The Importance of Charge Transfer between the Retinal Chromophore and the Protein Environment in Bacteriorhodopsin: A Theoretical Analysis on Reduced and Oxidized Chromophores

Abstract— The importance of charge transfer(CT) between the retinal chromophore and the protein environment in the ground state of bacteriorhodopsin(BR) has been verified by using ab initio and semiempirical molecular orbital methods. We hypothesize that the chromophore is stabilized in BR by highest occupied molecular orbital-lowest unoccupied molecular orbital(HOMO-LUMO) interaction with the protein environment. If sufficient charge is transferred between two sites due to the strong HOMO-LUMO interaction, the chromophore might be treated as a one-electron reduced species(when it behaves as an electron acceptor), or as a one-electron oxidized one (when it acts as an electron donor).In both optimized geometries, the -conjugated systems exhibit a drastic decrease in bond alternation. To estimate the rotational barrier for thermal isomerization between the al-trans and the 13,15-dicis form, the potential energy curve around these two bonds was computed. The first -_* transition energy was also calculated for an inspection of the opsin shift. The barrier height and the transition energy became much lower as a result of the chromophore reduction. The site selectivity in photo- and thermal isomerization and the opsin shift in BR can be well explained by considering CT from the protein environment to the chromophore.     

Tracking the Amide I and αCOO− Terminal ν(C=O) Raman Bands in a Family of l-Glutamic Acid-Containing Peptide Fragments: A Raman and DFT Study

The E-hook of β-tubulin plays instrumental roles in cytoskeletal regulation and function. The last six C-terminal residues of the βII isotype, a peptide of amino acid sequence EGEDEA, extend from the microtubule surface and have eluded characterization with classic X-ray crystallographic techniques. The band position of the characteristic amide I vibration of small peptide fragments is heavily dependent on the length of the peptide chain, the extent of intramolecular hydrogen bonding, and the overall polarity of the fragment. The dependence of the E residue’s amide I ν(C=O) and the αCOO− terminal ν(C=O) bands on the neighboring side chain, the length of the peptide fragment, and the extent of intramolecular hydrogen bonding in the structure are investigated here via the EGEDEA peptide. The hexapeptide is broken down into fragments increasing in size from dipeptides to hexapeptides, including EG, ED, EA, EGE, EDE, DEA, EGED, EDEA, EGEDE, GEDEA, and, finally, EGEDEA, which are investigated with experimental Raman spectroscopy and density functional theory (DFT) computations to model the zwitterionic crystalline solids (in vacuo). The molecular geometries and Boltzmann sum of the simulated Raman spectra for a set of energetic minima corresponding to each peptide fragment are computed with full geometry optimizations and corresponding harmonic vibrational frequency computations at the B3LYP/6-311++G(2df,2pd) level of theory. In absence of the crystal structure, geometry sampling is performed to approximate solid phase behavior. Natural bond order (NBO) analyses are performed on each energetic minimum to quantify the magnitude of the intramolecular hydrogen bonds. The extent of the intramolecular charge transfer is dependent on the overall polarity of the fragment considered, with larger and more polar fragments exhibiting the greatest extent of intramolecular charge transfer. A steady blue shift arises when considering the amide I band position moving linearly from ED to EDE to EDEA to GEDEA and, finally, to EGEDEA. However, little variation is observed in the αCOO− ν(C=O) band position in this family of fragments.     

四溴双酚-A与牛血清白蛋白相互作用的光谱学及电化学研究

采用荧光光谱、同步荧光光谱、三维光谱和循环伏安曲线法研究了溴化阻燃剂四溴双酚-A(TBBPA)与牛血清白蛋白(BSA)的相互作用。研究表明,TBBPA对BSA的内源荧光有显著的猝灭作用,根据不同温度下TBBPA对BSA的荧光猝灭作用及室温的循环伏安曲线,证实猝灭机理为静态猝灭。运用位点模型计算出结合常数KA和结合位点数n,说明TBBPA与BSA仅有1个结合位点。由ΔH0和ΔS0分别为-33.06 kJ/mol和-64.73 J/(mol.K),推断范德华力或氢键在二者结合过程中起主要作用。并通过同步荧光光谱和三维光谱研究了TBBPA对BSA构象的影响,结果表明,TBBPA分子的引入改变了BSA疏水腔内疏水微环境,从而导致BSA的构象发生变化。     

Dienophilic behavior of the vinylic (C=C) and the carbonyl (C=O) bonds of ketenes in reactions with 1,3-diazabuta-1,3-dienes

[reaction: see text] Ab initio and density functional studies (DFT) on cycloaddition reactions of 1,3-diazabuta-1,3-dienes with ketenes are reported. The vinylic (C=C) and the carbonyl (C=O) units of the ketenes are found to participate in concerted asynchronous [4 + 2] cycloaddition reactions. The transition states (3t, 4t, and 7t) for these paths have been located on the PE surface at the correlated levels of ab initio calculations. A reasonable mechanism for the formation of [4 + 2] and [2 + 2] adducts is presented.     

A Study on the Interaction of the DAS-K with Bovine Serum Albumin by On-line Ultrafiltration and Chemiluminescence

Potassium dehydroandrographolide succinate （DAS-K） has antibacterial and antiviral effects. It has been used widely for the treatment of virus pneumonia, malaria and respiratory infections. In this work, a novel flow-injection chemiluminescence （CL） method for the determination of DAS-K was proposed. The method is based on the reaction between DAS-K and hexacyanoferrate（III） in alkaline solution to give weak CL signal, which is enhanced by rhodamine B. The experimental conditions for the CL reaction were optimized and the possible reaction mechanism was discussed. Under the optimum conditions, the concentration of DAS-K is proportional to the CL intensity in the range of 0.1-80 μmol·L^-1 with a detection limit of 0.05 μmol·L^-1. The interaction of the DAS-K with bovine serum albumin by on-line ultrafiltration and flow-injection chemiluminescence was studied. The concentrations of unbound DAS-K from ultra filter tube were determined by the flow-injection CL method. The binding parameters were estimated by the Scatchard plot and Klotz plot. The proposed system proved that FIA-CL coupled with on-line ultrafiltration sampling was a fast and simple technique for the study of drug-protein interaction.     

视网膜脱离后PVR的形成与氧自由基和锌、铜关系的研究

为探讨氧自由基和锌、铜在视网膜脱离后增殖性玻璃体视网膜病变 (PVR)中的作用 ,收集了 48例视网膜脱离患者视网膜下液 (SRF) ,利用紫外分光光度计测定了SRF中LPO的含量和SOD的活性 ,用原子吸收光谱法测定了Zn、Cu的含量。结果表明 ,随着PVR程度及玻璃体浑浊的加重、病程的延长 ,LPO含量增加 ,SOD活性明显下降 ,P <0 0 5 ,差异有统计学意义。提示SRF中LPO、Zn、Cu含量及SOD活性的改变与视网膜脱离后PVR的发生、发展有密切关系。     

Study of rotations around C=C and C-N bonds in dienic δ- aminocarbonyl compounds by the NMR method

Conclusions We determined the free activation energies of the rotations around the C =C and C -N bonds in some unsaturated aminocarbonyl compounds and studied their dependence on the substituents, number of double bonds, solvent, and the concentration. Explanations of the observed processes were proposed on the basis of the obtained data.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 9, pp. 2013–2022, September, 1973.     

用分光光度法研究牛血清白蛋白与曙红Y的结合反应

1　引　　言在酸性介质中 ,蛋白质与酸性染料发生结合反应 ,形成有色探针 ,用于蛋白质的定量测定已得到广泛应用。作者提出水溶性曙红Ｙ(ＥＹ)与牛血清白蛋白 (ＢＳＡ)在酸性溶液中结合 ,作为蛋白质的吸光探针 ,用于人血清中总蛋白质的测定 ,方法简便 ,灵敏度较高 ,干扰较少 ,结果与考马斯亮蓝方法一致。对结合反应的机理进行了研究 ,认为它们之间主要以静电引力而结合。疏水作用力对结合反应也有影响。拟定了最佳结合反应条件 ,对结合反应的参数进行了测定和计算 ,并讨论了染色反应的影响因素 ,对改进和发展蛋白质定量分析方法有重要意义。…     

A Case Study in the Chemical Engineering Freshman Course Using Enhanced Excel with Visual Basic and Power Point

A multicomponent gas-liquid system was considered as a case study project for the course Elementary Principles of Chemical Engineering. In this case study, students were responsible for preparing and using the graphical representation of vapor-liquid equilibrium (T_xy diagrams) for a variety of systems and conditions. The solution to this problem is designed as an interactive program utilizing Enhanced Excel, Visual Basic, and PowerPoint. Using a combination of these three software components necessitated the submission of the solution on a computer disk. Submitting only a printout of the same solution may not capture all of the information that is displayed when using generated events from interacting with the various software modules. By using Excel, freshman students can perform a what-if-analysis for which the problems solution is sought, with minimum efforts. Furthermore, students will have a decent exposure to the chemical engineering process considered for this case study. Moreover, Excel spreadsheets are useful and easier to modify for parametric studies on the overall process than any other computational tool or program.     

Milk-Compositional Study of Metabolites and Pathogens in the Milk of Bovine Animals Affected with Subclinical Mastitis

Bovine milk is an important food component in the human diet due to its nutrient-rich metabolites. However, bovine subclinical mastitis alters the composition and quality of milk. In present study, California mastitis testing, somatic cell count, pH, and electrical conductivity were used as confirmatory tests to detect subclinical mastitis. The primary goal was to study metabolome and identify major pathogens in cows with subclinical mastitis. In this study, 29 metabolites were detected in milk using gas chromatography–mass spectrometry. Volatile acidic compounds, such as hexanoic acid, hexadecanoic acid, lauric acid, octanoic acid, n-decanoic acid, tricosanoic acid, tetradecanoic acid, and hypogeic acid were found in milk samples, and these impart good flavor to the milk. Metaboanalyst tool was used for metabolic pathway analysis and principal component estimation. In this study, EC and pH values in milk were significantly increased (p < 0.0001), whereas fat (p < 0.04) and protein (p < 0.0002) significantly decreased in animals with subclinical mastitis in comparison to healthy animals. Staphylococcus aureus was the predominant pathogen found (n = 54), followed by Escherichia coli (n = 30). Furthermore, antibiotic sensitivity revealed that Staphylococcus aureus was more sensitive to gentamicin (79.6%), whereas Escherichia coli showed more sensitivity to doxycycline hydrochloride (80%).     

Bonding Properties of the 1,2-Semiquinone Radical-Anionic Ligand in the [M(CO)(4-n)(L)(n)(DBSQ)] Complexes (M = Re, Mn; DBSQ = 3,5-di-tert-butyl-1,2-benzosemiquinone; n = 0, 1, 2). A Comprehensive Spectroscopic (UV-Vis and IR Absorption, Resonance Raman, EPR) and Electrochemical Study

Rhenium and manganese complexes of the 3,5-di-tert-butyl-1,2-benzosemiquinone (DBSQ) ligand, [M(CO)(4)(DBSQ)], fac-[M(CO)(3)(L)(DBSQ)], and cis,trans-[M(CO)(2)(L)(2)(DBSQ)], with a widely varied nature of co-ligand(s) (L = THF, Me(2)CO, MeC(O)Ph, py, NEt(3), Ph(3)PO, SbPh(3), AsPh(3), PCy(3), P(OPh)(3), PPh(3), dppe-p, PPh(2)Et, P(OEt)(3), PEt(3)) were generated in solution and characterized as valence-localized molecules containing the radical-anionic DBSQ ligand bound to Re(I) or Mn(I) metal atoms. This is evidenced by the following. (i) Carbonyl stretching frequencies nu(C&tbd1;O) and average force constants k(av) are typical for Mn(I) or Re(I) carbonyls. (ii) Frequencies of the intra-dioxolene C=O bond stretching vibration, nu(C=O), lie within the 1400-1450 cm(-1) range which is diagnostic for coordinated semiquinones. (iii) EPR spectra indicate a very small spin density on the metal atom (0.2% < a(M)/A(iso) > 2.6%). (iv) Absorption spectra show Re(I) --> DBSQ MLCT electronic transitions characterized by a resonant enhancement of the Raman peaks due to the nu(C&tbd1;O) and intra-DBSQ nu(C=O) vibrations. (iv) Finally, the electrochemical pattern consists of DBSQ/DBQ and DBSQ/DBCat ligand-localized redox couples. All these properties are, in a limited range, dependent on the nature and, especially, the number of co-ligands L, indicating a small delocalization of the singly occupied MO of the DBSQ ligand over the metal atom. The extent of this delocalization may be finely tuned by changing the co-ligands, although in absolute terms, it remains rather limited, and the DBSQ ligand behaves toward Re(I) and Mn(I) as a very weak pi-acceptor only. The changes of the electronic properties of the metal center induced by the co-ligands are mostly compensated by more flexible M --> CO pi back-bonding as is manifested by large variations of the average C&tbd1;O stretching force constant.     

Theoretical Study of the Reaction Formalhydrazone with Singlet Oxygen. Fragmentation of the C=N Bond,Ene Reaction and Other Processes

Photobiologic and synthetic versatility of hydrazones has not yet been established with ¹O₂ as a route to commonly encountered nitrosamines. Thus, to determine whether the “parent” reaction of formalhydrazone and ¹O₂ leads to facile C=N bond cleavage and resulting nitrosamine formation, we have carried out CCSD(T)//DFT calculations and analyzed the energetics of the oxidation pathways. A [2 + 2] pathway occurs via diradicals and formation of 3‐amino‐1,2,3‐dioxazetidine in a 16 kcal/mol^?1 process. Reversible addition or physical quenching of ¹O₂ occurs either on the formalhydrazone carbon for triplet diradicals at 2–3 kcal mol^?1, or on the nitrogen (N(3)) atom forming zwitterions at ~15 kcal/mol^?1, although the quenching channel by charge‐transfer interaction was not computed. The computations also predict a facile conversion of formalhydrazone and ¹O₂ to hydroperoxymethyl diazene in a low‐barrier ‘ene’ process, but no 2‐amino‐oxaziridine‐O‐oxide (perepoxide‐like) intermediate was found. A Benson‐like analysis (group increment calculations) on the closed‐shell species are in accord with the quantum chemical results.     

Resonance Raman scattering with a forbidden but vibronically allowed electronic transition: Excitation profiles of combinations and overtones of copper tetraphenylporphyrin in the Q-band resonance

Resonance Raman scattering with the Q band of CuTPP shows a peculiar intensity pattern; bands due to combinations and overtones are strong, whereas the corresponding fundamentals are very weak. By a quantitative analysis of excitation profiles, this phenomenon has been fully accounted for on the basis of the vibronic theory of Raman intensities. Vibronic coupling parameters between the Q and B states of CuTPP have been obtained.     

难熔固体MX(M=Sc,Ti,V;X=C,N,O)电子结构和力学性质的密度泛函研究

采用密度泛函方法对MX(M=Sc,Ti,V;X=C,N,O)固体的体相电子结构和力学性质进行了系统研究.计算结果表明,对于金属原子相同的同一系列化合物,氮化物具有最大的体模量;进一步的研究可知,随着外界压力的增大,化合物由NaCl构型向CsCl构型转变由易到难的顺序依次是氧化物、氮化物和碳化物.本文还首次用密度泛函方法系统地计算了各化合物的能带结构和态密度,并对该类型化合物的导电性能进行了探讨.