The geometry of intermolecular interactions in some crystalline fluorine-containing organic compounds

Shimoni, Liat; Glusker, Jenny P.

doi:10.1007/bf02252897

Cited by 206 publications

(162 citation statements)

References 9 publications

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“…The most populated H···F distance (2.6 ; Figure 3) and CÀH···F angle (1408; Figure S5 in the Supporting Information) thus agree perfectly with geometries reported for H···F interactions in small-molecule crystal structures. [2,[42][43][44][45] Accordingly, we interpret our findings in terms of weak attractive CÀF···HÀC dipolar interactions, with more short-range interactions present in 3 and 4 self-pairs than in their 2 counterparts. This interpretation is corroborated by analysis of the occupancy of CÀF···HÀC interactions: that is, the ratio of times when the interaction is present relative to the total simulation time.…”

mentioning

confidence: 61%

Determinants of the Unexpected Stability of RNA Fluorobenzene Self Pairs

et al. 2008

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confidence: 61%

Determinants of the Unexpected Stability of RNA Fluorobenzene Self Pairs

et al. 2008

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“…[47,48] This question is of particular interest in the present case, because difluorotoluene might conceivably form two weakened hydrogen bonds with adenine. These would be a CÀF´´´HÀN and a CÀH´´´N interaction.…”

Section: Electronic Factorsmentioning

confidence: 97%

Mimicking the Structure and Function of DNA: Insights into DNA Stability and Replication

Kool

Morales

Guckian

2000

Angew. Chem. Int. Ed.

353

241

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The physical and chemical factors that allow DNA to perform its functions in the cell have been studied for several decades. Recent advances in the synthesis and manipulation of DNA have allowed this field to move ahead especially rapidly during the past fifteen years. One of the most common chemical approaches to the study of interactions involving DNA has been the use of DNA base analogues in which functional groups are added, deleted, blocked, or rearranged. Here we describe a different strategy, in which the polar natural DNA bases are replaced by nonpolar aromatic molecules of the same size and shape. This allows the evaluation of polar interactions (such as hydrogen bonding) with little or no interference from steric effects. We have used these nonpolar nucleoside isosteres as probes of noncovalent interactions such as DNA base pairing and protein - DNA recognition. We have found that, while base-pairing selectivity does depend on Watson - Crick hydrogen bonding in the natural pairs, it is possible to design new bases that pair selectively and stably in the absence of hydrogen bonds. In addition, studies have been carried out with DNA polymerase enzymes to investigate the importance of Watson - Crick hydrogen bonding in enzymatic DNA replication. Surprisingly, this hydrogen bonding is not necessary for efficient enzymatic synthesis of a base pair, and significant levels of selectivity can arise from steric effects alone. These results may have significant impact both on the study of basic biomolecular interactions and in the design of new, functionally active biomolecules.

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“…[15] The authors revealed that attractive CÀH¥¥¥FÀC interactions occur, but they are very weak. [15] Because of the importance of fluorine in biochemical environments and the common practice to replace a hydrogen atom or hydroxyl group by fluorine to generate a fluorinated enzyme substrate or inhibitor in a given enzymatic process, [16] subsequent CSD searches were carried out with more severe criteria for the F¥¥¥H distance. [17] According to a CSD analysis of Howard et al with R H¥¥¥F < 2.35 ä, short CÀH¥¥¥FÀC contacts occur somewhat more frequently than O/N À H¥¥¥F À C hydrogen bonds, but they are still relatively rare.…”

Section: Introductionmentioning

confidence: 98%

Weak Hydrogen Bridges: A Systematic Theoretical Study on the Nature and Strength of CH⋅⋅⋅FC Interactions

Hyla‐Kryspin

Haufe

Grimme

2004

Chemistry A European J

118

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We present a comparative study on the nature and strength of weak hydrogen bonding between the C(sp3)-H, C(sp2)-H, and C(sp)-H donor bonds and F-C(sp3) acceptors. The series of molecules CH3F.CH4 (2 a, 2 b), CH3F.C2H4 (3), CH3F.C2H2 (4), as well as model complexes of experimentally characterized 2-fluoro-2-phenylcyclopropane derivatives, C3H6.C3H5F (5 a, 5 b) and C3H5F.C3H5F (6) were investigated. Comparative studies were also performed for two conformers of the methane dimer (1 a, 1 b). The calculations were carried out in hierarchies of basis sets [SV(d,p), TZV(d,p), aug-TZV(d,p), TZV(2df,2pd), aug-TZV(2df,2pd), QZV(3d2fg,2pd), aug-QZV(3d2fg,2pdf)] by means of ab initio [HF, MP2, QCISD, QCISD(T)] methods and density functional theory (DFT/B3LYP, DFT/PBE). It is shown that well-balanced basis sets of at least TZV(2df,2pd) quality are needed for a proper description of the weakly bonded systems. In the case of 2, 3, 5, and 6, the dispersion interaction is the dominant term of the entire attraction, which is not accounted for at the B3LYP level. Significant electrostatic contributions are observed for 6 and 3. For 4, these forces have a dominating contribution to the hydrogen bonding. The C(sp)--H...F--C(sp(3)) interaction in 4, though weak, exhibits the same characteristics as conventional hydrogen bridges. Despite showing longer H.F/H contacts compared to 1 a, 2 a, and 5 a the bifurcated structures, 1 b, 2 b, 5 b, are characterized by larger dispersion interactions leading to stronger bonding. For the systems with only one H.F contact, the MP2/QZV(3d2fg,2pd) interaction energy increases in the order 2 a (-1.62 kJ mol(-1)), 3 (-2.79 kJ mol(-1)), 5 a (-5.97 kJ mol(-1)), 4 (-7.25 kJ mol(-1)), and 6 (-10.02 kJ mol(-1)). This contradicts the estimated proton donor ability of the C--H bonds (2 a<5 a<3<6<4).

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The geometry of intermolecular interactions in some crystalline fluorine-containing organic compounds

Cited by 206 publications

References 9 publications

Determinants of the Unexpected Stability of RNA Fluorobenzene Self Pairs

Determinants of the Unexpected Stability of RNA Fluorobenzene Self Pairs

Mimicking the Structure and Function of DNA: Insights into DNA Stability and Replication

Weak Hydrogen Bridges: A Systematic Theoretical Study on the Nature and Strength of CH⋅⋅⋅FC Interactions

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