Stability issues of covalently and noncovalently bonded peptide subunits

Perczel, András; Hudáky, Péter; Füzéry, Anna K.; Csizmadia, Imre G.

doi:10.1002/jcc.20028

Cited by 15 publications

(30 citation statements)

References 36 publications

(28 reference statements)

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“…The basis set superposition error (BSSE) energy, which is calculated by using the counterpoise procedure87 with H 2 O and C 60 as two fragments of the supermolecule, is roughly around 4.7 kcal mol −1 regardless of the complexes investigated; the value is about 73.3 % of the uncorrected binding energy, and such a large BSSE is not uncommon in other systems 88. 89 The counterpoise‐corrected binding energy, −2.03 kcal mol −1 , matches the RVS and KM/6‐311G interaction energies, −2.12 kcal mol −1 (Table 2).…”

Section: Resultsmentioning

confidence: 99%

Can a Single Molecule of Water be Completely Isolated Within the Subnano‐Space Inside the Fullerene C₆₀Cage? A Quantum Chemical Prospective

Varadwaj

2012

Chemistry A European J

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Based on an experimental observation, it has been controversially suggested in a study (Kurotobi et al., Science 2011, 33, 613) that a single molecule of water can completely be localized within the subnano-space inside the fullerene C(60) cage and, that neither the H atoms nor the O lone-pairs are linked, either via hydrogen bonding or through dative bonding, with the interior C-framework of the C(60) cage. To resolve the controversy, electronic structure calculations were performed by using the density functional theory, together with the quantum theory of atoms in molecules, the natural population and bond orbital analyses, and the results were analyzed by using varieties of recommended diagnostics often used to interpret noncovalent interactions. The present results reveal that the mechanically entrapped H(2)O molecule is not electronically innocent of the presence of the cage; each H atom of H(2)O is weakly O-H···C(60) bonded, whereas the O lone-pairs are O···C(60) bonded regardless of the conformations investigated. Exploration of various featured properties suggests that H(2)O@C(60) may be regarded as a unique system composed of both inter- and intramolecular interactions.

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Section: Resultsmentioning

confidence: 99%

Can a Single Molecule of Water be Completely Isolated Within the Subnano‐Space Inside the Fullerene C₆₀Cage? A Quantum Chemical Prospective

Varadwaj

2012

Chemistry A European J

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“…• The 6-31G(d) basis set, which is frequently used in the literature, [8,9,12,15,16,29,97,101,111,115,116], has turned out to be a very efficient one for calculating the geometry both at RHF and MP2.…”

Section: Discussionmentioning

confidence: 99%

“…In any bottom-up approach to the still unsolved protein folding problem [1][2][3][4], the characterization of the conformational behaviour of short peptides [5][6][7][8][9][10][11][12] constitutes an unavoidable first step. If high accuracy of the treatment is sought, numerically expensive methods must be used to calculate the physical properties of these protein subunits.…”

Section: Introductionmentioning

confidence: 99%

“…In any bottom-up attempt to understand the behavior of protein molecules (in particular, the still elusive protein folding process), [1][2][3][4][5] the characterization of the conformational preferences of short peptides [6][7][8][9][10][11][12][13] constitutes an unavoidable first step. Because of the lower numerical effort required and also to the manageability of their conformational space, the most frequently studied peptides are the shortest ones: the dipeptides, [14][15][16][17] in which a single amino acid residue is capped at both the N-and C-termini with neutral peptide groups.…”

Section: Introductionmentioning

confidence: 99%

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Efficient model chemistries for peptides. I. General framework and a study of the heterolevel approximation in RHF and MP2 with Pople split‐valence basis sets

Echenique

Alonso

2008

J Comput Chem

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We present an exhaustive study of more than 250 ab initio potential energy surfaces (PESs) of the model dipeptide HCO-L-Ala-NH2. The model chemistries (MCs) used are constructed as homo-and heterolevels involving possibly different RHF and MP2 calculations for the geometry and the energy. The basis sets used belong to a sample of 39 selected representants from Pople's split-valence families, ranging from the small 3-21G to the large 6-311++G(2df,2pd). The reference PES to which the rest are compared is the MP2/6-311++G(2df,2pd) homolevel, which, as far as we are aware, is the more accurate PES of a dipeptide in the literature. The aim of the study presented is twofold: On the one hand, the evaluation of the influence of polarization and diffuse functions in the basis set, distinguishing between those placed at 1st-row atoms and those placed at hydrogens, as well as the effect of different contraction and valence splitting schemes. On the other hand, the investigation of the heterolevel assumption, which is defined here to be that which states that heterolevel MCs are more efficient than homolevel MCs. The heterolevel approximation is very commonly used in the literature, but it is seldom checked. As far as we know, the only tests for peptides or related systems, have been performed using a small number of conformers, and this is the first time that this potentially very economical approximation is tested in full PESs. In order to achieve these goals, all data sets have been compared and analyzed in a way which captures the nearness concept in the space of MCs. * Corresponding author. E-mail address: pnique@unizar.es 1The most important results of the study are the following: First, that the convergence in method is not achieved in the RHF → MP2 step. Second that the transferability of basis set accuracy from RHF to MP2 is imperfect. These two conclusions lead us to discourage the use of RHF MCs for peptides. Regarding the relative efficiency of the Pople's basis sets, we recommend the inclusion of polarization functions in 1st-row atoms and we discourage the use of basis sets containing doubly-split polarization shells and no diffuse functions. Also, we have found that 6-31G(d) is very efficient for calculating the geometry, and that both the RHF and MP2 infinite basis set limits are approximately reached at 6-311++G(2df,2pd). Finally, related to the heterolevel approximation, we conclude that it is essentially correct for the description of the conformational behaviour of HCO-L-Ala-NH2 both at RHF and MP2. Nevertheless, we place a cautionary remark on the use of RHF geometries with MP2 single-points: Whereas this practice could be accurate enough for short peptides, the accumulation of errors may render it unreliable for longer chains and require the use of MP2 geometries.

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“…Thus increasing the expense and "accuracy" of a calculation may not always converge to the "correct" solution. As a consequence, the quality of the results does not steadily grow with the computational effort invested, but rather there exist certain tradeoffs that render the relation between them more involved [14-16]. Hence, not only the choice of the more efficient QC method for a given problem among the already existing ones, but also the design of novel model chemistries becomes 'more an art than a science' [17], based more on know-how and empiricism than in a set of systematic procedures.…”

Section: Introductionmentioning

confidence: 99%

The Quixote project: Collaborative and Open Quantum Chemistry data management in the Internet age

et al. 2011

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Computational Quantum Chemistry has developed into a powerful, efficient, reliable and increasingly routine tool for exploring the structure and properties of small to medium sized molecules. Many thousands of calculations are performed every day, some offering results which approach experimental accuracy. However, in contrast to other disciplines, such as crystallography, or bioinformatics, where standard formats and well-known, unified databases exist, this QC data is generally destined to remain locally held in files which are not designed to be machine-readable. Only a very small subset of these results will become accessible to the wider community through publication.In this paper we describe how the Quixote Project is developing the infrastructure required to convert output from a number of different molecular quantum chemistry packages to a common semantically rich, machine-readable format and to build respositories of QC results. Such an infrastructure offers benefits at many levels. The standardised representation of the results will facilitate software interoperability, for example making it easier for analysis tools to take data from different QC packages, and will also help with archival and deposition of results. The repository infrastructure, which is lightweight and built using Open software components, can be implemented at individual researcher, project, organisation or community level, offering the exciting possibility that in future many of these QC results can be made publically available, to be searched and interpreted just as crystallography and bioinformatics results are today.Although we believe that quantum chemists will appreciate the contribution the Quixote infrastructure can make to the organisation and and exchange of their results, we anticipate that greater rewards will come from enabling their results to be consumed by a wider community. As the respositories grow they will become a valuable source of chemical data for use by other disciplines in both research and education.The Quixote project is unconventional in that the infrastructure is being implemented in advance of a full definition of the data model which will eventually underpin it. We believe that a working system which offers real value to researchers based on tools and shared, searchable repositories will encourage early participation from a broader community, including both producers and consumers of data. In the early stages, searching and indexing can be performed on the chemical subject of the calculations, and well defined calculation meta-data. The process of defining more specific quantum chemical definitions, adding them to dictionaries and extracting them consistently from the results of the various software packages can then proceed in an incremental manner, adding additional value at each stage.Not only will these results help to change the data management model in the field of Quantum Chemistry, but the methodology can be applied to other pressing problems related to data in computational and experimental sc...

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Stability issues of covalently and noncovalently bonded peptide subunits

Cited by 15 publications

References 36 publications

Can a Single Molecule of Water be Completely Isolated Within the Subnano‐Space Inside the Fullerene C₆₀Cage? A Quantum Chemical Prospective

Can a Single Molecule of Water be Completely Isolated Within the Subnano‐Space Inside the Fullerene C₆₀Cage? A Quantum Chemical Prospective

Efficient model chemistries for peptides. I. General framework and a study of the heterolevel approximation in RHF and MP2 with Pople split‐valence basis sets

The Quixote project: Collaborative and Open Quantum Chemistry data management in the Internet age

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Stability issues of covalently and noncovalently bonded peptide subunits

Cited by 15 publications

References 36 publications

Can a Single Molecule of Water be Completely Isolated Within the Subnano‐Space Inside the Fullerene C60Cage? A Quantum Chemical Prospective

Can a Single Molecule of Water be Completely Isolated Within the Subnano‐Space Inside the Fullerene C60Cage? A Quantum Chemical Prospective

Efficient model chemistries for peptides. I. General framework and a study of the heterolevel approximation in RHF and MP2 with Pople split‐valence basis sets

The Quixote project: Collaborative and Open Quantum Chemistry data management in the Internet age

Contact Info

Product

Resources

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Can a Single Molecule of Water be Completely Isolated Within the Subnano‐Space Inside the Fullerene C₆₀Cage? A Quantum Chemical Prospective

Can a Single Molecule of Water be Completely Isolated Within the Subnano‐Space Inside the Fullerene C₆₀Cage? A Quantum Chemical Prospective