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The static and dynamic structures of DNA duplexes affected by 5S-Tg (Tg, Thymine glycol) epimers were studied using MD simulations and Markov State Models (MSMs) analysis. The results show that the 5S,6S-Tg base caused little perturbation to the helix, and the base-flipping barrier was determined to be 4.4 kcal mol−1 through the use of enhanced sampling meta-eABF calculations, comparable to 5.4 kcal mol−1 of the corresponding thymine flipping. Two conformations with the different hydrogen bond structures between 5S,6R-Tg and A19 were identified in several independent MD trajectories. The 5S,6R-Tg:O6HO6•••N1:A19 hydrogen bond is present in the high-energy conformation displaying a clear helical distortion, and near barrier-free Tg base flipping. The low-energy conformation always maintains Watson–Crick base pairing between 5S,6R-Tg and A19, and 5S-Tg base flipping is accompanied by a small barrier of ca. 2.0 KBT (T = 298 K). The same conformations are observed in the MSMs analysis. Moreover, the transition path and metastable structures of the damaged base flipping are for the first time verified through MSMs analysis. The data clearly show that the epimers have completely different influence on the stability of the DNA duplex, thus implying different enzymatic mechanisms for DNA repair.

The reaction of HO• radical with DNA is intensively studied both mechanistically and analytically for lesions formation. Several aspects related to the reaction paths of purine moieties with the formation of 5',8-cyclopurines (cPu), 8-oxopurines (8-oxo-Pu), and their relationship are not well understood. In this study, we investigated the reaction of HO• radical with a 21-mer double-stranded oligodeoxynucleotide (ds-ODNs) in γ-irradiated aqueous solutions under various oxygen concentrations and accurately quantified the six purine lesions (i.e., four cPu and two 8-oxo-Pu) by LC-MS/MS analysis using isotopomeric internal standards. In the absence of oxygen, 8-oxo-Pu lesions are only ∼4 times more than cPu lesions. By increasing oxygen concentration, the 8-oxo-Pu and the cPu gradually increase and decrease, respectively, reaching a gap of ∼130 times at 2.01 × 10-4 M of O2. Kinetic treatment of the data allows to estimate the C5' radical competition between cyclization and oxygen trapping in ds-ODNs, and lastly the rate constants of the four cyclization steps. Tailored computational studies by means of dispersion-corrected DFT calculations were performed on the CGC and TAT in their double-strand models for each cPu diastereoisomer along with the complete reaction pathways of the cyclization steps. Our findings reveal unheralded reaction mechanisms that resolve the long-standing issues with C5' radical cyclization in purine moieties of DNA sequences.

Despite their great success in recognizing small molecules in vitro, nucleic acid aptamers are rarely used in clinical settings. This is partially due to the lack of structure-based mechanistic information. In this work, atomistic molecular dynamics simulations are used to study the static and dynamic supramolecular structures relevant to the process of the wild-type (wt) nucleic acid aptamer recognition and binding of ATP. The effects brought about by mutation of key residues in the recognition site are also explored. The simulations reveal that the aptamer displays a high degree of rigidity and is structurally very little affected by the binding of ATP. Interaction energy decomposition shows that dispersion forces from π-stacking between ATP and the G6 and A23 nucleobases in the aptamer binding site plays a more important role in stabilizing the supramolecular complex, compared to hydrogen-bond interaction between ATP and G22. Moreover, metadynamics simulations show that during the association process, water molecules act as essential bridges connecting ATP with G22, which favors the dynamic stability of the complex. The calculations carried out on three mutated aptamer structures confirm the crucial role of the hydrogen bonds and π-stacking interactions for the binding affinity of the ATP nucleic acid aptamer.

Selective C–H oxidation is thought to be a highly suitable strategy for building synthetic blocks and generating bioactive compounds. Noncovalent DNA catalysis for C–H bond cleavage is studied for the first time in order to delineate the so-called ‘oxidation enhancement effect’ on oxidatively generated damage in DNA duplex structures. Herein, DFT methods have been used to gain insight into the reactivity of the 5-hydroxy-6-peroxyl-5,6-dihydrothymine radical using ten single-stranded and duplex DNA models. Reliable M06-2X/6-31+G(d,p) calculations indicate that hydrogen bonding between the complementary base pairs significantly enhances the reactivity of the thymine peroxyl radical in duplex DNA models towards the C1′–H1′ bond. An excellent linear relationship of the reaction activation barrier vs. the difference between the bond dissociation free energies (BDFE) of the C–H and O–H bonds is observed. With the noted role of charge transfer from LPO4′ on 2-deoxyribose to its adjacent C1′–H1′ anti-bonding orbital, a hyperconjugation effect is proposed to explain the reason why the barrier heights are close to each other for the studied duplex DNA models. The difference in the reactivity of the thymine peroxyl radical in the duplex and related single-strand DNA models is rationalized in terms of the preparatory energy and the optimal σC1′–H1′ and oxyl-p based π*-orbital interactions.

supplements for Coordinated path-following control for networked unmanned surface vehicles by Dong-Liang Chen, Guo-Ping Liu, Ru-Bo Zhang and Xingru Qu in International Journal of Advanced Robotic Systems

Oxidative damage to RNA has been linked to change or loss of RNA function and development of many human age-related diseases. However, knowledge on the nature of RNA oxidative damage is relatively limited. In this study, oxidative damage to RNA is investigated under anaerobic and aerobic conditions by exploring the properties and reactions of 5-hydroxyl-2'-uridin-6-yl and its peroxyl diastereoisomers in the RNA strand, respectively. Selective addition of OH to the nucleic base from the 5'-end is studied at the molecular level for the first time, explaining the large number of the 5S-isomer available for further reactions. Our results provide clear evidence that the efficiency of C2'-H2' bond activation in the peroxyl isomers is lower than in the carbon radical species. An exception is observed for the isomer cis-(5S,6R)-A1, whose internucleotidyl H2'-abstraction barrier is far smaller than that in the corresponding C6-yl radical. However, analysis of the equilibrium species distribution reveals that the amount of cis-(5S,6R)-A1 is very small among the peroxyl diastereoisomers, and hence the resulting products from direct strand scission should be a less important component in RNA oxidative damage. The species with maximum distribution is the cis-(5S,6R)-B1 isomer, which is derived from cis-(5S,6R)-A1 and has a moderate intranucleotidyl H2'-abstraction barrier. More importantly, the reaction is mildly exothermic. These results show that the main fraction of the intranucleotidyl H2'-abstraction intermediates can be formed from the cis-(5S,6R)-B1 isomer. The absolute reduction potentials, the hydrogen atom binding energies, and the key structural parameters of the C6-peroxyl species are used to understand the diverse reactivity of the cis-(5S,6R) diastereoisomers toward the C2'-H2' bonds activation. The present study shows that in addition to the selectivity of the OH radical addition, there is a strong correlation between the conformation of the modified uracil base and its reactivity in RNA oxidative damage.

A pair of linear two-dimensional conjugated non-fullerene acceptors, named as TVIDTPDI and TVIDTzPDI, which have the same perylene diimide end-capping groups, but different in two-dimensional conjugated central core (the dithienyl vinylene-fused indacenodithiophene or dithienyl vinylene-fused indacenodithiazole), were successfully synthesized and evaluated as acceptor materials in organic solar cells (OSCs). Such core units in these small acceptors play a decisive role in the formation of the nanoscale separation of the blend films, which were systematically investigated through absorption spectra, electrochemical properties, density functional theory calculations, AFM images, and charge mobility measurement by space-charge-limited current SCLC method. By incorporation of the dithienyl vinylene-fused indacenodithiazole-based core, TVIDTzPDI showed better planarity in the core unit with a dihedral 45.4° and 49.6° angle of between central core and the PDI. Moreover, the TVIDTzPDI blend with PTB7-Th displays higher and more balanced mobilities (μh = 4.56 × 10−4 and μe = 6.12 × 10−4 cm2 V−1 s−1) in comparison with those of TVIDTPDI blend with PTB7-Th. Therefore, the TVIDTzPDI/PTB7-Th based OSCs showed a higher PCE of 2.09% than that of the TVIDTPDI/PTB7-Th devices (1.50%). The purpose of this study is to provide a facile strategy to design PDI-based two-dimensional conjugated small molecular acceptors and understand the impact of installing the two dimensional core and more electron-deficient thiazole unit in such small molecular acceptors.

The multi-autonomous underwater vehicle (AUV) distributed task allocation model of a contract net, which introduces an equilibrium coefficient, has been established to solve the multi-AUV distributed task allocation problem. A differential evolution quantum artificial bee colony (DEQABC) optimization algorithm is proposed to solve the multi-AUV optimal task allocation scheme. The algorithm is based on the quantum artificial bee colony algorithm, and it takes advantage of the characteristics of the differential evolution algorithm. This algorithm can remember the individual optimal solution in the population evolution and internal information sharing in groups and obtain the optimal solution through competition and cooperation among individuals in a population. Finally, a simulation experiment was performed to evaluate the distributed task allocation performance of the differential evolution quantum bee colony optimization algorithm. The simulation results demonstrate that the DEQABC algorithm converges faster than the QABC and ABC algorithms in terms of both iterations and running time. The DEQABC algorithm can effectively improve AUV distributed multi-tasking performance.

A pair of isomeric hexafluorinated oligomers (Th6FSe and Se6FTh), which are with the same aromatic compositions (difluorobenzothiadiazoles central core, IDT units, and donor end-capped groups), but differ in the π-bridge position (selenophene and thiophene), were designed and successfully synthesized. The potential of the resulted oligomers as donor materials for BHJ-OSCs was systematically investigated through optical absorption, AFM, TEM, GIXD, charge mobility measurement, and photovoltaic device fabrication. It was found that the π-bridge sequences in the resulted oligomers play a subtle but key role in device performances. Moreover, as a result of increase of crystalline content and desired phase separation after rapid SVA or combined TA and SVA treatment, the device performance of the resultant devices undergo significant enhancement. Notably, the Se6FTh devices showed a best PCE of ca. 9.3% with SVA+TA treatment, which is the highest PCE of BHJ-OSCs based on donor end-capped oligomers. These primary...

Fluorinated carbonates have attracted increasing attention in high-voltage lithium ion battery applications. Under free and electric fields, their structure-related solvent dynamic properties such as charge and discharge rate, however, are rarely reported. Herein, solutions including linear fluorinated carbonates have been simulated using joint MD/DFT calculations. For the first time, the dielectric constants of the four pure fluorinated carbonates have been predicted to be ca. 5.4 (4: ethyl-2,2,2-trifluoroethyl carbonate)-12.1 (7: di-1,1,2,2,2-pentafluoroethyl carbonate), which are dependent on the number of fluorine atoms. Minor difference in the solvation free energies and few contact ion associations were observed in the ETFEC and DTFEC solvents. Their comparable viscosity values were found through calculations of ion diffusivity and conductivity. In the electric fields, the Li

The synthesis of a series of tetrafluorine-substituted, wide-bandgap, small molecules consisting of various π-conjugated spacers (furan, thiophene, selenophene) between indacenodithiophene as the electron-donating core and the electron-deficient difluorobenzothiadiazole unit is reported and the effect of the π-conjugated spacers on the photovoltaic properties is investigated. The alteration of the π-conjugated spacer enables fine-tuning of the photophysical properties and energy levels of the small molecules, and allows the adjustment of the charge-transport properties, the morphology of the photoactive films, as well as their photovoltaic properties. Moreover, most of these devices exhibit superior device performances after CH2Cl2 solvent annealing than without annealing, with a high fill factor (0.70–0.75 for all cases). Notably, the devices based on the new molecule BIT4FTh (with thiophene as the spacer) show an outstanding PCE of 8.7% (with an impressive FF of 0.75), considering its wide-bandgap (1.81 eV), which is among the highest efficiencies reported so far for small-molecules-based solar cells. The morphologies of the photoactive layers with/without CH2Cl2 solvent annealing are characterized by atomic force microscopy, transmission electron microscopy and two-dimensional grazing incidence X-ray diffraction analysis. The results reported here clearly indicate that highly efficient small-molecules-based solar cells can be achieved through rational design of their molecular structure and optimization of the phase-separated morphology via an adapted solvent–vapor annealing process.

The reactivity of thymine peroxy radicals in DNA and their fate are studied using the reliable DFT methods. The most accessible H1' abstraction by the C6-peroxyl once reported experimentally is effectively competitive to the crosslinking reaction between the C6-peroxyl and the C5 or C6 on the 5'-adjacent thymine base. The rare transfer of the ObH1' group to the C1' radical from the formed hydroperoxide happens with a very strong heat release. Afterwards, the parallel reactions including the H1' and H2' abstractions by the C6-alkoxyl in an inter-nucleotidyl manner lead to direct formation of thymine glycol. After the H1' abstraction by the C6-alkoxyl, the apyrimidinic site can be formed on C1' through effective N1-glycosidic bond rupture. The geometric rearrangements and the orbital interaction between the H donor and the σ-type H acceptor are used to explain the difference of the H2' abstraction barriers by C6-alkoxyl. Hence, new radical reaction paths for the formation of DNA oxidation products are suggested, which are strongly different from the previously suggested paths with the tetraoxide intermediate.

Here we report the synthesis of a pair of D1–A-bridge–D2-bridge–A–D1 type small molecules BIT4FDT and BIT4FTT which have different π-conjugated bridges between indacenodithiophene (IDT) as the electron-donating core and the electron-deficient difluorobenzothiadiazole unit and investigated the effects of the π-conjugated bridges on their photovoltaic properties. We found that the molecule BIT4FTT, containing thieno[3,2-b]thiophene which has two fused thiophene rings as the π-conjugated bridges, exhibits different photophysical properties, HOMO/LUMO energy levels, charge carrier mobilities and morphologies of blend films, and photovoltaic properties compared with the analogous system BIT4FDT which has 2,2′-bithiophene rings as the conjugated bridges. Moreover, the devices based on the two molecules after CH2Cl2 solvent annealing exhibited superior device performance to those not subjected to CH2Cl2 solvent annealing. The PCE of BHJ-OSC devices based on BIT4FTT and PC71BM increased from 5.85% to 7.57% (Jsc = 11.33 mA cm−2, Voc = 0.89 V, and FF = 0.75) after exposure to CH2Cl2 vapor due to the obvious increase of both Jsc and FF. Interestingly, the devices based on BIT4FDT and PC71BM showed a weaker response to solvent vapor annealing and much lower PCEs in comparison with those based on BIT4FTT. The results indicate that highly efficient small-molecule solar cells can be achieved using fused aromatic bridges and a suitable solvent vapor annealing process.

Multiple Unmanned Underwater Vehicles Is a typical combinatorial optimization problem, to achieve multiple AUV, coordinated, collaborative tasks to complete complex jobs subsea. Through analyzing the ant colony optimization algorithm, the paper proposed An Meta-heuristic ant colony optimization algorithm the Implementation to solve the multi AUVs to achieve the task allocation problem, and had simulation test based on the consolidated analyze the advantages of multiple unmanned underwater vehicle .results show that the ant colony optimization algorithms in solving multi-task allocation problem of multiple unmanned underwater vehicle showed a good performance.

A family of narrow band gap extended π-conjugated D2-A2-D1-A1-D1-A2-D2 type small molecules based on diketopyrrolopyrrole derivatives as the stronger acceptor core (A1) coupled with indacenodithiophene (IDT; D1) and difluorobenzothiadiazole (A2) are synthesized, and their properties as donor materials in solution-processed small-molecule organic solar cells are investigated. The impacts of replacing the thiophene ring by a more electron-deficient thiazole ring and inserting thiophene spacer between electron-donating (D1) and electron-accepting (A1 and A2) aromatic moieties on bulk properties, such as the photophysical properties, the HOMO/LUMO energy level, charge carrier mobilities, and the morphologies of blend films, as well as optimization on device performance via solvent vapor annealing are investigated. NDPPFBT shows outstanding efficiencies up to 7.00% after THF vapor annealing for 60 s because of a very high fill factor (FF) of 0.73 and high Voc of 0.89 V. The reported efficiency is among one of ...

A series of tetrafluorine-substituted small molecules with a D1-A-D2-A-D1 linear framework based on indacenodithiophene and difluorobenzothiadiazole is designed and synthesized for application as donor materials in solution-processed small-molecule organic solar cells. The impacts of thiophene π-bridge and multiple fluorinated modules on the photophysical properties, the energy levels of the highest occupied molecular orbitals (HOMO) and lowest unoccupied molecular orbitals (LUMO), charge carrier mobility, the morphologies of blend films, and their photovoltaic properties as electron donor material in the photoactive layer are investigated. By incorporating multiple fluorine substituents of benzothiadiazole and inserting two thiophene spacers, the fill factor (FF), open-circuit voltage, and short-circuit current density are dramatically improved in comparison with fluorinated-free materials. With the solvent vapor annealing treatment, further enhancement in charge carrier mobility and power conversion efficiency (PCE) are achieved. Finally, a high PCE of 8.1% with very-high FF of 0.76 for BIT-4F-T/PC71BM is achieved without additional additive, which is among one of the highest reported for small-molecules-based solar cells with PCE over 8%. The results reported here clearly indicate that high PCE in solar cells based small molecules can be significantly increased through careful engineering of the molecular structure and optimization on the morphology of blend films by solvent vapor annealing.

Combined with practical research project, a novel discharge method using high voltage pulsed power technology was put into practice for a special kind of underground sonic source device. The sonic source guaranteed large power as well as broad and thick sonic wave. Simulation as well as field test confirmed the correctness and effectiveness of the design method.

This paper present a hybrid, hierarchical control architecture for mission re-planning and plan repair of autonomous underwater vehicle (AUV) navigating in dynamic and uncertain marine environment. The proposal carries out a component-oriented part-based control architecture structured in three parts: situation reasoning, re-planning trigger and hierarchical re-planning layer. Situation reasoning using the unstructured real-word information obtained by sorts of sensor detectes and recognizes uncertain event. According the event types and influence degree, the re-planning trigger decides the re-planning level. Hierarchical re-planning layer contains mission re-planning, task re-planning and behavior re-planning. Different re-planning level depends on the result of re-planning trigger. Preliminary versions of the architecture have been integrated and tested in a marine simulation environment.

This paper proposed a novel design method for a special kind of non-linear filters based on building block technique. Due to the introduction of such technique, the filter was successfully separated from the math model of the specific problem to be investigated thus can be designed independently. The difficult but important task of checking the correctness of the deigned filter was solved for a class of non-linear filters based on point selection technique. Simulation results proved the correctness and the effectiveness of the proposed design method.

Speech under G-force which produced when speaker was under different acceleration of gravity was analyzed and researched, considered as principal part and stressed part to research. An isolated word recognition approach was proposed which combined difference subspace means with dynamic time warping technique. The method recognized speech under G-force by constructing a difference subspace to remove the stressed part. Dynamic time warping technique was adopted to make all feature vectors of one word in the training set have equal length, and a corresponding decision criterion was suggested. For a small vocabulary including 15 words, the method obtained the average recognition rate of 98.3%, which almost equal to the rate in normal environment. The method not only worked well in normal conditions but also had good performance for speech under G-force.

Adjustable autonomy is an important mechanism in advanced robotic system. With this mechanism, robot can cooperate with operators, and the efficiency of mission is improved. In order to evaluate the advantages of the adjustable autonomy mechanism, a method of evaluating autonomous performance of Unmanned Surface Vehicle (USV) is proposed. This method considers two aspects in navigation task: the effectiveness of the task and the complexity of the environment. Several specific evaluation indicators are put forward, and the weights of indicators are determined by eigenvector method. Then a comprehensive evaluation value of task effectiveness and the environment complexity are calculated respectively. In two groups of the simulation experiment, USV performs navigation task in complicated marine environment. By comparing experimental data in different two modes, it can be seen that the performance of task in adjustable autonomy mode is better than that in full autonomy mode.

With the portable ECG device develops rapidly, the ECG waveform detection is particularly important. As far as we know, the goal of most researchers is designing a new, real-time, high efficiency, perfect effect ECG detection algorithm. In order to obtain better detection accuracy, a new type of algorithm which combines differential threshold and the wavelet transform is designed, the method uses improved version of the differential threshold method to detect the QRS wave group, and then the P, T-wave is identified by biorthogonal wavelet transform. Dozens of MIT-BIT test data show that the algorithm fully meets the testing requirements, achieve the desired goal and obtain good results.

Data manifold represented in the reality is intrinsically in tensor form and so tensor-based subspace algorithms can preserve the intrinsic spatial structure information. They are beneficial for data representation and classification and have been widely used in recent years. In this paper, a new algorithm called Tensor based Isometric Projection (TIsoProjection) is proposed. The proposed algorithm can naturally describe the spatial relationship between the column vectors and the row vectors. Also it solves the small sample size (SSS) problem. Experiments on the ORL and YaleB demonstrate that the proposed algorithm can achieve higher recognition rate.

DNA strand scission and base release in 3'dTMP, induced by H and OH radical addition to thymine, is studied at the DFT B3LYP/6-31+G(d,p) level in the gas phase and in solution. In particular the mechanism of H atom transfer subsequent to radical formation, from C2' on the sugar to the C6 site on the base, is explored. Bulk solvation is found to lower the barrier by up to 5 kcal mol(-1) and the reaction energy by up to 12 kcal mol(-1) for the hydroxyl radical adducts. The strengths of the N1-C1'(N1-glycosidic bond) and C3'-O(P) bonds are calculated, showing that homolytic bond breaking processes are largely favored in both cases. The barrier for C3'-O(P) bond rupture is approximately 18.2 kcal mol(-1), and its breakage is preferred by 10-15 kcal mol(-1) over that of N1-glycosidic bond cleavage in both the gas phase and solvents, which is consistent with the changes in C3'-O(P) and N1-C1' bond lengths during the H transfer reactions. Mulliken spin densities, NPA charges, and vertical electron affinities are calculated to clarify the reactive properties of the intramolecular H-transfer radicals.

The mechanism of formation of azetidine and oxetane in (6-4) photoproducts between thymine and imine-type cytosine is studied using the MPWB1K and B3LYP functionals together with the 6-31G(d,p) and 6-311++G(d,p) basis sets, in vacuum and bulk solvent. The photoinduced cycloaddition displays favorable energy barriers in the triplet excited state for formation of both azetidine and oxetane. The stepwise cycloaddition in the triplet excited state involves the initial formation of a diradical followed by ring closure via singlet-triplet interaction. The distinguishing feature in the formation of azetidine compared to that of oxetane is an intermediate H3' back-transfer to N3', which is a low-barrier exothermic reaction, and thus shifts the energy balance toward azetidine formation.

Time-delay estimation is an important research topic of sound localization. According to the specificity of time-delay in sound localization, a fast and efficient time-delay estimation algorithm is proposed based on the principle of fast linear cross correlation. Relative to the original time-delay estimation algorithm based on fast linear cross correlation, the proposed algorithm has enormous advantages in the time complexity and space complexity. The computing speed is twice faster than the original time-delay estimation algorithm, while the size of the memory space used is half of the original time-delay estimation algorithm.

Currently, integrating adjustable autonomy framework are increasingly involved in future warfighters in complex task environments. The adjustable autonomy system must know what the user is doing, what needs to be done in the present situation, and the comparative strengths for of the human and the system in each task. Towards reasoning the situation, we are working on situation reasoning in an integrating adjustable autonomy framework of unmanned surface platform. This article provides a summary of various related work, ranging from situation awareness to performance capacity level assessment and impact assessment. In the end, we use visualization to display the process of the situation reasoning.

Swarm Intelligence which emerges from interactions of simple individuals can be used to solve many problems. The foraging task in ant system is often considered as the prototype of cooperative behavior in Swarm Intelligence. The foraging model in swarm robots which considers the random feature of individual robot is built using the mean field method. Then the conflict between robots which influences the performance is observed. To solve this problem, a modified foraging strategy based on pheromone is proposed. From the simulations in Starlogo platform, it is shown that the modified method can reduces the conflict of robots and increase the performance of the system.

Grind-hardening is a new integrated machining technology which utilizes grinding heat to quench the non-quenched steel directly. In this paper, the technology is applied in the process of rack form grinding. A comprehensive numerical model is developed to simulate the temperature distributions of the rack under the dry grind-hardening conditions with finite element method(FEM). The temperature dependency of the thermal properties, the triangular heat distribution of the heat flux, latent heat and the air convection are taken into account. The simulated hardness penetration depth(HPD) is deduced from the local temperature distribution, time history of workpiece according to martensitic phase transformation theory. This provides a reliable method for the proper selection of process parameters in order to produce enough heat at the contact zone, enabling the treatment of the rack.

In order to estimate the energy partition within the workpiece, an integral approximation solution of energy partition is found in the grind-hardening process. Heat transfer models of the abrasive grain, workpiece, chips and fluid were analyzed by using the integral approximation method. The present model can calculate the energy partition with and without film boiling in the grinding zone. The temperature underneath the surface of the workpiece was measured using semi--natural thermocouple method. The workpiece background temperature calculated by the present model agreed very well with the experimental results. Energy partition model can be used to calculate the grinding temperature for controlling thermal damage and predicting the harden layer depth in grinding.

RNA strand scission and base release in 3'-uridine monophosphate (UMP), induced by OH radical addition to uracil, is studied at the DFT B3LYP/6-31+G(d,p) level in the gas phase and in solution. In particular, the mechanism of hydrogen-atom transfer subsequent to radical formation, from C2' on the sugar to the C6 site on the base, is explored. The barriers of (C2'-)H2'(a) abstraction by the C6 radical site range from 11.2 to 20.0 kcal mol(-1) in the gas phase and 14.1 to 21.0 kcal mol(-1) in aqueous solution, indicating that the local surrounding governs the hydrogen-abstraction reaction in a stereoselective way. The calculated N1-C1' (N1-glycosidic bond) and beta-phosphate bond strengths show that homolytic and heterolytic bond-breaking processes are largely favored in each case, respectively. The barrier for beta-phosphate bond rupture is approximately 3.2-4.0 kcal mol(-1) and is preferred by 8-12 kcal mol(-1) over N1-glycosidic bond cleavage in both the gas phase and solution. The beta-phosphate bond-rupture reactions are exothermal in the gas phase and solution, whereas N1-C1' bond-rupture reactions require both solvation and thermal corrections at 298 K to be energetically favored. The presence of the ribose 2'-OH group and its formation of low-barrier hydrogen bonds with oxygen atoms of the 3'-phosphate linkage are highly important for hydrogen transfer and the subsequent bond-breakage reactions.

DNA damages caused by a 5-hydroxy-5,6-dihydrothymine-6-yl radical (5-OHT-6yl) abstracting a C20 hydrogen from a neighboring sugar (inter-H abstraction) have been theoretically investigated using hybrid DFT in gas phase and in water solution. The inter-H abstraction was here shown to be comparable in energy (24 kcal mol 1) with the intra-H abstraction in which the 5-OHT-6yl abstracts a C20 hydrogen from its own sugar. The effect of a neutrally or a negatively charged phosphate group was also studied and the results show no significant impact on the activation energy of the hydrogen abstraction whereas base release and strand break reactions are affected.

Low-energy electrons (LEE) are well known to induce nucleic acid damage. However, the damage mechanisms related to charge state and structural features remain to be explored in detail. In the present work, we have investigated the N1-glycosidic and C3'-O(P) bond ruptures of 3'-UMP (UMP=uridine monophosphate) and the protonated form 3'-UMPH with -1 and zero charge, respectively, based on hybrid density functional theory (DFT) B3 LYP together with the 6-31+G(d,p) basis set. The glycosidic bond breakage reactions of the 3'UMP and 3'UMPH electron adducts are exothermic in both cases, with barrier heights of 19-20 kcal mol(-1) upon inclusion of bulk solvation. The effects of the charge state on the phosphate group are marginal, but the C2'-OH group destabilizes the transition structure of glycosidic bond rupture of 3'-UMPH in the gas phase by approximately 5.0 kcal mol(-1). This is in contrast with the C3'-O(P) bond ruptures induced by LEE in which the charge state on the phosphate influences the barrier heights and reaction energies considerably. The barrier towards C3'-O(P) bond dissociation in the 3'UMP electron adduct is higher in the gas phase than the one corresponding to glycosidic bond rupture and is dramatically influenced by the C2'-OH group and bulk salvation, which decreases the barrier to 14.7 kcal mol(-1). For the C3'-O(P) bond rupture of the 3'UMPH electron adduct, the reaction is exothermic and the barrier is even lower, 8.2 kcal mol(-1), which is in agreement with recent results for 3'-dTMPH and 5'-dTMPH (dTMPH=deoxythymidine monophosphate). Both the Mulliken atomic charges and unpaired-spin distribution play significant roles in the reactions.

DNA strand scission and base release in 3'dTMP, induced by H and OH radical addition to thymine, is studied at the DFT B3LYP/6-31+G(d,p) level in the gas phase and in solution. In particular the mechanism of H atom transfer subsequent to radical formation, from C2' on the sugar to the C6 site on the base, is explored. Bulk solvation is found to lower the barrier by up to 5 kcal mol(-1) and the reaction energy by up to 12 kcal mol(-1) for the hydroxyl radical adducts. The strengths of the N1-C1'(N1-glycosidic bond) and C3'-O(P) bonds are calculated, showing that homolytic bond breaking processes are largely favored in both cases. The barrier for C3'-O(P) bond rupture is approximately 18.2 kcal mol(-1), and its breakage is preferred by 10-15 kcal mol(-1) over that of N1-glycosidic bond cleavage in both the gas phase and solvents, which is consistent with the changes in C3'-O(P) and N1-C1' bond lengths during the H transfer reactions. Mulliken spin densities, NPA charges, and vertical electron affinities are calculated to clarify the reactive properties of the intramolecular H-transfer radicals.

The intramolecular radical cross-link reactions of 8,5′-cyclo-purines and 6,5′-cyclo-pyrimidines have been studied using the DFT B3LYP formalism with 6-31+G(d,p) and 6-311++G(d,p) basis sets, and including CPCM bulk solvation effects. In aqueous solution, the largest free energy barrier is 11.1 kcal/mol for dT → 6,5′-cycloT and the smallest 9.4 kcal/mol for dA → 8,5′-cycloA . Partial radical transfer occurs from the deoxyribose moiety to the connected base upon the formation of the transition structures. The unpaired spin density of the products is mainly localized on N7 in the 8,5′-cyclo-purines and on C5 in the 6,5′-cyclo-pyrimidines. The reaction free energies range from −4.3 kcal/mol (dC → 6,5′-cycloC ) to −9.7 kcal/mol (dG → 8,5′-cycloG ).

Structures and binding energies of the cyclic forms of the uracil–water and thymine–water complexes, in their lowest-lying triplet state, were determined using the UB3LYP/6-311++G(d,p) method. The calculated binding energies, ranging from −20 to −30 kJ/mol, are about 1–3 kJ/mol smaller than those of the corresponding complexes in the singlet state. Proton affinities (PAs) at oxygen atoms and deprotonation enthalpies (DPEs) of the NH and CH groups of triplet uracil and thymine were evaluated at the same level. Compared to the singlet counterparts, DPEs of the NH bonds of triplet pyrimidine nucleobases are found to be slightly smaller, whereas DPEs of the C5H5 and C6H6 bonds are significantly decreased by 100 and 47 kJ/mol, respectively. PAs at oxygen of the triplet bases are slightly increased by 2–7 kJ/mol, relative to the singlet values. Again, it has been found that the most stable cyclic hydrogen bond is formed at the O-site characterized by the smallest PA and at the NH site having the smallest DPE. A certain correlation has been found between the hydrogen bonding energies in the studied complexes and the PAs and DPEs of the sites involved in the interaction. The calculated frequency shifts of hydrogen stretching modes confirm the established bond characteristics. A NBO analysis was also carried to probe further the interaction of the triplet uracil and water. Protonation at O-sites and NH-deprotonation significantly influence the vertical singlet–triplet gap of uracil.

The [2+2] cycloreversion reaction of formylcyclobutane radical anion (c-C4H7-CHO•-) has been investigated at the UB3LYP level with the augmented Dunning's correlation-consistent polarized valence double-ζ basis set supplied with four even-tempered sp shells. Very diffuse p−π*-like singly occupied orbitals (SOMO) are found for the c-C4H7-CHO•- and product CH2CHCHO•- radical anions, necessitating the use of a rather diffuse basis set for mechanistic study. The respective electron affinities of c-C4H7-CHO and CH2CHCHO are calculated to be 5.4 and 16.1 kcal/mol, showing the ability to bind an extra electron. The intermediate structure •(CH2)3CHCHO- is found to be a valence-bound distonic anion apt to the elimination of C2H4. The present two-step “rotating” cycloreversion mechanism for c-C4H7-CHO•- is formally similar to the biradical one for neutral cyclobutane structures, but with evidently lower potential barrier. For efficient electron-attachment catalysis, the extra electron should be trapped by suitable ...

In this paper, the aqueous adiabatic electron affinity (AEA) of Uracil (U) and internal reorganization energy λ i of the self-exchange electron transfer (ET) reaction between Uracil and Uracil anion radical (U − ) in aqueous solution were studied. The effect of the solvation was studied with the recently developed hybrid quantum molecular chemical method, ONIOM. In all calculations, the geometrical optimization for U and U − was performed at B3LYP/6-31++G(d) level. As for the solvent surroundings, the seven water molecules as the first hydration shell were adopted and treated with B3LYP, PM3 and AMBER methods, namely, ONIOM (B3LYP:B3LYP), ONIOM (B3LYP:PM3) and ONIOM (B3LYP:Amber) methods, respectively. The values of AEA for Uracil, predicted by the above three methods, are small positive ones. The geometrical differences between neutral and anion radical molecules of U originate mainly from those of dihedral angles. According to the corresponding dipole moment values, the excess electron in U − should be trapped dominantly by dipole-bound way. The calculated λ i values by ONIOM (B3LYP:B3LYP) and ONIOM (B3LYP:PM3) are close to each other within 0.89%. The λ i value from ONIOM (B3LYP:Amber) is in agreement with the one from SCRF-CPCM very well. Finally, the calculation results of the detailed geometries and molecular interaction mode effect of U and U − and related water molecules in the hydration shell were discussed.

The oxidation damage to telomeric DNA is closely associated with cellular life-span. In order to obtain the information about the factors related to the oxidation damage of telomeric DNA, electron structure of base stacks and effects of base sequence for telomeric ssDNA units of human, plant, and chlamydomonas were studied with a combined method of quantum and molecular mechanics in this paper. The results showed the following. (i) From the energies of the fragments, it can be seen that telomeric ssDNA sequences are more stable than the corresponding non-telomeric ones. B-type telomeric ssDNAs are more stable than the corresponding A-type ones too. The stability of telomeric DNA fragments is mainly from the contribution of G/G and G/A stacks. The results also showed that the electron correlation energy plays an important role in the stacking systems. (ii) The HOMOs of the series –G 3 AT n – ( n =2–4) are mainly localized at 5′-G(1). The LUMOs of the same series are from the contributions from 5′-T(1) and 5′-T(2). (iii) The E HOMO values increase and E LUMO values decrease with the increase of the number n in –G n – and –G 3 AT n – ( n =1–4) for the same ssDNA type (A or B) and sequence direction (telomere or non-telomere), which results in the decrease of Δ E ( E LUMO − E HOMO ) values with the increase of n . The Δ E values of A-type sequences are always smaller than those of the corresponding B-type ones, which means that the former are more easy to be excited. The E HOMO values of A-type fragments are always higher than those of the corresponding B-type ones so that the former are of more stronger tendency to donate electrons than the cases of the latter. (iv) The different effects of base A, stacked at the 3′terminal and 5′terminal of –GGG–, on frontier orbital energies and components were discussed. (v) These results will be helpful to understand the fact that telomeric DNA prefers B-type conformation at the stationary state to make organism more stable for withstanding reactive oxygen species stress from cell metabolism damage.