Browsing by Subject "CORRELATION-ENERGY"

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  • Rauhalahti, Markus; Taubert, Stefan; Sundholm, Dage; Liegeois, Vincent (2017)
    Magnetically induced current density susceptibilities and ring-current strengths have been calculated for neutral and doubly charged persubstituted benzenes C6X6 and C6X62+ with X = F, Cl, Br, I, At, SeH, SeMe, TeH, TeMe, and SbH2. The current densities have been calculated using the gauge-including magnetically induced current (GIMIC) method, which has been interfaced to the Gaussian electronic structure code rendering current density calculations using effective core potentials (ECP) feasible. Relativistic effects on the ring-current strengths have been assessed by employing ECP calculations of the current densities. Comparison of the ring-current strengths obtained in calculations on C6At6 and C6At62+ using relativistic and non-relativistic ECPs show that scalar relativistic effects have only a small influence on the ring-current strengths. Comparisons of the ring-current strengths and ring-current profiles show that the C6I62+, C6At62+, C-6(SeH)(6)(2+), C-6(SeMe)(6)(2+), C-6(TeH)(6)(2+), C-6(TeMe)(6)(2+), and C-6(SbH2)(6)(2+) dications are doubly aromatic sustaining spatially separated ring currents in the carbon ring and in the exterior of the molecule. The C6I6+ radical cation is also found to be doubly aromatic with a weaker ring current than obtained for the dication.
  • 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.
  • Reidelbach, Marco; Zimmer, Christoph; Meunier, Brigitte; Rich, Peter R.; Sharma, Vivek (2021)
    Cellular respiration is a fundamental process required for energy production in many organisms. The terminal electron transfer complex in mitochondrial and many bacterial respiratory chains is cytochrome c oxidase (CcO). This converts the energy released in the cytochrome c/oxygen redox reaction into a transmembrane proton electrochemical gradient that is used subsequently to power ATP synthesis. Despite detailed knowledge of electron and proton transfer paths, a central question remains as to whether the coupling between electron and proton transfer in mammalian mitochondrial forms of CcO is mechanistically equivalent to its bacterial counterparts. Here, we focus on the conserved span between H376 and G384 of transmembrane helix (TMH) X of subunit I. This conformationally-dynamic section has been suggested to link the redox activity with the putative H pathway of proton transfer in mammalian CcO. The two helix X mutants, Val380Met (V380M) and Gly384Asp (G384D), generated in the genetically-tractable yeast CcO, resulted in a respiratory-deficient phenotype caused by the inhibition of intra-protein electron transfer and CcO turnover. Molecular aspects of these variants were studied by long timescale atomistic molecular dynamics simulations performed on wild-type and mutant bovine and yeast CcOs. We identified redox- and mutation-state dependent conformational changes in this span of TMH X of bovine and yeast CcOs which strongly suggests that this dynamic module plays a key role in optimizing intra-protein electron transfers.
  • Lehtola, Susi (2019)
    We present the implementation of a variational finite element solver in the HelFEM program for benchmark calculations on diatomic systems. A basis set of the form chi nlm mu nu phi=Bn mu Ylm nu phi is used, where (mu, nu, phi) are transformed prolate spheroidal coordinates, B-n(mu) are finite element shape functions, and Ylm are spherical harmonics. The basis set allows for an arbitrary level of accuracy in calculations on diatomic molecules, which can be performed at present with either nonrelativistic Hartree-Fock (HF) or density functional (DF) theory. Hundreds of DFs at the local spin density approximation (LDA), generalized gradient approximation (GGA), and the meta-GGA level can be used through an interface with the Libxc library; meta-GGA and hybrid DFs are not available in other fully numerical diatomic program packages. Finite electric fields are also supported in HelFEM, enabling access to electric properties. We introduce a powerful tool for adaptively choosing the basis set by using the core Hamiltonian as a proxy for its completeness. HelFEM and the novel basis set procedure are demonstrated by reproducing the restricted open-shell HF limit energies of 68 diatomic molecules from the first to the fourth period with excellent agreement with literature values, despite requiring orders of magnitude fewer parameters for the wave function. Then, the electric properties of the BH and N-2 molecules under finite field are studied, again yielding excellent agreement with previous HF limit values for energies, dipole moments, and dipole polarizabilities, again with much more compact wave functions than what were needed for the literature references. Finally, HF, LDA, GGA, and meta-GGA calculations of the atomization energy of N-2 are performed, demonstrating the superb accuracy of the present approach.
  • Kuleta, Patryk; Lasham, Jonathan; Sarewicz, Marcin; Ekiert, Iwona; Sharma, Vivek; Ekiert, Robert; Osyczka, Artur (2021)
    Hemes are common elements of biological redox cofactor chains involved in rapid electron transfer. While the redox properties of hemes and the stability of the spin state are recognized as key determinants of their function, understanding the molecular basis of control of these properties is challenging. Here, benefiting from the effects of one mitochondrial disease-related point mutation in cytochrome b, we identify a dual role of hydrogen bonding (H-bond) to the propionate group of heme bH of cytochrome bc1, a common component of energy-conserving systems. We found that replacing conserved glycine with serine in the vicinity of heme bH caused stabilization of this bond, which not only increased the redox potential of the heme but also induced structural and energetic changes in interactions between Fe ion and axial histidine ligands. The latter led to a reversible spin conversion of the oxidized Fe from 1/2 to 5/2, an effect that potentially reduces the electron transfer rate between the heme and its redox partners. We thus propose that H-bond to the propionate group and heme-protein packing contribute to the fine-tuning of the redox potential of heme and maintaining its proper spin state. A subtle balance is needed between these two contributions: While increasing the H-bond stability raises the heme potential, the extent of increase must be limited to maintain the low spin and diamagnetic form of heme. This principle might apply to other native heme proteins and can be exploited in engineering of artificial hemecontaining protein maquettes.
  • 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.
  • Taubert, Stefan; Sundholm, Dage; Pichierri, Fabio (2010)
  • Taubert, Stefan; Sundholm, Dage; Pichierri, Fabio (2010)
  • Taubert, Stefan; Sundholm, Dage; Pichierri, Fabio (2010)
  • 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.
  • 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.
  • Sundholm, Dage; Wirz, Lukas N.; Schwerdtfeger, Peter (2015)
    A new family of cavernous all-carbon structures is proposed. These molecular cage structures are constructed by edge subdivisions and leapfrog transformations from cubic polyhedra or their duals. The obtained structures were then optimized at the density functional level. These hollow carbon structures represent a new class of carbon allotropes which could lead to many interesting applications.
  • Haapanen, Outi; Djurabekova, Amina; Sharma, Vivek (2019)
    Respiratory complex I performs the reduction of quinone (Q) to quinol (QH(2)) and pumps protons across the membrane. Structural data on complex I have provided spectacular insights into the electron and proton transfer paths, as well as into the long (similar to 30 angstrom) and unique substrate binding channel. However, due to missing structural information on Q binding modes, it remains unclear how Q reduction drives long range (similar to 20 nm) redox-coupled proton pumping in complex I. Here we applied multiscale computational approaches to study the dynamics and redox chemistry of Q and QH(2). Based on tens of microseconds of atomistic molecular dynamics (MD) simulations of bacterial and mitochondrial complex I, we find that the dynamics of Q is remarkably rapid and it diffuses from the N2 binding site to another stable site near the entrance of the Q channel in microseconds. Analysis of simulation trajectories also reveal the presence of yet another Q binding site 25-30 angstrom from the N2 center, which is in remarkable agreement with the electron density observed in recent cryo electron microscopy structure of complex I from Yarrowia lipolytica. Quantum chemical computations on the two Q binding sites closer to the entrance of the Q tunnel reveal redox-coupled protonation reactions that may be important in driving the proton pump of complex I.