Browsing by Subject "BASIS-SETS"

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  • 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.
  • Keshavarz, Fatemeh; Shcherbacheva, Anna; Kubecka, Jakub; Vehkamäki, Hanna; Kurten, Theo (2019)
    The effect of dust aerosols on accretion reactions of water, formaldehyde, and formic acid was studied in the conditions of earth's troposphere at the DLPNO-CCSD(T)/aug-cc-pVTZ//omega B97X-D/6-31++G** level of theory. A detailed analysis of the reaction mechanisms in the gas phase and on the surface of mineral dust, represented by mono- and trisilicic acid, revealed that mineral dust has the potential of decreasing reaction barrier heights. Specifically, at 0 K, mineral dust can lower the apparent energy barrier of the reaction of formaldehyde with formic acid to zero. However, when the entropic contributions to the reaction free energies were accounted for, mineral dust was found to selectively enhance the reaction of water with formaldehyde, while inhibiting the reaction of formaldehyde and formic acid, in the lower parts of the troposphere (with temperatures around 298 K). In the upper troposphere (with temperatures closer to 198 K), mineral dust catalyzes both reactions and also the reaction of methanol with formic acid. Despite the intrinsic potential of mineral dust, calculation of the catalytic enhancement parameter for a likely range of dust aerosol concentrations suggested that dust aerosols will not contribute to secondary organic aerosol formation via dimerization of closed-shell organic compounds. The main reason for this is the relatively low absolute concentratign of tropospheric dust aerosol and its inefficiency in increasing the effective reaction rate coefficients.
  • Berndt, Torsten; Herrmann, Hartmut; Kurten, Theo (2017)
    Criegee intermediates (CIs), mainly formed from gas-phase ozonolysis of alkenes, are considered as atmospheric oxidants besides OH and NO3 radicals as well as ozone. Direct CI measurement techniques are inevitably needed for reliable assessment of CIs' role in atmospheric processes. We found that CIs from ozonolysis reactions can be directly probed by means of chemical ionization mass spectrometry with a detection limit of about 10(4)-10(5) molecules cm(-3). Results from quantum chemical calculations support the experimental findings. The simplest CI, CH2OO, is detectable as an adduct with protonated ethers, preferably with protonated tetrahydrofuran. Kinetic measurements yielded k(CH2OO + SO2) = (3.3 +/- 0.9) X 10(-11) and k(CH2OO + acetic acid) = (1.25 +/- 0.30) x 10(-10) cm(3) molecule(-1) s(-1) at 295 +/- 2 K, in very good agreement with recent measurements using diiodomethane photolysis for CH2OO generation. CIs from the ozonolysis of cydohexene, acting as surrogate for cyclic terpenes, are followed as protonated species (CI)H+ using protonated amines as reagent ions. Kinetic investigations indicate a different reactivity of cydohexene-derived CIs compared with that of simple CIs, such as CH2OO. It is supposed that the aldehyde group significantly influences the CI reactivity of the cydohexene-derived CIs. The direct CI detection method presented here should allow study of the formation and reactivity of a wide range of different CIs formed from atmospheric ozonolysis reactions.
  • Draper, Danielle C.; Myllys, Nanna; Hyttinen, Noora; Moller, Kristian H.; Kjaergaard, Henrik G.; Fry, Juliane L.; Smith, James N.; Kurten, Theo (2019)
    NO3 radical oxidation of most monoterpenes is a significant source of secondary organic aerosol (SOA) in many regions influenced by both biogenic and anthropogenic emissions, but there are very few published mechanistic studies of NO3 chemistry beyond simple first generation products. Here, we present a computationally derived mechanism detailing the unimolecular pathways available to the second generation of peroxy radicals following NO3 oxidation of Delta-3-carene, defining generations based on the sequence of peroxy radicals formed rather than number of oxidant attacks. We assess five different types of unimolecular reactions, including peroxy and alkoxy radical (RO2 and RO) hydrogen shifts, RO2 and RO ring closing (e.g., endoperoxide formation), and RO decomposition. Rate constants calculated using quantum chemical methods indicate that this chemical system has significant contribution from both bimolecular and unimolecular pathways. The dominant unimolecular reactions are endoperoxide formation, RO H-shifts, and RO decomposition. However, the complexity of the overall reaction is tempered as only 1 or 2 radical propagation pathways dominate the fate of each radical intermediate. Chemical ionization mass spectrometry (CIMS) measurements using the NO3- reagent ion during Delta-3-carene + NO3 chamber experiments show products consistent with each of the three types of unimolecular reactions predicted to be important from the computational mechanism. Moreover, the SIMPOL group contribution method for predicting vapor pressures suggests that a majority of the closed-shell products inferred from these unimolecular reactions are likely to have low enough vapor pressure to be able to contribute to SOA formation.
  • Lehtola, Susi (2019)
    Although many programs have been published for fully numerical Hartree-Fock (HF) or density functional (DF) calculations on atoms, we are not aware of any programs that support hybrid DFs, which are popular within the quantum chemistry community due to their better accuracy for many applications, or that can be used to calculate electric properties. Here, we present a variational atomic finite element solver in the HelFEM program suite that overcomes these limitations. A basis set of the type chi nlm(r,theta,phi) = r(-1) Bn (r) Upsilon(m)(1) ((r) over cap is used, where B-n(r) are finite element shape functions and Upsilon(m)(1) are spherical harmonics, which allows for an arbitrary level of accuracy. HelFEM supports nonrelativistic HF and DF calculations even with hybrid functionals, which are not available in other commonly available program packages. Hundreds of functionals at the local spin-density approximation (LDA), generalized-gradient approximation (GGA), as well as the meta-GGA levels of theory are included through an interface with the Libxc library. Electric response properties are achievable via finite field calculations. We introduce an alternative grid that yields faster convergence to the complete basis set limit than commonly used alternatives. We also show that high-order Lagrange interpolating polynomials yield the best convergence, and that excellent agreement with literature HF limit values for electric properties, such as static dipole polarizabilities, can be achieved with the present approach. Dipole moments and dipole polarizabilities at finite field are also reported with the PBE, PBEh, TPSS, and TPSSh functionals. Finally, we show that a recently published Gaussian basis set is able to reproduce absolute HF and DF energies of neutral atoms, cations, as well as anions within a few dozen microhartrees.
  • Zanca, Tommaso; Kubecka, Jakub; Zapadinsky, Evgeni; Passananti, Monica; Kurten, Theo; Vehkamäki, Hanna (2020)
    Identification of atmospheric molecular clusters and measurement of their concentrations by atmospheric pressure interface time-of-flight (APi-TOF) mass spectrometers may be affected by systematic error due to possible decomposition of clusters inside the instrument. Here, we perform numerical simulations of decomposition in an APi-TOF mass spectrometers and formation in the atmosphere of a set of clusters which involve a representative kind of highly oxygenated organic molecule (HOM), with the molecular formula C10H16O8. This elemental composition corresponds to one of the most common mass peaks observed in experiments on ozone-initiated autoxidation of alpha-pinene. Our results show that decomposition is highly unlikely for the considered clusters, provided their bonding energy is large enough to allow formation in the atmosphere in the first place.
  • Rong, Mark K.; van Duin, Koen; van Dijk, Tom; de Pater, Jeroen J. M.; Deelman, Berth-Jan; Nieger, Martin; Ehlers, A. W.; Slootweg, J. Chris; Lammertsma, Koop (2017)
    Highly stable iminophosphanes, obtained from alkylating nitriles and reaction of the resulting nitrilium ions with secondary phosphanes, were explored as tunable P-monodentate and 1,3-P,N bidentate ligands in rhodium complexes. X-ray crystal structures are reported for both k1 and k2 complexes with the counterion in one of them being an unusual anionic coordination polymer of silver triflate. The iminophosphane-based ruthenium(II)-catalyzed hydration of benzonitrile in 1,2-dimethoxyethane (180 degrees C, 3 h) and water (100 degrees C, 24 h) and under solvent free conditions (180 degrees C, 3 h) results in all cases in the selective formation of benzamide with yields of up to 96%, thereby outperforming by far the reactions in which the common 2-pyridyldiphenylphosphane is used as the 1,3-P,N ligand.
  • Sokka, Iris Katariina; Ekholm, Filip S.; Johansson, Mikael P. (2019)
    Monomethyl auristatin E and monomethyl auristatin F are widely used cytotoxic agents in antibody-drug conjugates (ADCs), a group of promising cancer drugs. The ADCs specifically target cancer cells, releasing the auristatins inside, which results in the prevention of mitosis. The auristatins suffer from a potentially serious flaw, however. In solution, the molecules exist in an equal mixture of two conformers, cis and trans. Only the trans-isomer is biologically active and the isomerization process, i.e., the conversion of cis to trans is slow. This significantly diminishes the efficiency of the drugs and their corresponding ADCs, and perhaps more importantly, raises concerns over drug safety. The potency of the auristatins would be enhanced by decreasing the amount of the biologically inactive isomer, either by stabilizing the transisomer or destabilizing the cis-isomer. Here, we follow the computer-aided design strategy of shifting the conformational equilibrium and employ high-level quantum chemical modeling to identify promising candidates for improved auristatins. Coupled cluster calculations predict that a simple halogenation in the norephedrine/phenylalanine residues shifts the isomer equilibrium almost completely toward the active trans-conformation, due to enhanced intramolecular interactions specific to the active isomer.
  • Wirtanen, T.; Muuronen, M.; Hurmalainen, J.; Tuononen, H. M.; Nieger, M.; Helaja, J. (2016)
    With an excess of a strong acid, 2,3-dichloro-5,6-dicyano-1,4-quinone (DDQ) is shown to promote metal-free intermolecular oxidative dehydrogenative (ODH) 3,3'-coupling of 2-aryl-benzo[b]furans and 2-aryl-benzo[b]thiophenes up to 92% yield as demonstrated with 9 substrates. Based on the analysis of oxidation potentials and molecular orbitals combined with EPR, NMR and UV-Vis observations, the studied reaction is initiated by a DDQ-substrate charge transfer complex and presumably proceeds via oxidation of the substrate into an electrophilic radical cation that further reacts with another molecule of a neutral substrate. The coupling reactivity can easily be predicted from the oxidation potential of the substrate and the morphology of its frontier molecular orbitals. The intermolecular ODH coupling reaction allowed a concise total synthesis of the natural product shandougenine B.
  • Johansson, Mikael P.; Swart, Marcel (2013)
    By analysing the properties of the electron density in the structurally simple perhalogenated ethanes, X3C–CY3 (X, Y = F, Cl), a previously overlooked non-covalent attraction between halogens attached to opposite carbon atoms is found. Quantum chemical calculations extrapolated towards the full solution of the Schrödinger equation reveal the complex nature of the interaction. When at least one of the halogens is a chlorine, the strength of the interaction is comparable to that of hydrogen bonds. Further analysis shows that the bond character is quite different from standard non-covalent halogen bonds and hydrogen bonds; no bond critical points are found between the halogens, and the σ-holes of the halogens are not utilised for bonding. Thus, the nature of the intramolecular halogen···halogen bonding studied here appears to be of an unusually strong van der Waals type.
  • Rauhalahti, M.; Munoz-Castro, A.; Sundholm, D. (2016)
    spherical and cavernous carbocage molecule exhibiting faces with larger ring sizes than regular fullerenes is a suitable species for investigating how molecular magnetic properties depend on the structure of the molecular framework. The studied all-carbon gaudiene (C-72) is a highly symmetrical molecule with three-and four-fold faces formed by twelve membered rings. Here, we attempt to unravel the magnetic response properties of C-72 by performing magnetic shielding and current density calculations with the external magnetic field applied in different directions. The obtained results indicate that the induced current density flows mainly along the chemical bonds that are largely perpendicular to the magnetic field direction. However, the overall current strength for different directions of the magnetic field is nearly isotropic differing by only 10% indicating that C-72 can to some extent be considered to be a spherical aromatic molecule, whose current density and magnetic shielding are ideally completely isotropic. The induced magnetic field is found to exhibit long-range shielding cones in the field direction with a small deshielding region located perpendicularly to the field outside the molecule. The magnetic shielding is isotropic inside the molecular framework of C-72, whereas an orientation-dependent magnetic response appears mainly at the exterior of the molecular cage.
  • Reiter, Kevin; Weigend, Florian; Wirz, Lukas N.; Dimitrova, Maria; Sundholm, Dage (2019)
    Molecular structures of toroidal carbon nanotubes (TCNTs) have been constructed and optimized at the density functional theory (DFT) level. The TCNT structures have been constrained by using point groups with high symmetry. TCNTs consisting of only hexagons (polyhex) with armchair, chiral, and zigzag structures as well as TCNTs with pentagons and heptagons have been studied. The employed method for constructing general polyhex TCNTs is discussed. Magnetically induced current densities have been calculated using the gauge-including magnetically induced currents (GIMIC) method. The strength of the magnetically induced ring currents has been obtained by integrating the current density passing a plane cutting the ring of the TCNT. The main pathways of the current density have been identified by visualizing the current density. The calculations show that the strength of the diatropic ring current of polyhex TCNTs with an armchair structure generally increases with the size of the TCNT, whereas TCNTs with a zigzag structure sustain very weak diatropic ring currents. Some of the TCNTs with pentagons and heptagons sustain a strong diatropic ring current, whereas other TCNT structures with pentagons and heptagons sustain paratropic ring currents that are, in most cases, relatively weak. We discuss the reasons for the different behaviors of the current density of the seemingly similar TCNTs.
  • Wirz, Lukas N.; Dimitrova, Maria; Fliegl, Heike; Sundholm, Dage (2018)
    The topology of twisted molecular rings is characterized by the linking number, which is equal to the sum of the twist-a local property of the molecular frame-and the writhe-a global parameter, which represents the bending of the molecular ring. In this work, we investigate a number of cyclic all-trans C40H40 annulenes with varying twisting numbers for a given linking number and their dications. The aromatic character is assessed by calculating ring-current strength susceptibilities using the gauge-including magnetically induced currents (GIMIC) method, which makes it possible to conduct a systematic study of the relation between the topology and aromaticity of twisted molecules. We found that the aromatic properties of the investigated Mobius twisted molecules are not only dependent on the linking number as previously suggested but also depend strongly on the partitioning of the linking number into the twist and writhe contributions.
  • Duarte, Luis; Khriachtchev, Leonid (2017)
    We report on the identification of the complexes of two noble-gas hydrides, HXeCCXeH and HXeCC, with acetylene. These complexes were prepared by photolysis (250 nm) and annealing (55-65 K) of HCCH/Xe matrices. The experimentally observed monomer-to-complex shifts of the H-Xe stretching modes of the HXeCCXeH center dot center dot center dot HCCH (about +17 cm(-1)) and HXeCC center dot center dot center dot HCCH complexes (from +20 to +46 cm(-1)) indicate the stabilization of the H-Xe bond relatively to the monomers. The CCSD/cc-pVTZ calculations predict two structures for each complex. The HXeCCXeH center dot center dot center dot HCCH complex has quasi T-shaped and linear structures, with the H-Xe stretching modes blue-shifted and red-shifted by about +27 and -9 cm(-1), respectively. The HXeCC center dot center dot center dot HCCH complex has bent and T-shaped structures, with the H-Xe stretching modes blue-shifted by about +46 and +42 cm(-1), respectively. Based on the calculations, the experimental bands of the HXeCCXeH center dot center dot center dot HCCH and HXeCC center dot center dot center dot HCCH complexes are assigned to the quasi T-shaped and bent structures, respectively. Complexes of an open-shell noble-gas hydride and of a molecule with two noble-gas atoms are reported for the first time.
  • Benkyi, Isaac; Fliegl, Heike; Valiev, Rashid R.; Sundholm, Dage (2016)
    Magnetically induced current densities have been calculated and analyzed for a number of synthesized carbachlorins and carbaporphyrins using density functional theory and the gauge including magnetically induced current (GIMIC) method. Aromatic properties have been determined by using accurate numerical integration of the current flow yielding reliable current strengths and pathways that are related to the degree of aromaticity and the aromatic character of the studied molecules. All investigated compounds are found to be aromatic. However, the obtained aromatic pathways differ from those previously deduced from spectroscopic data and magnetic shielding calculations. For all studied compounds, the ring current divides into an outer and an inner branch at each pyrrolic subring, showing that all pi-electrons of the pyrrolic rings take part in the delocalization pathway. The calculations do not support the common notion that the main share of the current takes the inner route at the pyrrolic rings without an inner hydrogen and follows an 18 pi aromatic pathway. The aromatic pathways of the investigated carbaporphyrins and carbachlorins are very similar, since the current strength via the C-beta=C-beta' bond of the cyclopentadienyl ring of the carbaporphyrins is almost as weak as the current density passing the corresponding saturated C beta-C-beta' bond of the carbachlorins.
  • Rico del Cerro, Daniel; Mera-Adasme, Raúl; King, Alistair W. T.; Perea-Buceta, Jesus E.; Heikkinen, Sami; Hase, Tapio; Sundholm, Dage; Wähälä, Kristiina (2018)
    Comprehensive spectroscopic kinetic studies illustrate an alternative mechanism for the traditional free-carbene intermediated H/D exchange reaction of 1,3-dialkylimidazolium salts under neutral (D2O) and acidic conditions (DCl/D2O 35wt% solution). The deuteration of high purity [bmim]Cl in D2O is studied at different temperatures, in absence of catalyst or impurities, to yield an activation energy. DFT transition-state modelling, of a small water cluster and [bmim] cation, also yields an activation energy which strongly supports the proposed mechanism. The presence of basic impurities are shown to significantly enhance the exchange reaction, which brings into question the need for further analysis of technical purities of ionic liquids and the implications for a wide range of chemical reactions in such media.
  • Valiev, Rashid R.; Fliegl, Heike; Sundholm, Dage (2017)
    Magnetic and spectroscopic properties of a number of formally antiaromatic carbaporphyrins, carbathiaporphyrins and isophlorins with 4n pi electrons have been investigated at density functional theory and ab initio levels of theory. The calculations show that the paratropic contribution to the magnetically induced ring-current strength susceptibility and the magnetic dipole-transition moment between the ground and the lowest excited state are related. The vertical excitation energy (VEE) of the first excited state decreases with increasing ring-current strength susceptibility, whereas the VEE of the studied higher-lying excited states are almost independent of the size of the ring-current strength susceptibility. Strong antiaromatic porphyrinoids, based on the magnitude of the paratropic ring-current strength susceptibility, have small energy gaps between the highest occupied and lowest unoccupied molecular orbitals and a small VEE of the first excited state. The calculations show that only the lowest S-0 -> S-1 transition contributes signficantly to the magnetically induced ring-current strength susceptibility of the antiaromatic porphyrinoids. The decreasing optical gap combined with a large angular momentum contribution to the magnetic transition moment from the first excited state explains why molecules III-VII are antiaromatic with very strong paratropic ring-current strength susceptibilities. The S-0 -> S-1 transition is a magnetic dipole-allowed electronic transition that is typical for antiaromatic porphyrinoids with 4n pi electrons.
  • Fathi-Rasekh, Mahtab; Rohde, Gregory T.; Hart, Mason D.; Nakakita, Toshinori; Zatsikha, Yuriy V.; Valiev, Rashid R.; Barybin, Mikhail V.; Nemykin, Victor N. (2019)
    Two isomeric ruthenium(II)/5,10,15,20-tetraphe-nylporphyrin complexes featuring axially coordinated redox-active, low-optical gap 2- or 6-isocyanoazulene ligands have been isolated and characterized by NMR, UV-vis, and magnetic circular dichroism (MCD) spectroscopic methods, high-resolution mass spectrometry, and single-crystal X-ray crystallography. The UV-vis and MCD spectra support the presence of the low-energy, azulene-centered transitions in the Q band region of the porphyrin chromophore. The first coordination sphere in new L2RuTPP complexes reflects compressed tetragonal geometry. The redox properties of the new compounds were assessed by electrochemical and spectroelectrochemical means and correlated with the electronic structures predicted by density functional theory and CASSCF calculations. Both experimental and theoretical data are consistent with the first two reduction processes involving the axial azulenic ligands, whereas the oxidation profile (in the direction of increasing potential) is exerted by the ruthenium ion, the porphyrin core, and the axial azulenic moieties.
  • Sundholm, Dage; Rabaa, Hassan; Chiheb, Mohammed; Balch, Alan L. (2019)
    Calculations have been performed at the MP2 and DFT levels for investigating the reasons for the difficulties in synthesizing bis(isocyanide)gold(I) halide complexes. Three-coordinated gold(I) complexes of the type (R3P)(2)(AuX)-X-I (1) can be synthesized, whereas the analogous isocyanide complexes (RNC)(2)(AuX)-X-I (2) are not experimentally known. The molecular structures of (R3P)(2)(AuX)-X-I (X = Cl, Br, and I) and (RNC)(2)(AuX)-X-I with X = halide, cyanide, nitrite, methylthiolate, and thiocyanate are compared and structural differences are discussed. Calculations of molecular properties elucidate which factors determine the strength of the gold-ligand interactions in (RNC)(2)(AuX)-X-I. The linear bonding mode of RNC favors a T-shaped geometry instead of the planar Y-shaped trigonal structure of (R3P)(2)(AuX)-X-I complexes that have been synthesized. An increased polarity of the Au-X bond in 2 leads to destabilization of the Y-shaped structure. Chalcogen-containing ligands or cyanide appear to be good X-ligand candidates for synthesis of (RNC)(2)(AuX)-X-I complexes.
  • Valiev, Rashid R.; Fliegl, Heike; Sundholm, Dage (2015)
    Magnetically induced current densities have been calculated for dioxaporphyrin, dithiaporphyrin, true carbaporphyrins, and N-confused porphyrins using the gauge-including magnetically induced current (GIMIC) method. The current-strength susceptibilities (current strengths) have been obtained by numerically integrating the current flow passing selected chemical bonds. The current strength calculations yield very detailed information about the electron delocalization pathways of the molecules. The strength of the ring-current that circles around the porphyrinoid macroring is used to estimate the degree of molecular aromaticity. The studied porphyrinoid structures have been obtained by replacing the NH and N groups of porphin with formally isoelectronic moieties such as O, S, CH and CH2. Replacing an NH moiety of trans-porphin with isoelectronic O and S does not significantly change the current strengths and pathways, whereas substitution of N with an isoelectronic CH group leads to significant changes in the current pathway and current strengths. CH2 groups cut the flow of diatropic currents, whereas in strongly antiaromatic molecules a significant fraction of the paratropic ring-current is able to pass the sp(3) hybridized inner carbons. N-confused porphyrinoids sustain a ring current whose strength is about half the ring-current strength of porphin with the dominating current flow along the outer pathway via the NH moiety. When no hydrogen is attached to the inner carbon of the inverted pyrrolic ring, the current prefers the inner route at that ring.