Browsing by Subject "GAUSSIAN-BASIS SETS"

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  • Shao, Yihan; Mei, Ye; Sundholm, Dage; Kaila, Ville R. I. (2020)
    Quantum chemical calculations are important for elucidating light-capturing mechanisms in photobiological systems. The time-dependent density functional theory (TDDFT) has become a popular methodology because of its balance between accuracy and computational scaling, despite its problems in describing, for example, charge transfer states. As a step toward systematically understanding the performance of TDDFT calculations on biomolecular systems, we study here 17 commonly used density functionals, including seven long-range separated functionals, and compare the obtained results with excitation energies calculated at the approximate second order coupled-cluster theory level (CC2). The benchmarking set includes the first five singlet excited states of 11 chemical analogues of biochromophores from the green fluorescent protein, rhodopsin/bacteriorhodopsin (Rh/bR), and the photoactive yellow protein. We find that commonly used pure density functionals such as BP86, PBE, M11-L, and hybrid functionals with 20-25% of Hartree-Fock (HF) exchange (B3LYP, PBE0) have a tendency to consistently underestimate vertical excitation energies (VEEs) relative to the CC2 values, whereas hybrid density functionals with around 50% HF exchange such as BHLYP, PBE50, and M06-2X and long-range corrected functionals such as CAM-B3LYP, omega PBE, omega PBEh, omega B97X, omega B97XD, BNL, and M11 overestimate the VEEs. We observe that calculations using the CAM-B3LYP and omega PBEh functionals with 65% and 100% long-range HF exchange, respectively, lead to an overestimation of the VEEs by 0.2-0.3 eV for the benchmarking set. To reduce the systematic error, we introduce here two new empirical functionals, CAMh-B3LYP and omega hPBE0, for which we adjusted the long-range HF exchange to 50%. The introduced parameterization reduces the mean signed average (MSA) deviation to 0.07 eV and the root mean square (rms) deviation to 0.17 eV as compared to the CC2 values. In the present study, TDDFT calculations using the aug-def2-TZVP basis sets, the best performing functionals relative to CC2 are omega hPBE0 (rms = 0.17, MSA = 0.06 eV); CAMh-B3LYP (rms = 0.16, MSA = 0.07 eV); and PBE0 (rms = 0.23, MSA = 0.14 eV). For the popular range-separated CAM-B3LYP functional, we obtain an rms value of 0.31 eV and an MSA value of 0.25 eV, which can be compared with the rms and MSA values of 0.37 and -0.31 eV, respectively, as obtained at the B3LYP level.
  • Valiev, Rashid R.; Benkyi, Isaac; Konyshev, Yuri; Fliegl, Heike; Sundholm, Dage (2018)
    Magnetically induced current densities and ring-current pathways have been calculated at density functional theory (DFT) and second-order Moller-Plesset perturbation theory (MP2) levels of theory for a set of expanded porphyrins consisting of five or six pyrrolic rings. The studied molecules are sapphyrin, cyclo [6]pyrrole, rubyrin, orangarin, rosarin, and amethyrin. Different functionals have been employed to assess the functional dependence of the ring-current strength susceptibility. Vertical singlet and triplet excitation energies have been calculated at the second-order approximate coupled cluster (CC2), expanded multiconfigurational quasi-degenerate perturbation theory (XMC-DPT2), and time-dependent density functional theory levels. The lowest electronic transition of the antiaromatic molecules was found to be pure magnetic transitions providing an explanation for the large paratropic contribution to the total current density. Rate constants for different nonradiative deactivation channels of the lowest excited states have been calculated yielding lifetimes and quantum yields of the lowest excited singlet and triplet states. The calculations show that the spin-orbit interaction between the lowest singlet (S-0) and triplet (T-1) states of the antiaromatic molecules is strong, whereas for the aromatic molecule the spin-orbit coupling vanishes. The experimentally detected fluorescence from S-2 to S-0 of amethyrin has been explained. The study shows that there are correlations between the aromatic character and optical properties of the investigated expanded porphyrins.
  • Leverentz, Hannah R.; Siepmann, J. Ilja; Truhlar, Donald G.; Loukonen, Ville; Vehkamäki, Hanna (2013)
  • Lehtola, Susi (2020)
    recently developed finite-element approach for fully numerical atomic structure calculations [S. Lehtola, Int. J. Quantum Chem. 119, e25945 (2019)] is extended to the description of atoms with spherically symmetric densities via fractionally occupied orbitals. Specialized versions of Hartree-Fock as well as local density and generalized gradient approximation density functionals are developed, allowing extremely rapid calculations at the basis-set limit on the ground and low-lying excited states, even for heavy atoms. The implementation of range separation based on the Yukawa or complementary error function (erfc) kernels is also described, allowing complete basis-set benchmarks of modern range-separated hybrid functionals with either integer or fractional occupation numbers. Finally, the computation of atomic effective potentials at the local density or generalized gradient approximation levels for the superposition of atomic potentials (SAP) approach [S. Lehtola, J. Chem. Theory Comput. 15, 1593 (2019)] that has been shown to be a simple and efficient way to initialize electronic structure calculations is described. The present numerical approach is shown to afford beyond micro-Hartree accuracy with a small number of numerical basis functions, and to reproduce the literature results for the ground states of atoms and their cations for 1
  • Lehtola, Susi; Dimitrova, Maria; Sundholm, Dage (2020)
    We present fully numerical electronic structure calculations on diatomic molecules exposed to an external magnetic field at the unrestricted Hartree-Fock limit, using a modified version of a recently developed finite-element programme, HelFEM. We have performed benchmark calculations on a few low-lying states of H-2, HeH+, LiH, BeH+, BH and CH+ as a function of the strength of an external magnetic field parallel to the molecular axis. The employed magnetic fields are in the range of B = [0, 10] B-0 atomic units, where B-0 approximate to 2.35 x 10(5) T. We have compared the results of the fully numerical calculations to ones obtained with the LONDON code using a large uncontracted gauge-including Cartesian Gaussian (GICG) basis set with exponents adopted from the Dunning aug-cc-pVTZ basis set. By comparison to the fully numerical results, we find that the basis set truncation error (BSTE) in the GICG basis is of the order of 1 kcal/mol at zero field, that the BSTE grows rapidly in increasing magnetic field strength, and that the largest BSTE at B = 10 B-0 exceeds 1000 kcal/mol. Studies in larger Gaussian-basis sets suggest that reliable results can be obtained in GICG basis sets at fields stronger than B = B-0, provided that enough higher-angular-momentum functions are included in the basis.
  • Myllys, Nanna; Ponkkonen, Tuomo; Passananti, Monica; Elm, Jonas; Vehkamäki, Hanna; Olenius, Tinja (2018)
    The role of a strong organobase, guanidine, in sulfuric acid-driven new-particle formation is studied using state-of-the-art quantum chemical methods and molecular cluster formation simulations. Cluster formation mechanisms at the molecular level are resolved, and theoretical results on cluster stability are confirmed with mass spectrometer measurements. New-particle formation from guanidine and sulfuric acid molecules occurs without thermodynamic barriers under studied conditions, and clusters are growing close to a 1:1 composition of acid and base. Evaporation rates of the most stable clusters are extremely low, which can be explained by the proton transfers and symmetrical cluster structures. We compare the ability of guanidine and dimethylamine to enhance sulfuric acid-driven particle formation and show that more than 2000-fold concentration of dimethylamine is needed to yield as efficient particle formation as in the case of guanidine. At similar conditions, guanidine yields 8 orders of magnitude higher particle formation rates compared to dimethylamine. Highly basic compounds such as guanidine may explain experimentally observed particle formation events at low precursor vapor concentrations, whereas less basic and more abundant bases such as ammonia and amines are likely to explain measurements at high concentrations.
  • Rauhalahti, Markus; Sundholm, Dage; Johansson, Mikael P. (2021)
    The magnetically induced current density of an intriguing naphthalene-fused heteroporphyrin has been studied, using the quantum-chemical, gauge-including magnetically induced currents (GIMIC) method. The ring-current strengths and current-density pathways for the heteroporphyrin, its Pd complex, and the analogous quinoline-fused heteroporphyrin provide detailed information about their aromatic properties. The three porphyrinoids have similar current-density pathways and are almost as aromatic as free-base porphyrin. Notably, we show that the global ring current makes a branch at three specific points. Thus, the global current is composed of a total of eight pathways that include 22 pi-electrons, with no contributions from 18-electron pathways.
  • Bizzarri, Claudia; Arndt, Andreas P.; Kohaut, Stephan; Fink, Karin; Nieger, Martin (2018)
    A mononuclear and two dinuclear heteroleptic Cu(I) complexes have been successfully prepared, using the chelating bis [(2-diphenylphosphino)phenyl] ether (DPEPhos) and pyrid-2'-yl-1H-1,2,3-triazole as chelating ligands. They show good luminescence in solution at room temperature with long-lived excited states. Furthermore, bimolecular quenching experiments of these new complexes with the catalyst Ni(cyclam)Cl-2 encourage the use of such compounds as photosensitizers for the photoreduction of carbon dioxide. (C) 2018 Elsevier B.V. All rights reserved.
  • Wikström, Mårten Karl Fredrik; Krab, Klaas; Sharma, Vivek (2018)
    This review focuses on the type A cytochrome c oxidases (C cO), which are found in all mitochondria and also in several aerobic bacteria. C cO catalyzes the respiratory reduction of dioxygen (O2) to water by an intriguing mechanism, the details of which are fairly well understood today as a result of research for over four decades. Perhaps even more intriguingly, the membrane-bound C cO couples the O2 reduction chemistry to translocation of protons across the membrane, thus contributing to generation of the electrochemical proton gradient that is used to drive the synthesis of ATP as catalyzed by the rotary ATP synthase in the same membrane. After reviewing the structure of the core subunits of C cO, the active site, and the transfer paths of electrons, protons, oxygen, and water, we describe the states of the catalytic cycle and point out the few remaining uncertainties. Finally, we discuss the mechanism of proton translocation and the controversies in that area that still prevail.
  • Shahi, Chandra; Bhattarai, Puskar; Wagle, Kamal; Santra, Biswajit; Schwalbe, Sebastian; Hahn, Torsten; Kortus, Jens; Jackson, Koblar A.; Peralta, Juan E.; Trepte, Kai; Lehtola, Susi; Nepal, Niraj K.; Myneni, Hemanadhan; Neupane, Bimal; Adhikari, Santosh; Ruzsinszky, Adrienn; Yamamoto, Yoh; Baruah, Tunna; Zope, Rajendra R.; Perdew, John P. (2019)
    Semilocal approximations to the density functional for the exchange-correlation energy of a many-electron system necessarily fail for lobed one-electron densities, including not only the familiar stretched densities but also the less familiar but closely related noded ones. The Perdew-Zunger (PZ) self-interaction correction (SIC) to a semilocal approximation makes that approximation exact for all one-electron ground- or excited-state densities and accurate for stretched bonds. When the minimization of the PZ total energy is made over real localized orbitals, the orbital densities can be noded, leading to energy errors in many-electron systems. Minimization over complex localized orbitals yields nodeless orbital densities, which reduce but typically do not eliminate the SIC errors of atomization energies. Other errors of PZ SIC remain, attributable to the loss of the exact constraints and appropriate norms that the semilocal approximations satisfy, suggesting the need for a generalized SIC. These conclusions are supported by calculations for one-electron densities and for many-electron molecules. While PZ SIC raises and improves the energy barriers of standard generalized gradient approximations (GGAs) and meta-GGAs, it reduces and often worsens the atomization energies of molecules. Thus, PZ SIC raises the energy more as the nodality of the valence localized orbitals increases from atoms to molecules to transition states. PZ SIC is applied here, in particular, to the strongly constrained and appropriately normed (SCAN) meta-GGA, for which the correlation part is already self-interaction-free. This property makes SCAN a natural first candidate for a generalized SIC. Published under license by AIP Publishing.
  • Niskanen, Johannes; Sahle, Christoph J.; Ruotsalainen, Kari O.; Müller, Harald; Kavcic, Matjaz; Zitnik, Matjaz; Bucar, Klemen; Petric, Marko; Hakala, Mikko; Huotari, Simo (2016)
    In this paper we report an X-ray emission study of bulk aqueous sulfuric acid. Throughout the range of molarities from 1 M to 18 M the sulfur K beta emission spectra from H2SO4 (aq) depend on the molar fractions and related deprotonation of H2SO4. We compare the experimental results with results from emission spectrum calculations based on atomic structures of single molecules and structures from ab initio molecular dynamics simulations. We show that the S K beta emission spectrum is a sensitive probe of the protonation state of the acid molecules. Using non-negative matrix factorization we are able to extract the fractions of different protonation states in the spectra, and the results are in good agreement with the simulation for the higher part of the concentration range.
  • Blum, Markus; Feil, Christoph M.; Nieger, Martin; Gudat, Dietrich (2021)
    A diphosphine with an unsupported PP bond connecting two carbon-free "inorganic" 1,3,2,4,5-diazaphosphadisilolidine rings was prepared by reductive coupling of a P-chloro-substituted monocyclic precursor molecule. VT-EPR studies revealed that the diphosphine exists in solution, like other compounds of this kind, in dynamic equilibrium with the corresponding phosphinyl radicals. Determination of the radical concentration from the EPR spectra permitted to calculate thermochemical parameters for the homolytic PP bond fission. The results disclose that both the enthalpy and entropy of dissociation are higher than in topologically related bi(diazaphospholidines). The impact of the entropy term allows explaining that, regardless of the presence of an energetically rather stable PP bond, the onset of dissociation is observable even at ambient temperature. Irradiation experiments showed that radical formation cannot only be induced thermally, but also by photolysis.
  • Dimitrova, Maria; Sundholm, Dage (2018)
    We have investigated the aromatic properties of seven low-lying isomers of [10]annulene and of the recently synthesized dicupra[10]annulene compounds that were crystallised with two or four lithium counterions (Wei et al., J. Am. Chem. Soc., 2016, 138, 60-63). The molecular structures of the [10]annulene conformers and the dicupra[10]annulenes with bulky trimethylsilyl (TMS) and phenyl groups, as well as the corresponding unsubstituted dicupra[10]annulenes were optimised using density functional theory, employing a semiempirical dispersion correction to consider van der Waals interactions. The structures of the hydrocarbon annulenes were subsequently optimised at the SCS-MP2/def2-QZVPD level. Single-point coupled-cluster calculations with explicit treatment of the electron correlation CCSD(F12)(T) were performed to obtain the relative energies of the hydrocarbon annulenes. Four of the conformations lie close in energy relative to each other. Three substituted and three unsubstituted dicupra[10]annulene structures with either four, two or no Li+ counterions were investigated. Magnetically induced current densities calculated using the GIMIC program were used for the assessment of the aromatic properties of the studied molecules. The conformations of [10] annulene with lowest energies are non-aromatic. The calculations revealed that the electron donation of the lithium atoms to the dicupra[10]annulene core significantly affects the electronic and molecular structures of the dicupra[10]annulenes. The annulene ring is non-planar for all studied dicupra[10]annulenes except for the unsubstituted one with four Li+ counterions, which was also found to be the only molecule that sustains a strong diatropic ring current around the dicupra[10]annulene ring. The other five dicupra[10]annulenes sustain very weak net ring currents and can be considered non-aromatic.
  • Dimitrova, Maria; Fliegl, Heike; Sundholm, Dage (2017)
    Four polycyclic molecules have been investigated at the DFT B3LYP/def2-TZVP level of theory using calculated magnetically induced current densities as an indicator of their (anti)aromaticity. Complicated current pathways were found in dibenzo[a,e]pentalene and its three heterocyclic analogues each containing two boron and two nitrogen atoms. The antiaromatic character of the pentalene moiety is weaker in the hydrocarbon molecule and in 5,11-dihydrobenzo[d]benzo[4,5][1,2,3]azadiborolo[3,2-b][1,2,3]azadiborole as compared to the pentalene molecule. The antiaromatic character of the pentalene moiety is completely absent in the other two heterocyclic structures. In 6,12-dihydrobenzo[d]benzo[4,5][1,2,3]diazaborolo[2,1-a][1,2,3]diazaborole all four molecular rings are aromatic according to the ring-current criterion, and in 6,12-dihydrobenzo[d]benzo[3,4][1,2,5]azadiborolo[1,2-a][1,3,2]diazaborole, the diazaborole ring is aromatic, while the azadiborole ring is antiaromatic. In all four molecules the six-membered rings are aromatic sustaining a weaker ring current than benzene does.