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  • 1
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 109 (1998), S. 2604-2608 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The difficulty of widely used density functionals in describing the dissociation behavior of some homonuclear and heteronuclear diatomic radicals is analyzed. It is shown that the self-interaction error of these functionals accounts for the problem—it is much larger for a system with a noninteger number of electrons than a system with an integer number of electrons. We find the condition for the erroneous dissociation behavior described by approximate density functionals: when the ionization energy of one dissociation partner differs from the electron affinity of the other partner by a small amount, the self-interaction error will lead to wrong dissociation limit. Systems with a noninteger number of electrons and hence the large amount of self-interaction error in approximate density functionals arise also in the transition states of some chemical reactions and in some charge-transfer complexes. In the course of analysis, we derive a scaling relation necessary for an exchange-correlation functional to be self-interaction free. © 1998 American Institute of Physics.
    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 112 (2000), S. 3483-3492 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A new practical approach to studying enzyme reactions by combining ab initio QM/MM calculations with free energy perturbation is presented. An efficient iterative optimization procedure has been developed to determine optimized structures and minimum energy paths for a system with thousands of atoms on the ab initio QM/MM potential: the small QM sub-system is optimized using a quasi-Newton minimizer in redundant internal coordinates with ab initio QM/MM calculations, while the large MM sub-system is minimized by the truncated Newton method in Cartesian coordinates with only molecular mechanical calculations. The above two optimization procedures are performed iteratively until they converge. With the determined minimum energy paths, free energy perturbation calculations are carried out to determine the change in free energy along the reaction coordinate. Critical to the success of the iterative optimization procedure and the free energy calculations is the smooth connection between the QM and MM regions provided by a recently proposed pseudobond QM/MM approach [J. Chem. Phys. 110, 46 (1999)]. The methods have been demonstrated by studying the initial proton transfer step in the reaction catalyzed by the enzyme triosephosphate isomerase (TIM). © 2000 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 110 (1999), S. 46-54 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A major challenge for combined quantum mechanical and molecular mechanical methods (QM/MM) to study large molecules is how to treat the QM/MM boundary that bisects some covalent bonds. Here a pseudobond approach has been developed to solve this problem for ab initio QM/MM calculations: a one-free-valence atom with an effective core potential is constructed to replace the boundary atom of the environment part and to form a pseudobond with the boundary atom of the active part. This pseudobond, which is described only by the QM method, is designed to mimic the original bond with similar bond length and strength, and similar effects on the rest of the active part. With this pseudobond approach, some well-known deficiencies of the link atom approach have been circumvented and a well-defined potential energy surface of the whole QM/MM system has been provided. The construction of the effective core potential for the pseudobond is independent of the molecular mechanical force field and the same effective core potential is applicable to both Hartree–Fock and density functional methods. Tests on a series of molecules yield very good structural, electronic, and energetic results in comparison with the corresponding full ab initio quantum mechanical calculations. © 1999 American Institute of Physics.
    Type of Medium: Electronic Resource
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  • 4
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 109 (1998), S. 10107-10110 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A generalized adiabatic connection is developed for density functional theory. The method extends the well-known adiabatic connection formula and provides a general link between the Kohn–Sham and the physical system. When the complimentary error function is used as a special case, the expression for the exchange-correlation functional does not have the 1/r12 Coulomb component. The exact contributions from the physical system and the noninteracting system are established: The physical system limit has a dominant contribution, while the noninteracting system limit has no contribution. © 1998 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 107 (1997), S. 1218-1226 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The evaluation of the Coulomb interaction of the electron density with itself dominates the cost of a density-functional theory calculation, due to its quadratic scaling with the size of the system. A similar problem is found in simulations of systems of particles, where the cost is dominated by the particle–particle interactions. Recently, we have presented a simple method for the particle–particle problem [J. M. Pérez-Jordá and W. Yang, Chem. Phys. Lett. 247, 484 (1995)]. In this paper, our scheme is generalized to densities, in particular for calculations with Gaussian basis functions. Near linear scaling is observed for molecules with about 400 first-row atoms. CPU time savings of up to one order of magnitude are observed for these molecules. The method distinguishes between localized and diffuse distributions in a much simpler way than in other proposed approaches. © 1997 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 102 (1995), S. 7549-7556 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A unique definition of atomic charges in molecules is presented based on a variational principle involving the electrostatic potential energy. The method requires only the electron density as input, and does not rely on an arbitrary set of fitting points as do conventional electrostatic potential fitting procedures. The dipole moments and electrostatic potentials calculated from atomic charges obtained from this method agree well with those from self-consistent-field calculations. The new method also provides a spherical-atom potential model that may be useful in future generation molecular simulation force fields. © 1995 American Institute of Physics.
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 101 (1994), S. 3298-3300 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The conventional Ewald expression for the electrostatic energy and forces is recast in a form that can be evaluated to high accuracy in order N log(N) steps using fast Fourier transforms. The fast Fourier Poisson method does not rely on interpolation approaches or Taylor/multipole expansions, and can be easily integrated with conventional molecular dynamics algorithms.
    Type of Medium: Electronic Resource
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  • 8
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 84 (1986), S. 3320-3323 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The density matrix that leads to a minimum kinetic energy for a given density is considered as a convex superposition of pure states. It is shown that the conditions of stationarity of the kinetic energy and collapse to the given density require that each of the pure state wave functions involved be a single determinant in the same eigenspace of a particular, n-electron Hamiltonian and that all of the orbitals are eigenfunctions of the same effective one-electron Hamiltonian. The potential function arises originally as a Lagrange multiplier associated with the density constraint. In some cases it can (at least in principle) be determined. The role of electron–electron interactions and possible treatment of excited states are considered.
    Type of Medium: Electronic Resource
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  • 9
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 83 (1985), S. 2334-2336 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: As previously shown [M. Levy and J. P. Perdew, Phys. Rev. A (in press)], the customary Hohenberg–Kohn density functional, based on the universal functional F[ ρ], does not exhibit naively expected scaling properties. Namely, if ρλ=λ3ρ(λr) is the scaled density corresponding to ρ(r), the expected scaling, not satisfied, is T[ρλ]=λ2T[ρ] and V[ρλ]=λV[ρ], where T and V are the kinetic and potential energy components. By defining a new functional of ρ and λ, F[ ρ, λ], it is now shown how the naive scaling can be preserved. The definition is F[ρ(r), λ]=〈λ3N/2 Φminρλ (λr1... λrN)|Tˆ(r1...rN) +Vee(r1...rN)| λ3N/2Φminρλ(λr1...λrN)〉, where λ3N/2 Φminρλ(λr1... λrN) is that antisymmetric function Φ which yields ρλ(r)=λ3ρ(λr) and simultaneously minimizes 〈Φ|Tˆ(r1...rN) +λVee(r1...rN)|Φ〉. The corresponding variational principle is EvG.S.=Infλ, ρ(r){∫ drv(r) ρλ(r)+λ2T[ ρ(r)] +λVee[ ρ(r)]}, where EvG.S. is the ground-state energy for potential v(r). One is thus allowed to satisfy the virial theorem by optimum scaling just as if the naive scaling relations were correct for F[ ρ].
    Type of Medium: Electronic Resource
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  • 10
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 116 (2002), S. 515-524 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: An empirical method has been designed to account for the van der Waals interactions in practical molecular calculations with density functional theory. For each atom pair separated at a distance R, the method adds to the density functional electronic structure calculations an additional attraction energy EvdW=−fd(R)C6R−6, where fd(R) is the damping function which equals to one at large value of R and zero at small value of R. The coefficients C6 for pair interactions between hydrogen, carbon, nitrogen, and oxygen atoms have been developed in this work by a least-square fitting to the molecular C6 coefficients obtained from the dipole oscillator strength distribution method by Meath and co-workers. Two forms of the damping functions have been studied, with one dropping to zero at short distances much faster than the other. Four density functionals have been examined: Becke's three parameter hybrid functional with the Lee-Yang-Parr correlation functional, Becke's 1988 exchange functional with the LYP correlation functional, Becke's 1988 exchange functional with Perdew and Wang's 1991 (PW91) correlation functional, and PW91 exchange and correlation functional. The method has been applied to three systems where the van der Waals attractions are known to be important: rare-gas diatomic molecules, stacking of base pairs and polyalanines' conformation stabilities. The results show that this empirical method, with the damping function dropping to zero smoothly, provides a significant correction to both of the Becke's hybrid functional and the PW91 exchange and correlation functional. Results are comparable to the corresponding second-order Møller-Plesset calculations in many cases. © 2002 American Institute of Physics.
    Type of Medium: Electronic Resource
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