Solubility of <Emphasis Type="Italic">d</Emphasis>-element salts in organic and aqueous–organic solvents: II. Effect of halocomplex formation on solubility of cobalt bromide and chloride and nickel chloride

Solubility of salts in the systems MCl₂–H₂O–Solv (M = Co, Ni) and CoBr₂–H₂O–Solv (Solv = dimethyl sulfoxide, dimethyl formamide, and dimethyl acetamide) at 25°C was measured experimentally. Dominating species of cobalt and nickel halides existing in various concentration regions were identified by analysis of electron absorption spectra. It was shown that the major factor defining solubility is the interaction of halocomplexes of metal ions with solvent molecules.     

A comparative DFT study of Fe3+ and Fe2+ ions adsorption on (100) and (110) surfaces of pyrite: An electrochemical point of view

Pyrite acts as a catalyst in the mineral processing, and the speed of ferric ion reduction and mineral decomposition increases with increasing cathodic points. In this study, the ferric ion interaction on the (100) and (110) surfaces of pyrite was studied using the density functional theory calculations. The analysis of stability, density of states, and electron density were performed to understand the interaction between the ferric ion and pyrite surfaces. The results showed that pyrite surface is chemically active and tends to absorb ferric ion between two surface sulfur atoms. The hyperconjugation between the 3d orbital of ferric ion and the 3p or 3d orbitals of surface atoms provides the conditions for the Fe³⁺ ion adsorption. The molecular orbital (MO) and electron density analyses indicate that the 3p orbitals of S atoms play a more important role in bonds formations relative to the 3d orbitals. The (110) surface is more active, and the adsorption energy is larger than that of surface (100), which is the result of decreased cation coordination and the presence of sulfur at the surface. Subsequently, the interaction of the Fe²⁺ ion, as product of Fe³⁺ ion reduction and its competitor for adsorption, on the surfaces was studied. The Fe^{2 +} ion adsorbs stronger at the surface of (110), and the adsorption energies at (100) and (110) surfaces were obtained as −24 and −47 kcal/mol, respectively. In general, the Fe³⁺ ion is a stronger oxidizing agent than Fe²⁺ on pyrite surfaces.     

Dissociation of disulfide‐intact somatostatin ions: the roles of ion type and dissociation method

The dissociation chemistry of somatostatin‐14 was examined using various tandem mass spectrometry techniques including low‐energy beam‐type and ion trap collision‐induced dissociation (CID) of protonated and deprotonated forms of the peptide, CID of peptide‐gold complexes, and electron transfer dissociation (ETD) of cations. Most of the sequence of somatostatin‐14 is present within a loop defined by the disulfide linkage between Cys‐3 and Cys‐14. The generation of readily interpretable sequence‐related ions from within the loop requires the cleavage of at least one of the bonds of the disulfide linkage and the cleavage of one polypeptide backbone bond. CID of the protonated forms of somatostatin did not appear to give rise to an appreciable degree of dissociation of the disulfide linkage. Sequential fragmentation via multiple alternative pathways tended to generate very complex spectra. CID of the anions proceeded through CH₂? S cleavages extensively but relatively few structurally diagnostic ions were generated. The incorporation of Au(I) into the molecule via ion/ion reactions followed by CID gave rise to many structurally relevant dissociation products, particularly for the [M+Au+H]²⁺ species. The products were generated by a combination of S? S bond cleavage and amide bond cleavage. ETD of the [M+3H]³⁺ ion generated rich sequence information, as did CID of the electron transfer products that did not fragment directly upon electron transfer. The electron transfer results suggest that both the S? S bond and an N? C_α bond can be cleaved following a single electron transfer reaction. Copyright © 2009 John Wiley & Sons, Ltd.     

Ab initio study of the topology of the charge distribution of H3SiO(H)AlH3 conformers

The topologic properties of the electronic charge distribution of conformers of H₃SiO(H)AlH₃ molecule hydroxyl groups of zeolites are reported. The studied properties—total density, Laplacian density, and bond ellipticity—were evaluated at the position of the critical points of the O Si, O Al, and O H bonds, by using Hartree–Fock and second‐order Møller–Plesset levels of theory, and the STO/6‐31+G(d,p) standard basis set. For the H₃SiO(H)AlH₃ molecule, four conformers are identified. It is demonstrated that for these conformers, the total density and Laplacian density remain almost constant by effect of the rotations of the T H bonds, T=(Si, Al), around the corresponding O T bonds, respectively. However, these rotations induce sensible variations in the ellipticity at the position of the critical point of the O Al bonds, which are reflected in the OH bond distance, OH vibrational mode, and the stabilization energy of conformers. These results lead to a linear relationship between the magnitude of the bond ellipticity at the critical point of the O Al bonds and the frequency values of the OH bonds, with a correlation coefficient of r²=0.98. In addition, a good linear relationship between the ellipticity of the O Al bond and the pattern of the stabilization energy of conformers was also found. © 1999 John Wiley & Sons, Inc. Int J Quant Chem 76: 1–9, 2000     

Thermochemistry of Complex Formation of Endofullerene Li<Superscript>+</Superscript>@C<Subscript>60</Subscript> with the Triflate Ion

The density functional theory method at the M06-2X/6-31G(d,p) level was used to calculate the optimal geometry and thermodynamic parameters of formation of the Li⁺CF₃SO₃^? and Li⁺@C₆₀(CF₃SO₃^?) ion pairs, as well as topological characteristics of the electron density distribution in the critical point (3,?1) of bonds between lithium cation endofullerene Li⁺@C₆₀, and the triflate anion in a vacuum and in chlorobenzene.     

Application of Bader’s atoms in molecules theory to the description of coordination bonds in the complex compounds of Ca2+ and Mg2+ with methylidene rhodanine and its anion

In the framework of Bader??s atoms in molecules theory a complete analysis of the distribution function of electron density in molecules of complexes of Ca²⁺ and Mg²⁺ with methylidene rhodanine and its anion was carried out. The role of mutual polarization of the metal cation and the ligand in the formation of coordination bonds was demonstrated. The accumulation of electron density in the interatomic space of coordination bonds is assumed to be a consequence of the deformation of the ligand electron shell under the influence of the cation electric field. Based on the magnitude and sign of the Laplacian and the electron energy density at the critical points of coordination bonds the interactions were classified the in terms of the atoms in molecules theory. The energy of the coordination bonds was evaluated using the Espinoza??s formula. The stability of metal-containing rings was considered basing on the values of the bond ellipticity.     

Probing the weakest bond and the cleavage of p‐chlorobenzaldehyde diperoxide energetic molecule via quantum chemical calculations and theoretical charge density analysis

A high‐level ab initio Hartree‐Fock/Møller‐Plesset 2 and density functional theory quantum chemical calculations were performed on p‐chlorobenzaldehyde diperoxide energetic molecule to understand its bond topological, electrostatic, and energetic properties. The optimized molecular geometry for the basis set 6‐311G** exhibit chair diperoxide ring and planar aromatic side rings. Although the diperoxide ring bear same type of side rings, surprisingly, both the rings are almost perpendicular to each other, and the dihedral angle is 96.1°. The MP2 method predicts the O? O bond distance as ～1.466 Å. The charge density calculation reveals that the C? C bonds of chlorobenzaldehyde ring have rich electron density and the value is ～2.14 e Å^?3. The maximum electron density of the O? O bonds does not lie along the internuclear axes; in view of this, a feeble density is noticed in the ring plane. The high negative values of laplacian of C? C bonds (approximately ?22.4 e Å^?5) indicate the solidarity of these bonds, whereas it is found too small (approximately ?1.8 e Å^?5 for MP2 calculation) in O? O bonds that shows the existence of high degree of bond charge depletion. The energy density in all the C? C bonds are found to be uniform. A high electronegative potential region is found at the diperoxide ring which is expected to be a nucleophilic attack area. Among the bonds, the O? O bond charge is highly depleted and it also has high bond kinetic energy density; in consequence of this, the molecular cleavage is expected to happen across these bonds when the material expose to any external stimuli such as heat or pressure treatment. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Nitrogen incorporation in saturated aliphatic C6–C8 hydrocarbons and ethanol in low‐pressure nitrogen plasma generated by a hollow cathode discharge ion source

Ion/molecule reactions of saturated hydrocarbons (n‐hexane, cyclohexane, n‐heptane, n‐octane and isooctane) in 28‐Torr N₂ plasma generated by a hollow cathode discharge ion source were investigated using an Orbitrap mass spectrometer. It was found that the ions with [M+14]⁺ were observed as the major ions (M: sample molecule). The exact mass analysis revealed that the ions are nitrogenated molecules, [M+N]⁺ formed by the reactions of N₃⁺ with M. The reaction, N₃⁺ + M → [M+N]⁺ + N₂, were examined by the density functional theory calculations. It was found that N₃⁺ abstracts the H atom from hydrocarbon molecules leading to the formation of protonated imines in the forms of R′R″C?NH₂⁺ (i.e. C–H bond nitrogenation). This result is in accord with the fact that elimination of NH₃ is the major channel for MS/MS of [M+N]⁺. That is, nitrogen is incorporated in the C–H bonds of saturated hydrocarbons. No nitrogenation was observed for benzene and acetone, which was ascribed to the formation of stable charge‐transfer complexes benzene????N₃⁺ and acetone????N₃⁺ revealed by density functional theory calculations. Copyright © 2016 John Wiley & Sons, Ltd.     

Peptide cation-radicals. A computational study of the competition between peptide N-Calpha bond cleavage and loss of the side chain in the [GlyPhe-NH2 + 2H]+. cation-radical

Cation‐radicals and dications corresponding to hydrogen atom adducts to N‐terminus‐protonated N_α‐glycylphenylalanine amide (Gly‐Phe‐NH₂) are studied by combined density functional theory and Møller‐Plesset perturbational computations (B3‐MP2) as models for electron‐capture dissociation of peptide bonds and elimination of side‐chain groups in gas‐phase peptide ions. Several structures are identified as local energy minima including isomeric aminoketyl cation‐radicals, and hydrogen‐bonded ion‐radicals, and ylid‐cation‐radical complexes. The hydrogen‐bonded complexes are substantially more stable than the classical aminoketyl structures. Dissociations of the peptide N? C_α bonds in aminoketyl cation‐radicals are 18–47 kJ mol^?1 exothermic and require low activation energies to produce ion‐radical complexes as stable intermediates. Loss of the side‐chain benzyl group is calculated to be 44 kJ mol^?1 endothermic and requires 68 kJ mol^?1 activation energy. Rice‐Ramsperger‐Kassel‐Marcus (RRKM) and transition‐state theory (TST) calculations of unimolecular rate constants predict fast preferential N? C_α bond cleavage resulting in isomerization to ion‐molecule complexes, while dissociation of the C_α? CH₂C₆H₅ bond is much slower. Because of the very low activation energies, the peptide bond dissociations are predicted to be fast in peptide cation‐radicals that have thermal (298 K) energies and thus behave ergodically. Copyright © 2003 John Wiley & Sons, Ltd.     

Spectroscopic and DFT studies of photoactivatable Mn(I) tricarbonyl complexes

A combined experimental study and density functional theory calculations of fac‐[MnBr (CO)₃L] complexes (L = 2‐(2′‐pyridyl)benzimidazole ligand, furnished with either morpholine (L^morph) or phthalimido (L^phth) side‐chain) were performed using different spectral and analytical tools. The synthesized complexes released carbon monoxide upon the exposure to LED source light at 468 nm. Illumination of fac‐[MnBr (CO)₃L] (10 μM) in the myoglobin solution (Mb) produced about 25 μM MbCO. The plateau of the CO release process is attained within 25 min. With the aid of time‐dependent density functional theory calculations, the observed lowest energy absorption transition at ~ 400 nm has a ground‐state composed of d (Mn)/π (pyridyl) and excited‐state of ligand π*‐orbitals forming MLCT/π‐π^*. Natural population analyses of fac‐[MnBr (CO)₃L] were carried out to get information about the strength of Mn–CO bonds, electronic arrangment and natural charge of manganese ion.     

DFT studies and AIM analysis of intramolecular N–H···O hydrogen bonds in 3-aminomethylene-2 methoxy-5,6-dimethyl-2-oxo-2,3-dihydro-2λ5-[1,2]oxaphosphinin-4-one and its derivatives

The intramolecular N–H···O hydrogen bonds in 3-aminomethylene-2 methoxy-5,6-dimethyl-2-oxo-2,3-dihydro-2λ⁵-[1,2]oxaphosphinin-4-one and its derivatives (F, H, Li, -BeH) were studied by DFT (density functional theory) methods. The results of calculations were obtained at B3LYP/6-311++G(d,p) level on model species, with the resonance-assisted hydrogen bonds (RAHB). Topological parameters such an electron density, its Laplacian, kinetic electron energy density, potential electron energy density, and total electron energy density at the bond critical points (BCP) of H···O/N–H contact bonds from Bader’s ‘Atoms in molecules’ (AIM) theory were analyzed in details. The energy of the N–H···O interactions studied here was found rather weak (E _HB = 2.53–12.08 kcal/mol). The results of AIM ellipticity indicated π-delocalization over all six atoms within ring.     

Theoretical study of substituents effects on characteristics of resonance-assisted hydrogen bond in (Z)-(thionitrosomethylene)hydrazine and its derivatives in ground and electronic excited state

The molecular geometry, intramolecular hydrogen bond strength, vibrational frequencies, ¹H NMR chemical shift, and nuclear quadrupole resonance parameters of ¹⁴N, ³⁵S and ²H atoms and several well-established indices of aromaticity in (Z)-(thionitrosomethylene)hydrazine molecule and its derivatives were studied by density functional theory method. The results of calculations were obtained at B3LYP/6-311++G** level of approximation on model species, with the resonance-assisted hydrogen bonds. A set of simple and mostly common substituents having different properties in resonance effect according to values of substituents constants were chosen to simulate the influence of substitution in R position of title molecule on the quasi-delocalization and H-bonding. The following substituents have been taken into consideration: F, Cl, NO₂, OCH₃, OCF₃, SCH₃, SH, and OH. The excited-state properties of intramolecular hydrogen bonding in substituted systems have been investigated theoretically using the time-dependent density functional theory method. Also, the possible charge transfer and the topological properties of investigated molecule and its derivatives were studied by means of natural bond orbital and atoms in molecules (AIM) theory. The energy of the N–H···S interactions studied here was found medium in strength ( \( E_{\text{HB}}^{*} \)  = ?36.5 to ?45.3 kJ mol^?1). The electron density (ρ), Laplacian (?² ρ) properties and the total electron energy density (HC), estimated by AIM calculations, indicate that H···S bond possesses low ρ, positive ?² ρ and HC < 0 which are in agreement with partially covalent character of HB.     

<Emphasis Type="Italic">Ab Initio</Emphasis> calculations of 3-(trichlorogermyl)propanoylamide structure and nature of its Ge←O coordination bond

Calculations of 3-(trichlorogermyl)propanoylamide molecule containing a Ge←O coordination bond were performed by RHF/6-31G(d) method with full and partial geometry optimization. Its total energy 2.22 kcal mol⁻¹ is lower than that of the molecule with tetracoordinated germanium atoms. Germanium and oxygen atoms initiate the formation of a coordination Ge←O bond in this molecule and are conductors of the electron density transfer from the atoms nearest to the oxygen on the atoms of the germanium coordination polyhedron. No electron density transfer occurs from the oxygen atom to germanium. Upon decrease in the Ge...O distance the axial Ge-Cl bond is polarized much stronger than the equatorial bonds. In the crystalline state of the substance these molecules are fixed in an energetically unfavorable structure.     

Bonding situations in tricoordinated beryllium phenyl complexes

The bonding situation in the tricoordinated beryllium phenyl complexes [BePh₃]⁻, [(pyridine)BePh₂] and [(trimethylsilyl-N-heterocyclic imine)BePh₂] is investigated experimentally and computationally. Comparison of the NMR spectroscopic properties of these complexes and of their structural parameters, which were determined by single crystal X-ray diffraction experiments, indicates the presence of π-interactions. Topology analysis of the electron density reveals elliptical electron density distributions at the bond critical points and the double bond character of the beryllium-element bonds is verified by energy decomposition analysis with the combination of natural orbital for chemical valence. The present beryllium-element bonds are highly polarized and the ligands around the central atom have a strong influence on the degree of π-delocalization. These results are compared to related triarylboranes.     

Energetics and electronic rearrangements of proton transfer in (H3NHOH2)+

Proton transfer between N and O in the hydrogen-bonded system (H₃NHOH₂)⁺ is studied by ab initio molecular orbital methods. Potential energy curves are calculated at the hartree–Fock level using the 4–31G basis set for hydrogen bond lengths R(NO) varying from the equilibrium value of 2.664 to 3.10 Å. Short hydrogen bonds are associated with asymmetric single-well potentials in which the minimum corresponds to the NH? O configuration. For longer R(NO) separations, the potential is of double-well form, including both N? HO and NH? O as minima. It is found that the height of the energy barrier to proton transfer is sensitive to both stretches and bends of the hydrogen bond. Continuous changes in the electron density are monitored at various stages of proton transfer via density difference maps and Mulliken population analyses. The initial loss of density from the proton-accepting molecule during the first half of the transfer is accelerated during the second half. A correlation is drawn between the energetics of transfer in a number of systems and the net charge lost by the proton-acceptor group.     

Molecular and crystal structure of the intracomplex 2-[(dibutylboryloxy)(Butyl) borylamino]-4-methylpyridine with boron atoms of differing hybridization in the chelate ring

X-ray diffraction has been used to establish the crystalline and molecular structure of the intracomplex 2-[(dibutylboryloxy)(butyl)borylamino]4-methylpyridine. In the crystal, the molecule forms weak intermolecular N(H)...O hydrogen bonds. The bicyclic portion of the molecule is nearly planar. From the bond lengths in the ring, which incorporates boron atoms of differing hybridization (sp³ and sp²), it follows that delocalization of electron density extends only over the amidine fragment. Quantum chemical calculations (MO LCAO, version CNINDO/2) show that the electron density at the endocyclic nitrogen of the aminopyridine system coordinated with boron is lower than that at the endocyclic nitrogen of the aminopyridine.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 1, pp. 173–177, January, 1991.     

Resonant dissociative electron capture by the simplest amino acids and dipeptides

The formation of ions from amino acids (glycine and alanine) and dipeptides (glycylglycine, alanylalanine, and glycylalanine) under the resonant electron capture conditions was studied by negative ion resonant electron capture mass spectrometry. The isobaric ions were found, their effective yield curves were experimentally separated, and the elemental composition was determined. The thermochemical aspect of ion formation was considered, and probable dissociative channels of fragmentation ion formation and their structures were established on the basis of this aspect. Bond cleavage reactions only and H-shift processes were revealed. The rearrangements occur presumably through the stage of formation of intramolecular hydrogen bonds. The cross-sections of formation of ions [M − H]⁻ were measured in the energy range 1.1–1.3 eV. The metastable decay channels of ions [M − H]⁻ and [M − COOH]⁻ were found in the energy range 4.5–7.5 eV for dipeptides, which enabled establishing the genetic relationship between the parental and daughter ions and revealing hidden fragmentation pathways.     

Nature of Alkali- and Coinage-Metal Bonds versus Hydrogen Bonds

We have quantum chemically studied the structure and nature of alkali- and coinage-metal bonds (M-bonds) versus that of hydrogen bonds between A−M and B⁻ in archetypal [A−M⋅⋅⋅B]⁻ model systems (A, B=F, Cl and M=H, Li, Na, Cu, Ag, Au), using relativistic density functional theory at ZORA-BP86-D3/TZ2P. We find that coinage-metal bonds are stronger than alkali-metal bonds which are stronger than the corresponding hydrogen bonds. Our main purpose is to understand how and why the structure, stability and nature of such bonds are affected if the monovalent central atom H of hydrogen bonds is replaced by an isoelectronic alkali- or coinage-metal atom. To this end, we have analyzed the bonds between A−M and B⁻ using the activation strain model, quantitative Kohn-Sham molecular orbital (MO) theory, energy decomposition analysis (EDA), and Voronoi deformation density (VDD) analysis of the charge distribution.     

Theoretical study on the mechanisms of the nucleophilic substitution reactions of hydrosulfide ion and halomethanes

Three species involved in the nucleophilic substitution reaction of hydrosulfide ion and halomethanes are investigated by ab initio calculations. Geometries for stationary structures along the reaction paths are fully performed with the second‐order Møller–Plesset perturbation approximation with the cc‐pVDZ basis set. The monomer geometries determined by the MP2 method match the experimental results very well. Single point energy calculations are carried out at the coupled cluster with perturbative triple excitations CCSD (T) theory with aug‐cc‐pVDZ basis set. Halomethanes have three conformers here, which lead to the three product channels, HSCH₃ + F^?1, HSCH₃ + Cl^?1, and HSCH₃ + Br^?1. The investigation encompasses the six complexes formed among three channels, respectively. By selecting the six complexes as the model, we investigate the binding energy, topological property of the electron charge density and their Laplacian in detail theoretically. Electrostatic density potential maps of halomethanes are generated for the determination of attractive interaction sites. It is proved that the similar misshaped electron clouds of the three halogen atoms result in the similar properties of the carbon‐halogen bonds, and reveals that the product ion‐dipole complexes interactions are predominantly electrostatic in nature. The calculated results predict the binding energy of the most stable complex in six complexes is ?47.06 kcal/mol at the MP2 level of theory. The second channel has the lowest energy barrier, which is ?3.63 kcal/mol at the CCSD (T) levels of theory, is expected to be the most important pathway. It occurs via C? Cl cleavage accompanied by C? S bond formation. The other two channels have higher energy barriers and are expected to have smaller rates. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Relationships between structure,ionization profile and sensitivity of exogenous anabolic steroids under electrospray ionization and analysis in human urine using liquid chromatography–tandem mass spectrometry

The relationships between the ionization profile, sensitivity, and structures of 64 exogenous anabolic steroids (groups I–IV) was investigated under electrospray ionization (ESI) conditions. The target analytes were ionized as [M + H]⁺ or [M + H–nH₂O]⁺ in the positive mode, and these ions were used as precursor ions for selected reaction monitoring analysis. The collision energy and Q3 ions were optimized based on the sensitivity and selectivity. The limits of detection (LODs) were 0.05–20 ng/mL for the 64 steroids. The LODs for 38 compounds, 14 compounds and 12 compounds were in the range of 0.05–1, 2–5 and 10–20 ng/mL, respectively. Steroids including the conjugated keto‐functional group at C3 showed good proton affinity and stability, and generated the [M + H]⁺ ion as the most abundant precursor ion. In addition, the LODs of steroids using the [M + H]⁺ ion as the precursor ion were mostly distributed at low concentrations. In contrast, steroids containing conjugated/unconjugated hydroxyl functional groups at C3 generated [M + H ? H₂O]⁺ or [M + H ? 2H₂O]⁺ ions, and these steroids showed relatively high LODs owing to poor stability and multiple ion formation. An LC‐MS/MS method based on the present ionization profile was developed and validated for the determination of 78 steroids (groups I–V) in human urine. Copyright © 2015 John Wiley & Sons, Ltd.