Energy loss of hydrogen- and helium-ion beams in DNA: calculations based on a realistic energy-loss function of the target

We have calculated the electronic energy loss of proton and α-particle beams in dry DNA using the dielectric formalism. The electronic response of DNA is described by the MELF-GOS model, in which the outer electron excitations of the target are accounted for by a linear combination of Mermin-type energy-loss functions that accurately matches the available experimental data for DNA obtained from optical measurements, whereas the inner-shell electron excitations are modeled by the generalized oscillator strengths of the constituent atoms. Using this procedure we have calculated the stopping power and the energy-loss straggling of DNA for hydrogen- and helium-ion beams at incident energies ranging from 10 keV/nucleon to 10 MeV/nucleon. The mean excitation energy of dry DNA is found to be I = 81.5 eV. Our present results are compared with available calculations for liquid water showing noticeable differences between these important biological materials. We have also evaluated the electron excitation probability of DNA as a function of the transferred energy by the swift projectile as well as the average energy of the target electronic excitations as a function of the projectile energy. Our results show that projectiles with energy ?100 keV/nucleon (i.e., around the stopping-power maximum) are more suitable for producing low-energy secondary electrons in DNA, which could be very effective for the biological damage of malignant cells.     

Unravelling coherent dynamics and energy dissipation in photosynthetic complexes by 2D spectroscopy

Spectroscopic studies of light harvesting and the subsequent energy conversion in photosynthesis can track quantum dynamics happening on the microscopic level. The Fenna-Matthews-Olson complex of the photosynthetic green sulfur bacteria Chlorobium tepidum is a prototype efficient light-harvesting antenna: it stores the captured photon energy in the form of excitons (collective excitations), which are subsequently converted to chemical energy with almost 100% efficiency. These excitons show an elaborate relaxation pattern involving coherent and incoherent pathways. We make use of the complex chirality and fundamental symmetries of multidimensional optical signals to design new sequences of ultrashort laser pulses that can distinguish between coherent quantum oscillations and incoherent energy dissipation during the exciton relaxation. The cooperative dynamical features, which reflect the coherent nature of excitations, are amplified. The extent of quantum oscillations and their timescales in photosynthesis can be readily extracted from the designed signals, showing that cooperativity is maintained during energy transport in the Fenna-Matthews-Olson complex. The proposed pulse sequences may also be applied to reveal information on the robustness of quantum states in the presence of fluctuating environments in other nanoscopic complexes and devices.     

Solid state approach in biophoton research

Main characteristics of the delayed luminescence (DL) emitted in the seconds range from biological systems is analyzed. The correlation between change in DL and cell's organization, and similarity with some characteristics of DL from solid state system suggest to connect DL in biological system to decay of collective electron states, formed during energy and charge transport along the macromolecular ordered structures which form the cell. Results of a proposed soliton model are discussed, together with some phenomenological evidence which emphasize the possibility of using DL measurements as an intrinsic probe in biophysical investigations.     

Suppressing Energy Loss due to Triplet Exciton Formation in Organic Solar Cells: The Role of Chemical Structures and Molecular Packing

In the most efficient solar cells based on blends of a conjugated polymer (electron donor) and a fullerene derivative (electron acceptor),ultrafast formation of charge‐transfer (CT) electronic states at the donor‐acceptor interfaces and efficient separation of these CT states into free charges, lead to internal quantum efficiencies near 100%. However, there occur substantial energy losses due to the non‐radiative recombinations of the charges, mediated by the loweset‐energy (singlet and triplet) CT states; for example, such recombinations can lead to the formation of triplet excited electronic states on the polymer chains, which do not generate free charges. This issue remains a major factor limiting the power conversion efficiencies (PCE) of these devices. The recombination rates are, however, difficult to quantify experimentally. To shed light on these issues, here, an integrated multi‐scale theoretical approach that combines molecular dynamics simulations with quantum chemistry calculations is employed in order to establish the relationships among chemical structures, molecular packing, and non‐radiative recombination losses mediated by the lowest‐energy charge‐transfer states.     

Protein strain in blue copper proteins studied by free energy perturbations.

Free energy perturbations have been performed on two blue copper proteins, plastocyanin and nitrite reductase. By changing the copper coordination geometry, force constants, and charges, we have estimated the maximum energy with which the proteins may distort the copper coordination sphere. By comparing this energy with the quantum chemical energy cost for the same perturbation on the isolated copper complex, various hypotheses about protein strain have been tested. The calculations show that the protein can only modify the copper-methionine bond length by a modest amount of energy-<5 kJ/mol-and they lend no support to the suggestion that the quite appreciable difference in the copper coordination geometry encountered in the two proteins is a result of the proteins enforcing different Cu-methionine bond lengths. On the contrary, this bond is very flexible, and neither the geometry nor the electronic structure change appreciably when the bond length is changed. Moreover, the proteins are rather indifferent to the length of this bond. Instead, the Cu(II) coordination geometries in the two proteins represent two distinct minima on the potential surface of the copper ligand sphere, characterized by different electronic structures, a tetragonal, mainly sigma-bonded, structure in nitrite reductase and a trigonal, pi-bonded, structure in plastocyanin. In vacuum, the structures have almost the same energy, and they are stabilized in the proteins by a combination of geometric and electrostatic interactions. Plastocyanin favors the bond lengths and electrostatics of the trigonal structure, whereas in nitrite reductase, the angles are the main discriminating factor. Proteins 1999;36:157-174.     

Solitons and energy transfer along protein molecules

It is shown that the energy released in the hydrolysis of ATP molecules can be transferred in the form of vibration solitons along α-helical protein molecules. The vibration solitons are collective excitations travelling along a chain of successively arranged peptide groups and corresponding to amide I vibrations. The exceptional stability of solitons in one-dimensional structures can account for the small probability of their energy transforming into that of disordered heat motion.     

Paramagnetic effects in NMR for protein structures and ensembles: Studies of metalloproteins

Paramagnetic effects on the NMR spectra are known to encode information on structure, electronic properties and dynamics hardly accessible with any other technique, especially in the field of biological systems. Paramagnetism-based restraints are conveniently used for the de novo determination of protein structures, the structural refinement starting from crystallographic models, and for the determination of the internal arrangement of domains with known structures. Conformational variability can also be profitably interrogated including the possibility of uncovering the presence of states with very low population. The recent advances in the quantum chemistry treatment of paramagnetic NMR effects has provided new momentum to the field, allowing for the refinement of protein structures at the metal coordination site to an unprecedented resolution.     

Do we live in a quantum world? Advances in multidimensional coherent spectroscopies refine our understanding of quantum coherences and structural dynamics of biological systems

The issue of quantum effects in biological functions reduces to determining the relevant length and/or time scales over which phase relationships (coherence) in the wave properties of matter are conserved and lead to observable interference effects. Recent advances in femtosecond laser-based two-dimensional spectroscopy and coherent control have made it possible to directly determine the relevant timescales of quantum coherence in biological systems and even manipulate such effects, respectively, and also provide direct information on the interactions between the different degrees of freedom (electronic and nuclear) with sufficient time resolution to catch the very chemical processes driving biological functions in action. The picture that is emerging is that there are primary events in biological processes that occur on timescales commensurate with quantum coherence effects.     

Phototautomerism of the GC base pair of DNA

Electronic spectra and ground and excited state electronic structures of normal G and rare tautomeric G1z.sbnd;C1 base pairs as well as of the individual rare tautomeric bases (purines and pyrimidines) have been studied using the VE-PPP molecular orbital method. The nature and consequences of the lowest energy purine-localized and purine to pyrimidine charge transfer type π?π1 singlet excitations of the base pairs have been investigated. The results indicate that in these excited states, particularly in the charge transfer excited state, the probability for the GC base pair to change over to G1C1 would be larger than in the ground state. The likeliness of the relevance of results obtained experimentally by other workers from the study of a model system to the GC base pair is discussed.     

Protein contributions to redox potentials of homologous rubredoxins: an energy minimization study.

The energetic contributions of the protein to the redox potential in an iron-sulfur protein are studied via energy minimization, comparing homologous rubredoxins from Clostridium pasteurianum, Desulfovibrio gigas, Desulfovibrio vulgaris, and Pyrococcus furiosus. The reduction reaction was divided into 1) the change in the redox site charge without allowing the protein to respond and 2) the relaxation of the protein in response to the new charge state, focusing on the latter. The energy minimizations predict structural relaxation near the redox site that agrees well with that in crystal structures of oxidized and reduced P. furiosus rubredoxin, but underpredicts it far from the redox site. However, the relaxation energies from the energy-minimized structures agree well with those from the crystal structures, because the polar groups near the redox site are the main determinants and the charged groups are all located at the surface and thus are screened dielectrically. Relaxation energies are necessary for good agreement with experimentally observed differences in reduction energies between C. pasteurianum and the other three rubredoxins. Overall, the relaxation energy is large (over 500 mV) from both the energy-minimized and the crystal structures. In addition, the range in the relaxation energy for the different rubredoxins is large (300 mV), because even though the structural perturbations of the polar groups are small, they are very near the redox site. Thus the relaxation energy is an important factor to consider in reduction energetics.     

Collective Electronic Excitations in Thin Ag Films on Ni(111)

The collective electronic excitations in thin Ag films deposited onto the Ni(111) surface were studied by high-resolution electron energy loss spectroscopy. A broad loss peak at 7.7 eV was assigned to the Ag multipole plasmon, in excellent agreement with calculations based on s-d polarization model. Ag multipole plasmon was excited only at grazing incidence. Furthermore, a strong dependence on the impinging energy exists. Multipole plasmon could be measured only for a very strict range of primary electron beam energies and it was excited by electrons scattered at a reflection plane located just underneath the jellium edge. Such mode was found to be dramatically more sensible to the state of the surface with respect to ordinary surface plasmon. Moreover, we report experimental evidence of interference effects in surface plasmon excitation.     

Resonance Raman enhancement of FeIV=O stretch in high-valent iron porphyrins: an insight from TD-DFT calculations

Density functional theory (DFT) has been applied to explain the origin of resonance Raman enhancement associated with the Fe(IV)=O stretch observed in iron(IV)oxo porphyrins. To accomplish this electronic excitations of the Im-(Por)Fe(IV)=O model were computed in the 1.5-4.0 eV spectral range using time-dependent DFT (TD-DFT). All electronic transitions having dominant pi-->pi* character were analyzed and assigned in terms of one-electron excitations. It was found that the most intense Soret band has a multi-component character, but the pi (a(2u))-->pi*(d(xz),d(yz)) and pi (a(1u))-->pi*(d(xz),d(yz)) electronic excitations are primarily responsible for observed resonance enhancement of the Fe(IV)=O stretch.     

肼基单胺氧化酶抑制剂活性与电子结构构效关系的计算分析

采用量子化学方法,在DFT/B3LYP/6-31G*基组水平上对肼基单胺氧化酶抑制剂进行了几何构型优化和电子结构计算.根据计算结果,分析了肼基单胺氧化酶抑制剂的抑制活性与电子结构的构效关系,结果表明,肼基单胺氧化酶抑制剂衍生物的活性与最低空轨道的能量E_LUMO与最高占据轨道的能量E_HOMO的差值、分子偶极矩和苯环上5位碳原子电荷密度有显著相关性.     

Theoretical analysis of the electronic properties of the sex pheromone and its analogue derivatives in the female processionary moth Thaumetopoea pytiocampa

In the present work, the distribution of the electronic charge density of the natural sex pheromone, the (Z)-13-hexadecen-11-ynyl acetate, in the female processionary moth, Thaumetopoea pytiocampa, and its nine analogue derivatives was studied within the framework of the Density Functional Theory and the Atoms in Molecules (AIM) Theory at B3LYP/6-31G *//B3LYP/6-31++G * * level. Additionally, molecular electrostatic potential (MEP) maps of the previously mentioned compounds were computed and compared. Furthermore, the substitution of hydrogen atoms from the methyl group in the acetate group by electron withdrawing substituents (i.e., halogen atoms) as well as the replacement effect of hydrogen by electron donor substituents (+I effect) as methyl group, were explored. The key feature of the topological distribution of the charge density in analogue compounds, such as the variations of the topological properties encountered in the region formed by neighbouring atoms from the substitution site were presented and discussed. Using topological parameters, such as electronic charge density, Laplacian, kinetic energy density, and potential energy density evaluated at bond critical points (BCP), we provide here a detailed analysis of the nature of the chemical bonding of these molecules. In addition, the atomic properties (population, charge, energy, volume, and dipole moment) were determined on selected atoms. These properties were analyzed at the substitution site (with respect to the natural sex pheromone) and related to the biological activity and to the possible binding site with the pheromone binding protein, (PBP). Moreover, the Laplacian function of the electronic density was used to locate electrophilic regions susceptible to be attacked (by deficient electron atoms or donor hydrogen). Our results indicate that the change in the atomic properties, such as electronic population and atomic volume, are sensitive indicators of the loss of the biological activity in the analogues studied here. The crucial interaction between the acetate group of the natural sex pheromone and the PBP is most likely to be a hydrogen bonding and the substitution of hydrogen atoms by electronegative atoms in the pheromone molecule reduces the hydrogen acceptor capacity. This situation is mirrored by the diminish of the electronic population on carbon and oxygen atoms at the carbonylic group in the halo-acetate group. Additionally, the modified acetate group (with electronegative atoms) shows new charge concentration critical points or regions of concentration of charge density in which an electrophilic attack can also occur. Finally, the use of the topological analysis based in the charge density distribution and its Laplacian function, in conjunction with MEP maps provides valuable information about the steric volume and electronic requirement of the sex pheromone for binding to the PBP.     

Excited-State Lifetimes of Far-Infrared Collective Modes in Proteins

Vibrational excitations of low frequency collective modes are essential for functionally important conformational transitions in proteins. Here we report the first direct measurement on the lifetime of vibrational excitations of the collective modes at 87 pm (115 cm^-1) in bacteriorhodopsin, a transmembrane protein. The data show that these modes have extremely long lifetime of vibrational excitations, over 500 picoseconds, accommodating 1500vibrations. We suggest that there is a connection between this relativelyslow anharmonic relaxation rate of approximately 10 g sec^-1 and thesimilar observed rate of conformational transitions in proteins, which require require multi-level vibrational excitations and energy exchanges with othervibrational modes and collisional motions of solvent molecules.     

Structures, energies and bonding in neutral and charged Li microclusters

Structural and chemical properties of charged and neutral Lithium microclusters are investigated for [Formula: see text]. A total of 18 quantum conformational spaces are randomly walked to produce candidate structures for local minima. Very rich potential energy surfaces are produced, with the largest structural complexity predicted for anionic clusters. Analysis of the electron charge distributions using the quantum theory of atoms in molecules (QTAIM) predicts major stabilizing roles of Non-nuclear attractors (NNAs) via NNA···Li interactions with virtually no direct Li···Li interactions, except in the least stable configurations. A transition in behavior for clusters containing more than seven nuclei is observed by using the recently introduced quantum topology to determine in a quantum mechanically consistent fashion the number of spatial dimensions each cluster has. We experiment with a novel scheme for extracting persistent structural motifs with increase in cluster size. The new structural motifs correlate well with the energetic stability, particularly in highlighting the least stable structures. Quantifying the degree of covalent character in Lithium bonding independently agrees with the observation in the transition in cluster behavior for lithium clusters containing more than seven nuclei. Good correlation with available experimental data is obtained for all properties reported in this work.     

Quantum dots as a sensor for quantitative visualization of surface charges on single living cells with nano-scale resolution

We developed a technique using quantum dot (QD) as a sensor for quantitative visualization of the surface charge on biological cells with nano-scale resolution. The QD system was designed and synthesized using amino modified CdSe/ZnS nanoparticles. In a specially designed buffer solution, they are positively charged and can homogeneously disperse in the aqueous environment to label all the negative charges on the surfaces of living cells. Using a wide-field optical sectioning microscopy to achieve 2D/3D imaging of the QD-labeled cells, we determined the charge densities of different kinds of cells from normal to mutant ones. The information about the surface charge distribution is significant in evaluating the structure, function, biological behavior and even malignant transformation of cells.