Simulation of pH-Dependent Conformational Transitions in Membrane Proteins: The CLC-ec1 Cl−/H+ Antiporter

Intracellular transport of chloride by members of the CLC transporter family involves a coupled exchange between a Cl⁻ anion and a proton (H⁺), which makes the transport function dependent on ambient pH. Transport activity peaks at pH 4.5 and stalls at neutral pH. However, a structure of the WT protein at acidic pH is not available, making it difficult to assess the global conformational rearrangements that support a pH-dependent gating mechanism. To enable modeling of the CLC-ec1 dimer at acidic pH, we have applied molecular dynamics simulations (MD) featuring a new force field modification scheme—termed an Equilibrium constant pH approach (ECpH). The ECpH method utilizes linear interpolation between the force field parameters of protonated and deprotonated states of titratable residues to achieve a representation of pH-dependence in a narrow range of physiological pH values. Simulations of the CLC-ec1 dimer at neutral and acidic pH comparing ECpH-MD to canonical MD, in which the pH-dependent protonation is represented by a binary scheme, substantiates the better agreement of the conformational changes and the final model with experimental data from NMR, cross-link and AFM studies, and reveals structural elements that support the gate-opening at pH 4.5, including the key glutamates Glu_in and Glu_ex.     

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     

NMR investigation of the dihydrogen-bonding and proton-transfer equilibria between the hydrido carbonyl anion [HRe2(CO)9]- and fluorinated alcohols

The interaction of fluorinated alcohols with the anionic hydrido complex [HRe2(CO)9]- (1) has been investigated by NMR spectroscopy. According to the acidic strength of the alcohols, the interaction may result not only in the formation of dihydrogen-bonded ROH...[HRe2(CO)9]- adducts 2, but also in proton transfer to give the neutral species [H2Re2(CO)9] (3). With the weaker acid trifluoroethanol (TFE) evidence for the occurrence of the dihydrogen-bonding equilibrium was obtained by 2D 1H NOESY. The dependence of the hydride chemical shift on TFE concentration at different temperatures provided values for the constants of this equilibrium, from which the thermodynamic parameters were evaluated as deltaH(degrees) = -2.6(2) kcal mol(-1), deltaS(degrees) = -9.3(2) cal mol(-1) K(-1). This corresponds to a rather low basicity factor (E(j) = 0.64). Variable-temperature T1 measurements allowed the proton-hydride distance in adduct 2 a to be estimated (1.80 angstroms). In the presence of hexafluoroisopropyl alcohol (HFIP) simultaneous occurrence of both dihydrogen-bonding and proton-transfer equilibria was observed, and the equilibria shifted versus the protonated product 3 with increasing HFIP concentration and decreasing temperature. Reversible proton transfer between the alcohol and the hydrido complex occurs on the NMR timescale, as revealed by a 2D 1H EXSY experiment at 240 K. For the more acidic perfluoro-tert-butyl alcohol (PFTB) the protonation equilibrium was further shifted to the right. Thermal instability of 3 prevented the acquisition of accurate thermodynamic data for these equilibria. The occurrence of the proton-transfer processes (in spite of the unfavorable pK(a) values) can be explained by the formation of homoconjugated RO...HOR- pairs which stabilize the alcoholate anions.     

A cyclam core dendrimer containing dansyl and oligoethylene glycol chains in the branches: protonation and metal coordination

We have synthesized a dendrimer (1) consisting of a 1,4,8,11-tetraazacyclotetradecane (cyclam) core, appended with four benzyl substituents that carry, in the 3- and 5-positions, a dansyl amide derivative (of type 2), in which the amide hydrogen is replaced by a benzyl unit that carries an oligoethylene glycol chain in the 3- and 5-positions. All together, the dendrimer contains 16 potentially luminescent moieties (eight dansyl- and eight dimethoxybenzene-type units) and three distinct types of multivalent sites that, in principle, can be protonated or coordinated to metal ions (the cyclam nitrogen atoms, the amine moieties of the eight dansyl units, and the 16 oligoethylene glycol chains). We have studied the absorption and luminescence properties of 1, 2, and 3 in acetonitrile and the changes taking place upon titration with acid and a variety of divalent (Co2+, Ni2+, Cu2+, Zn2+), and trivalent (Nd3+, Eu3+, Gd3+) metal ions as triflate and/or nitrate salts. The results obtained show that: 1) double protonation of the cyclam ring takes place before protonation of the dansyl units; 2) the oligoethylene glycol chains do not interfere with protonation of the cyclam core and the dansyl units in the ground state, but affect the luminescence of the protonated dansyl units; 3) the first equivalent of metal ion is coordinated by the cyclam core; 4) the interaction of the resulting cyclam complex with the appended dansyl units depends on the nature of the metal ion; 5) coordination of metal ions by the dansyl units follows at high metal-ion concentrations; 6) the effect of the metal ion depends on the nature of the counterion. This example demonstrates that dendrimers may exhibit complete functionality resulting from the integration of the specific properties of their component units.     

精氨酸侧链和核酸碱基间离子氢键作用强度分析

采用MP2/6-31+G(d,p)方法优化得到了22个由精氨酸侧链与碱基尿嘧啶、 胸腺嘧啶、 胞嘧啶、 鸟嘌呤及腺嘌呤形成的氢键复合物的气相稳定结构, 使用包含BSSE校正的MP2/aug-cc-pVTZ方法计算得到了复合物的气相结合能, 通过MP2/6-31+G(d,p)方法和PCM模型优化得到了复合物的水相稳定结构, 采用MP2/aug-cc-pVTZ方法和PCM模型计算得到了复合物的水相结合能. 研究发现, 精氨酸侧链与碱基间的离子氢键作用强度与单体间电荷转移量、 氢键临界点电子密度及二阶作用稳定化能密切相关. 与中性氢键相比, 离子氢键作用具有更显著的共价作用成分. 研究还发现, 精氨酸侧链和碱基间形成的氢键复合物的稳定性次序可以通过氢键受体碱基分子上氧原子和氮原子的质子化反应焓变进行预测, 质子化反应焓变越负, 形成的氢键复合物越稳定.     

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。     

Protonation state and free energy calculation of HIV-1 protease–inhibitor complex based on electrostatic polarisation effect

The protonation states of catalytic Asp25/25′ residues remarkably affect the binding mechanism of the HIV-1 protease–inhibitor complex. Here we report a molecular dynamics simulation study, which includes electrostatic polarisation effect, to investigate the influence of Asp25/25′ protonation states upon the binding free energy of the HIV-1 protease and a C₂-symmetric inhibitor. Good agreements are obtained on inhibitor structure, hydrogen bond network, and binding free energy between our theoretical calculations and the experimental data. The calculations show that the Asp25 residue is deprotonated, and the Asp25′ residue is protonated. Our results reveal that the Asp25/25′ residues can have different protonation states when binding to different inhibitors although the protease and the inhibitors have the same symmetry. This study offers some insights into understanding the protonation state of HIV-1 protease–inhibitor complex, which could be helpful in designing new inhibitor molecules.     

TBT/CuPc复合薄膜的制备及能量/电荷转移研究

在4,7-二(4-三-苯胺基)-2,1,3-苯并噻二唑[4,7-bis(4-triphenylamino)-2,1,3-benzothiadiazole,TBT]和酞菁铜(copper phthalocyanine,CuPc)的混合硝基甲烷溶液中,采用质子化-共电沉积( PCD)的方法制备得到了TBT∶CuPc共混复合...     

Reactions of Doubly Ionized Benzene with Nitrogen and Water: A Nitrogen‐Mediated Entry into Superacid Chemistry

Even in the highly diluted gas phase, rather than electron transfer the benzene dication C₆H₆²⁺ undergoes association with dinitrogen to form a transient C₆H₆N₂²⁺ dication which is best described as a ring‐protonated phenyl diazonium ion. Isotopic labeling studies, photoionization experiments using synchrotron radiation, and quantum chemical computations fully support the formation of protonated diazonium, which is in turn a prototype species of superacidic chemistry in solution. Additionally, reactions of C₆H₆²⁺ with background water involve the transient formation of diprotonated phenol and, among other things, afford a long‐lived C₆H₆OH₂²⁺ dication, which is attributed to the hydration product of Hogeveen’s elusive pyramidal structure of C₆H₆²⁺, as the global minimum of doubly ionized benzene. Nitrogen is essential for the formation of the C₆H₆OH₂²⁺ dication in that it mediates the formation of the water adduct, while the bimolecular encounter of the C₆H₆²⁺ dication with water only leads to (dissociative) electron transfer.