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Ab initio many-body perturbation theory within the GW approximation is a Green's function formalism widely used in the calculation of quasiparticle excitation energies of solids. In what has become an increasingly standard approach, Kohn–Sham eigenenergies, generated from a DFT calculation with a strategically-chosen exchange–correlation functional “starting point”, are used to construct G and W, and then perturbatively corrected by the resultant GW self-energy. In practice, there are several ways to construct the GW self-energy, and these can lead to variations in predicted quasiparticle energies. For example, for ZnO and TiO2, the GW fundamental gaps reported in the literature can vary by more than 1 eV depending on the GW code used. In this work, we calculate and analyze GW quasiparticle (QP) energies of these and other systems with three different GW codes: BERKELEYGW, ABINIT and YAMBO. Through a systematic analysis of the GW implementation of these three codes, we identify the primary origin of major discrepancies between codes reported in prior literature to be the different implementations the Coulomb divergence in the Fock exchange term and the frequency integration scheme of the GW self-energy. We then eliminate these discrepancies by using common numerical methods and algorithms, demonstrating that the same quasiparticle energies for a given material can be obtained with different codes, within numerical differences ascribable to the technical details of the underling implementations. This work will be important for users and developers in assessing the precision of future GW applications and methods.

The dispersion of the electronic states of epitaxial graphene (Gr) depends significantly on the strength of the bonding with the underlying substrate. We report on empty electron states in cobalt-intercalated Gr grown on Ir(111), studied by angle-resolved inverse photoemission spectroscopy and x-ray absorption spectroscopy, complemented with density functional theory calculations. The weakly bonded Gr on Ir preserves the peculiar spectroscopic features of the Gr band structure, and the empty spectral densities are almost unperturbed. Upon intercalation of a Co layer, the electronic response of the interface changes, with an intermixing of the Gr π* bands and Co d states, which breaks the symmetry of π/σ states, and a downshift of the upper part of the Gr Dirac cone. Similarly, the image potential of Ir(111) is unaltered by the Gr layer, while a downward shift is induced upon Co intercalation, as unveiled by the image state energy dispersion mapped in a large region of the surface Brillouin zone. [ABSTRACT FROM AUTHOR]

Spontaneous condensation of excitons is a long-sought phenomenon analogous to the condensation of Cooper pairs in a superconductor. It is expected to occur in a semiconductor at thermodynamic equilibrium if the binding energy of the excitons--electron (e) and hole (h) pairs interacting by Coulomb force--overcomes the band gap, giving rise to a new phase: the "excitonic insulator" (EI). Transition metal dichalcogenides are excellent candidates for the EI realization because of reduced Coulomb screening, and indeed a structural phase transition was observed in few-layer systems. However, previous work could not disentangle to which extent the origin of the transition was in the formation of bound excitons or in the softening of a phonon. Here we focus on bulk MoS2 and demonstrate theoretically that at high pressure it is prone to the condensation of genuine excitons of finite momentum, whereas the phonon dispersion remains regular. Starting from first-principles many-body perturbation theory, we also predict that the self-consistent electronic charge density of the EI sustains an out-of-plane permanent electric dipole moment with an antiferroelectric texture in the layer plane: At the onset of the EI phase, those optical phonons that share the exciton momentum provide a unique Raman fingerprint for the EI formation. Finally, we identify such fingerprint in a Raman feature that was previously observed experimentally, thus providing direct spectroscopic confirmation of an ideal excitonic insulator phase in bulk MoS2 above 30 GPa. [ABSTRACT FROM AUTHOR]

We report on the electronic properties of an artificial system obtained by the intercalation of equiatomic FeCo layers under graphene grown on Ir(111). Upon intercalation, the FeCo film grows epitaxially on Ir(111), resulting in a lattice-mismatched system. By performing density functional theory calculations, we show that the intercalated FeCo layer leads to a pronounced corrugation of the graphene film. At the same time, the FeCo intercalated layers induce a clear transition from a nearly undisturbed to a strongly hybridized graphene π-band, as measured by angle-resolved photoemission spectroscopy. A comparison of experimental results with the computed band structure and the projected density of states unveils a spin-selective hybridization between the π band of graphene and FeCo-3d states. Our results demonstrate that the reduced dimensionality, as well as the hybridization within the FeCo layers, induces a narrowing and a clear splitting of Fe 3d-up and Fe 3d-down-spin bands of the confined FeCo layers with respect to bulk Fe and Co. [ABSTRACT FROM AUTHOR]

In this work we show the possibility to extract Kohn-Sham orbitals, orbital energies, and exchange correlation potentials from accurate Quantum Monte Carlo (QMC) densities for atoms (He, Be, Ne) and molecules (H2, Be2, H2O, and C2H4). The Variational Monte Carlo (VMC) densities based on accurate Jastrow Antisymmetrised Geminal Power wave functions are calculated through different estimators. Using these reference densities, we extract the Kohn-Sham quantities with the method developed by Zhao, Morrison, and Parr (ZMP) [Phys. Rev. A 50, 2138 (1994)]. We compare these extracted quantities with those obtained form CISD densities and with other data reported in the literature, finding a good agreement between VMC and other high-level quantum chemistry methods. Our results demonstrate the applicability of the ZMP procedure to QMC molecular densities, that can be used for the testing and development of improved functionals and for the implementation of embedding schemes based on QMC and Density Functional Theory. [ABSTRACT FROM AUTHOR]

We combine density functional theory and many body perturbation theory to investigate the electronic properties of Si(100) and Ge(100) surfaces terminated with halogen atoms (–I, –Br, –Cl, –F) and other chemical functionalizations (–H, –OH, –CH3) addressing the absolute values of their work function, electronic affinity and ionization potential. Our results point out that electronic properties of functionalized surfaces strongly depend on the chemisorbed species and much less on the surface crystal orientation. The presence of halogens at the surface always leads to an increment of the work function, ionization potential and electronic affinity with respect to fully hydrogenated surfaces. On the contrary, the presence of polar –OH and –CH3 groups at the surface leads to a reduction of the aforementioned quantities with respect to the H-terminated system. Starting from the work functions calculated for the Si and Ge passivated surfaces, we apply a simple model to estimate the properties of functionalized SiGe surfaces. The possibility of modulating the work function by changing the chemisorbed species and composition is predicted. The effects induced by different terminations on the band energy line-up profile of SiGe surfaces are then analyzed. Interestingly, our calculations predict a type-II band offset for the H-terminated systems and a type-I band offset for the other cases. [ABSTRACT FROM AUTHOR]

The article explains the ab initio optical absorption spectra of various size-expanded xDNA base assemblies. The optical response is found to get highly affected by the modifications of the frontier electron orbitals.

The study of the optical absorption spectra of DNA bases and base pairs, carried out by means of time dependent density functional theory is described. The spectra for the isolated bases are compared and used to assess the accuracy of the method and the quality of the exchange correlation functional and this approach turns out to be a reliable tool to describe the response of the nucleobases.

Fifty years ago Walter Kohn speculated that a zero-gap semiconductor might be unstable against the spontaneous generation of excitons–electron–hole pairs bound together by Coulomb attraction. The reconstructed ground state would then open a gap breaking the symmetry of the underlying lattice, a genuine consequence of electronic correlations. Here we show that this excitonic insulator is realized in zero-gap carbon nanotubes by performing first-principles calculations through many-body perturbation theory as well as quantum Monte Carlo. The excitonic order modulates the charge between the two carbon sublattices opening an experimentally observable gap, which scales as the inverse of the tube radius and weakly depends on the axial magnetic field. Our findings call into question the Luttinger liquid paradigm for nanotubes and provide tests to experimentally discriminate between excitonic and Mott insulators. [ABSTRACT FROM AUTHOR]

G-quadruplex is a quadruple helical form of nucleic acids that can appear in guanine-rich parts of the genome. The basic unit is the G-tetrad, a planar assembly of four guanines connected by eight hydrogen bonds. Its rich topology and its possible relevance as a drug target for a number of diseases have stimulated several structural studies. The superior stiffness and electronic π-π overlap between consecutive G-tetrads suggest exploitation for nanotechnologies. Here we inspect the intimate link between the structure and the electronic properties, with focus on charge transfer parameters. We show that the electronic couplings between stacked G-tetrads strongly depend on the three-dimensional atomic structure. Furthermore, we reveal a remarkable correlation with the topology: a topology characterized by the absence of syn-anti G-G sequences can better support electronic charge transfer. On the other hand, there is no obvious correlation of the electronic coupling with usual descriptors of the helix shape. We establish a procedure to maximize the correlation with a global helix shape descriptor. [ABSTRACT FROM AUTHOR]

The accurate calculation of electronic excited states of large and electronically correlated biological chromophores in their complex protein environment still represents a challenge for quantum chemistry. Two ab initio techniques are recently emerging as candidates to correctly tackle this issue: Quantum Monte Carlo (QMC) calculations for the ground state geometry optimization, and Many Body Green’s Function Theory (MBGFT) for exited state energies. In the present work we use the Variational Monte Carlo (VMC) to carry out structural optimizations and we present an extension of MBGFT to complex environments, using a Quantum Mechanics/Molecular Mechanics framework. This technique is applied to evaluate the optical properties of the retinal protonated Schiff base (RPSB) chromophore in rhodopsin, the protein responsible for dim light vision in the vertebrates. Vertical energies for the bright excitation of RPSB calculated solving the Bethe-Salpeter equation in gas phase and in the protein environment correspond to 2.19eV and 2.58eV, respectively. These data are in fair agreement with the available experimental findings. The comparison between these excitation energies and that obtained for a gas phase calculation on a retinal geometry obtained in the protein environment (2.03eV) reveals the essential role of the protein field in the spectral tuning of the molecule. The proposed VMC/MBGFT methodologies can therefore be applied to obtain a reliable ab initio evaluation of optical properties of biological chromophores. [ABSTRACT FROM AUTHOR]

We investigate from first principles the electronic and optical properties of edge-modulated armchair graphene nanoribbons, including both quasiparticle corrections and excitonic effects. Exploiting the oscillating behavior of the ribbon energy gap, we show that minimal width-modulations are sufficient to obtain confinement of both electrons and holes, thus forming optically active quantum dots with unique properties, such as the coexistence of dotlike and extended excitations and the fine tunability of optical spectra, with great potential for optoelectronic applications. [ABSTRACT FROM AUTHOR]

We present an efficient scheme to calculate the chiroptical response of molecular systems within time dependent density functional theory using either a real-time propagation or a frequency-dependent Sternheimer method. The scheme avoids the commonly used sum over empty orbitals and has a very favorable scaling with system size. Moreover, the method is general and can be easily implemented. In the present work, we implemented it using a real-space pseudo-potential representation of the wave-functions and Hamiltonian. The specific use of non-local pseudo-potentials implies that a gauge correction term in the angular momentum operator must be included to ensure that the total scheme is fully gauge invariant. Applications to small organic chiral molecules are shown and discussed, addressing some deficiencies of present exchange–correlation functionals to describe the absolute position of the excitations. However, the shape or sign of the dichroism spectra comes out in excellent agreement with available experiments. [ABSTRACT FROM AUTHOR]

We present calculations on energy- and time-resolved two photon photoemission spectra of images states in Cu(1 0 0) and Cu(1 1 1) surfaces. The surface is modeled by a 1D effective potential and the states are propagated within a real-space, real-time method. To obtain the energy-resolved spectra we employ a geometrical approach based on a subdivision of space into two regions. We treat electronic inelastic effects by taking into account the scattering rates calculated within a GW scheme. To get further insight into the decaying mechanism we have also studied the effect of the variation of the classical Hartree potential during the excitation. This effect turns out to be small. [Copyright &y& Elsevier]

Gas-phase action spectroscopy shows unambiguously that the low-energy absorptions by tetramethylthiotetrathiafulvalene and tetrathianaphthalene cations in solution phase are due to monomers and not π-dimers. [ABSTRACT FROM AUTHOR]

In view of their applicability in optoelectronics, we review here the relevant structural, electronic, and optical features of the inorganic Pb-free halide perovskite class. In particular, after discussing the reasons that have motivated their introduction in opposition to their more widely investigated organic-inorganic counterparts, we highlight milestones already achieved in their synthesis and characterization and show how the use of ab initio ground and excited state methods is relevant in predicting their properties and in disclosing yet unsolved issues which characterize both ternary and quaternary stoichiometry double-perovskites. [ABSTRACT FROM AUTHOR]

Abstract: The suitability of the time-dependent density-functional theory (TDDFT) approach for the theoretical study of the optical properties of biomolecules is demonstrated by several examples. We critically discuss the limitations of available TDDFT implementations to address some of the present open questions in the description of the excited-state dynamics of biological complexes. The key objective of the present work is to address the performance of TDDFT in the linear response regime of the bio-molecular systems to the visible or near UV radiation – measured by, e.g. optical absorption or optical dichroism spectra. Although these spectra are essentially determined by the electronic degrees of freedom of small, optically active regions within the usually large biological systems, they can also be strongly influenced by environment effects (solvent, hosting protein, temperature, etc.). Moreover, many key biological processes consist of photo-induced dynamics (photoisomerisation, etc.), and their description requires a coupled treatment of electronic and nuclear degrees of freedom. We illustrate these aspects with a selection of paradigmatic biomolecular systems: chromophores in fluorescent proteins, porphyrins, DNA basis, the azobenzene dye, etc. To cite this article: A. Castro et al., C. R. Physique 10 (2009). [Copyright &y& Elsevier]

Carbon nanotubes continue to be model systems for studies of confinement and interactions. This is particularly true in the case of so-called "ultraclean" carbon nanotube devices offering the study of quantum dots with extremely low disorder. The quality of such systems, however, has increasingly revealed glaring discrepancies between experiment and theory. Here, we address the outstanding anomaly of exceptionally large orbital magnetic moments in carbon nanotube quantum dots. We perform low temperature magnetotransport measurements of the orbital magnetic moment and find it is up to 7 times larger than expected from the conventional semiclassical model. Moreover, the magnitude of the magnetic moment monotonically drops with the addition of each electron to the quantum dot directly contradicting the widely accepted shell filling picture of single-particle levels. We carry out quasiparticle calculations, both from first principles and within the effective-mass approximation, and find the giant magnetic moments can only be captured by considering a self-energy correction to the electronic band structure due to electron-electron interactions. [ABSTRACT FROM AUTHOR]

Density functional theory provides the most widespread framework for the realistic description of the electronic structure of solids, but the description of strongly correlated systems has remained so far elusive. We consider a particular limit of electrons and ions in which a one-band description becomes exact all the way from the weakly correlated metallic regime to the strongly correlated Mott-Hubbard regime. We provide a necessary condition a density functional should fulfill to describe Mott-Hubbard behavior in this one-band limit and show that it is not satisfied by standard and widely used local, semilocal, and hybrid functionals. We illustrate the condition in the case of few-atom systems and provide an analytic approximation to the exact exchange-correlation potential based on a variational wave function which shows explicitly the correct behavior, combining in a neat way lattice and continuum methods. [ABSTRACT FROM AUTHOR]

Despite its simple crystal structure, layered boron nitride features a surprisingly complex variety of phonon-assisted luminescence peaks. We present a combined experimental and theoretical study on ultraviolet-light emission in hexagonal and rhombohedral bulk boron nitride crystals. Emission spectra of high-quality samples are measured via cathodoluminescence spectroscopy, displaying characteristic differences between the two polytypes. These differences are explained using a fully first-principles computational technique that takes into account radiative emission from "indirect," finite-momentum excitons via coupling to finite-momentum phonons. We show that the differences in peak positions, number of peaks, and relative intensities can be qualitatively and quantitatively explained, once a full integration over all relevant momenta of excitons and phonons is performed.

Spontaneous condensation of excitons is a long-sought phenomenon analogous to the condensation of Cooper pairs in a superconductor. It is expected to occur in a semiconductor at thermodynamic equilibrium if the binding energy of the excitons-electron (e) and hole (h) pairs interacting by Coulomb force-overcomes the band gap, giving rise to a new phase: the "excitonic insulator" (EI). Transition metal dichalcogenides are excellent candidates for the EI realization because of reduced Coulomb screening, and indeed a structural phase transition was observed in few-layer systems. However, previous work could not disentangle to which extent the origin of the transition was in the formation of bound excitons or in the softening of a phonon. Here we focus on bulk [Formula: see text] and demonstrate theoretically that at high pressure it is prone to the condensation of genuine excitons of finite momentum, whereas the phonon dispersion remains regular. Starting from first-principles many-body perturbation theory, we also predict that the self-consistent electronic charge density of the EI sustains an out-of-plane permanent electric dipole moment with an antiferroelectric texture in the layer plane: At the onset of the EI phase, those optical phonons that share the exciton momentum provide a unique Raman fingerprint for the EI formation. Finally, we identify such fingerprint in a Raman feature that was previously observed experimentally, thus providing direct spectroscopic confirmation of an ideal excitonic insulator phase in bulk [Formula: see text] above 30 GPa., Competing Interests: The authors declare no competing interest., (Copyright © 2021 the Author(s). Published by PNAS.)

The structures of three negatively charged forms (anionic keto-1 and enol-1 and dianionic enol-2) of oxyluciferin (OxyLuc), which are the most probable emitters responsible for the firefly bioluminescence, have been fully relaxed at the variational Monte Carlo (VMC) level. Absorption energies of the S 1 ← S 0 vertical transition have been computed using different levels of theory, such as TDDFT, CC2, and many-body Green's function theory (MBGFT). The use of MBGFT, by means of the Bethe-Salpeter (BS) formalism, on VMC structures provides results in excellent agreement with the value (2.26(8) eV) obtained by action spectroscopy experiments for the keto-1 form (2.32 eV). To unravel the role of the quality of the optimized ground-state geometry, BS excitation energies have also been computed on CASSCF geometries, inducing a non-negligible blue shift (0.08 and 0.07 eV for keto-1 and enol-1 forms, respectively) with respect to the VMC ones. Structural effects have been analyzed in terms of over- or undercorrelation along the conjugated bonds of OxyLuc by using different methods for the ground-state optimization. The relative stability of the S 1 state for the keto-1 and enol-1 forms depends on the method chosen for the excited-state calculation, thus representing a fundamental caveat for any theoretical study on these systems. Finally, Kohn-Sham HOMO and LUMO orbitals of enol-2 are (nearly) bound only when the dianion is embedded into a solvent (water and toluene in the present work); excited-state calculations are therefore meaningful only in the presence of a dielectric medium which localizes the electronic density. The combination of VMC for the ground-state geometry and BS formalism for the absorption spectra clearly outperforms standard TDDFT and quantum chemistry approaches.

Despite most of the applications of anatase nanostructures rely on photoexcited charge processes, yet profound theoretical understanding of fundamental related properties is lacking. Here, by means of ab initio ground and excited-state calculations, we reveal, in an unambiguous way, the role of quantum confinement effect and of the surface orientation, on the electronic and optical properties of anatase nanosheets (NSs). The presence of bound excitons extremely localized along the (001) direction, whose existence has been recently proven also in anatase bulk, explains the different optical behavior found for the two orientations - (001) and (101) - when the NS thickness increases. We suggest also that the almost two-dimensional nature of these excitons can be related to the improved photoconversion efficiency observed when a high percentage of (001) facet is present in anatase nanocrystals.

Photoinitiated phenomena play a crucial role in many living organisms. Plants, algae, and bacteria absorb sunlight to perform photosynthesis, and convert water and carbon dioxide into molecular oxygen and carbohydrates, thus forming the basis for life on Earth. The vision of vertebrates is accomplished in the eye by a protein called rhodopsin, which upon photon absorption performs an ultrafast isomerisation of the retinal chromophore, triggering the signal cascade. Many other biological functions start with the photoexcitation of a protein-embedded pigment, followed by complex processes comprising, for example, electron or excitation energy transfer in photosynthetic complexes. The optical properties of chromophores in living systems are strongly dependent on the interaction with the surrounding environment (nearby protein residues, membrane, water), and the complexity of such interplay is, in most cases, at the origin of the functional diversity of the photoactive proteins. The specific interactions with the environment often lead to a significant shift of the chromophore excitation energies, compared with their absorption in solution or gas phase. The investigation of the optical response of chromophores is generally not straightforward, from both experimental and theoretical standpoints; this is due to the difficulty in understanding diverse behaviours and effects, occurring at different scales, with a single technique. In particular, the role played by ab initio calculations in assisting and guiding experiments, as well as in understanding the physics of photoactive proteins, is fundamental. At the same time, owing to the large size of the systems, more approximate strategies which take into account the environmental effects on the absorption spectra are also of paramount importance. Here we review the recent advances in the first-principle description of electronic and optical properties of biological chromophores embedded in a protein environment. We show their applications on paradigmatic systems, such as the light-harvesting complexes, rhodopsin and green fluorescent protein, emphasising the theoretical frameworks which are of common use in solid state physics, and emerging as promising tools for biomolecular systems.

G-quadruplex is a quadruple helical form of nucleic acids that can appear in guanine-rich parts of the genome. The basic unit is the G-tetrad, a planar assembly of four guanines connected by eight hydrogen bonds. Its rich topology and its possible relevance as a drug target for a number of diseases have stimulated several structural studies. The superior stiffness and electronic π-π overlap between consecutive G-tetrads suggest exploitation for nanotechnologies. Here we inspect the intimate link between the structure and the electronic properties, with focus on charge transfer parameters. We show that the electronic couplings between stacked G-tetrads strongly depend on the three-dimensional atomic structure. Furthermore, we reveal a remarkable correlation with the topology: a topology characterized by the absence of syn - anti G-G sequences can better support electronic charge transfer. On the other hand, there is no obvious correlation of the electronic coupling with usual descriptors of the helix shape. We establish a procedure to maximize the correlation with a global helix shape descriptor.

In this letter, we report the singlet ground state structure of the full carotenoid peridinin by means of variational Monte Carlo (VMC) calculations. The VMC relaxed geometry has an average bond length alternation of 0.1165(10) Å, larger than the values obtained by DFT (PBE, B3LYP, and CAM-B3LYP) and shorter than that calculated at the Hartree-Fock (HF) level. TDDFT and EOM-CCSD calculations on a reduced peridinin model confirm the HOMO-LUMO major contribution of the Bu(+)-like (S2) bright excited state. Many Body Green's Function Theory (MBGFT) calculations of the vertical excitation energy of the Bu(+)-like state for the VMC structure (VMC/MBGFT) provide an excitation energy of 2.62 eV, in agreement with experimental results in n-hexane (2.72 eV). The dependence of the excitation energy on the bond length alternation in the MBGFT and TDDFT calculations with different functionals is discussed.

The accurate determination of the geometrical details of the dark state of 11- cis retinal in rhodopsin represents a fundamental step for the rationalization of the protein role in the optical spectral tuning in the vision mechanism. We have calculated geometries of the full retinal protonated Schiff base chromophore in the gas phase and in the protein environment using the correlated variational Monte Carlo method. The bond length alternation of the conjugated carbon chain of the chromophore in the gas phase shows a significant reduction when moving from the β -ionone ring to the nitrogen, whereas, as expected, the protein environment reduces the electronic conjugation. The proposed dark state structure is fully compatible with solid-state NMR data reported by Carravetta et al. [ J. Am. Chem. Soc . 2004 , 126 , 3948-3953]. TDDFT/B3LYP calculations on such geometries show a blue opsin shift of 0.28 and 0.24 eV induced by the protein for S 1 and S 2 states, consistently with literature spectroscopic data. The effect of the geometrical distortion alone is a red shift of 0.21 and 0.16 eV with respect to the optimized gas phase chromophore. Our results open new perspectives for the study of the properties of chromophores in their biological environment using correlated methods.

We present a combined investigation of the dynamics and optics of triplex DNA, based on classical molecular dynamics and time-dependent density functional theory. Our approach is devised to include the effects of conformational fluctuations on the electronic structure and optical excitations of the system. We find that the structural flexibility has a strong role in the determination of the optical signals. Our results allow us to unravel the peculiar fingerprints of Watson-Crick and Hoogsteen H-bonding in the optical absorption spectra. We find a specific optical absorption feature that is due to the simultaneous presence of the two H-bonding patterns in C(+)GC triplets. While this peculiar triplet signal is wiped out in some structures that are representative of the finite-temperature dynamics, it can be recovered in an average view, so that it is a pristine result of this work.

The optical properties of the flavylium state of the cyanin dye are simulated numerically by combining Car-Parrinello molecular dynamics and linear-response time-dependent density functional theory calculations. The spectrum of the dye calculated in the gas phase is characterized by two peaks in the yellow and in the blue (green and violet), using a GGA-PBE (hybrid-B3LYP) DFT functional, which would bring about a greenish (bright orange) color incompatible with the dark purple hue observed in nature. Describing the effect of the water solvent through a polarizable continuum model does not modify qualitatively the resulting picture. An explicit simulation of both solvent and thermal effects using ab initio molecular dynamics results instead in a spectrum that is compatible with the observed coloration. This result is analyzed in terms of the spectroscopic effects of the molecular distortions induced by thermal fluctuations.

Synchrotron radiation circular dichroism (SRCD) spectra were recorded for a family of 12 DNA duplexes that all contain nine adenines (A) and nine thymines (T) in each strand but in different combinations. The total number of AT Watson-Crick (WC) base pairs is constant (18), but the number of cross-strand (CS) hydrogen bonds between A and T varies between 0 and 16, the maximum possible. Eleven of the duplexes have one or more A tracts, and one duplex has T tracts. The signals due to hybridization were found from subtraction of spectra of single strands from spectra of the duplexes. The residual spectrum of the T-tract duplex T(9)A(9):A(9)T(9) (5'-3':3'-5') significantly differs from that of the A-tract duplex A(9)T(9):T(9)A(9), but only below 210 nm, which suggests that the signal in this region depends on the superhelicity of the duplex. A principal component analysis of all residual spectra reveals that spectra of A-tract duplexes can be obtained to a good approximation as a linear combination of just two basis spectra. The first component is assigned to the spectrum of 18 WC and 8 CS pairs, whereas the second component is that of 8 CS pairs. This interpretation is supported by separate experiments on duplexes of varying lengths but with similar arrangements of the A and T's and by experiments on two other duplex families of 14 and 30 base pairs. The best correlation is obtained by the assumption that cross-strand interactions occur as long as there are two adenine neighbors in a strand. Our data indicate that a circular dichroism spectrum of a duplex containing only A and T can simply be inferred from the number of WC base pairs and the number of CS interactions, and we provide reference spectra for these two interactions. Finally, time dependent density functional theory calculations of the circular dichroism spectra for an isolated WC base pair and two different CS base pairs (between adenine N-6 amine and thymine O-4 or between adenine C-2-H and thymine O-2) were performed to provide some additional support for the interpretation of the experimental spectra. We find large differences between the two calculated CS spectra. However, there is a reasonable qualitative agreement between the calculated WC and the C-2-H...O-2 CS spectra and those deduced from the experimental data.

We identify excitonic confinement in one-dimensional molecular chains (i.e., polyacetylene and H2) as the main driving force for the saturation of the chain polarizability as a function of the number of molecular units. This conclusion is based on first principles time-dependent density-functional theory calculations using a recently developed exchange-correlation kernel that accounts for excitonic effects. The failure of simple local and semilocal functionals is shown to be linked to the lack of memory effects, spatial ultranonlocality, and self-interaction corrections. These effects get smaller as the gap reduces, in which case such simple approximations do perform better.

We performed first-principles calculations of the optical response of the green fluorescent protein (GFP) within a combined quantum-mechanical molecular-mechanics and time-dependent density-functional theory approach. The computed spectra are in excellent agreement with experiments assuming the presence of two, protonated and deprotonated, forms of the photoreceptor in a approximately 4:1 ratio, which supports the conformation model of photodynamics in GFP. Furthermore, we discuss charge transfer, isomerization, and environment effects. The present approach allows for systematic studies of excited-state electron-ion dynamics in biological systems.