Properties of Hydrogen-Bonded Complexes Obtained from the B3LYP Functional with 6-31G(d,p) and 6-31+G(d,p) Basis Sets: Comparison with MP2/6-31+G(d,p) Results and Experimental Data

Bene, Janet E. Del; Person, Willis B.; Szczepaniak, Krystyna

doi:10.1021/j100027a005

Cited by 397 publications

(218 citation statements)

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“…The agreement between the MP2(full) calculated and TCID measured values improves to 26.0 ± 6.7 and 17.0 ± 5.0 kJ/ mol when BSSE corrections are not included, consistent with previous TCID studies on similar proton-bound dimers [29][30][31]. This is also consistent with previous theoretical studies of hydrogen-bonded complexes [68][69][70][71][72][73][74][75], which have shown that at least triple-zeta-quality basis sets are required to accurately describe systems where there can be significant intramolecular noncovalent interactions, and the BSSE corrections can get rather large for MP2 calculations when flexible but still unsaturated basis sets are used. Based on the comparisons between theory and experiment, it is clear that B3LYP theory describes the base-pairing interactions in the proton-bound dimers more accurately, whereas MP2(full) underestimates the strength of the base-pairing interactions in all complexes.…”

Section: Comparison Of Experiments and Theorysupporting

confidence: 90%

Base-Pairing Energies of Proton-Bound Dimers and Proton Affinities of 1-Methyl-5-Halocytosines: Implications for the Effects of Halogenation on the Stability of the DNAi-Motif

Rodgers

2015

J. Am. Soc. Mass Spectrom.

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Abstract. (CCG) n •(CGG) n trinucleotide repeats have been found to be associated with fragile X syndrome, the most widespread inherited cause of mental retardation in humans. The (CCG) n •(CGG) n repeats adopt i-motif conformations that are preferentially stabilized by base-pairing interactions of noncanonical proton-bound dimers of cytosine (C + •C). Halogenated cytosine residues are one form of DNA damage that may be important in altering the structure and stability of DNA or DNA-protein interactions and, hence, regulate gene expression. Previously, we investigated the effects of 5-halogenation and 1-methylation of cytosine on the base-pairing energies (BPEs) using threshold collision-induced dissociation (TCID) techniques. In the present study, we extend our work to include proton-bound homo-and heterodimers of cytosine, 1-methyl-5-fluorocytosine, and 1-methyl-5-bromocytosine. All modifications examined here are found to produce a decrease in the BPEs. However, the BPEs of all of the proton-bound dimers examined significantly exceed those of Watson-Crick G•C, neutral C•C base pairs, and various methylated variants such that DNA i-motif conformations should still be preserved in the presence of these modifications. The proton affinities (PAs) of the halogenated cytosines are also obtained from the experimental data by competitive analysis of the primary dissociation pathways that occur in parallel for the proton-bound heterodimers. 5-Halogenation leads to a decrease in the N3 PA of cytosine, whereas 1-methylation leads to an increase in the N3 PA. Thus, the 1-methyl-5-halocytosines exhibit PAs that are intermediate.

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Section: Comparison Of Experiments and Theorysupporting

confidence: 90%

Base-Pairing Energies of Proton-Bound Dimers and Proton Affinities of 1-Methyl-5-Halocytosines: Implications for the Effects of Halogenation on the Stability of the DNAi-Motif

Rodgers

2015

J. Am. Soc. Mass Spectrom.

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“…28 Both CHA and CP results point out that this effect is directly caused by the BSSE rather than by the supposed poor behavior of the actual functionals used to describe these kinds of systems. 29 By studying the PES one can extract information mainly in terms of nuclear relaxation, i.e., how the nuclear positions move according to the electronic potential. To gain a deeper insight into how the BSSE affects the electronic distribution at a given nuclear arrangement ͑electronic relaxation͒ one is driven to study the electron density and its topology.…”

Section: Resultsmentioning

confidence: 99%

Effect of basis set superposition error on the electron density of molecular complexes

Salvador¹,

Fradera²,

Duran³

2000

The Journal of Chemical Physics

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The Chemical Hamiltonian Approach ͑CHA͒ versions of the Roothaan and Kohn-Sham equations, labeled CHA/F and CHA/DFT, respectively, have been used to obtain the basis set superposition error ͑BSSE͒-corrected first-order electron density of the hydrogen fluoride dimer with several basis sets. We have analyzed the effect of BSSE in terms of the electronic relaxation, i.e., the redistribution of the electron density due to the inclusion of the CHA correction at a frozen geometry, along with the subsequent nuclear relaxation process. Critical points of the charge density have been located and characterized to compare the conventional, uncorrected first-order electron density against the BSSE-corrected density at each level of theory. Contour difference maps between BSSE-corrected and uncorrected densities on the molecular plane have also been plotted to gain insight into the effects of BSSE correction on the electron density.

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“…59 It has been found that the B3LYP H-bonding geometries are in very good agreement with MP2 geometries. [60][61][62][63][64][65] Geometry optimizations were performed without any symmetry constraints, and using the Opt = Tight convergence option which is usually necessary to guarantee reasonable convergence and reliability of calculated frequencies. Geometries were not optimized, however, on the counterpoise-corrected ͑CP͒ surface.…”

Section: Methodsmentioning

confidence: 99%

Cooperative effects in two-dimensional ring-like networks of three-center hydrogen bonding interactions

Parra

Bulusu

Zeng

2005

The Journal of Chemical Physics

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Cooperative effects in two-dimensional cyclic networks containing intermolecular three-centered hydrogen bonding interactions of the type H 1 …A…H 2 are investigated by means of ab intio molecular orbital and density functional theory calculations. Ring-like clusters consisting of three and up to nine monomers of the cis-cis isomer of carbonic acid H 2 CO 3 are used as basic models, where each unit acts simultaneously as a double hydrogen-bond donor and double hydrogen-bond acceptor. Cooperative effects based on binding energies are evident for ͑H 2 CO 3 ͒ n , where n goes from 2 to 9. Thus, the ZPVE-corrected dissociation energy per bifurcated hydrogen bond increases from 11.52 kcal/ mol in the dimer to 20.42 kcal/ mol in the nonamer, i.e., a 77% cooperative enhancement. Cooperative effects are also manifested in such indicators as geometries, and vibrational frequencies and intensities. The natural bond orbital analysis method is used to rationalize the results in terms of the substantial charge delocalization taking place in the cyclic clusters. Cooperativity seems close to reaching an asymptotic limit in the largest ring considered, n = 9.

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Properties of Hydrogen-Bonded Complexes Obtained from the B3LYP Functional with 6-31G(d,p) and 6-31+G(d,p) Basis Sets: Comparison with MP2/6-31+G(d,p) Results and Experimental Data

Cited by 397 publications

References 0 publications

Base-Pairing Energies of Proton-Bound Dimers and Proton Affinities of 1-Methyl-5-Halocytosines: Implications for the Effects of Halogenation on the Stability of the DNAi-Motif

Base-Pairing Energies of Proton-Bound Dimers and Proton Affinities of 1-Methyl-5-Halocytosines: Implications for the Effects of Halogenation on the Stability of the DNAi-Motif

Effect of basis set superposition error on the electron density of molecular complexes

Cooperative effects in two-dimensional ring-like networks of three-center hydrogen bonding interactions

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