Revised mechanism of carboxylation of ribulose‐1,5‐biphosphate by rubisco from large scale quantum chemical calculations

Here, we describe a computational approach for studying enzymes that catalyze complex multi‐step reactions and apply it to Ribulose 1,5‐bisphosphate carboxylase–oxygenase (Rubisco), the enzyme that fixes atmospheric carbon dioxide within photosynthesis. In the 5‐step carboxylase reaction, the substrate Ribulose‐1,5‐bisphosphate (RuBP) first binds Rubisco and undergoes enolization before binding the second substrate, CO₂. Hydration of the RuBP.CO₂ complex is followed by C C bond scission and stereospecific protonation. However, details of the roles and protonation states of active‐site residues, and sources of protons and water, remain highly speculative. Large‐scale computations on active‐site models provide a means to better understand this complex chemical mechanism. The computational protocol comprises a combination of hybrid semi‐empirical quantum mechanics and molecular mechanics within constrained molecular dynamics simulations, together with constrained gradient minimization calculations using density functional theory. Alternative pathways for hydration of the RuBP.CO₂ complex and associated active‐site protonation networks and proton and water sources were investigated. The main findings from analysis of the resulting energetics advocate major revision to existing mechanisms such that: hydration takes place anti to the CO₂; both hydration and C C bond scission require early protonation of CO₂ in the RuBP.CO₂ complex; C C bond scission and stereospecific protonation reactions are concerted and, effectively, there is only one stable intermediate, the C3‐gemdiolate complex. Our main conclusions for interpreting enzyme kinetic results are that the gemdiolate may represent the elusive Michaelis–Menten‐like complex corresponding to the empirical K_m (=K_c) with turnover to product via bond scission concerted with stereospecific protonation consistent with the observed catalytic rate. © 2018 Wiley Periodicals, Inc.     

NMR and potentiometric determination of the high pK values and protonation sequence of dipyridino-hexaaza-28-crown-8 and its interactions with selenate,sulfate and nitrate ions in aqueous solution

The aqueous protonation and anion-binding SeO ₂ ^–/4 SO _2– ⁴ , and NO _– ³ ) constants of the macrocyclic polyamine ligand, dipyridino-hexaaza-28-crown-8(L), were measured in 0.1M KCl using a potentiometric titration technique. The protonation sequence of the aza groups of L was studied in D₂O from the chemical shifts of the nonlabile protons so as to find the charge distribution geometry as a function of pD. The study indicates that in 0.1M KC1 fully protonated L forms stable l: 1 complexes with SeO _2– ⁴ (logK=3.68) and SO _2– ⁴ (logK=3.55), but not with NO _– ³ (logK < l.5). All of the amine pK values were above 6.3, thus allowing the use of the protonated form of this ligand over a wide pH range.     

卟吩质子化过程结构变化的理论研究

用ＡＭ１ＭＯ方法计算了质子化卟吩的构型，并通过结构分析、电荷布局分析和前线轨道分析，讨论了其质子化过程的构型变化及Ｒａｍａｎ光谱变化的原因。     

Syntheses, structures, and reactivities of homometallic rare-earth-metal multimethyl methylidene and oxo complexes

Unsolvated, trinuclear, homometallic, rare-earth-metal multimethyl methylidene complexes [{(NCN)Ln(μ(2)-CH(3))}(3)(μ(3)-CH(3))(μ(3)-CH(2))] (NCN = L = [PhC{NC(6)H(4)(iPr-2,6)(2)}(2)](-); Ln = Sc (2a), Lu (2b)) have been synthesized by treatment of [(L)Ln{CH(2)C(6)H(4)N(CH(3))(2)-o}(2)] (Ln = Sc (1a), Lu (1b)) with two equivalents of AlMe(3) in toluene at ambient temperature in good yields. Treatment of 1 with three equivalents of AlMe(3) gives the heterometallic trinuclear complexes [(L)Ln(AlMe(4))(2)] (Ln = Sc (3a), Lu (3b)) in good yields. Interestingly, 2 can also be generated by recrystallization of 3 in THF/toluene, thereby indicating that the THF molecule can also induce C-H bond activation of 2. Reaction of 2 with one equivalent of ketones affords the trinuclear homometallic oxo-trimethyl complexes [{(L)Ln(μ(2) -CH(3))}(3) (μ(3)-CH(3))(μ(3)-O)] (Ln = Sc(4a), Lu(4b)) in high yields. Complex 4b reacts with one equivalent of cyclohexanone to give the methyl abstraction product [{(L)Lu(μ(2) -CH(3) )}(3) (μ(3) -OC(6)H(9))(μ(3)-O)] (5b), whereas reaction of 4b with acetophenone forms the insertion product [{(L)Lu(μ(2)-CH(3))}(3){μ(3)-OCPh(CH(3))(2)}(μ(3)-O)] (6b). Complex 4a is inert to ketone under the same conditions. All these new complexes have been characterized by elemental analysis, NMR spectroscopy, and confirmed by X-ray diffraction determination.     

Thermodynamic behavior of polyelectrolytes with the lower critical solution temperature (LCST) phenomenon

A series of vinyl polymers with L-valine and L-leucine residues, and related copolymers with N-isopropylacrylamide, were studied in aqueous solution at different temperatures (25, 30 and 35°C) and at two ionic strengths (0.01 M and 0.1 M NaCl). The protonation behavior revealed great differences between the polymers that were attributed to the size of the hydrophobic lateral group. Macromolecular shrinkage, occurring above a critical degree of protonation β, was related to hydrophobic forces outweighing the electrostatic repulsions between COO – groups. Low salt concentrations increased the electrostatic potential while high temperatures increased the hydrophobic interaction at lower β. The release of fewer water molecules structured around the polymer chain, responsible for the lower critical solution temperature phenomenon, revealed lower entropy changes at higher temperatures. The reversible configuration of graft polymer chains instantly responded to changes in pH and temperature, modifying the water filtration rates through the pores of cellulose membranes.     

Conformers of gaseous protonated glycine

Ab initio geometry optimizations were performed on gaseous protonated glycine using the second-order Møller–Plesset perturbation theory with the 6-31G*, 6-31G**, 6-31+G**, and 6-311+G** basis sets. Eight energy minima and 12 saddle points in the low-energy region of the electronic potential energy surface were characterized. The global minimum was an amino N-protonated conformer containing an ionic H bond between the (SINGLE BOND)NH₃⁺ and O(DOUBLE BOND)C(DIAGONAL BOND)(DIAGONAL BOND) groups. The lowest energy O-protonated conformer was stabilized by a conjugative attraction between the nitrogen lone-pair electrons and the positively charged planar fragment (SINGLE BOND)C(OH)₂⁺. Relative electronic energies of the nine N- and 11 O-protonated species fall in the ranges of 0–10 and 30–40 kcal mol⁻¹. At room temperature the equilibrium distribution contained the most stable N-protonated conformer almost exclusively. Additional subjects for investigation include the effects of basis set and electron correlation on the predicted structures, nonbonded interactions that influence the relative stability of protonated conformers, conformational interconversions based on intrinsic reaction coordinate calculations, and kinetic pathways for protonation and associated changes in Gibbs free energy. The work provides geometric, energetic, and thermodynamic data pertinent to the study of gas-phase ion chemistry of amino acids and peptides. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1862–1876, 1998     

含邻手性碳原子双键亲电加成反应的立体选择性模型

本文主要介绍了预测邻位具有手性中心π体系亲电加成反应的立体选择性模型,尤其是α,β-不饱和羰基化合物亲核共轭加成形成的烯醇负离子及其类似物和硝基烯烃亲核加成形成的氮酸根类中间体的烷基化和动力学控制质子化反应的立体选择性模型。立体位阻效应控制的Zimmerman前过渡态模型主要适用于底物构象受限的环状或联烯型烯醇负离子的动力学质子化。对于构象转化相对灵活的直链底物,Houk基于量子化学计算研究提出了亲电试剂的进攻角度或接触角在经过环状过渡态时是锐角还是钝角决定了亲电加成反应的立体选择性控制(Houk模型)。而Fleming模型首次将烯丙基A-1,3张力引入各类烯醇负离子烷基化和质子化的过渡态。Mohrig模型在考虑A-1,3张力的基础上,将吸电子取代基与即将形成的σ键反式共平面,主要阐述了立体电子效应对酯的烯醇负离子动力学控制质子化立体选择性的影响,后来又提出了金属离子参与的立体电子效应控制的六元环状半椅式模型。本文希望对理解亲电加成反应的立体化学控制提供一些有用的信息。     

Michael Addition of Thiols to á,(a)-Unsaturated Carbonyl Compounds Catalyzed by Bifunctional Organocatalysts:Asymmetric Michael Addition and Asymmetric Protonation

Recently the hydrogen-bond activated reactions have attracted much attention.1 Takemoto2 reported a highly enantioselective Michael addition of manolate to nitroolefins catalyzed by a bifunctional organocatalyst with tertiary amine and thiourea moiety. As we known,stereoselective conjugate additions of thiols are interesting due to the standpoint of biological and synthetic importance, however, only very limited good results have been obtained except for the works of Shibasaki3, Kanemasa4 and Deng5 et al.In this letter, we report an efficient catalytic asymmetric Michael reactions of thiols to a,a-unsaturated carbonyl compounds promoted by bifunctional organocatalysts. A series of organocatalysts with chiral amine and thiourea structures were designed and synthesized and have been successfully applied in the conjugated additions of thiols to a,a-unsaturated imides and enones.The reactions got quantitative yields and the ee values were up to 84%. It is noteworthy that the a-asymmetric protonation (up to 43% ee) also could be achieved.The Michael addition between aromatic thiols and a,a-unsaturated carbonyl compounds isdescribed as follows:Works to further increase the enantioselectivity is under investigation in our laboratory.     

Differential protonation and dynamic structure of doxylamine succinate in solution using 1H and 13C NMR

A protonation and dynamic structural study of doxylamine succinate, a 1:1 salt of succinic acid with dimethyl-[2-(1-phenyl-1-pyridin-2-yl-ethoxy)ethyl]amine, in solution using one- and two-dimensional 1H and 13C NMR experiments at variable temperature and concentration is presented. The two acidic protons of the salt doxylamine succinate are in 'intermediate' exchange at room temperature, as evidenced by the appearance of a broad signal. This signal evolves into two distinct signals below about -30 degrees C. A two-dimensional 1H-1H double quantum filtered correlation experiment carried out at -55 degrees C shows protonation of one of the acidic protons to the dimethylamine nitrogen. A two-dimensional rotating frame 1H-1H NOE experiment at the same temperature reveals that the other proton remains with the succinate moiety. Comparison of the 1H and 13C chemical shifts and the 13C T1 relaxation times of the salt with those of the free base further substantiate the findings.