Dissociative electron attachment to phosphoric acid esters: the direct mechanism for single strand breaks in DNA

We use dibutyl phosphate to simulate the behavior of the phosphate group in DNA towards the attack of low energy electrons. We find that the compound undergoes effective dissociative electron attachment within a low energy resonant feature at 1 eV and a further resonance peaking at 8 eV. The dissociative electron attachment (DEA) reactions are associated with the direct cleavage of the C-O and the P-O bond but also the excision of the PO-, PO3-, H2PO3- units. For the phosphate group coupled in the DNA network these reactions represent single strand breaks. We hence propose that the most direct mechanism of single strand breaks occurring in DNA at subexcitation energies (< 4 eV) is due to DEA directly to the phosphate group.     

低能电子致DNA链断裂的纳剂量蒙特卡罗模拟

为了对DNA损伤进行纳剂量蒙特卡罗模拟,先根据D.Emfietzoglou给出的介电响应理论和Born修正模型计算了低能电子与液态水的非弹性反应截面,在Geant4-DNA的基础上建立了纳剂量蒙特卡罗程序的物理模块,同时参照国际纳剂量蒙特卡罗程序使用的模型参数建立了纳剂量蒙特卡罗程序的前化学模块、化学模块、DNA几何模块及DNA损伤模块。利用本程序,采用H. Nikjoo给出的对电子均匀照射DNA情形的模拟方法,还模拟计算了不同能量电子均匀照射DNA所导致的DNA链断裂产额,并与已公布的实验数据进行比对,二者符合良好。     

低能电子致DNA链断裂的纳剂量蒙特卡罗模拟

为了对DNA损伤进行纳剂量蒙特卡罗模拟,先根据D.Emfietzoglou给出的介电响应理论和Born修正模型计算了低能电子与液态水的非弹性反应截面,在Geant4-DNA的基础上建立了纳剂量蒙特卡罗程序的物理模块,同时参照国际纳剂量蒙特卡罗程序使用的模型参数建立了纳剂量蒙特卡罗程序的前化学模块、化学模块、DNA几何模块及DNA损伤模块。利用本程序,采用H. Nikjoo给出的对电子均匀照射DNA情形的模拟方法,还模拟计算了不同能量电子均匀照射DNA所导致的DNA链断裂产额,并与已公布的实验数据进行比对,二者符合良好。     

Role of secondary low-energy electrons in the concomitant chemoradiation therapy of cancer

Solid films of DNA with and without the chemotherapeutic agent cisplatin bonded to guanine were bombarded with electrons of 1, 10, 100, and 60,000 eV causing single and double strand breaks. In the presence of cisplatin this damage was increased by factors varying from 1.3 to 4.4 owing to an increase in bond dissociation triggered by the formation of transient anions. This mechanism may lie at the basis of the efficiency of concomitant cisplatin-radiation therapy.     

Real-time observation of nonadiabatic surface dynamics: the first picosecond in the dissociation of NO on iridium

Ultrafast laser pulses on Ir{111} cause a highly temperature-dependent redshift of the intramolecular stretch frequency of adsorbed NO. The time-resolved spectral changes are driven by charge transfer of hot electrons to the NO 2pi*d antibonding orbital, which leads to bending of NO and internal bond weakening. The nonadiabatic change in the NO adsorption geometry follows the charge transfer within a time scale of 700 femtoseconds. This geometrical change is the same as the mechanism predicted for thermally induced dissociation.     

Effect of a magnetic field on the track structure of low-energy electrons: a Monte Carlo study

The increasing use of MRI-guided radiation therapy evokes the necessity to investigate the potential impact of a magnetic field on the biological effectiveness of therapeutic radiation beams. While it is known that a magnetic field, applied during irradiation, can improve the macroscopic absorbed dose distribution of electrons in the tumor region, effects on the microscopic distribution of energy depositions and ionizations have not yet been investigated. An effect on the number of ionizations in a DNA segment, which is related to initial DNA damage in form of complex strand breaks, could be beneficial in radiation therapy. In this work we studied the effects of a magnetic field on the pattern of ionizations at nanometric level by means of Monte Carlo simulations using the Geant4-DNA toolkit. The track structure of low-energy electrons in the presence of a uniform static magnetic field of strength up to 14 T was calculated for a simplified DNA segment model in form of a water cylinder. In the case that no magnetic field is applied, nanodosimetric results obtained with Geant4-DNA were compared with those from the PTB track structure code. The obtained results suggest that any potential enhancement of complexity of DNA strand breaks induced by irradiation in a magnetic field is not related to modifications of the low-energy secondary electrons track structure.     

DNA strand breaks induced by concerted interaction of H radicals and low-energy electrons

We propose a mechanism of DNA single strand breaks induced by low-energy electrons. Density functional theory calculations have been performed on a neutral, hydrogenated, and/or negatively charged nucleotide of cytosine in the gas phase to identify barriers for the phosphate-sugar O–C bond cleavage. Attachment of the first excess electron induces intermolecular proton transfer to cytosine. The resulting neutral radical of hydrogenated cytosine binds another excess electron, and the excess charge is localized primarily on the C6 atom. A barrier encountered for proton transfer from the C2’ atom of the adjacent sugar unit to the C6 atom of cytosine is 3.6 and 5.0 kcal/mol, based on the MPW1K and B3LYP electronic energies corrected for zero-point vibrations, respectively. The proton transfer is followed by a barrier-free sugar-phosphate C–O bond cleavage. The proton transfer is impossible for the neutral nucleotide, as there is no local minimum for the product. In the case of anionic and hydrogenated nucleotides the same barrier determined at the B3LYP level is as large as 29.3 and 22.4 kcal/mol respectively. This illustrates that the consecutive hydrogenation and electron attachment make the nucleotide of cytosine susceptible to a strand break. The rate of the C–O bond cleavage in the anion of hydrogenated nucleotide of cytosine is estimated to be ca. 10¹⁰  s^-1. The proposed mechanism proceeds through bound anionic states, not through metastable states with finite lifetimes and discrete energy positions with respect to the neutral target. The results suggest that at least for DNA without hydration even very low-energy electrons may cleave the DNA backbone.     

Effect of intense, ultrashort laser pulses on DNA plasmids in their native state: strand breakages induced by in situ electrons and radicals

Single strand breaks are induced in DNA plasmids, pBR322 and pUC19, in aqueous media exposed to strong fields generated using ultrashort laser pulses (820 nm wavelength, 45 fs pulse duration, 1 kHz repetition rate) at intensities of 1-12 TW?cm(-2). The strong fields generate, in situ, electrons and radicals that induce transformation of supercoiled DNA into relaxed DNA, the extent of which is quantified. Introduction of electron and radical scavengers inhibits DNA damage; results indicate that OH radicals are the primary (but not sole) cause of DNA damage.     

DNA damage induced by low-energy electrons: electron transfer and diffraction

Thin films of the short single strand of DNA, GCAT, in which guanine (G) or adenine (A) have been removed, were bombarded under vacuum by 4 to 15 eV electrons. The fragments corresponding to base release and strand breaks (SB) were analyzed by high performance liquid chromatography and their yields compared with those obtained from unmodified GCAT. From such a comparison, it is shown that, using GCAT as a model system, (1) most SB result from electron capture by DNA bases followed by electron transfer to the phosphate group and (2) the initial capture probability depends on the coherence of the electron wave within the tetramer.     

Ion-induced electron production in tissue-like media and DNA damage mechanisms

This work is the first stage in the development of an inclusive approach to calculation of the DNA damage caused by irradiation of biological tissue by ion/proton beams. The project starts with an analysis of ionization caused by the projectiles and the characteristics of secondary electrons produced in tissue-like media. We consider interactions with the medium on a microscopic level and this allows us to obtain the energy spectrum and abundance of secondary electrons as functions of the projectile’s kinetic energy. The physical information obtained in this analysis is related to biological processes responsible for the DNA damage induced by the projectile. In particular, we consider double strand breaks of DNA caused by secondary electrons and free radicals, and local heating in the ion’s track. The heating may enhance the biological effectiveness of electron/free radical nteractions with the DNA and may even be considered as an independent mechanism of DNA damage. Numerical estimates are performed for the case of carbon-ion beams. The obtained dose-depth curves are compared with results of the MCHIT model based on the GEANT4 toolkit.     

Bond- and site-selective loss of H- from pyrimidine bases

Electron attachment to gas phase thymine and uracil leads to H- loss within a broad and structured feature in the energy range between about 5 and 12 eV consisting of 4 overlapping resonances. By using thymine and uracil methylated at the N1 and N3 positions, respectively, and taking into account recent results from partly deuterated thymine, we find that by tuning the electron energy, H- loss turns out to be not only bond selective, i.e., (C-H) versus (N-H) bonds, but also site selective (N1 versus N3 site). Such a bond and site selectivity by energy has not been observed before in dissociative electron attachment. Implications for the mechanism of strand breaks observed in plasmid DNA are considered.     

笼状团簇Mg12B24结构与性质的密度泛函理论研究

运用杂化密度泛函B3LYP方法,在6-31G*水平上优化得到了一种Mg₁₂B₂₄团簇的笼状稳定结构,其IR最强吸收峰位于205.23 cm^-1,Raman谱的最强峰位于242.63 cm^-1. Mg₁₂B₂₄团簇笼状结构中B原子主要是sp杂化轨道参与成键,Mg原子主要是s轨道参与成键.团簇中B原子层堆积了大量的电子,表明MgB₂的超导作用主要发生在B原子层;B原子层电子存在较强的离域性,也为超导电性提供了条件;Mg原子起了提供电子的作用.     

Anisotropic Stark effect of carbon monoxide: emergent orbital cooperativity

ABSTRACT

Applying external electric fields to molecules gives rise to spectral shifting and splitting, a phenomenon known as the Stark effect. However, a fundamental question of how electronic structures of molecules are modified by electric fields is still not well understood. By applying electric fields to a carbon monoxide molecule, herein we have successfully addressed the fundamental question at orbital scales and discovered that the Stark effect exhibits anisotropic characters depending on the direction of the electric fields with respect to the molecular axis. Based on the fact that applying electric fields along the molecular axis always preserved the orthogonality between the sigma and pi electrons, we found that orbital resemblance-based cooperativity can only operate within either the sigma system in which sigma electrons somehow prefer to resemble each other or the pi electron system in which the 1π electrons experience polarization-based self-resemblance. However, switching the electric field vertical to the molecular axis breaks down the orthogonality between the sigma system and pi electron systems, opening up electronic channels that allow σ electron systems to resemble π electrons. Such orbital cooperativity represents a new physical effect beyond the conventional Stark effect. Moreover, we have found that applying electric fields to the molecule would modify its molecular orbital diagram, depending on the directions of the electric fields; the electric field along the carbon-to-oxygen direction basically retains the MO diagram of the free CO molecule, with noticeable intra-orbital electron redistributions, whereas the oxygen-to-carbon electric field does create new states of molecular orbital contributions.     

Dynamics of hydrogen in hydrogenated amorphous silicon

The problem of hydrogen diffusion in hydrogenated amorphous silicon (a-Si:H) is studied semiclassically. It is found that the local hydrogen concentration fluctuations-induced extra potential wells, if intense enough, lead to the localized electronic states in a-Si:H. These localized states are metastable. The trapping of electrons and holes in these states leads to the electrical degradation of the material. These states also act as recombination centers for photo-generated carriers (electrons and holes) which in turn may excite a hydrogen atom from a nearby Si-H bond and breaks the weak (strained) Si-Si bond thereby apparently enhancing the hydrogen diffusion and increasing the light-induced dangling bonds.     

Frequency-upconverted organic crystal

The fluorescent characteristics of Troger's base have been investigated experimentally. A one-photon-induced fluorescent spectrum was observed, and the peak wavelength was at 337 nm with a full width at half-maximum of ~85nm . The violet radiation of the Troger's base crystal could result from the pi(*) -pi transition of the benzenoid pi bond. Two-photon-pumped frequency-upconverted fluorescence was obtained, which is a wideband emission with the main peak wavelength at 337 nm and a subordinate peak. Donor groups and acceptor groups of electrons in the aromatic rings strengthen the two-photon-pumped frequency-upconverted fluorescence.     

Quantum thermal conductance of electrons in a one-dimensional wire

We use an electron thermometer to measure the temperature rise of approximately 2 x 10(5) electrons in a two-dimensional box, due to heat flow into the box through a ballistic one-dimensional (1D) constriction. Using a simple model we deduce the thermal conductance kappa(Vg) of the 1D constriction, which we compare to its electrical conductance characteristics; for the first four 1D subbands the heat carried by the electrons passing through the wire is proportional to its electrical conductance G(Vg). In the vicinity of the 0.7 structure this proportionality breaks down, and a plateau at the quantum of thermal conductance pi(2)k(2/B)T/3h is observed.     

介质势垒放电(DBD)等离子体中NO荧光发射谱研究

利用介质阻挡放电 (DBD)等离子体技术对大气污染物NO分子进行了光谱研究 ,得到了低气压条件下放电等离子体在 2 1 0～ 2 80nm光谱范围内的荧光发射谱。该谱明显的表现为双峰结构 ,谱线均成对出现 ,强度分布符合Frank Condon原理 ,且最大峰值位置出现在 2 36nm处 ,将该组谱线归属为NO分子的A2 ΣA →X2 Π1 / 2 ,2 / 3 跃迁。荧光产生过程为 :基态NO分子与高能电子发生非弹性碰撞被激发至激发态A2 Σ 后自发跃迁回基态同时辐射出荧光。通过测量等离子体中NO分子和N2 分子 337nm谱线强度随时间的变化关系 ,初步证实了放电等离子体中存在的NO分子的分解机制为 :e NO→N O e,N NO→N2 O ,O NO→NO2 hν。     

不同LET辐射致DNA集簇性损伤的研究

利用辐照质粒DNA构象变化的分子模型,以DNA糖苷酶Fpg和AP核酸内切酶EndoIII识别并切割辐射所致DNA碱基损伤,将其转换为DNA断裂损伤,通过电泳分析DNA分子构象变化,研究比较γ射线、质子和7Li离子诱发DNA集簇性损伤。50Gy以上高剂量γ辐射对质粒DNA的损伤主要表现为单链断裂(SSB)和很少比例的双链断裂(DSB),并能产生一定水平的集簇性损伤。相比之下,高能质子束和高LET的7Li离子直接所致DNA的断裂损伤以及所产生的集簇性碱基损伤比γ射线的要严重,质子10Gy照射就可诱发明显的集簇损伤。     

DNA damage induced by laser-hematoporphyrin derivative

Irradiation caused DNA single-strand breaks in S180 cells in the presence oflaser-hematoporphyrin derivative(HPD).The number of single strand breaks was 3.69 ×10~(10)break dolton~(-1).The analysis of base composition of DNA showed that the effect of laser-HPDirradiation on guanine was the highest,being 5-12 times as high as those of the three others(adenine,cytosine and thymine).It was different from the nature of DNA damage caused by γ-ray irradiation.