Grand canonical Monte Carlo simulations of water in protein environments

The grand canonical simulation algorithm is considered as a general methodology to sample the configuration of water molecules confined within protein environments. First, the probability distribution of the number of water molecules and their configuration in a region of interest for biochemical simulations, such as the active site of a protein, is derived by considering a finite subvolume in open equilibrium with a large system serving as a bulk reservoir. It is shown that the influence of the bulk reservoir can be represented as a many-body potential of mean force acting on the atoms located inside the subvolume. The grand canonical Monte Carlo (GCMC) algorithm, augmented by a number of technical advances to increase the acceptance of insertion attempts, is implemented, and tested for simple systems. In particular, the method is illustrated in the case of a pure water box with periodic boundary conditions. In addition, finite spherical systems of pure water and containing a dialanine peptide, are simulated with GCMC while the influence of the surrounding infinite bulk is incorporated using the generalized solvent boundary potential [W. Im, S. Berneche, and B. Roux, J. Chem. Phys. 114, 2924 (2001)]. As a last illustration of water confined in the interior of a protein, the hydration of the central cavity of the KcsA potassium channel is simulated.     

129Xe NMR spectrum of xenon inside C(60)

Xenon was inserted into C(60) by heating C(60) in 3000 atm of xenon gas at 650 degrees C. The Xe@C(60) was separated from the empty C(60) by using HPLC. The (13)C resonance for Xe@C(60) is shifted downfield by 0.95 ppm (192 Hz). (129)Xe NMR showed a line 179.2 ppm downfield from xenon gas.     

Double-salt formation in crystal structures containing [Co(en)3]Cl3

The structures of three racemic double salts of [Co(en)₃]Cl₃ (en is ethane-1,2-diamine, C₂H₈N₂), namely, bis[tris(ethane-1,2-diamine-κ²N,N′)cobalt(III)] hexaaquasodium(I) heptachloride, [Co(en)₃]₂[Na(H₂O)₆]Cl₇, bis[tris(ethane-1,2-diamine-κ²N,N′)cobalt(III)] hexaaquapotassium(I) heptachloride, [Co(en)₃]₂[K(H₂O)₆]Cl₇, and ammonium bis[tris(ethane-1,2-diamine-κ²N,N′)cobalt(III)] heptachloride hexahydrate, (NH₄)[Co(en)₃]₂Cl₇·6H₂O, have been determined, and the structural similarities with the parent compound, tris(ethane-1,2-diamine-κ²N,N′)cobalt(III) trichloride tetrahydrate, [Co(en)₃]Cl₃·4H₂O, are highlighted. All four compounds crystallize in the trigonal space group Pc1. When compared with the parent compound, the double salts show a modest increase in the unit-cell volume. The structure of the chiral derivative [Λ-Co(en)₃]₂[Na(H₂O)₆]Cl₇ has also been redetermined at cryogenic temperatures (120 K) and the disorder noted in a previous report has been accounted for.     

Thermal decomposition of [Co(NH3)5Cl]Cl2

The thermal decomposition of [Co(NH₃)₅Cl]Cl₂ was studied under non-isothermal conditions, in dynamic air and argon atmospheres. The kinetics of the particular stages of [Co(NH₃)₅Cl]Cl₂ thermal decomposition were evaluated from the dynamic weight loss data by means of the modified Coats-Redfern method. TheD _n andR _n models were selected as the models best fitting the experimental TG curves. These models suggest that the kinetics and macromechanism of [Co(NH₃)₅Cl]Cl₂ decomposition can be governed by diffusive and/or phase boundary processes. The values of the activation energy,E _a, and the pre-exponencial factor,A, of the particular stages of the thermal decomposition were calculated.     

Thermal decomposition of [Co(NH3)5Cl]Cl2

Simultaneous TG-DTG-DTA studies on [Co(NH₃)₅Cl]Cl₂ under non-isothermal conditions were carried out in dynamic air and argon atmospheres in the temperature range 293–1273 K. Thermogravimetric measurements under quasi-isothermal conditions were also made. On the basis of the experimental data (weight loss, X-ray diffraction, reflectance spectroscopy and chemical analysis), the probable decomposition sequences are presented. The data indicate that the thermal decomposition of [Co(NH₃)₅Cl]Cl₂ occurs in three stages in argon and four stages in air.The changes in the morphology of crystalline [Co(NH₃)₅Cl]Cl₂ powder in the course of its thermal decomposition in air were followed by scanning electron microscopy.

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Zusammenfassung In dynamischer Luft- und ArgonatmosphÄre wurden im Temperaturbereich 293–1273 K unter nichtisothermen Bedingungen simultane TG-DTG-DTA Untersuchungen an [Co(NH₃)₅Cl]Cl₂ durchgeführt, ebenso auch thermogravimetrische Untersuchungen unter quasi-isothermen Bedingungen. Auf der Grundlage der experimentellen Daten (Gewichtsverlust, Röntgendiffraktion, Reflexionsspektroskopie und chemische Analyse) wurde eine wahrscheinliche Zersetzungssequenz erstellt. Es zeigte sich, da\ die thermische Zersetzung in Argon in drei Schritten, in Luft dagegen in vier Schritten verlÄuftDie VerÄnderung der Morphologie kristallinen [Co(NH₃)₅Cl]Cl₂-Pulvers im Verlaufe seiner thermischen Zersetzung in Luft wurde durch Scanning-Elektronenmikroskopie verfolgt.

     

Thermal decomposition of [Co(NH3)6]Cl3

The thermal decomposition reactions of [Co(NH₃)₆]Cl₃ were determined in dynamic argon and air atmospheres. The investigations were carried out with simultaneous TG-DTG-DTA measurements under non-isothermal conditions, thermogravimetry under quasi-isothermal conditions, reflectance spectroscopy, absorption spectroscopy, X-ray diffraction and chemical analysis. The data show that the thermal decomposition of [Co(NH₃)₆]Cl₃ occurs in three and four stages in argon and air atmospheres, respectively. The determined sequences are in agreement with that proposed by Simons and Wendlandt [2, 5].The changes in the morphology of the studied complex crystalline powder in the course of thermal decomposition in air were followed by scanning electron microscopy.

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Zusammenfassung In bewegter Argon- und Luftatmosphäre wurden die Zersetzungsreaktionen für [Co(NH₃)₆]Cl₃ bestimmt. Zu den Untersuchungen wurden folgende Methoden zu Hilfe gezogen: simultane TG-DTG-DTA-Messungen unter nichtisothermen Bedingungen, Thermogravimetrie unter quasi-isothermen Bedingungen, Remissionsspektroskopie, Absorptionsspektroskopie, Röntgendiffraktion und chemische Analyse. Die Ergebnisse zeigen, daß sich [Co(NH₃)₆]Cl₃ in Argon in drei und in Luft in vier Schritten thermisch zersetzt. Die festgestellten Sequenzen stehen in Übereinstimmung mit den von Simon und Wendlandt [2, 5] vorgeschlagenen. Veränderungen in der Morphologie des untersuchten Komplexkristallpulvers wurden über die thermische Zersetzung in Luft mittels Scanning-Elektronen-Mikroskopie beobachtet.

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[Co(NH₃)₆]Cl₃. , , - , , , . , , , , , , .

     

Solid-state 129Xe and 131Xe NMR study of the perxenate anion XeO(6)4-

Results of the first solid-state 131Xe NMR study of xenon-containing compounds are presented. The two NMR-active isotopes of xenon, 129Xe (I=1/2) and 131Xe (I=3/2), are exploited to characterize the xenon magnetic shielding and quadrupolar interactions for two sodium perxenate salts, Na4XeO6.xH2O (x=0, 2), at an applied magnetic field strength of 11.75 T. Solid-state 129/131Xe NMR line shapes indicate that the local xenon environment in anhydrous Na4XeO6 adopts octahedral symmetry, but upon hydration, the XeO6(4-) anion becomes noticeably distorted from octahedral symmetry. For stationary, anhydrous samples of Na4XeO6, the heteronuclear 129/131Xe-23Na dipolar interaction is the principal contributor to the breadth of the 129/131Xe NMR lines. For stationary and slow magic-angle-spinning samples of Na4XeO(6).2H2O, the anisotropic xenon shielding interaction dominates the 129Xe NMR line shape, whereas the 131Xe NMR line shape is completely dominated by the nuclear quadrupolar interaction. The xenon shielding tensor is approximately axially symmetric, with a skew of -0.7+/-0.3, an isotropic xenon chemical shift of -725.6+/-1.0 ppm, and a span of 95+/-5 ppm. The 131Xe quadrupolar coupling constant, 10.8+/-0.5 MHz, is large for a nucleus at a site of approximate Oh symmetry, and the quadrupolar asymmetry parameter indicates a lack of axial symmetry. This study demonstrates the extreme sensitivity of the 131Xe nuclear quadrupolar interaction to changes in the local xenon environment.     

A double quantum (129)Xe NMR experiment for probing xenon in multiply-occupied cavities of solid-state inclusion compounds

A method is presented for detecting multiple xenon atoms in cavities of solid-state inclusion compounds using (129)Xe double quantum NMR spectroscopy. Double quantum filtered (129)Xe NMR spectra, performed on the xenon clathrate of Dianin's compound were obtained under high-resolution Magic-Angle Spinning (MAS) conditions, by recoupling the weak (129)Xe-(129)Xe dipole-dipole couplings that exist between xenon atoms in close spatial proximity. Because the (129)Xe-(129)Xe dipole-dipole couplings are generally weak due to dynamics of the atoms and to large internuclear separations, and since the (129)Xe Chemical Shift Anisotropy (CSA) tends to be relatively large, a very robust dipolar recoupling sequence was necessary, with the symmetry-based SR26 dipolar recoupling sequence proving appropriate. We have also attempted to measure the (129)Xe-(129)Xe dipole-dipole coupling constant between xenon atoms in the cavities of the xenon-Dianin's compound clathrate and have found that the dynamics of the xenon atoms (as investigated with molecular dynamics simulations) as well as (129)Xe multiple spin effects complicate the analysis. The double quantum NMR method is useful for peak assignment in (129)Xe NMR spectra because peaks arising from different types of absorption/inclusion sites or from different levels of occupancy of single sites can be distinguished. The method can also help resolve ambiguities in diffraction experiments concerning the order/disorder in a material.     

Synthesis, characterization, and glutathionylation of cobalamin model complexes [Co(N4PyCO2Me)Cl]Cl2 and [Co(Bn-CDPy3)Cl]Cl2

Synthetic Co(III) complexes containing N5 donor sets undergo glutathionylation to generate biomimetic species of glutathionylcobalamin (GSCbl), an important form of cobalamin (Cbl) found in nature. For this study, a new Co(III) complex was synthesized derived from the polypyridyl pentadentate N5 ligand N4PyCO(2)Me (1). The compound [Co(N4PyCO(2)Me)Cl]Cl(2) (3) was characterized by X-ray crystallography, UV-vis, IR, (1)H NMR, and (13)C NMR spectroscopies and mass spectrometry (HRMS). Reaction of 3 with glutathione (GSH) in H(2)O generates the biomimetic species [Co(N4PyCO(2)Me)(SG)](2+) (5), which was generated in situ and characterized by UV-vis and (1)H NMR spectroscopies and HRMS. (1)H NMR and UV-vis spectroscopic data are consistent with ligation of the cysteine thiolate of GSH to the Co(III) center of 5, as occurs in GSCbl. Kinetic analysis indicated that the substitution of chloride by GS(-) occurs by a second-order process [k(1) = (10.1 ± 0.7) × 10(-2) M(-1) s(-1)]. The observed equilibrium constant for formation of 5 (K(obs) = 870 ± 50 M(-1)) is about 3 orders of magnitude smaller than for GSCbl. Reaction of the Co(III) complex [Co(Bn-CDPy3)Cl]Cl(2) (4) with GSH generates glutathionylated species [Co(Bn-CDPy3)(GS)](2+) (6), analogous to 5. Glutathionylation of 4 occurs at a similar rate [k(2) = (8.4 ± 0.5) × 10(-2) M(-1) s(-1)], and the observed equilibrium constant (K(obs) = 740 ± 47 M(-1)) is slightly smaller than for 5. Glutathionylation showed a significant pH dependence, where rates increased with pH. Taken together, these results suggest that glutathionylation is a general reaction for Co(III) complexes related to Cbl.     

Acceleration of Monte Carlo simulations through spatial updating in the grand canonical ensemble

A new grand canonical Monte Carlo algorithm for continuum fluid models is proposed. The method is based on a generalization of sequential Monte Carlo algorithms for lattice gas systems. The elementary moves, particle insertions and removals, are constructed by analogy with those of a lattice gas. The updating is implemented by selecting points in space (spatial updating) either at random or in a definitive order (sequential). The type of move, insertion or removal, is deduced based on the local environment of the selected points. Results on two-dimensional square-well fluids indicate that the sequential version of the proposed algorithm converges faster than standard grand canonical algorithms for continuum fluids. Due to the nature of the updating, additional reduction of simulation time may be achieved by parallel implementation through domain decomposition.     

Inclusion Complex Formation of Thiacalix[4]arene and Xe in Aqueous Solution Studied by Hyperpolarized 129Xe NMR

The inclusion complex formation of 4-sulfothiacalix[4]arene sodium salt (STCAS) and Xe has been investigated by using hyperpolarized ¹²⁹Xe NMR spectroscopy. Our new continuous-flow type hyperpolarizing system has advantageous capabilities that can supply hyperpolarized gases continuously and directly to a sample solution in a NMR tube. Consequently saturated Xe concentration in the aqueous solution of STCAS is maintained during the NMR experiment, and ¹²⁹Xe NMR spectra can be obtained in remarkably short time. STCAS concentration dependence of ¹²⁹Xe chemical shift has been analyzed in an elaborated way by a computer method as well as a simple graphic method that we have proposed. The association constant K:13.6±0.8 M⁻¹ at 25 °C was obtained, and further analysis of the temperature dependence has successfully given thermodynamic parameters of enthalpy (ΔH) and entropy (ΔS) for the inclusion complex formation: ΔH = −11.9±1.9 kJ mol⁻¹ and ΔS = −17.4±5.8 JK⁻¹ mol⁻¹. The energetic aspects of complex formation are discussed from the size effect and from the molecular theory of standard entropy, and a release of definite number of water molecules from STCAS cavity is suggested in the inclusion complex formation with Xe.     

Synthesis of the chiral tripyridyldiamine ligand Bn-CDPy3 and characterization of its Co(III) complex [Co(Bn-CDPy3)Cl]Cl2

Synthesis of the tripyridyldiamine Bn-CDPy3, a chiral pentadentate ligand, and characterization of its low-spin Co(iii) complex [Co(Bn-CDPy3)Cl]Cl(2) by X-ray crystallography, (1)H NMR, (13)C NMR, IR and UV-vis spectroscopy as well as molar conductivity and mass spectrometry, is described.     

pH-Driven Variation of the Outer-Sphere Binding Mode of cis-[Co(Ad)(en)2Cl]Cl (en-Ethylendiamine, Ad-Adeninate) with p-Sulfonatothiacalix[4]arene

The non-symmetrical cobalt (III) complex cis-[Co(Ad)(en)₂Cl]Cl (1Cl), possessing two flexible ethylendiaminate chelate rings (en) and monodentate N(9)-bound adeninate (Ad^-) was chosen as the guest of p-sulfonatothiacalix[4]arene (STCA) to study the inclusion complex formation at wide range of pH 2–10. It was shown by ¹H, NOE NMR methods and pH-metric procedure, that pH-driven variation of the inclusion mode of 1 ⁺ into calixarene cavity is the result of the protonation of 1 ⁺ via adeninate moiety.     

An NMR study on the shielding of the 129Xe isotope of xenon dissolved in thermotropic liquid crystals

The variation of the nuclear shielding of the ¹²⁹Xe isotope in natural xenon dissolved in various liquid crystals and liquid crystal mixtures has been studied over the temperature range from 300 to 360 K. The temperature dependence is linear in the isotropic phase of the liquid crystals. An abrupt change in the shielding is observed when passing through the nematic-isotropic and smectic A-nematic phase transitions as well as when the liquid crystal director rotates by 90° in the so-called critical mixture of ZLI 1167 and EBBA. This is interpreted as being mainly the consequence of the shielding anisotropy of xenon arising from the deformation of its electronic distribution. The shift changes observed for 4,4'-di-n-heptylazoxybenzene at the nematic-isotropic phase transition on the one hand and at the smectic A-nematic phase transition on the other are found to be opposite in sign, reflecting the change in the liquid crystal structure.     

NMR study on (+/-)-1-[3-(2-methoxyphenoxy)-2-hydroxypropyl]-4-[(2,6-dimethylphenyl)aminocarbonylmethyl]piperazine dihydrochloride salt

(+/-)-1-[3-(2-Methoxyphenoxy)-2-hydroxypropyl]-4-[(2,6-dimethylphenyl)aminocarbonylmethyl]piperazine dihydrochloride salt was studied spectroscopically. Complete NMR assignments for dihydrochloride salt were made using DEPT, H-H COSY, as well as HMQC and HMBC heteronuclear correlation techniques.     

Thermal decomposition of the [Co(NH3)6]Cl3, Co[(NH3)4Cl2]Cl,K3[Fe(C2O4)3]3H2O and Fe(CH3COO)3 in argon and air atmosphere

Kinetic parameters (apparent activation energy, reaction order, pre-exponential factor (Z) in the Arrhenius equation) for thermal decomposition of the [Co(NH₃)₆]Cl₃, Co[(NH₃)₄Cl₂]Cl, K₃[Fe(C₂O₄)₃]3H₂O and Fe(CH₃COO)₃ are reported. They have been calculated on the DTA and TG data according to Coats-Redfern's model. Both, decomposition data obtained in argon and in air atmosphere have been considered and the results are compared.

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Zusammenfassung Es werden die kinetischen Parameter (scheinbare Aktivierungsenergie, Reaktionsordnung, prÄexponentieller Faktor (Z) der Arrhenius-Gleichung) der thermischen Zersetzung von [Co(NH₃)₆]Cl₃, [Co(NH₃)₄Cl₂]Cl, K₃[Fe(C₂O₄)₃]3H₂O und Fe(CH₃COO)₃ beschrieben, die entsprechend dem Coats-Redfern-Modell auf der Basis der DTA- und TG-Daten errechnet wurden. Die Zersetzung wurde sowohl in Argon als auch in Luft durchgeführt und die erhaltenen Daten miteinander verglichen.

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Helpful comments from Professor W. Wojciechowski and financial support from Institute for Low Temperatures and Structure Research Polish Academy of Sciences (CPBP 01.12) are greatefully acknowledged.     

NMR and kinetic studies of the interactions of [Au(cis-DACH)Cl2]Cl and [Au(cis-DACH)2]Cl3 with potassium cyanide in aqueous solution

The interactions of [Au(cis-DACH)Cl₂]Cl and [Au(cis-DACH)₂]Cl₃ [where cis-DACH is cis-1,2-diaminocyclohexane] with enriched KCN were carried out in CD₃OD and D₂O, respectively. The reaction pathways of these complexes were studied by ¹H, ¹³C, ¹⁵N NMR, UV spectrophotometry, and electrochemistry. The kinetic data for the reaction of cyanide with [Au(cis-DACH)₂]Cl₃ are k = 18 M^?1s^?1, ?H^≠ = 11 kJ M^?1, ?S^≠ = ?185 JK^?1 M^?1, and E_a = 13 kJ M^?1 with square wave voltammetric (SWV) peak +1.35 V, whereas the kinetic data for the reaction of cyanide ion with [Au(cis-DACH)Cl₂]Cl are k = 148 M^?1s^?1, ?H^≠ = 39 kJM^?1, ?S^≠ = ?80 JK^-1 M^?1, and E_a = 42 kJM^?1 along with SWV peak +0.82 V, indicating much higher reactivity of [Au(cis-DACH)Cl₂]Cl toward cyanide than [Au(cis-DACH)₂]Cl₃. The interaction of these complexes with potassium cyanide resulted in an unstable [Au(¹³CN)₄]^? species which readily underwent reductive elimination reaction to generate [Au(¹³CN)₂]^? and cyanogen.