Kinetic Isotope and Collision Energy Effects in the Dissociation of Chloride and Bromide Adducts of Aliphatic Alcohols, Benzaldehyde, and 2,4-Pentanedione

2003 ◽  
Vol 56 (5) ◽  
pp. 415 ◽  
Author(s):  
Rodinei Augusti ◽  
Xubin Zheng ◽  
M. Turowski ◽  
R. Graham Cooks

A tandem-in-space triple quadrupole mass spectrometer was used to measure kinetic isotopic effects (KIEs) for the dissociation of chloride and bromide adducts of several compounds that bind halide anions via either hydrogen bonds or by nucleophilic attachment. Two isotopomers of each adduct were simultaneously mass-selected in the first quadrupole and dissociated by collision with argon in the second quadrupole. The KIEs were measured by comparing the extents of dissociation of the lighter versus the heavier isotopomeric adducts. In most cases, lower collision energies and multiple collision conditions favoured larger KIE values, an expected feature of easily dissociated cluster ions considering zero-point energies (ZPEs). The larger chloride adduct of cyclohexanol gave greater KIEs compared with the smaller alcohols, a consequence of slower dissociation due to the larger number of degrees of freedom. Dissociation of the chloride adducts gave greater KIEs than the corresponding bromide adducts, a result that is also consistent with expectations based on ZPEs. Both the chloride and bromide adducts of 2,4-pentanedione, when dissociated at 6 eV collision energy under single-collision conditions, displayed normal KIEs (1.0460 ± 0.0012 and 1.0092 ± 0.0035 respectively). These and the alcohol results were correctly predicted by the ZPEs calculated using commonly applied ab initio Hartree–Fock (HF) and B3LYP density functional theory (DFT) methods with large basis sets (6–311 containing both polarization and diffuse functions). Geometry optimization calculations for the 2,4-pentanedione chloride adduct using either the Restricted Hartree–Fock (RHF) method with a 6–31G* basis set or using the more accurate 6–31++G** method showed that, in the most stable form, the chloride is bonded at multiple sites by a molecule of 2,4-pentanedione. In this structure, chloride binds weakly to both the methylene and the methyl hydrogen atoms. Collision-induced dissociation furnishes chloride and 2,4-pentanedione anion ([M – H]–) as competitive negatively charged products, which is consistent with the proposed structure. It is interesting that the intermolecular KIEs in this study tend to be normal, while intramolecular isotope effects in halides, notably of the type M1Cl+M2 are inverse, as a consequence of the lower ZPEs associated with the heavier isotopomers. The difference in the two systems is that the stronger bonds are found in the products in the case of M1Cl+M2 dissociation but in the reactants in the case of MCl– dissociation.


Molecules ◽  
2021 ◽  
Vol 26 (16) ◽  
pp. 5058
Author(s):  
Maciej Spiegel ◽  
Andrzej Gamian ◽  
Zbigniew Sroka

Polyphenolic compounds are now widely studied using computational chemistry approaches, the most popular of which is Density Functional Theory. To ease this process, it is critical to identify the optimal level of theory in terms of both accuracy and resource usage—a challenge we tackle in this study. Eleven DFT functionals with varied Hartree–Fock exchange values, both global and range-separated hybrids, were combined with 14 differently augmented basis sets to calculate the reactivity indices of caffeic acid, a phenolic acid representative, and compare them to experimental data or a high-level of theory outcome. Aside from the main course, a validation of the widely used Janak’s theorem in the establishment of vertical ionization potential and vertical electron affinity was evaluated. To investigate what influences the values of the properties under consideration, linear regression models were developed and thoroughly discussed. The results were utilized to compute the scores, which let us determine the best and worst combinations and make broad suggestions on the final option. The study demonstrates that M06–2X/6–311G(d,p) is the best fit for such research, and, curiously, it is not necessarily essential to include a diffuse function to produce satisfactory results.



2010 ◽  
Vol 7 (2) ◽  
pp. 449-455
Author(s):  
S. D. S. Chauhan ◽  
A.K. Sharma ◽  
R. Kumar ◽  
D. Kulshreshtha ◽  
R. Gupta ◽  
...  

Vibrational frequencies of aniline in gas phase have been calculated and each of their modes of vibration assigned properly at RHF and DFT with 6-31G(d) basis set. In the present study, it has been observed that the 6-31G(d) basis set at both RHF and DFT levels of calculations provides better agreement to the experimental findings as compared to other basis sets. Simultaneously, Density functional theory is found to be superior to its counterpart Hartree Fock method.



2013 ◽  
Vol 12 (07) ◽  
pp. 1350066 ◽  
Author(s):  
JABER JAHANBIN SARDROODI ◽  
ALIREZA RASTKAR ◽  
NEGAR RAD YOUSEFNIA ◽  
JAFAR AZAMAT

The effects of short-range electron correlation, long-range electron exchange, local and nonlocal parts of density, higher order gradients of density, and adding some percentage of Hartree–Fock exchange to the functional on the prediction of geometrical parameters were investigated. A copper complex namely 1,2-bis(1,4,7-triaza-1-cyclononyl) ethane copper (II) with Jahn–Teller distortion in octahedral geometry was used to evaluate the performance of 50 commonly available density functionals. The standard 3-21G basis set was used for all light elements, while pseudo potential LANL2DZ was used for the copper atom. The best bond lengths and bond angles were obtained using M05-2x and OP functionals respectively. Also in order to more accurate survey the performance of B3LYP, we used this functional with two all-electron basis sets (6-31G and 3-21G) and three basis sets involving effective core potentials (LANL2DZ/3-21G, LANL2DZ, and LACVP).



1998 ◽  
Vol 53 (10) ◽  
pp. 1223-1235
Author(s):  
Inge Warttmann ◽  
Günter Häfelinger

AbstractAb initio Hartree-Fock (HF) and density functional (DFT) optimizations on the test m olecule osmiumtetracarbonyldihydride (13) with various basis sets show that the lanl2mb pseudopotential basis set for osmium leads in the HF approximation to more reliable molecular geometries than the DFT calculations. This HF procedure was used for the optimizations of molecular geometries of three isomeric 4,4,4,4,17,17,17,17-octacarbonyl-4,17-diosma[7.7]ortho-, meta- and paracyclophanes 1 to 3, of which 3 was found to be predestined for formation of various host-guest complexes with possible guests benzene (4), fluorobenzene (5), 1,3,5- trifluorobenzene (6), 1,2,4,5-tetrafluorobenzene (7), hexafluorobenzene (8), fluoroanil (9), tetrafluoroethene (10), tetracyanoethene (11) and aniline (12). Results of optimized hostguest geometries are presented graphically for inclusions and associations of guest 4 to 12 with 3. Calculated lanl2mb interaction energies, after correction for basis set superposition error (BSSE), remain favourable only for inclusion of 5 and associations of 5, 10, 11 and 12. Additionally lanl2dz single point calculations for inclusion, which may not need BSSE correction because of the improved basis set, are favourable for 6 and 12. According to lanl2mb HOMO and LUMO energies, 3 may as well easily donate or accept electrons. This may be an interpretation to the surprising effect, that Mulliken total charges are positive on the electron accepting guest molecules 4 to 11. There are geometrical peculiarities in the optimized host-guest complexes for inclusion and association. Fluorine atoms of 5 to 10 and nitrogen atoms of a cyano group of 11 and the amino group of 12 like to come close to one or two carbonyl groups. Similar distances of 2.70 Å to 3.57 Å between the O atom of the carbonyl group and the F atom or N atom appear in all optimizations of inclusion and association of 5 to 12 except in the case of association of tetrafluoroethene (10).



2016 ◽  
Vol 15 (01) ◽  
pp. 1650006 ◽  
Author(s):  
Nabil Omri ◽  
Mohammed Yahyaoui ◽  
Ridha Banani ◽  
Sabri Messaoudi ◽  
Fathi Moussa ◽  
...  

Tryptophan methyl ester (Trp-ME) degrades with singlet oxygen and produce compounds which are photosensitizers and may react to form other derivatives such as N’-Formylkynurénine (NFK) and kynurenine, which are the final products of this oxidation. In order to study and optimize the molecular structure of NFK and determine its different thermodynamic properties, we performed a conformational analysis by DFT/B3LYP method with 3-21G basis set. Six most stable conformations were observed through the analysis of the potential energy surfaces, obtained by a relaxed scan of the dihedral angles. The most stable form of NFK has been registered for D[Formula: see text], D[Formula: see text], D[Formula: see text], D[Formula: see text], D[Formula: see text], and D[Formula: see text]. The study was conducted by HF and DFT/B3LYP with 6-31G(d,p), 6-3[Formula: see text](d,p) and 6-31[Formula: see text](d,p) basis sets, on the optimized geometry of the most stable conformation and its thermodynamic and orbital properties. Two absorption bands were recorded at [Formula: see text][Formula: see text]nm and at [Formula: see text][Formula: see text]nm and were also determined by TD-DFT method. They showed good agreement with the UV experimental spectrum which confirms that it is a powerful tool to determine the dynamic and static properties of molecules. The surface of the electrostatic potential (ESP) of the NFK was also analyzed.



2016 ◽  
Vol 14 (01) ◽  
pp. 1650002 ◽  
Author(s):  
Jakub Bielecki ◽  
Ewelina Lipiec

Raman spectroscopy (including surface enhanced Raman spectroscopy (SERS) and tip enhanced Raman spectroscopy (TERS)) is a highly promising experimental method for investigations of biomolecule damage induced by ionizing radiation. However, proper interpretation of changes in experimental spectra for complex systems is often difficult or impossible, thus Raman spectra calculations based on density functional theory (DFT) provide an invaluable tool as an additional layer of understanding of underlying processes. There are many works that address the problem of basis set dependence for energy and bond length consideration, nevertheless there is still lack of consistent research on basis set influence on Raman spectra intensities for biomolecules. This study fills this gap by investigating of the influence of basis set choice for the interpretation of Raman spectra of the thymine molecule calculated using the DFT/B3LYP framework and comparing these results with experimental spectra. Among 19 selected Pople’s basis sets, the best agreement was achieved using 6-31[Formula: see text](d,p), 6-31[Formula: see text](d,p) and 6-11[Formula: see text]G(d,p) sets. Adding diffuse functions or polarized functions for small basis set or use of a medium or large basis set without diffuse or polarized functions is not sufficient to reproduce Raman intensities correctly. The introduction of the diffuse functions ([Formula: see text]) on hydrogen atoms is not necessary for gas phase calculations. This work serves as a benchmark for further research on the interaction of ionizing radiation with DNA molecules by means of ab initio calculations and Raman spectroscopy. Moreover, this work provides a set of new scaling factors for Raman spectra calculation in the framework of DFT/B3LYP method.



2018 ◽  
Vol 55 (6A) ◽  
pp. 63
Author(s):  
Pham Le Nhan ◽  
Nguyen Tien Trung

Density functional theory (DFT) calculations using numerical basis sets were employed to predict the solvation energies, Gibbs free energies and pKa values of a series of 5-substituted uracil derivatives. Obtained results show that solvation energies are not significantly different between DFT methods using the numerical (DNP) and Gaussian basis set (aug-cc-pVTZ). It is noteworthy that the independent and suitable solvation energy of proton of -258.6 kcal/mol has been proposed for the evaluation of pKa values in conjunction with the numerical basis set. In addition, the calculated pKa values suggest that the anti-conformation of 5-formyluracil is the most stable form in the aqueous solution. 



2005 ◽  
Vol 04 (03) ◽  
pp. 823-832 ◽  
Author(s):  
JUAN F. VAN DER MAELEN URÍA ◽  
JAVIER RUIZ ◽  
SANTIAGO GARCÍA-GRANDA

The experimental geometry obtained from single-crystal X-ray diffraction data for a metalladiphosphanyl carbene precursor is compared with the results of theoretical calculations made at the ab initio level by using Hartree–Fock (HF) and Density Functional Theory (DFT) methods over the carbene itself. Theoretical geometry optimizations for the singlet ground state of [ Mn(CO)4(PH2)2C: ]+ have been performed with several hybrid functionals and basis sets. Calculated geometries showed a perfect C 2v symmetry in the highest levels of calculation and were somewhat relaxed when compared with the experimental ones; for instance, with the largest basis set, the P–C–P angle found was 124.8°, whereas C–P bond distances were both 1.667 Å, compared to 103.5(3)° and 1.718(5) Å, respectively, from the experimental data. The absence of a ligand attached to the C : atom in the calculated structure, which is present in the form of iodine in the experimental complex, is probably responsible, to a certain extent, for the discrepancies. In addition to the structural computations, in order to theoretically quantify the highly electrophilic character expected for the carbene, electron affinities were calculated and found to be between 6.24 eV and 6.97 eV at different DFT levels of calculation, which confirmed the expectations. In this respect, a comparison with the analogous [Ru(CNH)4(PH2)2C:]2+ carbene is also made, showing the possibility of experimentally trapping the manganese carbene.



2018 ◽  
Vol 96 (3) ◽  
pp. 336-339 ◽  
Author(s):  
Delano P. Chong

The equilibrium bond lengths of 41 small molecules are calculated by Gaussian09 and ADF2013 programs. We use five different basis sets: 6-31G*, cc-pVDZ, 6-311G+(2d,p), cc-pVTZ, and cc-pVQZ, for six different methods: Hartree-Fock, MP2, MP3, CCSD, CCSD(T), and B3LYP. The reliability of each level of theory on 89 bond lengths compared with CCSD(T)/cc-pVQZ is examined in terms of the mean absolute deviation. In particular, basis set dependence of the relative reliability of the two popular methods MP2 versus B3LYP is important to computational chemists. In addition, the efficient even-tempered basis set of Slater-type orbital called et-pVQZ, available in the ADF2013 program, is tested with the popular density functional B3LYP.



1993 ◽  
Vol 48 (1-2) ◽  
pp. 109-116 ◽  
Author(s):  
Jiahu Wang ◽  
Vedene H. Smith, Jr.

Abstract The spin densities of the nitroxides H2NO, (CH3)HNO and (CH3)2 NO have been studied by iterative CI methods. Calculations at different geometries with various basis sets were performed. It is found that the spin distribution is delocalized within the N-O group, and substitution of the hydrogen atoms on the nitroxyl group by methyl groups changes the spin distribution significantly. Electron correlation, as well as the basis-set quality, plays an important role for the fluctuation of spin populations in the nitroxide radicals. It has been found that the spin density map can be predicted fairly well when correlation was included at certain levels and reasonable quality basis sets were employed. The spin polarization mechanism has been studied through a core excitation method. The superiority of local-spin-density (LSD) theory over the unrestricted Hartree-Fock (UHF) method in spin property studies is discussed.



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