Browsing by Subject "BASIS-SETS"

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  • Donsbach, Carsten; Reiter, Kevin; Sundholm, Dage; Weigend, Florian; Dehnen, Stefanie (2018)
    The use of ionic liquids (C(n)C(1)Im)[BF4] with long alkyl chains (n=10,12) in the ionothermal treatment of Na-2[HgTe2] led to lamellar crystal structures with molecular macrocyclic anions [Hg8Te16](8-) (1), the heaviest known topological relative of porphyrin. [Hg8Te16](8-) differs from porphyrin by the absence of an electronic pi-system, which prevents a global aromaticity. Quantum chemical studies reveal instead small ring currents in the pyrrole-type five-membered rings that indicate weak local (sigma) aromaticity. As a result of their lamellar nature, the compounds are promising candidates for the formation of sheets containing chalcogenidometalate anions.
  • Schlindwein, Simon H.; Sibold, Carlo; Schenk, Mareike; Ringenberg, Mark R.; Feil, Christoph M.; Nieger, Martin; Gudat, Dietrich (2020)
    The ability of 3-(diphenylphosphinomethyl)-benzene-1,2-dithiol (pbdtH(2)) to act as ditopic ligand was probed in reactions with selected group-10-metal complexes. Reactions with [(cod)PdCl2] afforded a mixture of products identified as [Pd(pbdtH)(2)], [Pd-2(mu(2)-pbdt)(2)] and [Pd-3(mu(2)-pbdt)(2)Cl-2]. The polynuclear complexes could be isolated after suitably adjusting the reaction conditions, and heating of a mixture in a microwave reactor effected partial conversion into a further complex [Pd-3(mu(2)-pbdt)(3)]. Reaction of pbdtH(2) with [Ni(H2O)(6)Cl-2] gave rise to a complex [Ni-2(mu(2)-pbdt)(2)], which was shown to undergo two reversible 1e(-)-reduction steps. Reaction of [Pd(pbdtH)(2)] with [Au(PPh3)Cl] afforded heterotrinuclear [PdAu2(mu(2)-pbdt)(2)(PPh3)]. All complexes were characterized by analytical, spectroscopic and single-crystal X-ray diffraction studies. Their molecular structures confirm the ability of the pbdt(2-) unit to support simultaneous P,S- and S,S-chelating coordination to two metal centers.
  • Matovic, Jelena; Järvinen, Juulia; Bland, Helena C.; Sokka, Iris K.; Imlimthan, Surachet; Ferrando, Ruth Mateu; Huttunen, Kristiina M.; Timonen, Juri; Peräniemi, Sirpa; Aitio, Olli; Airaksinen, Anu J.; Sarparanta, Mirkka; Johansson, Mikael P.; Rautio, Jarkko; Ekholm, Filip S. (2020)
    Boron neutron capture therapy (BNCT) for cancer is on the rise worldwide due to recent developments of in-hospital neutron accelerators which are expected to revolutionize patient treatments. There is an urgent need for improved boron delivery agents, and herein we have focused on studying the biochemical foundations upon which a successful GLUT1-targeting strategy to BNCT could be based. By combining synthesis and molecular modeling with affinity and cytotoxicity studies, we unravel the mechanisms behind the considerable potential of appropriately designed glucoconjugates as boron delivery agents for BNCT. In addition to addressing the biochemical premises of the approach in detail, we report on a hit glucoconjugate which displays good cytocompatibility, aqueous solubility, high transporter affinity, and, crucially, an exceptional boron delivery capacity in the in vitro assessment thereby pointing toward the significant potential embedded in this approach.
  • Kurten, Theo; Moller, Kristian H.; Nguyen, Tran B.; Schwantes, Rebecca H.; Misztal, Pawel K.; Su, Luping; Wennberg, Paul O.; Fry, Juliane L.; Kjaergaard, Henrik G. (2017)
    Oxidation of monoterpenes (C10H16) by nitrate radicals (NO3) constitutes an important source of atmospheric secondary organic aerosol (SOA) and organonitrates. However, knowledge of the mechanisms of their formation is incomplete and differences in yields between similar monoterpenes are poorly understood. In particular, yields of SOA and organonitrates from alpha-pinene + NO3 are low, while those from Delta(3)-carene + NO3 are high. Using computational methods, we suggest that bond scission of the nitrooxy alkoxy radicals from Delta(3)-carene lead to the formation of reactive keto-nitrooxy-alkyl radicals, which retain the nitrooxy moiety and can undergo further reactions to form SOA. By contrast, bond scissions of the nitrooxy alkoxy radicals from alpha-pinene lead almost exclusively to the formation of the relatively unreactive and volatile product pinonaldehyde (C10H16O2), thereby limiting organonitrate and SOA formation. This hypothesis is supported by laboratory experiments that quantify products of the reaction of alpha-pinene + NO3 under atmospherically relevant conditions.
  • Duarte, Luis; Khriachtchev, Leonid (2017)
    We report on the aromatic noble-gas hydride, C6H5CCXeH, identified in a xenon matrix using infrared spectroscopy and extensive quantum chemical calculations. This molecule is prepared by 250-nm photolysis of phenylacetylene (C6H5CCH) isolated in a xenon matrix and subsequent thermal mobilization of hydrogen atoms at about 40 K. The characteristic H-Xe stretching mode of C6H5CCXeH is observed at about 1500 cm(-1), and a number of other fundamentals also appear in the experimental spectra. The assignment is supported by deuteration experiments providing predictable shifts of the vibrational frequencies. The experimental and calculated spectra are in a good agreement. C6H5CCXeH is computationally lower in energy than the C6H5CC + Xe + H fragments by about 0.60 eV at the M06-2X/aug-cc-pVTZ-PP level of theory, which allows its formation at low temperatures. C6H5CCXeH is the first aromatic noble-gas hydride and the first halogen-free aromatic noble-gas compound.
  • Sundholm, Dage; Berger, Raphael J. F.; Fliegl, Heike (2016)
    Magnetically induced current susceptibilities and current pathways have been calculated for molecules consisting of two pentalene groups annelated with a benzene (1) or naphthalene (2) moiety. Current strength susceptibilities have been obtained by numerically integrating separately the diatropic and paratropic contributions to the current flow passing planes through chosen bonds of the molecules. The current density calculations provide novel and unambiguous current pathways for the unusual molecules with annelated aromatic and antiaromatic hydrocarbon moieties. The calculations show that the benzene and naphthalene moieties annelated with two pentalene units as in molecules 1 and 2, respectively, are unexpectedly antiaromatic sustaining only a local paratropic ring current around the ring, whereas a weak diatropic current flows around the C-H moiety of the benzene ring. For 1 and 2, the individual five-membered rings of the pentalenes are antiaromatic and a slightly weaker semilocal paratropic current flows around the two pentalene rings. Molecules 1 and 2 do not sustain any net global ring current. The naphthalene moiety of the molecule consisting of a naphthalene annelated with two pentalene units (3) does not sustain any strong ring current that is typical for naphthalene. Instead, half of the diatropic current passing the naphthalene moiety forms a zig-zag pattern along the C-C bonds of the naphthalene moiety that are not shared with the pentalene moieties and one third of the current continues around the whole molecule partially cancelling the very strong paratropic semilocal ring current of the pentalenes. For molecule 3, the pentalene moieties and the individual five-membered rings of the pentalenes are more antiaromatic than for 1 and 2. The calculated current patterns elucidate why the compounds with formally [4n + 2] p-electrons have unusual aromatic properties violating the Huckel pi-electron count rule. The current density calculations also provide valuable information for interpreting the measured H-1 NMR spectra.
  • Molina, V.; Rauhalahti, M.; Hurtado, J.; Fliegl, H.; Sundholm, D.; Munoz-Castro, A. (2017)
    [trans-Cu(mu-OH)(mu-dmpz)](6) (1) exhibits six Cu(II) centers effectively coupled through a ligand mediated mechanism leading to a diamagnetic ground state over a wide temperature range. Here we investigate further magneto-structural correlations based on the possible free electron precession along such a copper-based ring-like nanocoil mediated by bridging ligands. We find that in 1, mediated antiferro-magnetic coupling leads to characteristics that induce aromatic ring behavior through evaluation of both induced currents and shielding of cones from a relativistic density functional theory level. According to our gauge calculations including magnetically induced current densities and an induced magnetic field, a sizable ring current strength susceptibility is obtained for the cyclic Cu-N-N-Cu and Cu-O-Cu pathways, allowing a magnetic exchange between the copper centers. Our study suggests that [Cu-6(dmPz)(6)(OH)(6)] consisting of an aromatic ring structure displays aromaticity and superexchange along the Cu-O-Cu and Cu-N-N-Cu backbones, which accounts for 80% and 20% of the overall ring current strength susceptibility, respectively. This reveals the presence of particular aromatic ring characteristics in coordination compounds without a direct metal-metal bond, where several formally paramagnetic centers are antiferromagnetically-coupled through supporting ligands. We envisage that our findings can be extended to other examples depicting ligand-mediated interaction between metal centers.
  • Baryshnikov, Glib; Valiev, Rashid R.; Nasibullin, Rinat T.; Sundholm, Dage; Kurten, Theo; Ågren, Hans (2020)
    The recently synthesized cyclo[18]carbon molecule has been characterized in a number of studies by calculating electronic, spectroscopic, and mechanical properties. However, cyclo[18] carbon is only one member of the class of cyclo[n]carbons-standalone carbon allotrope representatives. Many of the larger members of this class of molecules have not been thoroughly investigated. In this work, we calculate the magnetically induced current density of cyclo[n]carbons in order to elucidate how electron delocalization and aromatic properties change with the size of the molecular ring (n), where n is an even number between 6 and 100. We find that the Hiickel rules for aromaticity (4k + 2) and antiaromaticity (4k) become degenerate for large C-n rings (n > 50), which can be understood as a transition from a delocalized electronic structure to a nonaromatic structure with localized current density fluxes in the triple bonds. Actually, the calculations suggest that cyclo[n]carbons with n > 50 are nonaromatic cyclic polyalkynes. The influence of the amount of nonlocal exchange and the asymptotic behavior of the exchange-correlation potential of the employed density functionals on the strength of the magnetically induced ring current and the aromatic character of the large cyclo[n]carbons is also discussed.
  • Lehtola, Susi (2019)
    Electronic structure calculations, such as in the Hartree-Fock or Kohn-Sham density functional approach, require an initial guess for the molecular orbitals. The quality of the initial guess has a significant impact on the speed of convergence of the self-consistent field (SCF) procedure. Popular choices for the initial guess include the one-electron guess from the core Hamiltonian, the extended Huckel method, and the superposition of atomic densities (SAD). Here, we discuss alternative guesses obtained from the superposition of atomic potentials (SAP), which is easily implementable even in real-space calculations. We also discuss a variant of SAD which produces guess orbitals by purification of the density matrix that could also be used in real-space calculations, as well as a parameter-free variant of the extended Huckel method, which resembles the SAP method and is easy to implement on top of existing SAD infrastructure. The performance of the core Hamiltonian, the SAD, and the SAP guesses as well as the extended Huckel variant is assessed in nonrelativistic calculations on a data set of 259 molecules ranging from the first to the fourth periods by projecting the guess orbitals onto precomputed, converged SCF solutions in single- to triple-zeta basis sets. It is shown that the proposed SAP guess is the best guess on average. The extended Huckel guess offers a good alternative, with less scatter in accuracy.
  • Popov, Georgi; Bačić, Goran; Mattinen, Miika; Manner, Toni; Lindström, Hannu; Seppänen, Heli; Suihkonen, Sami; Vehkamäki, Marko; Kemell, Marianna; Jalkanen, Pasi; Mizohata, Kenichiro; Räisänen, Jyrki; Leskelä, Markku; Koivula, Hanna Maarit; Barry, Seán T.; Ritala, Mikko (2020)
    Atomic layer deposition (ALD) is a viable method for depositing functional, passivating, and encapsulating layers on top of halide perovskites. Studies in that area have only focused on metal oxides, despite a great number of materials that can be made with ALD. This work demonstrates that, in addition to oxides, other ALD processes can be compatible with the perovskites. We describe two new ALD processes for lead sulfide. These processes operate at low deposition temperatures (45-155 degrees C) that have been inaccessible to previous ALD PbS processes. Our processes rely on volatile and reactive lead precursors Pb(dbda) (dbda = rac-N-2,N-3-di-tertbutylbutane-2,3-diamide) and Pb(btsa)(2) (btsa = bis(trimethylsilyl)amide) as well as H2S. These precursors produce high quality PbS thin films that are uniform, crystalline, and pure. The films exhibit p- type conductivity and good mobilities of 10-70 cm(2) V-1 s(-1). Low deposition temperatures enable direct ALD of PbS onto a halide perovskite CH3NH3PbI3 (MAPI) without its decomposition. The stability of MAPI in ambient air is greatly improved by capping with ALD PbS. More generally, these new processes offer valuable alternatives for PbS-based devices, and we hope that this study will inspire more studies on ALD of non-oxides on halide perovskites.
  • Rong, Mark K.; Holtrop, Flip; Bobylev, Eduard O.; Nieger, Martin; Ehlers, Andreas W.; Slootweg, J. Chris; Lammertsma, Koop (2021)
    Novel seven-membered cyclic imine-based 1,3-P,N ligands were obtained by capturing a Beckmann nitrilium ion intermediate generated in situ from cyclohexanone with benzotriazole, and then displacing it by a secondary phosphane under triflic acid promotion. These "cycloiminophosphanes" possess flexible non-isomerizable tetrahydroazepine rings with a high basicity; this sets them apart from previously reported iminophophanes. The donor strength of the ligands was investigated by using their P-kappa(1)- and P,N-kappa(2)-tungsten(0) carbonyl complexes, by determining the IR frequency of the trans-CO ligands. Complexes with [RhCp*Cl-2](2) demonstrated the hemilability of the ligands, giving a dynamic equilibrium of kappa(1) and kappa(2) species; treatment with AgOTf gives full conversion to the kappa(2) complex. The potential for catalysis was shown in the Ru-II-catalyzed, solvent-free hydration of benzonitrile and the Ru-II- and Ir-I-catalyzed transfer hydrogenation of cyclohexanone in isopropanol. Finally, to enable access to asymmetric catalysts, chiral cycloiminophosphanes were prepared from l-menthone, as well as their P,N-kappa(2)-Rh-III and a P-kappa(1)-Ru-II complexes.
  • Valiev, Rashid R.; Fliegl, Heike; Sundholm, Dage (2018)
    Aromatic properties of two recently synthesized dithienothiophene-bridged (DTT) [34]octaphyrins have been investigated by calculating magnetically induced current densities and vertical excitation energies. These intriguing molecules have been proposed to be the first synthesized neutral bicycloaromatic compounds. The triplet state of their dications was even suggested to be Baird-type bicycloaromatic rendering them very interesting as a new prototype of molecules possessing simultaneously the two rare types of aromaticity. Here, we investigate computationally the aromatic properties of the neutral as well as the singly and doubly charged DTT-bridged [34]octaphyrins. Our study provides unambiguous information about changes in the aromatic properties of the DTT-bridged [34]octaphyrins upon oxidation. The calculations identify two independent diatropic ring currents in the neutral DTT-bridged [34]octaphyrins, showing that they are indeed bicycloaromatic. The current-density flow of the two independent ring currents of the bicycloaromatic compounds are visualized and individual aromatic pathways are quantified by performing numerical integration. The calculations show that two independent diatropic ring currents can indeed be sustained by molecules consisting of two aromatic rings that share a common set of π electrons. The current density calculations on the singly charged DTT-bridged [34]octaphyrins show that they are weakly antiaromatic, which does not agree with the suggested aromatic character deduced from spectroscopical studies. The triplet state of the two DTT-bridged [34]octaphyrin cations with very similar molecular structures have unexpectedly different aromatic character. One of them is Baird-type bicycloaromatic, whereas the triplet state of the other dication has one aromatic and one nonaromatic ring, which could not be resolved from available spectroscopical data. Calculations of excitation energies reveal that a simple model cannot be employed for interpreting the electronic excitation spectra of the present molecules, because more than 20 excited states contribute to the spectra above 2.5 eV (500 nm) showing the importance of computations. The present work illustrates how detailed information about molecular aromaticity can nowadays be obtained by scrutinizing calculated current densities.
  • Orozco-Ic, Mesias; Celaya, Christian A.; Sundholm, Dage (2020)
    Magnetic response properties of 1,2,3,5-tetrazine derivatives including the newly synthesized 4,6-diphenyl-1,2,3,5-tetrazine have been studied computationally at the density functional theory (DFT) level. Calculations of magnetically induced current densities and induced magnetic fields show that the unsubstituted 1,2,3,5-tetrazine is almost as aromatic as benzene. Separating the magnetic shielding functions into molecular orbital components provided additional insights into the magnetic response. The aromatic character estimated from magnetically induced current densities and induced magnetic fields shows that NICS pi zz(0) values and ring-current strengths yield about the same degree of aromaticity, whereas NICSzz(0) and NICSzz(1) values are contaminated by sigma electron contributions. The studied 1,2,3,5-tetrazine derivatives are less aromatic than the unsubstituted one. Calculations of magnetic response properties of 4,6-diphenyl-1,2,3,5-tetrazine showed that it is the least aromatic among the studied molecules according to the ring-current criterion, while 4,6-[1,2,3,5]-ditetrazinyl-1,2,3,5-tetrazine is as aromatic as 4,6-dimethyl-1,2,3,5-tetrazine and slightly less aromatic than the unsubstituted 1,2,3,5-tetrazine.
  • Mera-Adasme, Raul; Xu, Wen-hua; Sundholm, Dage; Mendizabal, Fernando (2016)
    Solar power is a strong alternative to the currently used fossil fuels in order to satisfy the world's energy needs. Among them, dye-sensitized solar cells (DSSC) represent a low-cost option. Efficient and cheap dyes are currently needed to make DSSCs competitive. Computational chemistry can be used to guide the design of new light-absorbing chromophores. Here, we have computationally studied the lowest excited states of ZnPBAT, which is a recently synthesized porphyrinoid chromophore with high light-absorption efficiency. The calculations have been performed at ab initio correlated levels of theory employing second-order coupled clusters (CC2) and algebraic diagrammatic construction using second order (ADC(2)) methods and by performing density functional theory (DFT) calculations using the time-dependent DFT (TDDFT) approach for excitation energies. The ultraviolet-visible (UV-vis) spectrum calculated at the ADC(2) and CC2 levels agrees well with the experimental one. The calculations show that ZnPBAT has six electronic transitions in the visible range of the absorption spectrum. The ab initio correlated calculations and previously reported experimental data have been used to assess the performance of several well-known density functionals that have been employed in the present TDDFT study. Solvent effects have been estimated by using the conductor-like screening model (COSMO). The influence of the addition of a TiO2 cluster to the chromophore systems has also been investigated. The results indicate that both CAM-B3LYP and Becke's "half-and-half'' (BHLYP) density functionals are appropriate for the studies of excitation energies in the blue range of the visible spectrum for these kinds of porphyrinoid chromophores, whereas the excitation energies of the Q band calculated at the ab initio correlated level are more accurate than those obtained in the present TDDFT calculations. The inclusion of solvent effects has a modest influence on the spectrum of the protonated form of the studied chromophores, whereas solvent models are crucial when studying the absorption spectrum of the anionic chromophore. The calculated UV-vis spectrum for the chromophore anion is not significantly affected by attaching a TiO2 cluster to it.
  • Boom, Devin H. A.; de Boed, Ewoud J. J.; Nicolas, Emmanuel; Nieger, Martin; Ehlers, Andreas W.; Jupp, Andrew R.; Slootweg, J. Chris (2020)
    The reaction of the intramolecular frustrated Lewis pair (FLP) tBu2PCH2BPh2 with the amine-boranes NH3·BH3 and Me2NH·BH3 leads to the formation of the corresponding FLP-H2 adducts as well as novel five-membered heterocycles that result from capturing the in situ formed amino-borane by a second equivalent of FLP. The sterically more demanding tBu2PCH2BMes2 does not form such a five-membered heterocycle when reacted with Me2NH·BH3 and its H2 adduct liberates dihydrogen at elevated temperatures, promoting the metal-free catalytic dehydrogenation of amine-boranes.
  • Hirvonen, Viivi; Myllys, Nanna; Kurtén, Theo; Elm, Jonas (2018)
    The role of covalently bound dimer formation is studied using highlevel quantum chemical methods. Reaction free energy profiles for dimer formation between common oxygen-containing functional groups are calculated, and based on the Gibbs free energy differences between transition states and reactants, we show that none of the studied two-component gas-phase reactions are kinetically feasible at 298.15 K and 1 atm. Therefore, the catalyzing effect of water, base, or acid molecules is calculated, and sulfuric acid is identified to lower the activation free energies significantly. We find that the reactions yielding hemiacetal, peroxyhemiacetal, alpha-hydroxyester, and geminal diol products occur with activation free energies of less than 10 kcal/mol with sulfuric acid as a catalyst, indicating that these reactions could potentially take place on the surface of sulfuric acid clusters. Additionally, the formed dimer products bind stronger onto the pre-existing cluster than the corresponding reagent monomers do. This implies that covalent dimerization reactions stabilize the existing cluster thermodynamically and make it less likely to evaporate. However, the studied small organic compounds, which contain only one functional group, not able to form dimer are products that are stable against evaporation at atmospheric conditions. Calculations of dimer formation onto a cluster surface and the clustering ability of dimer products should be extended to large terpene oxidation products in order to estimate the real atmospheric significance.
  • Valiev, Rashid R.; Fliegl, Heike; Sundholm, Dage (2017)
    Magnetizabilities and magnetically induced ring-current strength susceptibilities have been calculated at the Hartree-Fock, density functional theory and second order Moller-Plesset levels for a number of antiaromatic closed-shell carbaporphyrins, carbathia-porphyrins and isophlorins. The calculations yield a linear relation between magnetizabilities and ring-current strength susceptibilities. The calculations show that the porphyrinoids with the largest ring-current strength susceptibility are closed-shell paramagnetic molecules with positive magnetizabilities. The closed-shell paramagnetism is due to the large paramagnetic contribution to the magnetizability originating from the strong paratropic ring current in the antiaromatic porphyrinoids.
  • Iyer, Siddharth; Reiman, Heidi; Moller, Kristian H.; Rissanen, Matti P.; Kjaergaard, Henrik G.; Kurten, Theo (2018)
    The oxidation of biogenically emitted volatile organic compounds (BVOC) plays an important role in the formation of secondary organic aerosols (SOA) in the atmosphere. Peroxy radicals (RO2) are central intermediates in the BVOC oxidation process. Under clean (low-NOx) conditions, the main bimolecular sink reactions for RO2 are with the hydroperoxy radical (HO2) and with other RO2 radicals. Especially for small RO2, the RO2 + HO2 reaction mainly leads to closed-shell hydroperoxide products. However, there exist other known RO2 + HO2 and RO2 + RO2 reaction channels that can recycle radicals and oxidants in the atmosphere, potentially leading to lower-volatility products and enhancing SOA formation. In this work, we present a thermodynamic overview of two such reactions: (a) RO2 + HO2 -> RO + OH + O-2 and (b) R'O-2 + RO2 -> R'O + RO + O-2 for selected monoterpene + oxidant derived peroxy radicals. The monoterpenes considered are alpha-pinene, beta-pinene, limonene, trans-beta-ocimene, and Delta(3)-carene. The oxidants considered are the hydroxyl radical (OH), the nitrate radical (NO3), and ozone (O-3). The reaction Gibbs energies were calculated at the DLPNO-CCSD(T)/def2-QZVPP//omega B97X-D/aug-cc-pVTZ level of theory. All reactions studied here were found to be exergonic in terms of Gibbs energy. On the basis of a comparison with previous mechanistic studies, we predict that reaction a and reaction b are likely to be most important for first-generation peroxy radicals from O-3 oxidation (especially for beta-pinene), while being less so for most first-generation peroxy radicals from OH and NO3 oxidation. This is because both reactions are comparatively more exergonic for the O-3 oxidized systems than their OH and NO3 oxidized counterparts. Our results indicate that bimolecular reactions of certain complex RO, may contribute to an increase in radical and oxidant recycling under high HO2 conditions in the atmosphere, which can potentially enhance SOA formation.