Cations of halogenated methanes: adiabatic ionization energies, potential energy surfaces, and ion fragment appearance energies

The DFT-B3LYP and G3X model chemistry were used to predict the cation structures and energetics of fluorinated, chlorinated, and brominated methanes. Ion–complex structures between methylene cations and HX (X = F, Cl, Br) were found for all H-containing cations, and [CHF–FH]⁺, [CF₂–FH]⁺, [CCl₂–ClH]⁺, and [CCl₂–FH]⁺ structures are more stable than their normal tetravalent structures. Several cations should also be better described as ion–complex structures between methyl cations and halogen atoms, e.g., [CF₃–Br]⁺. Transition states connecting normal and ion–complex structures were also located, and potential energy diagrams were constructed for decomposition of methane cations and to predict the fragmentation pathways. The G3X energies were used to predict the adiabatic ionization energies (IE_as) and ion fragment appearance energies (AEs) from methanes. Many of the experimental AEs correspond to the energies of transition states instead of the thermodynamic dissociation limits. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

On the metal ion selectivity of PNP-lariat ether—an insight from density functional theory calculations

The complexes of Li⁺, Na⁺, K⁺, Be²⁺, Mg²⁺, and Ca²⁺ metal cations with [N₃P₃R₄O(CH₂CH₂O)₄] (R?=?H(1), NMe₂(2), NC(NMe₂)₂(3)) PNP-lariat ethers were systematically studied in the gas phase by using density functional theory (DFT) B3LYP-D3/6-311+G(3df,2p)//B3LYP/6-31+G(d,p) method. The gas phase cation affinities were calculated to span the wide range between 64.2 and 496.1 kcal mol^?1 in order K⁺?<?Na⁺?<?Li⁺?<?Ca²⁺?<?Mg²⁺?<?Be²⁺. The structural and electronic properties of 1–3 and their complexes were investigated and effects of electron-donor substituents were analyzed. The electron-donor substituents were found to promote the cation affinity. Sidearm coordinative interaction with the crown ether-complexed metal ion has been noticed. The nature of the metal–ligand interactions was investigated using Bader’s Quantum theory of atoms in molecule. It has been found that the Be²⁺–N bonds are partly covalent in nature while other coordinate bonds are of the electrostatic nature. The electron density at the bond critical points was found to be consistent with cation affinity. Natural bond orbital analysis was performed on the optimized geometries. The results showed that the stabilization interaction energies are caused by the donation of O/N lone pair electrons to the LP* orbitals of the metal cations. The amount of charge transfer follows the cation affinity order. The largest charge transfer and associated second-order perturbation stabilization energy were observed for Be²⁺ complexes.

     

ELECTRON SPIN RESONANCE OR Pd(I). III: The Nature of the Metal-ligand Bonds in Square Planar Complexes of Palladium(I)

Abstract

ESR spectra for a variety of palladium(I) complexes produced in the powders and the frozen solutions of palladium(II) complexes by γ -ray irradiation have been interpreted in terms of the nature of the metal-ligand bonds. It has been found that the covalency for the palladium-ligand σ-bond increases in the order of Pd[sbnd]O, Pd[sbnd]Cl < Pd[sbnd]N < Pd[sbnd]S, Pd[sbnd]C, and that the nature of the metal-ligand bond in palladium(I) complexes is very similar to that in copper(II) complexes. The ratio of the magnitude of the ligand field splitting for palladium(I) complex to that for the copper(II) complex with the same ligand has been estimated from the comparison of their g values.     

Investigation of structural and biological properties of N-heterocyclic carbene silver(I) and palladium(II) complexes

abstract

Computational investigations were done on bis(1-allyl-3-benzyl-2,3-dihydro-1H-benzo[d]imidazol-2-yl)silver(I), bis(1-benzyl-3-butyl-2,3-dihydro-1H-benzo[d]imidazol-2-yl)silver(I), bis(1-allyl-3-benzyl-2,3-dihydro-1H-benzo[d]imidazol-2-yl)dibromidepalladium(II), and bis(1-benzyl-3-butyl-2,3-dihydro-1H-benzo[d]imidazol-2-yl)dibromidepalladium(II) complexes. Related complexes were optimized at different six calculation levels which are HF/6-31G(LANL2DZ), HF/6-31G(d,p)(LANL2DZ), B3LYP/6-31G(LANL2DZ), B3LYP/6-31G(d,p)(LANL2DZ), M062X/6-31G(LANL2DZ) and M062X/6-31G(d,p)(LANL2DZ) levels in vacuo. IR and NMR spectrum are calculated and examined in detail. Energy diagram of molecular orbitals, contour diagram of frontier molecular orbitals, molecular electrostatic potential maps and the harmonic surface of related molecules are examined in detail. Finally, interactions between mentioned complexes and related proteins (1BNA, 1JNX, and 2ING) are investigated in detail. As a result, it is found that biological and anti-cancer properties of silver N-heterocyclic carbene complexes are higher than those of palladium complexes.     

Quantum chemical analysis of possible fragmentation of [M + H]<Superscript>+</Superscript> and [M + Na]<Superscript>+</Superscript> complexes of monosubstituted methane,cyclohexane, and benzene derivatives in mass spectrometric studies

The formation and fragmentation energies of the proton and sodium cation complexes with monosubstituted methane, cyclohexane, and benzene derivatives in which carbon atoms are bonded to substituents (NH₂, OH, F, Cl, Br, ONO₂, NO₂, COOH, CN, and Ph) were calculated by the B3LYP/6-31G(d) method. For [M + Na]⁺ complexes, the formation energies are much lower (and differ from one another to a much lesser extent), while the dissociation energies are much higher, than the corresponding energies of the [M + H]⁺ complexes. Na⁺ cation shows a lower selectivity toward localization at functional groups in molecules compared to H⁺. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 2, pp. 246–249, February, 2008.     

Solvation of Metal Cations in Non-aqueous Liquids

The role that alkali cations in non-aqueous solvents play in organic reactions continues to be a topic of interest. In particular it has been observed that these cations can alter the stereoselectivity of organic reactions. Our interest is to first understand the nature of cation–ether complexes, then to investigate the role that the cation plays in the reaction. We have used the electronic structure techniques Hartree-Fock (HF), Second-order Møller-Plesset perturbation theory (MP2), and the Becke three-parameter exchange functional coupled with the nonlocal correlation functional of Lee, Yang, and Parr (B3LYP) to study the structure and properties of tetrahydrofuran (THF) and dimethyl ether (DME) solvation complexes with Li⁺, Na⁺, K⁺, Cu⁺, and MgCl⁺. The values calculated for DME complexes were compared with existing experimentally determined data. The B3LYP/6-31⁺G^? model chemistry was found to be the most accurate and efficient method of modeling the cation–DME molecular system. The energetic trends observed in the DME results were also observed in the THF data. Based on the accuracy of the calculations and the computational cost of the calculations, B3LYP was found to be the most desirable method of modeling these types of systems.     

A theoretical study of cation--π interactions: Li+, Na+, K+, Be2+, Mg2+ and Ca2+ complexation with mono- and bicyclic ring-fused benzene derivatives

DFT (B3LYP functional) and MP2 methods using 6-311+G(2d,2p) basis set have been employed to examine the effect of ring fusion to benzene on the cation--π interactions involving alkali metal ions (Li⁺, Na⁺, and K⁺) and alkaline earth metal ions (Be²⁺, Mg²⁺ and Ca²⁺). Our present study indicates that modification of benzene (π-electron source) by fusion of monocyclic or bicyclic (or mixture of these two kinds of rings) strengthens the binding affinity of both alkali and alkaline earth metal cations. The strength of interaction decreases in the following order: Be²⁺ > Mg²⁺ > Ca²⁺ > Li⁺ > Na⁺ > K⁺ for any considered aromatic ligand. The interaction energies for the complexes formed by divalent cations are 4–6 times larger than those for the complexes involving monovalent cations. The structural changes in the ring wherein metal ion binds are examined. The distance between ring centroid and the metal ion is calculated for all of the complexes. Strained bicyclo[2.1.1]hexene ring fusion has substantially larger effect on the strength of cation--π interactions than the monocyclic ring fusion for all of the cations due to the π-electron localization at the central benzene ring.     

Theoretical investigation of the structure and properties of H2B=NH2...Mn+, HB≡NH...Mn+, and Borazine...Mn+ complexes (M = Alkaline and Earth Alkaline Metals)

The nature of H₂B=NH₂...M ⁿ⁺, HB=NH...M ⁿ⁺, and Borazine...M ⁿ⁺ interactions were studied with ab-initio calculations. The interaction energies were calculated at B3LYP/6-31G(d, p) level. The calculations suggest that the size and charge of cation are two influential factors that affect the nature of interaction. The theory of atoms in molecules (AIM) and natural bond orbital (NBO) analysis of complexes indicate that the variation of densities and the extent of charge shifts upon complexation correlate well with the obtained interaction energies.     

Density functional theory study of calix[4]arene‐N‐azacrown‐5, calix[4]arene‐N‐phenyl‐azacrown‐5, and their complexes with alkali‐metal cations: Na+, K+, and Rb+

Theoretical studies of 1,3‐alternate‐25,27‐bis(1‐methoxyethyl)calix[4]arene‐azacrown‐5 ( L₁ ), 1,3‐alternate‐25,27‐bis(1‐methoxyethyl)calix[4]arene‐N‐phenyl‐azacrown‐5 ( L₂ ), and the corresponding complexes M⁺/ L of L₁ and L₂ with the alkali‐metal cations: Na⁺, K⁺, and Rb⁺ have been performed using density functional theory (DFT) at B3LYP/6‐31G* level. The optimized geometric structures obtained from DFT calculations are used to perform natural bond orbital (NBO) analysis. The two main types of driving force metal–ligand and cation–π interactions are investigated. The results indicate that intermolecular electrostatic interactions are dominant and the electron‐donating oxygen offer lone pair electrons to the contacting RY* (1‐center Rydberg) or LP* (1‐center valence antibond lone pair) orbitals of M⁺ (Na⁺, K⁺, and Rb⁺). What's more, the cation–π interactions between the metal ion and π‐orbitals of the two rotated benzene rings play a minor role. For all the structures, the most pronounced changes in geometric parameters upon interaction are observed in the calix[4]arene molecule. In addition, an extra pendant phenyl group attached to nitrogen can promote metal complexation by 3D encapsulation greatly. In addition, the enthalpies of complexation reaction and hydrated cation exchange reaction had been studied by the calculated thermodynamic data. The calculated results of hydrated cation exchange reaction are in a good agreement with the experimental data for the complexes. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Computationally rational design of metal-involving halogen bonds with π-covalency: Structures and bonding analysis

Traditional π-covalent interactions have been proved in the non-metal halogen bond adducts formed by chloride and halogenated triphenylamine-based radical cations. In this study, we have rationally designed two metal-involving halogen bond adducts with π-covalency property, such as [L1-Pd···I-PTZ]⁺ (i.e., 1) and [L2-Pd···I-PTZ]⁺ (i.e., 2), in which the square-planar palladium complexes serve as halogen bond acceptor and 3,7-diiodo-10H-phenothiazine radical cation (i.e., [I-PTZ]^•+) acts as halogen bond donor. Noncovalent interaction analysis and quantum theory of atoms in molecules analysis revealed that there are notable halogen bond interactions along the Pd···I direction without genuine chemical bond formed in both designed adducts. Energy decomposition analysis together with natural orbital for chemical valence calculations were performed to gain insight into their bonding nature, which demonstrated the presence of remarkable π-covalent interactions and σ-covalent interactions in both 1 and 2. We therefore proposed a new strategy for building the metal-involving halogen bonds with π-covalency property, which will help the further development of new types of halogen bonds.     

A DFT study of molecular structures and tautomerizations of 2-benzoylpyridine semicarbazone and picolinaldehyde N-oxide thiosemicarbazone and their complexations with Ni(II), Cu(II), and Zn(II)

The structure optimizations of picolinaldehyde N-oxide thiosemicarbazone (Hpiotsc), 2-benzoylpyridine semicarbazone (H2BzPS), their imino tautomers and their complexes with Ni(II), Cu(II), and Zn(II) were carried out using DFT calculations. The structures of Hpiotsc and H2BzPS ligands, transition states of their tautomerizations were obtained at the B3LYP/6-31+G(d,p) level and their thermodynamic properties were derived from the frequency calculations at the same level of theory. The B3LYP/LANL2DZ-optimized structures of Hpiotsc and H2BzPS complexes with Ni(II), Cu(II), and Zn(II), and the thermodynamic properties of their complexations derived from the B3LYP/LANL2DZ-frequency calculations were obtained. The B3LYP/LANL2DZ-optimized geometrical parameters for the [Ni(Hpiotsc)₂]²⁺, [Cu(Hpiotsc).Cl₂], and [Zn(Hpiotsc).Cl₂] complexes show good agreement with their corresponding X-ray crystallographic data.     

A study on interaction of Be, Mg and Ca with phenylalanine: Binding energies, metal ion affinities and IR signature of complex stability

The interaction between divalent metal cations and amino acids plays an important role in many biological processes. In present report, we have examined the effect of metal cations (Be⁺⁺, Mg⁺⁺ and Ca⁺⁺) interaction on structures, binding energies (BE), metal ion affinities (MIA) and infrared (IR) spectra of phenylalanine (Phe) molecule by density functional theory (DFT) calculations at B3LYP/6-311++G(d,p) level. Nine different ground state isomers of Phe molecule have been optimized at B3LYP/6-311++G (d,p) level of theory. The relative ground state energies of these nine isomers are lying between 0.0-1.9 kcal/mol with respect to the ground state energy of most stable Phe isomer. Seven most stable complexes of Phe molecule with Be⁺⁺, Mg⁺⁺ and Ca⁺⁺ [Phe+M]⁺⁺ (M = Be⁺⁺, Mg⁺⁺ and Ca⁺⁺) were studied. The calculated values of metal ion affinity (MIA), BE and the Gibbs free energies of each [Phe+M] ⁺⁺ complexes were found to be in the order of Be⁺⁺ > Mg⁺⁺ > Ca⁺⁺. Among the seven [Phe+M]⁺⁺ complexes, the most stable conformer has charge solvation structure where the metal cations coordinated through tridentate bonds with -N, -O atoms and benzene ring (N/O/Ring). The [Phe+Be]⁺⁺ complex has maximum MIA value, 353.3 kcal/mol than that of [Phe+Mg]⁺⁺ and [Phe + Ca]⁺⁺ complexes. Thus, the complex [Phe+Be]⁺⁺ is energetically more stable than that of [Phe+Mg]⁺⁺ and [Phe + Ca]⁺⁺. The IR spectra of each seven conformers of [Phe+M]⁺⁺ complexes have been also calculated. The wavnumber position of (-CO) stretching mode was used to determine the charge/salt bridge structures of the [Phe+M]⁺⁺ complex. The most stable [Phe+M]⁺⁺ complex has been also verified through the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) analysis.     

Computational studies of the structure and cation-anion interactions in 1-ethyl-3-methylimidazolium lactate ionic liquid

Quantum chemical calculations of the structures and cation-anion interaction of 1-ethyl-3-methylimidazolium lactate ([Emim][LAC]) ion pair at the B3LYP/6-31++G** theoretical level were performed. The relevant geometrical characteristics, energy properties, intermolecular H-bonds (H-bonds), and calculated IR vibrations with respect to isolated ions were systematically discussed. The natural bond orbital (NBO) and atoms in molecule (AIM) analyses were also employed to understand the nature of the interactions between cation and anion. The five most stable geometries were verified by analyzing the relative energies and interaction energies. It was found that the most of the C-H···O intermolecular H-bonds interactions in five stable conformers have some covalent character in nature. The elongation and red shift in IR spectrum of C-H bonds which involve in H-bonds is proved by electron transfers from the lone pairs of the carbonyl O atom of [LAC] to the C-H antibonding orbital of the [Emim]+. The interaction modes are more favorable when the carbonyl O atoms of [LAC] interact with the C2-H of the imidazolium ring and the C-H of the ethyl group through the formation of triple H-bonds.     

Quantum simulation on donor and acceptor II calix[4]arene substrate and alkali metal ions: the driven inclusion

The energetic and structural optimized of a calix[4]arene with and without alkali-metal cations are presented with performance of various quantum chemical methods such as Hartree--Fock, second order Møller-Plesset perturbation theory, and density functional theory. The geometry optimizations have been carried out with the 3-21G (Li⁺--Cs⁺) and 3-21G(d,p) (Li⁺--K⁺) and the 3-21G basis sets for Cs⁺ and Rb⁺. Additional single-point energy ab initio calculations for Li⁺–K⁺ were carried out at HF/6--31G, HF/6-31G (d,p), HF/6--311G(d,p) for complexes of Li⁺ and Na⁺. The calculations were carried out to analyze the complexation of calix[4]arene with alkali metal cationic species (Li⁺, Na⁺, K⁺, Rb⁺, and Cs⁺). Assumption to isolate the effects of the aromatic core and cation-π interactions. Particular emphasis has been on conformational binding selectivity and the structural characterization of the complexes, the smaller cation as Li⁺ and Na⁺ has been placed in the lower rim's of the calix[4]arene's cavity. The large cations like K⁺, Rb⁺, and Cs⁺ take placed in upper rim and the endo (inclusive) complexation is driven by cation-π interactions, that reflect a superior interaction with two phenol rings. The endo complexation of Cs⁺ with calix[4]arene is in agreement with X-ray diffraction data. The binding modes of calixarene-cation systems are studied to involve cooperative effects between cation-π and electrostatic forces.     

Low‐dimensional compounds containing bioactive ligands. IV. Unusual ionic forms of 5‐chloroquinolin‐8‐ol

Bis(5‐chloro‐8‐hydroxyquinolinium) tetrachloridopalladate(II), (C₉H₇ClNO)₂[PdCl₄], (I), catena‐poly[dimethylammonium [[dichloridopalladate(II)]‐μ‐chlorido]], {(C₂H₈N)[PdCl₃]}_n, (II), ethylenediammonium bis(5‐chloroquinolin‐8‐olate), C₂H₁₀N₂²⁺·2C₉H₅ClNO⁻, (III), and 5‐chloro‐8‐hydroxyquinolinium chloride, C₉H₇ClNO⁺·Cl⁻, (IV), were synthesized with the aim of preparing biologically active complexes of Pd^II and Ni^II with 5‐chloroquinolin‐8‐ol (ClQ). Compounds (I) and (II) contain Pd^II atoms which are coordinated in a square‐planar manner by four chloride ligands. In the structure of (I), there is an isolated [PdCl₄]²⁻ anion, while in the structure of (II) the anion consists of Pd^II atoms, lying on centres of inversion, bonded to a combination of two terminal and two bridging Cl⁻ ligands, lying on twofold rotation axes, forming an infinite [–μ₂‐Cl–PdCl₂–]_n chain. The negative charges of these anions are balanced by two crystallographically independent protonated HClQ⁺ cations in (I) and by dimethylammonium cations in (II), with the N atoms lying on twofold rotation axes. The structure of (III) consists of ClQ⁻ anions, with the hydroxy groups deprotonated, and centrosymmetric ethylenediammonium cations. On the other hand, the structure of (IV) consists of a protonated HClQ⁺ cation with the positive charge balanced by a chloride anion. All four structures are stabilized by systems of hydrogen bonds which occur between the anions and cations. π–π interactions were observed between the HClQ⁺ cations in the structures of (I) and (IV).     

Gas-Phase studies of valinomycin-alkali metal cation complexes: attachment rates and cation affinities

Reactions of laser-desorbed Na⁺, K⁺, Rb⁺, and Cs⁺ with thermally vaporized valinomycin generate metal-ligand complexes in a Fourier transform ion cyclotron resonance trapping cell, proving that complexes can form via gas-phase ion-molecule reactions. Although desorption of intact pre-formed complexes cannot be ruled out, this route appears minor. Relative rate constants for the complexation reactions show strong dependence on the charge densities of the cations. Competition experiments between valinomycin and the synthetic ionophores 18-crown-6 (18C6) and [2.2.2]-cryptand ([2.2.2]) show that valinomycin has a higher intrinsic alkali metal cation affinity than either 18C6 or [2.2.2], in contrast to the complex formation constants observed in methanol, where K+ affinities are in the order [2.2.2] > 18C6 > valinomycin.     

Quantum chemical study of the interaction between selenium analog of methimazole as an anti-thyroid drug and metal cations

Energetic and structural properties of complexes formed from interaction between selenium analog of methimazole (MSeI) as an anti-thyroid drug and M^z+ (Li⁺, Na⁺, K⁺, Be²⁺, Mg²⁺ and Ca²⁺) cations have been investigated using B3LYP, M062X, PBE1PBE, and MP2 methods with 6-311++G(d,p) and 6-311++G(2d,2p) basis sets. Two planar and perpendicular complexes were predicted from interaction of MSeI and M^z+ cations. From the Gibbs free energy difference between the planar and perpendicular forms of MSeI–M^z+ complexes, it is found that the perpendicular forms are the predominant ones. In addition, the comparison of interaction energies shows that the order of energies increases in the following order: K⁺ < Na⁺ < Li⁺ < Ca²⁺ < Mg²⁺ < Be²⁺. The results of natural bond orbital analysis showed that the charge transfer occurs from MSeI to metal cations. The atom in molecule analysis shows that the charge density and its Laplacian at the Se–M^z+ bond critical point of the MSeI–M²⁺ complexes are greater than the MSeI–M¹⁺ ones. Also, it was revealed that the Se–M^z+ interactions in perpendicular complexes of alkali and alkaline metal cations are electrostatic and partially covalent in nature, respectively.     

Theoretical study on conformational features and cation-binding properties of a diquinone calix[4]arene

Theoretical studies of a diquinone calix[4]arene and its interactions with the cations Li⁺, Na⁺, K⁺ and Ag⁺ have been performed. Conformational features and cation-binding properties were evaluated with the restricted hybrid Becke three-parameter exchange functional method using the 6-31G(d) basis set and its relativistic effective core potentials. To model the effect of medium, the polarisable continuum model was also used. Four typical conformations of the parent diquinone calix[4]arene were studied. The calculated results show that the most stable conformers are 1,3-alternate and partial cone in the gas phase and in CH₂Cl₂ solution, respectively. The optimised geometric structures were used to perform natural bond orbital analysis. The two main types of driving force metal–ligand and cation–π interactions are investigated. The calculated binding energy for cations (Li⁺, Na⁺, K⁺ and Ag⁺) is discussed. The calculated results indicate that cone complexes are the most stable.     

Complexes of AgI with cationic ligands: bis[(pyridylmethyl)ammonio]silver(I) salts

Bis­[(2-pyridyl­methyl)­ammonio]silver(I) trinitrate, [Ag(C₆H₉N₂)₂](NO₃)₃, (I), and bis{bis­[(4-pyridyl­methyl)­ammonio]silver(I)} hexakis­(perchlorate) dihydrate, [Ag(C₆H₉N₂)₂]₂(ClO₄)₆·2H₂O, (II), are rare examples of complexes with cationic ligands. In (I), the Ag⁺ cation has a T-shaped [2+1] coordination involving the pyridine N atoms and a nitrate O atom, while in (II) there are three independent two-coordinate Ag complex cations (two with the Ag atoms on independent inversion centres) and disordered ClO₄⁻ ions. The crystal structures reveal the role of hydrogen bonding in stabilizing these complexes.