Interaction studies of cysteine with Li+, Na+, K+, Be2+, Mg2+, and Ca2+ metal cation complexes

The coordination geometries, electronic features, metal ion affinities, entropies, and the energetics of Li⁺, Na⁺, K⁺, Be²⁺, Mg²⁺, and Ca²⁺ metal cations with different possible conformations of cysteine complexes were studied. The complexes were optimized using density functional theory (B3LYP) and second order Moller–Plesset Perturbation (MP2) theory methods using 6‐311 + +G** basis set. The interactions of the metal cations at different nucleophilic sites of cysteine conformations were considered after a careful selection among several binding sites. All the metal cations coordinate with cysteine in a tridentate manner and also the most preferred position for the interaction. It is found that, the overall structural parameters of cysteine are not altered by metal ion substitution, but, the metal ion‐binding site has undergone a noticeable change. All the complexes were characterized by an electrostatic interaction between ligand and metal ions that appears slightly more pronounced for lithium and beryllium metal complexes. The metal ion affinity (MIA) and basis set superposition error (BSSE) corrected interaction energy were also computed for all the complexes. The effect of metal cations on the infrared (IR) stretching vibrational modes of amino N? H bond, side chain thiol group S? H bond, hydroxyl O? H bond, and Carbonyl C?O bond in cysteine molecules have also been studied. The nature of the metal ion‐ligand bond and the coordination properties were examined using natural bond order (NBO) at bond critical point (electron density and their Laplacian of electron density) through Atoms in Molecules (AIM) analyses. Copyright © 2010 John Wiley & Sons, Ltd.     

Investigation of the π–π stacking interactions without direct electrostatic effects of substituents: the aromatic∥aromatic and aromatic∥anti-aromatic complexes

Stability of the π–π stacking interactions in the ben∥substituted-ben and ben∥substituted-COT complexes was studied using the computational quantum chemistry methods (where ben and COT are benzene and cyclooctatetraene, ∥ denotes π–π stacking interaction, substituted-ben and substituted-COT are benzene and cyclooctatetraene which substituted with four ethynyl-X groups, respectively, and X = OH, CH₃, H, F, CF₃, CN and NO₂). In these complexes electron-withdrawing substituents lead to larger binding energies and electron-donating ones lead to weaker interactions compared to X = H. There are meaningful correlations between the Hammett constants and binding energies. The atoms in molecules (AIM) analysis shows that formation of these complexes is accompanied by increase in the electron charge densities at the ring critical points of the substituted-ben and substituted-COT rings which leads to increase/decrease of the π–π stacking interactions in the ben∥substituted-ben/ben∥substituted-COT complexes. The charge transfer occurs from benzene to substituted-ben in the ben∥substituted-ben complexes and from substituted-COT to benzene (with the exception of X = CN) in the ben∥substituted-COT ones. Nuclear magnetic resonance calculations demonstrate that interactions of the more aromatic substituted-ben/less anti-aromatic substituted-COT rings with benzene in the ben∥substituted-ben/ben∥substituted-COT complexes can be helpful to enhance strength of the π–π stacking interactions. Thus, regardless of ring size, the π–π stacking interaction is an aromatic–aromatic interaction and π electron cloud properties of interacting rings affect on the strength of this interaction.     

Effects of interaction between the chelate rings and π‐conjugated systems in fused salphen complexes on UV‐Vis‐NIR spectra

Dinuclear (Zn₂, Ni₂, and NiZn) complexes of fused salphen with acene‐type annelation were synthesized from 3,7‐diformyl‐2,6‐dihydroxynaphthalene. The spectroscopic properties of these complexes were compared with those of their constitutional isomers with phene‐type annelation. The acene‐type complexes exhibited a characteristic absorption band in the near‐infrared region that showed a noticeable solvent effect. Time‐dependent density functional theory calculations suggested that the absorption arose from a π → π* transition localized at the naphthalene ring, which was perturbed by the adjoining chelate rings. Effects of the connection topology in the fused salphen complexes are discussed by comparison with those of polycyclic aromatic hydrocarbons.     

Recognition of aromatic amino acids and proteins with p‐sulfonatocalix[4]arene – A luminescence and theoretical approach

The host–guest interaction of p‐sulfonatocalix[4]arene (p‐SC4) with aromatic amino acids (AAs) and two proteins has been studied using UV–Vis absorption, fluorescence, and theoretical methods. Spectral studies supported by binding constant and calculated binding energy (BE) values show that p‐SC4 binds more strongly with tyrosine compared with other AAs. The application of Bader's theory of atoms in molecule shows the involvement of various types of noncovalent interactions in the formation of the host–guest complexes. Both tyrosine and histidine have strong electrostatic interaction with the sulfonato group and other two AAs have dominant π?π interaction with the aromatic rings of calixarene. In addition, the role of C?H···O, C?H···π and lone pair···π (lp···π) interactions in the stabilization of p‐SC4‐AA complexes has also been realized from the atoms in molecule analysis. The electron density at the bond critical points varies with the calculated BEs and trend in BEs is in good agreement with the experimental binding constant values. The work has been extended to the binding of p‐SC4 with proteins, bovine serum albumin and ovalbumin. Ovalbumin exhibits stronger binding with p‐SC4 than bovine serum albumin. Copyright © 2012 John Wiley & Sons, Ltd.     

Mutual influence between triel bond and cation–π interactions: an ab initio study

Using ab initio calculations, the cooperative and solvent effects on cation–π and B···N interactions are studied in some model ternary complexes, where these interactions coexist. The nature of the interactions and the mechanism of cooperativity are investigated by means of quantum theory of atoms in molecules (QTAIM), noncovalent interaction (NCI) index and natural bond orbital analysis. The results indicate that all cation–π and B···N binding distances in the ternary complexes are shorter than those of corresponding binary systems. The QTAIM analysis reveals that ternary complexes have higher electron density at their bond critical points relative to the corresponding binary complexes. In addition, according to the QTAIM analysis, the formation of cation–π interaction increases covalency of B···N bonds. The NCI analysis indicates that the cooperative effects in the ternary complexes make a shift in the location of the spike associated with each interaction, which can be regarded as an evidence for the reinforcement of both cation–π and B···N interactions in these systems. Solvent effects on the cooperativity of cation–π and B···N interactions are also investigated.     

Interaction of cations with 2′‐deoxythymidine nucleoside and analysis of the nature and strength of cation bonds

Binding of Mg²⁺, Ca²⁺, Zn²⁺, and Cu⁺ metal ions with 2′‐deoxythymidine (dT) nucleoside was studied using a density functional theory method and a 6‐311++G(d,p) basis set. This work demonstrated that the interaction of dT with these cations is tri‐coordinated η (O2, O4′, O5′). Among the four types of cations, Zn²⁺ cation exhibited the most tendency to interact with the dT. Cations via their interaction with dT can affect the N‐glycosidic bond length, the values of pseudorotation of the sugar ring, the orientation of the base unit with respect to the sugar ring, and the acidity of the O5′H, O3′H, and N3H groups in the dT nucleoside. Natural bond orbital analysis was performed to calculate the charge transfer and natural population analysis of the complexes. Quantum theory of atoms in molecules was also applied to determine the nature of interactions. It was shown that in dT–Mg²⁺ and dT–Ca²⁺ complexes, the bonds are electrostatic (closed‐shell) interactions, although they are partially covalent and partially electrostatic interactions in dT–Zn²⁺ and dT–Cu⁺ complexes. Copyright © 2011 John Wiley & Sons, Ltd.     

Oxidized metabolites from cyclopenta‐fused polycyclic aromatic hydrocarbons (CP‐PAHs). A DFT model study of their carbocations formed by epoxide ring opening

A density functional theory (DFT) study aimed at understanding structure–reactivity relationships in the oxidized metabolites of cyclopenta‐fused polycyclic aromatic hydrocarbons (CP‐PAHs) is reported. Epoxidation at various positions was examined in order to identify the most stable epoxide in each class of CP‐PAHs. Relative energies of the carbocations resulting from O‐protonation and epoxide ring opening were analyzed and compared, taking into account the available biological activity data on these compounds. Geometrical, electronic, and conformational issues were considered. Charge delocalization modes in the resulting carbocations were deduced via the natural population analysis (NPA)‐derived changes in charges. Computational results pointed to the importance of the unsaturated cyclopenta ring on the reactivity of these compounds. The reported bioactivity of this highly mutagenic/carcinogenic family of PAHs was observed to parallel their relative carbocation stabilities. A different behavior was observed in crowded non‐planar structures possessing a distorted aromatic system. A covalent adduct formed between a CP‐PAH epoxide and a purine base was computed inside a DNA fragment employing the ONIOM method. Copyright © 2010 John Wiley & Sons, Ltd.     

Modelling the interaction in a benzene dimer

The interaction between aromatic rings is a fundamental problem in material science and biochemistry. These interactions are generally found to stabilise protein molecules and the double helical structure of DNA, and they also play an important role in the recognition processes in biological and non-biological systems. However, the complexity and variety in the structures and components of aromatic compounds are major obstacles to investigating their interactions. In this study, the simplest case of aromatic interactions, which is the interaction between two benzene rings, is modelled using a continuous approximation. Assuming a constant atomic surface density and modelling the structure of a benzene molecule as a combination of two rings, namely an inner carbon ring and an outer hydrogen ring, the van der Waals interaction between any two benzene rings can be obtained as the sum of four interactions. The major result obtained here is an analytical expression for the potential energy which can then be used to predict equilibrium configurations for two interacting benzene molecules. Moreover, we find that at sufficiently large distances between the two benzene molecules, the orientational angle φ at which the interaction energy is a minimum can be approximated by the arctan of the ratio of two separation distances in two mutually perpendicular directions.     

Interaction of water‐soluble triphenylphosphines with β‐cyclodextrin: a quantum chemistry study

The interaction of β‐cyclodextrin (β‐CD) with meta‐trisulfonated triphenylphosphine derivatives bearing one or two methyl (or methoxy) groups on the aromatic rings has been investigated by PM3 calculations. The results show that phosphine molecules interact with β‐CD having either an unsubstituted sulfophenyl group or a substituted sulfophenyl group at the para and/or meta‐position. The presence of one methyl or methoxy group in the ortho‐position on each aromatic ring prevents the formation of an inclusion complex between meta‐trisulfonated triphenylphosphine derivatives and β‐CD. The deeply included phosphines in the β‐CD cavity show significant van der Waals interactions with β‐CD. These interactions are at the origin of the high association constants between these molecules and β‐CD. Phosphines exhibiting small association constants interact with β‐CD by forming H‐bonds and weak (or null) van der Waals interactions. Copyright © 2011 John Wiley & Sons, Ltd.     

Density functional theory study of the bis‐3‐benzo‐crown ethers and their complexes with alkali metal cations Na+, K+, Rb+ and Cs+

The binding interactions of bis‐3‐benzo‐15‐crown‐5 ethers and bis‐3‐benzo‐18‐crown‐6 ethers (neutral hosts) with a series of alkali metal cations Na⁺, K⁺, Rb⁺ and Cs⁺ (charged guests) were investigated using quantum chemical density functional theory. Different optimized structures, binding energies and various thermodynamic parameters of free crown ethers and their metal cation complexes were obtained based on the Becke, three‐parameter, Lee–Yang–Parr functional using mixed basis set (C, H, O, Na⁺ and K⁺ using 6‐31 g, and the heavier cation Rb⁺ and Cs⁺ using effective core potentials). Natural bond orbital analysis is conducted on the optimized geometric structures. The main types of driving force host–guest interactions are investigated. The electron donating O offers a lone pair of electrons to the contacting LP* (1‐center valence antibond lone pair) orbitals of metal cations. The bis‐3‐benzocrown ethers are assumed to have sandwich‐like conformations, considering the binding energies to gauge the exact interactions with alkali cations. It is found that there are two different types of complexes: one is a tight ion pair and the other is a separated ion pair. Copyright © 2011 John Wiley & Sons, Ltd.     

Vibrational spectra and potential energy distributions for 1‐benzyl‐1H‐imidazole by normal coordinate analysis

The Fourier‐transform (FT) Raman and infrared (IR) spectra of the crystallized novel pharmaceutical molecule 1‐benzyl‐1H‐imidazole (BI) were recorded and analyzed. The geometry, intermolecular hydrogen bond, and harmonic vibrational wavenumbers of BI were investigated with the help of B3PW91 density functional theory (DFT) methods. The detailed interpretation of the vibrational spectra was carried out with the aid of normal coordinate analysis (NCA) following the scaled quantum mechanical force field methodology (SQMFF). The aromaticities of the imidazole and phenyl rings were studied using the standard harmonic oscillator model of aromaticity (HOMA) index. Natural bond orbital (NBO) analysis on BI was carried out to demonstrate the various intramolecular interactions that are responsible for the stabilization of this molecule leading to its medicinal activity. The potential energy profile corresponding to the torsion around the bridge bonds connecting the two rings was drawn to explain the steric and/or electronic effects using potential energy surface (PES) scan studies. The pronounced double‐bond localization in the imidazole ring upon intermolecular H‐bonding appears to be the cause for its enhanced aromaticity. Copyright © 2008 John Wiley & Sons, Ltd.     

Theoretical prediction of size‐expansion effect on the C8‐site activity in the modified guanine‐cytosine analogs

Homo/hetero ring‐expanded DNA analogs have been shown to be rationally modified DNA motifs with improved physical or biological properties. In this work, using density functional theory, the stability of these artificial DNA base pairs was examined with regard to three aspects associated with DNA damage, namely deprotonation, H‐abstraction, and H‐radical addition. The effect of size expansion on C8 activity was investigated because C8‐oxidative guanine (G) is one of the most important products of DNA damage. Computational results indicate that the insertion of an aromatic spacer ring in G considerably decreases the electron density over the C8 site, leading to easier deprotonation or H‐abstraction from the C8 site and more difficult H ^. ‐radical attack on the C8 site. However, the opposite phenomenon is observed if the spacer ring is antiaromatic, because of the increased electron density over the C8 site. Moreover, these effects are more prominent the larger the aromaticity or antiaromaticity of the spacer ring. Further analyses, using natural bond orbitals (NBOs) and the nucleus‐independent chemical shift (NICS) index of aromaticity, indicate that the changes of the electron distribution over the C8 site arise because the aromatic spacer ring, involved in the conjugation structure, increases the electron delocalization from the electron‐rich imidazole ring to the diatropic six‐membered rings, while the antiaromatic spacer ring acts as an electron‐donating group, not only inhibiting the above electron delocalization, but also slightly increasing the electron density over the C8 site. The improved stability of these size‐expanded base pairs in different DNA‐damaged environments may encourage their use in practical applications. Copyright © 2009 John Wiley & Sons, Ltd.     

The study on interactions between 1‐ethyl‐3‐methylimidazolium chloride and benzene/pyridine /pyrrole/thiophene

The density functional theory was used to investigate the interactions between 1‐ethyl‐3‐methylimidazolium chloride ([EMIM]Cl) and benzene/pyridine/pyrrole/thiophene. The complexes formed between [EMIM]Cl and benzene/pyridine/pyrrole/thiophene were optimized at the ωB97XD/6‐31++G** level, and the optimized complexes were further analyzed by natural bond orbital, atoms in molecules, and noncovalent interaction. The calculated results show that the interaction energy between ionic liquid and benzene/pyridine/pyrrole/thiophene is in the order pyrrole > pyridine > thiophene > benzene. The major interactions between ionic liquid and benzene/pyridine/pyrrole/thiophene are hydrogen bonding and π‐π interaction, accompanied by C···H, N···H, H···H, and S···H weak interactions. Both cation and anion of ionic liquid are involved in interactions with aromatic compounds.     

Design and interaction mechanism of ligand targeted with folate receptor α and β

Four compounds 1 to 4 (folic acid, methotrexate and 2 dyes) were used to interact with folate receptor (FR)α and FRβ. The interaction structures and binding energies of the bound complexes were investigated. In order to analyze the differences between FRα and FRβ complexes, the details of the weak intermolecular interactions were analyzed, and the frontier orbital properties of the FR complexes were studied by a dispersion complemented density functional tight‐binding method. By comparing the different interaction properties of the 4 compounds with FRα and FRβ, the basic strategies for design of novel compound targeted with FR subtype were suggested. Further, a novel compound with high selectively with FRα based on compound 3 was designed to illustrate our conclusion. These data should be helpful for the design of novel molecules with extreme discerningly with FRα and FRβ.     

Cation sitting in aromatic cages: ab initio computational studies on tetramethylammonium–(benzene)n (n=3–4) complexes

Quantum chemistry study was performed on interaction between tetramethylammonium (TMA) and aromatic cages by means of the MP2 method to show how TMA sits in an aromatic cage that is composed of benzenes. The MP2 calculations on TMA–(benzene)_n complexes demonstrate that the more the benzene molecules in the aromatic cage, the stronger the binding strength between the cage and TMA. In details, the structure of TMA–(benzene)_n (n = 1–4) complexes can be easily constructed by superimposing n TMA‐benzene complexes via TMA, and the binding energies of the TMA–(benzene)_n complexes are the sum of the n corresponding TMA‐benzene systems. For instance, the distances between the N of TMA and the plane of the benzene ring are 4.238, 4.252, 4.264 ,and 4.276 Å, respectively, for TMA–(benzene)_n (n = 1–4) complexes, and the BSSE corrected binding energies at MP2/6‐311++G** level are ?8.8, ?17.3, ?25.8 and ?34.3 kcal/mol, respectively, for TMA– (benzene)_n (n = 1–4) complexes. Thus, this study provides us useful information on how a cation interacts with an aromatic cage in terms of complex geometry and binding strength. Copyright © 2007 John Wiley & Sons, Ltd.     

A Study on Spectro-Analytical Aspects,DNA – Interaction,Photo-Cleavage,Radical Scavenging,Cytotoxic Activities,Antibacterial and Docking Properties of 3 – (1 – (6 – methoxybenzo [d] thiazol – 2 – ylimino) ethyl) – 6 – methyl – 3H – pyran - 2, 4 – dione and its Metal Complexes

The focus of the present work is on the design, synthesis, characterization, DNA-interaction, photo-cleavage, radical scavenging, in-vitro cytotoxicity, antimicrobial, docking and kinetic studies of Cu (II), Cd (II), Ce (IV) and Zr (IV) metal complexes of an imine derivative, 3 – (1 – (6 – methoxybenzo [d] thiazol – 2 – ylimino) ethyl) – 6 – methyl – 3H – pyran – 2, 4 – dione. The investigation of metal ligand interactions for the determination of composition of metal complexes, corresponding kinetic studies and antioxidant activity in solution was carried out by spectrophotometric methods. The synthesized metal complexes were characterized by EDX analysis, Mass, IR, ¹H-NMR, ¹³C-NMR and UV–Visible spectra. DNA binding studies of metal complexes with Calf thymus (CT) DNA were carried out at room temperature by employing UV-Vis electron absorption, fluorescence emission and viscosity measurement techniques. The results revealed that these complexes interact with DNA through intercalation. The results of in vitro antibacterial studies showed the enhanced activity of chelating agent in metal chelated form and thus inferring scope for further development of new therapeutic drugs. Cell viability experiments indicated that all complexes showed significant dose dependent cytotoxicity in selected cell lines. The molecular modeling and docking studies were carried out with energy minimized structures of metal complexes to identify the receptor to metal interactions.     

TDDFT study on the excited‐state hydrogen bonding of N‐(2‐hydroxyethyl)‐1,8‐naphthalimide and N‐(3‐hydroxyethyl)‐1,8‐naphthalimide in methanol solution

The time‐dependent density functional theory method was performed to investigate the excited‐state hydrogen‐bonding dynamics of N‐(2‐hydroxyethyl)‐1,8‐naphthalimide (2a) and N‐(3‐hydroxyethyl)‐1,8‐naphthalimide (3a) in methanol (meoh) solution. The ground and excited‐state geometry optimizations, electronic excitation energies, and corresponding oscillation strengths of the low‐lying electronically excited states for the complexes 2a + 2meoh and 3a + 2meoh as well as their monomers 2a and 3a were calculated by density functional theory and time‐dependent density functional theory methods, respectively. We demonstrated that the three intermolecular hydrogen bonds of 2a + 2meoh and 3a + 2meoh are strengthened after excitation to the S₁ state, and thus induce electronic spectral redshift. Moreover, the electronic excitation energies of the hydrogen‐bonded complexes in S₁ state are correspondingly decreased compared with those of their corresponding monomer 2a and 3a. In addition, the intramolecular charge transfer of the S₁ state for complexes 2a + 2meoh and 3a + 2meoh were theoretically investigated by analysis of molecular orbital. Copyright © 2014 John Wiley & Sons, Ltd.     

The geometry and electronic structure of Aristolochic acid: possible implications for a frozen resonance

Molecular mutagens and carcinogens are structures which carry chemical and electronic properties that disturb and interact with the genomic machinery. Principally, a rule of thumb for carcinogens is that carcinogens are expected to introduce covalent irreversible bonding to one or several types of DNA bases, causing errors in the reading frame for the polymerases. 8‐methoxy‐6‐nitrophenanthro[3,4‐d][1,3]dioxole‐5‐carboxylic acid, better known as Aristolochic acid (AA1) is a recognized carcinogen which causes urotherial cancer and is found in certain plants. Its structure is particularly interesting given that it is closely related to phenanthrene in its polycyclic arrangement, and has four functional groups, a carboxyl‐, a nitro‐, a methoxy‐ and a dioxolane group. In this work, the structure of AA1 has been resolved at the MPWPW91 density functional theory method in combination with Aug‐cc‐pVDZ basis sets. A geometry analysis shows that in AA1 the carboxyl group's torsion is caused by steric strain from the nitro group, which elevates the molecular plane of the first phenanthrene ring with 0.1Å. The wavefunction analysis of AA1 shows that the ring deformation enhances a double π‐bond localization in the first ring, adjacent to the dioxalane group, and results in a decrease of ring aromaticity and induces a potentially frozen resonance. Intermolecular and intramolecular interactions were characterized by atoms in molecules and reduced density gradient analysis. This study brings novel information on the geometry and electronic structure of AA1, which are important for the further knowledge of its transformation in vivo and in situ. Copyright © 2013 John Wiley & Sons, Ltd.     

Silver‐capped silicon nanopillar platforms for adsorption studies of folic acid using surface enhanced Raman spectroscopy and density functional theory

The study of the interactions of folic acid (FA) with surface enhanced Raman scattering substrates is relevant for understanding its adsorption mechanism and for fabricating analytical devices for detection of malignant cells over‐expressing folate receptors. This paper presents a study of the adsorption of FA on silver‐capped silicon nanopillar substrates employing surface enhanced Raman scattering spectroscopy and density functional theory calculations. The experimentally observed vibrations from free FA and FA bound to the Ag surface display different vibrational spectra indicating chemical interaction of the molecule with the metal surface. Density functional theory calculations show that the Ag–FA interaction is primarily through the nitrogen from the pteridine ring anchoring to the Ag metal surface. To investigate the Ag–FA binding behavior further, the adsorption isotherm of FA on the silver‐capped silicon nanopillar surface is estimated. The results show a positive cooperative Ag–FA binding mechanism. That is, adsorbed FA increases the affinity of new incoming FA molecules. Copyright © 2015 John Wiley & Sons, Ltd.     

Raman,FT‐IR,and DFT studies of 3,5‐pyrazoledicarboxylic acid and its Ce(III) and Nd(III) complexes

3,5‐Pyrazoledicarboxylic acid was used as a ligand for the synthesis of its Ce(III) and Nd(III) complexes. The complexes of Ce(III) and Nd(III) with 3,5‐pyrazoledicarboxylic acid were synthesized and their compositions were determined by elemental analysis. Vibrational study in the solid state of 3,5‐pyrazoledicarboxylic acid and its new Ce(III) and Nd(III) complexes was performed by IR and Raman spectroscopy. The changes observed between the IR and Raman spectra of the ligand and of the complexes allowed us to establish the coordination mode of the metal in both complexes. The comparative vibrational analysis of the free ligand and its lanthanide(III) complexes gave evidence that 3,5‐pyrazoledicarboxylic acid binds Ln(III) through the deprotonated carboxylic oxygens. The density functional theory (DFT) calculated geometries, harmonic vibrational modes and Raman scattering activities of the ligand were in good agreement with the experimental data, and a complete vibrational assignment is being proposed. The experimental IR and Raman bands of the ligand were assigned to normal modes on the basis of DFT calculations. The effect of the intramolecular hydrogen bonds in the ligand on vibrational mode positions is also discussed. The characteristic IR and Raman bands of 3,5‐pyrazoledicarboxylic acid and its lanthanide complexes were specified and discussed. Copyright © 2006 John Wiley & Sons, Ltd.