水素結合－π電子系相関型有機伝導体の開発とその水素/重水素同位体効果

Using a combination of high resolution and dipolar solid state 15N NMR we have determined H/D isotope effects on the nitrogen-hydron (L = H, D) distances and 15N chemical shielding tensors of strongly hydrogen bonded bisisocyanide salts of the type [(CO)5Cr−C⋮N···L···N⋮C−Cr(CO)5]- X+, where X+ = AsPh4+ (2) and X+ = NPr4+ (3). These compounds have been modeled theoretically by the linear system [C⋮N···L···N⋮C]-Li+ (1). The crystal field acting on the anion was generated by a variety of fixed C···Li distances. For the calculation of dynamical corrections of geometries and NMR chemical shifts, an iterative procedure based on the crude adiabatic approximation was employed, consisting of (i) ab initio calculation of the energy hypersurface at the MP2/6-31+G(d,p) level, (ii) solution of the Schrödinger equation for the anharmonic collinear hydron motion, and (iii) NMR chemical shift calculations using the IGLO-method. The two hydrogen bond distances r1 ≡ N···L and r2 ≡ L···N are found to change in a correlated way when H is replaced by D, as a function of X+, i.e., of the electric field at the hydrogen bond site. The correlation r1 = f(r2) established here experimentally and theoretically for very strong NHN-hydrogen bonds shows a good agreement with a correlation established previously (Steiner, Th. J. Chem. Soc., Chem. Commun. 1995, 1331) based on the neutron diffraction structures of a number of weakly hydrogen bonded solids. A plot of the sum q2 = r1 + r2corresponding in a linear hydrogen bond to the heavy atom separationas a function of the proton dislocation from the hydrogen bond center q1 = 1/2(r1−r2) exhibits a minimum value at about 2.54 Å for the symmetric low-barrier hydrogen bond at q1 = 0. This situation is realized experimentally for 2. When q1 ≠ 0 anharmonic single well hydrogen bonds are obtained, typical for 3. The geometric H/D isotope effects can be split into a primary effect referring to the hydron position q1 = 1/2(r1−r2) and a secondary effect referring to the heavy atom position q2. Secondary effects have been reported previously by Ubbelohde. Both isotope effects are shown to be related in a simple empirical way to the hydrogen bond geometries and to the isotopic fractionation factors. Finally, it is shown that the chemical shielding of the nuclei in the hydrogen bridge is a qualitative probe for the primary and secondary geometric isotope effects.

Hydrogen/deuterium isotope effects on the 15N NMR chemical shifts and geometries of low-barrier hydrogen bonds in the solid state

The configuration and hydrogen-bonding network of side-chain amides in a 35 kDa protein were determined by measuring differential and trans-hydrogen-bond H/D isotope effects by using the isotopomer-selective (IS)-TROSY technique, which leads to a reliable recognition and correction of erroneous rotamers that are frequently found in protein structures. First, the differential two-bond isotope effects on carbonyl (13)C' shifts, which are defined as Delta(2)Delta(13)C'(ND) = (2)Delta(13)C'(ND(E))-(2)Delta(13)C'(ND(Z)), provide a reliable means for the configuration assignment for side-chain amides, because environmental effects (hydrogen bonds and charges, etc.) are greatly attenuated over the two bonds that separate the carbon and hydrogen atoms, and the isotope effects fall into a narrow range of positive values. Second and more importantly, the significant variations in the differential one-bond isotope effects on (15)N chemical shifts, which are defined as Delta(1)Delta(15)N(D) = (1)Delta(15)N(D(E))-(1)Delta(15)N(D(Z)) can be correlated with hydrogen-bonding interactions, particularly those involving charged acceptors. The differential one-bond isotope effects are additive, with major contributions from intrinsic differential conjugative interactions between the E and Z configurations, H-bonding interactions, and charge effects. Furthermore, the pattern of trans-H-bond H/D isotope effects can be mapped onto more complicated hydrogen-bonding networks that involve bifurcated hydrogen-bonds. Third, the correlations between Delta(1)Delta(15)N(D) and hydrogen-bonding interactions afford an effective means for the correction of erroneous rotamer assignments of side-chain amides. Rotamer correction by differential isotope effects is not only robust, but also simple and can be applied to large proteins.

I’ve started so I’ll finish. Mechanism and kinetic isotope effects for protiodecarboxylation of indoles.

Isotope effects on the stability of the hydrogen-bonded C2H2 NCH, H2O XH3 (X = N, P, As) and F2CH2 NH3 complexes

The primary and secondary deuterium isotope effects on proton and carbon chemical shifts were measured for a number of natural pigments and their derivatives, which contain the perylenequinone system and present a phenol–quinone tautomerism, cercosporin 1, isocercosporin 2, phleichrome 3, isophleichrome 4, cladochrome E 5, elsinochromes 6–8, hypocrellin 9, noranhydrocercosporin 10 and noranhydrophleichrome 11. Deuterium isotope effects on protons were also measured for 1,4-dihydroxyanthraquinone 12, methyl 4-(1,4-dihydroxy-9,10-dioxo-9,10-dihydroanthracen-2-yl)butanoate 13, N-acetyldaunomycin 15, daunomycinone 16, naphthazarin 17 and a number of intramolecularly hydrogen-bonded enols from β-diketones, β-ketoesters and o-hydroxyacyl aromatic compounds 19–24. The primary isotope effects Δδ(1H,2H) on OH proton shift and 1H chemical shifts of OH groups are correlated and can be used to estimate the strength of the hydrogen bonds in solution. The secondary isotope effects on proton and carbon nuclei are transmitted along the whole extended conjugated perylenequinone system. Long-range effects over eleven bonds and over seven bonds were observed in compounds 1–11 and in 12–18. The perturbation of the equilibrium due to the presence of deuterium was considered and calculations were performed in order to evaluate the amount of this contribution to the isotope effect. The variation with temperature of primary and secondary effects, from 25 °C down to –70 °C, was studied for compounds 1, 3, 6, 12 and 17, and for acetylacetone 22 and benzoylacetone 23. Parameters from a number of X-ray analyses, for example the O · · · O distances (as suggested by Gilli et al., J. Am. Chem. Soc., 1991, 113, 4917), gave evidence of a substantial parallelism between the liquid and the solid phase. The strength of the hydrogen bond in perylenequinones depends on the planarity of the two naphthalene units rather than on the distortion of the polycyclic ring.

The paper deals with the use of isotope effects on chemical shifts in characterizing intramolecular hydrogen bonds. Both so-called resonance-assisted (RAHB) and non-RAHB systems are treated. The importance of RAHB will be discussed. Another very important issue is the borderline between “static” and tautomeric systems. Isotope effects on chemical shifts are particularly useful in such studies. All kinds of intramolecular hydrogen bonded systems will be treated, typical hydrogen bond donors: OH, NH, SH and NH+, typical acceptors C=O, C=N, C=S C=N−. The paper will be deal with both secondary and primary isotope effects on chemical shifts. These two types of isotope effects monitor the same hydrogen bond, but from different angles.

H/F substitution for advanced molecular ferroelectrics

Elements, Atoms, and Electrons Matter and Elements Atoms Atomic Structure Isotopes The Periodic Table Electron Structure of Atoms Covalent Bonding and Molecules Interactions between Atoms Covalent Bonds Are Formed by Sharing Outer Electrons Formulae of Compounds Covalent Bonds Formed by Combining Atomic Orbitals Single Overlap, the Sigma-Bond Double Overlap, the Pi-Bond Molecules with s- and p-Bonds Hybrid Molecular Orbitals Forces Within and Between Molecules Ionic Bonding Polar Covalent Bonds Dipole-Dipole Forces The Hydrogen Bond van der Waals Forces The Hydrophobic Effect Coordinate Bonds Chemical Reactions Rates of Reaction Factors Affecting Rate of Reaction Rate Equations Integrated Forms of Rate Equations Zero-Order Reactions Integrated Form of the Zero-Order Rate Equation First-Order Reactions The Integrated Form of the First-Order Rate Equation Second-Order Reactions Integrated Forms of Second-Order Rate Equations Pseudo-First-Order Reactions Reversible Reactions Equilibrium Water The Water Molecule Ice Water Solutions The Mole Concept Calculating Molar Masses Molarity Colloidal Solutions Diffusion and Osmosis Acids, Bases, and Buffers Ionisation of Water The Hydrogen Ion Acids and Bases Strong Acids and Strong Bases Weak Acids and Weak Bases Ka and Kb Relationship between Ka and Kb pH, pOH, pKw, pKa, pKb Solutions of Weak Acids and Bases Salts and Salt Hydrolysis Buffer Systems Calculating the pH Values of Buffers Indicators Titrations Gases Pressure Measurement of Pressure Ideal Gas Laws Partial Pressures Solubility of Gases Diffusion in Gases Aliphatic Carbon Compounds Simple Molecules Containing Carbon Organic Compounds Alkanes and Alkyl Groups Alkenes Alcohols Thiols Aldehydes and Ketones Carboxylic Acids Amines Lipids, Sugars, and Linkages between Reactive Groups Fatty Acids Esters Glycerol Esters Hemiacetals and Hemiketals Simple Sugars Chirality in Simple Sugars Straight-Chain Sugars Spontaneously Form Rings Sugar Hydroxyls Can Be Chemically Modified Sugars Are Joined Together by Glycosidic Bonds Aromatic Carbon Compounds and Isomerism Benzene Bioactive Aromatic Compounds Isomerism Structural Isomerism Chain, Positional, and Functional Group Isomerism Tautomerism Stereoisomerism Geometrical Isomerism Optical Isomerism Organic and Biological Reaction Mechanisms Reactive Sites and Functional Groups Describing Reaction Mechanisms Bimolecular Nucleophilic Substitution Electrophilic Addition to a Nonpolar Double Bond Elimination to Form an Alkene Nucleophilic Addition to a Polar Double Bond Free Radical Reactions Carbon-Carbon Bond Formation in Biosynthesis Sulphur and Phosphorus The Electron-Shell Structure and Valency of Phosphorus and Sulphur Sulphur The Thiol Group and Thiol Esters Phosphate, Pyrophosphate, and Polyphosphate Phosphate Esters The Role of Phosphate Esters and ATP in Cellular Energy Metabolism Oxidation and Reduction Reactions Oxidation Is Linked to Reduction The Chemical Changes in the REDOX Process Splitting REDOX Reactions Standardising REDOX Half-Reactions Predicting Electron Flow Free Energy and Standard Reduction Potentials Redox Reactions and Nonstandard Conditions Metals in Biology General Properties of Metals in Biology Some Properties of Alkali Metals The Alkaline Earth Metals Transition Metals Role of Metal as Oxygen Carrier Metals Facilitate Biocatalysis The Role of Metal Ions as Charge Carriers The Toxicity of Metals Energy The First Law of Thermodynamics Units of Energy Measurement of Energy Internal Energy, U, and Enthalpy, H Calorimetry Hess's Law Enthalpies of Formation The Second Law of Thermodynamics Free Energy Interaction of DeltaH with TDeltaS Reactions and Equilibrium DeltaG and Equilibrium Activation Energy The Effect of the Temperature on Reaction Rate The Arrhenius Equation Catalysis Enzyme Catalysis Kinetics of Enzyme Reactions Finding Vmax and KM Light Light Is Part of the Electromagnetic Spectrum Wavelength and Frequency The Quantum Theory of Light The Absorption of Light The Relationship between Light Absorption and Concentration The Spectrophotometer The Fate of Absorbed Light Appendix: Derivations of Equations Index

The x-ray diffraction studies of the title complex were carried out at room temperature and 14 K for H/D (in hydrogen bridge) isotopomers. At 82 K a phase transition takes place leading to a doubling of unit cells and alternation of the hydrogen bond lengths linking tetramethylpyrazine (TMP) and chloranilic acid molecules. A marked H/D isotope effect on these lengths was found at room temperature. The elongation is much smaller at 14 K. The infrared isotopic ratio for O-H(D)...N bands equals to 1.33. The four tunnel splittings of methyl librational ground states of the protonated complex required by the structure are determined at a temperature T=4.2 K up to pressures P=4.7 kbars by high resolution neutron spectroscopy. The tunnel mode at 20.6 microeV at ambient pressure shifts smoothly to 12.2 microeV at P=3.4 kbars. This is attributed to an increase of the strength of the rotational potential proportional to r(-5.6). The three other tunnel peaks show no or weak shifts only. The increasing interaction with diminishing intermolecular distances is assumed to be compensated by a charge transfer between the constituents of deltae/e approximately 0.02 kbar(-1). The phase transition observed between 3.4 and 4.7 kbars leads to increased symmetry with only two more intense tunneling bands. In the isotopomer with deuterated hydrogen bonds and P=1 bar all tunnel intensities become equal in consistency with the low temperature crystal structure. The effect of charge transfer is confirmed by a weakening of rotational potentials for those methyl groups whose tunnel splittings were independent of pressure. Density functional theory calculations for the model TMP.(HF)2 complex and fully ionized molecule TMP+ point out that the intramolecular rotational potential of methyl groups is weaker in the charged species. They do not allow for the unequivocal conclusions about the role of the intermolecular charge transfer effect on the torsional frequencies.

H/D isotope effect between adsorbed water (H2O, D2O, and HDO) and H2O- and D2O-ice Ih(0 0 0 1) basal surfaces based on the combined plane wave and localized basis set method

THE substitution of deuterium for hydrogen has a characteristic effect on the bond lengths in hydrogen compounds, depending on the type of linkage involved. The effect has been described for ionic and covalent linkages1. In the case of structures involving intermolecular hydrogen bonds, no theoretical prediction of the effect could be made, because the nature of the hydrogen bond is not fully understood.

The CU_A domain is the initial point of entry for electrons into cytochrome c oxidase. In order to explain fast rates of intramolecular electron transfer (ET) over long distances, it has been suggested that the ET reorganization energy is less than 0.6 eV. This issue was investigated by attaching a ruthenium(II)-bisbipyridyl-imidazole complex to a single surface histidine of the Thermus thermophilus CU_A domain. Photoexcitation results in rapid ET between the ruthenium complex and the copper site. This was done over a range of driving forces by employing a series of substituted bipyridines. An analysis of the driving force dependence of the ET rate suggests that the total reorganization energy for this CU_A fragment is about 0.7 eV, almost as high as for azurin. The degree of solvent exposure of the active site may be the factor responsible for the higher reorganization energy. In addition, the effect of distance on ET rate was investigated. Two variants of ruthenium-modified CU_A were examined, in which the labeled sites are two positions apart. The observed ET rates only differ by an order of magnitude, drastically less than what theory would predict. It appears that geometric factors other than length influence ET coupled through hydrogen bonds. The role of hydrogen bonds in ET was studied in more detail with ruthenium-modified azurin. Changes in the ET rate were observed for different degrees of deuterium incorporation in the system. For wild-type azurin, the greatest effect (k_H/k_D ≈ 0.7) is seen when the protein is subjected to rigorous exchange under denaturing conditions, then returned to a normal buffer as a control for the solvent isotope effect on the reorganization energy. This is the expected outcome if deuteration of internal, difficult to exchange hydrogen bonds results in improved coupling along the path.

Deuterium equilibrium isotope effects (EIEs) for a cage diol and 2,6-dihydroxyacylaromatics and complexes thereof containing intra- or intermolecular hydrogen bonds have been calculated using harmonic and anharmonic vibrational frequencies using Gaussian '03 and the HF, B3LYP, and MP2 levels of theory. The predicted isotope effects have been compared with experimental NMR data, and the origins of the isotope effects have been characterized in terms of zero-point vibrational energy differences and enthalpic and entropic contributions to the free energy difference between labeled species. Reliable free energy predictions based upon harmonic frequencies were found for systems whose isotope effects are governed by bond stretching effects and for systems whose isotope effects are determined by low-frequency vibrational modes. In contrast, thermochemical predictions based upon anharmonic frequencies were found to be far less consistent. Vibrational entropy is predicted to play an important role in modulating and, in some cases, governing isotopic site preferences in hydroxyl-derived intra- and intermolecular hydrogen bonds.

Crystal structure and spectroscopic properties of N-methylmorpholine betaine phosphate