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  • 1. Guo, J. D.
    et al.
    Luo, Yi
    KTH, Superseded Departments, Biotechnology.
    A theoretical study of the photo-oxidation of a fluorene-based two-photon chromophore2003In: Journal of Molecular Structure: THEOCHEM, ISSN 0166-1280, Vol. 635, p. 1-9Article in journal (Refereed)
    Abstract [en]

    The infrared and optical absorption spectra of a fluorene-based two-photon chromophore AF50 (N,N-diphenyl-7-2-(4-pyridinyl)-ethenyl-9,9-di-n-decyl-9H-fluorene-2-amine) and its photo-oxidation products after ultra-violet exposure have been calculated using hybrid density functional theory. Our calculations have provided very useful information about the nature of the read/write process of AF50 and its possible final products.

  • 2. Jansik, B.
    et al.
    Schimmelpfennig, B.
    Norman, P.
    Macak, P.
    Ågren, Hans
    KTH, Superseded Departments, Biotechnology.
    Ohta, K.
    Relativistic effects on linear and non-linear polarizabilities of the furan homologues2003In: Journal of Molecular Structure: THEOCHEM, ISSN 0166-1280, Vol. 633, no 03-feb, p. 237-246Article in journal (Refereed)
    Abstract [en]

    First principles calculations including relativistic effects are carried out for dipole moments, polarizabilities, first- and second-order hyperpolarizabilities for the series of furan homologues XC4H4, X = O, S, Se, Te, at three different levels of theory; time-dependent Dirac-Hartree-Fock (DHF), time-dependent Hartree-Fock with a Douglas-Kroll transformed one-component Hamiltonian, and time-dependent Hartree-Fock using effective-core potentials. By comparison with the corresponding non-relativistic results, the influence of relativistic effects on the properties as well as the accuracy of previously reported calculations on these molecules using effective-core potentials for selenium and tellurium can be addressed. The obtained results indicate that relativistic effects can be described with comparable accuracy at all three employed levels, and that non-scalar effects, which are explicitly treated only at the time-dependent DHF level, are of minor importance. Frequency dispersion and relativity are found to be additive at the single-determinant level. We find that relativistic effects cannot make up for the earlier identified mismatch between theory and experiment for the non-linear polarizabilities of the heavier homologues. A Bishop-Kirtman analysis of vibrational effects indicates that the same can be said about these.

  • 3.
    Lin, Na
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Zhao, Xian
    Cheng, Xiu-Feng
    Jiang, Min-Hua
    Quantum chemical investigation on one- and two-photon absorption properties for a series of donor-pi-acceptor-type compounds with trivalent boron as an acceptor2007In: Journal of Molecular Structure: THEOCHEM, ISSN 0166-1280, Vol. 820, no 1-3, p. 98-106Article in journal (Refereed)
    Abstract [en]

    In this paper, one- and two-photon absorption properties as well as the transition nature of a series of donor-pi-acceptor-type compounds with trivalent boron as an acceptor have been theoretically studied by using INDO/SDCI method. Our calculations indicate that the four o-methyl moieties on the two mesityl groups play an important part in protecting the trivalent boron from being attacked by oxygen in the air. The trivalent boron containing group can be an all-right electron-acceptor with some bulky groups attached to it. On the basis of geometry optimization and UV-vis spectra, the positions and strengths of two-photon absorption for these molecules were reported.

  • 4. Norman, P.
    et al.
    Ågren, H.
    Geometry optimization of core electron excited molecules1997In: Journal of Molecular Structure: THEOCHEM, ISSN 0166-1280, Vol. 401, no 1-2, p. 107-115Article in journal (Refereed)
    Abstract [en]

    We demonstrate the feasibility of calculations of geometries and potential energy surfaces of core ionized and core excited states of molecular species including full optimization of all electronic and nuclear degrees of freedom. We show by examples that geometry optimization leads to symmetry broken nuclear conformations for ionization/excitation of symmetry delocalized core orbitals. Comparisons between results with the equivalent cores approximation and with full optimization pinpoint the role of the valence-core penetration to obtain the correct optimum geometry, especially along weaker bending and torsion modes. © 1997 Elsevier Science B.V.

  • 5.
    Oprea, Corneliu I.
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Damian, Alina
    Girtu, Mihai A.
    Theoretical study of neutral and reduced hexacyanobutadiene2007In: Journal of Molecular Structure: THEOCHEM, ISSN 0166-1280, Vol. 804, no 1-3, p. 111-116Article in journal (Refereed)
    Abstract [en]

    The molecular structure and the electronic densities of neutral and anionic hexacyanobutadiene (HCBD), trans-C-4(CN)(6), as well as the electron affinity (EA) of HCBD have been studied using density functional theory (DFT) and perturbation theory (MP2) procedures. The optimized geometries showed that the HCBD molecule is not planar, with a 140 degrees torsion angle about the central C-C bond. While the optimized geometries are not very sensitive to the choice of either the method or the basis set, the adiabatic electron affinity varies significantly with both. All the DFT computed electron affinities overestimate the experimental value, the best results being obtained with the BLYP functional, whereas the MP2 calculations heavily underestimate it. At the NIP2 level, the EA value obtained after projecting out the major spin contaminating component (PMP2) is a good estimate of the EA, within 0.11 eV of the experiment. Although other studies suggested that single-point PMP2 calculations over DFT-optimized geometries could be a valuable alternative for the study of larger systems at low computational effort, our results indicate that this approach can increase the spin contamination and should be used with caution.

  • 6.
    Riihimäki, Eva-Stina
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Inorganic Chemistry.
    Martínez, José Manuel
    Physical Chemistry Department, University of Seville.
    Kloo, Lars
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Inorganic Chemistry.
    An evaluation of non-periodic boundary condition models in molecular dynamics simulations using prion octapeptides as probes2006In: Journal of Molecular Structure: THEOCHEM, ISSN 0166-1280, Vol. 760, no 1-3, p. 91-98Article in journal (Refereed)
    Abstract [en]

    Molecular dynamics simulations have been performed under periodic boundary conditions and using four non-periodic solvation models. The biomolecular probe in these simulations was a single repeat of the copper-binding octapeptide in the human prion protein, PHGGGWGQ. Although the alternative non-periodic solvation models enable a reduction in computational time, the dynamical disadvantages are considerable when using any of these four non-periodic models. For simulations of systems similar to the test system, periodic boundary conditions are a better alternative than any of the four local models.

  • 7.
    Rinkevicius, Zilvinas
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Time-dependent closed and open-shell density functional theory from the perspective of partitioning techniques and projections2009In: Journal of Molecular Structure: THEOCHEM, ISSN 0166-1280, Vol. 914, no 1-3, p. 50-59Article in journal (Refereed)
    Abstract [en]

    The formalism of time-dependent density functional theory and density functional response functions is reviewed from the perspective of partitioning techniques and projections, the hallmark of the school of quantum chemistry represented by P.O. Lowdin. Extension to open-shell density functional theory is described, reviewing some of its common problems. Sample calculations on hyper-Raleigh scattering in the diamagnetic and paramagnetic complexes of copper bound to (glycyl)glycine dipeptide are presented.

  • 8. Rizzo, A.
    et al.
    Ruud, K.
    Norman, P.
    Relativistic effects on Sternheimer shieldings and the polarizabilities of the electric-field gradient at the nucleus: HX (X = F,Cl,Br,I,At) and Br 22003In: Journal of Molecular Structure: THEOCHEM, ISSN 0166-1280, Vol. 633, no 2-3, p. 163-176Article in journal (Refereed)
    Abstract [en]

    We investigate the relativistic effects on the electric field gradient (EFG) at the nucleus, the generalized Stemheimer shielding constants, and the EFG polarizabilities using analytic quadratic response theory at the four-component Dirac-Hartree-Fock level of theory. Particular attention is paid to the basis set requirements for calculations at the four-component level of theory of these higher-order properties involving operators that probe both the near-nucleus and the outer regions of the electron density. Our results show that relativistic effects become non-negligible for the hydrogen halides starting with hydrogen bromide and the heavier members of the group 17 halides. Interestingly, the relativistic effects are much more pronounced for the heavy-atom in hydrogen bromide, being about 10% for most of the generalized EFG polarizabilities, than in the homonuclear diatomic molecule Br2, where relativistic effects in general are much less than 10%.

  • 9. Rundgren, Henrik
    et al.
    Mark, Pekka
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Laaksonen, Aatto
    Molecular dynamics simulations of conserved Hox protein hexapeptides - II. Folded structures in water solution2007In: Journal of Molecular Structure: THEOCHEM, ISSN 0166-1280, Vol. 805, no 1-3, p. 61-70Article in journal (Refereed)
    Abstract [en]

    MD simulations of Hox protein N-terminal hexapeptides TFDWMK (Hox B1) and LFPWMR (Hox B8) are performed in water solution and complemented with simulations where the aromatic residues phenylalanine (F) and tryptophan (W) are successively replaced by alanine (A). Results from this study give support that different hexapeptides can form similar folded structures in water, stabilized mainly by internal hydrogen bonding where the arrangement of the aromatic side chains together with the methionine (M) side chain forming a hydrophobic core covers and protects the internal hydrogen bonds from water. Replacement of the aromatic side chains with Alanine did not lead to unfolding, but rather the hexapeptides were slightly changing their conformations where the Methionine side chain together with the peptide backbone protected the internal hydrogen bonds and the hexapeptides remain folded. Our results give support that these hexapeptides are able to remain folded to some extent even without the aromatic side chains.

  • 10. Rundgren, Henrik
    et al.
    Mark, Pekka
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Laaksonen, Aatto
    Molecular dynamics simulations of conserved Hox protein hexapeptides. I. Folding behavior in water solution2007In: Journal of Molecular Structure: THEOCHEM, ISSN 0166-1280, Vol. 810, no 1-3, p. 113-120Article in journal (Refereed)
    Abstract [en]

    Molecular dynamics simulations of hexapeptides TFDWMK and LFPWMR; the highly conserved regions of Hox proteins Hox B1 and Hox B8, respectively, are carried out starting from extended structures to investigate their conformational space in water solution. In addition, we have studied TADWMK and TADAMK, where the aromatic residues Phenylalanine and Tryptophan were successively substituted for Alanine to investigate effects from the presence/absence of aromatic amino acids and interactions between them to folding behavior. The backbone of the hexapeptides in all simulations folds to a similar conformation found in experimental studies in solution. Intramolecular, hydrophobically driven interactions between the aromatic residues and internal hydrogen bonds are found to stabilize the conformations.

  • 11. Seal, Prasenjit
    et al.
    Jha, Prakash Chandra
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Chakrabarti, Swapan
    Static first order hyperpolarizabilities of DNA base pairs: A configuration interaction study2008In: Journal of Molecular Structure: THEOCHEM, ISSN 0166-1280, Vol. 855, no 1-3, p. 64-68Article in journal (Refereed)
    Abstract [en]

    We have investigated the role of H-bonding on the static first-order hyperpolarizabilities of DNA base pairs, namely, adenine-thymine (AT) and guanine-cytosine (GC). To interpret the effect of long-range dipolar interaction on this optical coefficient, the configuration interaction method has been implemented in these systems. Remarkably, the static first-order hyperpolarizability values gradually increases for the AT base pair as one increases the H-bonding distance between the DNA bases, whereas a reverse trend is observed for the GC base pair where the hyperpolarizability values pass through a minimum.

  • 12. Sun, Y. H.
    et al.
    Zhao, K.
    Wang, Chuankui
    KTH, Superseded Departments, Biotechnology.
    Luo, Yi
    KTH, Superseded Departments, Biotechnology.
    Ren, Y.
    Tao, X. T.
    Jiang, M. H.
    Two-photon absorption properties of multi-branched bis-(styryl)benzene based organic chromophores2004In: Journal of Molecular Structure: THEOCHEM, ISSN 0166-1280, Vol. 682, no 03-jan, p. 185-189Article in journal (Refereed)
    Abstract [en]

    Two-photon absorption (TPA) cross-sections of a series of multi-branched trans-stilbene charge transfer compounds with benzene as the coupling center have been theoretically investigated using analytical response theory at the random phase approximation level. It shows that the TPA cross-sections of compounds with a quasi-one-dimensional geometrical arrangement can be enhanced through the pure electronic coupling of different branches. The effects of different combination of donor/acceptor substitutions on the TPA cross-sections have also been discussed.

  • 13.
    Wang, Yanhua
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Wang, Chuankui
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Vibrational contributions to nonlinear optical properties of methanol, ethanol and propanol2005In: Journal of Molecular Structure: THEOCHEM, ISSN 0166-1280, Vol. 717, no 1-3, p. 223-230Article in journal (Refereed)
    Abstract [en]

    Static and dynamic vibrational contributions to the linear polarizability and the first and second nonlinear hyperpolarizabilities of methanol, ethanol and propanol have been calculated. Both the pure vibrational contribution and the zero-point vibrational averaging contribution have been determined by adopting the perturbation treatment of Bishop and Kirtman at the Hartree-Fock level. The pure vibrational contribution is quite important at the static limit, while in the optical region it varies for different nonlinear optical processes. The zero-point vibrational averaging contribution is a quite large correction to the electronic nonlinear optical (NLO) properties, especially for the second hyperpolarizability at finite fundamental frequencies. Vibrational analysis shows that the swinging modes at around 300 cm(-1) and the C-H stretching modes at around 3160 cm(-1) often give large contributions.

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