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Ab initio study of the complexes of halogen-containing molecules RX (X=Cl, Br, and I) and NH3: towards understanding the nature of halogen bonding and the electron-accepting propensities of covalently bonded halogen atoms.

Ab initio calculations have been performed on a series of complexes formed between halogen-containing molecules and ammonia to gain a deeper insight into the nature of halogen bonding. It appears that the dihalogen molecules form the strongest halogen-bonded complexes with ammonia, followed by HOX; the charge-transfer-type contribution has been demonstrated to dominate the halogen bonding in these complexes. For the complexes involving carbon-bound halogen molecules, our calculations clearly indicate that electrostatic interactions are mainly responsible for their binding energies. Whereas the halogen-bond strength is significantly enhanced by progressive fluorine substitution, the substitution of a hydrogen atom by a methyl group in the CH(3)X...NH(3) complex weakened the halogen bonding. Moreover, remote substituent effects have also been noted in the complexes of halobenzenes with different para substituents. The influence of the hybridization state of the carbon atom bonded to the halogen atom has also been examined and the results reveal that halogen-bond strengths decrease in the order HC triple bond CX > H(2)C=CHX approximately O=CHX approximately C(6)H(5)X > CH(3)X. In addition, several excellent linear correlations have been established between the interaction energies and both the amount of charge transfer and the electrostatic potentials corresponding to an electron density of 0.002 au along the R-X axis; these correlations provide good models with which to evaluate the electron-accepting abilities of the covalently bonded halogen atoms. Finally, some positively charged halogen-bonded systems have been investigated and the effect of the charge has been discussed.

Algorithms↗

Bitumen morphologies by phase-detection atomic force microscopy.

Summary Bitumen is a complex mixture of hydrocarbons for which microstructural knowledge is incomplete. In an effort to detail this microstructure, 13 bitumens were analysed by phase-detection atomic force microscopy. Based on morphology, the bitumens could be classified into three distinct groups. One group showed fine domains down to 0.1 microm, another showed domains of about 1 microm, and a third group showed up to four different domains or phases of different sizes and shapes. No correlation was found between the atomic force microscopy morphology and the composition based on asphaltenes, polar aromatics, naphthene aromatics and saturates. A high correlation was found between the area of the 'bee-like' structures and the vanadium and nickel content in bitumen, and between the atomic force microscopy groups and the average size of molecular planes made of fused aromatics. The morphology and the molecular arrangements in bitumen thus appear to be partly governed by the molecular planes and the polarity defined by metallic cations.

Journal Article↗

Synthesis, Structure, Magnetic Properties, and (1)H NMR Studies of a Moderately Antiferromagnetically Coupled Binuclear Copper(II) Complex.

A binuclear Cu(II) complex of [(Cu(2)(HAP)(2)IPA)(OH)(H(2)O)](ClO(4))(2).H(2)O (HAP = 3-amino-1-propanol; IPA = 2-hydroxy-5-methylisophthalaldehyde) has been synthesized and characterized by X-ray crystallography, by solid state magnetic susceptibility, and in solution by (1)H NMR studies. The binuclear copper(II) complex crystallizes in the orthorhombic system, space group Pbcn, a = 27.9972(9) Å, b = 8.8713(3) Å, c = 19.5939(6) Å, and Z = 8. The two copper(II) atoms in this binuclear Cu(II) complex are bridged by the oxygen atoms of the phenolate and hydroxy groups. The axial position at one Cu atom is occupied by a water molecule while another Cu has weak interaction with a perchlorate group. The coordination geometries around the two Cu atoms are distorted square pyramid and square planar. The solid state magnetic susceptibility measurement reveals a moderate antiferromagnetic exchange interaction between the two Cu atoms with a -2J value of 113 +/- 9 cm(-)(1). The variable-temperature (1)H NMR studies in CD(3)CN solution show that the observed relatively sharp hyperfine shifted signals follow a Curie behavior. The exchange coupling constant (-2J) obtained in solution by using chemical shift as a function of temperature also reveals a moderate antiferromagnetic exchange interaction between two Cu(II) ions. An analysis of the relaxation data shows that the reorientational correlation time (tau(c)) is dominated probably by a combination of electronic relaxation time tau(s) and rotational correlation time (tau(r)) due to an exchange-modulated dipolar mechanism for this moderately antiferromagnetically coupled binuclear copper(II) system.

Journal Article↗

Degradable polyethylenimine-alt-poly(ethylene glycol) copolymers as novel gene carriers.

An ideal gene carrier requires both safety and transfection efficiency. Polyethylenimine (PEI) is a well-known cationic polymer, which has high transfection efficiency owing to its buffering capacity. But it has been reported that PEI is cytotoxic in many cell lines and non-degradable. In this study, we synthesized degradable PEI-alt-poly(ethylene glycol) (PEG) copolymers using Michael-type addition reactions as a new gene carrier and characterized them. These copolymers were complexed with plasmid DNA and the resulting complexes were characterized by dynamic light scattering, gel retardation and atomic force microscopy to determine particle sizes, complex formation and complex shape, respectively. Cytotoxicity and transfection efficiency of the copolymers were also checked in cultured HeLa human cervix epithelial carcinoma cells, HepG2 human hepatoblastoma cell line and MG63 human osteosarcoma cells. PEG to PEI ratio in the copolymers was near 1 and the molecular weight of the copolymer ranged from around 8000 to 12,900. These copolymers degraded rapidly at 37 degrees C in 0.1 M phosphate buffered saline (PBS, pH 7.4). The complete copolymer/DNA complex was formed at an N/P ratio of 12, producing a complex resistant to DNase I. Particle sizes decreased with increasing N/P ratio and PEG molecular weight, exhibiting a minimum value of 75 nm at an N/P ratio of 45 with PEI-alt-PEG (700). Cytotoxicity study showed that copolymers exhibited no cytotoxic effects on cells even at high copolymer concentration. Also, transfection efficiency was influenced by PEG molecular weight and, in case of PEI-alt-PEG (258), the transfection efficiency was higher than that for PEI 25 K in HepG2 and MG63, whereas it was lower than that for PEI 25K in HeLa cells.

Cell Line, Tumor↗

Hydrogen atom vs electron transfer in catecholase-mimetic oxidations by superoxometal complexes. Deuterium kinetic isotope effects.

Dioximato-cobalt(II), -iron(II) and -manganese(II) complexes (1)-(6), acting as functional catecholase and phenoxazinone synthase models, exhibit a deuterium kinetic isotope effect predicted by theory (k4H/k4D < or = 3) in the catalytic oxidative dehydrogenation of 3,5-di-tert-butylcatechol and 2-aminophenol by O2. KIEs in the range of (k4H/k4D approximately 1.79-3.51) are observed with (1) and (2) as catalysts, pointing to hydrogen atom transfer in the rate-determining step from the substrate hydroxy group to the metal-bound superoxo ligand. Less significant KIEs (1.06-1.20) are exhibited by catalysts systems (3)-(6), indicating that proton-coupled electron transfer is the preferred route in those cases.

Aminophenols↗

Complex formation between reduced D-amino acid oxidase and pyridine carboxylates.

Picolinate binds to a reduced form of D-amino acid oxidase, and the complex formed has a broad absorption band around 600 nm as in the case of the purple intermediate of the enzyme with a substrate. The dissociation constant at 25 degrees C was 35 microns at pH 7.0. The pH dependence (pH 8.3-pH 6.4) of the dissociation constant indicates that one proton is associated with the complex formation, and picolinate protonated at the N atom binds to the reduced enzyme. Resonance Raman spectra of the complex support that picolinate in the complex is a cationic form protonated at the N atom. Nicotinate also binds to the reduced enzyme, but isonicotinate does not.

Animals↗

PLASS: protein-ligand affinity statistical score--a knowledge-based force-field model of interaction derived from the PDB.

We have developed PLASS (Protein-Ligand Affinity Statistical Score), a pair-wise potential of mean-force for rapid estimation of the binding affinity of a ligand molecule to a protein active site. This scoring function is derived from the frequency of occurrence of atom-type pairs in crystallographic complexes taken from the Protein Data Bank (PDB). Statistical distributions are converted into distance-dependent contributions to the Gibbs free interaction energy for 10 atomic types using the Boltzmann hypothesis, with only one adjustable parameter. For a representative set of 72 protein-ligand structures, PLASS scores correlate well with the experimentally measured dissociation constants: a correlation coefficient R of 0.82 and RMS error of 2.0 kcal/mol. Such high accuracy results from our novel treatment of the volume correction term, which takes into account the inhomogeneous properties of the protein-ligand complexes. PLASS is able to rank reliably the affinity of complexes which have as much diversity as in the PDB.

Computational Biology↗

Characterization of dioxygenated cobalt(II)-carnosine complexes by Raman and IR spectroscopy.

Raman and IR studies are carried out on carnosine (beta-alanyl-L-histidine, Carnos) and its complexes with cobalt(II) at different metal/ligand ratios and basic pH. Binuclear complexes that bind molecular oxygen are formed and information regarding the O-O bridge is obtained from the Raman spectra. When the Co(II)/Carnos ratio is <or=1, peroxobinuclear complexes are the predominant species and two forms (monobridged and dibridged) are identified by the presence of two Raman peaks in the nuO-O region (750-850 cm(-1)). These peroxo complexes can be oxidized to yield a superoxo complex when the metal slightly exceeds the Carnos concentration, and there are consequent shifts of the nuO-O band to higher wavenumbers. In addition, the chelated species in the 2 : 1 Co(II)/Carnos system is found to bind oxygen to a lesser degree. With respect to the coordination sites, each Co(II) ion of the binuclear dioxygenated complexes is bound to one oxygen atom and four nitrogen atoms: N(pi) and N(tau) of two Carnos molecules, the peptide, and the terminal amino nitrogen atoms. Conversely, when the metal/ligand ratio is 2, in addition to the dioxygenated complexes, a complex is formed in which the imidazole moiety of Carnos binds two different cobalt ions because the N(pi) and N(tau) nitrogens are both deprotonated.

Carnosine↗

Control of heme metabolism with synthetic metalloporphyrins.

Studies with synthetic metal-porphyrin complexes in which the central iron atom of heme is replaced by other elements indicate that those heme analogues that cannot be enzymatically degraded to bile pigments possess novel biological properties that may have considerable clinical as well as experimental value. Such studies have revealed the important role that the central metal atom plays in determining the physiological and pharmacological properties of metal-porphyrin complexes; and they have demonstrated that the form in which animals and humans are exposed to trace metals, i.e., inorganic, organified, porphyrin-chelated, etc., can be of great importance in determining the biological responses that such elements elicit, especially with respect to actions on heme synthesis and degradation and cytochrome P-450 formation and function. Study of the biological properties of synthetic metalloporphyrins represents a potentially fruitful area of research and the results may have significant value for basic as well as clinical disciplines.

5-Aminolevulinate Synthetase↗

Photoinduced amino-imino tautomerization reaction in 2-aminopyrimidine and its methyl derivatives with acetic acid.

The electronic absorption and fluorescence spectra of 2-aminopyrimidine (2APM), 2-amino-4-methylpyrimidine (2A4MPM), and 2-amino-4,6-dimethylpyrimidine (2ADMPM) with acetic acid (AcOH) were measured in isooctane (2,2,4-trimethylpentane) at room temperature. From the absorption spectra, a hydrogen-bonded complex formation of the 2APM/AcOH, 2A4MPM/AcOH, and 2ADMPM/AcOH systems was recognized in isooctane. The enthalpy changes (-DeltaH) for the complex formation were estimated to be ca. 41.2-45.1 kJ mol-1 and increased in proportion to the numbers of the methyl group introduced into the 2APM. The -DeltaH values refer to the formation of the hydrogen-bonded 1:1 complex between the ring nitrogen atom and NH2 group of the aminopyrimidine and the OH and CO groups of AcOH, respectively. In the 2A4MPM/AcOH double hydrogen-bonded complex the OH group of AcOH is thought to be linked to the ring nitrogen at the 1-postion of 2A4MPM. The fluorescence spectral results indicate that the double proton transfer reaction takes place during the excited state, and gives rise to an imino-tautomer vibration emission, from analogy with the fluorescences of 1-methyl-2(1H)-pyrimidinimine (MPMI), 1,4-dimethyl-2(1H)-pyrimidinimine (DMPMI), and 1,4,6-trimethyl-2(1H)-pyrimidinimine (TMPMI). The fluorescence quantum yields of the imino-tautomers also increased in proportion to the numbers of the methyl group introduced into the 2APM.

Acetates↗

Diastereopure Fe(II) and Zn(II) complexes derived from a tridentate N,N',N-bis(methyl-L-prolinate)-substituted pyridine ligand.

A series of mononuclear iron(II) and zinc(II) complexes of the new chiral Py(ProMe)2 ligand (Py(ProMe)2 = 2,6-bis[[(S)-2-(methyloxycarbonyl)-1-pyrrolidinyl]methyl]pyridine) have been prepared. The molecular geometry in the solid state (X-ray crystal structures) of the complexes [FeCl2(Py(ProMe)2)] (1), [ZnCl2(Py(ProMe)2)] (2), [Fe(OTf)2(Py(ProMe)2)] (3), [Fe(Py(ProMe)2)(OH2)2](OTf)2 (4), and [Zn(OTf)(Py(ProMe)2)](OTf) (5) are reported. They all show a meridional NN'N coordination of the Py(ProMe)2 ligand. The bis-chloride derivatives 1 and 2 represent neutral isostructural five-coordinated complexes with a distorted geometry around the metal center. Unusual seven-coordinate iron(II) complexes 3 and 4 having a pentagonal bipyramidal geometry were obtained using weakly coordinating triflate anions. The reaction of Zn(OTf)2 with the Py(ProMe)2 ligand afforded complex 5 with a distorted octahedral geometry around the zinc center. All complexes were formed as single diastereoisomers. In the case of complexes 3-5, the oxygen atoms of both carbonyl groups of the ligand are also coordinated to the metal. The stereochemistry of the coordinated tertiary amine donors in complexes 3-5 is of opposite configuration as in complexes 1 and 2 as a result of the planar penta-coordination of the ligand Py(ProMe)2. Complexes 1, 2, and 5 have an overall -configuration at their metal center, while the Fe(II) ion in complexes 3 and 4 has the opposite delta-configuration (crystal structures and CD measurements). The magnetic moments of iron complexes 1, 3, and 4 correspond to that of high-spin d6 Fe(II) complexes. The solution structures of complexes 1-5 were characterized by means of UV-vis, IR, conductivity, and CD measurements and their electrochemical behavior. These studies showed that the coordination environment of 1 and 2 observed in the solid state is maintained in solution. In coordinating solvents, the triflate anion (3, 5) or water (4) co-ligands of complexes 3-5 are replaced by solvent molecules with retention of the original pentagonal bipyramidal and octahedral geometry, respectively.

Crystallography, X-Ray↗

Experimental observation of competing pathways in the relaxation of ICl* in a He supersonic expansion.

Differing caging mechanisms of electronically excited ICl within He...ICl complexes are investigated using laser-induced fluorescence and two-laser, pump-probe spectroscopy. A continuum signal is observed in laser-induced fluorescence spectra recorded with excitation energies that access regions above the I 2P3/2 + Cl 2P3/2 dissociation limit. We show that this signal is associated with transitions of the He ...ICl(X,v" = 0) complex with a linear equilibrium geometry to the continuum of states correlating with the repulsive, inner wall of the ICl(A 3pi1) potential. The dissociating ICl(A) molecule within the complex undergoes kinematic one-atom caging, ejecting the weakly bound He atom, and re-stabilizing the molecule in high lying vibrational levels within the A electronic state with very little rotational excitation. At higher excitation energies, weak LIF features superimposed on the continuum fluorescence signals are observed in preliminary investigations. When fixing an excitation laser on one of these features, at 18,012 cm(-1), I35Cl(B,v' = 2,3) vibrational levels are formed with little rotational excitation. This feature is associated with transitions of the linear He...I35Cl(X,v" = 0) complex to intermolecular states associated with the ICl(B) diabat that are coupled with those in the ICl(B') adiabat formed by an avoided curve crossing. The I35Cl(B,v') products are formed via a non-adiabatic one-atom caging mechanism of ICl* molecules within linear He...I35Cl* complexes.

Journal Article↗

Atomic resolution structures of resting-state, substrate- and product-complexed Cu-nitrite reductase provide insight into catalytic mechanism.

Copper-containing nitrite reductases catalyze the reduction of nitrite to nitric oxide (NO), a key step in denitrification that results in the loss of terrestrial nitrogen to the atmosphere. They are found in a wide variety of denitrifying bacteria and fungi of different physiology from a range of soil and aquatic ecosystems. Structural analysis of potential intermediates in the catalytic cycle is an important goal in understanding enzyme mechanism. Using "crystal harvesting" and substrate-soaking techniques, we have determined atomic resolution structures of four forms of the green Cu-nitrite reductase, from the soil bacterium Achromobacter cycloclastes. These structures are the resting state of the enzyme at 0.9 A, two species exhibiting different conformations of nitrite bound at the catalytic type 2 Cu, one of which is stable and also has NO present, at 1.10 A and 1.15 A, and a stable form with the product NO bound side-on to the catalytic type 2 Cu, at 1.12 A resolution. These structures provide incisive insights into the initial binding of substrate, its repositioning before catalysis, bond breakage (O-NO), and the formation of a stable NO adduct.

Achromobacter cycloclastes↗

[Role of histidine in ligand binding ability of hemoglobin gene].

The atomic and electronic structures of heme complexes with His, Gly, and Cys residues (Heme-His, Heme-Gly, and Heme-Cys) in the fifth coordination position of the Fe atom and with oxygen and nitrogen oxide molecules in the sixth Fe position were studied by the semiempirical quantum-chemical method PM3. A comparative analysis of internuclear distances showed that the strength of chemical bonding between the ligand molecules (oxygen and nitrogen oxide) is greater for Heme-Cys than for Heme-His and Heme-Gly complexes. Consequently, the strengthening of the chemical bond of the oxygen (or nitrogen oxide) molecule with Heme-Cys substantially weakens the chemical bond in the ligand molecule. The Mulliken population analysis showed that the electronic density of ligand (oxygen or nitrogen oxide) p-orbitals is transferred to the d-orbitals of the Fe atom, whose charge, calculated according to the Mulliken analysis, formally becomes negative. In the Heme-His complex with oxygen, this charge is substantially greater than in the complex with NO, and the oxygen molecule becomes polarized. No oxygen polarization is observed in the Heme-Cys complex, and the electron density (judging from the change in the Fe charge) is transferred to the coordinated sulfur atom. This is also characteristic of Heme-Cys complexes with nitrogen oxide. An analysis of charges on the atoms indicates that the character of chemical bonding of the oxygen molecule in Heme-Cys and Heme-Gly complexes is similar and basically differs from that in the case of the Heme-His complex. The English version of the paper: Russian Journal of Bioorganic Chemistry, 2004, vol. 30, no. 2; see also http://www.maik.ru.

Hemoglobins↗

Development of novel mixed-ligand oxotechnetium [SNS/S] complexes as potential 5-HT1A receptor imaging agents.

The "3 + 1" ligand system [SN(R)S/S combination] was applied in order to synthesize neutral mixed-ligand oxotechnetium complexes of the general formula 99mTcO[SN(R)S]/[S] as potential 5-HT1A receptor imaging agents. The complexes are carrying the 1-(2-methoxyphenyl)piperazine moiety, a fragment of the true 5-HT1A antagonist WAY 100635, either on the monodentate ligand [S] or on the tridentate ligand [SN(R)S]. The complexes MO[EtN(CH2CH2S)2] [o-MeOC6H4N(CH2CH2)2NCH2CH2S] (3), MO[o- MeOC6H4N(CH2CH2)2N(CH2)3N(CH2CH2S)2][PhS] (6) and MO[o-MeOC6H4N(CH2CH2)2N(CH2)3N(CH2CH2S)2] [PhCH2CH2S] (9), where M = 99mTc, were prepared at tracer level using 99mTc glucoheptonate as precursor. For structural characterization, the analogous oxorhenium (M = Re, 1, 4 and 7, respectively) and oxotechnetium (M = 99gTc, 2, 5 and 8, respectively) complexes were prepared by ligand exchange reactions. All products were characterized by elemental analysis and spectroscopic methods. Complexes 1, 4 and 7 were further characterized by crystallographic analysis. For 1, the coordination geometry about rhenium can be described as trigonally distorted square pyramidal (tau = 0.36), while for 4 and 7, as distorted trigonal bipyramidal (tau = 0.66 and tau = 0.61, respectively). The coordination sphere about oxorhenium in all complexes is defined by the SNS donor atom set of the tridentate ligand and the sulfur atom of the monodentate coligand. The structure of the 99mTc complexes 3, 6 and 9 was established by comparative HPLC using authentic oxorhenium and oxotechnetium samples. The binding affinity of oxorhenium compounds for the 5-HT1A receptor subtype was determined in rat brain hippocampal preparations (IC50 = 6-31 nM). Preliminary tissue distribution data in healthy mice revealed the ability of all three 99mTc complexes to cross the intact blood-brain barrier (0.49-1.15% ID at 1 min p.i.). In addition, complexes 6 and 9 showed significant brain retention. These promising results have demonstrated that the SNS/S mixed-ligand system can be used in the development of 99mTc complexes as potential 5-HT1A receptor imaging agents.

Animals↗

Gas phase, solution, and solid state alkali ion binding by the [NbE8](3-) (E = As, Sb) complexes: synthesis, structure, and spectroscopy.

Toluene solutions of Nb(toluene)(2) react with ethylenediamine solutions of K(3)E(7) (E = As, Sb) in the presence of 2,2,2-crypt to give [NbAs(8)](3-) (2) and [NbSb(8)](3-) (3) ions, respectively, in low yields. The (133)Cs NMR spectroscopy, ESIMS results (negative ion mode), and single-crystal X-ray structures of the ions are reported. The complexes have S(8)-like E(8) rings with Nb atoms in the center. The 1:1 complex of 2 with Cs+ was observed in solution and also in the gas phase as the oxidized ion [CsNbAs(8)](1-). The anion 2 selectively binds to Cs(+) in solution even in the presence of excess Na(+). Other gas-phase ions formed include [Cs(2)(NbAs(8))](1-), [KCs(NbAs(8))](1-), [KCs(NbAs(8))(2)](1-), [KNbAs(8)](1-), and [K(2)NbAs(8)](1-).

Journal Article↗

Structures of HCN-Mgn (n=2-6) complexes from rotationally resolved vibrational spectroscopy and ab initio theory.

High-resolution infrared laser spectroscopy has been used to determine the structures of HCN-Mgn complexes formed in helium nanodroplets. The magnesium atoms are first added to the droplets to ensure that the magnesium complexes are preformed before the HCN molecule is added. The vibrational frequencies, structures, and dipole moments of these complexes are found to vary dramatically with cluster size, illustrating the nonadditive nature of the HCN-magnesium interactions. All of the complexes discussed here have the nitrogen end of the HCN pointing towards the magnesium clusters. For Mg3, the HCN binds to the "threefold" site, yielding a symmetric top spectrum. Although the HCN-Mg4 complex also has C3v symmetry, the HCN sits "on-top" of a single magnesium atom. These structures are confirmed by both ab initio calculations and measurements of the dipole moments. Significant charge transfer is observed in the case of HCN-Mg4, indicative of charge donation from the lone pair on the nitrogen of HCN into the lowest unoccupied molecular orbital of the Mg4.

Journal Article↗

Iron, ferritin, and nutrition.

Ferritin, a major form of endogenous iron in food legumes such as soybeans, is a novel and natural alternative for iron supplementation strategies where effectiveness is limited by acceptability, cost, or undesirable side effects. A member of the nonheme iron group of dietary iron sources, ferritin is a complex with Fe3+ iron in a mineral (thousands of iron atoms inside a protein cage) protected from complexation. Ferritin illustrates the wide range of chemical and biological properties among nonheme iron sources. The wide range of nonheme iron receptors matched to the structure of the iron complexes that occurs in microorganisms may, by analogy, exist in humans. An understanding of the chemistry and biology of each type of dietary iron source (ferritin, heme, Fe2+ ion, etc.), and of the interactions dependent on food sources, genes, and gender, is required to design diets that will eradicate global iron deficiency in the twenty-first century.

Animals↗