Insufficient description of dispersion in B3LYP and large basis set superposition errors in MP2 calculations can hide peptide conformers

Holroyd, Leo F.; Mourik, Tanja van

doi:10.1016/j.cplett.2007.05.072

Cited by 116 publications

(148 citation statements)

References 31 publications

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“…Although three different methodologies to explore the conformational energy landscape of YGG were used in this study, the authors stated that the large changes in the relative stability of the obtained conformers indicate that B3LYP/6-31+G(d) as well as MP2/6-31+G(d) may not give correct structures and energetics for molecules containing interactions with p-electron clouds. Also, B3LYP/6-31+G(d) and MP2/6-31+G(d) calculations predicted markedly different structures for the tyrosilglycine (YG) dipeptide [21]. The same conformational behaviour discrepancy between these two methods was observed for a number of other molecules containing an aromatic ring in addition to a flexible side chain, WG [17][18][19] and WGG [18,19].…”

Section: Introductionmentioning

confidence: 61%

Structure of isolated tyrosyl-glycyl-glycine tripeptide. A comparative conformational study with peptides containing an aromatic ring

et al. 2010

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The potential energy surface (PES) of tyrosyl-glycyl-glycine (YGG) tripeptide in solution was explored using EDMC (Electrostatically Driven Monte Carlo) and in the gas-phase by means of ab initio quantum chemical calculations. The theoretical computational analysis revealed that this tripeptide possesses a significant molecular flexibility. A C 7 backbone conformation was the most energetically preferred for the central Gly residue, using both methodologies. Some new stable conformers that have not been previously reported were identified in the gas phase as well. This study points out the interplay of backbone and side-chain contributions in determining the relative stabilities of energy minima. In addition, the peptide backbone of YGG was compared with other small peptides containing aromatic side-chains (Phe-Gly-Gly and Trp-Gly-Gly). The comparison with experimental X-ray results was also satisfactory.

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Section: Introductionmentioning

confidence: 61%

Structure of isolated tyrosyl-glycyl-glycine tripeptide. A comparative conformational study with peptides containing an aromatic ring

et al. 2010

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“…In fact, for this kind of unsaturated, heterocyclic systems displaying intramolecular H-bonds, DFT methodologies (including B3LYP with any type of basis set), even considering both polarisation and diffuse functions, cannot fully describe this type of close contacts, which are often determinant of the conformational equilibrium. This is due to the ineffective representation of dispersive interactions [37], leading to an underestimation of weak H-bonds (of dispersive nature) [38] such as the one present in conformer 2CA-3. On the other hand, it is well known that the 6-31G* basis set, within a DFT approach, overestimates strong (electrostatic) intramolecular H-type interactions [39].…”

Section: Conformational Analysismentioning

confidence: 99%

Conformational behaviour of antioxidant chromones. A vibrational spectroscopy study

Machado

Valero

Domingos

et al. 2012

Vibrational Spectroscopy

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a b s t r a c tChromone and two carboxylic derivatives -chromone-2-carboxylic acid (2CA) and chromone-3-carboxylic acid (3CA) -were investigated as to their conformational preferences by vibrational spectroscopy -Raman, FTIR and INS -combined to density functional theory and plane-wave calculations. INS experiments allowed to clearly detect intramolecular hydrogen-type close contacts in these systems. A natural bond orbital (NBO) analysis was performed, including calculation of the second-order perturbation energies (E (2) ) and orbital occupancies, to provide theoretical evidence of the stabilisation due to the * i → * j donor-acceptor interaction. A complete assignment of the vibrational spectra was achieved for all compounds, allowing us to determine their most stable conformers and establish their H-bonding profile. 3CA was shown to display a particularly strong intramolecular H-bond, which can explain its singular conformational behaviour and abnormally high pK a value.

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“…Despite the availability of alternative methods of BSSE correction in the literature ͑see also below͒, [14][15][16][17] the simple and robust method described above was used. This procedure has shown perfect results in the case of benzene planarity, 26 Tyr-Gly energy profiles, 24 and conformations of normal alkanes. 23 Figure 2 represents a division of the Ace͑Gly͒ 10 NH 2 molecule into parts.…”

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confidence: 99%

“…[20][21][22] The importance of intramolecular BSSE has only been understood rather recently. [23][24][25][26] For example, in 2007, Holroyd and van Mourik 24 showed that large intramolecular BSSE values are responsible for producing the minimum in the MP2 / 6-31+ G͑d͒ energy profile of the Tyr-Gly molecule. Even calculations on the small benzene molecule have been found to be BSSE dependent.…”

mentioning

confidence: 99%

“…These results show that intramolecular BSSE can be the major error source in modern quantum chemical calculations of the shape of ͑bio͒molecules. [23][24][25][26] In this Communication, we attempt to estimate the accuracy of the DFT approach to biopolymer conformations. Cal- culation of BSSE is used to determine the deviation of the current results from the complete basis set ͑CBS͒ limit.…”

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confidence: 99%

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Communications: Is quantum chemical treatment of biopolymers accurate? Intramolecular basis set superposition error (BSSE)

Balabin

2010

The Journal of Chemical Physics

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The accuracy of quantum chemical treatment of biopolymers by means of density functional theory is brought into question in terms of intramolecular basis set superposition error (BSSE). Secondary structure forms—β-strands (C5; fully extended conformation), repeated γ-turns (C7), 310-helices (C10), and α-helices (C13)—of homopolypeptides (polyglycine and polyalanine) are used as representative examples. The studied molecules include Ace(Gly)5NH2, Ace(Gly)10NH2, Ace(Ala)5NH2, and Ace(Ala)10NH2. The counterpoise correction procedure was found to produce reliable estimations for the BSSE values (other methods of BSSE correction are discussed). The calculations reported here used the B3LYP, PBE0 (PBE1PBE), and BMK density functionals with different basis sets [from 6-31G(d) to 6-311+G(3df,3pd)] to estimate the influence of basis set size on intramolecular BSSE. Calculation of BSSE was used to determine the deviation of the current results from the complete basis set limit. Intramolecular BSSE was found to be nonadditive with respect to biopolymer size, in contrast to claims in recent literature. The error, which is produced by a basis set superposition, was found to exceed 4 kcal mol−1 when a medium-sized basis set was used. This indicates that this error has the same order of magnitude as the relative energy differences of secondary structure elements of biopolymers. This result makes all recent reports on the gas-phase stability of homopolypeptides and their analogs questionable.

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Insufficient description of dispersion in B3LYP and large basis set superposition errors in MP2 calculations can hide peptide conformers

Cited by 116 publications

References 31 publications

Structure of isolated tyrosyl-glycyl-glycine tripeptide. A comparative conformational study with peptides containing an aromatic ring

Structure of isolated tyrosyl-glycyl-glycine tripeptide. A comparative conformational study with peptides containing an aromatic ring

Conformational behaviour of antioxidant chromones. A vibrational spectroscopy study

Communications: Is quantum chemical treatment of biopolymers accurate? Intramolecular basis set superposition error (BSSE)

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