated using Hartree-Fock ͑HF͒ theory. Here, a density functional theory ͑DFT͒ based implementation of the EFP method is presented for water as a solvent. In developing the DFT based EFP method for water, all molecular properties ͑multipole moments, polarizability tensors, screening parameters, and fitting parameters for the exchange repulsion potential͒ are recalculated and optimized, using the B3LYP functional. Initial tests for water dimer, small water clusters, and the glycine-water system show good agreement with ab initio and DFT calculations. Several computed properties exhibit marked improvement relative to the Hartree-Fock based method, presumably because the DFT based method includes some dynamic electron correlation through the corresponding functional.

show abstract

“…For example, the effective fragment potential ͑EFP͒ method treats solvent molecules as rigid fragments represented in terms of multipoles and polarizability tensors determined from ab initio calculations, and has been used successfully in a variety of solution chemistry applications. [38][39][40][41][42][43][44][45][46][47][48][49][50][51][52][53][54][55] Carter and co-workers have developed a hybrid method that combines a high-level wave function model based on atom center basis functions, such as configuration interaction, with a planewave DFT model chemistry for studies of metallic crystals. [56][57][58][59][60][61] The frozen DFT ͑FDFT͒ and constrained DFT ͑CDFT͒ schemes of Wesolowski et al are also QM:QM models.…”

Section: Introductionmentioning

confidence: 99%

QM:QM electronic embedding using Mulliken atomic charges: Energies and analytic gradients in an ONIOM framework

Hratchian

Parandekar

Raghavachari

et al. 2008

The Journal of Chemical Physics

105

View full text Add to dashboard Cite

An accurate first-principles treatment of chemical reactions for large systems remains a significant challenge facing electronic structure theory. Hybrid models, such as quantum mechanics:molecular mechanics (QM:MM) and quantum mechanics:quantum mechanics (QM:QM) schemes, provide a promising avenue for such studies. For many chemistries, including important reactions in materials science, molecular mechanics or semiempirical methods may not be appropriate, or parameters may not be available (e.g., surface chemistry of compound semiconductors such as indium phosphide or catalytic chemistry of transition metal oxides). In such cases, QM:QM schemes are of particular interest. In this work, a QM:QM electronic embedding model within the ONIOM (our own N-layer integrated molecular orbital molecular mechanics) extrapolation framework is presented. To define the embedding potential, we choose the real-system low-level Mulliken atomic charges. This results in a set of well-defined and unique embedding charges. However, the parametric dependence of the charges on molecular geometry complicates the energy gradient that is necessary for the efficient exploration of potential energy surfaces. We derive an efficient form for the forces where a single set of self-consistent field response equations is solved. Initial tests of the method and key algorithmic issues are discussed.

show abstract

Vanadate complex spectroscopy at the RNase A active site

Cited by 13 publications

References 27 publications

Comparison of the Effective Fragment Potential Method with Symmetry-Adapted Perturbation Theory in the Calculation of Intermolecular Energies for Ionic Liquids

Comparison of the Effective Fragment Potential Method with Symmetry-Adapted Perturbation Theory in the Calculation of Intermolecular Energies for Ionic Liquids

Density functional theory based effective fragment potential method

QM:QM electronic embedding using Mulliken atomic charges: Energies and analytic gradients in an ONIOM framework

Contact Info

Product

Resources

About