A new mechanism for the Favorskii rearrangement

The title reaction was investigated by the use of ONIOM-RB3LYP calculations. A reaction system composed of alpha-chlorocyclohexanone, a methoxide ion and 8 MeOH solvent molecules was adopted. Two reaction channels, the semibenzilic acid mechanism (A) and cyclopropanone mechanism (B), were compared. B is found to be more favorable than A. The rate-determining step of B is the (MeOH)(3) addition transition state (TS3B) to the cyclopropanone intermediate. While TS3B involves a concerted function of MeO(-) addition and proton relays, it has a large activation energy. A new route was found, where the chloride ion evolved at the cyclopropane formation step (TS2B) works as a nucleophile to the cyclopropanone intermediate. Thus, a cyclopentane-carbonyl chloride intermediate is formed with a small activation energy. A new cyclopropanone mechanism is proposed.     

Synthesis and characterization of AU2Se6 (A = K, Cs)

Two new ternary uranium selenides, AU(2)Se(6) (A = K, Cs), were prepared using the reactive flux method. Single crystal X-ray diffraction was performed on single crystals. The compounds crystallize in the orthorhombic Immm space group, Z = 2. CsU(2)Se(6) has cell parameters of a = 4.046(2) A, b = 5.559(3) A, and c = 24.237(12) A. KU(2)Se(6) has cell parameters of a = 4.058(3) A, b = 5.556(4) A, and c = 21.710(17) A. The compounds are isostructural to the previously reported KTh(2)Se(6). The two-dimensional layered structure is related to ZrSe(3) with the alkali metals residing in the interlayer space. The oxidation states of uranium and selenium were evaluated using X-ray photoelectron spectroscopy (XPS). Uranium was found to be tetravalent, while selenium was found to be in two oxidation states, one of which is -2. The other oxidation state is similar to that found in a polyselenide network. While this structure is known, our work examines how the structure changes through the transactinide series.     

Direct quantitative determination of cyanamide by stable isotope dilution gas chromatography-mass spectrometry

Cyanamide is a multifunctional agrochemical used, for example, as a pesticide, herbicide, and fertilizer. Recent research has revealed that cyanamide is a natural product biosynthesized in a leguminous plant, hairy vetch (Vicia villosa). In the present study, gas chromatography-mass spectrometry (GC-MS) equipped with a capillary column for amines was used for direct quantitative determination of cyanamide. Quantitative signals for ((14)N(2))cyanamide, ((15)N(2))cyanamide (internal standard for stable isotope dilution method), and m-(trifluoromethyl)benzonitrile (internal standard for correcting errors in GC-MS analysis) were recorded as peak areas on mass chromatograms at m/z 42 (A(42)), 44 (A(44)), and 171 (A(IS)), respectively. Total cyanamide content, ((14)N(2))cyanamide plus ((15)N(2))cyanamide, was determined as a function of (A(42)+A(44))/A(IS). Contents of ((14)N(2))cyanamide and ((15)N(2))cyanamide were then calculated by multiplying the total cyanamide content by A(42)/(A(42)+A(44)) and A(44)/(A(42)+A(44)), respectively. The limit of detection for the total cyanamide content by the GC-MS analysis was around 1ng. The molar ratio of ((14)N(2))cyanamide to ((15)N(2))cyanamide in the injected sample was equal to the observed A(42)/A(44) value in the range from 0.1 to 5. It was, therefore, possible to use the stable isotope dilution method to quantify the natural cyanamide content in samples; i.e., the natural cyanamide content was derived by subtracting the A(42)/A(44) ratio of the internal standard from the A(42)/A(44) ratio of sample spiked with internal standard, and then multiplying the resulting difference by the amount of added ((15)N(2))cyanamide (SID-GC-MS method). This method successfully gave a reasonable value for the natural cyanamide content in hairy vetch, concurring with the value obtained by a conventional method in which cyanamide was derivatized to a photometrically active compound 4-cyanimido-1,2-naphthoquinone and analyzed with reversed-phase HPLC (CNQ-HPLC method). The determination range of cyanamide in the SID-GC-MS method was almost the same as that in the CNQ-HPLC method; however, the SID-GC-MS method was much simpler than the CNQ-HPLC method.     

Total synthesis of deamido bleomycin a(2), the major catabolite of the antitumor agent bleomycin

Metabolic inactivation of the antitumor antibiotic bleomycin is believed to be mediated exclusively via the action of bleomycin hydrolase, a cysteine proteinase that is widely distributed in nature. While the spectrum of antitumor activity exhibited by the bleomycins is believed to reflect the anatomical distribution of bleomycin hydrolase within the host, little has been done to characterize the product of the putative inactivation at a chemical or biochemical level. The present report describes the synthesis of deamidobleomycin demethyl A(2) (3) and deamido bleomycin A(2) (4), as well as the respective aglycones. These compounds were all accessible via the key intermediate N(alpha)-Boc-N(beta)-[1-amino-3(S)-(4-amino-6-carboxy-5-methylpyrimidin-2-yl)propion-3-yl]-(S)-beta-aminoalanine tert-butyl ester (16). Synthetic deamido bleomycin A(2) was shown to be identical to the product formed by treatment of bleomycin A(2) with human bleomycin hydrolase, as judged by reversed-phase HPLC analysis and (1)H NMR spectroscopy. Deamido bleomycin A(2) was found to retain significant DNA cleavage activity in DNA plasmid relaxation assays and had the same sequence selectivity of DNA cleavage as bleomycin A(2). The most significant alteration of function noted in this study was a reduction in the ability of deamido bleomycin A(2) to mediate double-strand DNA cleavage, relative to that produced by BLM A(2).     

Excited-state dynamics of acetylene excited to individual rotational level of the V04K01 subband

Dynamics of the IR emission induced by excitation of the acetylene molecule using the (3(2)K(a) (0,1,2),A (1)A(u)<--4(1)l(a) (1),X (1)Sigma(g) (+)) transition was investigated. The observed IR emission was assigned to transitions between the ground-state vibrational levels. Acetylene fluorescence quenching induced by external electric and magnetic fields acting upon the system prepared using the (3(4)K(a) (1),A (1)A(u)<--0(0)l(a) (0),X (1)Sigma(g) (+)) excitation was also studied. External electric field creates an additional radiationless pathway to the ground-state levels, coupling levels of the A (1)A(u) excited state to the quasiresonant levels of the X (1)Sigma(g) (+) ground state. The level density of the ground state in the vicinity of the excited state is very high, thus the electric-field-induced transition is irreversible, with the rate constant described by the Fermi rule. Magnetic field alters the decay profile without changing the fluorescence quantum yield in collisionless conditions. IR emission from the CCH transient was detected, and was also affected by the external electric and magnetic fields. Acetylene predissociation was demonstrated to proceed by the direct S(1)-->S(0) mechanism. The results were explained using the previously developed theoretical approach, yielding values of the relevant model parameters.     

Application of a stepwise flow ratiometry without phase separation to the determination of the chloroform/water distribution coefficients of volatile diazines

The chloroform/water distribution coefficients (K(D)) of sixteen diazine compounds were determined by a stepwise flow ratiometry. An aqueous solution of analyte was delivered and merged with chloroform. The flow rate ratio of both the phases was varied stepwise under a constant total (chloroform+aqueous) flow rate. The analyte was extracted to chloroform while both the phases, which were segmented by each other, were passing through an extraction coil. The segmented stream was then led to a UV/Vis detector directly without phase-separation. The absorbance of the chloroform and aqueous phases (A(o) and A(a), respectively) was each measured at the maximum absorption wavelength of the analyte. The plots of A(-1) against R(f), (AR(f))(-1) against R(f)(-1), and AR(f) against A gave straight lines, where A was A(o), A(a) or the sum of them (A(S)). The K(D) of the analyte was calculated from the slopes and intercepts of the plots. The log K(D) values obtained for the analytes (-0.5-1.4) were agreed well with the values measured by a shake-flask method. The present method is simple, rapid (5 min/determination) and applicable to the volatile compounds with reasonable precision (standard deviation of log K(D)<0.07).     

Synthesis and crystal structure of hexahydrobis[(1,3-p-dimethylaminobenzyl)-1,3-diazepine]-2-selenone, C23H32N4Se.

In the title compound, C23H32N4Se, was synthesized and its crystal structure was determined by single crystal X-ray diffraction. The compound crystallizes in orthorhombic system, space group Pbca, a = 10.9960(10)A, b = 14.9460(9)A, c = 27.565(5)A and Z = 2. According to X-ray crystallographic studies, the diazepine ring is observed to be in a disordered state. The site-occupancy of the major compenent refined to 0.53(1). The C=Se bond length of 1.862(4)A is a double bond character. The dihedral angle between the two phenyl rings is 37.7(2) degrees.     

From VO2 (B) to VO2 (A) nanobelts: first hydrothermal transformation, spectroscopic study and first principles calculation

The phase transition process from VO(2) (B) to VO(2) (A) was first observed through a mild hydrothermal approach, using hybrid density functional theory (DFT) calculations and crystallographic VO(2) topology analysis. All theoretical analyses reveal that VO(2) (A) is a thermodynamically stable phase and has a lower formation energy compared with the metastable VO(2) (B). For the first time, X-ray absorption spectroscopy (XAS) of the V L-edge and O K-edge was performed on different VO(2) phases, and the differences in the electronic structure of the two polymorphic forms provide further experimental evidence of the more stable VO(2) (A). Consequently, transformation from VO(2) (B) to VO(2) (A) is much easier to be realized from a dynamical point of view. Notably, the transformation of VO(2) (B) into VO(2) (A) show the sequence VO(2) (B)-high-temperature VO(2) (A(H)) phase-low-temperature VO(2) (A) phase, which was achieved by hydrothermal treatment, respectively. Also, an alternative synthesis route was proposed based on the above hydrothermal transformation, and VO(2) (A) was successfully prepared via the simple one-step hydrothermal method by hydrolysis of VO(acac)(2) (acac = acetylacetonate). Therefore, VO(2) nanostructures with controlled phase compositions can be obtained in high yields. Through elucidating the structural evolution in the crystallographic shear mechanism, we can easily guide the design of other metal oxide nanostructures with controllable phases.     

Self-Inclusion Complexes Derived from Cyclodextrins: Synthesis and Characterization of 6(A),6(B)-Bis-O-[p-(allyloxy)phenyl]-Substituted beta-Cyclodextrins

The syntheses, structures, and spectroscopic properties of 6(A),6(B)-bis-O-[p-(allyloxy)phenyl]-substituted beta-cyclodextrins have been investigated. Selective activation of the 6(A),6(B)-hydroxy groups was carried out by treating heptakis(2,3-di-O-methyl)-beta-cyclodextrin (1) with 2,4-dimethoxybenzene-1,5-disulfonyl chloride to give 6(A),6(B)-bissulfonate ester 2 in a yield of only 3%. This material was treated with sodium p-(allyloxy)phenoxide in DMF to form 6(A),6(B)-bis-O-[p-(allyloxy)phenyl]-heptakis(2,3-di-O-methyl)-beta-cyclodextrin (3), which had two isomers. One (3A) has the two p-(allyloxy)phenyl arms directed away from the cyclodextrin cavity, and the other (3B) has one of the p-(allyloxy)phenyl groups through the cavity to form a self-inclusion complex. When either 3A or 3B was treated with methyl iodide and sodium hydride, the resulting permethylated 6(A),6(B)-bis-O-[p-(allyloxy)phenyl]heptakis(2,3-di-O-methyl)-6(C),6(D),6(E),6(F),6(G)-penta-O-methyl-beta-cyclodextrin (4) was composed of two isomers, in which 4B is a self-inclusion complex. 3A and 3B also can be converted into a mixture of 3A and 3B in strong base but not when melted in the absence of base. 4A and 4B do not isomerize. Detailed 1D and 2D NMR spectroscopic studies were carried out to characterize the structures of these new compounds, and molecular mechanics techniques were used to explain the experimental facts.     

An ionically driven molecular IMPLICATION gate operating in fluorescence mode

An asymmetrically core-extended boron-dipyrromethene (BDP) dye was equipped with two electron-donating macrocyclic binding units with different metal ion preferences to operate as an ionically driven molecular IMPLICATION gate. A Na(+)-responsive tetraoxa-aza crown ether (R(2)) was integrated into the extended pi system of the BDP chromophore to trigger strong intramolecular charge transfer (ICT(2)) fluorescence and guarantee cation-induced spectral shifts in absorption. A dithia-oxa-aza crown (R(1)) that responds to Ag(+) was attached to the meso position of BDP in an electronically decoupled fashion to independently control a second ICT(1) process of a quenching nature. The bifunctional molecule is designed in such a way that in the absence of both inputs, ICT(1) does not compete with ICT(2) and a high fluorescence output is obtained (In(A)=In(B)=0-->Out=1). Accordingly, binding of only Ag(+) at R(1) (In(A)=1, In(B)=0) as well as complexation of both receptors (In(A)=In(B)=1) also yields Out=1. Only for the case in which Na(+) is bound at R(2) and R(1) is in its free state does quenching occur, which is the distinguishing characteristic for the In(A)=0 and In(B)=1-->Out=0 state that is required for a logic IMPLICATION gate and Boolean operations such as IF-THEN or NOT.     

Metallobleomycin-mediated cleavage of DNA not involving a threading-intercalation mechanism.

The DNA cleavage properties of metallobleomycins conjugated to three solid supports were investigated using plasmid DNA, relaxed covalently closed circular DNA, and linear duplex DNA as substrates. Cleavage of pBR322 and pSP64 plasmid DNAs by Fe(II).BLM A(5)-CPG-C(2) was observed with efficiencies not dissimilar to that obtained using free Fe(II).BLM A(5). Similar results were observed following Fe(II).BLM A(5)-CPG-C(2)-mediated cleavage of a relaxed plasmid, a substrate that lacks ends or negative supercoiling capable of facilitating strand separation. BLMs covalently tethered to solid supports, including Fe(II).BLM A(5)-Sepharose 4B, Fe(II).BLM A(5)-CPG-C(6), and Fe(II).BLM A(5)-CPG-C(2), cleaved a 5'-(32)P end labeled linear DNA duplex with a sequence selectivity identical to that of free Fe(II).BLM A(5); cleavage predominated at 5'-G(82)T(83)-3' and 5'-G(84)T(85)-3'. To verify that these results could also be obtained using other metallobleomycins, supercoiled plasmid DNA and a linear DNA duplex were employed as substrates for Co(III).BLM A(5)-CPG-C(2). Free green Co(III).BLM A(5) was only about 2-fold more efficient than green Co(III).BLM A(5)-CPG-C(2) in effecting DNA cleavage. A similar result was obtained using Cu(II).BLM A(5)-CPG-C(2) + dithiothreitol. In addition, the conjugated Co.BLM A(5) and Cu.BLM A(5) cleaved the linear duplex DNA with a sequence selectivity identical to that of the respective free metalloBLMs. Interestingly, when supercoiled plasmid DNA was used as a substrate, conjugated Fe.BLM A(5) and Co.BLM A(5) were both found to produce Form III DNA in addition to Form II DNA. The formation of Form III DNA by conjugated Fe.BLM A(5) was assessed quantitatively. When corrected for differences in the intrinsic efficiencies of DNA cleavage by conjugated vs free BLMs, conjugated Fe.BLM A(5) was found to produce Form III DNA to about the same extent as the respective free Fe.BLM A(5), arguing that this conjugated BLM can also effect double-strand cleavage of DNA. Although previous evidence supporting DNA intercalation by some metallobleomycins is convincing, the present evidence indicates that threading intercalation is not a requirement for DNA cleavage by Fe(II).BLM A(5), Co(III).BLM A(5), or Cu(I).BLM A(5).     

Design of biomolecular interface for detecting carbohydrate and lectin weak interactions

A hybrid functional biomolecular interface designed at a molecular size level is very effective at capturing an analyte with high sensitivity even if the interaction is very weak, as when detecting proteins with carbohydrate. We designed and processed a protein (lectin) recognition molecular interface taking the following points into consideration: (1) the height (molecular length) difference between the capturing and spacer molecules; (2) the ratio of capturing molecules in the recognition interface. When the height difference between the maltoside part (Concanavalin A (Con A) recognition group) and the OH group terminated spacer molecules exceeded (>(CH(2))(6)), the association rate constant (k(a)) became larger (k(a)(1/Ms): ～2.6 times) and the dissociation constant (K(D)) became much smaller (K(D)(M): 1.0 × 10(-6): ～0.17 times) compared with the similar heights (lengths) of both molecular interfaces. With regard to maltoside density, a 100% maltoside monolayer was unsuitable for detecting Con A. We constructed a nanostructured recognition site with a maltoside part of 10%, which was the most suitable ratio for Con A detection. The binding interaction between Con A and the maltoside group was changed from monovalent binding to bivalent binding when the maltoside part was diluted in the recognition interface. From electrochemical measurements, even though there was a small amount of maltoside component on the suitable recognition monolayer, quality similar to that of 100% maltoside was observed.     

Development of a New Distyrylbenzene-Derivative Amyloid-β-aggregation and Fibril Formation Inhibitor

Several new amyloid-β (Aβ) aggregation inhibitors were synthesized according to our theory that a hydrophilic moiety could be attached to the Aβ-recognition unit for the purpose of preventing amyloid plaque formation. A distyrylbenzene-derivative, DSB(EEX)(3), which consider the Aβ recognition unit (DSB, 1,4-distyrylbenzene) and expected to bind to amyloid fibrils (β-sheet structure), was combined with the hydrophilic aggregation disrupting element (EEX) (E, Glu; X, 2-(2-(2-aminoethoxy)ethoxy)acetic acid). This DSB(EEX)(3) compound, compared to several others synthesized similarly, was found to be the most active for reducing Aβ toxicity toward IMR-32 human neuroblastoma cells. Moreover, its inhibition of Aβ-aggregation or fibril formation was directly confirmed by transmission electron microscopy and atomic force microscopy. These results suggest that the Aβ aggregation inhibitor DSB(EEX)(3) disrupts clumps of Aβ protein and is a likely candidate for drug development to treat Alzheimer's disease.     

Quantitative Aspects of Electrochemical Detection of Amyloid‐β Aggregation

The tyrosine based electrochemical analysis of synthetic amyloid‐β (Aβ) peptide – an analog of natural peptide implicated in Alzheimer's disease pathogenesis – was applied for a quantitative estimation of peptide aggregation in vitro. The analysis was carried out by square wave voltammetry (SWV) on carbon screen printed electrodes (SPE). The electrooxidation peak current (I_p) for Aβ42 peptide in different aggregation states was directly compared with the size and structure of Aβ42 aggregates occurring in the analyzed sample. Dynamic light scattering (DLS) and thioflavin T (ThT) based fluorescence assay were employed to estimate the size and structure of Aβ42 aggregates. The I_p was found to decrease in a linear fashion when the average diameter of aggregates and the relative ThT fluorescence in Aβ42 solutions exceeded 35 nm and 3, respectively, while being nearly constant below these values. It was suggested that the electrooxidation current is mostly generated by peptide monomers and that a depletion of the monomer pool due to inclusion of Aβ42 molecules in aggregates is responsible for the decrease of electrooxidation current. The direct electrochemistry is emerging as a method complementary to methods based on aggregates’ detection and commonly employed for monitoring Aβ aggregation. The work further enlarges the basis for application of the cost‐effective and rapid electrochemical techniques, such as SWV on carbon SPE, to in vitro studies of Aβ aggregation.     

A new synthetic pathway of segmented tri-block copolyether

A new synthetic pathway of A–B–A tri-block copolyether which is composed of a hydrophilic poly(oxyethylene) unit as an A part and a hydrophobic poly(oxy-2-methyl-trimethylene) unit as a B part is proposed. Telechelic α-tosyl-ω-tosyloxypoly(oxy-2-methyl-trimethylene) derived from tosylation of poly(oxy-2-methyl-trimethylene glycol) (PMTG) was allowed to react with poly(ethylene glycol) (PEG) in the presence of sodium hydroxide. T_g of the resulting A–B–A tri-block copolyether (PEMG) (M?_n = 1600) was ?72°C and its specific gravity [D₄¹⁵] was 1.055.     

Probing the solvent accessibility and electron density of adenine: oxidation of 7-deazaadenine in bent DNA and purine doublets

The effect of DNA bending on nucleobase electron transfer was investigated by studying the oxidation of double-stranded sequences containing seven repeats of the known bent sequence d(GGCA(1)A(2)A(3)A(4)A(5)A(6)C) where 7-deazaadenine (zA) was substituted at the A(3) position. Native gel electrophoresis was used to show that the sequence remained bent upon substitution of zA, which provides for oxidation of the sequence by Ru(bpy)(3)(3+) (bpy = 2,2'-bipyridine). The Ru(III) oxidant was generated by photolysis of Ru(bpy)(3)(2+) in the presence of ferricyanide, and the oxidation was visualized by high-resolution gel electrophoresis of the radiolabeled DNA sequence following base treatment. Cleavage of the DNA strand at the guanine residues and at the zA residues was observed. Comparison of the oxidation of zA in bent DNA versus the normal B form showed that hybridization of the B form sequence to its Watson-Crick complement produced a reduction in cleavage by a factor of 5.19 +/- 0.46 while hybridization of the bent sequence only reduced cleavage by a factor of 1.58 +/- 0.23. This result implies that the zA in the double-stranded, bent sequence is much more solvent-exposed than in normal B-form DNA. When the zA occurred in a B-form 5'-zA-G doublet, the reactivity was 6.63 +/- 0.10 times higher for the zA compared to the G. This implies an even greater effect of a 3'-guanine on the oxidation potential of zA than in the well-known 5'-GG doublet.     

Conformational control of the Q(A) to Q(B) electron transfer in bacterial reaction centers: evidence for a frozen conformational landscape below -25 degrees C

The competition between the P(+)Q(A)(-) --> PQ(A) charge recombination (P, bacteriochlorophyll pair acting as primary photochemical electron donor) and the electron transfer to the secondary quinone acceptor Q(A)(-)Q(B) --> Q(A)Q(B)(-) (Q(A) and Q(B), primary and secondary electron accepting quinones) was investigated in chromatophores of Rb. capsulatus, varying the temperature down to -65 degrees C. The analysis of the flash-induced pattern for the formation of P(+)Q(A)Q(B)(-) shows that the diminished yield, when lowering the temperature, is not due to a homogeneous slowing of the rate constant k(AB) of the Q(A)(-)Q(B) --> Q(A)Q(B)(-) electron transfer but to a distribution of conformations that modulate the electron transfer rate over more than 3 orders of magnitude. This distribution appears "frozen", as no dynamic redistribution was observed over time ranges > 10 s (below -25 degrees C). The kinetic pattern was analyzed to estimate the shape of the distribution of k(AB), showing a bell-shaped band on the high rate side and a fraction of "blocked" reaction centers (RCs) with very slow k(AB). When the temperature is lowered, the high rate band moves to slower rate regions and the fraction of blocked RCs increases at the expense of the high rate band. The RCs that recombine from the P(+)Q(A)Q(B)(-) state appear temporarily converted to a state with rapid k(AB), indicating that the stabilized state described by Kleinfeld et al. (Biochemistry 1984, 23, 5780-5786) is still accessible at -60 degrees C.     

Total synthesis of oxidized phospholipids. 3. The (11E)-9-hydroxy-13-oxotridec-11-enoate ester of 2-lysophosphatidylcholine

A total synthesis of (11E)-9-hydroxy-13-oxotridec-11-enoate ester of 2-lysophosphatidylcholine (HOT-PC) was devised to facilitate identification of this oxidized phospholipid. A lactone, 8-(3-oxo-1H,6H-2-oxinyl)octanoic acid (1), believed to be generated through an intermediate (11E)-9-hydroxy-13-oxotridec-11-enoic acid (HOT), is produced upon autoxidation of linoleic acid. A synthesis of lactone 1 methyl ester was accomplished from HOT involving a novel trans-cis isomerization that is driven to completion by cyclization to a hemiacetal. An alternative route to this carbon skeleton was also achieved that provides the lactone 1 itself.     

Optical Stark spectroscopy of the B̃(1)A(')(000)←X̃(1)A(')(000) system of copper hydroxide

The B?(1)A(')(000)←X?(1)A(')(000) band system of a cold beam of CuOH has been studied field-free and in the presence of a static electric field. The Stark tuning of the low-J levels of the X?(1)A(')(000) state were analyzed to give a value of 3.968(32) D for the a-component of the permanent electric dipole moment, μ(a). An upper limit of 0.3 D for μ(a)(B?(1)A(')) is established from the lack of observable Stark tuning for the low-J levels of the B?(1)A(')(000) state. The experimental value for μ(a)(X?(1)A(')) is compared to theoretical predictions and other Cu-containing molecules. A molecular orbital correlation diagram is used to rationalize the large change in μ(a) upon excitation. The electronegativity of OH was determined to be 2.81 from a comparison of the determined μ(a) with the experimental μ values for CuF, CuO, and CuS.     

Protein-cofactor interactions in bacterial reaction centers from Rhodobacter sphaeroides R-26: effect of hydrogen bonding on the electronic and geometric structure of the primary quinone. A density functional theory study

The effect of hydrogen bonding to the primary quinone (Q(A) and Q(*)(-)(A)) in bacterial reaction centers was studied using density functional theory (DFT) calculations. The charge neutral state Q(A) was investigated by optimizing the hydrogen atom positions of model systems extracted from 15 different X-ray structures. From this analysis, mean values of the H-bond lengths and directions were derived. It was found that the N(delta)-H of His M219 forms a shorter H-bond to Q(A) than the N-H of Ala M260. The H-bond of His M219 is linear and more twisted out of the quinone plane. The radical anion Q(*)(-)(A) in the protein environment was investigated by using a mixed quantum mechanics/molecular mechanics (QM/MM) approach. Two geometry optimizations with a different number of flexible atoms were performed. H-bond lengths were obtained and spectroscopic parameters calculated, i.e. the hyperfine and nuclear quadrupole couplings of magnetic nuclei coupled to the radical. Good agreement was found with the results provided by EPR/ENDOR spectroscopy. This implies that the calculated lengths and directions of the H-bonds to Q(*)(-)(A) are reliable values. From a comparison of the neutral and reduced state of Q(A) it was concluded that the H-bond distances are shortened by approximately 0.17 Angstroms (His M219) and approximately 0.13 Angstroms (Ala M260) upon single reduction of the quinone. It is shown that the point-dipole approximation can not be used for an estimation of H-bond lengths from measured hyperfine couplings in a system with out-of-plane H-bonding. In contrast, the evaluation of the nuclear quadrupole couplings of (2)H nuclei substituted in the hydrogen bonds yields H-bond lengths close to the values that were deduced from DFT geometry optimizations. The significance of hydrogen bonding to the quinone cofactors in biological systems is discussed.