A growing string method for determining transition states: comparison to the nudged elastic band and string methods

Interpolation methods such as the nudged elastic band and string methods are widely used for calculating minimum energy pathways and transition states for chemical reactions. Both methods require an initial guess for the reaction pathway. A poorly chosen initial guess can cause slow convergence, convergence to an incorrect pathway, or even failed electronic structure force calculations along the guessed pathway. This paper presents a growing string method that can find minimum energy pathways and transition states without the requirement of an initial guess for the pathway. The growing string begins as two string fragments, one associated with the reactants and the other with the products. Each string fragment is grown separately until the fragments converge. Once the two fragments join, the full string moves toward the minimum energy pathway according to the algorithm for the string method. This paper compares the growing string method to the string method and to the nudged elastic band method using the alanine dipeptide rearrangement as an example. In this example, for which the linearly interpolated guess is far from the minimum energy pathway, the growing string method finds the saddle point with significantly fewer electronic structure force calculations than the string method or the nudged elastic band method.     

The Henicosaphosphide Iodides of Potassium and Rubidium,K4P21I and Rb4P21I

The novel ternary polyphosphides M₄P₂₁I (M = K, Rb) have been synthesized from the elements in single crystalline form, representing further examples for the formation of mixed crystals between simple salts and binary phosphides. They form as ruby‐red platelets and dark‐red prisms, respectively, and are only slightly sensitive to moisture and oxygen. The compounds are isotypic (Ccmm (no 63); Z = 4; oP104; K₄P₂₁I: a = 12.853Å; b = 21.795Å; c = 9.748Å; 1168 hkl, R = 0.033; Rb₄P₂₁I: a = 13.281Å; b = 21.868Å; c = 9.771Å; 777 hkl, R = 0.053) and feature corrugated 2D networks formed from two different types of polymerized P₇ units. The networks form large cavities filled by M⁺ and I^‐ ions. Zigzag chains of condensed trigonal M₆ prisms, centered by the I^‐ anions, separate the polyphosphide nets. The mean homoatomic P‐P bond length (d = 2.216Å) corresponds to a P‐P single bond. However, the individual P‐P distances vary with position and function (2.126 ‐ 2.247Å) and these are compared with those of the isolated P₂₁^‐3 anion.     

PHOTOSENSITIZING PROPERTIES OF BACTERIOCHLOROPHYLLIN a and BACTERIOCHLORIN a, TWO DERIVATIVES OF BACTERIOCHLOROPHYLL a

Abstract The photosensitizing properties of two water soluble derivatives of bacteriochlorophyll a , bacteriochlorophyllin a and bacteriochlorin a (lacking the central Mg-ion) were investigated and compared to those of hematoporphyrin derivatives. At physiological pH the oxygen consumption rate of histidine, tryptophan, dithiothreitol and guanosine upon illumination was 3 to 4 times higher when bacteriochlorin a was used as photosensitizer than when hematoporphyrin derivatives were used. Especially bacteriochlorin a proved to be an effective sensitizer for the killing of L929 cells. Because bacteriochlorin a has an absorption maximum at 765 nm in phosphate buffered saline (allowing a light penetration in tissue about ten times larger than at 630 nm) and a high molar absorption coefficient (32 000 M cm⁻¹) it has promising possibilities for the application in photodynamic therapy.     

Zwitterionic and cationic bis(phosphine) platinum(II) complexes: structural,electronic, and mechanistic comparisons relevant to ligand exchange and benzene C-H activation processes

Structurally similar but charge-differentiated platinum complexes have been prepared using the bidentate phosphine ligands [Ph(2)B(CH(2)PPh(2))(2)], ([Ph(2)BP(2)], [1]), Ph(2)Si(CH(2)PPh(2))(2), (Ph(2)SiP(2), 2), and H(2)C(CH(2)PPh(2))(2), (dppp, 3). The relative electronic impact of each ligand with respect to a coordinated metal center's electron-richness has been examined using comparative molybdenum and platinum model carbonyl and alkyl complexes. Complexes supported by anionic [1] are shown to be more electron-rich than those supported by 2 and 3. A study of the temperature and THF dependence of the rate of THF self-exchange between neutral, formally zwitterionic [Ph(2)BP(2)]Pt(Me)(THF) (13) and its cationic relative [(Ph(2)SiP(2))Pt(Me)(THF)][B(C(6)F(5))(4)] (14) demonstrates that different exchange mechanisms are operative for the two systems. Whereas cationic 14 displays THF-dependent, associative THF exchange in benzene, the mechanism of THF exchange for neutral 13 appears to be a THF independent, ligand-assisted process involving an anchimeric, eta(3)-binding mode of the [Ph(2)BP(2)] ligand. The methyl solvento species 13, 14, and [(dppp)Pt(Me)(THF)][B(C(6)F(5))(4)] (15), each undergo a C-H bond activation reaction with benzene that generates their corresponding phenyl solvento complexes [Ph(2)BP(2)]Pt(Ph)(THF) (16), [(Ph(2)SiP(2))Pt(Ph)(THF)][B(C(6)F(5))(4)] (17), and [(dppp)Pt(Ph)(THF)][B(C(6)F(5))(4)] (18). Examination of the kinetics of each C-H bond activation process shows that neutral 13 reacts faster than both of the cations 14 and 15. The magnitude of the primary kinetic isotope effect measured for the neutral versus the cationic systems also differs markedly (k(C(6)H(6))/k(C(6)D(6)): 13 = 1.26; 14 = 6.52; 15 approximately 6). THF inhibits the rate of the thermolysis reaction in all three cases. Extended thermolysis of 17 and 18 results in an aryl coupling process that produces the dicationic, biphenyl-bridged platinum dimers [[(Ph(2)SiP(2))Pt](2)(mu-eta(3):eta(3)-biphenyl)][B(C(6)F(5))(4)](2) (19) and [[(dppp)Pt](2)(mu-eta(3):eta(3)-biphenyl)][B(C(6)F(5))(4)](2) (20). Extended thermolysis of neutral [Ph(2)BP(2)]Pt(Ph)(THF) (16) results primarily in a disproportionation into the complex molecular salt [[Ph(2)BP(2)]PtPh(2)](-)[[Ph(2)BP(2)]Pt(THF)(2)](+). The bulky phosphine adducts [Ph(2)BP(2)]Pt(Me)[P(C(6)F(5))(3)] (25) and [(Ph(2)SiP(2))Pt(Me)[P(C(6)F(5))(3)]][B(C(6)F(5))(4)] (29) also undergo thermolysis in benzene to produce their respective phenyl complexes, but at a much slower rate than for 13-15. Inspection of the methane byproducts from thermolysis of 13, 14, 15, 25, and 29 in benzene-d(6) shows only CH(4) and CH(3)D. Whereas CH(3)D is the dominant byproduct for 14, 15, 25, and 29, CH(4) is the dominant byproduct for 13. Solution NMR data obtained for 13, its (13)C-labeled derivative [Ph(2)BP(2)]Pt((13)CH(3))(THF) (13-(13)()CH(3)()), and its deuterium-labeled derivative [Ph(2)B(CH(2)P(C(6)D(5))(2))(2)]Pt(Me)(THF) (13-d(20)()), establish that reversible [Ph(2)BP(2)]-metalation processes are operative in benzene solution. Comparison of the rate of first-order decay of 13 versus the decay of d(20)-labeled 13-d(20)() in benzene-d(6) affords k(13)()/k(13-d20)() approximately 3. The NMR data obtained for 13, 13-(13)()CH(3)(), and 13-d(20)() suggest that ligand metalation processes involve both the diphenylborate and the arylphosphine positions of the [Ph(2)BP(2)] auxiliary. The former type leads to a moderately stable and spectroscopically detectable platinum(IV) intermediate. All of these data provide a mechanistic outline of the benzene solution chemistries for the zwitterionic and the cationic systems that highlights their key similarities and differences.     

Darstellung, 19F-NMR-spektroskopischer Nachweis und Untersuchung zur Bildung der metallgemischten Clusteranionen [(Mo6−nWnCl)F]2−, n = 0−6

Preparation, ¹⁹F NMR Spectroscopic Evidence and Study of the Formation of Metal-Mixed Cluster Anions [(Mo_6?nW_nCl )F ]^2?, n = 0?6 The complete system of metal-mixed octahedral cluster ions [(Mo_6?nW_nCl)F]^2?, n = 0?6, is prepared by tempering Mo powder with WCl₆ at 600°C. A mixture containing inclusively the geometric isomers (n = 2, 3, 4) all ten possible species is transferred into the tetra-n-butylammonium salts (TBA)₂[(Mo_6?nW_nCl)F]. In the ¹⁹F nmr spectrum the 24 expected signals are observed, assigned on the basis of their chemical shifts, multiplicities and intensities, and confirmed by a 2D-¹⁹F-¹⁹F COSY spectrum. From the integrated intensities the distribution of the different components is derived revealing a non-statistical formation, in that isomers with Mo…?Mo or W…?W atoms in trans-positions in comparision to those with mixed Mo…?W axes are favoured, and that especially the homoleptic compounds Mo₆ and W₆ are present to an over-average extent. Evaluation of ¹⁹F chemical shifts reveals that F bound to W which is in antipodal position to Mo resonates at higher field compared to F bound to W in a W…?W arrangement, caused by an increased shielding, which is synonymous to a positive antipodal-effect by Mo. Vice versa F bound to Mo with an antipodal W resonates at lower field compared with F bound to Mo in an Mo…?Mo arrangement caused by an increased deshielding and synonymous a negative antipodal-effect by W. The chemical shifts, resulting from antipodal-effects, are different for the compounds within the [(Mo_6?nW_nCl)F]^2? - system. The difference of the antipodal effect of successive substitution products results in characteristic values designated as antipodal shift constants, depending on the kind of substituents, which is valid for other cluster systems, too.     

Primary reaction dynamics of halorhodopsin,observed by sub-picosecond IR – vibrational spectroscopy

The primary all-trans to 13-cis chromophore isomerization of the light driven chloride pump halorhodopsin has been studied by means of transient absorption spectroscopy in the visible and mid-infrared regime at a time resolution of better than 100 and 220 fs, respectively. The picosecond vibrational dynamics are dominated by two time constants, i.e., 2 and 7.7 ps in accordance with the biphasic decay of the retinal excited electronic state and electronic ground state formation with 1.5 and 6.6 ps. The transient vibrational spectra of the participating electronic states strongly suggest the existence of two distinct S₁ populations as a result of an early branching reaction. It is shown that the 13-cis product is formed with the fast time constant, whereas the all-trans educt state is repopulated via both time constants. Concomitant protein dynamics are indicated by spectral changes on a similar time scale in the amide region.     

Comparison of reversed-phase liquid chromatography and hydrophilic interaction/cation-exchange chromatography for the separation of amphipathic alpha-helical peptides with L- and D-amino acid substitutions in the hydrophilic face

Mixed-mode hydrophilic interaction/cation-exchange chromatography (HILIC/CEX) is a novel high-performance technique which has excellent potential for peptide separations. Separations by HILIX/CEX are carried out by subjecting peptides to linear increasing salt gradients in the presence of high levels of acetonitrile, which promotes hydrophilic interactions overlaid on ionic interactions with the cation-exchange matrix. In the present study, HILIC/CEX has been compared to reversed-phase liquid chromatography (RP-HPLC) for separation of mixtures of diastereomeric amphipathic alpha-helical peptide analogues, where L- and D-amino acid substitutions were made in the centre of the hydrophilic face of the amphipathic alpha-helix. Unlike RP-HPLC, temperature had a substantial effect on HILIC/CEX of the peptides, with a rise in temperature from 25 to 65 degrees C increasing the retention times of the peptides as well as improving resolution. Our results again highlight the potential of HILIC/CEX as a peptide separation mode in its own right as well as an excellent complement to RP-HPLC.     

Three-state 2',7'-difluorofluorescein excited-state proton transfer reactions in moderately acidic and very acidic media

2',7'-Difluorofluorescein (Oregon Green 488, OG488) is a novel fluorescein dye derivative which presents important advantages for improving the fluorimetric applications in the biomedical and biochemical sciences. In aqueous solution it displays four prototropic forms, namely cation (C), neutral (N), monoanion (M), and dianion (D). In previous works, we found (J. Phys. Chem. A 2005, 109, 734-747, 2840-2846) that OG488 undergoes excited-state proton transfer reactions, which may affect the results from applications using this dye. We established that the excited-state proton transfer (ESPT) reactions between neutral, monoanionic, and dianionic forms of OG488 are promoted by acetate buffer, and we characterized the ground and excited species involved. We also solved the kinetics of the prototropic reactions using global compartmental analysis. In the present paper, we extend our study on the ESPT reactions of OG488 to acidic media, in which only the three prototropic species cation, neutral, and monoanion coexist. We have solved the kinetics of the three-state ESPT reaction by means of global three-compartmental analysis of a fluorescence decay surface in moderately acidic media (pH between 1.1 and 3.0), recovering the kinetic and spectral parameters of this three-state system. This system is one of the most complex solved to date, due to the strong overlap of the absorption and emission spectra of the neutral and monoanionic forms of OG488. We also found that the cation behaves as "super" photoacid, showing a very high deprotonation rate constant (1.04 x 10(11) s(-1)) and an enhanced acidity. Therefore, we also carried out experiments at very high perchloric acid concentrations, dealing with some other effects which become noteworthy at these [H(+)]. The presence of xanthylium cation quenching due to "free" water molecules, and the reduction in the amount of water clusters acting as proton acceptors, are processes which alter notably the time course of the excited-species in this high [H(+)] range.     

Determination of 8-hydroxy-2'-deoxyguanosine in untreated urine by capillary electrophoresis with UV detection

A capillary electrophoresis method with UV detection was developed for the determination of 8-hydroxy-2'-deoxyguanosine (8-OHdG) in untreated urine samples. The calibration graph for 8-OHdG in urine is linear in the concentration range 10-500 mg/l. and the detection limit is 5 mg/l (17 microM). 8-OHdG was determined in urine from oncological patients treated by radiation therapy. Its concentrations relative to creatinine were found to be in the range 10-47 microg 8-OHdG/l mg creatinine (4-19 micromol 8-OHdG/mmol creatinine). The overall time of the analysis of a urine sample was less than 15 min.     

Die Struktur des Pentaphenyldisilans

Structure of Pentaphenyldisilane For the first time Pentaphenyldisilane was prepared by Gilman and Goodman. It is produced by the reaction of Ph₃SiLi with Ph₂ClSiH. The crystal structure presents an ideally staggered conformation. The distance d(Si? Si) = 235.7 pm corresponds to a normal single bond length. This emphasizes the complete relief of the central Si? Si bond by the insertion of only one hydrogen atom.