DFT Study of the Mechanism and Regioselectivity of 1,3-Pentadiene with Methyl Acrylate Using Theoretical Approaches

<正>Ab initio density functional theory (DFT) calculations have been used to study regioselectivity in the Diels-Alder (DA) cycloaddition reaction between 1,3-pentadiene and methyl acrylate. The DFT calculations were performed with the B3LYP functional and 6-311+G~(**) basis set. Two synchronous transition structures corresponding to the formation of different regioisomers associated with the two reaction channels have been located. The DFT calculations generated transition geometries with a very small degree of asynchronicity. The present analysis shows that these reactions have normal electron demand (NED) character. Moreover, the results obtained from energetic and electronic approaches with the exception of Houk's rule confirm that ortho regioisomer is the major product.     

Endonuclease-based Method for Detecting the Sequence Specific DNA Binding Protein on Double-stranded DNA Microarray

The double-stranded DNA (dsDNA) probe contains two different protein binding sites. One is for DNA- binding proteins to be detected and the other is for a DNA restriction enzyme. The two sites were arranged together with no base interval. The working principle of the capturing dsDNA probe is described as follows: the capturing probe can be cut with the DNA restriction enzyme (such as EcoR I) to cause a sticky terminal, if the probe is not bound with a target protein, and the sticky terminal can be extended and labeled with Cy3-dUTP by DNA polymerase. When the probe is bound with a target protein, the probe is not capable to be cut by the restriction enzyme because of space obstruction. The amount of the target DNA binding proteins can be measured according to the variations of fluorescent signals of the corresponding probes.     

AN INVESTIGATION ON THE ab initio CALCULATION OF INTERMOLECULAR INTERACTION——NON-BONDED INTERACTION IN THE HYDROGEN BOND COMPLEX (HF)_2

An ab initio calculation of the hydrogen bond complex (HF)_2 is given with the 6-311 G~(**) basis set, according to which the potential surface around the balance point of the distancès and the orientations between two HF molecules is obtained. The atomic charges in the system are calculated with the PD/LSF method (potential-derived/least-square-fitting method) and then an analysis of the hydrogen bond interaction between two HF molecules is given with the (exp-6-1) potential function, by means of which it is shown that the main interaction between them is not an electro-static but a charge transfer one. The potential curve between two HF molecules is like a Morse function.     

Structures,Aromaticity and Raman Spectroscopy of Double Hanging Ring Molecules[(GnHn-1^m)(GnHn-1^m)](G=C,Si,Ge;n=3,5,6,7,8;m=+1,-1,0,+1,+2)

Theoretical calculations of Double Hanging Ring Molecule(DHRM) [(GnHn-1^m)(GnHn-1^m)](G=C,Si,Ge;n=3,5,6,7,8;m=+1,-1,0,+1,+2) were performed via Gaussian 09 with the method of Density Functional Theory(DFT). Geometrical optimization, Potential Energy surface Scan(PES), Degree of Aromaticity(DOA) and Nucleus Independent Chemical Shift(NICS) were computed to study the optimal structures and aromaticity of DHRMs. Ring Stretching Vibration Raman Spectroscopy(RSVRSF) was predicted to seek the relation between RSVRSF and aromaticity of DHRMs. The results show optimal structures of DHRMs[(GnH(n-1)~m)(GnH(n–1)~m)](n = 3, 5~8);DA = 90° is the stable structure when n = 3, 7, 8;while n = 5 corresponds to DA = 30°, n = 6 corresponds to DA = 50°;the correlation between DOA and NICS of DHRMs is quadratic;the value of RSVRSF of DHRM approximates to its corresponding single ring molecule, which could act as characteristic frequency of ring molecule to identify its aromaticity;the correlation between RSVRSF and DOA is quadratic, and that between RSVRSF and NICS is linear.     

A comparative study on p-doping behavior of polythiophenes with CH_3SO_3H

Four kinds of polythiophenes have been doped with CH3SO3H in CHCl3 under air,oxygen,and nitrogen. In the doping of two types of poly(3-hexylthiophene)s,P3HexTh(Zn/Ni)and P3HexTh(Fe)with different contents of a head-to-tail unit,the p-doping occurs at a similar rate.The reaction between poly(3-dodecylthiophene),P3DodTh,and the acid takes place more rapidly.P3OBuTh with a butoxy substituent undergoes more facile p-doping and receives photochemical reaction with CHCl3,and this reaction obeys a pseudo-first-order rate law with a rate constant kobs of 1.42×10-5s-1at room tempera- ture.     

Influence of aliphatic amide terminals on the thermoresponsive properties of hyperbranched polyethylenimines

Acetamide(C2), propionamide(C3), butyramide(C4), isobutyramide(i-C4), isovaleramide(i-C5) and trimethylacetamide(t-C5) groups each were introduced to the terminals of hyperbranched polyethylenimine(HPEI) through the amidation reaction between HPEI and the corresponding anhydride. Moreover, HPEIs terminated with two kinds of amides were also prepared. The first amide was fixed to be i-C4 with 52% degree of amidation(DA), and the second amide varied from C2, C3, C4, i-C5 to t-C5. All the polymers were characterized by 1H-NMR. Turbidimetry measurements were performed for these polymers in water at different temperatures. With respect to the polymers bearing only one kind of amide group, except C2, all the other amide groups could render thermoresponsive properties to HPEI. The specific ordering of these amide groups to reduce the cloud point temperature(Tcp) was as follows: i-C5 t-C5 C4 i-C4 C3. Moreover, the more branched i-C4 and t-C5 were better groups than their less branched isomers C4 and i-C5 in the Tcp range of 12-51 °C to render the sharper phase transition to the thermoresponsive polymers. As for the polymers bearing two kinds of amide groups, the further introduction of C2, C3, C4, i-C5 or t-C5 could effectively endow HPEI bearing 52% of i-C4 with thermoresponsive properties. The specific ordering of these second amide groups to reduce the Tcp was as follows: i-C5 C4 i-C4 C3 C2. C4, i-C5 and t-C5 were all effective second amide groups to prepare the thermoresponsive polymers with sharper phase transition.     

A comparative study on p-doping behavior of polythiophenes with CH<Subscript>3</Subscript>SO<Subscript>3</Subscript>H

Four kinds of polythiophenes have been doped with CH3SO3H in CHCl3 under air, oxygen, and nitrogen. In the doping of two types of poly(3-hexylthiophene)s, P3HexTh(Zn/Ni) and P3HexTh(Fe) with different contents of a head-to-tail unit, the p-doping occurs at a similar rate. The reaction between poly(3-dodecylthiophene), P3DodTh, and the acid takes place more rapidly. P3OBuTh with a butoxy substituent undergoes more facile p-doping and receives photochemical reaction with CHCl3, and this reaction obeys a pseudo-first-order rate law with a rate constant kobs of 1.42×10-5 s-1 at room temperature.     

以乙二胺为手臂分子制备的DNA修饰电极及其伏安性能

Carboxyl was formed on the surface of glassy carbon electrode(GCE) by electrochemical oxidation. Ethylenediamine(En) was used as the arm molecule to link carboxyl with dsDNA using 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide hydrochloride (EDC) and N- hydroxysuccinimide (NHS) as the activators to prepare dsDNA modified electrode(dsDNA/En/GCE). It was shown that dsDNA couM be covalently immobilized on the surface of GCE. ssDNA modified electrode(ssDNA/En/GCE) was obtained via the thermal denaturation of dsDNA/En/GCE. The dsDNA/En/GCE and ssDNA/En/GCE were characterized by voltammetry with methylene blue(MB) as the indicator. The results indicated that the currents of the redox peaks of MB at ssDNA/En/GCE were larger than those at dsDNA/En/GCE, and the currents of the redox peaks at En/GCE were the smallest. The peak-currents of MB at the DNA modified electrode had good reproducibility after multi-denaturation and hybridization cycles.     

Ab Initio Study on the Mechanism of Cycloaddition Reaction between Silylene Carbene （H_2Si=C：） and Acetone

The mechanism of cycloaddition reaction between singlet silylene carbene and acetone has been investigated with CCSD(T)//MP2/6-31G method. From the potential energy profile, it can be predicted that the reaction has two competitive dominant reaction pathways. One consists of two steps: (1) the two reactants (R1, R2) firstly form a four-membered ring intermediate (INT4) through a barrier-free exothermic reaction of 585.9 kJ/mol; (2) Then intermediate (INT4) isomerizes to CH3-transfer product (P4.1) via a transition state (TS4.1) with energy barrier of 5.3 kJ/mol. The other is as follows: on the basis of intermediate (INT4) created between R1 and R2, intermediate (INT4) further reacts with acetone (R2) to form the intermediate (INT5) through a barrier-free exothermic reaction of 166.3 kJ/mol; Then, intermediate (INT5) isomerizes to a silicic bis-heterocyclic product (P5) via a transition state (TS5), for which the barrier is 54.9 kJ/mol. The presented rule of this reaction: the [2+2] cycloaddition effect between the π orbital of silylene carbene and the π orbital of π-bonded compounds leads to the formation of a four-membered ring intermediate (INT4); The unsaturated property of C atom from carbene in the four-membered ring intermediate (INT4) results in the generation of CH3-transfer product (P4.1) and silicic bis-heterocyclic compound (P5).     

无胶筛分芯片电泳研究贝类毒素-软骨藻酸与寡聚DNA的相互作用

近年来,我国日趋严重的赤潮已给海洋渔业带来了极大的损失,也对人类的健康构成威胁．赤潮毒素可对海洋养殖产生严重的污染,食用贝类所富集的贝类毒素严重损害食用者身体健康．根据其中毒症状,贝类毒素被分为4大类：引起腹泻性中毒(Diarrhetic Shellfish Poisoning,DSP)的贝类毒素;引起麻痹性中毒(Paralytic Shellfish Poisoning,PSP)的贝类毒素;     

Dynamic-light-scattering-based sequence-specific recognition of double-stranded DNA with oligonucleotide-functionalized gold nanoparticles

An ultrasensitive and simple dynamic-light-scattering (DLS) assay for the sequence-specific recognition of double-stranded DNA (dsDNA) was developed based on detection of the average diameter change of Au nanoparticle (AuNP) probes modified with oligonucleotides 5'-TTTCTCTTCCTT- CTCTTC-(T)(12)-SH-3' (Oligo 1) and 5'-TTCTTTCTTTTCTTTTTC-(T)(12)- SH-3' (Oligo 2). The target dsDNA was composed of two complementary oligonucleotides: 5'-AAAGAGAAGGAAGAGAAGAAGAAAGAAAAGAAAAAG-3' (Oligo 3) and 3'-TTTCTCTTCCTTCTCTTCTTCTTTCTTTTCTTTTTC-5' (Oligo 4). Hybridization of the two AuNPs-Oligo probes with the target dsDNA induced aggregation of the target dsDNA by forming triplex DNA, which accordingly increased the average diameter. This diameter change could then be detected by DLS. The average diameter was proportional to the target dsDNA concentration over the range from 593 fM to 40 pM, with a detection limit of 593 fM. Moreover, the assay had good sequence specificity for the target dsDNA.     

Trinuclear copper(II) complex showing high selectivity for the hydrolysis of 2'-5' over 3'-5' for UpU and 3'-5' over 2'-5' for ApA ribonucleotides

The cooperative action of multiple Cu(II) nuclear centers is shown to be effective and selective in the hydrolysis of 2'-5' and 3'-5' ribonucleotides. Reported herein is the specific catalysis by two trinuclear Cu(II) complexes of L3A and L3B. Pseudo first-order kinetic studies reveal that the L3A trinuclear Cu(II) complex effects hydrolysis of Up(2'-5')U with a rate constant of 28 x 10(-)(4) min(-)(1) and Up(3'-5')U with a rate constant of 0.5 x 10(-)(4) min(-)(1). The hydrolyses of Ap(3'-5')A and Ap(2'-5')A proceed with rate constants of 24 x 10(-)(4) min(-)(1) and 0.5 x 10(-)(4) min(-)(1) respectively. The L3A trinuclear Cu(II) complex demonstrates high specificity for Up(2'-5')U and Ap(3'-5')A. Similar studies with the more rigid L3B trinuclear Cu(II) complex shows no selectivity and yields lower rate constants for hydrolysis. The selectivity observed with the L3A ligand is attributed to the geometry of the ligand-bound diribonucleotide which ultimately dictates the proximity of the attacking hydroxyl and the phosphoester to a Cu(II) center for activation and subsequent hydrolysis.     

Decoupling optical and potentiometric band gaps in pi-conjugated materials

Syntheses, optical spectroscopy, potentiometric studies, and electronic structural calculations are reported for two classes of conjugated (porphinato)metal oligomers that feature a meso-to-meso ethyne-bridged linkage topology. One set of these systems, bis[(5,5'-10,20-bis[3,5-bis(3,3-dimethyl-1-butyloxy)phenyl]porphinato)zinc(II)]ethyne (DD), 5,15-bis[[5'-10',20'-bis[3,5-di(3,3-dimethyl-1-butyloxy)phenyl]porphinato)zinc(II)]ethynyl]-10,20-bis[3,5-di(9-methoxy-1,4,7-trioxanonyl)phenyl]porphinato)zinc(II) (DDD), and 5,15-bis[[15' '-(5'-10',20'-bis[3,5-bis(3,3-dimethyl-1-butyloxy)phenyl]porphinato)zinc(II)]-[(5' '-10' ',20' '-bis[3,5-di(9-methoxy-1,4,7-trioxanonyl)phenyl]porphinato)zinc(II)]ethyne]ethynyl]-10,20-bis[3,5-di(9-methoxy-1,4,7-trioxanonyl)phenyl]porphinato)zinc(II) (DDDDD), constitute highly soluble analogues of previously studied examples of this structural motif having simple 10,20-diaryl substituents, while a corresponding set of conjugated oligomers, [(5-10,20-bis[3,5-bis(3,3-dimethyl-1-butyloxy)phenyl]porphinato)zinc(II)]-[(5'-15'-ethynyl-10',20'-bis[10,20-bis(heptafluoropropyl)porphinato)zinc(II)]ethyne (DA), 5,15-bis[[5'-10',20'-bis[3,5-di(3,3-dimethyl-1-butyloxy)phenyl]porphinato)zinc(II)]ethynyl]-10,20-bis(heptafluoropropyl)porphinato]zinc(II) (DAD), and 5,15-bis[[15' '-(5'-10',20'-bis[3,5-bis(3,3-dimethyl-1-butyloxy)phenyl]porphinato)zinc(II)]-[(5' '-(10' ',20' '-bis(heptafluoropropyl)porphinato)zinc(II)]ethyne]ethynyl]-10,20-bis[3,5-di(9-methoxy-1,4,7-trioxanonyl)phenyl]porphinato)zinc(II) (DADAD), features alternating electron-rich and electron-poor (porphinato)zinc(II) units. Electrooptic and computational data for these species demonstrate that it is possible to engineer conjugated oligomeric structures that possess highly delocalized singlet (S1) excited states yet manifest apparent one-electron oxidation and reduction potentials (E1/20/+ and E1/2-/0 values) that are essentially invariant with respect to those elucidated for their constituent monomeric precursors.     

Solution self-assembly, spontaneous deprotonation, and crystal structures of bipyrazolate-bridged metallomacrocycles with dimetal centers

A series of nanosized cavity-containing bipyrazolate-bridged metallomacrocycles with dimetal centers, namely, {[(bpy)M]8L4}(NO3)8 [L=3,3',5,5'-tetramethyl-4,4'-bipyrazolyl, Pd, Pt; 1,4-bis-4'-(3',5'-dimethyl)-pyrazolylbenzene), Pd; and 1,4-bis-4'-(3',5'-dimethyl)-pyrazolylbiphenyl, Pd], {[(phen)M]8L4}(NO3)8 [L=3,3',5,5'-tetramethyl-4,4'-bipyrazolyl, Pd, Pt; 1,4-bis-4'-(3',5'-dimethyl)-pyrazolylbenzene, Pd; and 1,4-bis-4'-(3',5'-dimethyl)-pyrazolylbiphenyl, Pd], {[(bpy)Pd]6L3}(NO3)6 [L=1,4-bis-4'-(3',5'-dimethyl)-pyrazolylbenzene,], {[(phen)Pd]6L3}(NO3)6 [L=1,4-bis-4'-(3',5'-dimethyl)-pyrazolylbenzene,], {[(bpy)Pd]4L2}(NO3)4 [L=1,3-bis-4'-(3',5'-dimethyl)-pyrazolylbenzene, and 1,2-bis-4'-(3',5'-dimethyl)-pyrazolylbenzene,], and {[(phen)Pd]4L2}(NO3)4 [L=1,3-bis-4'-(3',5'-dimethyl)-pyrazolylbenzene, and 1,2-bis-4'-(3',5'-dimethyl)-pyrazolylbenzene,] (where bpy=2,2'-bipyridine and phen=1,10-phenanthroline) have been synthesized through a directed self-assembly approach that involves spontaneous deprotonation of the 1H-bipyrazolyl ligands in aqueous solution. These complexes, with weak Pd(II)...Pd(II) or Pt(II)...Pt(II) interactions, have been characterized by elemental analysis, 1H and 13C NMR, cold-spray ionization or electrospray ionization mass spectrometry, UV-visible spectroscopy, and luminescence spectroscopy. Complexes and have also been characterized by single-crystal X-ray diffraction analysis.     

2′-5′寡腺苷酸的有机合成与修饰

本文主要综述了三方面的内容:(1)2′-5′寡腺苷酸的生物学意义。(2)2′-5′寡腺苷酸的有机合成,特别是磷酸三酯法和铅离子(Pb~(++))催化法。(3)2′-5′寡腺苷酸结构与功能的关系,如5′端磷酸基,3′端羟基以及碱基与功能的关系。     

2-芳胺基-5-[5′-氨基-1′-(4″-氯苯基)-1′,2′,3′-三唑-4′-基]-1,3,4-噻二唑的合成~≠

1-[5’-氨基-1’-(4”-氯苯基)-1,2,3-三唑-4’-甲酰基]-4-芳基-3-氨基硫脲在浓硫酸催化下环化得到2-芳胺基-5-[5’-氨基-1’-(4”-氯苯基)-1’,2’,3’,-三唑-4’-基]-1,3,4-噻二唑2a～i,依次法合成了九个标题化合物,收率为30～74％。化合物2i的结构用X-光衍射单晶分析确证。     

Total synthesis of 2',3',4',5',5' '-(2)h(5)-ribonucleosides: the key building blocks for NMR structure elucidation of large RNA

The diastereospecific chemical syntheses of uridine-2',3',4',5',5' '-(2)H(5) (21a), adenosine-2',3',4',5',5' '-(2)H(5) (21b), cytidine-2',3',4',5',5' '-(2)H(5)(2)H(5) (21c), and guanosine-2',3',4',5',5' '-(2)H(5) (21d) (>97 atom % (2)H at C2', C3', C4', and C5'/C5' ') have been achieved for their use in the solution NMR structure determination of oligo-RNA by the Uppsala "NMR-window" concept (refs 4a-c, 5a, 6), in which a small (1)H segment is NMR-visible, while the rest is made NMR-invisible by incorporation of the deuterated blocks 21a-d. The deuterated ribonucleosides 21a-d have been prepared by the condensation of appropriately protected aglycone with 1-O-acetyl-2,3,5-tri-O-(4-toluoyl)-alpha/beta-D-ribofuranose-2,3,4,5,5'-(2)H(5) (19), which has been obtained via diastereospecific deuterium incorporation at the C2 center of appropriate D-ribose-(2)H(4) derivatives either through an oxidation-reduction-inversion sequence or a one-step deuterium-proton exchange in high overall yield (44% and 24%, respectively).     

苯并噻唑偶氮吡唑和苯并噻唑偶氮嘧啶的合成

2-氨基苯并噻唑重氮盐与丙二腈偶联, 生成2-(苯并噻唑腙基)-丙二腈, 然后分别与水合肼, 苯肼和硝酸胍反应, 形成相应的4'-(苯并噻唑-2-偶氮)-3',5'-二氨基吡唑, 4'-(苯并噻唑-2-偶氮)-3',5'-二氨基-2'-苯并吡唑和5'-(苯并噻唑-2-偶氮)-2',4',6'-三氨基嘧啶.     

Rational modification of a selection strategy leads to deoxyribozymes that create native 3'-5' RNA linkages

We previously used in vitro selection to identify several classes of deoxyribozymes that mediate RNA ligation by attack of a hydroxyl group at a 5'-triphosphate. In these reactions, the nucleophilic hydroxyl group is located at an internal 2'-position of an RNA substrate, leading to 2',5'-branched RNA. To obtain deoxyribozymes that instead create linear 3'-5'-linked (native) RNA, here we strategically modified the selection approach by embedding the nascent ligation junction within an RNA:DNA duplex region. This approach should favor formation of linear rather than branched RNA because the two RNA termini are spatially constrained by Watson-Crick base pairing during the ligation reaction. Furthermore, because native 3'-5' linkages are more stable in a duplex than isomeric non-native 2'-5' linkages, this strategy is predicted to favor the formation of 3'-5' linkages. All of the new deoxyribozymes indeed create only linear 3'-5' RNA, confirming the effectiveness of the rational design. The new deoxyribozymes ligate RNA with k(obs) values up to 0.5 h(-1) at 37 degrees C and 40 mM Mg2+, pH 9.0, with up to 41% yield at 3 h incubation. They require several specific RNA nucleotides on either side of the ligation junction, which may limit their practical generality. These RNA ligase deoxyribozymes are the first that create native 3'-5' RNA linkages, which to date have been highly elusive via other selection approaches.