Addendum to SAM1 results previously published

Holder, Alvin A.; Dennington, Roy D.; Jie, Caoxian

doi:10.1016/s0040-4020(01)80782-1

Cited by 49 publications

(26 citation statements)

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“…We also include four recently developed functionals [12][13][14] and fourteen other density functionals with varying percentages of Hartree-Fock exchange. [15][16][17][18][19][20][21][22][23][24][25][26][27][28][29][30][31][32][33] The semiempirical molecular orbital (SEMO) methods we test are all based on neglect of diatomic differential overlap (NDO), and include AM1 [34][35][36][37], MNDO [38,39], PM3 [40] and the newer PM6 method. [41] We also test an iterative extended Hückel theory (IEHT) method: self-consistent-charge density-functional tight-binding (SCC-DFTB) theory as implemented in two software packages, DFTB/DYLAX [42][43][44] and the more recent DFTB+ release.…”

Section: Introductionmentioning

confidence: 99%

Assessment of density functionals, semiempirical methods, and SCC-DFTB for protonated creatinine geometries

Settergren

Bühlmann

Amin

2008

Journal of Molecular Structure: THEOCHEM

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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 selfconsistent-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.

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Section: Introductionmentioning

confidence: 99%

Assessment of density functionals, semiempirical methods, and SCC-DFTB for protonated creatinine geometries

Settergren

Bühlmann

Amin

2008

Journal of Molecular Structure: THEOCHEM

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“…Of the forty-two methods used in this study, six were semiempirical calculations that used AM1, [47,50] PM3, [48] and SAM1 [49,50] Hamiltonians. The 16 ab initio Hartree ± Fock (HF) calculations used several basis sets including Truhlar×s MIDI!, [51] and ML, [52] Dunning×s LANL2DZ, [53] cc-pVDZ, [54] cc-pVTZ, [55] and Pople×s 6-31G, [56] and 6-311G.…”

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confidence: 99%

Experimental and Theoretical Multiple Kinetic Isotope Effects for an S_N2 Reaction. An Attempt to Determine Transition‐State Structure and the Ability of Theoretical Methods to Predict Experimental Kinetic Isotope Effects

Fang

Gao

Ryberg

et al. 2003

Chemistry A European J

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The secondary alpha-deuterium, the secondary beta-deuterium, the chlorine leaving-group, the nucleophile secondary nitrogen, the nucleophile (12)C/(13)C carbon, and the (11)C/(14)C alpha-carbon kinetic isotope effects (KIEs) and activation parameters have been measured for the S(N)2 reaction between tetrabutylammonium cyanide and ethyl chloride in DMSO at 30 degrees C. Then, thirty-nine readily available different theoretical methods, both including and excluding solvent, were used to calculate the structure of the transition state, the activation energy, and the kinetic isotope effects for the reaction. A comparison of the experimental and theoretical results by using semiempirical, ab initio, and density functional theory methods has shown that the density functional methods are most successful in calculating the experimental isotope effects. With two exceptions, including solvent in the calculation does not improve the fit with the experimental KIEs. Finally, none of the transition states and force constants obtained from the theoretical methods was able to predict all six of the KIEs found by experiment. Moreover, none of the calculated transition structures, which are all early and loose, agree with the late (product-like) transition-state structure suggested by interpreting the experimental KIEs.

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“…The energies of the structures were initially calculated by using the SAM1 geometry-optimization method (24)(25)(26) in the AMPAC 5.0 (27) program. This was followed by single-point gas-phase energy calculations with AM1 (28) and with the SM2.1/AM1 solvation model (29) to correct the single-point gas-phase energies to a water dielectric.…”

Section: Methodsmentioning

confidence: 99%

Interresidue hydrogen bonding in a peptide nucleic acid.RNA heteroduplex.

Torres

Bruce

1996

Proc. Natl. Acad. Sci. U.S.A.

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Previous molecular mechanics calculations suggest that strands of peptide nucleic acids (PNAs) and complementary oligonucleotides form antiparallel duplexes stabilized by interresidue hydrogen bonds. In the computed structures, the amide carbonyl oxygen nearest the nucleobase (07') forms an interresidue hydrogen bond with the backbone amide proton of the following residue, (n + 1)Hl'. Of the 10 published two dimensional 1H NMR structures of a hexameric PNA-RNA heteroduplex, PNA(GAACTC)-r(GAGUUC), 9 exhibit two to five potential interresidue hydrogen bonds. In our minimized average structure, created from the coordinates of these 10 NMR structures, three of the five possible interresidue hydrogen bond sites within the PNA backbone display the carbonyl oxygen (07') and the amide proton (n + 1)H1' distances and N1'-H1'-(n -1)07' angles optimal for hydrogen bond formation. The finding of these interresidue hydrogen bonds supports the results of our previous molecular mechanics calculations.In viable peptide nucleic acids (PNAs), the ribose-phosphodiester backbone of oligonucleotides is replaced with a peptidic backbone consisting ofN-(2-aminoethyl)glycine units, with the glycine nitrogen connected to a purine or pyrimidine base by an acetyl linker (Scheme 1) (1-5). These neutral, homomorphous DNA analogs recognize their DNA and RNA complements by Watson-Crick and Hoogsteen base pairing, thereby maintaining the specificity associated with natural oligonucleotides. This type of PNA has been shown to bind target DNA or RNA strand(s) with a greater affinity than observed between innate oligonucleotide strands. These polymeric structures also display greater stability against nuclease activity and greater sensitivity to base-pair mismatches when compared with their DNA and RNA oligonucleotide counterparts. These features make these PNAs attractive as putative genetic regulatory agents. Much interestThe publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. §1734 solely to indicate this fact.

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Addendum to SAM1 results previously published

Cited by 49 publications

References 1 publication

Assessment of density functionals, semiempirical methods, and SCC-DFTB for protonated creatinine geometries

Assessment of density functionals, semiempirical methods, and SCC-DFTB for protonated creatinine geometries

Experimental and Theoretical Multiple Kinetic Isotope Effects for an S_N2 Reaction. An Attempt to Determine Transition‐State Structure and the Ability of Theoretical Methods to Predict Experimental Kinetic Isotope Effects

Interresidue hydrogen bonding in a peptide nucleic acid.RNA heteroduplex.

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Addendum to SAM1 results previously published

Cited by 49 publications

References 1 publication

Assessment of density functionals, semiempirical methods, and SCC-DFTB for protonated creatinine geometries

Assessment of density functionals, semiempirical methods, and SCC-DFTB for protonated creatinine geometries

Experimental and Theoretical Multiple Kinetic Isotope Effects for an SN2 Reaction. An Attempt to Determine Transition‐State Structure and the Ability of Theoretical Methods to Predict Experimental Kinetic Isotope Effects

Interresidue hydrogen bonding in a peptide nucleic acid.RNA heteroduplex.

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Experimental and Theoretical Multiple Kinetic Isotope Effects for an S_N2 Reaction. An Attempt to Determine Transition‐State Structure and the Ability of Theoretical Methods to Predict Experimental Kinetic Isotope Effects