Molecular mechanics calculations of conjugated amides and an ab initio investigation of acrylamide and its β-amino derivative: Conformational analysis and rotational barriers

Conformations and rotational barriers in a series of conjugated primary and tertiary amides have been analyzed by a modified MM2(91) force field, which treats the amide nitrogen as part of the conjugated system by redefining the atom type for the nitrogen. Ab initio molecular orbital calculations at the MP2/6-31G* level have been performed on the stable conformers and transition structures of acrylamide and β-trans-aminoacrylamide. The results have been used, with published experimental and computational data, to generate parameters for the MM2 force field. The force field has been applied to various conjugated amides, such as reduced nicotinamide adenine dinucleotide (NADH) and NAD⁺ analogues, nicotinamide, urea, vinylogous urea derivatives, and nucleic acid bases. The fundamental difference between primary and tertiary conjugated amides with respect to both conformation and barrier is highlighted. © 1996 by John Wiley & Sons, Inc.     

钯-8-羟基喹啉-5-磺酸络合物电极反应和十二烷基硫酸钠的增敏机理

钯 8 羟基喹啉 5 磺酸形成的络合物的峰电流 (pH 8.6 ,- 0 .6 8V)具有吸附特性 ,为不可逆电极反应过程。其电子转移数 (n)、电子转移系数 (α)及饱和吸附量 (Γs)分别为 2、0 .4 6和 2 .2× 10 - 9mol cm2 ;钯 与8 羟基喹啉 5 磺酸的络合比为 1∶2 ;稳定常数 (K)为 8.73× 10 7。加入阴离子表面活性剂十二烷基硫酸钠未形成三元络合物 ,催化电流是由与十二烷基硫酸钠共吸附在电极表面上的超氧阴离子自由基氧化了络合物的电极反应中间体所产生的。     

Study of Photochemical Reactions of Coniferyl Alcohol. II. Comparative Structural Study of a Photochemical and Enzymatic Polymer of Coniferyl Alcohol

The structure of the polymer synthesized by UV irradiation of coniferyl alcohol was studied, using UV-visible, Raman, IR, H-NMR and ¹³C-NMR spectroscopy. The photochemical polymer was compared with the structure of the polymer obtained by peroxidase-catalyzed polymerization of coniferyl alcohol. General similarity of the spectra of the two polymers was shown. However, differences in the fine structure of particular regions of the NMR spectra, as well as in certain bands in the Raman and IR spectra, could be explained through the various bond types and organization within the polymers. These results are consistent with molecular mass distribution of the polymers. Two fractions of enzymatic polymer correspond to the main two fractions of photochemical polymer. The later polymer has additional fractions that are probably the main reason for the observed spectral differences.     

Preparation and redox properties of N,N,N-1,3,5-trialkylated flavin derivatives and their activity as redox catalysts

Eight different flavin derivatives have been synthesized and the electronic effects of substituents in various positions on the flavin redox chemistry were investigated. The redox potentials of the flavins, determined by cyclic voltammetry, correlated with their efficiency as catalysts in the H2O2 oxidation of methyl p-tolyl sulfide. Introduction of electron-withdrawing groups increased the stability of the reduced catalyst precursor.     

Molecular structure and barriers to internal rotation of α-naphthalenesulfonyl chloride: a study by gas-phase electron diffraction and quantum chemical calculations

α-Naphthalenesulfonyl chloride, α-NaphSC, was studied by gas-phase electron diffraction (GED) and quantum chemical calculations (HF/6-311 + G**, HF/aug-cc-pVDZ, B3LYP/cc-pVDZ, B3LYP/cc-pVTZ, B3LYP/aug-cc-pVDZ, B3LYP/aug-cc-pVTZ, MP2/cc-pVDZ, and MP2/cc-pVTZ). The calculations predict the existence of two conformers with C ₁ (I) and C _s (II) symmetries. The most stable conformer I has an enantiomer. The experimental data of α-NaphSC obtained at 370(5) K could be best fitted by a C ₁ symmetry model indicating that only this form exists in the gas-phase. In this model the C_α–S–Cl plane deviates from the perpendicular orientation relative to the plane of the naphthalene skeleton. Under the applied experimental conditions, the mole fraction of a second less stable conformer II of α-NaphSC predicted by calculations is no more than 1 %. The following geometrical parameters of conformer I were obtained from the experiment (Å and °; uncertainties are in parentheses): r _h1(C–H) = 1.082(6), r _h1(C–C)_cp = 1.407(3), r _h1(C–S) = 1.764(5), r _h1(S–O)_av = 1.425(3), r _h1(S–Cl) = 2.051(5), ∠C–C_α–C = 122.5(1), ∠C_α–S–Cl = 101.5(10); C9–C1–S–Cl = 71.4(21). The calculated barriers to internal rotation of the sulfonyl chloride group exceed considerably the thermal energy values corresponding to the temperatures of the GED experiments. Natural bond orbitals analysis of the electron density distribution was carried out to explain the peculiarities of the molecular structure of the studied compound and the deviation from the structures of β-NaphSHal molecules and their benzene analogs.     

Laser-induced alignment and anti-alignment of rotationally excited molecules

We numerically investigate the post-pulse alignment of rotationally excited diatomic molecules upon nonresonant interaction with a linearly polarized laser pulse. In addition to the simulations, we develop a simple model which qualitatively describes the shape and amplitude of post-pulse alignment induced by a laser pulse of moderate power density. In our treatment we take into account that molecules in rotationally excited states can interact with a laser pulse not only by absorbing energy but also by stimulated emission. The extent to which these processes are present in the interaction depends, on the one hand, on the directionality of the molecular angular momentum (given by the M quantum number), and on the other hand on the ratio of transition frequencies and pulse duration (determined by the J number). A rotational wave packet created by a strong pulse from an initially pure state contains a broad range of rotational levels, over which the character of the interaction can change from non-adiabatic to adiabatic. Depending on the laser pulse duration and amplitude, the transition from the non-adiabatic to the adiabatic limit proceeds through a region with dominant rotational heating, or alignment, for short pulses and a large region with rotational cooling, and correspondingly preferred anti-alignment, for longer pulses.     

Reaction of Red Phosphorus with Allylbenzene in Superbasic System KOH-DMSO

Abstract

Red phosphorus reacts with allylbenzene in the superbase system KOH-DMSO (130°C, 3 h, Ar) to give a mixture of bis(1-methyl-2-phenylethyl)phosphane (1), bis(1-methyl-2-phenylethyl)phosphane oxide (2), and 1-methyl-2-phenylethylphosphinic acid (3). Secondary phosphane oxide 2 and phosphinic acid 3 have been isolated from this mixture in 35% and 32% yield, respectively. Microwave activation of the reaction (200 W, 30 min) affords secondary phosphane 1 as the main product in 48% yield.

GRAPHICAL ABSTRACT      

DFT study of polymorphism of the DNA double helix at the level of dinucleoside monophosphates

We apply DFT calculations to deoxydinucleoside monophosphates (dDMPs) which represent minimal fragments of the DNA chain to study the molecular basis of stability of the DNA duplex, the origin of its polymorphism and conformational heterogeneity. In this work, we continue our previous studies of dDMPs where we detected internal energy minima corresponding to the “classical” B conformation (BI‐form), which is the dominant form in the crystals of oligonucleotide duplexes. We obtained BI local energy minima for all existing base sequences of dDMPs. In the present study, we extend our analysis to other families of DNA conformations, successfully identifying A, BI, and BII energy minima for all dDMP sequences. These conformations demonstrate distinct differences in sugar ring puckering, but similar sequence‐dependent base arrangements. Internal energies of BI and BII conformers are close to each other for nearly all the base sequences. The dGpdG, dTpdG, and dCpdA dDMPs slightly favor the BII conformation, which agrees with these sequences being more frequently experimentally encountered in the BII form. We have found BII‐like structures of dDMPs for the base sequences both existing in crystals in BII conformation and those not yet encountered in crystals till now. On the other hand, we failed to obtain dDMP energy minima corresponding to the Z family of DNA conformations, thus giving us the ground to conclude that these conformations are stabilized in both crystals and solutions by external factors, presumably by interactions with various components of the media. Overall the accumulated computational data demonstrate that the A, BI, and BII families of DNA conformations originate from the corresponding local energy minimum conformations of dDMPs, thus determining structural stability of a single DNA strand during the processes of unwinding and rewinding of DNA. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem 110:2548–2559, 2010