Biomedical subjects

John P Perdew

Publications and source records attributed to John P Perdew.

15 recordsLinked to original sources

PubMed2006

Relevance of the slowly varying electron gas to atoms, molecules, and solids.

We present a Thomas-Fermi-inspired density scaling under which electron densities of atomic, molecular, or condensed matter become both large and slowly varying, so that semiclassical approximations and second-order density gradient expansions are asymptotically exact for the kinetic and exchange energies. Thus, even for atoms and molecules, density-functional approximations should recover the universal second-order gradient expansions in this limit. We also explain why common generalized gradient approximations for exchange do not.

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PubMed2006

Spurious fractional charge on dissociated atoms: pervasive and resilient self-interaction error of common density functionals.

Semilocal density functional approximations for the exchange-correlation energy can improperly dissociate a neutral molecule XY (Y not =X) to fractionally charged fragments X(+q)...Y(-q) with an energy significantly lower than X0...Y0. For example, NaCl can dissociate to Na(+0.4)...Cl(-0.4). Generally, q is positive when the lowest-unoccupied orbital energy of atom Y0 lies below the highest-occupied orbital energy of atom X0. The first 24 open sp-shell atoms of the Periodic Table can form 276 distinct unlike pairs XY, and in the local spin density approximation 174 of these display fractional-charge dissociation. Finding these lowest-energy solutions with standard quantum chemistry codes, however, requires special care. Self-interaction-corrected (SIC) semilocal approximations are exact for one-electron systems and also reduce the spurious fractional charge q. The original SIC of Perdew and Zunger typically reduces q to 0. A scaled-down SIC with better equilibrium properties sometimes fails to reduce q all the way to 0. The desideratum of "many-electron self-interaction freedom" is introduced as a generalization of the one-electron concept.

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PubMed2006

Scaling down the Perdew-Zunger self-interaction correction in many-electron regions.

Semilocal density functional approximations (DFAs) for the exchange-correlation energy suffer from self-interaction error, which is believed to be the cause of many of the failures of common DFAs, such as poor description of charge transfer and transition states of chemical reactions. The standard self-interaction correction (SIC) of Perdew and Zunger mends some of these failures but spoils such essential properties as thermochemistry and equilibrium bond lengths. The Perdew-Zunger SIC seems to overcorrect many-electron systems. In this paper, we propose a modified SIC, which is scaled down in many-electron regions. The new SIC has an improved performance for many molecular properties, including total energies, atomization energies, barrier heights of chemical reactions, ionization potentials, electron affinities, and bond lengths. The local spin-density approximation (LSDA) benefits from SIC more than higher-level functionals do. The scaled-down SIC has only one adjustable parameter. Rationalization of the optimal value of this parameter enables us to construct an almost-nonempirical version of the scaled-down SIC-LSDA, which is significantly better than uncorrected LSDA and even better than the uncorrected generalized gradient approximation. We present an analysis of the formal properties of the scaled-down SIC and define possible directions for further improvements. In particular, we find that exactness for all one-electron densities does not guarantee correct asymptotics for the exchange-correlation potential of a many-electron system.

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PubMed2006

The performance of semilocal and hybrid density functionals in 3d transition-metal chemistry.

We investigate the performance of contemporary semilocal and hybrid density functionals for bond energetics, structures, dipole moments, and harmonic frequencies of 3d transition-metal (TM) compounds by comparison with gas-phase experiments. Special attention is given to the nonempirical metageneralized gradient approximation (meta-GGA) of Tao, Perdew, Staroverov, and Scuseria (TPSS) [Phys. Rev. Lett. 91, 146401 (2003)], which has been implemented in TURBOMOLE for the present work. Trends and error patterns for classes of homologous compounds are analyzed, including dimers, monohydrides, mononitrides, monoxides, monofluorides, polyatomic oxides and halogenides, carbonyls, and complexes with organic pi ligands such as benzene and cyclopentadienyl. Weakly bound systems such as Ca(2), Mn(2), and Zn(2) are discussed. We propose a reference set of reaction energies for benchmark purposes. Our all-electron results with quadruple zeta valence basis sets validate semilocal density-functional theory as the workhorse of computational TM chemistry. Typical errors in bond energies are substantially larger than in (organic) main group chemistry, however. The Becke-Perdew'86 [Phys. Rev. A 38, 3098 (1988); Phys. Rev. B 33, 8822 (1986)] GGA and the TPSS meta-GGA have the best price/performance ratio, while the TPSS hybrid functional achieves a slightly lower mean absolute error in bond energies. The popular Becke three-parameter hybrid B3LYP underbinds significantly and tends to overestimate bond distances; we give a possible explanation for this. We further show that hybrid mixing does not reduce the width of the error distribution on our reference set. The error of a functional for the s-d transfer energy of a TM atom does not predict its error for TM bond energies and bond lengths. For semilocal functionals, self-interaction error in one- and three-electron bonds appears to be a major source of error in TM reaction energies. Nevertheless, TPSS predicts the correct ground-state symmetry in the vast majority of cases and rarely fails qualitatively. This further confirms TPSS as a general purpose functional that works throughout the periodic table. We also give workstation timing comparisons for the 645-atom protein crambin.

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PubMed2005

Binding energy curves from nonempirical density functionals. I. Covalent bonds in closed-shell and radical molecules.

Binding or potential energy curves have been calculated for the ground-state diatomics H(2)(+), He(2)(+), LiH(+), H(2), N(2), and C(2), for the transition state H(3), and for the triplet first excited state of H(2) using the nonempirical density functionals from the first three rungs of a ladder of approximations: the local spin density (LSD) approximation, the Perdew-Burke-Ernzerhof (PBE) generalized gradient approximation (GGA), and the Tao-Perdew-Staroverov-Scuseria (TPSS) meta GGA. Good binding energy curves in agreement with coupled cluster or configuration interaction calculations are found from the PBE GGA and especially from the TPSS meta GGA. Expected exceptions are the symmetric radicals H(2)(+) and He(2)(+), where the functionals suffer from self-interaction error, and the exotically bonded C(2). Although the energy barrier for the reaction H(2) + H --> H + H(2) is better in PBE than in TPSS, the transition state H(3) is a more properly positioned and curved saddle point of the energy surface in TPSS. The triplet first excited state of H(2) obeys the Aufbau principle and thus is one of the exceptional excited states that are computable in principle from the ground-state functional. The PBE GGA and TPSS meta GGA are useful not only for chemical applications but also for the construction of higher-rung nonempirical functionals that can further improve the binding energy curves.

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PubMed2005

Binding energy curves from nonempirical density functionals II. van der Waals bonds in rare-gas and alkaline-earth diatomics.

Binding energy curves have been calculated for the ground-state rare-gas diatomics Ne(2) and Ar(2) and for the alkaline-earth diatomic Be(2) using the nonempirical density functionals from the first three rungs of a ladder of approximations: the local spin density (LSD) approximation, the Perdew-Burke-Ernzerhof (PBE) generalized gradient approximation (GGA), and the Tao-Perdew-Staroverov-Scuseria (TPSS) meta-GGA. Binding energy curves in reasonable agreement with those constructed from experiment are found from PBE and TPSS, which incorporate inhomogeneity corrections that satisfy the Lieb-Oxford bound and so describe the short-range part of the van der Waals interaction. At large internuclear separation, these functionals produce an exponentially decaying attraction in place of the correct long-range -C(6)/R(6). Basis-set and exchange-only effects are also discussed.

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PubMed2005

Proper gaussian basis sets for density functional studies of water dimers and trimers.

The accuracy of the Perdew-Burke-Ernzerhof and Tao-Perdew-Staroverov-Scuseria density functionals for describing noncovalent interaction energies in small water clusters is studied by testing 11 basis sets on a reduced test set proposed by Dahlke and Truhlar (J. Phys. Chem. B 2005, 109, 15677). We have also tested variants of the Perdew-Burke-Ernzerhof functional and the Becke98 hybrid functional. While moderate basis sets give converged density functional theory results for covalent dissociation energies, this is not true for noncovalent interaction energies. Our results show that density functionals give converged interaction energies with aug-cc-pVTZ and aug-cc-pVQZ basis sets. Gradual simplification of the basis set introduces an increasing overbinding effect. The best agreement with the high-level result was obtained by the Perdew-Burke-Ernzerhof functional at the basis set limit. The converged Tao-Perdew-Staroverov-Scuseria interaction energies show a systematic underbinding effect that can be compensated by a somewhat systematic overbinding basis set effect of smaller basis sets such as 6-31+G(d,2p). The inclusion of the diffuse functions in the oxygen basis set is very important, while the inclusion of the f functions practically does not influence the results. Improvement can be obtained by adding more hydrogen p functions to the 6-31+G basis set.

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PubMed2005

Nonempirical construction of current-density functionals from conventional density-functional approximations.

Density-functional approximations for the exchange-correlation energy Exc[n] of a many-electron ground state are highly developed and widely useful. When a paramagnetic current jp(r) is present, Vignale and Rasolt have extended the Kohn-Sham theorems and presented an additive correction valid to second order in the gauge-invariant vorticity nu=Delta x (jp/n):Exc[n, jp]=Exc[n, jp=0] + DeltaE(VR)(xc)[n, nu]. Apart from spin-polarization effects, their correction is unambiguous for a generalized gradient approximation (GGA). But for a meta-GGA (MGGA), one needs to know how to go back from the orbital kinetic energy density tau([n, jp];r) to tau([n,0];r); we show how to do this here. Numerical tests on the degeneracies for open-shell atoms show that current-density corrections reduce the error of GGA from 2 to 1 kcal/mol, and of MGGA from 5 to 2 kcal/mol.

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PubMed2005

Prescription for the design and selection of density functional approximations: more constraint satisfaction with fewer fits.

We present the case for the nonempirical construction of density functional approximations for the exchange-correlation energy by the traditional method of "constraint satisfaction" without fitting to data sets, and present evidence that this approach has been successful on the first three rungs of "Jacob's ladder" of density functional approximations [local spin-density approximation (LSD), generalized gradient approximation (GGA), and meta-GGA]. We expect that this approach will also prove successful on the fourth and fifth rungs (hyper-GGA or hybrid and generalized random-phase approximation). In particular, we argue for the theoretical and practical importance of recovering the correct uniform density limit, which many semiempirical functionals fail to do. Among the beyond-LSD functionals now available to users, we recommend the nonempirical Perdew-Burke-Ernzerhof (PBE) GGA and the nonempirical Tao-Perdew-Staroverov-Scuseria (TPSS) meta-GGA, and their one-parameter hybrids with exact exchange. TPSS improvement over PBE is dramatic for atomization energies of molecules and surface energies of solids, and small or moderate for other properties. TPSS is now or soon will be available in standard codes such as GAUSSIAN, TURBOMOLE, NWCHEM, ADF, WIEN, VASP, etc. We also discuss old and new ideas to eliminate the self-interaction error that plagues the functionals on the first three rungs of the ladder, bring up other related issues, and close with a list of "do's and don't's" for software developers and users.

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PubMed2005

Estimation, computation, and experimental correction of molecular zero-point vibrational energies.

For accurate thermochemical tests of electronic structure theory, accurate true anharmonic zero-point vibrational energies ZPVE(true) are needed. We discuss several possibilities to extract this information for molecules from density functional or wave function calculations and/or available experimental data: (1) Empirical universal scaling of density-functional-calculated harmonic ZPVE(harm)s, where we find that polyatomics require smaller scaling factors than diatomics. (2) Direct density-functional calculation by anharmonic second-order perturbation theory PT2. (3) Weighted averages of harmonic ZPVE(harm) and fundamental ZPVE(fund) (from fundamental vibrational transition frequencies), with weights (3/4, 1/4) for diatomics and (5/8,3/8) for polyatomics. (4) Experimental correction of the PT2 harmonic contribution, i.e., the estimate ZPVE(true)PT2 + (ZPVE(fund)expt - ZPVE(fund)PT2) for ZPVE(true). The (5/8,3/8) average of method 3 and the additive correction of method 4 have been proposed here. For our database of experimental ZPVE(true), consisting of 27 diatomics and 8 polyatomics, we find that methods 1 and 2, applied to the popular B3LYP and the nonempirical PBE and TPSS functionals and their one-parameter hybrids, yield polyatomic errors on the order of 0.1 kcal/mol. Larger errors are expected for molecules larger than those in our database. Method 3 yields errors on the order of 0.02 kcal/mol, but requires very accurate (e.g., experimental, coupled cluster, or best-performing density functional) input harmonic ZPVE(harm). Method 4 is the best-founded one that meets the requirements of high accuracy and practicality, requiring as experimental input only the highly accurate and widely available ZPVE(fund)expt and producing errors on the order of 0.05 kcal/mol that are relatively independent of functional and basis set. As a part of our study, we also test the ability of the density functionals to predict accurate equilibrium bond lengths and angles for a data set of 21 mostly polyatomic molecules (since all calculated ZPVEs are evaluated at the correspondingly calculated molecular geometries).

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PubMed2005

Test of a nonempirical density functional: short-range part of the van der Waals interaction in rare-gas dimers.

It is known that the nonempirical generalized gradient approximation (GGA) of Perdew, Burke, and Ernzerhof (PBE) provides a much more realistic description of the short-range part of the van der Waals (vdW) interaction than does the local spin density (LSD) approximation. In the present work, the ability of the higher-level nonempirical meta-GGA of Tao, Perdew, Staroverov, and Scuseria (TPSS) to describe vdW interaction is tested self-consistently in ten rare-gas dimers with Z< or =36. The one-parameter hybrid version (TPSSh) of the TPSS exchange-correlation functional is also included in this test. Calculations show that both TPSS and TPSSh functionals correctly yield vdW bonds in these dimers and significantly improve the prediction of bond lengths, binding energies, and harmonic vibrational frequencies over LSD. The rather close agreement of TPSS with PBE for these dimers confirms a principle of the TPSS construction: preservation of the PBE large-gradient behavior. More importantly, it suggests that TPSS can serve as a platform on which to construct a still-higher level of nonempirical functionals. Compared with the PBE GGA, TPSS, and TPSSh yield a slightly weaker binding. As for normally bonded molecules, TPSSh yields the most accurate vibrational frequencies. The typically too-long bond lengths and too-small binding energies of TPSS meta-GGA suggest the need for some long-range vdW interaction correction even in this class of systems. The effect of basis-set superposition error on the calculated properties of these vdW systems is investigated. We also show that the relatively strong anharmonic effects in the rare-gas dimers are described remarkably well by the Morse potential.

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PubMed2004

Electrical response of molecular chains from density functional theory.

The electrical response of molecular chains is dramatically overestimated by local and semilocal density functionals. We show that Kohn-Sham density-functional theory yields accurate linear and nonlinear polarizabilities when the exact exchange energy is employed together with the corresponding exact Kohn-Sham potential upsilonx(r). We further show that approximations to upsilonx(r) that are very accurate for the ground-state energy can nevertheless fail badly for the response because of potential barriers that have little effect on the ground-state energy but strongly affect the electron mobility.

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PubMed2004

Meta-generalized gradient approximation: explanation of a realistic nonempirical density functional.

Tao, Perdew, Staroverov, and Scuseria (TPSS) have constructed a nonempirical meta-generalized gradient approximation (meta-GGA) [Phys. Rev. Lett. 91, 146401 (2003)] for the exchange-correlation energy, imposing exact constraints relevant to the paradigm densities of condensed matter physics and quantum chemistry. Results of their extensive tests on molecules, solids, and solid surfaces are encouraging, suggesting that this density functional achieves uniform accuracy for diverse properties and systems. In the present work, this functional is explained and details of its construction are presented. In particular, the functional is constructed to yield accurate energies under uniform coordinate scaling to the low-density or strong-interaction limit. Its nonlocality is displayed by plotting the factor F(xc) that gives the enhancement relative to the local density approximation for exchange. We also discuss an apparently harmless order-of-limits problem in the meta-GGA. The performance of this functional is investigated for exchange and correlation energies and shell-removal energies of atoms and ions. Non-self-consistent molecular atomization energies and bond lengths of the TPSS meta-GGA, calculated with GGA orbitals and densities, agree well with those calculated self-consistently. We suggest that satisfaction of additional exact constraints on higher rungs of a ladder of density functional approximations can lead to further progress.

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PubMed2003

Climbing the density functional ladder: nonempirical meta-generalized gradient approximation designed for molecules and solids.

The electron density, its gradient, and the Kohn-Sham orbital kinetic energy density are the local ingredients of a meta-generalized gradient approximation (meta-GGA). We construct a meta-GGA density functional for the exchange-correlation energy that satisfies exact constraints without empirical parameters. The exchange and correlation terms respect two paradigms: one- or two-electron densities and slowly varying densities, and so describe both molecules and solids with high accuracy, as shown by extensive numerical tests. This functional completes the third rung of "Jacob's ladder" of approximations, above the local spin density and GGA rungs.

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PubMed2003

Simple iterative construction of the optimized effective potential for orbital functionals, including exact exchange.

For exchange-correlation functionals that depend explicitly on the Kohn-Sham orbitals, the potential V(xcsigma)(r) must be obtained as the solution of the optimized effective potential (OEP) integral equation. This is very demanding and has limited the use of orbital functionals. We demonstrate that instead the OEP can be obtained iteratively by solving the partial differential equations for the orbital shifts that exactify the Krieger-Li-Iafrate approximation. Unoccupied orbitals do not need to be calculated. Accuracy and efficiency of the method are shown for atoms and clusters using the exact-exchange energy. Counterintuitive asymptotic limits of the exact OEP are presented.

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