Molecular model of LH1 light-harvesting complex of the photosynthetic center of Thermochromatium tepidum bacteria

A three-dimensional all-atom structure of the LH1 light-harvesting complex of the photosynthetic center of the Thermochromatium tepidum bacteria was constructed with molecular modeling techniques.     

Origin‐independent sum over states simulations of magnetic and electronic circular dichroism spectra via the localized orbital/local origin method

Although electronic and magnetic circular dichroism (ECD, MCD) spectra reveal valuable details about molecular geometry and electronic structure, quantum‐chemical simulations significantly facilitate their interpretation. However, the simulated results may depend on the choice of coordinate origin. Previously (?těpánek and Bou?, J. Comput. Chem. 2013, 34, 1531), the sum‐over‐states (SOS) methodology was found useful for efficient MCD computations. Approximate wave functions were “resolved” using time‐dependent density functional theory, and the origin‐dependence was avoided by placing the origin to the center of mass of the investigated molecule. In this study, a more elegant way is proposed, based on the localized orbital/local origin (LORG) formalism, and a similar approach is also applied to generate ECD intensities. The LORG‐like approach yields fully origin‐independent ECD and MCD spectra. The results thus indicate that the computationally relatively cheap SOS simulations open a new way of modeling molecular properties, including those involving the origin‐dependent magnetic dipole moment operator. © 2015 Wiley Periodicals, Inc.     

Molecular electric properties in electronic excited states: multipole moments and polarizabilities of H2O in the lowest1 B 1 and3 B 1 excited states

Summary The dipole and quadrupole moments and the dipole polarizability tensor components are calculated for the¹ B ₁ and³ B ₁ excited states of the water molecule by using the complete active space (CAS) SCF method and an extended basis set of atomic natural orbitals. The dipole moment in the lowest¹ B ₁ (0.640 a.u.) and³ B ₁ (0.416 a.u.) states is found to be antiparallel to that in the ground electronic state of H₂O. The shape of the quadrupole moment ellipsoid is significantly modified by the electronic excitation to both states investigated in this paper. All components of the excited state dipole polarizability tensor increase by about an order of magnitude compared to their values in the ground electronic state. The present results are used to discuss some aspects of intermolecular interactions involving molecules in their excited electronic states.     

Computation of magnetic circular dichroism by sum‐over‐states summations

Magnetic circular dichroism (MCD) spectroscopy has been established as a convenient method to study electronic structure, in particular for small symmetric organic molecules. Newer applications on more complex systems are additionally stimulated by the latest availability of precise quantum‐chemical techniques for the spectral simulations. In this work, a sum over states (SOS) summation is reexamined as an alternative to the derivative techniques for the MCD modeling. Unlike in previous works, the excited electronic states are calculated by the time‐dependent density functional theory (TDDFT). A gradient formulation of the MCD intensities is also proposed, less dependent on the origin choice than the standard expressions. The dependencies of the results on the basis set, number of electronic states, and coordinate origin are tested on model examples, including large symmetric molecules with degenerate electronic states. The results suggest that the SOS/TDDFT approach is a viable and accurate technique for spectral simulation. It may even considerably reduce the computational time, if compared with the traditional MCD computational procedures based on the response theory. © 2013 Wiley Periodicals, Inc.     

Unexpected properties of non‐autoionizing doubly excited states of the H2 molecule

We present accurate calculations of the non‐autoionizing and doubly excited states of the H₂ molecule using full configuration interaction with Hartree–Fock molecular orbitals and Heitler–London atomic orbitals. We consider the united atom configurations from He(2p2p) up to He(2p8g) and dissociation products from H₂(2p + 2p) up to H₂(2p + 6?). Born–Oppenheimer calculations are carried out with extended and optimized Slater‐type orbitals for a total of 40 states, 10 for each symmetry, covering the internuclear distances from the united atom to dissociation, which, for some states, is reached beyond 100 a₀. Occurrences of repulsive states cleanly interlaced between bound states with many vibrational levels are reported. Some of the potential minima are deep enough to accommodate many vibrational levels (up to 50). Noteworthy large equilibrium minima, like R_eq = 46.0 a₀ in the state dissociating as (2p + 6h) and with 18 vibrational levels. The occurrence of vertical excitations from the singly excited manifolds is analyzed. Several states present double minima generated by avoided crossings, some with a strong ionic character. © 2016 Wiley Periodicals, Inc.     

Electron paramagnetic resonance of the excited states of the three-spins-1/2 ZnTPP–3-NOPy complex

EPR spectra of the excited quartet and doublet molecular states of (tetraphenylporphinato)zinc(II)covalently bounded to 3-(N-nitronyl-notroxide) pyridine stable radical are modeled in terms of the spin-Hamiltonian given by the sum of the contributions from the radical and triplet moieties, and the interaction between them. The later is represented by anisotropic point dipolar and isotropic exchange electron spin–spin interactions. It is shown that the high field (W-band) EPR spectra depend on energy separation between the electronic doublet (D) and quartet (Q) states. This dependence was utilized to estimate the upper limit of the intensity of exchange interaction between the radical and porphyrin moieties.     

Theoretical study of the electronic excited states of tetracyanoethylene and its radical anion.

The low-lying electronic states of tetracyanoethylene (TCNE) and its radical anion were studied using multiconfigurational second-order perturbation theory (CASPT2) and extended atomic natural orbital (ANO) basis sets. The results obtained yield a full interpretation of the electronic absorption spectra, explain the spectral changes undergone upon reduction, give support to the occurrence of a bound excited state for the anionic species, and provide valuable information for the rationalization of the experimental data obtained with electron transmission spectroscopy.     

An ab initio study of excited states of guanine in the gas phase and aqueous media: Electronic transitions and mechanism of spectral oscillations

Ground state geometries of the four tautomeric forms keto‐N9H, keto‐N7H, enol‐N9H, and enol‐N7H of guanine were optimized in the gas phase at the RHF level using a mixed basis set consisting of the 4‐31G basis set for all the atoms except the nitrogen atom of the amino group for which the 6‐311+G* basis set was used. These calculations were also extended to hydrogen‐bonded complexes of three water molecules with each of the keto‐N9H (G9‐3W) and keto‐N7H (G7‐3W) forms of guanine. Relative stabilities of the four above‐mentioned tautomers of guanine as well as those of G9‐3W and G7‐3W complexes in the ground state in the gas phase were studied employing the MP2 correlation correction. In aqueous solution, relative stabilities of these systems were studied using the MP2 correlation correction and polarized continuum model (PCM) or the isodensity surface polarized continuum model (IPCM) of the self‐consistent reaction field (SCRF) theory. Geometry optimization in the gas phase at the RHF level using the 6‐31+G* basis set for all atoms and the solvation calculations in water at the MP2 level using the same basis set were also carried out for the nonplanar keto‐N9H and keto‐N7H forms of guanine. Thus, it is shown that among the different tautomers of guanine, the keto‐N7H form is most stable in the gas phase, while the keto‐N9H form is most stable in aqueous solution. It appears that both the keto‐N9H and keto‐N7H forms of guanine would be present in the ground state, particularly near the aqueous solution–air interface. Vertical excitation and excited state geometry optimization calculations were performed using configuration interaction involving single electron excitation (CIS). It is found that the absorption spectrum of guanine would arise mainly due to its keto‐N9H form but the keto‐N7H form of the same would also make some contribution to it. The enol‐N9H and enol‐N7H forms of the molecule are not expected to occur in appreciable abundance in the gas phase or aqueous media. The normal fluorescence spectrum of guanine in aqueous solution with a peak near 332 nm seems to originate from the lowest singlet excited state of the keto‐N7H form of the molecule while the fluorescence of oxygen‐rich aqueous solutions of guanine with a peak near 450 nm appears to originate from the lowest singlet excited state of the keto‐N9H form of the molecule. The origin of the slow damped spectral oscillation observed in the absorption spectrum of guanine has been explained. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 826–846, 2000     

Configurational stabilization of mixed-valence states in the star-burst tetranuclear ruthenium complex bridged with acetylene links

A new tetranuclear ruthenium complex in which a metal was bridged radially to three identical metals with acetylene links showed a mixed-valence state in cyclic voltammograms. The peak potential difference for the mixed-valence state was twice the potential difference for a mixed-valence state of the corresponding binuclear complex. This fact suggests stabilization of the mixed-valence state twice by configurational modification of redox centers. However, this is inconsistent with the prediction from the additive pair model of the redox interaction. A quantum chemical model of the redox interaction was presented, in which the potential difference was expressed by the overlap integral S and the nearest neighbor interaction energy between the reduced center and the oxidized one. Application of the theory gave a negative value of S, which demonstrated reasonably the stabilization of the mixed-valence state from a quantum chemical viewpoint.     

Exploring the electro‐optical properties of conjugated polymers based on oligo‐selenophene and oligo(3,4‐ethylenedioxyselenophene)

For seeking high‐efficiency narrow‐band‐gap donor materials to enhance short‐circuit current density for organic solar cells, a series of oligo‐selenophene (OS) and oligo(3,4‐ethylenedioxyselenophene) (OEDOS) with various chain lengths were designed and characterized using density functional theory (DFT) and time‐dependent DFT calculations. Based on the results, it can be seen that with increasing chain length of the oligomers in both syn‐ and anti‐adding manners, the bond length alternation is decreased which indicates that the π‐electron delocalization is increased. Also, when the chain length is increased the electronic energy gap and the optical energy gap are decreased. It can be concluded that the syn‐(OS)_n=10,14,15, anti‐(OS)_n=14 and anti‐(OEDOS)_n=7–12 oligomers can act as low‐band‐gap polymers. Therefore they can absorb more sunlight based on maximum wavelength (higher than 620 nm). Furthermore, a red shift in the simulated absorption spectra of (OS)_n and (OEDOS)_n donors is observed. It is found that (OS)_n=14,15 with syn configuration of the extended oligomers is the most suitable donor for the design of high‐performance organic solar cells possessing a narrow electronic band gap, high exciton lifetime and broad and intense absorption spectra that cover the solar spectrum leading to complete light‐harvesting efficiency.     

Induction and inversion of chirality in poly‐L‐lysine and methyl orange complex

The mechanism of complexation of poly‐L‐lysine (PLL) with methyl orange (MO) and the appearance of induced circular dichroism (ICD) were investigated as a function of dye concentration and temperature and compared with that of the PLL‐ethyl orange complex. The formation of stoichiometric complexes with uniform size and intensities of ICDs depended on the length of alkyl groups (methyl and ethyl) as determined from quartz crystal microbalance measurement, absorption spectra, and CD spectra data. Furthermore, at constant PLL concentration, a dependence of the inversion of the ICD on the MO concentration (CMO) was observed in the PLL‐MO complexes, which to our knowledge has not been reported for a constant dye concentration system. The positive ICD in the PLL‐MO complexes observed at CMO lower than 2.0 × 10^?5 M showed reversible changes in response to heating and cooling, whereas the negative ICD in PLL‐MO complexes observed at higher CMO inverted to positive ICD values in response to a decrease in temperature. These results demonstrate the alkyl group substituent in the dye, dye concentration, and temperature play important roles in the formation of PLL‐azo dye complex and ICD appearance. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011     

Contracted well-tempered Gaussian basis sets in SCF calculations on the ground and excited electronic states of neutral and ionized diatomic molecules containing first-row atoms

Summary Calculations were done on ground and excited states of C₂, C ₂ ⁺ , C ₂ ^– , N₂, N ₂ ⁺ , O₂, O ₂ ⁺ , O ₂ ^– , CO, CO⁺, CO²⁺, and CO^– using contracted well-tempered basis sets. The (14s 10p) basis sets were augmented with threed, one or twof, and oneg functions. Total energies, orbital energies, and spectroscopic constants were compared with the best available computational data.     

Theoretical study of the vertical excited states of benzene, pyrimidine, and pyrazine by the symmetry adapted cluster--configuration interaction method

The ground state and the excited states of benzene, pyrimidine, and pyrazine have been examined by using the symmetry adapted cluster-configuration interaction (SAC-CI) method. Detailed characterizations and the structures of the absorption peaks in the vacuum ultraviolet (VUV), low energy electron impact (LEEI), and electron energy loss (EEL) spectra were theoretically clarified by calculating the excitation energy and the oscillator strength for each excited state. We show that SAC-CI has the power to well reproduce the electronic excitation spectra (VUV, LEEI, and EEL) simultaneously to an accuracy for both the singlet and the triplet excited states originated from the low-lying pi --> pi*, n --> pi*, pi --> sigma* and n --> sigma* excited states of the titled compounds. The present results are compared with those of the previous theoretical studies by methods, such as EOM-CCSD(T), STEOM-CCSD, CASPT2 and TD-B3LYP, etc.     

Potential functions of inversion of R2CO (R=H, F, Cl) molecules in the lowest excited electronic states

The inversion potentials of R₂CO (R=H, F, Cl) molecules in the lowest excited electronic states were determined from experimental data using various model potential functions and approximations for the kinetic energy operator of inversion motion. The estimates of the heights of the barriers to inversion and the equilibrium values of the inversion coordinate for the H₂CO molecule in the S₁ and T₁ states are fairly stable. The results for the F₂CO and Cl₂CO molecules are strongly dependent on the approximation used; for these molecules, the most reliable parameters of the potential functions were chosen. The problem of qualitative characteristics of the shape of inversion potentials is discussed using the results ofab initio quantum-chemical calculations of the molecules under study. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 4, pp. 645–651, April, 1999.     

Molecular parameters of tetraatomic carbonyls X2CO and XYCO (X,Y = H,F, Cl) in the ground and lowest excited electronic states,part 1: A test of ab initio methods

Geometrical parameters of tetraatomic carbonyl molecules X₂CO and XYCO (X, Y = H, F, Cl) in the ground (S₀) and lowest excited singlet (S₁) and triplet (T₁) electronic states as well as values of barriers to inversion in S₁ and T₁ states and S₁ ← S₀ and T₁ ← S₀ adiabatic transition energies were systematically investigated by means of various quantum‐chemical techniques. The following methods were tested: HF, MP2, CIS, CISD, CCSD, EOM‐CCSD, CCSD(T), CR‐EOM‐CCSD(T), CASSCF, MR‐MP2, CASPT2, CASPT3, NEVPT2, MR‐CISD, and MR‐AQCC within cc‐pVTZ and cc‐pVQZ basis sets. The accuracy of quantum‐chemical methods was estimated in comparison with experimental data and rather accurate structures of excited electronic states were obtained. MP2 and CASPT2 methods appeared to be the most efficient and CCSD(T), CR‐EOM‐CCSD(T), and MR‐AQCC the most accurate. It was found that at equilibrium all the molecules under study are nonplanar in S₁ and T₁ electronic states with CO out‐of‐plane angle ranging from 34° (H₂CO, S₁) to 52° (F₂CO, T₁), and height of barrier to inversion varying from 300 (H₂CO, S₁) to 11,000 (F₂CO, T₁) cm^?1. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Water‐in‐Oil Micro‐Emulsion Enhances the Secondary Structure of a Protein by Confinement

A scheme is presented in which an organic solvent environment in combination with surfactants is used to confine a natively unfolded protein inside an inverse microemulsion droplet. This type of confinement allows a study that provides unique insight into the dynamic structure of an unfolded, flexible protein which is still solvated and thus under near‐physiological conditions. In a model system, the protein osteopontin (OPN) is used. It is a highly phosphorylated glycoprotein that is expressed in a wide range of cells and tissues for which limited structural analysis exists due to the high degree of flexibility and large number of post‐translational modifications. OPN is implicated in tissue functions, such as inflammation and mineralisation. It also has a key function in tumour metastasis and progression. Circular dichroism measurements show that confinement enhances the secondary structural features of the protein. Small‐angle X‐ray scattering and dynamic light scattering show that OPN changes from being a flexible protein in aqueous solution to adopting a less flexible and more compact structure inside the microemulsion droplets. This novel approach for confining proteins while they are still hydrated may aid in studying the structure of a wide range of natively unfolded proteins.     

FCclasses3: Vibrationally-resolved spectra simulated at the edge of the harmonic approximation

We introduce FCclasses3, a code to carry out vibronic simulations of electronic spectra and nonradiative rates, based on the harmonic approximation. Key new features are: implementation of the full family of vertical and adiabatic harmonic models, vibrational analysis in curvilinear coordinates, extension to several electronic spectroscopies and implementation of time-dependent approaches. The use of curvilinear valence internal coordinates allows the adoption of quadratic model potential energy surfaces (PES) of the initial and final states expanded at arbitrary configurations. Moreover, the implementation of suitable projectors provides a robust framework for defining reduced-dimensionality models by sorting flexible coordinates out of the harmonic subset, so that they can then be treated at anharmonic level, or with mixed quantum classical approaches. A set of tools to facilitate input preparation and output analysis is also provided. We show the program at work in the simulation of different spectra (one and two-photon absorption, emission and resonance Raman) and internal conversion rate of a typical rigid molecule, anthracene. Then, we focus on absorption and emission spectra of a series of flexible polyphenyl molecules, highlighting the relevance of some of the newly implemented features. The code is freely available at http://www.iccom.cnr.it/en/fcclasses/ .