N-Hydroxyurea dimers: A matrix isolation and theoretical study

The dimerization of N-hydroxyurea (NH₂CONHOH) has been investigated by FTIR matrix isolation spectroscopy and DFT(B3LYP)/6-311++G(2d,2p) calculations. The analysis of NH₂CONHOH/Ar matrix spectra and comparison with theoretical ones reveal the formation of two types of dimers with a strong OH⋯O hydrogen bond. There is an additional weak interaction between the oxygen atom of the OH group of the proton donor molecule and the NH or NH₂ group of the proton acceptor in both dimers, respectively. The identified structures correspond to local minima on the PES. The formation of the less stable structures not the most stable ones indicates that the creation of N-hydroxyurea dimers is related to the dipole-dipole interaction at the initial stage of the dimerization process, which favours generation of polar dimers.     

Thermodynamic study of the dimerization of 8-anilino-1-naphthalenesulfonic acid by isothermal titration calorimetry

Dimerization of the fluorescence probe, 8-anilino-1-naphthalenesulfonic acid (ANS) in aqueous media have been studied by isothermal titration calorimetry (ITC). ITC experiments carried out at different pHs show that dimerization constants are highly pH dependent, decreasing their values with increasing pH. No dimerization is detected over pH 7. Analyzing the dependence of K_dim on pH, using a model that only considers dimers between zwitterionic molecules of ANS, a value of 5.6 for the pK of anilinium moiety is obtained. It is in agreement with the pK determined spectrophotometrically. The dimerization process is enthalpically disfavored and entropically driven at all pH and temperatures studied, indicating that hydrophobic effect has an important role on the formation of dimers. Although dimerization constants are low, dimerization equilibria must be taken into account when the energetics of the interaction of ANS to a protein is studied at pH below 7.     

Steric Control in the π‐Dimerization of Oligothiophene Radical Cations Annelated with Bicyclo[2.2.2]octene Units

A Two series of oligothiophenes 2 (nT) (n=4,5), annelated with bicyclo[2.2.2]octene (BCO) units at both ends, and quaterthiophenes 3 a – c , annelated with various numbers of BCO units at different positions, were newly synthesized to investigate the driving forces of π‐dimerization and the structure–property relationships of the π‐dimers of oligothiophene radical cations. Their radical‐cation salts were prepared through chemical one‐electron oxidation by using nitrosonium hexafluoroantimonate. From variable‐temperature electron spin resonance and electronic absorption measurements, the π‐dimerization capability was found to vary among the members of the 2 (nT)^{+ .} SbF₆^? series and 3 ^{+ .} SbF₆^? series of compounds. To examine these results, density functional theory (DFT) calculations at the M06‐2X/6‐31G(d) level were conducted for the π‐dimers. This level of theory was found to successfully reproduce the previously reported X‐ray structure of ( 2 (3T))₂²⁺ having a bent π‐dimer structure with cis–cis conformations. The absorption bands obtained by time‐dependent DFT calculations for the π‐dimers were in reasonable agreement with the experimental spectra. The attractive and repulsive forces for the π‐dimerization were divided into four factors: 1) SOMO–SOMO interactions, 2) van der Waals forces, 3) solvation, and 4) Coulomb repulsion, and the effects of each factor on the structural differences and chain‐length dependence are discussed in detail.     

Synthesis, spectroscopic studies and crystal structure of a polyoxoanion cluster incorporating para-bromophenylimido ligand, (Bu4N)2[Mo6O18(NC6H4Br-p)]

An organic-inorganic hybrid compound, (Bu₄N)₂[Mo₆O₁₈(NAr)] (Ar = p-BrC₆H₄) has been synthesized via the DCC dehydrating protocol of the reaction of [α-Mo₈O₂₆]⁴⁻ with 4-bromoaniline hydrochloride in anhydrous acetonitrile, which has been characterized by UV-Vis spectra, ¹H NMR and single crystal X-ray diffraction study. By comparing the UV-Vis spectra, which were used to monitor the reaction, the optimum preparative condition for this compound was also determined. This compound crystallizes in the monoclinic space group P2₁/n, which is featured in a terminal para-bromophenylimido group linked to an Mo atom of a hexamolybdate cluster by a Mo-N triply bond. In addition, there are π-π dimerization of the neighboring cluster anions though the parallel aromatic rings in their crystals.     

Dielectric study of dipolar association in dilute solutions of nitrobenzene in benzene

The correlation factors R_p and R_s are determined for the dielectric polarization and the non-linear dielectric effect in dilute solutions of nitrobenzene in benzene. Assuming dipole association of the nitrobenzene molecules to be restricted to dimerization, we determined the concentration x₂ of dimers, their dipole moment μ_dim, and the equilibrium constant K_x and Gibbs energy ΔG of the dimerization process.     

Catalytic tail-to-tail dimerization of methyl acrylate using bis(triphenylphosphine)tricarbonyl ruthenium(0)

The complex Ru(CO)₃(PPh₃)₂ catalyzes the dimerization of methyl acrylate at 120–140°C to give tail-to-tail dimers containing predominantly dimethyl (E)-2-hexene-1,6-dioate together with small amounts of trimers and polymer. The reaction under hydrogen atmosphere selectively gave tail-to-tail dimers in improved yield without formation of trimers and polymer. Under these conditions a catalyst turnover number of 246 was obtained at 130°C in 6 h.     

Crystal structure and magnetic properties of the coupled spin dimer compound SrCu2(TeO3)2Cl2

Single crystals of the strontium copper tellurium oxochloride SrCu₂(TeO₃)₂Cl₂ were synthesized via solid-gas reactions in sealed evacuated silica tubes. The compound crystallizes in the monoclinic system, space group P2₁, a=7.215(2), b=7.2759(15), c=8.239(2) Å, β=96.56(4)°, Z=2. The building units are [SrO₆Cl₂] irregular polyhedra, [CuO₄] and [CuO₃Cl] square planes, [TeO₃E] tetrahedra and [TeO₃₊₁E] trigonal bipyramids; E being the 5s² lone pair of Te(IV). The Cu atoms can be regarded as forming a chain of weakly connected dimers. The magnetic susceptibility of the compound shows a broad maximum typical for antiferromagnetic spin fluctuations with a non-magnetic ground state. A Heisenberg spin model with coupled s=1/2 dimers leads to a satisfactory fitting of the experimental data.     

The First Examples of Unsymmetrically Substituted Anhydro Dimers of Salicylaldehyde

Three new nitro-substituted anhydro dimers of salicylaldehyde have been obtained, either by selective nitration of the parent dimer or by statistical dimerization of 3- and 5-nitrosalicylaldehydes. These constitute the first examples of dimers without identical substitution in the two rings and therefore without a C₂ axis.     

A novel hydrogen peroxide-dependent oxidation pathway of dopamine via 6-hydroxydopamine

In the presence of excess H₂O₂, oxidation of dopamine was diverted from the usual pigment-forming pathway to afford 6-hydroxydopamine and then a colorless reaction mixture comprising a polar non-extractable product. The latter was obtained in 20% yield by oxidation of 6-hydroxydopamine and was tentatively formulated as the novel 5-(2-aminoethyl)-2-hydroxy-5-(3-hydroxy-2-oxotetrahydro-1aH-oxireno[2,3]cyclopenta[1,2-b]pyrrol-3a(4H)-yl)cyclohex-2-ene-1,4-dione by extensive spectral analysis and conversion to a tetraacetyl derivative. Mechanistic experiments suggested that formation of the product proceeds via 6-hydroxydopamine by H₂O₂-dependent epoxidation and cyclization steps followed by dimerization and ring contraction with decarboxylation.     

A density functional theory study of dimers of hydrophosphoryl compounds and proton transfer in them

The structures of dimers of several types of dimethylphosphinous acid (CH₃)₂POH and dimethylphosphine oxide (CH₃)₂P(O)H and dimers of the corresponding perfluorinated derivatives (CF₃)₂POH and (CF₃)₂P(O)H were studied in detail by density functional theory with the PBE gradient-corrected functional and the TZ2p basis set. Fairly strong dimeric associates (2.50–10.5 kcal/mol) were shown to form thanks to O-H···O, O-H···P, and C-H···O H-bonds and dipole-dipole interactions of polar phosphoryl groups P → O of two monomer molecules. The existence of C-H···O and the absence of P-H···O H-bonds in (CH₃)₂P(O)H dimers was substantiated by an AIM (atoms in molecules) analysis of their structures according to Bader. The reaction coordinates were calculated for synchronous transfer of two protons in (CH₃)₂POH and (CF₃)₂P(O)H dimers. Both rearrangements were shown to occur via symmetrical six-membered planar transition states with activation barriers of less than 20 kcal/mol, which was much lower than for intramolecular transfer in the corresponding monomers (47 kcal/mol for the (CH₃)₂P(O)H → (CH₃)₂POH pair). The tautomeric transitions between the phosphinous acid and phosphine oxide forms observed experimentally in nonpolar media under mild conditions in the absence of molecules that could act as proton carriers were shown to proceed as bimolecular reactions with the intermediate formation of the corresponding dimers.     

Crystal structures of condensation products of 3,5-dibromosalicylic aldehyde with streptocide, norsulfazole, and ethazole

Crystal structures of 4-[(3,5-dibromo-2-hydroxy-benzylidene)-amino]-benzenesulfonamide (I), 4-[(3,5-dibromo-2-hydroxy-benzylidene)-amino]-N-thiazol-2-yl-benzenesulfonamide (II), and 4-[((3,5-dibromo-2-hydroxy-benzylidene)-amino]-N-(5-ethyl-1,3,4-thiadiazol-2-yl)-benzenesulfonamide (III) have been determined. The crystals of I are monoclinic, a = 8.645(2) Å, b = 12.622(3) Å, c = 14.414(3) Å; β = 104.31(3)°, space group P2₁/n, Z = 4, R = 0.0642. The crystals of II are also monoclinic, a = 10.313(2) Å, b = 11.288(2) Å, c = 15.766(3) Å; α = 99.37(3)°, space group P2₁/c, Z = 4, R = 0.0635. The crystals of III are triclinic, a = 10.567(2) Å, b = 10.849(2) Å, c = 18.432(4) Å; α = 75.97(3)°, β = 89.71(3)°, γ = 87.33(3)°, space group P-1, Z = 4, R = 0.0644. The asymmetric part of the unit cell of compounds I and II contains a single molecule of the Schiff’s base, while in III two independent azomethine molecules A and B. The studied compounds I–III adopt the E-configuration relatively to the double azomethine bond C=N. Owing to phenolic oxygen together with nitrogen and oxygen atoms of the sulfonamide group, compound I makes in a crystalline state a two-dimensional hydrogen bonded network parallel to the plane (1 0 1). Compound II forms centrosymmetric dimers in the crystals via N-H…N hydrogen bonds. These dimers, in their turn, are connected by hydrogen bonds O-H…O into infinite chains running along the double screw axis b. As in II, molecules and of compound III form centrosymmetric dimers through hydrogen bonding N-H…N. These dimers are linked into infinite chains running along the c axis by hydrogen bonds C-H…O. The π-π-stacking interaction of aromatic rings is observed in all the compounds studied.     

Ring-size controlled dimerization of synthetic zinc chlorophyll derivatives possessing a 1-azacycloalkyl group through mutual coordination of amino moiety to central zinc atom

Zinc methyl 3-devinyl-pyropheophorbides-a bearing a (1-azacycloalkyl)methyl group at the 3-position were prepared by chemically modifying naturally occurring chlorophyll-a. The azacyclobutylated molecules closely dimerized through double coordination of the 3¹-nitrogen atom to the central zinc atom in 1%(v/v) dichloromethane and hexane to give red-shifted visible absorption and reverse S-shaped circular dichroism (CD) bands. The azacyclopentyl analog formed similarly π–π interacted and A-ring overlapped dimers with relatively weakened and lengthened Zn–N bonds to show less split excitonic bands, and its cofacial and anti-parallel supramolecule giving S-shaped CD bands was inversely twisted by the insertion of a methylene group in the 1-azacycloalkyl moiety. One more methylene insertion as in the azacyclohexyl derivative induced a least coordination ability and no more dimerization, so the compound with the most sterically crowded 3¹-N was monomeric in the less polar organic solvent. Steric factor at around the 3¹-nitrogen atom controlled the dimerization and affected the supramolecular structure with excitonically coupling visible absorption and CD bands.     

Coumarins with an unprecedented tetracyclic skeleton and coumarin dimers from chemically engineered extracts of a marine-derived fungus

The unprecedented tetracyclic coumarin derivatives 1 and 2 and the coumarin dimers 3–5 were isolated from chemically engineered extracts (coumarin dimerization of natural extract) of the marine-derived fungus Eurotium rubrum. The structures of these compounds were established using NMR, MS and IR methods. The absolute configuration of 1 was determined by ECD calculations. The unprecedented tetracyclic coumarin skeleton was generated by domino-Knoevenagel-Diels-Alder reactions. Compounds 1–5 showed tyrosinase inhibitory activity (IC₅₀?=?1.7, 1.2, 4.9, 1.8 and 2.9?μM, respectively). The isolated coumarin derivatives 1–5 were not observed by HPLC analysis in crude extracts of E. rubrum, suggesting that chemically engineered extract generated these new coumarin derivatives with tyrosinase inhibitory activity.     

Dimerisation des polyphenyl-allenes-II : Formation et interconversion des dimeres cyclobutaniques du triphenyl-allene. stereoselectivite de la dimerisation des allenes

Progressive heating of triphenyl-allene 1 leads first to the kinetic dimers 3b and 3c, then the less stable dimer 3c undergoes thermal opening, and so isomerizes to 3a and 3b, which can equilibrate further. Finally, the diradicals 2 produced by thermal reopening of these dimers 3 can give the dihydronaphthacene 4 through recombination involving the ortho position of a phenyl group and dehydrogenation. The kinetically formed diradical, which gives 3b and 3c by conrotatory closures, is shown to possess structure 2a, and this fact suggests that the meeting of two allene molecules 1 must lead to a transition state of T_1,2 type, corresponding to optimum electronic and steric stabilization. The analysis of thermochemical data for the dimerization of aliene to 1,2-dimethylene cyclobutane demonstrates their compatibility with such a structure for the transition state. Stereochemistry of various polysubstituted allenes dimerizations appears to conform with the same factors of stability for the corresponding transition states.     

THE EFFECT OF PERIPHERAL SUBSTITUTION ON THE BATHOCHROMIC SHIFT OF THE Qy TRANSITION OF BACTERIOCHLOROPHYLL DIMERS; in vitro MODELS OF THE PROTEIN EFFECT ON THE SPECTRUM OF PIGMENT CENTERS IN THE LIGHT-HARVESTING COMPLEXES*

Abstract— The effect of chemical modifications in the side groups of the isocyclic ring V on the formation, optical absorption and circular dichroism of bacteriochlorophyll (Bchl) dimers was examined in a mixture of formamide and water containing TritonX–100 and variable amounts of pyridine. Substitution of the carbomethoxy group in the C13² position with a hydrogen atom, had no effect on the dimerization constant but increased the shift of the Q_y transition by 1000 cm^-1 with respect to the native Bchl. Substitution of the C13 hydrogen atom with OH decreased the shift of the Q_y transition by 400 cm^-1. The similarity between the spectra of the modified Bchl dimers and Bchl dimers in vivo indicates that protein binding to the side groups at Bchl dimers may profoundly affect the energy of their Q_y transition but have minor effects on the Q_y transitions of the monomelic Bchl.     

Magnetochemistry of dimers with iron group ions

General theory of matrix interactions of dimers of iron group ions is considered. Equations for calculation of matrix elements of the exchange energy of dimers and equations for calculation of the magnetic moments of dimers of different d ⁿ configurations and different exchange parameters are reported. The energies of the spin states of dimers are calculated with inclusion of exchange interactions of the first J ₀ and second J ₂ orders, and energy state diagrams for dimers with different spins and exchange energies are reported. For heterospin dimers, equations for calculation of the magnetic moment ?? and magnetic susceptibility ?? are introduced, and for homospin dimers, analytical formulas of calculation are presented. The tables of magnetic moments are calculated and their diagrams as a function of J ₀ for homospin dimers with spins S = 5/2, 2, 3/2, 1, and 1/2 are given. The experimental data are interpreted for Co²⁺ dimers as an example: the experimental and theoretical dependences of ?? and ?? on temperature are considered.     

Hydrogen-Bonded Dimers in Dipyrrinones and Acyldipyrrinones

Summary.  A crystal structure determination of the 9-acyl-dipyrrinone 9-butanoyl-2,3,7,8-tetramethyl-(10H)-dipyrrin-1-one indicates the presence of intermolecularly hydrogen-bonded dimers; however, in CHCl₃ solution the pigment is monomeric as determined by vapor pressure osmometry measurements. Lacking an alkyl group at C(8), the 9-acyl-dipyrrinone exhibits only a weak tendency to form dimers in CHCl₃ (K _A ∼ 60 M ⁻¹) as determined by analysis of variable temperature ¹H NMR data. In contrast, when the 9-acyl group is replaced by formyl or when the acyl group is fixed in a syn orientation to the pyrrole NH, the dipyrrinone is strongly prone to dimerization in CHCl₃. Received August 22, 2000. Accepted September 5, 2000     

Photoinduced polymerization and oligomerization of 4-vinylbenzophenone

The photopolymerizations of 4-vinylbenzophenone (VBP) in various solvents were investigated to make clear the photoininiation characteristics. It was found that direct photoirradiation produces polymers, oligomers (trimers), and dimers. The dimers were identified as trans- and cis-1,2-bis(4-benzoylphenyl)cyclobutanes. The fraction of trans-form in the cyclobutane dimers produced was about 80%, and was little affected by the reaction conditions. The quantum yields ([VBP] = 0.1M in benzene) was estimated to be 3 × 10^?2 for the dimerization and 2 × 10^?4 for the initiation of polymerization. The photoreactions via π,π^* triplet state of the monomer was suggested from the results.     

Theoretical Study of the Dimerization of Chlorophyll (a) and Its Hydrates: Implication for Chlorophyll (a) Aggregation

Dimeric structures chlorophyll (a) (Chla) and their mono‐ and dihydrated have been suggested to play an important role in the mechanism of photoreaction center chlorophyll special pairs PSI and PSII. Despite their functional importance, the molecular basis structures for interacting two Chla molecules and the structural stabilization role of H₂O in the formation of hydrated Chla dimer complexes is poorly understood. In this article, the different coordination modes between two interacting Chla molecules and the configurational (orientation and distance) features between the dimer and bound H₂O molecules are characterized by means of super molecule approach the density functional theory DFT. An estimation of the thermodynamic quantities is made for Chla dimerization and hydration processes. The results indicate that structure including ester linkages via H₂O hydrogen bonding is the most favorable conformation for the dihydrated chlorophyll (a) dimer at B3LYP/6‐31G*‐DCP level of calculation. The dispersion interaction is shown to be of great significance for the Chla dimer stabilization. In aqueous nonpolar solvent, the thermodynamics show that Chla has a slightly stronger driving force for full hydration than for dimerization and that hydration of the dimers is rather weakly exergonic. The tetrahydrated dimers having a similar arrangement to that in crystals of ethyl chlorophyllide (a) dihydrate are found to be more stable than the Chla dihydrated dimer. The data underscore the key role of H‐bonding in the stability of Chla‐H₂O adducts and, in particular, the great importance of the Chla monomeric dihydrated species in the hydration and dimerization of Chla in aqueous media. Clearly, the Chla dihydrates (Chla‐2 H₂O) are found more stable than the monohydrates (Chla‐H₂O) and the Chla dimers (Chla₂), owing to a particular structure in which cooperative interactions occur between the H₂O molecules and Chla. Calculations also indicate that the most thermodynamically preferred pathway for the formation of Chla dimer hydrates can be represented by two steps: the first corresponds to the formation of Chla monomeric dihydrates and the second is the dimerization of the dihydrates on to tetrahydrated Chla dimers. These results allow to obtain a new possible pathway for Chla dimer formation processes and could provide new insights to the aggregation of chlorophyll (a) in solution.     

Double versus single helical structures of oligopyridine-dicarboxamide strands. Part 2: The role of side chains

A series of heptameric oligoamides comprising 4-alkoxy-substituted 2,6-diaminopyridine and 2,6-pyridine-dicarbonyl units have been synthesized using convergent methods. The hybridization of these compounds into double helical dimers was studied in solution by ¹H NMR spectroscopy in CDCl₃ or DMSO-d₆ at various concentrations, and in the solid state using X-ray crystallographic analysis. Both solid state and solution data suggest that these compounds follow identical hybridization schemes. In CDCl₃, the oligomers possess dimerization constants considerably (up to 2000-fold) higher than related compounds having no alkoxy substituents on their 2,6-diaminopyridine units. The origin of this effect can be in part interpreted as a result of interactions between the 4-alkoxy side chains when they are present on all pyridine rings. For example, 4-benzyloxy-substituted oligomer 2 has a higher dimerization constant than 4-decyloxy and 4-methoxy-substituted analogues 1 and 3. The crystal structure of 2 reveals multiple aromatic-aromatic interactions between the benzyl side chains, both face-to-face and edge-to-face at various angles surrounding the duplex. In the solid state, these double helices are stacked on top of each other to form long channels filled with water molecules. The 4-methoxy and 4-decyloxy-substituted analogues 1 and 3 have similar dimerization constants, showing that interactions between side chains are not significant between purely aliphatic residues. Consequently, the high stability of the double helices formed by 1 and 3 compared to related compounds having alkoxy substituents on their 2,6-pyridine-dicarbonyl units only does not find its origin in interactions between side chains but in the direct effect of the alkoxy substituents upon main chain aryl-aryl interactions.