Origins of Structure and Energetics of van der Waals Clusters from ab Initio Calculations

Chałasiński, Grzegorz; Szczȩśniak, M. M.

doi:10.1021/cr00031a001

Cited by 807 publications

(533 citation statements)

References 72 publications

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“…Through this comparison, we aimed to assess the ability of commonly used exchange-correlation functionals to describe cooperative EDA interactions (note that some previous DFT studies have already been devoted to EDA systems [26,27]). Then, using the symmetry-adapted perturbation theory (SAPT), [28,29] we have evaluated the electrostatic, induction, exchange and dispersion contributions to the interaction energy in order to clarify their respective role in the stabilization of conventional and unconventional complexes of carbonyl dioxide with carbonyl compounds.…”

Section: Introductionmentioning

confidence: 99%

Theoretical insights on electron donor–acceptor interactions involving carbon dioxide

San‐Fabián

Ingrosso

Lambert

et al. 2014

Chemical Physics Letters

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Section: Introductionmentioning

confidence: 99%

Theoretical insights on electron donor–acceptor interactions involving carbon dioxide

San‐Fabián

Ingrosso

Lambert

et al. 2014

Chemical Physics Letters

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“…This is related not only to level of electron correlation estimation [11][12][13][14][15][16][17][18][19], corrections of basis superposition errors (BSSE) [20] and quality of applied basis set [11][12][13][14] (or its extrapolation to complete one) but also to non-additive contributions to molecular cluster stabilizations [12][13][14][15][16]. As it was nowadays documented [16] accurate values for manybody effects require extensions of electron correlation beyond MP2 levels since this approximation can only encounter non-additivity via correlated exchange and induction components [21,22]. However, due to fortunate compensation of errors such levels of theory as MP3, L-CCD or CCSD lead to substantially the same predictions as CCSD(T) one [16].…”

Section: Introductionmentioning

confidence: 99%

“…Unfortunately the size of analyzed systems prohibit application of advanced levels of theory as routine computations for broad range of nucleobases conformations. Bearing in mind formal restrictions of MP2 level [21,22] the qualitative estimation of non-additive nature of dinucleotide steps was characterized here for all ten unique dinucleotide steps adopting B-DNA conformations. Let consider schematic representation of model dinucleotide step as it is presented in Fig.…”

Section: Introductionmentioning

confidence: 99%

Non-additive interactions of nucleobases in model dinucleotide steps occurring in B-DNA crystals

Cysewski

2010

J Mol Model

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Non-additivity of base-base interactions in all ten possible model dinucleotide steps were analyzed on MP2/aug-cc-pvDZ quantum chemistry level. Selected conformations of four nucleobases exactly matched to ones occurring in B-DNA crystals. In most of 162 analyzed tetramers both threeand four-body contributions are negligible except of d(GpG) steps. However, in these dinucleotides both contributions are always of opposite signs and in all cases the sum of all non-additive part of intermolecular interactions do not exceed 2.6 kcal/mol. This stands for less than 5% of the overall binding energy of dinucleotide steps. Also replacements of guanine with 8-oxoguanine in d(GpG) systems introduces non-additivity of the same magnitude as for canonical dinucleotides. It is observed linear relationships between values of the total binding energy obtained in the tetramer basis set and estimated energy exclusively in dimers basis sets with assumption of pairwise additivities. For all analyzed dinucleotides steps there are also linear correlations between amount of non-additive contributions and magnitude of pairs interactions. Based on differences in electrostatic contribution to the total binding energy of four nucleobases and polarity of dinucleotide steps three distinct classes of dinucleotide steps were identified.Response to Reviewers: 1) I recommend to do a careful proofreading, there are many typos and some sentences are difficult to understand. Thank you. Careful proofreading was applied and text was modified accordingly.2) Page 3, Results and discussion Alltogether 162 dinucleotide steps were analyzed. The number of individual steps is variable, why is it so? Why there was 48 d(GpG) steps, but only 10 d(GpC) steps? What were the PDB codes of structures from which steps were chosen, and which steps (chain ID, res ID) were chosen? What was the resolution of these structures? This information could go to the Supplementary material.In supplementary material details related to analyzed structures are provided now. The differences in dinucleotide populations have strictly technical reason. Since in my previous work accepted for publication in Int.J.Quantum Chem. (DOI:10.1002/qua.22435) detailed analysis of d(GpG) steps were presented I have just included these data in this work. Consequently this dinucleotide is overrepresented. Since it constitutes its own class I do not think that such overrepresentation changes papers conclusions. On the other hand it is not necessary extending the number of other dinucleotide steps since the non-additivity is quite small and they were selected from broad range of data according to IIE and structural parameters diversities.3) Page 3, Results and discussion The numbers of steps are large enough to perform some statistical analysis of resulting energies. E.g. ANOVA could be performed to test whether the mean energies in dinucleotide steps differ significantly each from other. Also, is the distribution of energies for individual steps Gaussian or not? If not, some non-parametric ...

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“…The binding energies were appropriately corrected by the counterpoise (CP) calculations [12,13] such as CP-RNA and PNA-CP. The double strands are listed in decreasing order of binding energy in Table II and Table III.…”

Section: Resultsmentioning

confidence: 99%

“…In the present study, we used the PW91 functionals and the 6-31G** basis set. Because the binding energy between the two strands calculated in a finite basis set is subject to a basis set superposition error (BSSE), the binding energy was appropriately corrected by the counterpoise calculation [12,13]. All MO calculations were performed by the G03 program package [11].…”

Section: Details Of Calculationsmentioning

confidence: 99%

Hybridization energies of double strands composed of DNA, RNA, PNA and LNA

Natsume¹,

Ishikawa²,

Dedachi³

et al. 2007

Chemical Physics Letters

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The electronic properties of double strands composed of trimeric LNA, PNA, DNA and RNA single strands were investigated by density-functional molecular orbital calculations. The computed hybridization energies for the double strands involving PNA or LNA are larger than those for DNA-DNA and RNA-RNA. The larger stability is attributed to the presence of a larger positive charge of the hydrogen atoms contributing to the hydrogen bonds in the PNA-DNA and LNA-DNA doublestrands. These results are comparable to the experimental finding that PNA and LNA single strands display high affinity toward a complementary DNA or RNA single strand.

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Origins of Structure and Energetics of van der Waals Clusters from ab Initio Calculations

Cited by 807 publications

References 72 publications

Theoretical insights on electron donor–acceptor interactions involving carbon dioxide

Theoretical insights on electron donor–acceptor interactions involving carbon dioxide

Non-additive interactions of nucleobases in model dinucleotide steps occurring in B-DNA crystals

Hybridization energies of double strands composed of DNA, RNA, PNA and LNA

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