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Cobalamins, cobalt glyoximate complexes and nickel complexes with Triphos (bis(diphenylphosphinoethyl)phenylphosphine) and PPh2CH2CH2SEt ligands were studied with the DFT/BP86 method in connection with methyl transfer reactions. Geometries, methyl binding energies and redox potentials were determined for the studied complexes. Three- and four-coordinate structures were considered for nickel complex with PPh2CH2CH2SEt ligand, whereas four- and five-coordinate for its methyl derivative. On the basis of calculations, the possible mechanism of methyl transfer reaction between cobalt and nickel complexes was considered.

Methylcobalamin (MeCbl)-dependent enzyme methionine synthase (MetH), plays a critical role in the catalysis of methyl group transfer from methyltetrahydrofolate (CH3-H4folate) to homocysteine. It often performs a side reaction to generate cob(II)alamin through photolysis of the organometallic CoC σ bond. A hybrid QM/MM method has been applied to explore the photochemistry of MeCbl-bound MetH. The photolytic properties of MeCbl inside MetH are mediated by its manifold of low-lying excited states. The corresponding potential energy surfaces (PESs) of the electronically excited S1 state has been constructed as a function of axial bond lengths to elucidate the mechanism of photo-induced activation of CoC bond inside the enzyme. The analysis of the S1 PES has revealed that the two different electronic states of the S1 PES, namely metal-to-ligand charge transfer (MLCT) and the ligand field (LF), are relevant to the photodissociation of the CoC bond. There are two possible pathways identified, Path A and Path B, that connect the MLCT to LF state that represent possible photodissociation mechanisms. In the case of MetH, one possible photodissociation pathway (Path B) was identified based on the energetics of the MLCT and LF states. The energetically accessible Path B involves the initial detachment of the Co-NIm bond followed by a subsequent displacement of the CoC bond prior to the formation of cob(II)alamin / CH3 radical pair (RP). The photochemical data of base-on MeCbl in solution was compared with the computed result of MeCbl-bound MetH to understand the effect of the enzymatic environment on the photolytic properties of MeCbl.

Coenzyme B12 (adenosylcobalamin = AdoCbl)-dependent enzymes catalyze complex molecular transformations by employing radical chemistry. The initial step in the native catalytic cycle, upon substrate binding, involves homolytic cleavage of the Co–C bond of AdoCbl to form the Co(II)/Ado• radical pair (RP). Formation of Co(II)/Ado• is subsequently coupled with H atom abstraction from the substrate. Interestingly, these same RPs can be generated upon light absorption without presence of a substrate. Herein, the photochemistry associated with the mechanism of Co–C bond photocleavage inside the AdoCbl-dependent ethanolamine ammonia-lyase (EAL) was investigated using a combined time-dependent density functional theory and molecular mechanics (TD-DFT/MM) approach. Excited state potential energy surfaces (PESs), constructed as a function of axial bond lengths, were used to understand the photocleavage of the Co–C bond and to elucidate the mechanism of photodissociation for AdoCbl inside the enzyme. The S1 PES is ch...

Absorption and emission properties of six dithiinodiquinolines 1–6 (composed of 2,3- and/or 3,4-quinolinediyl units fused with 1,4-dithiin moiety) in methanol and cyclohexane solutions were studied. Differences in fluorescence properties of the compounds 1–6 are observed, depending on the type of condensed pattern of quinoline units. Emision bands of 1 and 2 occur at wavelengths over 500 nm are shifted systematically towards shorter waves when coming from 1,2 to 3,4 and 5,6. The compounds 1–6 posses long fluorescence lifetimes of several microseconds, which can be explained by an effective electronic conjugation in the excited state. In particular, the emission spectra of 3–6 in cyclohexane show two peaks characteristic for dual luminescence. The absorption and emission properties of compounds 1–6 were discussed in terms of DFT and TDDFT calculations. The geometry optimization of the excited nstates results in a planar structure as compared to a folded structure in the ground state of ditthiinodiquinolines 1–6.

Four novel cyclometalated iridium(III) complexes: [Ir(q-bt-Ph) 2 (phen)]PF 6 , [Ir(q-bt-Ph) 2 (acac)], [Ir(q-bt-Me) 2 (bpy)]PF 6 and [Ir(q-bt-Me) 2 (acac)] (where q-bt-Ph, q-bt-Me correspond to 2-(2,2’-bithien-5-yl)-4-phenylquinoline and 2-(2,2’-bithien-5-yl)-4-methylquinoline), are reported. The complexes were characterized by NMR, FTIR and HRMS. The optical, electrochemical properties and thermal stability of novel iridium(III) complexes were thoroughly investigated. The complexes emit a light in the narrow range of 693–707 nm. The optical study showed that replacement of fragment in the main quinoline ligand did not affect wavelength of the emitted light. On the other hand, the modification of the ancillary ligand and substituent in the quinoline ring caused the increase of the photoluminescence quantum yields. Electrochemical experiments demonstrate that the oxidation process for complexes [Ir(q-bt-Ph) 2 (phen)]PF 6 and [Ir(q-bt-Ph) 2 (acac)] was reversible (or quasi-reversible) and well detectable whereas for complexes with quinoline substituted by methyl group was irreversible, even at low temperature (−70 °C). The electrochemical and photophysical studies have been well confirmed by density functional theory (DFT) calculations. In addition, bulk heterojunction polymer solar cells based on complexes [Ir(q-bt-Ph) 2 (phen)]PF 6 and [Ir(q-bt-Ph) 2 (acac)] were fabricated. Only the solar cell incorporating [Ir(q-bt-Ph) 2 (acac)] exhibited a photovoltaic effect. The architecture of the cell was ITO/PEDOT:PSS/P3HT:PCBM:[Ir(q-bt-Ph) 2 (acac)]/Al. A power conversion efficiency of 0.25% was measured under 1 sun illumination using an AM 1.5G filter to simulate the solar spectrum.

Density functional theory (DFT/BP86) and the Polarizable Continuum Model (PCM/acetonitrile) for solvation have been applied to investigate the methyl transfer reaction from CH 3 I to Ni(PPh 2 CH 2 CH 2 SEt) 2 . Two different mechanisms were considered: S N 2 and radical one. The reaction paths for both examined mechanism were determined, and the geometries of possible substrates and products were compared.

The pKa values of isomeric sulfamoylquinolines 2a–8a and N,N-dimethylsulfamoylquinolines 2b–8b were determined by means of a UV–VIS spectroscopic method that uses absorbance diagrams, at constant ionic strength (0.15 M). For sulfamoylquinolines 2a–8a two pKa values – for basic function (Nring: −0.31 to 3.36) and for acid function (SO2NH2 group: 8.89–10.34) but only one in the case of N,N-dimethylsulfamoylquinolines 2b–8b (−0.05 to 3.07) – were obtained. The full geometry optimization in the 6–311 + G(d) basis set and the NBO population analysis were performed. Correlation between the experimentally determined and theoretically calculated (Sparc program) of pKa values as well as the differences between the calculated NBO population values for neutral and ionic forms were found for compounds 2a–7a and 2b–8b.

The DFT calculations for nitrosyl manganese and cobalt porphyrins were carried out with the use of several density functionals. The binding energy of nitrosyl ligand and spin state of nitrosyl-free manganese porphyrin were determined. The best values of binding energy are obtained from the OLYP functional. The NBO analysis of metal–nitrosyl bonding was performed. Electronic spectra of nitrosyl cobalt and manganese porphyrin were calculated with the TDDFT method. The calculated electronic transitions agree well with the experimental data except for the Soret band of (Por)Mn(NO), where they are 0.3–0.5 eV higher in energy than the experimental ones.

Complex fac-[RuCl3(NO)(P–N)] (1) was synthesized from the reaction of [RuCl3(H2O)2(NO)] and the P–N ligand, o-[(N,N-dimethylamino)phenyl]diphenylphosphine) in refluxing methanol solution, while complex mer,trans-[RuCl3(NO)(P–N)] (2) was obtained by photochemical isomerization of (1) in dichloromethane solution. The third possible isomer mer,cis-[RuCl3(NO)(P–N)] (3) was never observed in direct synthesis as well as in photo- or thermal-isomerization reactions. When refluxing a methanol solution of complex (2) a thermally induced isomerization occurs and complex (1) is regenerated. The complexes were characterized by NMR (31P{1H}, 15N{1H} and 1H), cyclic voltammetry, FTIR, UV–Vis, elemental analysis and X-ray diffraction structure determination. The 31P{1H} NMR revealed the presence of singlet at 35.6 for (1) and 28.3 ppm for (2). The 1H NMR spectrum for (1) presented two singlets for the methyl hydrogens at 3.81 and 3.13 ppm, while for (2) was observed only one singlet at 3.29 ppm. FTIR Ru–NO stretching in KBr pellets or CH2Cl2 solution presented 1866 and 1872 cm−1 for (1) and 1841 and 1860 cm−1 for (2). Electrochemical analysis revealed a irreversible reduction attributed to RuII–NO+ → RuII–NO0 at −0.81 V and −0.62 V, for (1) and (2), respectively; the process RuII → RuIII, as expected, is only observed around 2.0 V, for both complexes. Studies were conducted using 15NO and both complexes were isolated with 15N-enriched NO. Upon irradiation, the complex fac-[RuCl3(NO)(P–N)] (1) does not exchange 14NO by 15NO, while complex mer,trans-[RuCl3(NO)(P–N)] (2) does. Complex mer,trans-[RuCl3(15NO)(P–N)] (2′) was obtained by direct reaction of mer,trans-[RuCl3(NO)(P–N)] (2) with 15NO and the complex fac-[RuCl3(15NO)(P–N)] (1′) was obtained by thermal-isomerization of mer,trans-[RuCl3(15NO)(P–N)] (2′). DFT calculation on isomer energies, electronic spectra and electronic configuration were done. For complex (1) the HOMO orbital is essentially Ru (46.6%) and Cl (42.5%), for (2) Ru (57.4%) and Cl (39.0%) while LUMO orbital for (1) is based on NO (52.9%) and is less extent on Ru (38.4%), for (2) NO (58.2%) and Ru (31.5%).

Complete active space self-consistent field (CASSCF) computations followed by the second-order perturbation theory have been applied to investigate the electronic properties of a structural mimic of the reactant complex formed in the catalytic cycle of cobalamin-dependent methionine synthase (MetH). Two different structural models have been employed to analyze the reaction complex between methylcobalamin (MeCbl) and homocysteine (Hcy). The first model, referred to as the small model (SM), is based on a truncated corrin ring with inner conjugated macrocycle only and has symmetry constrain with respect to methylthiolate. The second is based on a full corrin ring, i.e., [Co(III)(corrin)]-Me(+)···(-)S-CH(3), without the side chains (which were replaced by hydrogen atoms) and referred to as the large model (LM). The active space chosen for both models includes all essential orbitals participating in the methyl transfer reaction. Although the CASSCF calculations are much more demanding for the LM (due to the structural complexity) than the SM, the results are fully consistent. The energetic of ionic and diradical states have been examined as a function of the C···S distance between the methyl group of MeCbl and the sulfur of the thiolate substrate for both models. The most important finding of the present work is the energetic variation of ionic and diradical states as a function of C···S distance. The two states cross each other at a C···S distance of 4.0 Å, i.e., for a distance shorter than ∼4.0 Å, the ionic state is energetically the lowest electronic state, while the diradical state becomes the lowest state at longer distances. However, the potential energy surface of the ionic state shows greater sensitivity with respect to the C···S distance than that of the diradical one. The former can be associated with S(N)2-type displacement, where the cleavage of the Co-C bond would be heterolytic, while the latter can be associated with an electron transfer (ET), where the cleavage is homolytic. Finally, the importance of this finding is briefly discussed in the context of MeCbl-dependent enzymatic catalysis.

Quantum chemical computations are used to study the electronic and structural properties of the cob(I)alamin intermediate of the cobalamin-dependent methionine synthase (MetH). QM(DFT)/MM calculations on the methylcobalamin (MeCbl) binding domain of MetH reveal that the transfer of the methyl group to the substrate is associated with the displacement of the histidine axial base (His759). The axial base oscillates between a His-on form in the Me-cob(III)lamin:MetH resting state, where the Co-N(His759) distance is 2.27 A, and a His-off form in the cob(I)alamin:MetH intermediate (2.78 A). Furthermore, QM/MM and gas phase DFT calculations based on an unrestricted formalism show that the cob(I)alamin intermediate exhibits a complex electronic structure, intermediate between the Co(I) and Co(II)-radical corrin states. To understand this complexity, the electronic structure of Im···[Cob(I)alamin] is investigated using multireference CASSCF/QDPT2 calculations on gas phase models where the axial histidine is modeled by imidazole (Im). It is found that the correlated ground state wave function consists of a closed-shell Co(I) (d(8)) configuration and a diradical contribution, which can be described as a Co(II) (d(7))-radical corrin (π*)(1) configuration. Moreover, the contribution of these two configurations depends on the Co-NIm distance. At short Co-NIm distances (

The paper presents a combined experimental and computational study of novel tricarbonyl complex – fac-[Re(CO)3(tp)2Cl] (tp = 1,2,4-triazolo-[1,5-a]pyrimidine). The compound has been characterized spectroscopically and structurally (by single-crystal X-ray diffraction). The absorption and emission spectra of the complex have been discussed on the basis of DFT and time-dependent (TD)DFT calculations.

Two novel tricarbonyl rhenium complexes based on the bidentate heterocyclic N–N ligands [bis(pyrazol-1-yl)methane(bpzm) and bis(3,5-dimethylpyrazol-1-yl)methane(bdmpzm)] have been synthesized by heating at reflux [Re(CO)5Cl] with the appropriate N–N ligand in toluene. The compounds have been characterized by IR and UV–Vis spectroscopy and X-ray analysis. Density functional theory (DFT) and time-dependent (TD) DFT calculations have been carried out for the [Re(CO)3(bdmpzm)Cl] complex.

The [(C6H6)RuCl(HPB)] and [(C6H6)RuCl2(C5H4NCOOH)] complexes have been prepared and studied by IR, UV–Vis spectroscopy and X-ray crystallography. The complexes was prepared in reaction of [(C6H6)RuCl2]2 with 2-(2′-hydroxyphenyl)-benzoxazole or 4-picolinic acid in methanol. The electronic spectra of the obtained compounds have been calculated using the TDDFT method. The luminescence property of the half sandwich complex [(C6H6)RuCl(HPB)] was studied by the DFT method and the mechanism was suggested.

This study was performed in order to explain different orientation in the reaction of quinolinyl sulfides with nitrating mixture, which converted on one hand quinolinyl sulfides 1, 3 and 5 to sulfoxides 2, 4 and 8, respectively, on the other hand, sulfides 6, 7 to the respective nitroderivatives 9 and 10. Competitive experiments showed following reactivity order: thianthrene 11 ≥ thianthrene 5-oxide 12 ≥ isothioquinanthrene 3 ≥ thioquinanthrene 1 ≥ 3,3′-diquinolinyl sulfide 5 ≥ 3,4′-diquinolinyl sulfide 6 ≥ 4,4′-diquinolinyl sulfide 7. Considering that NO2+ (as reactive form of nitrating mixture) attacks the most electronodonating (sulfur or carbon) center the reactivity order well correlates with the results of HOMO as well as MEP calculations.

The [(C6H6)RuCl(1,10-C12H8N2)]Cl complex has been prepared and studied by IR, UV–Vis, 1H NMR spectroscopy and X-ray crystallography. The complex was prepared in reaction of [(C6H6)RuCl2]2 with 1,10-phenatroline in acetone. The electronic spectrum of the compound has been calculated using the TDDFT method.

[(C6H6)Ru(1,2,4-triazole)3](CF3SO3)2 has been prepared and studied by IR, electronic and 1H NMR spectroscopy and X-ray crystallography. The complex was prepared by reaction of [(C6H6)RuCl2]2 with 1,2,4-triazole in the presence of AgCF3SO3 in methanol. The electronic spectrum of the compound has been calculated using the TDDFT method.

The DFT calculations on cobaltoporphyrin with nitric oxide as the axial ligand (PorCoNO, Por = porphyrin) were performed with the use of the B3LYP and BP86 functionals. The calculated Co–NO binding enthalpy is 12.2 kcal for the B3LYP functional and 35.2 kcal for BP86. The experimental binding enthalpy is equal 23.4 kcal. Calculated binding energy from CASPT2 method is 23.1 kcal, in very good agreement with experiment. The NBO charges indicate that the oxidation of PorCoNO occurs on the porphyrin ring. The spin densities of oxidized cobaltoporphyrin (PorCo+) obtained form the unrestricted wave functions show antiferromagnetic coupling of the electrons on the d z 2 cobalt orbital and π orbital of the porphyrin ring. The calculated oxidation potentials of nitrosyl cobaltoporphyrin from the B3LYP and BP86 functionals agree very well with the experimental values.

[(C6H6)RuCl2(pic)] complexes have been synthesized by the reaction of [(C6H6)RuCl2]2 with α-, β- and γ-picoline in methanolic solution. The prepared complexes have been studied by IR, UV–Vis and 1H NMR spectroscopy. The crystal structure of the complex with α-picoline was determined by X-ray crystallography. The electronic spectra of the compounds have been calculated by the TDDFT method.

The reactions of [ReOCl3(OAsPh3)(AsPh3)] and [ReOCl3(PPh3)2] with 1,10-phenanthroline (phen) have been examined and the complexes [ReOCl3(phen)] (1) and [ReCl2(phen)(PPh3)2](ReO4) (2) have been obtained. The crystal and molecular structures of 1 and 2 · 1 2 H 2 O have been determined. The geometric parameters of 1 and 2 have been examined with the density functional theory (DFT) method. The spin-allowed electronic transitions have been calculated with the time-dependent DFT method for [ReOCl3(phen)], [ReCl2(phen)(PPh3)2]+ cation and ReO 4 - anion, and the UV–Vis spectra of the title compounds have been discussed on this basis.

The calculations using the density functional theory (DFT) method were done on two diamagnetic oxo-bridged dinuclear rhenium complexes: [{Re(O)Br 2 (3,5-Me 2 pzH) 2 } 2 (μ-O)] ( 1 ) with a linear O Re–O–Re O core and [{Re(O)Br(3,5-Me 2 pzH)} 2 (μ-O)(μ-3,5-Me 2 pz) 2 ] ( 2 ) with a bent Re 2 O 3 unit (pzH monodentate N -pyrazole and pz bidentate N , N ′-pyrazole ligand). The optimized geometries of 1 and 2 agree with the X-ray structures. The MO sequence is almost the same for 1 with a linear O Re–O–Re O core and 2 with a bent Re 2 O 3 unit. The bending of Re 2 O 3 unit in 2 is a consequence of steric congestion introduced by two coordinated 3,5-dimethylopyrazole bridging ligands. Additional information about binding in the complexes 1 and 2 was obtained by NBO analysis.

The [{ReCl 4 (PPh 3 )}(μ-O){Re(O)(3,5-Me 2 pzH) 4 }] complex has been isolated as a product of the degradation of [ReCl 3 (3,5-Me 2 pzH) 2 (PPh 3 )] during slow crystallization from chloroform in air. Its crystal and molecular structure has been determined as well as spectroscopic investigations and density functional theory (DFT) calculations have been carried out. The UV–Vis spectrum of the dirhenium complex has been discussed on the basis of the spin-allowed electronic transitions calculated for [{ReCl 4 (PPh 3 )}(μ-O){Re(O)(3,5-Me 2 pzH) 4 }] with the time-dependent DFT (TDDFT) method.

The reactions of the [ReOCl3(AsPh3)(OAsPh3)] and [ReOCl3(PPh3)2] complexes with pyrazole (pzH) have been examined and two novel oxo compounds – [ReOCl2(pzH)2(OAsPh3)](ReO4) (1) and [{ReCl2(pzH)2}2(μ-O)] (2) – have been obtained. The crystal, molecular and electronic structures of 1 and 2 have been determined. The geometric parameters of 1 and 2 have been examined using the density functional theory (DFT) method. The spin-allowed singlet–singlet electronic transitions have been calculated with the time-dependent DFT method for the [ReOCl2(pzH)2(OAsPh3)]+ cation, ReO 4 - anion and [{ReCl2(pzH)2}2(μ-O)] complex, and the UV–Vis spectra of the title compounds have been discussed on this basis.

The five possible isomers of the [RuCl2(PPh3)2(HPz)2] were studied by DFT method. The isomer formed in the course of synthesis has lowest energy. The electronic spectrum of cis,cis,cis-[RuCl2(PPh3)2(HPz)2] was calculated by the TDDFT method with the PCM model in the solvent. On the basis of calculations the low energy band at 471 nm was assigned as LF transition, the band at 349 nm has MLCT character, the broad band with the shoulder at 270 nm results from LMCT, MLCT and intraligand/interligand LLCT transitions character.

The reaction of [(C6H6)RuCl2]2 with 7,8-benzoquinoline and 8-hydroxyquinoline in methanol were performed. The obtained complexes have been studied by IR, UV–VIS, 1H and 13C NMR spectroscopy and X-ray crystallography. In the reaction with 8-hydroxyquinoline the arene ruthenium(II) complex oxidized to Ru(III). The electronic spectra of the obtained compounds have been calculated using the TDDFT method. Magnetic properties of [Ru(C9H6NO)3] · CH3OH complex suggest the antiferromagnetic coupling of the ruthenium centers in the crystal lattice. EPR spectrum of [Ru(C9H6NO)3] · CH3OH compound indicates single isotropic line only characteristic for Ru3+ with spin equal to 1/2.

The reaction of [ReBr3(NO)(PPh3)2] complex with pyrazole (pzH) has been examined and a new rhenium nitrosyl – [ReBr3(NO)(PPh3)(pzH)] – has been obtained. The X-ray structure of the [ReBr3(NO)(PPh3)(pzH)] complex has been determined and its electronic structure has been calculated with the density functional theory (DFT) method with the use of B3LYP functional. Additional information about binding in the [ReBr3(NO)(PPh3)(pzH)] complex has been obtained by NBO analysis. The time-dependent DFT method (TDDFT) has been used for calculations of spin-allowed doublet–doublet electronic transitions of [ReBr3(NO)(PPh3)(pzH)], and on this basis the UV–Vis spectrum has been discussed.

The reactions of the complex [ReBr3(AsPh3)(OAsPh3)] with pyrazine (pyz) and pyridazine (pyd) have been examined and novel dinuclear rhenium oxocomplexes – [{ReOBr2(pyz)2}2(μ-O)] with a linear O Re–O–Re O backbone (1) and [{ReOBr2}2(μ-O)(μ-pyd)2] with a bent Re 2 O 3 4 + core (2) – have been obtained. The X-ray structures of the complexes 1 and 2 have been determined, and their electronic structures have been examined using the density functional theory (DFT) method. The UV–Vis spectra of 1 and 2 have been interpreted on the basis of the results of time-dependent DFT (TDDFT) calculations.

The reaction of the [RuCl2(PPh3)3] complex with picolines has been examined. New ruthenium(II) complexes – [RuCl2(C6H7N)4] have been obtained and characterized by IR, 1H NMR and UV–Vis measurements. The crystal structure of the [RuCl2(β-pic)4] complex has been determined. The electronic spectra of the complexes have been calculated by the TDDFT method.

The [ReOBr3(dppe)] (dppe=bis(diphenylophosphino)ethane) complex reacts with acetonitrile in the presence of excess of triphenylphpsphine to give a new monomeric nitrile rhenium(III) complex—[ReBr3(MeCN)(dppe)] (1). The reaction of 1 with gaseous nitric oxide leads to the mixed [ReBr3(NO)(dppe)]0.57[ReOBr3(dppe)]0.43 complex (2) with rhenium atoms on +2 and +5 oxidation states. This paper presents the synthesis, spectroscopic characterisation and X-ray structure of 1 and 2. The geometries of [ReBr3(NO)(dppe)] and [ReOBr3(dppe)] have been optimized using the density functional theory (DFT) and the electronic transitions of [ReBr3(NO)(dppe)] and [ReOBr3(dppe)] have been calculated with the time-dependent DFT method (TDDFT). The UV–vis spectrum of 2 has been interpreted on the basis of the experimental data for [ReOBr3(dppe)] and the calculated transitions for [ReOBr3(dppe)] and [Re(NO)Br3(dppe)].

The reactions of [NBu4]2[ReX5(NO)] (X = Cl, Br) with triphenylstibine have been examined and three new rhenium complexes – [ReCl2(NO)(SbPh3)3] (1), [ReBr2(NO)(SbPh3)3] (2) and [ReBr2Cl(SbPh3)3] (3) – have been obtained. The last one has been isolated in a low yield during slow recrystallization of the complex 2 from a mixture of chloroform and ethanol. The stibine rhenium nitrosyls have been characterized by IR and UV–vis spectroscopy. The X-ray structures of 1 and 3 have been determined. The geometric parameters of 1 have been examined using the density functional theory (DFT) method.

A new rhenium nitrosyl – [ReCl3(NO)(OPPh3)(pyz)] – has been obtained by two different routes: (i) in the substitution reaction of [ReCl3(NO)(OPPh3)(PPh3)] with pyrazine, and (ii) in the nitrosylation reaction of [ReOCl3(PPh3)2] by gaseous nitric oxide in the presence of an excess of pyrazine. The crystal, molecular and electronic structure of the [ReCl3(NO)(OPPh3)(pyz)] complex has been determined. The geometric parameters of [ReCl3(NO)(OPPh3)(pyz)] have been examined using the density functional theory (DFT) method. The UV–Vis spectrum of the pyrazine complex has been interpreted on the basis of the electronic transitions of [ReCl3(NO)(OPPh3)(pyz)] calculated with the time-dependent DFT method (TDDFT). The paper also includes the results of the DFT and TDDFT calculations for [ReCl3(NO)(OPPh3)(PPh3)].

The reaction of [RuCl3(NO)(PPh3)2] complex with pyrazole has been examined. The new ruthenium complex – [RuCl3(NO)(PPh3)(C3 H4N2)] has been obtained and characterised by IR and UV–Vis measurements. Crystal, molecular and electronic structures of the complexes have been determined. The electronic spectrum of the complex was calculated by the TDDFT method.

The aim of present study is to select the best methodology in the frame of the Density Functional Theory (DFT), which may be employed to study the cobalamin complexes. Our discussion is limited to two approaches, one in which hybrid B3LYP and UB3LYP functionals are used, and the second in which geometry parameters are calculated within LDA-VWN functional, and energies of the investigated systems are computed within RPBE functional. Results of performed calculations show that both methodologies can be successfully applied to study cobalamin derivatives. Probably because of the small ligand binding energies in the studied complexes, the B3LYP and UB3LYP functionals may be used only to predict the pattern of changes in the binding energies. The use of the RPBE functional, originally parameterized to reproduce in a proper way the chemisorption energies of the small molecules on the metallic surfaces, allows to improve their values so as they fit into experimental data. Geometry parameters of the investigated complexes computed within both approaches are in good agreement with the experimental values. Interatomic distances are a little overestimated while calculated within both hybrid functionals, what is in contrast to VWN functional results. The latter, in general, gives shorter distances as observed experimentally.

The X-ray structure of a new paramagnetic [ReCl3(pzH)3] complex (pzH=pyrazole) has been determined and its geometric parameters have been examined using the density functional theory (DFT) method. The UV–Vis spectrum of the complex has been discussed on the basis of the electronic transitions of [ReCl3(pzH)3] calculated with the time-dependent DFT method (TDDFT).

X-ray structures of new [ReCl3(pzH)2(PPh3)] and [ReCl3(3,5-Me2pzH)2(PPh3)] complexes (pzH=pyrazole) have been determined, and the geometric parameters of [ReCl3(pzH)2(PPh3)] have been examined using density functional theory (DFT) method. The UV–Vis spectra of the complexes have been discussed on the basis of the electronic transitions of [ReCl3(pzH)2(PPh3)] calculated with time-dependent DFT method (TDDFT).

The reactions of the (C6H6)RuCl2]2 complex with pyrazole and dimethylpyrazole have been examined. The ruthenium complexes, [(C6H6)RuCl(C3N2H4)2]Cl and [(C6H6)RuCl(C5N2H8)2], have been obtained and characterized by IR, UV–Vis and 1 H NMR measurements. Crystal, molecular and electronic structures of the complexes have been determined. The geometries of the complexes were optimized with the DFT method and their UV–VIS spectra were calculated with the TDDFT method. 2003 Elsevier Ltd. All rights reserved.

The electronic spectrum of Co-corrin was calculated with the TDDFT/B3LYP method. The calculated spectrum is compared to the experimental spectrum of vitamin B 12s which is known to be four coordinate in solution. Three basis sets were used in the calculations, one with the 6-311G*++ basis and two with the LANL2DZ+d basis on the cobalt atom. The results are similar for the several longest wave transitions in all the three bases. The bands at 700 and 554 nm are assigned as d→π ∗ transitions. The band at 460 nm has a prevailing d → d character. The bands at 385 and 300 nm are mainly of π→π ∗ and d→π ∗ character. The average energy error of calculated excitation energies for these bands is about 0.2 eV. The higher energy bands at 286 and 280 nm can be assigned as mainly d→π ∗ and π→π ∗ transitions from the calculated spectrum with the 6-311G*++ basis. In LANL2DZ+d the transitions to 4p orbitals dominate in this part of the spectrum. The problem with calculating the highest energy transitions in Co-corrin may be traced to the high-lying HOMO orbital of this molecule.

The electronic spectra of protonated and unprotonated metal-free corrins were calculated by the TDDFT method in the B3LYP version. Two low energy forms were found from geometry optimization for the protonated corrin, as well as for the unprotonated one. The calculated energies of electronic transitions are in good agreement with the experimental spectrum of synthetic corrin. The largest difference is 0.45 eV and the average difference 0.25 eV. The spectrum of the unprotonated corrin is similar to the spectrum of the protonated corrin with more pronounced n → π* transitions due to one more lone electron pair on nitrogen atoms.

High-level ab initio calculations were performed at the restricted Hartree–Fock (RHF) level of theory on carbazole and its N-methyl and N-ethyl derivatives. Single-point gauge-invariant atomic orbitals (SP GIAO) RHF NMR calculations on ab initio RHF optimized geometries were performed. The 6–31G* and 6–311++G** basis sets were used and some calculations were performed within a density functional theory using a recent B3PW91 hybrid functional. The theoretically predicted multinuclear magnetic resonance chemical shifts of carbazole and its N-methyl and N-ethyl derivatives in the gas phase are compared with experimental NMR data in CDCl3 solutions. A revised assignment of 13C NMR spectra of simple carbazoles is proposed. Copyright © 2000 John Wiley & Sons, Ltd.

The energy of CbFe(CO) 3 was calculated with RHF and CAS(12,12) methods as a function of Fe–Cb distance. RHF wave function was shown to be unstable in a wide range of Fe–Cb distances. Two types of UHF solutions were found, one which breaks the symmetry of the Fe–Cb bond, and another where the symmetry breaking in the ring also occurs. The symmetry breaking in Fe–carbonyl bonds was found to be important, too. The geometry of CbFe(CO) 3 was optimized with RHF and CAS(10,10) methods, while the Fe–Cb and Fe–CO distances were optimized also at the CASPT2 level. CAS(10,10) optimized Fe–C(Cb) bond lengths reproduce correctly the experimental trends while the RHF optimized geometry was found to be in disagreement with experiment. The rotational barrier calculated is equal to zero in all methods. The Fe(CO) 3 –Cb binding energy was calculated on CASPT2 level.

Density functional theory (DFT/BP86) and the polarized continuum model (PCM/ε = 20) have been applied to perform calculations for the A-cluster of acetyl-CoA synthase enzyme. The geometry optimization was carried out for the oxidized, one- and two-electron reduced A-cluster as well as for A-cluster with ligands important in the catalytic cycle, i.e., H2O, CO, CH3, OH(-), and H(+). The electronic structure of the studied species (spin densities and NBO charges) was analyzed and the metal-metal interactions were investigated with the use of Wiberg bond indices (WBIs). The pKa values and the reduction potentials have been determined. On the basis of the calculations, the mechanism of PCET reductive activation of the A-cluster has been proposed for the methylation catalytic step.

AM1 molecular orbital calculations were carried out for a series of compounds having the formula Ph-SO 2 -CR 1 R 2 -COOH, some of which possess a sweet taste. The minimum-energy conformation with an intramolecular hydrogen bond was found for each compound investigated.

In this study we have carried out semiempirical AM1 and PM3 calculations on a simplified penicillin molecule (i.e. methylpenicillin) in the presence of the Zn(II) ion to assess the probable complex structures and to gain additional information on the mechanism of the metal-ion promoted hydrolysis of penicillins. Theoretical investigations based on calculated heats of formation Δ H f predict formation of two complexes of comparable thermochemical stability in aqueous solutions of methylpenicillin in the presence of Zn(II): by the COO − group alone and by the COO − group and β-lactam ring nitrogen atom. The former structure, with four watermolecules, is slightly favoured Δ H f lower by 6.5 kcal mol −1 (AM1)and 10.7kcal mol −1 (PM3)). A complex involving binding to the C6 substituent described in some earlier works was not found. The calculated lengthening of the ligand C7-N4 bond upon coordination suggests easier Nu − attack at the β-lactam carbon atom, which facilitates the degradation of penicillin. The results also indicate that both methods can be applied to calculations on penicillins. Generally, the PM3 bond lengths are longer than the AM1 values; however, the former reproduces better the first coordination sphere of the Zn(II) ion.

The calculations for iron complexes with EDTA and NO, [FeII(edta)(NO)]2− and [FeIII(edta)(NO)]−, were performed with the DFT/B3LYP method. The lowest energy structure for the Fe(II) complex is six-coordinated with one carboxylate group unbound. The Fe–NO bond is here short and strengthen additionally by the charge shift to form FeIIINO. The low stability of the [FeIII(edta)(NO)]− complex can be interpreted in terms of the weak Fe–NO bond calculated for this species. Photoreduction of the [FeIII(edta)(H2O)]− or [FeIII(edta)(OH)]2− complex by EDTA in the NO atmosphere was studied and is suggested as convenient method of the [Fe(edta)(NO)]2− synthesis. The results of the [Fe(edta)(NO)]2− irradiation connotes also a possibility of alternative release NO or N2O in acidic or alkaline solution, respectively. The calculated electronic spectrum of [Fe(edta)(NO)]2− showed that low and medium energy bands are mainly of π NO ∗ / d → d / π NO ∗ , while transitions from free electron pairs of nitrogen and oxygen atoms to metal d and nitrosyl π NO ∗ orbitals are responsible for the high energy band. The former favors homolytic dissociation of the neutral NO molecule, whereas the latter heterolytic Fe–NO bond cleavage. In both cases excitation leads to weakening of the Fe–NO bond, enabling the pH effect on dissociation of neutral NO molecule or NO anion. This outcome allows to control the NOx delivery by two stimuli: light and solution pH.

The mechanism of Co-C bond photodissociation in methylcobalamin (MeCbl) and ethylcobalamin (EtCbl) has been examined by means of time-dependent density functional theory (TD-DFT). The present contribution extends our recent study (J. Phys. Chem. B 2007, 111, 2419-2422) where relevant excited states involved in the photolysis of MeCbl have been identified. To obtain reliable structural models, the high-resolution crystal structure of MeCbl was used as the source of initial coordinates. The full MeCbl was simplified by replacing the corrin side chains by H atoms and the resulting geometry was optimized. The model of EtCbl was generated from the simplified structure of MeCbl by replacing methyl group with ethyl. For both models, the low-lying singlet and triplet excited states have been computed along the Co-C coordinate at TD-DFT/BP86/6-31G(d) level of theory. These calculations reveal that the photodissociation process is mediated by the repulsive 3(sigmaCo-C-->sigma*Co-C) triplet state. The overall mechanism of photodissociation for both systems is similar but energetic details are different, reflecting the difference in Co-C bond strength in MeCbl and EtCbl. In both cases the key intermediate involved in Co-C bond photodissociation is identified as first excited state (S1). The S1 intermediate has mixed character: it can be described as predominantly dCo-->pi*corrin metal-to-ligand charge transfer (MLCT) state with contribution from sigma bond to corrin charge transfer (SBLCT) where upon electronic excitation the electron density shifts from the axial NIm-Co-C bonding to corrin ligand. The optimized geometry of the S1 indicates that the structure of the corrin remains essentially unchanged in comparison to ground state (S0). The major structural change occurs in the NIm-Co-C moiety, which becomes bent with elongated Co-C bond in S1 state. Finally, it is proposed that the photolysis of Co-C bond is in line with the mechanism of heme-CO photolysis, where participation of the dFe-->pi*porphyrin has been suggested.

Block condensation of MePOCI2 or MeP(NEt2)2 with appropriately protected tetra(thymidine methanephosphonates) of predetermined sense of chirality at asymmetric phosphonate centres gave two pairs of diastereomeric mixtures, namely (SpSpSpSpSpSpSp + SpSpSpRpSpSpSp) 5a and (RpRpRpRpRpRpRp + RpRpRpSpRpRpRp) 5b. A comparison of the CD spectra of 5a and 5b with those of octathymidylic acid (7) and a random mixture of diastereomers of octa(thymidine methanephosphonate) (6), and also a comparison of the Tm of complexes formed between 5a, 5b, 6 or 7, and pentadecadeoxyriboadenylic acid (8), indicates that octamer 5b and its complex with its complementary oligonucleotide has a well-ordered structure due to the 'outward' or 'pseudoequatorial' orientation of the methyl group of each internucleotide methanephosphonate function of Rp configuration. Results presented in this report clearly indicate that the stability of hybrids formed between octa(thymidine methanephosphonate) and pentadecadeoxyriboadenylic acid depends on the stereochemistry of each internucleotide methanephosphonate function and strongly suggests that stereoselective synthesis of P-chiral oligonucleotide analogues is an important goal.

This study was performed in order to explain different orientation in the reaction of quinolinyl sulfides with nitrating mixture, which converted on one hand quinolinyl sulfides 1, 3 and 5 to sulfoxides 2, 4 and 8, respectively, on the other hand, sulfides 6, 7 to the respective nitroderivatives 9 and 10. Competitive experiments showed following reactivity order: thianthrene 11 ≥ thianthrene 5-oxide 12 ≥ isothioquinanthrene 3 ≥ thioquinanthrene 1 ≥ 3,3′-diquinolinyl sulfide 5 ≥ 3,4′-diquinolinyl sulfide 6 ≥ 4,4′-diquinolinyl sulfide 7. Considering that NO2+ (as reactive form of nitrating mixture) attacks the most electronodonating (sulfur or carbon) center the reactivity order well correlates with the results of HOMO as well as MEP calculations.

The relevant excited states involved in the photolysis of methylcobalamin (MeCbl) have been examined by means of time-dependent density functional theory (TD-DFT). The low-lying singlet and triplet excited states have been calculated along the Co-C bond at the TD-DFT/BP86/6-31g(d) level of theory in order to investigate the dissociation process of MeCbl. These calculations have shown that the photodissociation is mediated by the repulsive 3(sigmaCo-C --sigma*Co-C) triplet state. The key metastable photoproduct involved in Co-C bond photolysis was identified as an S1 state having predominantly dCo --pi*corrin metal-ligand charge transfer (MLCT) character.

Retroviral integrases are essential for viral replication and represent an attractive chemotherapeutic target. In the current study, we demonstrated the activity of micromolar concentrations of dinucleotides against human immunodeficiency virus type 1 (HIV-1), HIV type 2 (HIV-2), simian immunodeficiency virus, and feline immunodeficiency virus integrases. The structure-activity relationship indicates that 5'-phosphorylation enhances potency and that phosphodiester and sugar modifications affect the inhibition of HIV-1 integrase. Base sequence selectivity was observed: pAC, pAT, and pCT were the most potent inhibitors, whereas pAA, pGA, and pGC showed low activity at 100 microM. The inhibition by pAC is consistent with the interaction of the enzyme with the 5' end of the noncleaved strand (5'-AC-3'). The linear and cyclic dinucleotides released by the 3'-processing reaction did not affect enzymatic activity at physiological concentrations. An increase in the length to trinucleotides or tetranucleotides enhanced potency by only 2-3-fold, suggesting that two neighboring bases may be sufficient for significant interactions. Inhibition of a truncated (50-212) integrase mutant and global inhibition of all nucleophiles in the 3'-processing reaction suggest that dinucleotides bind in the catalytic core. All of the active dinucleotides inhibited enzyme/DNA binding in their respective IC50 range. Although the dinucleotides tested showed no antiviral activity, these observations demonstrate the usefulness of dinucleotides in elucidating enzyme mechanisms and as potential ligands for cocrystallization and as lead structures for development of antivirals.