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
01 Jul 1995-The Journal of Physical Chemistry (American Chemical Society)-Vol. 99, Iss: 27, pp 10705-10707
TL;DR: In this paper, Youngatown State University, Youngatown, Ohio 44555, and University of Florida, Gainesville, Florida 32611 have published a study on the relationship between the two types of cancers.
Abstract: Author Institution: Youngatown State University, Youngatown, Ohio 44555; University of Florida, Gainesville, Florida 32611
Citations
More filters
TL;DR: In this paper, the hydrogen-bonding topology of two conformers of the benzene-(water) 8 cluster was characterized using Resonant Two-photon ionization, ultraviolet hole burning, and resonant ion-dip infrared (RIDIR) spectroscopy.
Abstract: Resonant two-photon ionization, ultraviolet hole-burning, and resonant ion-dip infrared (RIDIR) spectroscopy were used to assign and characterize the hydrogen-bonding topology of two conformers of the benzene-(water) 8 cluster. In both clusters, the eight water molecules form a hydrogen-bonded cube to which benzene is surface-attached. Comparison of the RIDIR spectra with density functional theory calculations is used to assign the two (water) 8 structures in benzene-(water) 8 as cubic octamers of D 2 d and S 4 symmetry, which differ in the configuration of the hydrogen bonds within the cube. OH stretch vibrational fundamentals near 3550 wave numbers provide unique spectral signatures for these “molecular ice cubes.”
421 citations
TL;DR: In this article, the authors investigated the possible sources of the discrepancy between theory and experiment regarding hydrogen bond lengths in adenine−thymine (AT) and guanine−cytosine (GC) base pairs at various levels (BP86, PW91, and BLYP) in combination with different Slater-type orbital (STO) basis sets.
Abstract: Up till now, there has been a significant disagreement between theory and experiment regarding hydrogen bond lengths in Watson−Crick base pairs. To investigate the possible sources of this discrepancy, we have studied numerous model systems for adenine−thymine (AT) and guanine−cytosine (GC) base pairs at various levels (i.e., BP86, PW91, and BLYP) of nonlocal density functional theory (DFT) in combination with different Slater-type orbital (STO) basis sets. Best agreement with available gas-phase experimental A−T and G−C bond enthalpies (−12.1 and −21.0 kcal/mol) is obtained at the BP86/TZ2P level, which (for 298 K) yields −11.8 and −23.8 kcal/mol. However, the computed hydrogen bond lengths show again the notorious discrepancy with experimental values. The origin of this discrepancy is not the use of the plain nucleic bases as models for nucleotides: the disagreement with experiment remains no matter if we use hydrogen, methyl, deoxyribose, or 5‘-deoxyribose monophosphate as the substituents at N9 and N...
403 citations
TL;DR: In this paper, the authors examined the hydrogen bonding between water and a series of small organic molecules via electronic structure calculations and found that acceptor sites corresponded closely to the positions of lone pairs as predicted by simple hybridization arguments.
Abstract: Hydrogen bonding between water and a series of small organic molecules was examined via electronic structure calculations. Several computational methods were examined, including both a hybrid density functional procedure (Becke3LYP) and second-order Moller−Plesset theory (MP2) coupled with a double-ζ basis set augmented by diffuse polarization functions on heteroatoms. The agreement between Becke3LYP and MP2 energies was generally good, as was the agreement with energies obtained using more sophisticated and costly methods. The energies and structures of 53 hydrogen-bonded complexes of water with various small organic molecules, including alcohols, thiols, ethers, thioethers, carboxylic acids, esters, amines, amides, nitriles, and nitro compounds, were then examined systematically using the Becke3LYP and MP2 procedures. The hydrogen bond geometries were generally linear, and acceptor sites corresponded closely to the positions of lone pairs as predicted by simple hybridization arguments. Structures with s...
385 citations
TL;DR: In this article, single and double proton transfer reactions in Watson−Crick Guanine−Cytosine (GC) and Adenine−Thymine (AT) radical cations have been studied using the hybrid density functional B3LYP method.
Abstract: Single and double proton-transfer reactions in Watson−Crick Guanine−Cytosine (GC) and Adenine−Thymine (AT) radical cations have been studied using the hybrid density functional B3LYP method. Calibration calculations for the formamidine−formamide dimer, a model system of AT, have shown that B3LYP compares well to the high level ab initio correlated method CCSD(T), both for the neutral and cationic systems. The single proton-transfer reaction is favorable in both the GC and AT radical cations; it takes place from the ionized monomer (guanine and adenine, respectively), which increases its acidity, to the neutral fragment. For the two systems, GC and AT, the nonproton transferred and single proton transferred structures are almost degenerate (ΔE = 1.2 kcal/mol), and the process presents low energy barriers (4.3 kcal/mol for GC and 1.6 kcal/mol for AT). The double proton-transfer reaction is less favorable than the single one, in contrast to what is observed for the neutral systems. The relative stability of ...
203 citations
TL;DR: In this article, the enthalpy difference between the hydrogen-bonded (HB) form and the lowest energy conformer in which the OH is rotated into the “away” position was defined.
Abstract: For a series of 61 2-substituted phenols, 2-X−PhOH, forming a total of 73 intramolecular hydrogen bonds, the intramolecular hydrogen bond enthalpy, ΔHintra-HB, has been determined by density functional theory (DFT) calculations on the B3LYP/6-31G(d,p)//B3LYP/6-31G(d,p) level. The ΔHintra-HB was defined as the enthalpy difference between the hydrogen-bonded (HB) form and the lowest-energy conformer in which the OH is rotated into the “away” position. The correlation of ΔHintra-HB with geometrical factors such as r(O−H), or r(OH···A), with A as the hydrogen bond accepting atom, was generally very poor, showing that none of these parameters can be used as an universal descriptor for the hydrogen bond strength. The relation between ΔHintra-HB and ν(O−H) intra-HB is also insignificant, in contrast with previous estimates. The data clearly demonstrate that the genuine ΔHintra-HB of a phenolic compound cannot be unequivocally derived by simple rotation of the OH group into the “away” orientation, because additio...
195 citations