QSPR ensemble modelling of the 1:1 and 1:2 complexation of Co2+, Ni2+, and Cu2+ with organic ligands: relationships between stability constants

Quantitative structure–property relationship (QSPR) modeling of stability constants for the metal:ligand ratio 1:1 (logK) and 1:2 (logβ2) complexes of 3 transition metal ions with diverse organic ligands in aqueous solution was performed using ensemble multiple linear regression analysis and substructural molecular fragment descriptors. The modeling was performed on the sets containing 396 and 132 (Co2+), 613 and 233 (Ni2+), 883 and 257 (Cu2+) logK and logβ2 values, respectively. The models have been validated in external fivefold cross-validations procedure as well as on the external test set containing new ligands recently reported in the literature. Predicted logK and logβ2 values were calculated as arithmetic means of several hundred individual models (consensus models) using their applicability domains in averaging. The root mean squared error of predictions varies from 0.94 to 1.2 (logK) and from 1.2 to 1.4 (logβ2) which is close to observed experimental systematic errors. Linear correlations between experimental logK values for pair of metal ions were evaluated. For all metal ions and ligands forming both 1:1 and 1:2 complexes the following ratio is observed: logβ2/logK = 1.8 ± 0.1, n = 492.

[1]  Alexandre Varnek,et al.  Substructural fragments: an universal language to encode reactions, molecular and supramolecular structures , 2005, J. Comput. Aided Mol. Des..

[2]  A. Varnek,et al.  QSPR ensemble modelling of alkaline-earth metal complexation , 2013, Journal of Inclusion Phenomena and Macrocyclic Chemistry.

[3]  A Varnek,et al.  "In silico" design of potential anti-HIV actives using fragment descriptors. , 2005, Combinatorial chemistry & high throughput screening.

[4]  G. Anderegg,et al.  Critical evaluation of stability constants of metal complexes of complexones for biomedical and environmental applications* (IUPAC Technical Report) , 2005 .

[5]  D. VanDerveer,et al.  Metal-ion-complexing properties of 2-(pyrid-2'-yl)-1,10-phenanthroline, a more preorganized analogue of terpyridyl. A crystallographic, fluorescence, and thermodynamic study. , 2012, Inorganic chemistry.

[6]  D. W. Price,et al.  Metal complexes of cyclen and cyclam derivatives useful for medical applications: a discussion based on thermodynamic stability constants and structural data. , 2007, Dalton transactions.

[7]  Jahan B. Ghasemi,et al.  QSPR Modeling of Stability Constants of the Li-Hemispherands Complexes Using MLR: A Theoretical Host-Guest Study , 2010 .

[8]  I. Tetko,et al.  ISIDA - Platform for Virtual Screening Based on Fragment and Pharmacophoric Descriptors , 2008 .

[9]  S. Cabaniss Quantitative structure-property relationships for predicting metal binding by organic ligands. , 2008, Environmental science & technology.

[10]  A. Yu. Tsivadze,et al.  Structure-property modelling of complex formation of strontium with organic ligands in water , 2006 .

[11]  Gheorghe Duca,et al.  Homogeneous Catalysis with Metal Complexes: Fundamentals and Applications , 2012 .

[12]  A. Varnek,et al.  Computer-aided design of new metal binders , 2008 .

[13]  Estimation of Stability Constants of Copper(II) Chelates with N-alkylated Amino Acids using Topological Indices , 1999 .

[14]  H. Stoeckli-Evans,et al.  Designed Molecules for Self-Assembly: The Controlled Formation of Two Chiral Self-Assembled Polynuclear Species with Predetermined Configuration. , 2001, Angewandte Chemie.

[15]  Ronald L. Bruening,et al.  Thermodynamic and kinetic data for macrocycle interactions with cations and anions , 1991 .

[16]  C. J. Coetzee Determination of formation constants of copper(II) di-carboxylates with a solid state copper(II) ion-selective electrode , 1989 .

[17]  H. Azab,et al.  Ternary complexes of nickel(II) withAMP,ADP andATP as primary ligands and some biologically important polybasic oxygen acids as secondary ligands , 1993 .

[18]  H. Azab,et al.  Metal Ion Complexes Containing Nucleobases and Some Zwitterionic Buffers , 2004 .

[19]  Jahan B. Ghasemi,et al.  Review of the quantitative structure–activity relationship modelling methods on estimation of formation constants of macrocyclic compounds with different guest molecules , 2011 .

[20]  Igor V. Tetko,et al.  Exhaustive QSPR Studies of a Large Diverse Set of Ionic Liquids: How Accurately Can We Predict Melting Points? , 2007, J. Chem. Inf. Model..

[21]  R. M. Smith,et al.  Critical evaluation of stability constants for nucleotide complexes with protons and metal ions and the accompanying enthalpy changes , 1991 .

[22]  Robert D. Hancock,et al.  Approaches to predicting stability constants a critical review , 1997 .

[24]  S. Ibrahim,et al.  Medium Effect and Thermodynamic Studies for the Proton−Ligand and Metal−Ligand Formation Constants of the Ternary Systems MII + Adenosine-5‘-triphosphate (ATP) + Asparagine , 2001 .

[25]  A. Martell,et al.  New multidentate ligands. XIII. Ethylenediaminetetra(methylenephosphonic) acid , 1971 .

[26]  H. Azab,et al.  Ternary Complexes in Solution. Comparison of the Coordination Tendency of Some Biologically Important Zwitterionic Buffers toward the Binary Complexes of Some Transition Metal Ions and Some Amino Acids , 1999 .

[27]  C. Kumar,et al.  Metal-enzyme frameworks: role of metal ions in promoting enzyme self-assembly on α-zirconium(IV) phosphate nanoplates. , 2013, Langmuir : the ACS journal of surfaces and colloids.

[28]  R. Hancock Critical ReviewApproaches to Predicting Stability ConstantsA Critical Review , 1997 .

[29]  H. Zhai,et al.  Prediction of association constants of cesium chelates based on Uniform Design Optimized Support Vector Machine , 2011 .

[30]  Stefano Fontana,et al.  Thermodynamic and structural properties of Gd(III) complexes with polyamino-polycarboxylic ligands: basic compounds for the development of MRI contrast agents , 2000 .

[31]  Joop A. Peters,et al.  Metal binding calixarenes with potential biomimetic and biomedical applications , 2011 .

[32]  F. Kálmán,et al.  Study of thermodynamic and kinetic stability of transition metal and lanthanide complexes of DTPA analogues with a phosphorus acid pendant arm , 2006 .

[33]  Alexandre Varnek,et al.  Stochastic versus Stepwise Strategies for Quantitative Structure-Activity Relationship GenerationHow Much Effort May the Mining for Successful QSAR Models Take? , 2007, J. Chem. Inf. Model..

[34]  Leslie D. Pettit,et al.  The IUPAC stability constants database , 2006 .

[35]  A. Sherry,et al.  Synthesis, potentiometric, kinetic, and NMR Studies of 1,4,7,10-tetraazacyclododecane-1,7-bis(acetic acid)-4,10-bis(methylenephosphonic acid) (DO2A2P) and its complexes with Ca(II), Cu(II), Zn(II) and lanthanide(III) ions. , 2008, Inorganic chemistry.

[36]  Michael A. Malcolm,et al.  Computer methods for mathematical computations , 1977 .

[37]  A. Varnek,et al.  Complexation of Mn2+, Fe2+, Y3+, La3+, Pb2+, and UO22+ with Organic Ligands: QSPR Ensemble Modeling of Stability Constants , 2012 .

[38]  R. M. Izatt,et al.  Thermodynamic and Kinetic Data for Macrocycle Interaction with Cations and Anions , 2010 .

[39]  Arthur E. Martell,et al.  Critical Stability Constants , 2011 .

[40]  Jide Xu,et al.  Rational design of sequestering agents for plutonium and other actinides. , 2003, Chemical reviews.

[41]  A. Toropova,et al.  QSPR Modeling of Complex Stability by Correlation Weighing of the Topological and Chemical Invariants of Molecular Graphs , 2004 .

[42]  Peter Warwick,et al.  Tutorial review. Approaches to predicting stability constants , 1995 .

[43]  Gheorghe Duca,et al.  Homogeneous Catalysis with Metal Complexes , 2012 .

[44]  D. N. Dhar,et al.  Applications of metal complexes of Schiff bases-A review , 2009 .

[45]  Sidney R. Cohen,et al.  Self-Assembly at the Air−Water Interface. In-Situ Preparation of Thin Films of Metal Ion Grid Architectures , 1998 .

[46]  Jahan B. Ghasemi,et al.  QSPR modeling of stability constants of diverse 15-crown-5 ethers complexes using best multiple linear regression , 2008 .

[47]  Paul Heinz Müller,et al.  Tafeln der mathematischen Statistik , 1973 .

[48]  N. Williams,et al.  Control of metal ion size-based selectivity through chelate ring geometry. metal ion complexing properties of 2,2'-biimidazole. , 2010, Inorganic chemistry.

[49]  A. Varnek,et al.  Quantitative Structure–Property Relationship (QSPR) Modeling of Normal Boiling Point Temperature and Composition of Binary Azeotropes , 2011 .

[50]  A. Gemant,et al.  Metal Ions in Biological Systems , 2018 .

[51]  A. Toropova,et al.  QSPR Modeling of Stability of Complexes of Adenosine Phosphate Derivatives with Metals Absent from the Complexes of the Teaching Access , 2001 .

[52]  C. Lawson,et al.  Solving least squares problems , 1976, Classics in applied mathematics.

[53]  A. Gergely,et al.  Critical survey of the stability constants of complexes of aliphatic amino acids (Technical Report) , 1993 .

[54]  R. M. Izatt,et al.  Handbook of metal ligand heats and related thermodynamic quantities , 1970 .

[55]  A. Toropova,et al.  QSPR Modeling of Complex Stability by Optimization of Correlation Weights of the Hydrogen Bond Index and the Local Graph Invariants , 2002 .

[56]  Abeer E. Attia,et al.  Potentiometric studies on the formation equilibria of binary and ternary complexes of some metal ions with dipicolinic acid and amino acids , 2000 .

[57]  Arthur E. Martell,et al.  Ligand design for selective complexation of metal ions in aqueous solution , 1989 .

[58]  G. Arena,et al.  Thermodynamic and spectroscopic properties of mixed complexes in aqueous solution. Copper(II) complexes of 2,2′-bipyridyl and dicarboxylic acids , 1978 .

[59]  E. M. Khairy,et al.  Ternary complexes involving copper(II) and amino acids, peptides and DNA constituents. The kinetics of hydrolysis of α-amino acid esters , 2002 .

[60]  H. Sigel,et al.  Acid-base and metal-ion-binding properties of 9-[2-(2-phosphonoethoxy)ethyl]adenine (PEEA), a relative of the antiviral nucleotide analogue 9-[2-(phosphonomethoxy)ethyl]adenine (PMEA). An exercise on the quantification of isomeric complex equilibria in solution. , 2005, Inorganic chemistry.

[61]  M. Ahmadvand,et al.  Simultaneous estimation of stability constants of Mg, Ba, Ca, and Sr complexes using a small subset of molecular descriptors , 2011 .

[62]  R. Mewis,et al.  Biomedical applications of macrocyclic ligand complexes , 2010 .

[63]  G. Anderegg,et al.  CRITICAL EVALUATION OF STABILITY CONSTANTS OF METAL COMPLEXES OF COMPLEXONES FOR BIOMEDICAL AND ENVIRONMENTAL APPLICATIONS , 2005 .

[64]  J. Vanbriesen,et al.  Biogeochemistry of chelating agents , 2005 .

[65]  Jahan B. Ghasemi,et al.  A quantitative structure–property relationships study of the stability constant of crown ethers by molecular modelling: new descriptors for lariat effect , 2011 .

[66]  S. Sammartano,et al.  Weak alkali and alkaline earth metal complexes of low molecular weight ligands in aqueous solution , 2008 .

[67]  A. Varnek,et al.  Quantitative Structure—Property Relationships in Solvent Extraction and Complexation of Metals , 2010 .

[68]  R. Hancock,et al.  Stability of ammonia complexes that are unstable to hydrolysis in water , 1985 .

[69]  Alexandre Varnek,et al.  Modeling of Ion Complexation and Extraction Using Substructural Molecular Fragments , 2000, J. Chem. Inf. Comput. Sci..

[70]  A. Varnek,et al.  Stability constants of complexes of Zn2+, Cd2+, and Hg2+ with organic ligands: QSPR consensus modeling and design of new metal binders , 2012, Journal of Inclusion Phenomena and Macrocyclic Chemistry.

[71]  Charles L. Lawson,et al.  Solving least squares problems , 1976, Classics in applied mathematics.

[72]  Meyer,et al.  Comprehensive Coordination Chemistry II Volume 832 || Nickel , 2004 .

[73]  Alexandre Varnek,et al.  New Approach for Accurate QSPR Modeling of Metal Complexation: Application to Stability Constants of Complexes of Lanthanide Ions Ln 3+ , Ag + , Zn 2+ , Cd 2+ and Hg 2+ with Organic Ligands in Water , 2012 .

[74]  A. Varnek,et al.  Structure—property modeling of metal binders using molecular fragments , 2004 .

[75]  M. Karelson,et al.  QSPR Modelling of Lanthanide‐Organic Complex Stability Constants , 2006 .

[76]  M. Khalil,et al.  Binary and ternary complexes of inosine. , 1998, Talanta.

[77]  N. Williams,et al.  Metal ion complexing properties of the highly preorganized ligand 2,9-bis(hydroxymethyl)-1,10-phenanthroline: a crystallographic and thermodynamic study. , 2008, Inorganic chemistry.

[78]  L. Pettit,et al.  Complex formation and stereoselectivity in the ternary systems copper(II)–D/L-histidine–L-amino-acids , 1977 .

[79]  A. Fazary,et al.  Potentiometric Studies on Binary and Ternary Complexes of Di- and Trivalent Metal Ions Involving Some Hydroxamic Acids, Amino Acids, and Nucleic Acid Components , 2004 .

[80]  K. Rissanen,et al.  Two‐Level Self‐Organisation of Arrays of [2×2] Grid‐Type Tetranuclear Metal Complexes by Hydrogen Bonding , 2001 .

[81]  Igor V. Tetko,et al.  Benchmarking of Linear and Nonlinear Approaches for Quantitative Structure-Property Relationship Studies of Metal Complexation with Ionophores , 2006, J. Chem. Inf. Model..

[82]  J. Hardy Metallosupramolecular Grid Complexes: Towards Nanostructured Materials with High-Tech Applications , 2013 .

[83]  R. Hancock,et al.  Factors affecting stabilities of chelate, macrocyclic and macrobicyclic complexes in solution , 1994 .

[84]  S. Ahmadi Application of GA-MLR method in QSPR modeling of stability constants of diverse 15-crown-5 complexes with sodium cation , 2012, Journal of Inclusion Phenomena and Macrocyclic Chemistry.

[85]  N. Raos,et al.  Estimation of Stability Constants of Coordination Compounds using Models Based on Topological Indices , 2009, Arhiv za higijenu rada i toksikologiju.

[86]  A. Mousavi Predicting Mercury(II) Binding by Organic Ligands: A Chemical Model of Therapeutic and Environmental Interests , 2011 .

[87]  Hans-Jörg Schneider,et al.  Binding mechanisms in supramolecular complexes. , 2009, Angewandte Chemie.

[88]  B. Prijs,et al.  Ternary complexes in solution. The stability increasing effect of the imidazole group on the formation of mixed Cu2+ complexes. , 1969, European journal of biochemistry.

[89]  G. J. Leigh Comprehensive coordination chemistry II From Biology to Nanotechnology , 2004 .

[90]  Jahan B. Ghasemi,et al.  QSPR probing of Na+ complexation with 15-crown-5 ethers derivatives using artificial neural network and multiple linear regression , 2012, Journal of Inclusion Phenomena and Macrocyclic Chemistry.

[91]  L. Pettit,et al.  Complex formation between unsaturated α-aminoacids and silver(I) and some divalent transition metal ions , 1975 .

[92]  F. Fülöp,et al.  Copper(II)-binding ability of stereoisomeric cis- and trans-2-aminocyclohexanecarboxylic acid-L-phenylalanine dipeptides. A combined CW/pulsed EPR and DFT study. , 2012, Inorganic chemistry.