Structure Prediction of Bis(amino acidato)copper(II) Complexes with a New Force Field for Molecular Modeling

Sabolović, Jasmina; Gomzi, Vjeran

doi:10.1021/ct9000203

Cited by 24 publications

(55 citation statements)

References 102 publications

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“…The effective-core potentials of Hay and Wadt [53][54][55] were used to describe the shielding effects of electrons in copper inner shells. [25][26][27][28]46,56] This functional/basis set was checked for several copper(II) amino acid complexes with and without water molecules and compared with the experimental crystal structures. The choice of the DFT method and functional/basis set used is based on previous studies of the energies and geometries of anhydrous and aquabis(amino acidato)copper(II) complexes.…”

Section: Computational Detailsmentioning

confidence: 99%

“…The choice of the DFT method and functional/basis set used is based on previous studies of the energies and geometries of anhydrous and aquabis(amino acidato)copper(II) complexes. [27,28] Cu(l-His) 2 is an electrically neutral molecule with a spin multiplicity of 2. [25,26] Also, this functional/ basis set has been checked for energetics of the bis(glycinato)copper(II) system by comparison with G3 calculations at the MP2 level.…”

Section: Computational Detailsmentioning

confidence: 99%

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Why Does the Coordination Mode of Physiological Bis(L‐histidinato)copper(II) Differ in the Gas Phase, Crystal Lattice, and Aqueous Solutions? A Quantum Chemical Study

2013

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In bis(L‐histidinato)copper(II), the amino acid L‐histidine can bind to copper(II) in glycine‐like (G), histamine‐like (H), and imidazole–propionic acid like (I) coordination modes. This complex is known as the predominant copper(II)–amino acid complex in human blood serum. Numerous experimental studies of this physiological complex reported several coordination modes to coexist in aqueous solutions, but without providing complete structures. This paper is the first to investigate the relative stability of all possible copper(II) coordination modes and conformations of isolated bis(L‐histidinato)copper(II), and several conformers surrounded with up to 22 water molecules by DFT/B3LYP calculations. The vibration wavenumbers of four bis(L‐histidinato)copper(II)·20H2O structures were calculated and assigned for IR and Raman spectra. Among 83 isolated conformers obtained, 37 are in trans configuration, 45 in cis configuration, and one exhibits a trigonal‐bipyramidal structure. The most stable isolated conformer has a trans‐GG coordination. A comparison between the known X‐ray crystal and B3LYP vacuum molecular structures of bis(L‐histidinato)copper(II) dihydrate showed that the X‐ray cis‐HG mode with an intramolecular apical Cu–Ocarboxylato bond is unstable under vacuum and thus is greatly affected by crystal‐lattice effects. In the systems with 20 water molecules, the lowest energy was estimated for the conformer with a cis‐HH coordination and two axial Cu–Ocarboxylato bonds. This structural finding complements previous experimental studies, which reported an HH coordination mode as the prevailing in aqueous solutions under physiological conditions. The axial Cu–Ocarboxylato bond, unformed in any of the 83 isolated conformers, is stabilized by intermolecular interactions. The arrangement of water molecules around the complex might affect the coordination mode formation and stability.

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Section: Computational Detailsmentioning

confidence: 99%

Section: Computational Detailsmentioning

confidence: 99%

Why Does the Coordination Mode of Physiological Bis(L‐histidinato)copper(II) Differ in the Gas Phase, Crystal Lattice, and Aqueous Solutions? A Quantum Chemical Study

2013

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“…1) show that the distance between a copper(II) ion and an axial water molecule in the complex with glycine should be about 2.4 Å . Sabolović and Gomzi, [46] using MD simulations with the FFWa-SPCE force field, obtained value of 2.6 Å for this distance. In our opinion the discrepancy is due to very small (8.07043Á10 25 ) attractive C 6 parameter of the Lennard-Jones 12-6 potential used in the FFWa-SPCE force field for copper(II).…”

Section: Resultsmentioning

confidence: 80%

“…The simulations were performed using the GROMACS program package, version 5.1.4. The FFWa‐SPCE force field developed for copper(II) complexes with aliphatic amino acids was used with some modifications. The FFWa‐SPCE force field parameters of Lennard‐Jones potential result in wrong distances between Cu(II) and an axial ligand (water molecule or oxygen of the β‐carboxylic group of aspartic acid).…”

Section: Methodsmentioning

confidence: 99%

Hydration of copper(II) amino acids complexes

et al. 2017

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Hydration of the copper(II) bis-complexes with glycine, serine, lysine, and aspartic acid was studied by DFT and MD simulation methods. The distances between copper(II) and water molecules in the 1st and 2nd coordination shells, the average number of water molecules and their mean residence times in the hydration shells were calculated. Good agreement was observed between the values obtained and those found by DFT and NMR relaxation methods. Influence of the functional groups of the ligands and the cis-trans isomerism of the complexes on the structural and dynamical parameters of the hydration shells was displayed and explained. Analysis of the MD trajectories reveals the competition for a copper(II) axial position between water molecules or water molecules and the functional chain groups of the ligands and confirms the suggestion on the pentacoordination of copper(II) in such complexes. MD simulations show that only one axial position of Cu(II) is basically occupied at each time step while in average the coordination number more than 5 is observed. © 2017 Wiley Periodicals, Inc.

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“…23 Therefore, MM parametrisations for metals have traditionally been restricted to specific metal sites (with a given set of ligands), for which accurate results can be obtained 24,25,26,27 or metal-specific force fields requiring specialised software. 23,28,29 There are several approaches to incorporate metal ions into MM force fields. The simplest one is to describe the interaction between the ion and its ligand entirely by non-bonded interactions, i.e.…”

Section: Introductionmentioning

confidence: 99%

Comparison of Methods to Obtain Force-Field Parameters for Metal Sites

Ryde

2011

J. Chem. Theory Comput.

118

183

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We have critically examined and compared various ways to obtain standard harmonic molecular-mechanics (MM) force-field parameters for metal sites in proteins, using the twelve most common Zn 2+ sites as test cases. We show that the parametrisation of metal sites is hard to treat with automatic methods. The choice of method is a compromise between speed and accuracy, and therefore depends on the intended use of the parameters. If the metal site is not of central interest in the investigation, e.g. a structural metal, far from the active site, a simple and fast parametrisation is normally enough, using either a non-bonded model with restraints or a bonded parametrisation based on the method of Seminario. On the other hand, if the metal site is of central interest in the investigation, a more accurate method is needed to give quantitative results, e.g. the method by Norrby and Liljefors. The former methods are semiautomatic and can be performed in seconds, once quantum mechanical (QM) geometry optimisation and frequency calculations have been performed, whereas the latter method typically takes several days and requires significant human intervention. All approaches require a careful selection of the atom types used. For a non-bonded model, standard atom types can be used, whereas for a bonded-model, it is normally wise to use special atom types for each metal ligand. For accurate results, new atom types for all atoms in the metal site can be used. Atomic charges should also be considered. Typically, QM restrained electrostatic potential charges are accurate and easy to obtain once the QM calculation is performed, and they allow for charge transfer within the complex. For negatively charged complexes, it should be checked that hydrogen atoms of the ligands get proper charges. Finally, water ligands pose severe problems for bonded models in force fields that ignore non-bonded interactions for atoms separated by two bonds. Complexes with a single water ligand can normally be accurately treated with a bonded potential, once it is ensured that the water H atoms have non-zero Lennard-Jones parameters. However, for metal sites with several water molecules, a non-bonded model with restraints (taken from the QM calculations) is more stable.

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Structure Prediction of Bis(amino acidato)copper(II) Complexes with a New Force Field for Molecular Modeling

Cited by 24 publications

References 102 publications

Why Does the Coordination Mode of Physiological Bis(L‐histidinato)copper(II) Differ in the Gas Phase, Crystal Lattice, and Aqueous Solutions? A Quantum Chemical Study

Why Does the Coordination Mode of Physiological Bis(L‐histidinato)copper(II) Differ in the Gas Phase, Crystal Lattice, and Aqueous Solutions? A Quantum Chemical Study

Hydration of copper(II) amino acids complexes

Comparison of Methods to Obtain Force-Field Parameters for Metal Sites

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