Literature DB >> 26619981

Zn Coordination Chemistry:  Development of Benchmark Suites for Geometries, Dipole Moments, and Bond Dissociation Energies and Their Use To Test and Validate Density Functionals and Molecular Orbital Theory.

Elizabeth A Amin1, Donald G Truhlar1.   

Abstract

We present nonrelativistic and relativistic benchmark databases (obtained by coupled cluster calculations) of 10 Zn-ligand bond distances, 8 dipole moments, and 12 bond dissociation energies in Zn coordination compounds with O, S, NH3, H2O, OH, SCH3, and H ligands. These are used to test the predictions of 39 density functionals, Hartree-Fock theory, and seven more approximate molecular orbital theories. In the nonrelativisitic case, the M05-2X, B97-2, and mPW1PW functionals emerge as the most accurate ones for this test data, with unitless balanced mean unsigned errors (BMUEs) of 0.33, 0.38, and 0.43, respectively. The best local functionals (i.e., functionals with no Hartree-Fock exchange) are M06-L and τ-HCTH with BMUEs of 0.54 and 0.60, respectively. The popular B3LYP functional has a BMUE of 0.51, only slightly better than the value of 0.54 for the best local functional, which is less expensive. Hartree-Fock theory itself has a BMUE of 1.22. The M05-2X functional has a mean unsigned error of 0.008 Å for bond lengths, 0.19 D for dipole moments, and 4.30 kcal/mol for bond energies. The X3LYP functional has a smaller mean unsigned error (0.007 Å) for bond lengths but has mean unsigned errors of 0.43 D for dipole moments and 5.6 kcal/mol for bond energies. The M06-2X functional has a smaller mean unsigned error (3.3 kcal/mol) for bond energies but has mean unsigned errors of 0.017 Å for bond lengths and 0.37 D for dipole moments. The best of the semiempirical molecular orbital theories are PM3 and PM6, with BMUEs of 1.96 and 2.02, respectively. The ten most accurate functionals from the nonrelativistic benchmark analysis are then tested in relativistic calculations against new benchmarks obtained with coupled-cluster calculations and a relativistic effective core potential, resulting in M05-2X (BMUE = 0.895), PW6B95 (BMUE = 0.90), and B97-2 (BMUE = 0.93) as the top three functionals. We find significant relativistic effects (∼0.01 Å in bond lengths, ∼0.2 D in dipole moments, and ∼4 kcal/mol in Zn-ligand bond energies) that cannot be neglected for accurate modeling, but the same density functionals that do well in all-electron nonrelativistic calculations do well with relativistic effective core potentials. Although most tests are carried out with augmented polarized triple-ζ basis sets, we also carried out some tests with an augmented polarized double-ζ basis set, and we found, on average, that with the smaller basis set DFT has no loss in accuracy for dipole moments and only ∼10% less accurate bond lengths.

Entities:  

Year:  2008        PMID: 26619981     DOI: 10.1021/ct700205n

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.006


  27 in total

1.  Density-functional expansion methods: evaluation of LDA, GGA, and meta-GGA functionals and different integral approximations.

Authors:  Timothy J Giese; Darrin M York
Journal:  J Chem Phys       Date:  2010-12-28       Impact factor: 3.488

2.  Methanethiol Binding Strengths and Deprotonation Energies in Zn(II)-Imidazole Complexes from M05-2X and MP2 Theories: Coordination Number and Geometry Influences Relevant to Zinc Enzymes.

Authors:  Douglas P Linder; Kenton R Rodgers
Journal:  J Phys Chem B       Date:  2015-09-04       Impact factor: 2.991

3.  Simulations of allosteric motions in the zinc sensor CzrA.

Authors:  Dhruva K Chakravorty; Bing Wang; Chul Won Lee; David P Giedroc; Kenneth M Merz
Journal:  J Am Chem Soc       Date:  2011-11-14       Impact factor: 15.419

4.  An assessment of DFT methods for predicting the thermochemistry of ion-molecule reactions of group 14 elements (Si, Ge, Sn).

Authors:  Igor S Ignatyev; Manuel Montejo; Juan Jesús López González
Journal:  J Mol Model       Date:  2013-11-08       Impact factor: 1.810

Review 5.  Metal Ion Modeling Using Classical Mechanics.

Authors:  Pengfei Li; Kenneth M Merz
Journal:  Chem Rev       Date:  2017-01-03       Impact factor: 60.622

Review 6.  Quantum mechanical investigations of organocatalysis: mechanisms, reactivities, and selectivities.

Authors:  Paul Ha-Yeon Cheong; Claude Y Legault; Joann M Um; Nihan Çelebi-Ölçüm; K N Houk
Journal:  Chem Rev       Date:  2011-06-28       Impact factor: 60.622

7.  Interaction between alkaline earth cations and oxo-ligands. DFT study of the affinity of the Ca2+ cation for carbonyl ligands.

Authors:  Leonardo Moreira da Costa; José Walkimar de Mesquita Carneiro; Gilberto Alves Romeiro; Lilian Weitzel Coelho Paes
Journal:  J Mol Model       Date:  2010-04-30       Impact factor: 1.810

8.  Zinc-binding structure of a catalytic amyloid from solid-state NMR.

Authors:  Myungwoon Lee; Tuo Wang; Olga V Makhlynets; Yibing Wu; Nicholas F Polizzi; Haifan Wu; Pallavi M Gosavi; Jan Stöhr; Ivan V Korendovych; William F DeGrado; Mei Hong
Journal:  Proc Natl Acad Sci U S A       Date:  2017-05-31       Impact factor: 11.205

9.  DFT studies of imino and thiocarbonyl ligands with the pentaaqua Mg²⁺ cation: affinity and associated parameters.

Authors:  Leonardo Moreira da Costa; Glaucio Braga Ferreira; José Walkimar de M Carneiro
Journal:  J Mol Model       Date:  2013-03-28       Impact factor: 1.810

10.  Quantum chemical study of silanediols as metal binding groups for metalloprotease inhibitors.

Authors:  Igor S Ignatyev; Manuel Montejo; Pilar Gema Rodríguez Ortega; Juan Jesús López González
Journal:  J Mol Model       Date:  2013-01-15       Impact factor: 1.810

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