The effect of diffuse functions on minimal basis set superposition errors for H‐bonded dimers

Alagona, Giuliano; Ghio, Caterina

doi:10.1002/jcc.540110805

Cited by 28 publications

(6 citation statements)

References 43 publications

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“…However, these large stabilization energies are the result of the incomplete description of the separated reactants that is achieved when a relatively small basis set such as 3-21G or 3-21G* is used. This is termed basis set superposition error (BSSE) (30), which has been discussed extensively in connection with calculations on water clusters (31). The BSSE leads to energies of separated reactants that are artificially too high, causing AE * and AH* to be too low or even negative, when these are calculated from the separated reactants.…”

Section: Resultsmentioning

confidence: 99%

Ab initio molecular orbital calculations on the neutral hydrolysis and methanolysis of azetidinones, including catalysis by water. Relationship to the mechanism of action of β-lactam antibiotics

Wolfe¹,

Kim²,

Yang³

1994

Can. J. Chem.

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The docking of penicillins to a computer model of the active site of the penicillin-binding protein of Streptornyces R61 produces structures that exhibit a four-centred interaction between the 0 -H of a serine residue and the (0)C-N of the p-lactam ring. If such a structure is a stationary point on the reaction coordinate for the acylation of the serine OH by the p-lactam carbonyl group, the acylation mechanism would appear to consist of 0-C and H-N bond formation, concerted with the cleavage of the C-N bond. The existence of this "N-protonation" mechanism, and the energetics of this mechanism in comparison to the usual "0-protonation" pathway in which proton transfer to oxygen and addition to the carbonyl group precede C-N bond fission, have been examined by ab initio M O calculations on the neutral hydrolysis and methanolysis of N-methylazetidinone, penam, and penam-3a-carboxylate. The geometries of reactants and transition structures have been optimized fully at the 3-21G or 3-21G* levels, the existence of transition structures has been confirmed by vibrational analysis, thermochemical data have been computed, and the one-point energies of all structures have been determined at the MP216-31G* level. The N-protonation mechanism is found to exist with all substrates, and to be preferred over the 0-protonation mechanism by over 5 kcallmol. The activation energies are 5 kcallmol lower in the bicyclic penam than in the monocyclic N-methylazetidinone, and attack from the convex face is preferred over attack from the concave face. The introduction of a 3a-carboxylate group, as in penicillin itself, results in an additional 5 kcallmol decrease in activation energy. The origins of these trends are discussed. Since the active sites of some penicillin-recognizing enzymes contain at least one water molecule, catalysis of the foregoing reactions by one water molecule has also been examined. The catalysis amounts to over 10 kcaVmol in both the N-and 0-protonation mechanisms, and the preference for the N-protonation mechanism is maintained. It is concluded that penicillin complexes to its receptor in such a manner as to allow acylation of the active site serine residue to proceed via the energetically most favourable mechanism. SAUL WOLFE, CHAN-KYUNG KIM et KIYULL YANG. Can. J. Chem. 72, 1033Chem. 72, (1994. L'ammage de pCnicillines au modble sur ordinateur du site actif de la protCine de liaison de la pCnicilline du Streptomyces R61 foumit des structures qui prCsentent une interaction 21 quatre centres entre le 0 -H de la sCrine et le (0)C-N du noyau p-lactame. Si une telle structure est un point stationnaire sur les coordonnCes rtactionnelles de l'acylation du OH de la sCrine par le groupe carbonyle du p-lactame, il semblerait que le mtcanisme d'acylation cornporterait la formation de liaisons 0-C et H-N concertCe avec un clivage de la liaison C-N. L'existence de ce mCcanisme de ccN-protonation, et les tnergies impliquCes dans ce mCcanisme, par comparaison avec la voie usuelle de ccO-protonation,, dans laquelle le trans...

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Section: Resultsmentioning

confidence: 99%

Ab initio molecular orbital calculations on the neutral hydrolysis and methanolysis of azetidinones, including catalysis by water. Relationship to the mechanism of action of β-lactam antibiotics

Wolfe¹,

Kim²,

Yang³

1994

Can. J. Chem.

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“…The three difference basis set predicted similar result for the relative energies of CCM monomers, but the binding energies (E binding ) of CCM/SeO 3 2− adduct showed large difference. Because the basis set extension accompanies with reducing extant of basis set superposition error BSSE, especially the adding diffuse functions is definitely beneficial effect in anion-neutral system 63 64 65 . The BSSE calculated by counterpoise method 66 67 can demonstrate this phenomenon (see “BSSE and selection of basis set” of support materials ).…”

Section: Methodsmentioning

confidence: 99%

The Comparative Studies of Binding Activity of Curcumin and Didemethylated Curcumin with Selenite: Hydrogen Bonding vs Acid-Base Interactions

Liao

Chen

et al. 2015

Sci Rep

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In this report, the in vitro relative capabilities of curcumin (CCM) and didemethylated curcumin (DCCM) in preventing the selenite-induced crystallin aggregation were investigated by turbidity tests and isothermal titration calorimetry (ITC). DCCM showed better activity than CCM. The conformers of CCM/SeO32− and DCCM/SeO32− complexes were optimized by molecular orbital calculations. Results reveal that the selenite anion surrounded by CCM through the H-bonding between CCM and selenite, which is also observed via IR and NMR studied. For DCCM, the primary driving force is the formation of an acid-base adduct with selenite showing that the phenolic OH group of DCCM was responsible for forming major conformer of DCCM. The formation mechanisms of selenite complexes with CCM or DCCM explain why DCCM has greater activity than CCM in extenuating the toxicity of selenite as to prevent selenite-induced lens protein aggregation.

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“…A study of polarization functions has already been carried out 22 as well as of minimal basis sets augmented with diffuse functions …”

Section: Referencesmentioning

confidence: 99%

An ab Initio Investigation of Lithium Ion Hydration

1996

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The structures, frequencies, and interaction energies of small lithium−water clusters, Li(H2O) n +, n = 1−4, were calculated by ab initio Hartree−Fock theory with small- and medium-sized basis sets (STO-3G, 3-21G, 6-31G*, 6-31G**, 6-31+G*, 6-31+G*(5d), 6-311G*). The interaction energies were corrected for basis set superposition error (BSSE) by Mayer's CHA/CE formalism. The CHA/CE/6-31+G*//HF/6-31+G* level gives an excellent description of the binding energy. The geometry and symmetric stretch frequency for Li(H2O)4 + of 248 cm-1 (255 cm-1 expt) are well described at the HF/6-31G* level. The choice of partition of the supermolecule was demonstrated to be of minor importance (±4 kJ/mol). The binding energies were rationalized on crowding around the ion and a weakening Li−O interaction. The first ab initio calculation (STO-3G, 3-21G, 6-31G*, 6-31+G*) of a full second-solvation sphere of a metal cation is presented ([Li(H2O)4 +](H2O) n , n = 4,8). The second solvation sphere of four waters raises the frequency of the Li−O vibration by 18 cm-1 (7%).

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The effect of diffuse functions on minimal basis set superposition errors for H‐bonded dimers

Cited by 28 publications

References 43 publications

Ab initio molecular orbital calculations on the neutral hydrolysis and methanolysis of azetidinones, including catalysis by water. Relationship to the mechanism of action of β-lactam antibiotics

Ab initio molecular orbital calculations on the neutral hydrolysis and methanolysis of azetidinones, including catalysis by water. Relationship to the mechanism of action of β-lactam antibiotics

The Comparative Studies of Binding Activity of Curcumin and Didemethylated Curcumin with Selenite: Hydrogen Bonding vs Acid-Base Interactions

An ab Initio Investigation of Lithium Ion Hydration

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