Dataset Information

Assessment of Density Functionals, Semiempirical Methods, and SCC-DFTB for Protonated Creatinine Geometries.

ABSTRACT: Creatinine concentrations in blood and urine can be used to detect renal insufficiencies and muscle diseases, but current chemical sensors cannot measure creatinine with sufficient selectivity and robustness because they lack a receptor that binds protonated creatinine (creatininium) selectively enough. As a first step toward identifying potential receptors for creatininium, we examine the accuracy of density functional theory (DFT) and wave function theory (WFT) calculations for creatininium cation geometries, evaluated against reference parameters from experiment. We tested twenty-one local and nonlocal density functionals, Hartree-Fock theory, four semiempirical molecular orbital (SEMO) methods of the neglect of differential overlap (NDO) type, and one self-consistent-field nonorthogonal tight-binding method (SCC-DFTB) as implemented in two closely related software packages. DFT and HF calculations were carried out with the MG3S augmented polarized triple-zeta basis set. We find that DFT significantly outperforms SEMO methods for our dataset, and both SCC-DFTB releases we tested (which gave almost identical results) were less accurate than 81% of the density functionals evaluated. The top five functionals for the creatininium structures we examined were MPW1B95, PBEh, mPW1PW, SVWN5, and B97-2, with MMUEs in bond length of 0.0126 Å, 0.0129 Å, 0.0133 Å, 0.0142 Å, and 0.0144 Å respectively, which indicates that all five functionals are similarly suitable for creatininium. The popular B3LYP functional has a MMUE of 0.0178 Å, which ranks it 16(th) overall. B3LYP also performs less favorably than the best local functional (SVWN5), which is less expensive.

SUBMITTER: Settergren NM

PROVIDER: S-EPMC2504755 | biostudies-literature | 2008

REPOSITORIES: biostudies-literature

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Assessment of Density Functionals, Semiempirical Methods, and SCC-DFTB for Protonated Creatinine Geometries.

Settergren Nicole M NM Bühlmann Philippe P Amin Elizabeth A EA

Theochem 20080101 1-3

Creatinine concentrations in blood and urine can be used to detect renal insufficiencies and muscle diseases, but current chemical sensors cannot measure creatinine with sufficient selectivity and robustness because they lack a receptor that binds protonated creatinine (creatininium) selectively enough. As a first step toward identifying potential receptors for creatininium, we examine the accuracy of density functional theory (DFT) and wave function theory (WFT) calculations for creatininium ca ...[more]

PMID: 19122761

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Project description:Phosphate chemistry is involved in many key biological processes yet the underlying mechanism often remains unclear. For theoretical analysis to effectively complement experimental mechanistic analysis, it is essential to develop computational methods that can capture the complexity of the underlying potential energy surface and allow for sufficient sampling of the configurational space. To this end, we report the parameterization of an approximate density functional theory, Self-Consistent-Charge Density-Functional Tight-Binding (SCC-DFTB) method for systems containing phosphorus. Compared to high-level density functional theory and ab initio (MP2 and G3B3) results, the standard second-order parameterization is shown to give reliable structures for a diverse set of phosphate compounds but inaccurate energetics. With the on-site third-order terms included, referred to as SCC-DFTBPA, calculated proton affinities of phosphate compounds are substantially improved, although it remains difficult to obtain reliable proton affinity for both phosphates and compounds that do not contain phosphorus, indicating that further improvement in the formulation of SCC-DFTB is still a challenge to meet. To make SCC-DFTB applicable to phosphate reactions in the current (on-site-third-order-only) formulation, a "reaction-specific" parameterization, referred to as SCC-DFTBPR, is developed based on hydrolysis reactions of model phosphate species. Benchmark calculations in both the gas-phase and solution-phase indicate that SCC-DFTBPR gives reliable structural properties and semi-quantitative energetics for phosphate hydrolysis reactions. Since the number of reaction-specific parameters is small, it is likely that SCC-DFTBPR is applicable to a broad set of phosphate species. Indeed, for 56 reaction exothermicities and 47 energy barriers related to RNA catalysis model reactions collected from the QCRNA database, which involve molecules rather different from those used to parameterize SCC-DFTBPR, the corresponding root-mean-square difference between SCC-DFTBPR and high-level DFT results is only 5.3 kcal/mol. We hope that the parameterized SCC-DFTB models will complement NDDO based reaction-specific models (e.g., AM1-d/PhoT) and high-level ab initio QM/MM methods in better understanding the mechanism of phosphate chemistry in condensed phase, particularly biological systems.

Dataset Information

Assessment of Density Functionals, Semiempirical Methods, and SCC-DFTB for Protonated Creatinine Geometries.

Publications

Assessment of Density Functionals, Semiempirical Methods, and SCC-DFTB for Protonated Creatinine Geometries.

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