Related Experiment Video
Updated: Mar 29, 2026

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
Published on: January 26, 2024
Structure Prediction of Bis(amino acidato)copper(II) Complexes with a New Force Field for Molecular Modeling
Jasmina Sabolović1, Vjeran Gomzi1
1Institute for Medical Research and Occupational Health, Ksaverska cesta 2, P.O. Box 291, HR-10001 Zagreb, Croatia, and Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia.
Abstract:
This article presents a new force field whose parameterization was based on experimental crystal data and quantum chemically obtained vacuum structures of a series of copper(II) complexes with aliphatic α-amino acids and their N-alkyl derivatives, along with the SPC/E water model. The ability of the new force field to reproduce and predict the structural properties of the copper(II) complexes in the gas phase, in simulated crystalline surroundings, and solvated in water is examined. Molecular dynamics (MD) simulations with the new force field yielded time-average structural coordinates of bis(glycinato)copper(II) [the only one of 25 modeled bis(amino acidato)copper(II) systems with published experimental structural data in aqueous solution at room temperature] within the experimental error values. The study of the cis-trans isomerization of bis(glycinato)copper(II) in aqueous medium at 300 K using the quantum chemical polarized continuum model revealed a small energy difference (5 kJ mol(-1)) between the solvated cis and trans minima, in line with the MD energy estimations. The new force field proved promising in predicting the association of the complexes in aqueous solution and formation of a nucleus of crystallization.
More Related Videos
14:44Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR
Published on: December 16, 2013
07:31Author Spotlight: Advancing Cell Membrane Biophysics - Exploring Interactions and Challenges Through Experimental and Computational Approaches
Published on: September 1, 2023
Related Concept Videos
Crystal Field Theory - Octahedral Complexes
To explain the observed behavior of transition metal complexes (such as colors), a model involving electrostatic interactions between the electrons from the ligands and the electrons in the unhybridized d orbitals of the central metal atom has been developed. This electrostatic model is crystal field theory (CFT). It helps to understand, interpret, and predict the colors, magnetic behavior, and some structures of coordination compounds of transition metals.
CFT focuses on...
Crystal Field Theory - Tetrahedral and Square Planar Complexes
Crystal field theory (CFT) is applicable to molecules in geometries other than octahedral. In octahedral complexes, the lobes of the dx2−y2 and dz2 orbitals point directly at the ligands. For tetrahedral complexes, the d orbitals remain in place, but with only four ligands located between the axes. None of the orbitals points directly at the tetrahedral ligands. However, the dx2−y2 and dz2 orbitals (along the Cartesian axes) overlap with the ligands less than the dxy,...
Valence Bond Theory
Predicting Molecular Geometry
Molecular Models
Conserved Binding Sites
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...