Ab initio benchmark calculations on Ca(II) complexes and assessment of density functional theory methodologies.

J Phys Chem A

Departamento de Química Física y Analítica, Facultad de Química Universidad de Oviedo, Oviedo, Spain.

Published: October 2011

A set of benchmark results for the geometries, binding energies, and protonation affinities of 24 complexes of small organic ligands with Ca(II) is provided. The chosen level of theory is CCSD(T)/CBS obtained by means of a composite procedure. The performance of four density functionals, namely, PW91, PBE, B3LYP, and TPSS and several Pople-type basis sets, namely, 6-31G(d), 6-31+G(d), 6-31+G(2d,p) and 6-311+G(d) have been assessed. Additionally, the nature of the metal ligand bonding has been analyzed by means of the Symmetry Adapted Perturbation Theory (SAPT). We have found that the B3LYP hybrid functional, in conjunction with either the polarized double-ζ 6-31+G(2d,p) or the triple-ζ 6-311+G(d) basis sets, yields the closest results compared to the benchmark data. The SAPT analysis stresses the importance of induction effects in the binding of these complexes and suggests that consideration of classical electrostatic contributions alone may not be reliable enough for the prediction of relative binding energies for Ca(II) complexes.

Download full-text PDF

Source
http://dx.doi.org/10.1021/jp205101zDOI Listing

Publication Analysis

Top Keywords

caii complexes
8
binding energies
8
basis sets
8
initio benchmark
4
benchmark calculations
4
calculations caii
4
complexes
4
complexes assessment
4
assessment density
4
density functional
4

Similar Publications

In homogeneous catalysis, uncovering structure-activity relationships remains very rare but invaluable to understand and rationally improve performances. Here, generalizable structure-activity relationships apply to a series of heterodinuclear polymerization catalysts featuring Co(III) and s-block metals M(I/II) (M=Na(I), K(I), Ca(II), Sr(II), Ba(II)). These are shown to apply to polycarbonate production by the ring-opening copolymerizations (ROCOP) of cyclohexene oxide (CHO) and carbon dioxide (CO), conducted at high (20 bar) and low (1 bar) CO pressures, and to polyester production by copolymerization of cyclohexene oxide and phthalic anhydride (PA).

View Article and Find Full Text PDF

The correlation of intracranial parenchymal calcium score and the severity of neurological clinical presentation in carbonic anhydrase deficiency type 2.

Brain Dev

December 2024

Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia; Division of Medical Genetics, Department of Pediatrics, King Saud University Medical City, Riyadh, Saudi Arabia. Electronic address:

Background: Carbonic anhydrase type II deficiency (CAII-D) syndrome is a rare autosomal recessive genetic disorder characterized by osteopetrosis, renal tubular acidosis, and brain calcifications. Understanding the clinical and radiological features of CAII-D is key to effective management.

Aim: This study aimed to comprehensively analyze and measure intracranial parenchymal calcium score in pediatric CAII-D in relation to the severity of neurological clinical presentation.

View Article and Find Full Text PDF

It has been previously established that breast cancer cells exhibit high expression of the monocarboxylate (lactate) transporters (MCT1 and/or MCT4) and carbonic anhydrase IX (CAIX) and form a functional metabolon for proton-coupled lactate export, thereby stabilizing intracellular pH. CD147 is the MCT accessory protein that facilitates the creation of the MCT/CAIX complex. This study describes how the small molecule Beta-Galactose 2C (BGal2C) blocks the physical and functional interaction between CAIX and either MCT1 or MCT4 in Xenopus oocytes, which reduces the rate of proton and lactate flux with an IC of ~90 nM.

View Article and Find Full Text PDF

Effect of Water Networks On Ligand Binding: Computational Predictions vs Experiments.

J Chem Inf Model

December 2024

Medicinal Chemistry Research Group, Drug Innovation Centre, HUN-REN Research Centre for Natural Sciences, Magyar tudósok krt. 2, Budapest 1117, Hungary.

Rational drug design focuses on the explanation and prediction of complex formation between therapeutic targets and small-molecule ligands. As a third and often overlooked interacting partner, water molecules play a critical role in the thermodynamics of protein-ligand binding, impacting both the entropy and enthalpy components of the binding free energy and by extension, on-target affinity and bioactivity. The community has realized the importance of binding site waters, as evidenced by the number of computational tools to predict the structure and thermodynamics of their networks.

View Article and Find Full Text PDF
Article Synopsis
  • The study explores how biochar interacts with arsenic (As) in saline-alkali environments and highlights the critical role of calcium ions (Ca(II)) in this process.
  • Both undissolved biochar (UOB) and dissolved biochar (DOB) alone are ineffective for arsenic immobilization, but when combined with Ca(II), they achieve significant immobilization rates of As(V).
  • Key mechanisms include the formation of calcium arsenate precipitates and ternary complexes, with changes in Ca(II) concentration and pH further influencing the effectiveness of arsenic immobilization.
View Article and Find Full Text PDF

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!