On the Karplus relation for 3J(POCC) of nucleotides

The original Karplus parameters for analysing ³J(POCC) magnitudes of nucleotides in terms of conformational properties of the O? C bond were taken from results for 3′,5′-nucleotides and applied to 3′→ 5′-oligonucleotides; the parameters were later modified to take account of ‘largey’ magnitudes of ³J(POCC) observed in 2′ → 5′-oligonucleotides. In this work the origin of this discrepancy is explained in terms of substituent electronegativity effects at C-1′, and quantified using the ¹³C NMR results of 2′,3′-cyclic mononucleotides. A new set of Karplus parameters suitable for analysing ³J(POCC) magnitudes in 3′- and 5′-nucleotides and 3′ → 5′-oligonucleotides is determined from ¹³C NMR measurements on 3′-nucleotides and available results for 3′,5′-cyclic mononucleotides. A method of dealing with J(P, C-1′) coupling in 2′-nucleotides, 2′,3′-cyclic nucleotides and 2′ → 5′-oligonucleotides using the same Karplus relationship is suggested.     

关于二氟乙炔的异构化反应的量子化学研究

用ａｂ ｉｎｉｔｉｏｎ方法讨论了Ｆ２Ｃ２的异构化反应机理，用ＨＦ／６－３１Ｇ和ＭＰ２／６－３１Ｇ优化Ｆ２ＣＣ和二氟乙炔（ＦＣ＝ＣＦ）的几何构型，并得到反庆Ｆ２ＣＣ＿ＦＣＣＦ的过渡态（ＦＣ（Ｆ）Ｃ）。文中用内禀反应坐方法做反应路径解析，二氟乙炔是二氟丙二烯酮分解反应的产物，用从头算方法优化二氟丙二烯酮并在Ｍｕｌｌｉｋｅｎ集居分析中，发现Ｆ２Ｃ＝Ｃ＝Ｃ＝Ｏ在分解反庆中先产生中间产Ｆ２ＣＣ，之后经过过渡     

High resolution fourier transform infrared spectrum of difluoroethyne,FCCF.

Difluoroethyne, monitored by FTIR spectroscopy, has been prepared in the vapour phase by vacuum pyrolysis and photolysis of difluoromaleic anhydride and pyrolysis of 3-bromo-3,3-difluoropropanoic trifluoroacetic anhydride. The infrared spectrum of difluoroethyne has been assigned at both low and high resolution and wavenumber values for all five fundamentals estimated. Difluoropropadienone was observed as a pyrolysis product and difluorocyclopropenone as a photolysis product.     

On the form of the single coulostatic decay curve

A plot of E/t ^1/2 versusE as obtained from a single coulostatic decay curve resembles a classical voltammogram. Calculations by digital simulation show that for a reversible electrode reaction the coulostatic voltammogram is shifted to potentials slightly negative of the reversible half-wave potential. Analysis of published data for the reduction of aqueous Pb(II) at a mercury electrode shows that the results were affected by heterogeneous electron transfer kinetics.     

A Karplus Equation for the Conformational Analysis of Organic Molecular Crystals

Vicinal scalar couplings (³J) are extensively used for the conformational analysis of organic compounds in the liquid state through empirical Karplus equations. In contrast, there are no examples of such use for the structural investigation of solids. With the support of first principles calculations, we demonstrate here that ¹³C‐¹³C ³J coupling constants (³J_CC) measured on a series of isotopically enriched solid amino acids and sugars can be related to dihedral angles by a simple Karplus‐like relationship, and we provide a parameterized Karplus function for the conformational analysis of organic molecular crystals. Under the experimental conditions discussed, torsional angles can be estimated from the experimental ³J_CC values with an accuracy of 10° using this function. These results open new perspectives towards the use of ³J_CC as a new analytical tool that could considerably simplify structure determination of functional organic solids.     

Self-consistent Karplus parametrization of 3J couplings depending on the polypeptide side-chain torsion chi1.

Recently proposed self-consistent 3J coupling analysis (Schmidt, J. M.; Blümel, M.; L?hr, F.; Rüterjans, H. J. Biomol. NMR 1999, 14, 1-12) has been carried out to calibrate Karplus parameters constituting the empirical dependence of 3J coupling constants on the chi1 dihedral angle in amino acid side chains. The procedure involves simultaneous least-squares optimization of six sets of three Karplus coefficients related to all six 3J coupling types accessible in 15N,13C-labeled proteins. A simple concept of fundamental and incremental component couplings is proposed to account for substituent effects, eventually yielding amino acid topology-specific Karplus parameters. The method is exemplified with recombinant Desulfovibrio vulgaris flavodoxin (147 amino acids, 16 kDa) with reference to a total of 749 experimental 3JHalpha,Hbeta, 3JN',Hbeta, 3JC',Hbeta, 3JHalpha,Cgamma, 3JN',Cgamma, and 3JC',Cgamma coupling constants. Unlike other parametrizations, the present method does not make reference to X-ray coordinates, so that the Karplus coefficients obtained are not influenced by differences between solution and crystal states. Cross validation using X-ray torsion angles demonstrates the improvement relative to previous parametrizations. The Karplus coefficients derived are applicable to other proteins, too. Parameter refinement also yields a series of chi1 torsion angles, providing valuable constraints for protein structure determination, as well as optional parameters of local angular mobility in the contexts of Gaussian random fluctuation or a three-site jump model. The procedure permits automatic stereospecific assignments of Hbeta and Cgamma chemical shifts. The majority of the flavodoxin side-chain conformations agrees with high-resolution X-ray structures of the protein. Marked deviations between NMR and X-ray datasets are attributed to different rotameric states due to crystal-packing effects and to conformational equilibria between multiple chi1 rotamers.     

On the Ne—Ne potential-energy curve and related properties

The construction of interatomic pair potentials according to the HFD (Hartree—Fock—dispersion) and the XC (exchange—Coulomb) models is reviewed briefly. A new XC potential is constructed for Ne; as in a successful application to Ar, the adjustable parameters in the model are fixed by fitting only second virial coefficient data. The new XC potential, two slight modifications of it, and five literature potentials, are compared with respect to their ability to predict the second virial coefficients and transport properties of dilute Ne gas, the Ne—Ne differential and total scattering cross sections, and the spectroscopic constants of the dimer. A reassessment of the experimental data leads to the conclusion that a literature HFD-C potential is less reliable than previously thought. The new potentials constructed in this paper appear preferable to the other potentials considered; they reproduce essentially all the experimental data used for test purposes to within experimental error.     

Resolving an apparent discrepancy between theory and experiment: spin-spin coupling constants for FCCF

Ab initio equation of motion coupled cluster singles and doubles (EOM-CCSD) and second-order polarization propagator approximation (SOPPA) calculations have been performed to evaluate spin-spin coupling constants for FCCF (difluoroethyne). The computed EOM-CCSD value of (3)J(F-F) obtained at the experimental geometry of this molecule supports the previously reported experimental value of 2.1 Hz, thereby resolving an apparent discrepancy between theory and experiment. This coupling constant exhibits a strong dependence on the C-C and C-F distances, and its small positive value results from a sensitive balance of paramagnetic spin-orbit (PSO) and spin-dipole (SD) terms. The three other unique FCCF coupling constants (1)J(C-C), (1)J(C-F), and (2)J(C-F) have also been reported and compared with experimental data. While (1)J(C-F) is in agreement with experiment, the computed value of (2)J(C-F) is larger than our estimate of the experimental coupling constant.     

Analysis of the Vorontsova equation for calculation of vicinal coupling constants: Criticism of the criticism of the Karplus equation

Analysis of the Vorontsova calculation of vicinal coupling constants in terms of angular and chemical shift dependence indicates some serious inconsistencies in this equation.     

On the maximum reaction rate and inflexion points on the DTG curve

The authors present some theoretical considerations concerning the influence of the form of the conversion functionf() on the values of the degree of conversion corresponding to the maximum value of the reaction rate (_max) as well as on the inflexion points (_inf) of the DTG curve. The obtained equations are characterized by a general validity no matter the form off().

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Zusammenfassung Es werden einige theoretische Überlegungen bezüglich des Einflusses der Form der Konversionsfunktionf() auf die Werte der Konversionsrate bei maximalen Reaktionsgeschwindigkeiten (_max) sowie auf Inflexionspunkte () der DTG-Kurve angestellt. Die erhaltenen Gleichungen sind unabhängig von der Form vonf() durch eine all-gemeine Gültigkeit charakterisiert.

     

On the universal behavior of some thermodynamic properties along the whole liquid-vapor coexistence curve

When thermodynamic properties of a pure substance are transformed to reduced form by using both critical- and triple-point values, the corresponding experimental data along the whole liquid-vapor coexistence curve can be correlated with a very simple analytical expression that interpolates between the behavior near the triple and the critical points. The leading terms of this expression contain only two parameters: the critical exponent and the slope at the triple point. For a given thermodynamic property, the critical exponent has a universal character but the slope at the triple point can vary significantly from one substance to another. However, for certain thermodynamic properties including the difference of coexisting densities, the enthalpy of vaporization, and the surface tension of the saturated liquid, one finds that the slope at the triple point also has a nearly universal value for a wide class of fluids. These thermodynamic properties thus show a corresponding apparently universal behavior along the whole coexistence curve.     

On the calculation and behavior of thermal rate coefficients for a curve crossing system

Here is used an expression, obtained from linear response theory, to carry out model calculations of thermal rate constants for a potential curve crossing system. An illustrative calculation is presented which employs a modified fast Fourier transform to study how the thermal rate coefficients are affected when non-adiabatic effects are considered. Finally an Arrhenius analysis is performed on the computed thermal rate coefficients.     

Oligosaccharide trans-glycoside 3JCOCC Karplus curves are not equivalent: effect of internal electronegative substituents

Density functional theory (DFT) calculations show that internal electronegative substituents perturb 3JCOCC Karplus curves by phase shifting them with respect to analogous pathways devoid of this substitution. Thus, the J-coupling maximum, which normally is observed near 180 degrees , is shifted by approximately 15 degrees . These findings suggest that the two types of inter-residue C-O-C-C coupling pathways observed in many oligosaccharides cannot be treated using a generalized 3JCOCC Karplus equation. Quantitative interpretations of trans-glycoside J-couplings to evaluate linkage conformations will need to take this effect into account.     

On the ambiguity of the reaction rate constants in multivariate curve resolution for reversible first-order reaction systems

If for a chemical reaction with a known reaction mechanism the concentration profiles are accessible only for certain species, e.g. only for the main product, then often the reaction rate constants cannot uniquely be determined from the concentration data. This is a well-known fact which includes the so-called slow-fast ambiguity.     

Conformational analysis: 3JHCOC and 3JHCCC Karplus relationships for methylene 1H nuclei

NAMFIS (NMR Analysis of Molecular Flexibility In Solution) was applied to 1‐[2‐(benzyloxy)phenyl]ethanone using quantitative ¹H‐¹H NOE distances and ³J proton‐carbon coupling constant (CC) restraints for averaged methylene proton ³J_HCOC and ³J_HCCC pathways H₂‐³J‐X imposed by density functional theory‐generated Karplus relationships. Comparison of the NOE‐only versus the NOE + CC conformational selections illustrates that the experimentally measured average ³J coupling constants of methylene protons can be used for solution conformational analysis, potentially valuable in the study of small‐molecule drugs and natural products which lack the typically studied H₁‐³J‐X Karplus relationships. Copyright © 2015 John Wiley & Sons, Ltd.     

On the accuracy of acid-base determinations from potentiometric titrations using only a few points from the titration curve

There are several procedures which use only a few points on the titration curve for the calculation of equivalence volumes in acid-base titrations. The accuracy of such determinations will depend on the positions of the points on the titration curve. The effects of errors in the stability constants and in the pH measurements on the accuracy of the analysis have been considered, and the results are used to establish the conditions under which these errors are minimized.     

On a nonelementary progress curve equation and its application in enzyme kinetics

The analytical equation describing progress curves of an enzyme catalyzed reaction acting upon the Michaelis-Menten mechanism has been known for the case in which only the free enzyme incurs a loss of its activity, either spontaneously or as a result of an irreversible inhibitor action. The solution of differential equations which defines the rates of enzyme inactivation and substrate utilization is expressed by a nonelementary function in equation of an implicit type that precludes direct calculation of the extent of reaction at any time. Previously, the implicit equations have been rearranged to the alternative formulas and solved by the Newton-Raphson method, but this procedure may fail when used upon the presented equation. For this reason the other root-finding numerical method was applied, and the enzyme kinetic parameters of such numerically solved implicit equation for the reaction mechanism of irreversibly inhibited acetylcholinesterase were fitted to the experimental data by a nonlinear regression computer program.