| Literature DB >> 31398800 |
Shuman Li1, Tianlv Xu1, Tanja van Mourik2, Herbert Früchtl3, Steven R Kirk4, Samantha Jenkins5.
Abstract
Next-generation quantum theory of atoms in molecules (QTAIM) was used to investigate the competition between hydrogen bonding and halogen bonding for the recently proposed (Y = Br, I, At)/halogenabenzene/NH3 complex. Differences between using the SR-ZORA Hamiltonian and effective core potentials (ECPs) to account for relativistic effects with increased atomic mass demonstrated that next-generation QTAIM is a much more responsive tool than conventional QTAIM. Subtle details of the competition between halogen bonding and hydrogen bonding were observed, indicating a mixed chemical character shown in the 3-D paths constructed from the bond-path framework set B. In addition, the use of SR-ZORA reduced or entirely removed spurious features of B on the site of the halogen atoms.Entities:
Keywords: DFT; ZORA; double-hybrid density functional theory; halogen bonding; halogenabenzene; halouracil; next-generation QTAIM
Mesh:
Substances:
Year: 2019 PMID: 31398800 PMCID: PMC6720212 DOI: 10.3390/molecules24162875
Source DB: PubMed Journal: Molecules ISSN: 1420-3049 Impact factor: 4.411
SR-ZORA results for the eigenvector following path lengths (H,H’) and (H*,H*’), bond-path length (BPL), geometric bond length (GBL), (Hσ,Hσ’) and (Hσ*,Hσ*’), metallicity ξ(r), stiffness S, and the total local energy density H(r) in a.u. for the (Y = Cl, Br, I, At)/NH3 system. Note the use of the bond notations “--“ (closed-shell BCP) and “-“ (shared-shell BCP). The corresponding results obtained with effective core potentials (ECPs) are provided in Table S4 of the Supplementary Materials.
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| (H,H’) | (H*,H*’) | (BPL, GBL) | (Hσ,Hσ’) | (Hσ*,Hσ*’) | ξ(rb) | S | |
|---|---|---|---|---|---|---|---|---|
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| C3--H14 | (5.390, 5.202) | (5.266, 5.286) | (4.927, 4.864) | (5.024, 4.928) | (4.968, 4.978) | 0.351 | 0.156 | 0.001 |
| N12-H14 | (2.161, 2.154) | (2.158, 2.158) | (1.877, 1.914) | (1.897, 1.897) | (1.897, 1.897) | −0.198 | 1.496 | −0.481 |
| C3-H8 | (2.317, 2.298) | (2.294, 2.321) | (2.007, 2.036) | (2.051, 2.039) | (2.041, 2.049) | −0.274 | 1.426 | −0.299 |
| C4-C3 | (3.105, 3.095) | (3.082, 3.119) | (2.586, 2.585) | (2.648, 2.631) | (2.637, 2.642) | −0.324 | 1.931 | −0.375 |
| Cl2-C3 | (3.876, 3.831) | (3.839, 3.860) | (3.421. 3.396) | (3.999, 3.983) | (3.859, 3.905) | −0.862 | 0.776 | −0.123 |
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| C3--H14 | (6.297, 5.619) | (5.870, 5.905) | (5.125, 4.991) | (5.347, 5.097) | (5.212, 5.223) | 0.329 | 0.115 | 0.001 |
| Br2--N12 | (6.429, 6.376) | (6.358, 6.437) | (6.107, 6.091) | (6.137, 6.133) | (6.129, 6.139) | 0.286 | 0.108 | 0.001 |
| N12-H14 | (2.157, 2.149) | (2.153, 2.153) | (1.876, 1.913) | (1.896, 1.896) | (1.896, 1.896) | −0.198 | 1.500 | −0.482 |
| C3-H8 | (2.294, 2.275) | (2.271, 2.298) | (2.008, 2.037) | (2.051, 2.038) | (2.040, 2.048) | −0.276 | 1.427 | −0.297 |
| C4-C3 | (3.062, 3.054) | (3.038, 3.079) | (2.587, 2.585) | (2.646, 2.627) | (2.634, 2.639) | −0.325 | 1.927 | −0.374 |
| Br2-C3 | (3.895, 3.859) | (3.871, 3.879) | (3.691, 3.666) | (3.716, 3.713) | (3.705, 3.724) | −1.103 | 0.717 | −0.088 |
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| I2--N12 | (6.213, 6.195) | (6.198, 6.202) | (5.986, 5.970) | (6.588, 6.584) | (6.495, 6.564) | 0.346 | 0.153 | 0.001 |
| C3-H8 | (2.250, 2.231) | (2.229, 2.252) | (2.010, 2.039) | (2.045, 2.035) | (2.036, 2.044) | −0.279 | 1.430 | −0.295 |
| C4-C3 | (3.007, 3.002) | (2.985, 3.026) | (2.589, 2.587) | (2.641, 2.624) | (2.632, 2.634) | −0.329 | 1.905 | −0.369 |
| I2-C3 | (4.363, 4.334) | (4.337, 4.343) | (4.025, 4.004) | (4.640, 4.638) | (4.542, 4.628) | −2.200 | 0.600 | −0.061 |
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| At6--N12 | (6.160, 6.142) | (6.143, 6.146) | (5.927, 5.914) | (5.948, 5.943) | (5.939, 5.944) | 0.357 | 0.158 | 0.001 |
| C5-H8 | (2.257, 2.238) | (2.237, 2.259) | (2.014, 2.043) | (2.051, 2.041) | (2.042, 2.050) | −0.280 | 1.429 | −0.292 |
| C4-C5 | (2.963, 2.957) | (2.939, 2.982) | (2.593, 2.591) | (2.644, 2.626) | (2.633, 2.636) | −0.329 | 1.910 | −0.367 |
| At6-C5 | (4.636, 4.616) | (4.622, 4.623) | (4.235, 4.208) | (4.272, 4.270) | (4.248, 4.265) | −22.03 | 0.486 | −0.046 |
The percentage difference of ∆{[(ECP) – (SR-ZORA)]/(ECP)} (%) for ∆(H,H’), ∆(H*,H*’), ∆(BPL), ∆(GBL), ∆(Hσ,Hσ’), ∆(Hσ*,Hσ*’), ∆ξ(r), ∆S, and ∆H(r) in a.u. of the (X = Cl, Br, I, At)/1-methyluracil/NH3 system; see Table S4 of the Supplementary Materials and Table 1 for the original ECP and SR-ZORA results, respectively, and the caption of Table 1 for further details.
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| ∆(H,H’) (%) | ∆(H*,H*’) (%) | ∆(BPL, GBL) (%) | ∆(Hσ,Hσ’) (%) | ∆(Hσ*,Hσ*’) (%) | ∆ξ(rb) (%) | ∆S (%) | ∆ |
|---|---|---|---|---|---|---|---|---|
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| ||||||||
| C3--H14 | (−0.242, 0.115) | (−0.171, −0.019) | (−0.102, 0.000) | (−0.259, 0.000) | (−0.202, −0.101) | −3.540 | −0.645 | 0.000 |
| N12-H14 | (0.231, 0.185) | (0.185, 0.185) | (−0.321, 0.000) | (−0.264, −0.264) | (−0.264, −0.264) | −5.319 | 8.502 | 8.031 |
| C3-H8 | (2.030, 1.921) | (1.966, 2.026) | (−0.200, 0.000) | (0.195, 0.049) | (0.098, 0.098) | −11.38 | 18.05 | 12.57 |
| C4-C3 | (2.908, 2.826) | (2.868, 2.895) | (0.039, 0.000) | (0.339, 0.303) | (0.265, 0.339) | −13.68 | 36.40 | 10.29 |
| Cl2-C3 | (3.003, 2.643) | (2.786, 2.746) | (0.175, 0.000) | (1.502, 1.872) | (1.656, 1.563) | −15.70 | 9.240 | 6.107 |
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| C3--H14 | (−0.671, −0.807) | (−1.224, −0.854) | (−0.039, 0.000) | (−0.300, 0.157) | (−0.192, −0.173) | −1.543 | −2.679 | 0.000 |
| Br2--N12 | (−0.047, 0.530) | (0.235, 0.294) | (0.000, 0.000) | (0.114, −0.114) | (−0.147, 0.065) | −4.380 | −5.882 | 50.00 |
| N12-H14 | (0.416, 0.371) | (0.370, 0.416) | (−0.267, 0.000) | (−0.264, −0.264) | (−0.264, −0.264) | −5.319 | 8.369 | 8.015 |
| C3-H8 | (1.587, 1.515) | (1.518, 1.627) | (−0.150, 0.000) | (0.097, 0.000) | (0.049, 0.049) | −11.74 | 18.32 | 12.90 |
| C4-C3 | (2.608, 2.553) | (2.597, 2.594) | (0.000, 0.000) | (0.264, 0.266) | (0.265, 0.265) | −13.64 | 36.34 | 10.31 |
| Br2-C3 | (2.209, 1.906) | (2.050, 1.946) | (0.135, 0.000) | (0.215, 0.242) | (0.135, 0.321) | −7.926 | 2.846 | 1.124 |
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| I2--N12 | (−2.339, −2.295) | (−2.243, −2.276) | (−0.050, 0.000) | (0.768, 0.813) | (−0.480, 1.515) | −2.065 | −2.000 | 0.000 |
| C3-H8 | (−0.852, −0.768) | (−0.814, −0.806) | (−0.100, 0.000) | (−0.196, −0.197) | (−0.197, −0.245) | −10.28 | 15.48 | 11.68 |
| C4-C3 | (−1.008, −0.975) | (−0.981, −1.035) | (0.000, 0.000) | (−0.152, −0.114) | (−0.152, −0.152) | −10.77 | 28.89 | 8.889 |
| I2-C3 | (−4.880, −4.965) | (−4.683, −4.827) | (−0.025, 0.000) | (1.003, 1.003) | (−0.643, 1.845) | −19.24 | 3.692 | 4.688 |
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| At6--N12 | (−2.564, −2.555) | (−2.452, −2.467) | (−0.034, 0.000) | (18.07, 18.13) | (12.62, 19.96) | −4.386 | −1.282 | 0.000 |
| C5-H8 | (−0.267, −0.314) | (−0.314, −0.311) | (−0.099, 0.000) | (−0.146, −0.196) | (−0.196, −0.196) | −10.24 | 15.29 | 11.78 |
| C4-C5 | (−0.407, −0.373) | (−0.376, −0.404) | (0.000, 0.000) | (−0.114, −0.114) | (−0.076, −0.114) | −10.40 | 27.92 | 8.706 |
| At6-C5 | (−7.042, −7.174) | (−7.040, −7.039) | (0.000, 0.000) | (23.23, 23.24) | (17.11, 25.71) | 1.432 | −0.621 | 2.128 |
Figure 1The { path-packets; (dark magenta) and ʹ (light magenta) for the (Y = Cl, Br, I, At)/halogenabenzene/NH3 system are presented in subfigures (a–d), respectively, calculated using ECPs (left panels) and with the SR-ZORA Hamiltonian (right panels).
Figure 2The {σ,σʹ} path-packets with a magnification factor of ×5 for the (Y = Cl, Br, I, At)/halogenabenzene/NH3 system are presented in subfigures (a–d), respectively; see the caption of Figure 1 for further details.
Figure 3The {σ,σʹ} path-packets with a magnification factor of ×5 for the (Y = Cl, Br, I, At)/halogenabenzene/NH3 system are presented in subfigures (a–d), respectively; see the caption of Figure 1 for further details.