Water induced weakly bound electrons in DNA

We have studied the effect of humidity on the electronic properties of DNA base pairs. We found that the hydrogen links of the nucleobases with water molecules lead to a shift of the pi electron density from carbon atoms to nitrogen atoms and can change the symmetry of the wave function for some nucleobases. As a result, the orbital energies are shifted which leads to a decrease in the potential barrier for the hole transfer between the G-C and A-T pairs from 0.7 eV for the dehydrated case to 0.123 eV for the hydrated. More importantly, the pi electron density redistribution activated by hydration is enhanced by the intrastrand interactions. This leads to a modification of the nucleobase chemical structures from the covalent type to a resonance structure with separated charges, where some pi electrons are not locked up into the covalent bonds. Within the (G-C)(2) sequences, there is overlapping of the electronic clouds of such unlocked electrons belonging to the stacked guanines, that significantly increases the electron coupling between them to V(DA)=0.095 eV against the V(DA)=0.025 eV for the dehydrated case. Consequently, the charge transfer between two guanines within the (G-C)(2) sequences is increased by 250 times due to hydration. The presence of nonbonded electrons suppress the band gap up to approximately 3.0 eV, that allows us to consider DNA as a narrow band gap semiconductor.     

New electronic and magnetic properties emerging from adsorption of organized organic layers

New electronic and magnetic properties are induced by the adsorption of closed packed monolayers on solid substrates. For many thiolated molecules self-assembled on gold, a surprisingly large paramagnetism is observed. In the case where the layers are made from chiral molecules, in addition an unexpectedly large electronic dichroism is observed, which manifests itself as spin specific electron transmission. This dichroism was observed for monolayers made from polyalanine and from DNA. Self-assembled monolayers of double-stranded DNA oligomers on gold interact with polarized electrons similarly to a strong and oriented magnetic field. The direction of the field for right-handed DNA is away from the substrate. Moreover, the layer shows very high paramagnetic susceptibility. Interestingly, thiolated single-stranded DNA oligomers on gold do not show this effect. All the observations can be rationalized by assuming organization induced charge transfer between the substrate and the organic layer. The charge transfer results in spin alignment of the transferred electrons/holes. While for achiral molecules the spin alignment varies among the domains, in the case of monolayer made from chiral molecules the alignment is the same across the entire sample. When magnetic field is applied, large magnetic moment is observed that results from orbital magnetism.     

Ground state structures and excited state dynamics of pyrrole-water complexes: ab initio excited state molecular dynamics simulations

Structures of the ground state pyrrole-(H2O)n clusters are investigated using ab initio calculations. The charge-transfer driven femtosecond scale dynamics are studied with excited state ab initio molecular dynamics simulations employing the complete-active-space self-consistent-field method for pyrrole-(H2O)n clusters. Upon the excitation of these clusters, the charge density is located over the farthest water molecule which is repelled by the depleted pi-electron cloud of pyrrole ring, resulting in a highly polarized complex. For pyrrole-(H2O), the charge transfer is maximized (up to 0.34 a.u.) around approximately 100 fs and then oscillates. For pyrrole-(H2O)2, the initial charge transfer occurs through the space between the pyrrole and the pi H-bonded water molecule and then the charge transfer takes place from this water molecule to the sigma H-bonded water molecule. The total charge transfer from the pyrrole to the water molecules is maximized (up to 0.53 a.u.) around approximately 100 fs.     

Environmental effects on the enhancement in natural and damaged DNA nucleobase acidity because of discrete hydrogen-bonding interactions

The present study uses density functional theory to carefully consider the effects of the environment on the enhancement in (natural and damaged) DNA nucleobase acidities because of multiple hydrogen-bonding interactions. Although interactions with one small molecule can increase the acidity of the nucleobases by up to 60 kJ mol-1 in the gas phase, the maximum increase in enzymatic-like environments is expected to be approximately 40 kJ mol-1, which reduces to approximately 30 kJ mol-1 in water. Furthermore, the calculated (simultaneous) effects of two, three, or four molecules are increasingly less than the sum of the individual (additive) effects with an increase in the number and acidity of the small molecules bound or the dielectric constant of the solvent. Regardless of these trends, our calculations reveal that additional hydrogen-bonding interactions will have a significant effect on nucleobase acidity in a variety of environments, where the exact magnitude of the effect depends on the properties of the small molecule bound, the nucleobase binding site, and the solvent. The maximum increase in nucleobase acidity because of interactions with up to four small molecules is approximately 80 kJ mol-1 in enzymatic-like environments (or 65 kJ mol-1 in water). These results suggest that hydrogen-bonding interactions likely play an important role in many biological processes by changing the physical and chemical properties of the nucleobases.     

Sigma and pi contributions to the induced magnetic field: indicators for the mobility of electrons in molecules

The authors discuss the role of the sigma and pi contributions to the induced magnetic field for simple hydrocarbons containing a double or a triple bond, as well as for benzene and cyclobutadiene. While the magnetic field induced by the sigma electrons is short-ranged, the pi system is responsible for the formation of long-range cones. These cones influence the chemical shift of atoms by additional shielding (for aromatic) or deshielding (for antiaromatic molecules) contributions. While the hydrogen atoms of benzene are found to lie within the deshielded region of the magnetic field induced by the pi electrons, they are shielded by the total induced magnetic field. The induced magnetic field of the pi electrons support Pople's model on the basis of first-principles calculations.     

Amphoteric doping of carbon nanotubes by encapsulation of organic molecules: electronic properties and quantum conductance

In order to investigate and optimize the electronic transport processes in carbon nanotubes doped with organic molecules, we have performed large-scale quantum electronic structure calculations coupled with a Green's function formulation for determining the quantum conductance. Our approach is based on an original scheme where quantum chemistry calculations on finite systems are recast to infinite, non-periodic (i.e., open) systems, therefore mimicking actual working devices. Results from these calculations clearly suggest that the electronic structure of a carbon nanotube can be easily manipulated by encapsulating appropriate organic molecules. Charge transfer processes induced by encapsulated organic molecules lead to efficient n- and p-type doping of the carbon nanotube. Even though a molecule can induce p and n doping, it is shown to have a minor effect on the transport properties of the nanotube as compared to a pristine tube. This type of doping therefore preserves the intrinsic properties of the pristine tube as a ballistic conductor. In addition, the efficient process of charge transfer between the organic molecules and the nanotube is shown to substantially reduce the susceptibility of the pi electrons of the nanotube to modification by oxygen while maintaining stable doping (i.e., no dedoping) at room temperature.     

Discrepancy between the spin distribution and the magnetic ground state for a triaminoxyl substituted triphenylphosphine oxide derivative

The magnetic interaction and spin transfer via phosphorus have been investigated for the tri-tert-butylaminoxyl para-substituted triphenylphosphine oxide. For this radical unit, the conjugation existing between the pi* orbital of the NO group and the phenyl pi orbitals leads to an efficient delocalization of the spin from the radical to the neighboring aromatic ring. This has been confirmed by using fluid solution high-resolution EPR and solid state MAS NMR spectroscopy. The spin densities located on the atoms of the molecule could be probed since (1)H, (13)C, (14)N, and (31)P are nuclei active in NMR and EPR, and lead to a precise spin distribution map for the triradical. The experimental investigations were completed by a DFT computational study. These techniques established in particular that spin density is located at the phosphorus (rho=-15x10(-3) au), that its sign is in line with the sign alternation principle and that its magnitude is in the order of that found on the aromatic C atoms of the molecule. Surprisingly, whereas the spin distribution scheme supports ferromagnetic interactions among the radical units, the magnetic behavior found for this molecule revealed a low-spin ground state characterized by an intramolecular exchange parameter of J=-7.55 cm(-1) as revealed by solid state susceptibility studies and low temperature EPR. The X-ray crystal structures solved at 293 and 30 K show the occurrence of a crystallographic transition resulting in an ordering of the molecular units at low temperature.     

Inelastic electron interaction (attachment/ionization) with deoxyribose

We have investigated experimentally the formation of anions and cations of deoxyribose sugar (C(5)H(10)O(4)) via inelastic electron interaction (attachment/ionization) using a monochromatic electron beam in combination with a quadrupole mass spectrometer. The ion yields were measured as a function of the incident electron energy between about 0 and 20 eV. As in the case of other biomolecules (nucleobases and amino acids), low energy electron attachment leads to destruction of the molecule via dissociative electron attachment reactions. In contrast to the previously investigated biomolecules dehydrogenation is not the predominant reaction channel for deoxyribose; the anion with the highest dissociative electron attachment (DEA) cross section of deoxyribose is formed by the release of neutral particles equal to two water molecules. Moreover, several of the DEA reactions proceed already with "zero energy" incident electrons. In addition, the fragmentation pattern of positively charged ions of deoxyribose also indicates strong decomposition of the molecule by incident electrons. For sugar the relative amount of fragment ions compared to that of the parent cation is about an order of magnitude larger than in the case of nucleobases. We determined an ionization energy value for C(5)H(10)O(4) (+) of 10.51+/-0.11 eV, which is in good agreement with ab initio calculations. For the fragment ion C(5)H(6)O(2) (+) we obtained a threshold energy lower than the ionization energy of the parent molecular ion. All of these results have important bearing for the question of what happens in exposure of living tissue to ionizing radiation. Energy deposition into irradiated cells produces electrons as the dominant secondary species. At an early time after irradiation these electrons exist as ballistic electrons with an initial energy distribution up to several tens of electron volts. It is just this energy regime for which we find in the present study rather characteristic differences in the outcome of electron interaction with the deoxyribose molecule compared to other nucleobases (studied earlier). Therefore, damage induced by these electrons to the DNA or RNA strands may start preferentially at the ribose backbone. In turn, damaged deoxyribose is known as a key intermediate in producing strand breaks, which are the most severe form of lesion in radiation damage to DNA and lead subsequently to cell death.     

Magnetic and Optoelectronic Properties of Gold Nanocluster–Thiophene Assembly

Nanohybrids consisting of Au nanocluster and polythiophene nanowire assemblies exhibit unique thermal‐responsive optical behaviors and charge‐transfer controlled magnetic and optoelectronic properties. The ultrasmall Au nanocluster enhanced photoabsorption and conductivity effectively improves the photocurrent of nanohybrid based photovoltaics, leading to an increase of power conversion efficiency by 14 % under AM 1.5 illumination. In addition, nanohybrids exhibit electric field controlled spin resonance and magnetic field sensing behaviors, which open up the potential of charge‐transfer complex system where the magnetism and optoelectronics interact.     

Electron density investigation of a push-pull ethylene (C14H24N2O2.H2O) by X-ray diffraction at T = 21 K

The electron charge distribution in a strongly twisted push-pull ethylene [PPE, 3-(1,3-diisopropyl-2-imidazolidinylidene)-2,4-pentanedione] has been determined by low temperature (T = 21 K) single-crystal X-ray diffraction analysis. The derived electronic properties are consistent with a zwitterionic molecule, as indicated by a charge transfer of 0.82(16) e from the push to the pull moieties and a charge polarization of 0.29(7) e on the olefinic bond. A dipole moment of 12(3) D has been determined, which compares well with ab initio theoretical results in terms of both modulus and orientation. The second moments, which have also been obtained with good precision, characterize PPE as a highly quadrupolar molecule. The special electronic features of the molecule confer particular topological properties to the electron density distribution, as evidenced by comparison with "standard" organic molecules. The crystallographic asymmetric unit of the present system includes one water molecule, which is hydrogen bonded to PPE. Its topological properties have also been investigated, together with an analysis of the hydrogen bonds involved.     

并五苯分子电荷注入导致自旋极化的密度泛函理论研究

用密度泛函理论研究了不带自旋的空穴注入并五苯后体系的自旋相关特性. 电荷注入后并五苯分子中存在自发自旋极化行为. 当注入电荷量达一定程度,分子磁矩随注入电荷量的增加呈线性增长,最大磁矩可达1μB. 注入电荷和并五苯分子的相互作用导致分子体系结构发生变化,同时电荷密度分布及自旋密度分布也发生了变化. 注入电荷先填充自旋劈裂的碳原子pz轨道.     

Charge transfer in the TCNQ-sexithiophene complex

Molecular crystals from thiophene molecules can be doped with TCNQ-F4 molecules for use in all-organic optoelectronic and semiconductor devices. The charge transfer and the molecular orbital energy level formation in between these two organic molecules are investigated here by density functional theory calculations. The isolated molecules are calculated nonbonded and bonded together, forming a charge transfer complex (CTC). The relaxed structure of the complex shows essentially coplanar and centered molecules with the alpha-sexithiophene rings tilted alternatingly by 4.8 degrees. The bond formation of these molecules results in a charge transfer of approximately 0.4 e from the alpha-sexithiophene to the TCNQ-F4 molecule. The highest occupied molecular orbital-lowest unoccupied molecular orbital gap width is reduced as compared to the isolated molecules due to the newly formed orbitals in the CTC. Upon adsorption on a Au(111) surface, electrons are transferred onto the molecule complex, thereby causing the molecular levels to align asymmetric with respect to the charge neutrality level. The theoretical results for the single molecule and CTC layer are compared to experimental photoemission and scanning tunneling spectroscopy results.     

Parameters for excess electron transfer in DNA. Estimation using unoccupied Kohn-Sham orbitals and TD DFT

We show that the energetics and electronic couplings for excess electron transfer (EET) can be accurately estimated by using unoccupied Kohn-Sham orbitals (UKSO) calculated for neutral pi stacks. To assess the performance of different DFT functionals, we use MS-PT2 results for seven pi stacks of nucleobases as reference data. The DFT calculations are carried out by using the local spin density approximation SVWN, two generalized gradient approximation functionals BP86 and BLYP, and two hybrid functionals B3LYP and BH&HLYP. Best estimations within the UKSO approach are obtained by the B3LYP and SVWN methods. TD DFT calculations provide less accurate values of the EET parameters as compared with the UKSO data. Also, the excess charge distribution in the radical anions is well described by the LUMOs of neutral systems. In contrast, spin-unrestricted DFT calculations of radical anions considerably overestimate delocalization of the excess electron. The excellent results obtained for the ground and excited states of the radical anions (excitation energy, transition dipole moment, electronic coupling, and excess electron distribution) by using UKSO of neutral dimers suggest an efficient strategy to calculate the EET parameters for DNA pi stacks.     

A three-state model for the photophysics of guanine

The nonadiabatic photochemistry of the guanine molecule (2-amino-6-oxopurine) and some of its tautomers has been studied by means of the high-level theoretical ab initio quantum chemistry methods CASSCF and CASPT2. Accurate computations, based by the first time on minimum energy reaction paths, states minima, transition states, reaction barriers, and conical intersections on the potential energy hypersurfaces of the molecules lead to interpret the photochemistry of guanine and derivatives within a three-state model. As in the other purine DNA nucleobase, adenine, the ultrafast subpicosecond fluorescence decay measured in guanine is attributed to the barrierless character of the path leading from the initially populated 1(pi pi* L(a)) spectroscopic state of the molecule toward the low-lying methanamine-like conical intersection (gs/pi pi* L(a))CI. On the contrary, other tautomers are shown to have a reaction energy barrier along the main relaxation profile. A second, slower decay is attributed to a path involving switches toward two other states, 1(pi pi* L(b)) and, in particular, 1(n(O) pi*), ultimately leading to conical intersections with the ground state. A common framework for the ultrafast relaxation of the natural nucleobases is obtained in which the predominant role of a pi pi*-type state is confirmed.     

The role of intermolecular polarization for the stability of lithium intercalation compounds of alpha- and beta-perylene

Lithium intercalation compounds of alpha- and beta-perylene are investigated by photoelectron spectroscopy. Spectroscopic data together with a Born-Haber cycle provide information on the formation enthalpy of those materials. This approach allows understanding the amount of charge transferred from the alkali metal atoms to the pi system, and illuminates the role of molecular versus solid-state properties in the formation of the intercalation compounds. In the bulk of alpha-perylene material, molecular dimerization survives upon intercalation which reduces the Madelung energy of the intercalation compound but increases the electron-accepting capability of the organic system and facilitates the ionization of lithium atoms in the molecular solid environment. The lower ionization potential results in a larger charge transfer (about two electrons per molecule) in alpha-perylene compared to the monomeric system, beta-perylene.     

Magnetless Device for Conducting Three‐Dimensional Spin‐Specific Electrochemistry

Electron spin states play an important role in many chemical processes. Most spin‐state studies require the application of a magnetic field. Recently it was found that the transport of electrons through chiral molecules also depends on their spin states and may also play a role in enantiorecognition. Electrochemistry is an important tool for studying spin‐specific processes and enantioseparation of chiral molecules. A new device is presented, which serves as the working electrode in electrochemical cells and is capable of providing information on the correlation of spin selectivity and the electrochemical process. The device is based on the Hall effect and it eliminates the need to apply an external magnetic field. Spin‐selective electron transfer through chiral molecules can be monitored and the relationship between the enantiorecognition process and the spin of electrons elucidated.     

Ring currents in the porphyrins: pi shielding, delocalisation pathways and the central cation

It is shown that the ipsocentric orbital-based model explains how the charge of the central cation drives the delocalisation pathway in metalloporphyrins. A positive charge +Ze at the centre of the porphin ring gives rise to a two-way radial transfer of charge within the pi structure of the porphin macrocycle. This manifests itself in a change of pathway of the global pi current, as Z increases from Z = 0, from an inner- through a bifurcated- to an outer-pathway. Changes of pathway can be interpreted in terms of a specific pi shielding effect whereby electrons in high-lying pi orbitals are screened from the central charge by the electrons in lower-lying orbitals of the same symmetry. These changes in pi structure are essentially independent of accompanying changes in the sigma structure.     

What governs the charge transfer in DNA? The role of DNA conformation and environment

Charge transfer in DNA has received much attention in the last few years due to its role in oxidative damage and repair in DNA and also due to possible applications of DNA in nanoelectronics. Despite intense experimental and theoretical efforts, the mechanism underlying long-range hole transport is still unresolved. This is in particular due to the sensitive dependence of charge transfer on the complex structure and dynamics of DNA and the interaction with the solvent, which could not be addressed adequately in the modeling approaches up to now. In this work, we study the factors governing hole transfer in detail, using a DFT-based fragment-orbital method, which allows to compute the charge transfer parameters along multinanosecond molecular dynamics simulations. Environmental effects are captured using a hybrid quantum mechanics-molecular mechanics (QM/MM) coupling scheme. This methodology allows to analyze several factors responsible for charge transfer in DNA in detail. The fluctuation of counterions, strongly counterbalanced by the surrounding water, leads to large oscillations of onsite energies, which govern the energetics of hole propagation along the DNA strand. In contrast, the electronic couplings depend only on DNA conformation and are not affected by the solvent. In particular, the onsite energies are strongly correlated between neighboring nucleobases, indicating that a conformational-gating type of mechanism may be induced by the collective environmental degrees of freedom.     

EPR study of radiation damage to DNA irradiated with synchrotron soft X-rays around nitrogen and oxygen K-edge

In order to obtain detailed insights into the physicochemical mechanism of DNA damage induction, “in situ” measurement of electron paramagnetic resonance (EPR) signal from DNA constituent nucleobases, guanine and adenine, has been performed in a vacuum using monochromatic synchrotron soft X-rays. We found that short-lived unpaired electron species arise only during irradiation to the evaporated thin film on a surface. The EPR spectrum of the short-lived species significantly depends on the photon energy irradiated, and the spin concentration obtained from the EPR spectra shows a similar fine structure to the X-ray photoabsorption spectra (X-ray absorption near edge structure; XANES). For the adenine sample, the spin concentration alters strikingly by water absorption on the sample surface. Trapping of photo- or Auger electrons into a newly generated potential in the nucleobases as the consequence of photoelectric effect is suggested as mechanisms of the induction of the short-lived species.     

Self-Organization of Magnetic Nanoparticles and Inclusion of Hydrogen by Borohydride Reduction

 Different structures of the interglobular space or voids between self-organized nanoparticles lead to differences in the measurable magnetic properties of single-domain particle chains of similar composition, grain size, and amorphous structure of the single globules. The volumes and radii of nanoparticles obtained by application of a magnetic field (3 to 15 nm) are larger than those determined without application of a magnetic field during the borohydride reduction process. Two types of hydrogen containing nanotubes with diameters of up to 2 (small-size containers) and 5 nm (large-size containers) are produced using as a driving force the domain wall formation energy between ferromagnetic nanoparticles with quantum size effected dimensions prepared by this reduction method at room temperature and ambient atmosphere. Nanoscale hydrogen containers can be used instead of MeH nanoparticle electrodes as perfect energy charge transfer media of high efficiency (close to 100%) using Li ion electrolytes. No influence on the electrode temperature and no participation of OH⁻ and H₂O in the main charge/discharge transfer reactions were observed.