Effect of charge distribution on electrostatic chromophore—protein interactions in Bacteriorhodopsin

Charge distributions of a protonated and unprotonated Schiff base model compound are determined using different quantum chemical methods. After fitting the model molecule onto the protonated retinal Schiff base in Bacteriorhodopsin, electrostatic interaction energies between the model molecule and protein are calculated. Interaction energies as well as the calculated pK_1/2 values of the model molecule are shown to depend considerably on the chosen charge distribution. Electrostatic potential derived partial charges determined at different ab initio levels reveal interaction energies between the model molecule and nearby residues such as ARG-82, ASP-85, and ASP-212, which are relatively method independent. Consequently, such charge distributions also result in pK_1/2 values for the model molecule that are very similar. Larger deviations in the electrostatic interaction energies, however, are found in the case of charge distributions derived according to the Mulliken population analysis. Nevertheless, some sets of Mulliken derived partial charges predicted pK_1/2 values for the model molecule that are close to those determined with electrostatic potential derived partial charges. This agreement, however, is only achieved because the individual errors of the contributing terms are approximately compensated. The use of the extended atom model is shown to be problematic. Although potential derived charges can correctly describe electrostatic interaction energies, they fail to predict pK_1/2 values. On the basis of the present investigation a new set of partial charges for the protonated and unprotonated retinal Schiff base is proposed to be used in molecular dynamics simulations and electrostatics calculations. © 1997 by John Wiley & Sons, Inc.     

Oxidation‐Induced C—H Functionalization: A Formal Way for C—H Activation

Cross‐coupling reactions have developed widely and provided a powerful means to synthesize a variety of compounds in each chemical field. The compounds which have C—H bonds are widespread in fossil fuels, chemical raw materials, biologically active molecules, etc. Using these readily‐ available substances as substrates is high atom‐ and step‐economy for cross‐coupling reactions. Over the past decades, our research group focused on finding and developing new strategies for C—H functionalization. Compared with classical C—H activation methods, for example, C—H bonds are deprotonated by strong base or converted into C—M bonds, oxidation‐induced C—H functionalization would be another pathway for C—H bond activation. This perspective shows a brief introduction of our recent works in this oxidation‐induced C—H functionalization. We categorized this approach of these C—H bond activations by the key intermediates, radical cations, radicals and cations.     

Nystatin—dextran conjugates: Synthesis and characterization

The coupling of nystatin (Nys), a water-insoluble antifungal agent, to dextran via an imine or amine bond was systematically investigated. Dextran was first oxidized to dialdehyde dextran using potassium periodate, purified from the oxidizing agent, and reacted with Nys to form the Schiff base. The Schiff base was reduced to the amine using borohydride. All reactions took place in water. The purification of the oxidized dextran from the oxidizing agent was essential to prevent oxidative degradation of Nys at the coupling step. The effects on the coupling yield of the following factors: dextran molecular weight, degree of oxidation (aldehyde content), Nys to dextran ratio, temperature, and reaction pH were studied. A 95% coupling yield was obtained at the optimized coupling conditions: pH 8.9 ± 0.1, 50% degree of oxidation, and initial ratio of Nys to dialdehyde dextran 1:2.5. In all experiments, dextran was decreased in molecular weight during the oxidation step. Both imine and amine forms of Nys-dextran conjugates were soluble in water and exhibited improved stability in aqueous solutions as compared to the unbound drug. The conjugates showed comparable minimum inhibitory concentration (MIC) values against Candida albicans and Cryptococcus neoformans. The conjugates were about 25 times less toxic than free Nys after a single injection in mice. © 1996 John Wiley & Sons, Inc.     

Chemical release control—Schiff bases of perfume aldehydes and aminostyrenes

Schiff bases of p- and m-aminostyrenes with perfume aldehydes such as citral, cinnamaldehyde, piperonal, vanillin, and ethyl vanillin were synthesized in ethanol in more than 50% yield. Water-soluble copolymers of these Schiff bases with N-vinyl-2-pyrrolidone or with N,N-dimethylacrylamide were obtained. The hydrolytic behavior of Schiff base monomers and copolymers to liberate perfume aldehydes was structure dependent, thereby affording chemical release control.     

The mass spectrometry of volatile derivatives—II: N-alkyl trifluoracetamides

Under electron-impact, N-alkyl trifluoracetamides exhibit peaks due to [CF₃]⁺ and [M ? CF₃]⁺. Ions corresponding to [COCF₃]⁺ are absent. The base peak in many straight chain derivatives occurs at m/e 126 due to alkyl radical loss from the molecular ion; the mass of this ion rising to m/e 140 in the α-substituted N-sec-butyltrifluoracetamide and to m/e 154 in the tert-butyl derivative. High resolution measurements on a number of peaks indicate that they originate by loss of HF from other fragment ions.     

1,4‐Diphenyl‐1,4‐di‐4‐pyridyl‐2,3‐diaza‐1,3‐butadiene: weak C—H·N and C—H·π hydrogen bonds

In the title compound, C₂₄H₁₈N₄, each Schiff base molecule is centrosymmetric and interacts with four neighbours via four C—H(Ph)·N(py) hydrogen bonds (py is pyridyl) and four C—H(py)·π(Ph) hydrogen bonds, leading to an interesting two‐dimensional hydrogen‐bonded layer architecture.     

Poly-N-benzylaniline prepared in perchloric acid——a new soluble semiconducting polymer

Chemical or electrochemical oxidation of N-benzylaniline in perehloric acid solution yieldsa highly colored polymer——poly-N-benzylaniline (PBAn).The polymer has good solubility in a num-ber of organic solvents in either acid or base form.At room temperature,conductivity measurementson pressed pellets of the acid form PBAn give a conductivity of 9.3×10~(-6) S·cm~(-1).The soluble polymerwas analyzed using a variety of common experimental techniques including UV-vis,IR,NMR,ESRspectroscopy,elemental analysis and electrochemieal analysis.All experimental results showed thatPBAn has a structure similar to polyaniline with the elimination of some benzyl groups.     

Relativity and the chemistry of UF6: A molecular Dirac—Hartree—Fock—CI study

The electronic structure and bonding of UF₆ and UF₆⁻ are studied within a relativistic framework using the MOLFDIR program package. A stronger bonding but more ionic molecule is found if one compares the relativistic with the nonrelativistic results. The first peak in the photoelectron spectrum of Karlsson et al. is assigned to the 12γ_8u component of the 4t_1u orbital, in agreement with other theoretical and experimental results. Good agreement is found between the experimental and theoretical 5f spectrum UF₆⁻. Some properties, like the dissociation energy and electron affinity, are calculated and the necessity of a fully relativistic framework is shown. The Breit interaction has an effect on the core spinors and the spin-orbit splitting of these spinors but the influence on the valence spectrum is negligible. © 1996 John Wiley & Sons, Inc.     

Mass spectra of halogenated esters 6—Methyl esters of some trihalogenated propanoic and butanoic acids

The mass spectral fragmentation of trihalogenated methyl esters, formed in the reactions of monochlorinated methyl propenoates and 2-butenoates with Cl₂, BrCl and Br₂, have been investigated. In most cases α-cleavage gives the base peak, [COOCH₃]⁺, the peaks originating from the subsequent losses of one or two halogen atoms also being abundant. The primary loss of a halogen atom is more prominent in the C₄ derivatives, Br˙ and Cl˙ being preferentially lost from the 2- and 3-positions, respectively. The McLafferty rearrangement yields in one case the base peak; the 2-halo compounds could in general be distinguished by that fragmentation. Typical for all 2-bromo-substituted methyl butanoates studied is the base peak, [C₃H₃]⁺, at m/z 39, and for some 3-halo compounds the peaks at m/z 95, [C₂H₄ClO₂]⁺ and 139, [C₂H₄BrO₂]⁺.     

Unraveling the Amine‐Induced Disproportionation Reaction of Perchlorinated Silanes—A DFT Study

A detailed quantum‐chemical study on the amine‐induced disproportionation reaction of perchlorinated silanes to neo‐Si₅Cl₁₂ is reported. The key intermediate in the resulting mechanistic scenario is a dichlorosilylene amine adduct, which is in tune with recent experimental findings. Yet, at variance with the generally accepted notion of silicon‐chain growth by concerted silylene insertion into Si?Cl bonds of lower silanes, the formation of neo‐Si₅Cl₁₂ follows more complex pathways. The reactivity is dominated by the Lewis–base character of the dichlorosilylene amine adduct and characterized by three elementary steps that bear close resemblance to the key elementary steps identified earlier for the chloride‐induced disproportionation of Si₂Cl₆. NBO and QTAIM analyses of the key reactive species SiCl₂ ? NMe₃ and SiCl₃^? provide a rationale for these striking similarities.     

Ni‐Catalyzed Chelation‐Assisted Direct Functionalization of Inert C—H Bonds

During the last two decades, impressive advancements have been achieved in transition metal‐catalyzed chelation‐assisted C—H functionalization reaction. While reactions in this field are still dominated by precious 4d or 5d metals (e.g., Pd, Rh, Ir), the 3d base metals (e.g., Ni, Co, Cu, Fe) have made significant headway partially due to their relatively large abundance, low cost, low toxicity as well as their occasionally occurred novel reactivity when compared to their noble cousins. This review will give a comprehensive summary on Ni‐catalyzed functionalization of inert C—H bonds assisted by chelation groups. For clarity, the content is classified by the newly formed chemical bonds, namely C—C, C—N, C—chalcogen and C—halogen bond formation.     

Resonance des Phospholes—Reaction Avec le n-Butyl Lithium

Seven phospholes were prepared by a two-step synthesis as previously described. On the basis of H and ³¹P NMR data, these phospholes were tentatively classified by their degree of aromaticity. Two of these were reacted with n-butyl lithium. Nucleophilic attacks were observed on the phosphorus atom and on the double bonds. These facts are explained by enhanced p—π and p_π—d_π conjugations between the phosphorus atom and the dienic system by comparison with vinyl phosphines. NMR data seem to support this view. The influence on δ ³¹P of substitution and cyclic delocalization of the lone pair of electrons on phosphorus is interpreted within the Letcher-Van Wazer formalism.     

Clusters of Ammonium Cation—Hydrogen Bond versus σ‐Hole Bond

MP2/6‐311++G(d,p) calculations were performed on the NH₄⁺ ??? (HCN)_n and NH₄⁺ ??? (N₂)_n clusters (n=1–8), and interactions within them were analyzed. It was found that for molecules of N₂ and HCN, the N centers play the role of the Lewis bases, whereas the ammonium cation acts as the Lewis acid, as it is characterized by sites of positive electrostatic potential, that is, H atoms and the sites located at the N atom in the extension of the H?N bonds. Hence, the coordination number for the ammonium cation is eight, and two types of interactions of this cation with the Lewis base centers are possible: N?H ??? N hydrogen bonds and H?N ??? N interactions that are classified as σ‐hole bonds. Redistribution of the electronic charge resulting from complexation of the ammonium cation was analyzed. On the one hand, the interactions are similar, as they lead to electronic charge transfer from the Lewis base (HCN or N₂ in this study) to NH₄⁺. On the other hand, the hydrogen bond results in the accumulation of electronic charge on the N atom of the NH₄⁺ ion, whereas the σ‐hole bond results in the depletion of the electronic charge on this atom. Quantum theory of “atoms in molecules” and the natural bond orbital method were applied to deepen the understanding of the nature of the interactions analyzed. Density functional theory/natural energy decomposition analysis was used to analyze the interactions of the ammonium ion with various types of Lewis bases. Different correlations between the geometrical, energetic, and topological parameters were found and discussed.     

Transferts Protoniques de Sels d'Ammonium Substitues—VII: Deprotonation de Sels de N-Methylpiperidinium en Solution Aqueuse

The deprotonation of N-methylpiperidinium salts BH_a^⊕, observed by means of the coalescence of the N-methyl doublet, is operated either by OH^?, or by the conjugate base B. The action of OH^? is predominant as the steric hindrance increases around H_a and is twice as fast in the axial direction.     

High-field NMR of ethylene—sulfur dioxide copolymers

Copolymers of ethylene and sulfur dioxide containing 40–60 wt-% sulfur dioxide have been analyzed by using 220 MHz high-resolution NMR, and it has been shown that they contain structures of the form, ? SO₂? (CH₂? CH₂)_n? SO₂? , where n is 1, 2, 3, 4, … The relative numbers of structures with n = 1, 2, 3, or 4 and above can be calculated from the NMR spectra. The fraction of ethylenes in longer blocks and the sulfur dioxide contents of the polymers can also be determined from the NMR data. The NMR results indicate that the distribution of ethylenes among the different structures is not that expected for a random copolymerization of ethylene and sulfur dioxide but that the arrangement of these structures within the copolymer is random.     

Spiro[4H‐pyran‐3,3′‐oxindoles] Derived from 1,2,3,4‐tetrahydroquinoline—Part 2

Reaction of 5,6‐dihydro‐4H‐pyrrolo[3,2,1‐ij ]quinoline‐1,2‐dione ( 3 ) with two equivalents of cyclic 1,3‐dicarbonyl compounds under acid catalysis generates spiro[4H‐pyran‐3,3′‐oxindoles] 7 . In contrast, though base catalysis also achieves double addition, the final products 8 result from subsequent ring opening of the five‐membered lactam via intramolecular attack by enolate; these products can be converted into the spiro[4H‐pyran‐3,3′‐oxindoles] by treatment with acid.     

Chemical Ionization—A Mass-Spectrometric Analytical Procedure of Rapidly Increasing Importance

The mode of ionization of a molecule has a strong influence on its behavior in the mass spectrometer and thus on the information that can be obtained from its mass spectrum. In chemical ionization a reagent gas, e.g. methane, is first ionized by electron impact. The ions formed in ion-molecule reactions, in particular [CH₅]⁺, [C₂H₅]⁺, and [C₃H₅]⁺, then react “chemically” with the substrate M in fast acid/base type reactions to form ions of the type [MH]⁺, [M(C₂H₅)]⁺, etc., which subsequently fragment to various extents. Alternatively, chemical ionization can be effected by charge exchange, in that ions of a reagent gas, e.g. [He]^+?, react with the substrate M to form molecular ions [M]^+·. Chemical ionization can thus be conducted in a more or less mild fashion and the extent of the fragmentation can be controlled over a very wide range.