Synthesis of the DNA-[Ru(tpy)(dppz)(CH(3)CN)](2+) conjugates and their photo cross-linking studies with the complementary DNA strand

We here report our studies on the conjugation of photoreactive Ru(2+) complex to oligonucleotides (ODNs), which give a stable duplex with the complementary target DNA strand. These functionalized DNA duplexes bearing photoreactive Ru(2+) complex can be specifically photolyzed to give the reactive aqua derivative, [Ru(tpy)(dppz)(H(2)O)](2+)-ODN (tpy = 2,2':6',2' '-terpyridine; dppz = dipyrido[3,2-a:2',3'-c]phenazine), in situ, which successfully cross-links to give photoproduct(s) in the duplex form with the target complementary DNA strand. Thus, the stable precursor of the aquaruthenium complex, the monofunctional polypyridyl ruthenium complex [Ru(tpy)(dppz)(CH(3)CN)](2+), has been site-specifically tethered to ODN, for the first time, by both solid-phase synthesis and postsynthetic modifications. (i) In the first approach, pure 3'-[Ru(tpy)(dppz)(CH(3)CN)](2+)-ODN conjugate has been obtained in 42% overall yield (from the monomer blocks) by the automated solid-phase synthesis on a support labeled with [Ru(tpy)(dppz)Cl](+) complex with subsequent liberation of the crude conjugate from the support under mild conditions and displacement of the Cl(-) ligand by acetonitrile in the coordination sphere of the Ru(2+) label. (ii) In the second approach, the single-modified (3'- or 5'- or middle-modified) or 3',5'-bis-modified Ru(2+)-ODN conjugates were prepared in 28-50% yield by an amide bond formation between an active ester of the metal complex and the ODNs conjugated with an amino linker. The pure conjugates were characterized unambiguously by ultraviolet-visible (UV-vis) absorption spectroscopy, enzymatic digestion followed by HPLC quantitation, polyacrylamide gel electrophoresis (PAGE), and mass spectrometry (MALDI-TOF as well as by ESI). [Ru(tpy)(dppz)(CH(3)CN)](2+)-ODNs form highly stabilized ODN.DNA duplexes compared to the unlabeled counterpart (DeltaT(m) varies from 8.4 to 23.6 degrees C) as a result of intercalation of the dppz moiety; they undergo clean and selective photodissociation of the CH(3)CN ligand to give the corresponding aqua complex, [Ru(tpy)(dppz)(H(2)O)](2+)-ODNs (in the aqueous medium), which is evidenced from the change of their UV-vis absorption properties and the detection of the naked Ru(2+)-ODN ions generated in the course of the matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometric analysis. Thus, when [Ru(tpy)(dppz)(CH(3)CN)](2+)-ODN conjugate was hybridized to the complementary guanine (G)-rich target strand (T), and photolyzed in a buffer (pH 6.8), the corresponding aqua complex formed in situ immediately reacted with the G residue of the opposite strand, giving the cross-linked product. The highest yield (34%) of the photo cross-linked product obtained was with the ODN carrying two reactive Ru(2+) centers at both 3'- and 5'-ends. For ODNs carrying only one Ru(2+) complex, the yield of the cross-linked adduct in the corresponding duplex is found to decrease in the following order: 3'-Ru(2+)-ODN (22%) > 5'-Ru(2+)-ODN (9%) > middle-Ru(2+)-ODN (7%). It was also found that the photo cross-coupling efficiency of the tethered Ru(2+) complex with the target T strand decreased as the stabilization of the resulting duplex increased: 3'-Ru(2+)-ODN (VI.T) (DeltaT(m)(b) = 7 degrees C) < 5'-Ru(2+)-ODN (V.T) (DeltaT(m)(b) = 16 degrees C) < middle-Ru(2+)-ODN (VII.T) (DeltaT(m)(b) = 24.3 degrees C, Table 2). This shows that, with the rigidly packed structure, as in the duplex with middle-Ru(2+)-ODN, the metal center flexibility is considerably reduced, and consequently the accessibility of target G residue by the aquaruthunium moiety becomes severely restricted, which results in a poor yield in the cross-coupling reaction. The cross-linked product was characterized by PAGE, followed by MALDI-TOF MS.     

Enhancement of the binding ability of a ligand for nucleobase recognition by introducing a methyl group.

The recognition ability of pteridine derivatives for nucleobases opposite an abasic (AP) site in an oligodeoxynucleotide (ODN) duplex is enhanced by using a propylene residue (Spacer-C3) as an AP site. The recognition ability is further enhanced both by attaching methyl groups to a fluorescent ligand and by measuring the fluorescence response at 5 degrees C; 6.2 x 10(6) M(-1) of the binding constant is attained between 2-amino-6,7-dimethyl-4-hydroxypteridine and guanine opposite the AP site in water.     

Thermal decomposition of multiply charged T-rich oligonucleotide anions in the gas phase. Influence of internal solvation on the arrhenius parameters for neutral base loss

Arrhenius activation parameters (E(a), A) for the loss of neutral nucleobases from a series of T-rich, doubly and triply deprotonated 15- and 20-mer oligodeoxynucleotides (ODN) containing a single reactive base (X = A or C) with the sequence, XT14, XT19 and T19X, have been determined using the blackbody infrared radiative dissociation technique. The A-containing anions are significantly more reactive (> or =3000 times) than the C-containing ions over the temperature range investigated. Importantly, the Arrhenius parameters for the loss of AH exhibit a strong dependence on size of the ODN and, to some extent, the charge state; the Arrhenius parameters increase with size and charge (Ea = 29-39 kcal mol(-1), A = 10(15)-10(20) s(-1)). In contrast, the parameters for the loss of CH are much less sensitive to size (Ea = 35-39 kcal mol(-1), A = 10(14)-10(17) s(-1)). The results are consistent with a greater contribution from the internal solvation of the reactive base to the Arrhenius parameters for the loss of A, compared with C, from the 15- and 20-mers. To further probe differences in internal solvation of A and C, hydrogen/deuterium exchange was carried out on AT19(-3), T19A(-3), CT19(-3) and T19C(-3) using D2O as the exchange reagent. However, the H/D exchange results did not reveal any differences in internal solvation within the ODN anions. Arrhenius parameters for the dissociation of noncovalent complexes of T20(-3) and the neutral nucleobase AH or CH have also been determined. Differences in the parameters indicate differences in the nature of the intermolecular interactions. It is proposed that neutral A-T interactions (i.e., base-base), which originate in solution, dominate in the case of (T20 + AH)(-3), while charge solvation, involving CH and a deprotonated phosphate group, is present for (T20 + CH)(-3).     

Unique charge transfer properties of the four-base pi-stacks in Z-DNA

To investigate the photoreactions of BrU in Z-DNA, the photoirradiation of 5'-d(C1G2C3G4BrU5G6C7G8)-3'/5'-d(C9mG10C11A12C13mG14C15G16)-3'(ODN 1-2) was investigated. In accord with previous observations, B-form ODN 1-2 with the 5'-GBrU sequence showed very weak photoreactivity. However, Z-form ODN 1-2 in 2 M NaCl underwent photoreaction to afford 5'-d(CGC)rGd(UGCG)-3' together with the formation of imidazolone (Iz) contained 5'-d(CIzCACmGCG)-3'. The results clearly indicate that structural changes caused by the B-Z transition dramatically increased the photoreactivity of ODN 1-2. Inspection of the molecular structure of Z-DNA suggests that there is unique four-base pi-stacks at the G4-BrU5-C11-mG10 in ODN 1-2. These results suggest that the intriguing possibility that the mG10 in a complementary strand located at the end of the four-base pi-stacks may act as an electron donor. To test the hypothesis of interstrand charge transfer from mG10 to BrU5 within the four-base pi-stacks in Z-DNA, ODN 1-3 samples in which the putative donor G10 residue was replaced with 8-methoxyguanine (moG) were prepared, since moG is known to trap cation radicals to yield Iz moieties in DNA. Photoirradiation of ODN 1-3 efficiently produced 5'-d(CGC)rGd(UGCG)-3' together with formation of 5'-d(CIzCACmGCG)-3'. These results clearly indicate that the interstrand charge transfer from mG10 to BrU5 initiates the photoreaction. In clear contrast, other replacements of G with moG did not enhance the photoreactivity. The present study revealed the presence of unique four-base pi-stacks in Z-DNA and photoirradition of BrU in Z-DNA causes efficient electron transfer from G within this cluster.     

Syntheses,crystallographic/computational characterizations,and reactions of the first 10-vertex arachno- and nido-phosphamonocarbaboranes

A synthetic sequence involving the initial reaction of a substituted phosphorus dihalide (RPCl(2), R = CH(3), C(6)H(5)) with the arachno-CB(8)H(13)(-) (1-) monoanion followed by an in situ dehydrohalogenation reaction initiated by Proton Sponge, resulted in phosphorus cage insertion to yield the first 10-vertex arachno- and nido-phosphamonocarbaboranes, exo-6-R-arachno-6,7-PCB(8)H(12) (2a, 2b) and PSH(+)6-R-nido-6,9-PCB(8)H(9)(-) (PSH+3a-, PSH+3b-) (R = C(6)H(5) (a), CH(3) (b)). Alternatively, 2a and 2b were synthesized in high yield as the sole product of the reaction of the arachno-4-CB(8)H(12)(2-) (1(2-)) dianion with RPCl(2). Crystallographic determinations of PSH+3a- and PSH+3b- in conjunction with DFT/GIAO computational studies of the anions have confirmed the expected nido cage framework based on an octadecahedron missing the six-coordinate vertex. DFT/GIAO computational studies have also shown that while the gross cage geometries of the exo-6-R-arachno-6,7-PCB(8)H(12) compounds 2a and 2b resemble the known isoelectronic arachno-6,9-SCB(8)H(12), the phosphorus and carbon atoms are in thermodynamically unfavorable adjacent positions on the six-membered puckered face. They also each have an endo-hydrogen at the P6-position arising from proton transfer to the basic phosphorus during the cage-insertion reaction. Possible stepwise reaction pathways that can account for the formation of both the arachno and nido products are discussed. Deprotonation of 2a and 2b resulted in the formation of their corresponding conjugate monoanions, 6-R-arachno-6,7-PCB(8)H(11)(-) (2a-, 2b-), in which the proton that had been attached to the P6 atom was removed. Reactions of 2a- with O(2), S(8), BH(3).THF, or Br(2) further demonstrated the basicity of the P6-phosphorus yielding the new arachno-substituted compounds, endo-6-O-exo-6-(C(6)H(5))-arachno-6,7-PCB(8)H(11)(-) (4a-), endo-6-S-exo-6-(C(6)H(5))-arachno-6,7-PCB(8)H(11)(-) (5a-), endo-6-BH(3)-exo-6-(C(6)H(5))-arachno-6,7-PCB(8)H(11)(-) (6a-), and endo-6-Br-exo-6-(C(6)H(5))-arachno-6,7-PCB(8)H(11) (7a), respectively, in which the O, S, BH(3), and Br substituents are bound to the phosphorus at the endo position.     

Thermal decomposition of ethanol. III. A computational study of the kinetics and mechanism for the CH3+C2H5OH reaction

The mechanism for the CH3+C2H5OH reaction has been investigated by the modified Gaussian-2 method based on the geometric parameters of the stationary points optimized at the B3LYP/6-311+G(d,p) level of theory. Five transition states have been identified for the production of CH4+CH3CHOH (TS1), CH4+CH3CH2O (TS2), CH4+CH2CH2OH (TS3), CH3OH+CH3CH2 (TS4), and CH3CH2OCH3+H (TS5) with the corresponding barriers 12.0, 13.2, 16.0, 44.7, and 49.9 kcal/mol, respectively. The predicted rate constants and branching ratios for the three lower-energy H-abstraction reactions were calculated using the conventional and variational transition state theory with quantum-mechanical tunneling corrections for the temperature range 300-3000 K. The predicted total rate constant, kt=8.36 x 10(-76) T(20.00) exp(5258/T) cm3 mol(-1) s(-1) (300-600 K) and 6.10 x 10(-25) T(4.10)exp(-4058/T) cm3 mol(-1) s(-1) (600-3000 K), agrees closely with existing experimental data in the temperature range 403-523 K. Similarly, the predicted rate constants for CH3+CH3CD2OH and CD3+C2H5OD are also in reasonable agreement with available low temperature kinetic data.     

A versatile approach towards regioselective platinated DNA sequences

Undesired N(7) platination of 2'-deoxyguanosine residues at predetermined sites in an oligodeoxynucleotide (ODN) sequence is prevented by applying the sterically demanding diphenylcarbamoyl (DPC) as an O(6)-protecting group. The presence of a base-labile oxalyl linker between the immobilized 3'-nucleotide and controlled pore glass (CPG) allows cleavage of the protected ODN from the support and leaves DPC protection unaffected. This method provides an ODN with specifically blocked guanine-N(7) sites for platination. In the hexanucleotides prepared in this study, 5'-GGBGGT-3'(for B=T, C and A), a platinum GG adduct is introduced at G4,G5. These site-specific platinated hexamers were isolated in a yield of 65 %, and were fully characterized by using reversed-phase HPLC (high performance liquid chromotography), LCMS (liquid chromatography-mass spectrometry), MALDI-TOF MS (matrix-assisted laser desorption/ionization time-of-flight mass spectrometry), PAGE (polyacrylamide gel electrophoresis) and Maxam-Gilbert sequencing analysis.     

Synthesis and characterization of the first examples of perfluoroalkyl-substituted trialkyloxonium salts, [(CH3)2OCF3]+[Sb2F11]- and [(CH3)2OCF(CF3)2]+[Sb2F11]-

In the superacidic HF/SbF(5) system, methyl trifluoromethyl ether forms at -78 degrees C the new tertiary oxonium salt [(CH(3))(2)OCF(3)](+)[Sb(2)F(11)](-), which was characterized by Raman and multinuclear NMR spectroscopy and its crystal structure. The same oxonium salt was also obtained by methylation of CH(3)OCF(3) with CH(3)F and SbF(5) in HF solution at -30 to -10 degrees C. Replacement of one methyl group in the trimethyloxonium cation by the bulkier and more electronegative trifluoromethyl group increases the remaining O-CH(3) bond lengths by 0.037(1) A and the sum of the C-O-C bond angles by about 4.5 degrees. Methylation of CH(3)OCF(CF(3))(2) with CH(3)F in HF/SbF(5) solution at -30 degrees C produces [(CH(3))(2)OCF(CF(3))(2)](+)[Sb(2)F(11)](-). The observed structure and vibrational and NMR spectra were confirmed by theoretical studies at the B3LYP/6-311++G(2d,2p) and the MP2/6-311++G(2d,p) levels.     

CH3CH2+O(3P)反应机理的理论研究

The reaction for CH3CH2+O(3P) was studied by ab initio method. The geometries of the reactants, intermediates, transition states and products were optimized at MP2/6-311+G(d,p) level. The corresponding vibration frequencies were calculated at the same level. The single-point calculations for all the stationary points were carried out at the QCISD(T)/6-311+G(d,p) level using the MP2/6-311+G(d,p) optimized geometries. The results of the theoretical study indicate that the major products are the CH2O＋CH3, CH3CHO+H and CH2CH2+OH in the reaction. For the products CH2O＋CH3 and CH3CHO+H, the major production channels are A1: (R)→IM1→TS3→(A) and B1: (R)→IM1→TS4→(B), respectively. The majority of the products CH2CH2+OH are formed via the direct abstraction channels C1 and C2: (R)→TS1(TS2)→(C). In addition, the results suggest that the barrier heights to form the CO reaction channels are very high, so the CO is not a major product in the reaction.     

Investigation of the initial fragmentation of oligodeoxynucleotides in a quadrupole ion trap: Charge level-related base loss

The charge state distribution and CID fragmentation of two series of deprotonated oligodeoxynucleotide (ODN) 9-mers (5'-GGTTXTTGG-3' and 5'-CCAAYAACC-3', X/Y = G, C, A, or T) have been studied in detail in an ion trap in an effort to understand the intrinsic properties of DNA in vacuo. The distribution of charge states (-2 to -6) is similar for both the X- and Y-series, with the most abundant being the -4 charge state. The T-rich X-series prefers higher charge states (-6 and -5) than does the Y-series. Calculations show that phosphate groups located nearest a thymine are more acidic than those near an adenine, cytosine, or guanine, thus explaining why the X-series prefers higher charge states. We use the term "charge level" to define the ratio of the charge state to the total number of phosphate groups present in the ODN. We find, consistent with previous studies, that the initial step of fragmentation is loss of nucleobase either as an anion or as a neutral. We observe the former for ODNs with charge levels greater than 50% and the latter for ODNs with charge levels below 50%. The overall anionic base loss follows the trend A(-) > G(-) approximately T(-) > C(-); electrostatic potential calculations indicate that this trend follows delocalization of electron density for each anion, with A(-) being the most stabilized through delocalization. For neutral base loss, thymine (TH) is rarely cleaved, while the preferences for AH, GH, and CH loss vary. Proton affinity (PA) calculations show that a nearby negatively charged phosphate enhances the PA of proximally located nucleobases; this PA enhancement probably plays a role in promoting neutral base loss. The trends differ by charge level. At a charge level of 37.5% (-3 charge state), AH loss is preferred over CH and GH loss, regardless of sequence. However, at a charge level of 25% (-2 charge state), the terminal bases are preferentially lost over the internal bases, regardless of identity. By reconstructing the ODN sequences from structurally informative (a-BH) and w ions, we are able to identify the charge locations for the -3 and -2 charge states. For the -3 charge state, one charge resides on each "most terminal" phosphate, with the third being in the middle. For the -2 charge state, each charge resides on the penultimate phosphate groups. We compare our data to earlier experiments in an effort to generalize trends.     

U-pin polyamide motif for recognition of the DNA minor groove

DNA-binding hairpin pyrrole-imidazole polyamides with gamma-aminobutyric acid as a turn-forming residue tolerate A.T or T.A base pairs under the turn. U-pins-polyamides with a different turn-have been synthesized and their DNA binding properties were studied. The two turn-forming residues are connected via the ring nitrogens using variable length aliphatic linkers ((CH(2))(n), n=3-6). Through optimization of the linker length and the substituents at the 2-position of the pyrrole residue on the U-turn, polyamides with G.C/C.G tolerant turns could be found, which bind to DNA in a predictable manner.     

CH3CH2,CH3CHCl,CH3CCl2与NO2反应微观动力学理论研究

运用量子化学密度泛函理论UB3LYP/6-311+G*和高级电子相关校正的偶合簇(CCSD(T)/6-311+G*)方法,对CH3CH2,CH3CHCl和CH3CCl2自由基与NO2反应的机理和动力学进行了理论研究,得到了体系的势能面信息和可能的反应机理.根据计算得到的各反应热力学参数及反应能垒,采用传统过渡态理论计算了各反应在温度T=298 K和T=700 K时的速率常数.研究结果表明,该类反应均通过1个中间体和1个过渡态生成产物,产物分别为CH3CHO+HNO,CH3CHO+ClNO和CH3CClO+ClNO.     

Experimental and theoretical studies of rate coefficients for the reaction O(3P)+C2H5OH at high temperatures

Rate coefficients of the reaction O(3P)+C2H5OH in the temperature range 782-1410 K were determined using a diaphragmless shock tube. O atoms were generated by photolysis of SO2 at 193 nm with an ArF excimer laser; their concentrations were monitored via atomic resonance absorption. Our data in the range 886-1410 K are new. Combined with previous measurements at low temperature, rate coefficients determined for the temperature range 297-1410 K are represented by the following equation: k(T)=(2.89+/-0.09)x10(-16)T1.62 exp[-(1210+/-90)/T] cm3 molecule(-1) s(-1); listed errors represent one standard deviation in fitting. Theoretical calculations at the CCSD(T)/6-311+G(3df, 2p)//B3LYP/6-311+G(3df) level predict potential energies of various reaction paths. Rate coefficients are predicted with the canonical variational transition state (CVT) theory with the small curvature tunneling correction (SCT) method. Reaction paths associated with trans and gauche conformations are both identified. Predicted total rate coefficients, 1.60 x 10(-22)T3.50 exp(16/T) cm3 molecule(-1) s(-1) for the range 300-3000 K, agree satisfactorily with experimental observations. The branching ratios of three accessible reaction channels forming CH3CHOH+OH (1a), CH2CH2OH+OH (1b), and CH3CH2O+OH (1c) are predicted to vary distinctively with temperature. Below 500 K, reaction 1a is the predominant path; the branching ratios of reactions 1b,c become approximately 40% and approximately 11%, respectively, at 2000 K.     

Efficient C2'alpha-hydroxylation of deoxyribose in protein-induced Z-form DNA

DNA local conformations are thought to play an important biological role in processes such as gene expression by altering DNA-protein interactions. Although left-handed Z-form DNA is one of the best-characterized and significant local structures of DNA, having been extensively investigated for more than two decades, the biological relevance of Z-form DNA remains unclear. This is presumably due to the lack of a versatile detection method in a living cell. Previously, we demonstrated that the incorporation of a methyl group at the guanine C8 position (m(8)G) dramatically stabilizes the Z-form of short oligonucleotides in a variety of sequences. To develop a photochemical method to detect Z-form DNA, we examined the photoreaction of 5-iodouracil-containing Z-form d(CGCG(I)UGCG)(ODN 1)/d(Cm(8)GCAm(8)GCG)(ODN 2) in 2 M NaCl and found stereospecific C2'alpha-hydroxylation occurred at G(4) to provide d(CGCrGUGCG), 5. Recently, Rich and co-workers [Schwartz et al. Science 1999, 284, 1841. Schwartz et al. Nat. Struct. Biol. 2001, 8, 761] found that an ubiquitous RNA editing enzyme, adenosine deaminase 1 (ADAR1), and tumor-associated protein DML-1 specifically bind to Z-form DNA. In the present study, we investigate the photoreactivity of octanucleotide ODN 1-2 in Z-form induced by Zalpha, which is the NH(2)-terminal domain of ADAR1 responsible for tight binding of ADAR1. Detailed product analysis revealed that the C2'alpha-hydroxylated products 5 and 6 produced significantly higher yields in Z-form ODN 1-2 induced by Zalpha compared with that in 2 M NaCl. Upon treatment with ribonuclease T1, 5 and 6 were quantitatively hydrolyzed at the 3'-phosphodiester bond of the rG residue to provide d(UGCG) as a common hydrolyzed fragment on the 3' side. Quantitative analysis demonstrated that the amount of photochemically formed 5 and 6 from ODN 1-2 directly correlated with the proportion of Z-form induced by Zalpha or NaCl. These results suggest that this photochemical and enzymatic procedure can be used as a specific probe for the existence of local Z-form structure in cellular DNA.     

Dipyrido[3,2-a:2′,3′-c]phenazine-Tethered Oligo-DNA: Synthesis and Thermal Stability of Their DNA⋅DNA and DNA⋅RNA Duplexes and DNA⋅DNA⋅DNA Triplexes

Dipyrido[3,2-a:2′,3′-c]phenazine (dppz) derivatives were conjugated to 9-mer and 18-mer DNA (ODN) at a site without nucleobase, either at the 5′- or 3′-end or at a internucleotide position, via linkers of 7, 12, or 18 atoms lengths. These dppz-linked ODNs were synthesized using novel backbone glycerol phosphoramidites: Glycerol, serving as artificial nucleoside without nucleobase, was modified to amines 10 , 23 , and 24 , which were suitable for the subsequent key reaction with dppz-carboxylic acid 3 (Schemes 2 and 3). The products of these reactions (see 5 – 7 ) were then transformed to the standard phosphoramidite derivatives (see 27 , 29 , and 30 ) or used for loading on a CPG support (see 28 , 31 , and 32 ). The dppz-modified ODNs were subsequently assembled in the usual manner using automated solid-phase DNA synthesis. The 9-mer ODN-dppz conjugates 35 – 43 were tested for their ability to form stable duplexes with target DNA or RNA strands (D11 ( 60 ) or R11 ( 61 )), while the 18-mer ODN-dppz conjugates 48 – 56 were tested for their ability to form stable triplexes with a DNA target duplex D24⋅D24 ( 62 ) (see Tables 1 and 2). The presence of the conjugated dppz derivative increases the stability of DNA⋅DNA and DNA⋅RNA duplexes, typically by a ΔT_m of 7.3 – 10.9° and 4.5 – 7.4°, respectively, when the dppz is tethered at the 5′- or 3′-terminal (Table 2). The dppz derivatives also stabilize triplexes when attached to the 5′- or 3′-end, with a ΔT_m varying from 3.8 – 11.1° (Table 3). The insertion of a dppz building block at the center of a 9-mer results in a considerably poorer stability of the corresponding DNA⋅DNA duplexes (ΔT_m=0.5 to 4.2°) and DNA⋅RNA duplexes (ΔT_m=−1.5 to 0.9°), while the replacement of one interior nucleotide by a dppz building unit in the corresponding 8-mer ODN does not reveal the formation of any duplex at all. Different types of modifications in the middle of the 18-mer ODN, in general, do not lead to any triplex formation, except when the dppz derivative is tethered to the ODN through a 12-atom-long linker (Entry 9 in Table 3).     

自由基HO2与C2H2反应势能面的理论研究

应用量子化学从头计算和密度泛函理论(DFT)对HO2+C2H2反应体系的反应机理进行了研究.在B3LYP/6-311G**和CCSD(T)/6-311G**水平上计算了HO2+ C2H2反应的二重态反应势能面.计算结果表明,主要反应方式为自由基HO2的H原子和C2H2分子中的C原子结合,经过一系列异构化,最后分解得到主要产物P1 (CH2O+ HCO).此反应是放热反应,化学反应热为-321.99 kJ·mol-1.次要产物为P2 (CO2 +CH3),也是放热反应.     

CH3CH2S自由基H迁移异构化及裂解反应的理论研究

采用密度泛函方法(B3LYP)在6-311+G(d,p)基组水平上研究了CH3CH2S自由基H迁移异构化以及裂解反应的微观动力学机理. 在QCISD(T)/6-311++G(d,p)//B3LYP/6-311+G(d,p)+ZPE水平上进行了单点能校正. 利用经典过渡态理论(TST)与变分过渡态理论(CVT)分别计算了在200~2000 K温度区间内的速率常数kTST和kCVT, 同时获得了经小曲率隧道效应模型(SCT)校正后的速率常数kCVT/SCT. 研究结果表明, CH3CH2S自由基1,2-H迁移、1,3-H迁移、C—C键断裂和β-C—H键断裂反应的势垒ΔE≠分别为149.74, 144.34, 168.79和198.29 kJ/mol. 当温度低于800 K时, 主要发生1,2-H迁移反应, 高于1800 K时, 主要表现为C—C键断裂反应, 在1300—1800 K范围内, 1,3-H迁移反应是优势通道, 在计算的整个温度段内, β-C—H键断裂反应可以忽略.     

Ab initio/GIAO-CCSD(T) study of propenoyl (H2C=CH-CO+) and isopentenoyl ((CH3)2C=CH-CO+) cations and their superelectrophilic protonated dications

Structures of superelectrophilic protonated propenoyl (H2C=CH-COH2+) and isopentenoyl ((CH3)2C=CH-COH2+) dications and their parent cations were calculated using ab initio methods at the MP2/6-311+G and MP2/cc-pVTZ levels. Energies were calculated using Gaussian-2 (G2) theory. The alpha-carbon (Calpha) protonated 3 and 7 were found to be the global minima for protonated propenoyl and isopentenoyl dications, respectively. 13C NMR chemical shifts of the cations were also calculated using the GIAO-CCSD(T), GIAO-MP2 and GIAO-SCF methods. 13C NMR chemical shifts of the related tert-butyl cation ((CH3)3C+) and protonated tert-butyl dication ((CH3)2CCH4(2+)) were also computed at the same level to compare and explore the effect of the additional charge in dications.     

Ab initio studies of alkyl radical reactions: Combination and disproportionation reactions of CH3 with C2H5, and the decomposition of chemically activated C3H8

This paper reports the first quantitative ab initio prediction of the disproportionation/combination ratio of alkyl+alkyl reactions using CH3+C2H5 as an example. The reaction has been investigated by the modified Gaussian-2 method with variational transition state or Rice-Ramsperger-Kassel-Marcus calculations for several channels producing (1) CH4+CH2CH2, (2) C3H8, (3) CH4CH3CH, (4) H2+CH3CHCH2, (5) H2+CH3CCH3, and (6) C2H6+CH2 by H-abstraction and association/decomposition mechanisms through singlet and triplet potential energy paths. Significantly, the disproportionation reaction (1) producing CH4+C2H4 was found to occur primarily by the lowest energy path via a loose hydrogen-bonding singlet molecular complex, H3CHC2H4, with a 3.5 kcal/mol binding energy and a small decomposition barrier (1.9 kcal/mol), instead of a direct H-abstraction process. Bimolecular reaction rate constants for the formation of the above products have been calculated in the temperature range 300-3000 K. At 1 atm, formation of C3H8 is dominant below 1200 K. Over 1200 K, the disproportionation reaction becomes competitive. The sum of products (3)-(6) accounts for less than 0.3% below 1500 K and it reaches around 1%-4% above 2000 K. The predicted rate constant for the disproportionation reaction with multiple reflections above the complex well, k1=5.04 x T(0.41) exp(429/T) at 200-600 K and k1=1.96 x 10(-20) T(2.45) exp(1470/T) cm3 molecule(-1) s(-1) at 600-3000 K, agrees closely with experimental values. Similarly, the predicted high-pressure rate constants for the combination reaction forming C3H8 and its reverse dissociation reaction in the temperature range 300-3000 K, k2(infinity)=2.41 x 10(-10) T(-0.34) exp(259/T) cm3 molecule(-1) s(-1) and k(-2)(infinity)=8.89 x 10(22) T(-1.67)exp(-46 037/T) s(-1), respectively, are also in good agreement with available experimental data.     

Potential energy surfaces, product distributions and thermal rate coefficients of the reaction of O(3P) with C2H4(X1Ag): a comprehensive theoretical study

The potential energy surface for the O((3)P) + C(2)H(4) reaction, which plays an important role in C(2)H(4)/O(2) flames and in hydrocarbon combustion in general, was theoretically reinvestigated using various quantum chemical methods, including G3, CBS-QB3, G2M(CC,MP2), and MRCI. The energy surfaces of both the lowest-lying triplet and singlet electronic states were constructed. The primary product distribution for the multiwell multichannel reaction was then determined by RRKM statistical rate theory and weak-collision master equation analysis using the exact stochastic simulation method. Intersystem crossing of the "hot" CH(2)CH(2)O triplet adduct to the singlet surface, shown to account for about half of the products, was estimated to proceed at a rate of approximately 1.5 x 10(11) s(-1). In addition, the thermal rate coefficients k(O + C(2)H(4)) in the T = 200-2000 K range were computed using multistate transition state theory and fitted by a modified Arrhenius expression as k(T) = 1.69 x 10(-16) x T(1.66) x exp(-331 K/T) . Our computed rates and product distributions agree well with the available experimental results. Product yields are found to show a monotonic dependence on temperature. The major products (with predicted yields at T = 300 K/2000 K) are: CH(3) + CHO (48/37%), H + CH(2)CHO (40/19%), and CH(2)(X(3)B(1)) + H(2)CO (5/29%), whereas H + CH(3)CO, H(2) + H(2)CCO, and CH(4) + CO are all minor (< or =5%).