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  • 1
    ISSN: 1432-0770
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Computer Science , Physics
    Notes: Abstract Nonlinear dynamical biomolecular systems can evidently be considered as prototypes of information processing devices at molecular level capable to solve problems of high computational complexity. Keeping in mind this goal the dynamics of biochemical system based on enzymatic oxidation of uric acid was considered. The system was studied in the version of distributed biomolecular structure having predetermined geometry of enzyme distribution on a porous planar medium. Being in the regime of stepwise dissipative structure formation this system demonstrated complicated modes of behaviour.
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 114 (2001), S. 652-660 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Shape corrections to the standard approximate Kohn-Sham exchange-correlation (xc) potentials are considered with the aim to improve the excitation energies (especially for higher excitations) calculated with time-dependent density functional perturbation theory. A scheme of gradient-regulated connection (GRAC) of inner to outer parts of a model potential is developed. Asymptotic corrections based either on the potential of Fermi and Amaldi or van Leeuwen and Baerends (LB) are seamlessly connected to the (shifted) xc potential of Becke and Perdew (BP) with the GRAC procedure, and are employed to calculate the vertical excitation energies of the prototype molecules N2, CO, CH2O, C2H4, C5NH5, C6H6, Li2, Na2, K2. The results are compared with those of the alternative interpolation scheme of Tozer and Handy as well as with the results of the potential obtained with the statistical averaging of (model) orbital potentials. Various asymptotically corrected potentials produce high quality excitation energies, which in quite a few cases approach the benchmark accuracy of 0.1 eV for the electronic spectra. Based on these results, the potential BP-GRAC-LB is proposed for molecular response calculations, which is a smooth potential and a genuine "local" density functional with an analytical representation. © 2001 American Institute of Physics.
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 113 (2000), S. 8478-8489 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Time-dependent density functional theory (TDDFT) is applied for calculation of the excitation energies of the dissociating H2 molecule. The standard TDDFT method of adiabatic local density approximation (ALDA) totally fails to reproduce the potential curve for the lowest excited singlet 1Σu+ state of H2. Analysis of the eigenvalue problem for the excitation energies as well as direct derivation of the exchange-correlation (xc) kernel fxc(r,r′,ω) shows that ALDA fails due to breakdown of its simple spatially local approximation for the kernel. The analysis indicates a complex structure of the function fxc(r,r′,ω), which is revealed in a different behavior of the various matrix elements K1c,1cxc (between the highest occupied Kohn–Sham molecular orbital ψ1 and virtual MOs ψc) as a function of the bond distance R(H–H). The effect of nonlocality of fxc(r,r′) is modeled by using different expressions for the corresponding matrix elements of different orbitals. Asymptotically corrected ALDA (ALDA-AC) expressions for the matrix elements K12,12xc(στ) are proposed, while for other matrix elements the standard ALDA expressions are retained. This approach provides substantial improvement over the standard ALDA. In particular, the ALDA-AC curve for the lowest singlet excitation qualitatively reproduces the shape of the exact curve. It displays a minimum and approaches a relatively large positive energy at large R(H–H). ALDA-AC also produces a substantial improvement for the calculated lowest triplet excitation, which is known to suffer from the triplet instability problem of the restricted KS ground state. Failure of the ALDA for the excitation energies is related to the failure of the local density as well as generalized gradient approximations to reproduce correctly the polarizability of dissociating H2. The expression for the response function χ is derived to show the origin of the field-counteracting term in the xc potential, which is lacking in the local density and generalized gradient approximations and which is required to obtain a correct polarizability. © 2000 American Institute of Physics.
    Type of Medium: Electronic Resource
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  • 4
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The Kohn–Sham (KS) solution is constructed from an accurate CI density and the KS exchange and correlation energies Ex and Ec, as well as the corresponding exchange and exchange-correlation energy densities εx(r) and εxc(r), which are obtained for the hydrogen abstraction reaction H+H2 and the symmetrical four-center exchange reaction H2+H2. The KS quantities are compared with those of the standard GGAs. Comparison shows that the GGA exchange functional represents both exchange and molecular nondynamical left–right correlation, while the GGA correlation functional represents only the dynamical part of the correlation. This role of the GGA exchange functional is especially important for the transition states (TS) of the reactions where the left–right correlation is enhanced. Standard GGAs tend to underestimate the barrier height for the reaction H+H2 and to overestimate it for the reaction H2+H2. For H2+H2 the Kohn–Sham orbital degeneracy in the square TS is represented with an equi-ensemble KS solution for both accurate KS/CI and GGA, while near the TS ensemble solutions with unequal occupations of the degenerate highest occupied orbitals are obtained. For the GGA ensemble solution a special ensemble formula for the GGA exchange functional is proposed. Application of this formula to the H2+H2 reaction reduces appreciably the reaction barriers calculated with GGAs and leads to much better agreement with the accurate value. The too low GGA barriers for the H+H2 reaction are attributed to overestimation of the dynamical correlation in the TS by the GGA correlation functionals. In order to correct this error, it is recommended to modify the dependence of the approximate correlation functionals on the local polarization ζ with the purpose of reducing the approximate correlation energy for intermediate ζ values, which are expected to characterize the TS's of radical abstraction reactions. © 1999 American Institute of Physics.
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 116 (2002), S. 6435-6442 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: An approximate Kohn–Sham (KS) exchange potential vxσCEDA is developed, based on the common energy denominator approximation (CEDA) for the static orbital Green's function, which preserves the essential structure of the density response function. vxσCEDA is an explicit functional of the occupied KS orbitals, which has the Slater vSσ and response vrespσCEDA potentials as its components. The latter exhibits the characteristic step structure with "diagonal" contributions from the orbital densities |ψiσ|2, as well as "off-diagonal" ones from the occupied–occupied orbital products ψiσψj(≠1)σ*. Comparison of the results of atomic and molecular ground-state CEDA calculations with those of the Krieger–Li–Iafrate (KLI), exact exchange (EXX), and Hartree–Fock (HF) methods show, that both KLI and CEDA potentials can be considered as very good analytical "closure approximations" to the exact KS exchange potential. The total CEDA and KLI energies nearly coincide with the EXX ones and the corresponding orbital energies cursive-epsiloniσ are rather close to each other for the light atoms and small molecules considered. The CEDA, KLI, EXX–cursive-epsiloniσ values provide the qualitatively correct order of ionizations and they give an estimate of VIPs comparable to that of the HF Koopmans' theorem. However, the additional off-diagonal orbital structure of vxσCEDA appears to be essential for the calculated response properties of molecular chains. KLI already considerably improves the calculated (hyper)polarizabilities of the prototype hydrogen chains Hn over local density approximation (LDA) and standard generalized gradient approximations (GGAs), while the CEDA results are definitely an improvement over the KLI ones. The reasons of this success are the specific orbital structures of the CEDA and KLI response potentials, which produce in an external field an ultranonlocal field-counteracting exchange potential. © 2002 American Institute of Physics.
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 112 (2000), S. 1344-1352 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: An approximate Kohn–Sham exchange-correlation potential νxcSAOP is developed with the method of statistical averaging of (model) orbital potentials (SAOP) and is applied to the calculation of excitation energies as well as of static and frequency-dependent multipole polarizabilities and hyperpolarizabilities within time-dependent density functional theory (TDDFT). νxcSAOP provides high quality results for all calculated response properties and a substantial improvement upon the local density approximation (LDA) and the van Leeuwen–Baerends (LB) potentials for the prototype molecules CO, N2, CH2O, and C2H4. For the first three molecules and the lower excitations of the C2H4 the average error of the vertical excitation energies calculated with νxcSAOP approaches the benchmark accuracy of 0.1 eV for the electronic spectra. © 2000 American Institute of Physics.
    Type of Medium: Electronic Resource
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  • 7
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The density functional definition of exchange and correlation differs from the traditional one. In order to calculate the density functional theory (DFT), quantities accurately, molecular Kohn–Sham (KS) solutions have been obtained from ab initio wave functions for the homonuclear diatomic molecules Li2, N2, F2. These afford the construction of the KS determinant Ψs and the calculation of its total electronic energy EKS and the kinetic, nuclear-attraction and Coulomb repulsion components Ts, V, WH as well as the (DFT) exchange energy Ex and correlation energy Ec. Comparison of these DFT quantities has been made on one hand with the corresponding Hartree–Fock (HF) quantities and on the other hand with local density approximation (LDA) and generalized gradient approximation (GGA). Comparison with HF shows that the correlation errors in the components T, V, and WH of the total energy are much larger for HF than KS determinantal wave functions. However, the total energies EKS and EHF appear to be close to each other, as well as the exchange energies Ex and ExHF and correlation energies Ec and EcHF. The KS determinantal wave function and the KS orbitals therefore correspond to much improved kinetic and Coulombic energies, while having only a slightly larger total correlation energy. It is stressed that these properties of the Kohn–Sham orbitals make them very suitable for use in the molecular orbital theories of chemistry. Comparison of the accurate Kohn–Sham exchange and correlation energies with LDA and GGA shows that the GGA exchange energies are consistently too negative, while the GGA correlation energies are not negative enough. It is argued that the GGA exchange functionals represent effectively not only exchange, but also the molecular non-dynamical correlation, while the GGA correlation functionals represent dynamical correlation only. © 1997 American Institute of Physics.
    Type of Medium: Electronic Resource
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  • 8
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The exchange-correlation potentials vxc which are currently fashionable in density functional theory (DFT), such as those obtained from the local density approximation (LDA) or generalized gradient approximations (GGAs), all suffer from incorrect asymptotic behavior. In atomic calculations, this leads to substantial overestimations of both the static polarizability and the frequency dependence of this property. In the present paper, it is shown that the errors in atomic static dipole and quadrupole polarizabilities are reduced by almost an order of magnitude, if a recently proposed model potential with correct Coulombic long-range behavior is used. The frequency dependence is improved similarly. The model potential also removes the overestimation in molecular polarizabilities, leading to slight improvements for average molecular polarizabilities and their frequency dependence. For the polarizability anisotropy we find that the model potential results do not improve over the LDA and GGA results. Our method for calculating frequency-dependent molecular response properties within time-dependent DFT, which we described in more detail elsewhere, is summarized. © 1996 American Institute of Physics.
    Type of Medium: Electronic Resource
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  • 9
    Electronic Resource
    Electronic Resource
    Springer
    Journal of structural chemistry 29 (1988), S. 349-356 
    ISSN: 1573-8779
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 10
    Electronic Resource
    Electronic Resource
    Springer
    Journal of structural chemistry 21 (1980), S. 272-276 
    ISSN: 1573-8779
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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