Four years ago we published the results of an extensive computational study of the structure and bonding in the inclusion complex of a He atom in an adamantane (C 10 H 16 ) cage, He@adam, by density functional theory (DFT) calculations at the B3LYP/6-311 + + GA C H T U N G T R E N N U N G (2d,2p) level. [1] Structure optimization of the free adamantane molecule confirmed that the equilibrium structure has T d symmetry and yielded a C À C bond length of 154.0 pm and a t Cs Ct C valence angle of 109.78 ( s C = secondary carbon atom, t C = tertiary carbon atom), both in excellent agreement with the experimental values, r a = 154.0(2) pm and q a = 109.8(7)8, respectively.[2] Structure optimization of the He@adam complex showed that it retained the T d symmetry of the adamantane cage (see Figure 1). The distance from the He atom to the four tertiary carbon atoms ( t C) was found to be 162.1 pm; the distance to the six secondary carbon atoms ( s C) was 184.4 pm.The sum of the van der Waals radii of a He atom (148 pm) [3] and of a spherically averaged methane molecule (201 pm) [4] suggests that He···C interactions should be strongly repulsive at distances shorter than 200 pm. Indeed, DFT calculations on the He···H 3 CH dimer optimized under C 3v symmetry with He···C distances fixed at values ranging from 320 to 160 pm, showed that the interaction energy increase monotonically with decreasing distance and reach a value of 177 kJ mol À1 at He···C = 162.1 pm.[1]The energy of formation of the complex, defined as the energy of the reaction given in Equation (1)
The molecular structures of phthalocyaninatozinc (HPc-Zn) and hexadecafluorophthalocyaninatozinc (FPc- Zn) are determined using the gas electron diffraction (GED) method and high-level density functional theory (DFT) quantum chemical calculations. Calculations at the B3LYP/6-311++G** level indicate that the equilibrium structures of HPc-Zn and FPc-Zn have D4h symmetry and yield structural parameters in good agreement with those obtained by GED at 480 and 523 degrees C respectively. The calculated force fields indicate that both molecules are flexible. Normal coordinate calculations on HPc-Zn yield five vibrational frequencies (one degenerate) in the range 22-100 cm(-1), and ten vibrational frequencies ranging from 13 to 100 cm(-1) (three degenerate) for FPc-Zn. The high-level force field calculations confirm most of the previous vibrational assignments, and some new ones are suggested. The out-of-plane vibration of the Zn atom in HPc-Zn was studied in detail optimizing models in which the distance from the Zn atom to the two symmetry equivalent diagonally opposed N atoms (h) was fixed. The calculations indicate that the vibrationally activated vertically displacement of the Zn atom is accompanied by distortion of the ligand from D4h to C2v symmetry. The average height, h, at the temperature of the GED experiment was calculated to be 14.5 pm. Small structural changes indicate that a full F substitution on the benzo-subunits do not significantly alter the geometry, however there are indications that the benzo-subunits may shrink slightly with perfluorination.
The molecular structure of phthalocyaninatotin(II), Sn(II)Pc, is determined by density functional theory (DFT/B3LYP) calculations using various basis sets and gas-phase electron diffraction (GED). The quantum chemical calculations show that Sn(II)Pc has C4V symmetry, and this symmetry is consistent with the structure obtained by GED at 427 degrees C. GED locates the Sn atom at h(Sn) ) 112.8(48) pm above the plane defined by the four isoindole N atoms, and a N-Sn bond length of 226.0(10) pm is obtained. Calculation at the B3LYP/ccpVTZ/cc-pVTZ-PP(Sn) level of theory gives h(Sn) ) 114.2 pm and a N-Sn bond length of 229.4 pm. The phthalocyanine (Pc) macrocycle has a slightly nonplanar structure. Generally, the GED results are in good agreement with the X-ray structures and with the computed structure; however, the comparability between these three methods has been questioned. The N-Sn bond lengths determined by GED and X-ray are significantly shorter than those from the B3LYP predictions. Similar trends have been found for C-Sn bonds for conjugated organometallic tin compounds. Computed vibrational frequencies give five low frequencies in the range of 18-54 cm-1, which indicates a flexible molecule.
The molecular structure of the trans isomer of metal-free phthalocyanine (H2Pc) is determined using the gas electron diffraction (GED) method and high-level quantum chemical calculations. B3LYP calculations employing the basis sets 6-31G**, 6-311++G**, and cc-pVTZ give two tautomeric isomers for the inner H atoms, a trans isomer having D2h symmetry and a cis isomer having C2v symmetry. The trans isomer is calculated to be 41.6 (B3LYP/6-311++G**, zero-point corrected) and 37.3 kJ/mol (B3LYP/cc-pVTZ, not zero-point corrected) more stable than the cis isomer. However, Hartree-Fock (HF) calculations using different basis sets predict that cis is preferred and that trans does not exist as a stable form of the molecule. The equilibrium composition in the gas phase at 471 degrees C (the temperature of the GED experiment) calculated at the B3LYP/6-311++G** level is 99.8% trans and 0.2% cis. This is in very good agreement with the GED data, which indicate that the mole fraction of the cis isomer is close to zero. The transition states for two mechanisms of the NH tautomerization have been characterized. A concerted mechanism where the two H atoms move simultaneously yields a transition state of D2h symmetry and an energy barrier of 95.8 kJ/mol. A two-step mechanism where a trans isomer is converted to a cis isomer, which is converted into another trans isomer, proceeds via two transition states of C(s) symmetry and an energy barrier of 64.2 kJ/mol according to the B3LYP/6-311++G** calculation. The molecular geometry determined from GED is in very good agreement with the geometry obtained from the quantum chemical calculations. Vibrational frequencies, IR, and Raman intensities have been calculated using B3LYP/6-311++G**. These calculations indicate that the molecule is rather flexible with six vibrational frequencies in the range of 20-84 cm(-1) for the trans isomer. The cis isomer might be detected by infrared matrix spectroscopy since the N-H stretching frequencies are very different for the two isomers.
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