Ring complexes of S-nitrosothiols with CU+: a density functional theory study

The density functional theory (DFT) method B3P86/6-311+G(2df,p) has been employed to investigate the complexes formed upon interaction of Cu(+) with nitrosylated cysteine (CysNO) and its decarboxylated (H(2)NCH(2)CH(2)SNO) and deaminated (HOOCCH(2)CH(2)SNO) derivatives. Optimized structures, relative enthalpies and relative free energies have been calculated and compared. In addition, the effects of binding an H(2)O molecule to the Cu(+) centre in the resulting complexes have also been considered. It is found that the most stable complexes are formed when Cu(+) coordinates to the S-nitrosothiol via S of the SNO group. This results in dramatic lengthenings of the SN bond with concomitant shortening of the NO bond. In contrast, when Cu(+) coordinates via the nitrogen of the SNO group, a shortening of the SN bond with lengthening of the NO bond is observed. These effects are tempered by the electron donating ability of other functional groups also coordinated with the Cu(+) centre in the complexes and on the coordination state of the Cu(+) ion.     

On the nature of spin- and orbital-resolved Cu+–NO charge transfer in the gas phase and at Cu(I) sites in zeolites

Electronic factors essential for NO activation by Cu(I) sites in zeolites are investigated within spin-resolved analysis of electron transfer channels (natural orbitals for chemical valence). NOCV analysis is performed for three DFT-optimized models of Cu(I)?CNO site in ZSM-5: [CuNO]⁺, (T1)CuNO, and (M7)CuNO. NO as a non-innocent, open-shell ligand reveals significant differences between independent deformation density components for ?? and ?? spins. Four distinct components are identified: (i) unpaired electron donation from NO ??_??* antibonding orbital to Cu_s,d; (ii) backdonation from copper d _yz to ??_??* antibonding orbital; (iii) donation from occupied ??_?? and Cu d _xz to bonding region, and (iv) donation from nitrogen lone-pair to Cu_s,d. Channel (i), corresponding to one-electron bond, shows-up solely for spin majority and is effective only in the interaction of NO with naked Cu⁺. Channel (ii) dominates for models b and c: it strongly activates NO bond by populating antibonding ??* orbital and weakens the N?CO bond in contrast to channel (i), depopulating the antibonding orbital and strengthening N?CO bond. This picture perfectly agrees with IR experiment: interaction with naked Cu⁺ imposes small blue-shift of NO stretching frequency while it becomes strongly red-shifted for Cu(I) site in ZSM-5 due to enhanced backdonation.     

1,2,3-propanetriol radicals formed during oxidative stress

The presented results attempt to approximate the proper structure of the radical formed as a result of the oxidation of 1,2,3-propanetriol. To fulfil the aim unstable radical originated in 1,2,3-propanetriol was trapped by PBN. Resulted spin adduct was measured using EPR spectroscopy and the isotropic hyperfine coupling constants a_iso(¹⁴N) and a_iso(¹H) were obtained by simulation of the EPR spectrum. The next step consisted of conducting a comparative analysis of EPR parameters, based on the calculations conducted at the DFT and MP2 methods level in open-shell formalism including solvent effects. For comparison, calculations were also carried out at the level of combined methods (UB3LYP/QCISD and UMP2/QCISD) in terms of the ONIOM formalism. Comparison of the experimental EPR data of the isotropic hyperfine coupling constants a_iso(¹⁴N) and a_iso(¹H) with the calculated parameters indicate that oxidation of 1,2,3-propanetriol leads to a carbon centred radical where unpaired electron is situated on the second (middle) carbon of 1,2,3-propanetriol. What is important, this conclusion could be made regardless of the chosen calculation method. However, it could be stated that for calculation of the isotropic hyperfine coupling constants a_iso(¹⁴N) and a_iso(¹H) of PBN/gly• adducts, UMP2 polarisable conductor calculation model with two ethanol molecules is explicitly defined.     

The hyperfine coupling constants of 19F: An ab initio MRD-CI basis set study

The isotropic (a_iso) and dipolar (A_dip) hyperfine coupling constants of ¹⁹F were obtained from MRD -CI wave functions using a variety of basis sets. In series I, increasing numbers of d functions were added to a 5s4p contracted Huzinaga/Dunning basis. In series II, the 5s3p basis set was uncontracted in several steps until 9s5p was reached, to which were added from one to three d-polarization functions. CI parameters (selection thresholds and the number of reference configurations) were also varied. A study of the R dependence of a_iso and A_dip was performed. The best values obtained at R_e are 260 G for a_iso and 308 G for A_dip, compared with experimental values of about 280 G for a_iso and 320 G for A_dip.     

Gehinderte Ligandenbewegungen in Übergangsmetallkomplexen : VII. Rotation der olefinliganden L = malein- und furmarsäuredimethylester in komplexen des typs C5H5Mn(CO)2L und C5H5Cr(CO)(NO)L

The restricted rotation of the olefin ligands L = dimethyl maleate and dimethyl fumarate in complexes of the type C₅H₅Mn(CO)₂L and C₅H₅Cr(CO)-(NO)L, respectively, has been investigated on the basis of their temperature-dependent ¹H NMR spectra. The olefinic ligand is arranged preferably in a position where the CC double bond is parallel to the plane of the cyclopentadienyl ring. The possible stereoisomers are discussed using this model. The ¹H NMR spectra of C₅H₅Cr(CO)(NO)(trans-CH₃OOCCHCHCOOCH₃) provide direct evidence that the configuration (R or S) at the metal is stable up to 120°C, and that the restricted motion of the olefin is exclusively rotation around the metal—olefin bond. The activation barriers of the olefin rotation are found to be appreciably lower in the C₅H₅Mn(CO)₂L complexes (ΔG^≠(T_C) 11–12 kcal mol^?1) than in the isoelectric C₅H₅Cr(CO)(NO)L compounds (ΔG^≠(T_C) 15–20 kcal mol^?1).     

Structure of valence band in cluster model for cytochrome-<Emphasis Type="Italic">c</Emphasis>-oxidase active centers

The electron structure of cluster model for active centers of cytochrome-c-oxidase has been calculated by DFT (PBE) method in 6-31G basis. The cluster model was constructed on the basis of experimental PDB-structure and included 1105 hemoprotein atoms. The valence band ceiling of cytochromeoxidase active centers is shown to be formed by the atoms of carbon and nitrogen from porphyrin ring of cytochrome heme a₃ and atoms of carbon and nitrogen from imidazol moieties of histidine connected with Cu atom in cytochrome a₃. D-orbitals of Cu and Fe atoms from heme a₃ and d-orbital of Fe atom from heme a contribute mainly to the orbital group. A conclusion is made that the catalytic activity of the structure is determined by these two types of orbitals. Cu d-orbitals of cytochrome a are substantially low in energy. It is suggested that Cu atoms of cytochrome a shift the chemical potential of d-orbitals belonging to the active center that results in their easier electron accepting and releasing. This can be a decisive factor in the electron transport process.     

Synthesis,characterization, thermal behavior,and DFT aspects of some oxovanadium(IV) complexes involving ONO-donor sugar Schiff bases

Seven new Schiff base complexes of oxovanadium(IV), [VO(L)(H₂O)], where H₂L = H₂bmpph-gls, H₂bumpph-gls, H₂iso-vmpph-gls, H₂pmpph-gls, H₂iso-bumpph-gls, H₂ampph-gls, and H₂vmpph-gls, have been synthesized by the reaction of VOSO₄·5H₂O and the said ligands in aqueous ethanol. The resulting complexes have been characterized on the basis of elemental analysis, vanadium determination, molar conductance, magnetic measurements, thermogravimetric (TG) analysis, infrared, electronic mass, and electron spin resonance studies. The thermal decomposition processes of one representative complex is discussed, and the order of reaction (n) and the activation energies (E_a) have been calculated from TG and differential TG curves. Molecular geometry optimizations, molecular surface electrostatic potentials, vibrational frequency calculations, bond lengths, bond angles and dihedral angles, and natural atomic charges obtained by natural bond orbital and Mulliken population analysis and calculations of molecular energies, highest occupied molecular orbital and lowest unoccupied molecular orbital were performed with the Gaussian 09 software package using density functional theory methods with Becke3–Lee–Yang–Parr (B3LYP) hybrid exchange–correlation functional and the standard 6-311G(+) basis set for (ampph-glsH₂) and LANL2DZ basis set for one of its complexes, [VO(ampph-gls)(H₂O)]. No imaginary frequency was found in the optimized model compounds, and hence it ensures that the molecule is in the lowest point of the potential energy surface, that is, an energy minimum. Finally calculated results were applied to simulate infrared spectra which show good agreement with observed spectra. Based on experimental and theoretical data, suitable square pyramidal structures have been proposed for these complexes.     

Theoretical study on the structures and properties of the isomers of Nn(CH)8−nH8 (n = 0–7)

With replacement of N atoms by CH groups in the most stable chain isomer of N8H8, 34 possible isomers of N_n(CH)_8−nH₈ (n = 0–7) have been designed and optimized at the B3LYP/6-311++G** level of theory. The natural bond orbital (NBO) and atoms in molecules (AIM) analysis are carried out to study the bonding nature and relative stabilities of these conformers. G3MP2 method is applied to calculate energies and heats of formation. The results indicate that the hyperconjugation effect from lone pairs of nitrogen atoms to germinal C–N bonds is the major factor which caused the change of the C–N bond length. With the more replacement of nitrogen atoms by CH groups, the heats of formation of the isomers of N_n(CH)_8−nH₈ (n = 0–7) decrease gradually, but the energies increase linearly.     

Energy decomposition analysis of the metal-oxime bond in [M{RC(NOH)C(NO)R}2] (M = Ni(II), Pd(II), Pt(II), R = CH3, H, F, Cl, Br, Ph, CF3)

Quantum chemical calculations using gradient-corrected DFT at the BP86/TZ2P+ level were carried out for the metal-dioxime complexes [M{RC(NOH)C(NO)R}₂]with M = Ni, Pd, Pt, R = CH₃, H, F, Cl, Br, Ph, CF₃. The nature of the metal-ligand bond was investigated with an energy decomposition analysis (EDA). The complexes with electron donating substituents R = H, CH₃ have the strongest metal-ligand interaction energies ΔE_int, as well as the largest bond dissociation energies. The analysis of the bonding situation revealed that the metal ← ligand σ donation is much stronger than the metal → ligand π backdonation. The breakdown of the orbital interactions into the contributions of orbitals with different symmetry indicates that the donation from the in-plane lone-pair donor-orbitals of nitrogen into the d_xy AO of the metal provides about one half of the stabilization which comes from ΔE_orb. Inspection of the EDA data indicates that the electrostatic term ΔE_elstat is more important for the trend of the metal-oxime interactions in [M{RC(NOH)C(NO)R}₂] than the orbital term ΔE_orb.     

A theoretical study of the structures and inversion barriers of CF3− and SiF3−

The structures and inversion barriers of CF₃^? and SiF₃^? have been calculated using ab initio SCF theory with several different basis sets and limited CI. The highest occupied molecular orbital of planar SiF₃^? is shown to have a₁′ symmetry, rather than the normally expected a₂″ symmetry. The best estimates of the inversion barriers are 119 kcal mol^?1 (CF₃^?) and 82 kcal mol ^?1 (SiF₃^?).     

Silylation as a protective method in acetylene chemistry. : Syntheses in the polyeneyne series,R3Si(CC)n(CHCH)4(CC)nSiR3 and H(CC)n(CHCH)4(CC)nH (n = 1, 2)

The Grignard reagents R₃Si(CC)_nMgBr (R = Me, n = 1; R = Et, n = 1,2) couple with cyclooctatetraene dibromide 1 in THF to give, as major products, the silyl-stabilised E, Z, Z, E-polyeneynes, Me₃SiCC(CHCH)₄CCSiMe₃3a, Et₃SiCC(CHCH)₄CCSiEt₃4a and Et₃Si(CC)₂(CHCH)₄(CC)₂SiEt₃6a together with minor proportions of configurational isomers Z, E, Z, Z 3c, all -E 3b, 4b, 6b and compounds in which a bicyclo-octadiene structure 2, 5 and 7 is retained. Irradiation converts the cis(Z)-rich isomers e.g. 3c into the all-trans(E) products. Treatment of the bissilyl compounds 3, 4 and 6 with aqueous base liberates the respective parent polyeneynes, H(CC)_n(CHCH)₄(CC)_nH, in each case.     

Metal complexes derived from hydrazoneoxime ligands: IV. Molecular and supramolecular structures of some nickel(II) complexes derived from diacetylmonoxime S-benzyldithiocarbazonate

Four new nickel(II) complexes, [{Ni(L)}₂], [NiL · HPyr], [NiL · HIm] and [Ni(HL)₂] · H₂O, derived from diacetylmonoxime-S-benzyldithiocarbazonate (H₂L) have been synthesized and characterized by elemental analyses, field desorption and electrospray ionization mass spectra, UV–Vis, infrared absorption spectra, as well as ¹H NMR spectra. X-ray molecular structures showed that the Ni(II) in both [NiL · HPyr] and [NiL · HIm] are in a distorted square planar environment and is coordinated to the dianionic NNS tridentate hydrazoneoxime ligand via deprotonated oximate nitrogen, hydrazone imine nitrogen, and thiolate sulphur. The fourth coordination sites are occupied, respectively, by the pyrazole and imidazole nitrogens. The oximate O1 of [NiL · HPyr] is involved in intramolecular hydrogen bond with the pyrazole NH proton as well as intermolecular hydrogen bond pyrazole C6H proton, forming a helical chain propagating along the b-axis. The structure is stabilized by a set of π?π and CH?π interactions. The molecular units in [NiL · HIm] are linked together by hydrogen bond formation between the oximate oxygen and imidazole NH proton, giving rise to an infinite zigzag chain extended along the a-axis. The chains are interconnected by π?π and CH?O interactions. In [Ni(HL)₂] · H₂O, the Ni(II) is in a distorted octahedral environment. The two mononegative hydrazoneoxime ligands are coordinated in the meridional configuration where the two thiol sulphur atoms and the two oxime nitrogen atoms are cis to each other, while the imine nitrogen atoms are trans. The oxime proton O2H is involved in a reciprocal bifurcated hydrogen bond formation with both N2 and S3 of the adjacent molecule giving rise to hydrogen bonded dimer. This dimeric structure is further stabilized by a pair of reciprocal CH?O interactions. A one dimensional chain of alternating dimeric unit and water molecule propagating along the c-axis is formed via hydrogen bond formation between the oxime O1 oxygen and the bridged water molecule proton.     

The borane analogy: CH ligand orientation in arachno- and closo-butterfly clusters

The model compound HB₂H₄CH is used as a means of examining the preferred CH ligand orientation when the borane butterfly fragment HB₄H₄⁺ fragment accommodates CH^? to give either a closo- or arachno-HB₄H₄CH cluster. The Fenske-Hall quantum chemical technique is used to explore cluster bonding first in terms of carbide protonation and then through the interaction of HB₄H₄⁺ and CH^?. BH is formally isolobal with Fe(CO)₃ and it is shown that the fragment-ligand orbital interactions and mechanism of CH bond weakening in HFe₄(CO)₁₂CH are modelled successfully using HB₄H₄CH.     

The photodissociation of physisorbed alkyl nitrites.: Λ-doublet population and alignment of desorbed NO

The photolysis of thin layers of tert- and iso-butyl nitrite, physisorbed on a transparent insulating MgF₂ surface, has been investigated. (1+1′)-Resonance-enhanced multiphoton ionization (REMPI) spectroscopy was used to characterize the desorbed NO. For high-J rotational levels, a preference for the Π(A″) Λ-doublet and a small degree of alignment is observed. The axis of alignment is found to be parallel to the plane of polarization of the photolysis laser and perpendicular to the surface normal, indicating a cartwheeling mode of desorption. The photofragment yield (PHOFRY) spectrum of iso-butyl nitrite is also reported.     

Experimental and calculated momentum densities for the valence orbitals of carbon tetrafluoride

Carbon tetraflouoride has been investigated by binary (e,2e) spectroscopy at 1200 eV impact energy. Binding energy spectra (10–60 eV) at azimuthal angles of 0° and 8° are reported and are found to be in quantitative agreement with a previous Green's function calculated spectrum. Momentum distributions corresponding to individual orbitals are also reported and compared with theoretical momentum distributions evaluated using double-zeta quality SCF wavefunctions. Excellent agreement between experimental and theories is found for the strongly bonding 3t₂ orbital and the antibonding 4a₁ orbital but agreement is less good for the outermost non-bonding orbitals. Intense structure due to molecular density (bond) oscillation is observed experimentally in the region above 1.0 a_o^?1 in the case of the non-bonding 4t₂ orbital. It is also notable that the measured 4a₁ momentum distribution exhibits an extremely well-defined “p” character with clear separation between the s and p components. Contour maps of the position-space and momentum-space orbital densities in the F-C-F plane of the molecule are used to provide a qualitative interpretation of the features observed in the momentum distribution. In order to further extend momentum-space chemical concepts to three-dimensional systems, constant density surface plots are also used to give a more comprehensive view of the density functions of the CF₈ molecule.     

Investigation of the electronic structure and the structural stability of selected penicillins by density functional calculations of 14N nuclear quadrupole resonance parameters

A computational study was carried out by density functional theory (DFT) to investigate the relative stability and reactivity in three selected penicillins: penicillin-G, penicillin-V and carbenicillin. The geometry of the investigated molecules was optimized at the B3LYP/6-31G(d) level of theory. Then, the nuclear quadrupole resonance (NQR) parameters of ¹⁴N and ²H nuclei and natural bond orbital (NBO) analysis in these molecules were calculated on the geometrically optimized models at the B3LYP level using 6-311++G(d,p) basis sets in the gas phase. The NBO analysis shows that the occupancy of the LP(N) decreases with increasing p character of the lone pair of nitrogen. A comparison between the results obtained for these penicillins and related 6-APA structures of them indicates that the presence of a bulky side group in the acyl side chain can lead to more stability of the β-lactam ring. On the other hand, NBO analysis was applied to rationalize the ¹⁴N NQR parameters in the charge distribution around nitrogen atoms. Inspection of the present results illustrates that the largest component of EFG tensor (q _zz ), the nuclear quadrupole coupling constant, C _Q, and the NQR frequency values of nitrogens decrease with decreasing occupancy values of LP(N). We suggest that the reason for this trend can be found in increasing contribution of delocalized electrons of nitrogen in the intramolecular interactions and hence stability of these structures increases in the order: PG < PV < CA. Finally, a good relationship is found between most of the calculated ²H NQR parameters and the related intramolecular hydrogen bonds.     

Structures and stabilities of [C3H3O]+ ions in the gas phase: A molecular orbital study

The relative energies of 11 [C₃H₃O]⁺ ions are calculated by different molecular orbital methods (MINDO/3, MNDO, ab initio with 3-21G and 4-31G* basis set and configuration interaction). The four most stable structures are: a ([CH₂?CH? CO]⁺), b c ([CH?C? CHOH]⁺) and d ([CH₂?C?COH]⁺); their relative energies at the CI/4-31G*//3-21G level are 0, 117, 171 and 218 kJ mol^?1, respectively. The isomerizations c→[CH?CH? CHO]⁺→[CH₂?C? CHO]⁺→ a and dissociations into [C₂H₃]⁺+CO and [HCO]⁺+C₂H₂ are explored. The calculated potential energy profile reveals that the energy-determining step is the 1,3-H migration c→[CH?CH? CHO]⁺. This explains the value of unity of the branching ratio and the spread of kinetic energy released for the two dissociation channels.     

Metal complexes derived from hydrazoneoxime ligands: III – Synthesis,characterization and electrospray ionization mass spectra of some nickel(II) complexes with aroylhydrazoneoximes

Five binuclear nickel(II) complexes [{Ni(L-R)}₂] derived from diacetylmonooxime aroylhydrazones (H₂L-R) have been prepared and characterized. In these complexes the oximate group functions as a bridge between the two nickel(II) ions. The corresponding octahedral bisligand complexes [Ni(HL-R)₂] have been also prepared and characterized. Reaction of [{Ni(L-R)}₂] with excess pyrazole (HPyr) afforded square planar [Ni(L-R)HPyr] complexes. The structure of [Ni(L-H)HPyr] (11), [Ni(L-CH₃O)HPyr] (13) and [Ni(L-Cl)HPyr] (14) have been determined by single-crystal X-ray diffraction. In these complexes, the Ni(II) is coordinated to the oximate nitrogen, hydrazone nitrogen and enolimine oxygen of the aroylhydrazoneoxime ligand, the fourth coordination site is occupied by pyrazole nitrogen. In 11 and 13 the molecular units are linked together by intramolecular NH?O hydrogen bonds forming a helical chain propagating along a and b axis respectively. The helical structure is stabilized by CH?O, CH?π and π?π noncovalent interactions. The structure of 14 consists of two independently crystallographic molecular units. The Ni1 molecular units are assembled together by CH?O and CH?Cl1 interactions forming a two dimensional sheet, while the Ni2 units are jointed together by CH?O and CH?C interactions forming a chain extending along b-axis which are enclosed between sheets of Ni1 units.