Potential Energy Surface of Cytosine and Tunneling Between Its Normal and Trans-imino Tautomer

The potential energy surface of H(13) proton in base cytosine of the DNA molecules is calculated at the Gaussian 98 MP2/6-311G(d,p) level. Two potential wells are found. One corresponds to the normal cytosine, while the other corresponds to its trans-imino tautomer. The estimated tunneling probability of the H(13) proton from one well to another well shows that the life time of the proton staying in one of these wells is about 600 yrs. It is too long to let tautomers of cytosine be in thermodynamical equilibrium in a room temperature gas phase experiment.     

氢键质子的运动与胞嘧啶的变异几率

运用Gaussian98 MP2/6 311G(d， p)级的从头计算法计算了DNA分子中胞嘧啶碱基中H13质子的势能曲面。 发现有两个势阱: 其中一个对应正常的胞嘧啶， 而另一个则对应它的顺式亚胺式互变异构体。 质子在这两个势阱的束缚对热扰动是稳定的。 质子在势阱中像单摆一样绕着离它最近的氮原子摆动， 还可以远离氮原子与其它碱基形成氢键。 估算出的H13质子从一个势阱到另一个势阱的穿透几率表明质子呆在其中一个势阱中的寿命大约是6×102 a， 这使胞嘧啶和它的顺式亚胺式互变异构体在室温气相实验中远不能达到热平衡。 对这些结果的生物学意义作了讨论。 The potential energy surface of the H13 proton in base cytosine of theDNA molecules is calculated ab initio at the Gaussian98 MP2/6 311G(d， p) level. Two potential wells are found. One corre sponds to the normal cytosine， while the other corresponds to its imino tautomer. The bindings of the proton in these wells are stable enough against the thermo disturbance. The motions of the proton in these wells are oscillations around the nearest nitrogen atom like the pendulum， and may move far away from the nitrogen atom to form the hydrogen bond with other bases. The estimated tunneling probability of the H13 proton from one well to another well shows that the life time of the proton staying in one of these wells is about 6×102 a. It is too long to let tautomers of cytosine be in thermodynamical equilibrium in a room temperature gas phase experiment. The biological significance of these results is discussed.     

Effective proton-proton interaction and metallization of hydrogen

The effective proton-proton interaction in metallic hydrogen has been calculated for various densities. In the potential of this interaction, which can be represented in the form of a series of perturbation theory in the electron-proton interaction, the second- and third-order terms are taken into account. The second-order term gives a comparatively shallow potential well with one minimum. The position of the minimum corresponds to the equilibrium mutual position of protons in metallic hydrogen. When the third-order term is additionally taken into account, the potential has two characteristic minima; the position of one of them corresponds to the distance between the protons in a hydrogen molecule. The depths of these potential wells depend on the density of the system. At fairly high densities, only the potential well corresponding to the equilibrium position of protons in the metallic phase holds in the proton-proton potential. Owing to the presence of two minima in the effective proton-proton potential, the density of hydrogen at the point of transition to the metallic state can be estimated. Analysis of the effective proton-proton interaction makes it also possible to estimate the possibility of the existence of metallic hydrogen in a stable state at quite low temperatures.     

洛莫司汀的1H、13C NMR全归属

应用~1H NMR、~(13)C NMR、DEPT135、~1H-~(13)C HMBC、~1H-~(13)C HSQC、~1H-~1H COSY和~1H-~1H NOESY等多种NMR技术,对文献报道的洛莫司汀(Lomustine)~1H和~(13)C NMR数据进行了修正与补充;特别是应用2D NMR对重叠程度较高的环己烷区进行了指认归属,并确定了其空间构型.     

NMR studies on hydrogen bonding and proton transfer in Mannich bases

A review of studies on the ortho Mannich bases containing various substituents in the phenyl ring on the basis of¹H,¹³C and¹⁵N nuclear magnetic resonance (NMR) spectra in various solvents over the temperature range 110–298 K is presented. Some new results are also included. The data gathered so far show that there is some critical (inversion) range of ΔpK _a (= pK _a(NH⁺) − pK _a(OH)) in which the proton transfer equilibrium appears. This inversion range is well reflected in the behaviour of secondary deuterium isotope effect in¹³C NMR spectra. A strong temperature effect on the strength of hydrogen bonding should be emphasized. The¹H chemical shift for trichloroderivative increases from 13.5 at room temperature up to 17 ppm at 130 K when the proton is equally shared between the bridging atoms (¹ J(¹H,¹⁵N) = 30–40 Hz). The potential for the proton motion in such bridges is discussed taking into account the behaviour in the ultraviolet and infrared spectra. The role of dimerization in proton transfer equilibria is shown. In addition the rotation of OH groups involved in hydrogen bond formation and nitrogen pyramidal inversion was studied by the¹H dynamical NMR spectra.     

A 13C field-cycling NMR relaxometry investigation of proton tunnelling in the hydrogen bond: dynamic isotope effects, the influence of heteronuclear interactions and coupled relaxation

Concerted double proton transfer in the hydrogen bonds of a carboxylic acid dimer has been studied using 13C field-cycling NMR relaxometry. Heteronuclear 13C-1H dipolar interactions dominate the 13C spin-lattice relaxation which is significantly influenced by the polarisation state of the 1H Zeeman reservoir. The methodology of field-cycling experiments for such heteronuclear spin-coupled systems is studied experimentally and theoretically, including an investigation of various saturation-recovery and polarisation-recovery pulse sequence schemes. A theoretical model of the spin-lattice relaxation of this coupled system is presented which is corroborated by experiment. Spectral density components with frequencies omega(C), omega(C) + omega(H), and omega(C) - omega(H) are mapped out experimentally from the magnetic field dependence of the 13C and 1H spin-lattice relaxation and the proton transfer rate at low temperature is determined from their widths. Any dynamic isotope effect on the proton tunnelling in the hydrogen bond arising from 13C enrichment in the skeletal framework of the dimer is found to be smaller than experimental uncertainties (approximately 5%).     

Proton radioactivity within the generalized liquid drop model with various versions of proximity potentials

In the present work, we systematically investigate the proton radioactivity half-lives of spherical proton emitters adopting a generalized liquid drop model(GLDM) with 16 different proximity potentials, of which the proximity potential Prox.77-13 gives the closest results to the experimental data. Combined with the previous conclusion that the GLDM with proximity potential Prox.77-13 can also best describe α decay half-lives, which makes the model more uniform and consistent.Further, we use the proximity potential Prox.77-13 in GLDM to predict the proton radioactivity half-lives of 14 spherical proton emitters that are allowed energetically but not yet observed experimentally or specifically quantified. Finally, we research the Geiger-Nuttall law for proton radioactivity. The results reveal that the Geiger-Nuttall law can also be well used to study the proton radioactivity half-lives of isotopes with the same orbital angular momentum l.     

具有潜在抗菌活性的环丙沙星衍生物的NMR谱研究

利用核磁共振谱,通过¹H-¹]H COSY, gHMBC and APT (Attached Proton Test)实验对所合成的新化合物1环丙基-6-氟-7-（4-苯乙酰氨基硫代甲酰基-1-哌嗪基）-1,4-二氢-4-氧代喹啉-3-羧酸的NMR谱进行了分析,并对其谱峰进行了详细归属.     

Polaron in a superlattice with δ-like potentials

The problem of the polaron spectrum is studied in a superlattice having narrow quantum wells and relatively wide potential barriers. A δ-like superlattice potential is chosen to solve the problem. This model is adequate, if the penetration depth of the electron wave function into the barrier region is much greater than the width of the quantum well. A weak-coupling polaron at low temperature is studied. Only volume phonons are considered. Expressions are obtained for the polaron mass and the shift of the polaron energy under these assumptions. To test the model, numerical calculations were performed for an InAs-GaSb superlattice, whose quantum wells are quite deep (the energy offset of the conduction bands in InAs and GaSb equals 830 meV), narrow (the width of a quantum well corresponds to the width of an InAs monolayer 6 Å), and the barrier width corresponding to the thickness of the GaSb layers equals 150 Å. The assumption that the penetration depth of the wave function is much greater than the barrier width holds well.     

Helicobacter pylori determination in non-municipal drinking water and epidemiological findings

BACKGROUND: Studies conducted in Europe as well as in North and South America have tried to link Helicobacter pylori colonization with the drinking water supply, especially since H. pylori is known to survive quite well in water. METHODS: In 2000, a cohort of 1884 grade-two children from two rural counties surrounding the city of Leipzig, Germany (77.4% of the 1991/1992 birth cohort) were tested for H. pylori colonization using the [13C]urea breath test. A parent-completed questionnaire elicited details on living conditions and lifestyle habits including questions on the children's drinking water from sources other than public water supplies, swimming in natural waters, etc. In a second independent study, samples of well water, taken from 157 private wells still used in the two counties, were being tested for the presence of H. pylori, using polymerase chain reaction (PCR) method to determine relevant target DNA fragments of H. pylori. RESULTS: In county I, 5.7% of the children and in county II 6.6% tested H. pylori-positive. Cluster analyses of the questionnaire data in both counties pointed to 'drinking water from other than municipal sources', as the closest H. pylori-associated cluster variable. The cluster estimations were supported by odds ratio (OR) calculations with an OR=16.4 (95% confidence interval (CI) 3.1,...,88.5) for county I and OR=4.0 (95% CI 1.3,...,12.4) for county II. The PCR analyses showed H. pylori DNA fragments in 10.8% of the wells in county I and 9.2% in county II. The detection limit was set at 10 DNA copies corresponding to 125 bacteria/L, the average infestation of these wells was 931 bacteria/L. CONCLUSION: Despite the fact that the microbiological and epidemiological data do not correspond except that both studies were conducted in the same geographical areas, the independent findings of H. pylori in well water in the same general areas where children do seem to drink water other than from the public water supply suggests that water may be an important source of H. pylori infection.     

A new two-dimensional pulse sequence for T(2)* measurements of protons in (13)C isotopomers

A new two-dimensional pulse sequence for T(2)* measurement of protons directly coupled to (13)C spins is proposed. The sequence measures the tranverse relaxation time of heteronuclear proton single-quantum coherence under conditions of free precession and is therefore well suited to evaluate relaxation losses of proton magnetization during preparation delays of heteronuclear pulse experiments in analytical NMR. The relevant part of the pulse sequence can be inserted as a "building block" into any direct or inverse detecting H,C correlation pulse sequence if proton spin-spin relaxation is to be investigated. In this contribution, the building block is inserted into a HETCOR as well as into a HMQC pulse sequence. Experimental results for the HETCOR-based sequence are given.     

Selective dephasing of OH and NH proton magnetization based on (1)H chemical-shift anisotropy recoupling

A method for selectively suppressing the signals of OH and NH protons in (1)H combined rotation and multiple-pulse spectroscopy (CRAMPS) and in (1)H-(13)C heteronuclear correlation (HETCOR) solid-state NMR spectra is presented. It permits distinction of overlapping CH and OH/NH proton signals, based on the selective dephasing of the magnetization of OH and NH protons by their relatively large (1)H chemical-shift anisotropies. For NH protons, the (14)N-(1)H dipolar coupling also contributes significantly to this dephasing. The dephasing is achieved by a new combination of heteronuclear recoupling of these anisotropies with (1)H homonuclear dipolar decoupling. Since the 180 degrees pulses traditionally used for heteronuclear dipolar and chemical-shift anisotropy recoupling would result in undesirable homonuclear dephasing of proton magnetization, instead the necessary inversion of the chemical-shift Hamiltonian every half rotation period is achieved by inverting the phases of all the pulses in the HW8 multiple-pulse sequence. In the HETCOR experiments, carefully timed (13)C 180 degrees pulses remove the strong dipolar coupling to the nearby (13)C spin. The suppression of NH and OH peaks is demonstrated on crystalline model compounds. The technique in combination with HETCOR NMR is applied to identify the CONH and NH-CH groups in chitin and to distinguish NH and aromatic proton peaks in a peat humin.     

Collision site effect on the radiation dynamics of cytosine induced by proton

By combing the time-dependent density functional calculations for electrons with molecular dynamics simulations for ions (TDDFT-MD) nonadiabatically in real time, we investigate the microscopic mechanism of collisions between cytosine and low-energy protons with incident energy ranging from 150 eV to 1000 eV. To explore the effects of the collision site and the proton incident energy on irradiation processes of cytosine, two collision sites are specially considered, which are N and O both acting as the proton receptors when forming hydrogen bonds with guanine. Not only the energy loss and the scattering angle of the projectile but also the electronic and ionic degrees of freedom of the target are identified. It is found that the energy loss of proton increases linearly with the increase of the incident energy in both situations, which are 14.2% and 21.1% of the incident energy respectively. However, the scattering angles show different behaviors in these two situations when the incident kinetic energy increases. When proton collides with O, the scattering angle of proton is larger and the energy lost is more, while proton captures less electrons from O. The calculated fragment mass distribution shows the high counts of the fragment mass of 1, implying the production of H⁺ fragment ion from cytosine even for proton with the incident energy lower than keV. Furthermore, the calculated results show that N on cytosine is easier to be combined with low-energy protons to form NH bonds than O.     

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.     

Resolution enhancement in spectra of natural products dissolved in weakly orienting media with the help of 1H homonuclear dipolar decoupling during acquisition: application to 1H-13C dipolar couplings measurements

In weakly orienting media such as poly-gamma-benzyl-L-glutamate (PBLG) a polymer that forms a chiral liquid crystal in organic solvents, the spectral resolution for embedded molecules is usually poor because of numerous (1)H, (1)H dipolar couplings that generally broaden proton spectra. Therefore (1)H, (13)C dipolar couplings are difficult or impossible to measure. Here, we incorporate Flip-Flop decoupling during detection into an HSQC experiment. Flip-Flop removes the (1)H, (1)H dipolar couplings and scales the chemical shifts of the protons as well as the (1)H, (13)C dipolar couplings during detection. A resolution gain by a factor 1.5-4.2 and improved signal intensity by an average factor of 1.6-1.7 have been obtained. This technique is demonstrated on (+)-menthol dissolved in a PBLG/CDCl(3) phase.     

Influence of external electric field on the transfer of protons in hydrogen-bonded systems

The LCAO MO self-consistent field method in combination with the 6-31** basis set is used to calculate sections of the potential energy surface for a proton in the NH₃…HCl system in the presence of an external electrostatic field. The field strength is varied in the range of 0.000 to 0.017 a. u. In the absence of the field, the potential of the proton in the isolated complex has one well, the N–Cl distance is equal to 2.92 Å, and the NH₃…H–Cl bond is a hydrogen bond. With increasing distance between the N and Cl atoms, a second well appears in the potential, with the well near the Cl atom remaining deeper. In the presence of an external electric field, with increasing its strength, the depth of the well near the N atom increases, while the height of the barrier for proton transfer from the chlorine to the nitrogen atom decreases. At a certain field strength, the well near the nitrogen atom becomes deeper than that near the chlorine atom, so the proton moves to the nitrogen, making the complex ionic. Thus, the external electric field can influence the type of chemical bond in NH₃…HCl system.     

Experiments and low-order modelling of intermittent transitions between clockwise and anticlockwise spinning thermoacoustic modes in annular combustors

Annular combustion chambers of gas turbines and aircraft engines are subject to unstable azimuthal thermoacoustic modes leading to high amplitude acoustic waves propagating in the azimuthal direction. For certain operating conditions, the propagating direction of the wave switches randomly. The strong turbulent noise prevailing in gas turbine combustors is a source of random excitation for the thermoacoustic modes and can be the cause of these switching events. A low-order model is proposed to describe qualitatively this property of the dynamics of thermoacoustic azimuthal modes. This model is based on the acoustic wave equation with a destabilizing thermoacoustic source term to account for the flame’s response and a stochastic term to account for the turbulent combustion noise. Slow-flow averaging is applied to describe the modal dynamics on times scales that are slower than the acoustic pulsation. Under certain conditions, the model reduces formally to a Fokker-Planck equation describing a stochastic diffusion process in a potential landscape with two symmetric wells: One well corresponds to a mode propagating in the clockwise direction, the other well corresponds to a mode propagating in the anticlockwise direction. When the level of turbulent noise is sufficient, the stochastic force makes the mode jump from one well to the other at random times, reproducing the phenomenon of direction switching. Experiments were conducted on a laboratory scale annular combustor featuring 12 hydrogen-methan flames. System identification techniques were used to fit the model on the experimental data, allowing to extract the potential shape and the intensity of the stochastic excitation. The statistical predictions obtained from the Fokker–Planck equation on the mode’s behaviour and the direction switching time are in good agreement with the experiments.     

Experimental aspects of proton NMR spectroscopy in solids using phase-modulated homonuclear dipolar decoupling

In this paper we demonstrate experimentally that the continuously phase-modulated homonuclear decoupling sequence DUMBO-1 is suitable for high-resolution proton NMR spectroscopy of rigid solids. Over a wide range of experimental conditions, we show on the model sample L-alanine as well as on small peptides that proton linewidths of less than 0.5 ppm can be obtained under DUMBO-1 decoupling. In particular the DUMBO-1 sequence yields well resolved proton spectra both at slow and fast MAS. The DUMBO-1 decoupling scheme can in principle be inserted in any multi-nuclear or multi-dimensional solid-state NMR experiment which requires a high-resolution 1H dimension. An example is provided with the 13C-1H MAS-J-HMQC experiment.