Effect of microhydration on the electronic structure of the chromophores of the photoactive yellow and green fluorescent proteins

Electronic structure calculations of microhydrated model chromophores (in their deprotonated anionic forms) of the photoactive yellow and green fluorescent proteins (PYP and GFP) are reported. Electron-detachment and excitation energies as well as binding energies of mono- and dihydrated isomers are computed and analyzed. Microhydration has different effects on the excited and ionized states. In lower-energy planar isomers, the interaction with one water molecule blueshifts the excitation energies by 0.1-0.2 eV, whereas the detachment energies increase by 0.4-0.8 eV. The important consequence is that microhydration by just one water molecule converts the resonance (autoionizing) excited states of the bare chromophores into bound states. In the lower-energy microhydrated clusters, interactions with water have negligible effect on the chromophore geometry; however, we also identified higher-energy dihydrated clusters of PYP in which two water molecules form hydrogen-bonding network connecting the carboxylate and phenolate moieties and the chromophore is strongly distorted resulting in a significant shift of excitation energies (up to 0.6 eV).     

Excited-State Electronic Structure with Configuration Interaction Singles and Tamm-Dancoff Time-Dependent Density Functional Theory on Graphical Processing Units

Excited-state calculations are implemented in a development version of the GPU-based TeraChem software package using the configuration interaction singles (CIS) and adiabatic linear response Tamm-Dancoff time-dependent density functional theory (TDA-TDDFT) methods. The speedup of the CIS and TDDFT methods using GPU-based electron repulsion integrals and density functional quadrature integration allows full ab initio excited-state calculations on molecules of unprecedented size. CIS/6-31G and TD-BLYP/6-31G benchmark timings are presented for a range of systems, including four generations of oligothiophene dendrimers, photoactive yellow protein (PYP), and the PYP chromophore solvated with 900 quantum mechanical water molecules. The effects of double and single precision integration are discussed, and mixed precision GPU integration is shown to give extremely good numerical accuracy for both CIS and TDDFT excitation energies (excitation energies within 0.0005 eV of extended double precision CPU results).     

QM/MM study of the absorption spectra of DsRed.M1 chromophores

We report geometries and vertical excitation energies for the red and green chromophores of the DsRed.M1 protein in the gas phase and in the solvated protein environment. Geometries are optimized using density functional theory (DFT, B3LYP functional) for the isolated chromophores and combined quantum mechanical/molecular mechanical (QM/MM) methods for the protein (B3LYP/MM). Vertical excitation energies are computed using DFT/MRCI, OM2/MRCI, and TDDFT as QM methods. In the case of the red chromophore, there is a general blue shift in the excitation energies when going from the isolated chromophore to the protein, which is caused both by structural changes and by electrostatic interactions with the environment. For the lowest ππ* transition, these two factors contribute to a similar extent to the overall DFT/MRCI shift of 0.4 eV. An enlargement of the QM region to include active‐site residues does not change the DFT/MRCI excitation energies much. The DFT/MRCI results are closest to experiment for both chromophores. OM2/MRCI and TDDFT overestimate the first vertical excitation energy by 0.3–0.5 and 0.2–0.4 eV, respectively, relative to the experimental or DFT/MRCI values. The experimental gap of 0.35 eV between the lowest ππ* excitation energies of the red (cis‐acylimine) and green (trans‐peptide) forms is well reproduced by DFT/MRCI and TDDFT (0.32 and 0.37 eV, respectively). A histogram spectrum for an equal mixture of the two forms, generated by OM2/MRCI calculations on 450 snapshots along molecular dynamics trajectories, matches the experimental spectrum quite well, with a gap of 0.23 eV and an overall blue shift of about 0.3 eV. DFT/MRCI appears as an attractive choice for calculating excitation energies in fluorescent proteins, without the shortcomings of TDDFT and computationally more affordable than CASSCF‐based approaches. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Coupled-cluster studies of the lowest excited states of the 11-cis-retinal chromophore

The first few excited states of the 11-cis-retinal (PSB11) chromophore have been studied at the coupled-cluster approximative singles and doubles (CC2) level using triple-zeta quality basis sets augmented with double sets of polarisation functions. The two lowest vertical excitation energies of 2.14 and 3.21 eV are in good agreement with recently reported experimental values of 2.03 and 3.18 eV obtained in molecular beam measurements. Calculations at the time-dependent density functional theory (TDDFT) level using the B3LYP hybrid functional yield vertical excitation energies of 2.34 and 3.10 eV for the two lowest states. Zero-point vibrational energy (ZPVE) corrections of -0.09 and -0.17 eV were deduced from the harmonic vibrational frequencies for the ground and excited states calculated at the density functional theory (DFT) and TDDFT level, respectively, using the B3LYP hybrid functional.     

The lowest singlet states of octatetraene revisited

The two lowest excited singlet states of all-trans-1,3,5,7-octatetraene, 2?(1)A(-)(g) and 1?(1)B(+)(u), are studied by means of high level ab initio methods computing the vertical and adiabatic excitation energies for both states and the vertical emission energy for the 1 (1)A(g)(-)←2?(1)A(-)(g) transition. The results confirm the known assignment of two energies, the 2?(1)A(-)(g) adiabatic excitation energy and the 2?(1)A(-)(g) vertical emission energy, for which well defined experimental values are available, with an excellent agreement between theory and experiment. In the experimental absorption spectrum, the maximum of the band describing the 1?(1)B(+)(u)←1?(1)A(g)(-) excitation is the first peak and it has been assigned to the (0-0) vibrational transition, but in literature it is normally compared with the theoretical vertical excitation energy. This comparison has been questioned in the past, but a conclusive demonstration of its lack of foundation has not been given. The analysis reported here, while confirming the assignment of the highest peak in the experimental spectrum to the (0-0) adiabatic transition, indicates that it cannot be used as a reference for the vertical excitation energy. The theoretical vertical excitation energies for the 2?(1)A(-)(g) and 1?(1)B(+)(u) states are found to be almost degenerate, with a value, ? 4.8 eV, higher than that normally accepted in the literature, 4.4 eV. The motivations which have induced in the past other authors to consider this a correct value are discussed and the origin of their feebleness are analyzed.     

Reduction of the virtual space for coupled-cluster excitation energies of large molecules and embedded systems

We investigate how the reduction of the virtual space affects coupled-cluster excitation energies at the approximate singles and doubles coupled-cluster level (CC2). In this reduced-virtual-space (RVS) approach, all virtual orbitals above a certain energy threshold are omitted in the correlation calculation. The effects of the RVS approach are assessed by calculations on the two lowest excitation energies of 11 biochromophores using different sizes of the virtual space. Our set of biochromophores consists of common model systems for the chromophores of the photoactive yellow protein, the green fluorescent protein, and rhodopsin. The RVS calculations show that most of the high-lying virtual orbitals can be neglected without significantly affecting the accuracy of the obtained excitation energies. Omitting all virtual orbitals above 50 eV in the correlation calculation introduces errors in the excitation energies that are smaller than 0.1 eV. By using a RVS energy threshold of 50 eV, the CC2 calculations using triple-ζ basis sets (TZVP) on protonated Schiff base retinal are accelerated by a factor of 6. We demonstrate the applicability of the RVS approach by performing CC2/TZVP calculations on the lowest singlet excitation energy of a rhodopsin model consisting of 165 atoms using RVS thresholds between 20 eV and 120 eV. The calculations on the rhodopsin model show that the RVS errors determined in the gas-phase are a very good approximation to the RVS errors in the protein environment. The RVS approach thus renders purely quantum mechanical treatments of chromophores in protein environments feasible and offers an ab initio alternative to quantum mechanics/molecular mechanics separation schemes.     

The electronic states of 1,2,3-triazole studied by vacuum ultraviolet photoabsorption and ultraviolet photoelectron spectroscopy, and a comparison with ab initio configuration interaction methods

The Rydberg states in the vacuum ultraviolet photoabsorption spectrum of 1,2,3-triazole have been measured and analyzed with the aid of comparison to the UV valence photoelectron ionizations and the results of ab initio configuration interaction (CI) calculations. Calculated electronic ionization and excitation energies for singlet, triplet valence, and Rydberg states were obtained using multireference multiroot CI procedures with an aug-cc-pVTZ [5s3p3d1f] basis set and a set of Rydberg [4s3p3d3f] functions. Adiabatic excitation energies obtained for several electronic states using coupled-cluster (singles, doubles, and triples) and complete active space self-consistent field procedures agree well with experimental values. Variations in bond lengths with the electronic state are discussed. The lowest energy UV band (～5.5-6.5 eV) is assigned to three electronically excited states and demonstrates the occurrence of a nonplanar upper state on the low energy side. A UV photoelectron spectrum with an improved resolution yielded adiabatic and vertical ionization energies and reorganization energies for several of the lowest cationic states. As well as excitations to the s, p, d-Rydberg states are the excitations consistent with an f-series.     

Excited state properties,fluorescence energies,and lifetimes of a poly(fluorene‐phenylene), based on TD‐DFT investigation

The structural and electronic properties of fluorene‐phenylene copolymer (FP)_n, n = 1–4 were studied by means of quantum chemical calculations based on density functional theory (DFT) and time dependent density functional theory (TD‐DFT) using B3LYP functional. Geometry optimizations of these oligomers were performed for the ground state and the lowest singlet excited state. It was found that (FP)_n is nonplanar in its ground state while the electronic excitations lead to planarity in its S₁ state. Absorption and fluorescence energies were calculated using TD‐B3LYP/SVP and TD‐B3LYP/SVP+ methods. Vertical excitation energies and fluorescence energies were obtained by extrapolating these values to infinite chain length, resulting in extrapolated values for vertical excitation energy of 2.89 and 2.87 eV, respectively. The S₁ ← S₀ electronic excitation is characterized as a highest occupied molecular orbital to lowest unoccupied molecular orbital transition and is distinguishing in terms of oscillator strength. Fluorescence energies of (FP)_n calculated from TD‐B3LYP/SVP and TD‐B3LYP/SVP+ methods are 2.27 and 2.26 eV, respectively. Radiative lifetimes are predicted to be 0.55 and 0.51 ns for TD‐B3LYP/SVP and TD‐B3LYP/SVP+ calculations, respectively. These fundamental information are valuable data in designing and making of promising materials for LED materials. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Improving convergence of experimental and computed vertical ionization energies using the ionization potential equation-of-motion coupled-cluster with singles and doubles method

Comparison of statistically evaluated experimental vertical ionization energies (IEs) for 53 medium-sized molecules (6-34 atoms) with ionization potential equation-of-motion coupled-cluster with singles and doubles (IP-EOMCCSD) computations shows that discrepancies between computed and experimental results can be accounted for with a combination of experimental and theoretical contributions. Discrepancies can be minimized by extrapolating computations to the complete basis set limit and correcting for vibrational zero-point energy (ZPE) while comparing with experimental IEs calculated as the intensity-weighted mean band position to account for band asymmetries. This procedure reduced the average discrepancy for ethylene, (E)-2-butene, 2,5-dihydrofuran, and pyrrole from 0.25 to 0.05 eV. Agreement between reported vertical IEs and computations without either making adjustments as described in this paper or using complete simulation of the ionization spectrum should be considered fortuitous. The comparisons made in this work show that estimates of vertical and adiabatic IE made using IP-EOMCCSD extrapolated to the complete basis set limit and corrected for vibrational ZPE can be used with reasonable confidence when experimental values are not available.     

A CASSCF/CASPT2 study on the low-lying excited states of HSiCN, HSiNC and their ions

Equilibrium geometries of low-lying electronic states of cyanosilylene (HSiCN), isocyanosilylene (HSiNC), and their ions have been investigated using the complete active space self-consistent field (CASSCF) approach. The harmonic vibrational frequencies on the optimized geometries were calculated using the multiconfiguration linear response (MCLR) method. Taking the further correlation effects into account, the complete active space perturbation theory of second-order (CASPT2) was carried out for the energetic correction. The CASPT2 calculations have been performed to obtain the vertical excitation energies of selected low-lying excited states of HSiCN and HSiNC. Computed results show that the singlet-triplet splittings are calculated to be 0.99 and 1.30 eV for HSiCN and HSiNC, respectively. The vertical excitation energies of the lowest singlet and triplet excited states in HSiCN are lower than those in HSiNC. The first vertical ionization energy of HSiCN (10.04 eV) is higher than that of HSiNC (9.97 eV). The ground-state adiabatic electron affinities are found to be rather high, and the value of HSiCN (1.85 eV) higher than that of HSiNC (1.52 eV). The existences of dipole-bound excited negative ion states have been discovered within HSiCN and HSiNC.     

Conductor‐like screening model for relaxed excited states: Implementation in the semiempirical method MSINDO

Two approaches to treat solvent polarization and reorientation effects for excited states of molecules and surfaces have been implemented in the recently developed MSINDO‐sCIS method (Gadaczek, Krause, Hintze, Bredow, J. Chem. Theory Comput. 2011, 7, 3675). They allow for an efficient calculation of analytical energy gradients and hence open the opportunity to investigate fluorescence effects or photochemical reactions in solution for large molecules that are difficult to treat with high‐level methods. Both approaches are based on the conductor‐like screening model (COSMO) (Klamt and Schüürmann, J. Chem. Soc., Perkin Trans. 1993, 2, 799) in combination with the configuration interaction singles (CIS) method (Foresman, Head‐Gordon, Pople, and Frisch, J. Phys. Chem. 1992, 96, 135). The paper gives a brief outline of the theoretical background. As a first application, solvent shifts of three well‐studied, environment‐sensitive fluorescent dyes (Kucherak, Didier, Mély, and Klymchenko, J. Phys. Chem. Lett. 2010, 1, 616) have been calculated and compared with experimental results and standard time‐dependent density functional theory. A statistical evaluation of MSINDO‐COSMO‐sCIS is provided for a set of 39 molecules suggested recently by Jacquemin et al. (Jacquemin, Planchat, Adamo, and Mennucci, J. Chem. Theory Comput. 2012, 8, 2359). Calculated vertical and adiabatic excitation energies and fluorescence energies are compared to experimental data. © 2014 Wiley Periodicals, Inc.     

The lowest 2A' excited state of the water-hydroxyl complex

Vertical and adiabatic excitation energies of the lowest (2)A(') excited state in the water-hydroxyl complex have been determined using coupled cluster, multireference configuration interaction, multireference perturbation theory, and density-functional methods. A significant redshift of about 0.4 eV in the vertical excitation energy of the complex compared to that of the hydroxyl radical monomer is found with the coupled cluster calculations validating previous results. Electronic excitation leads to a structure with near-equal sharing of the hydroxyl hydrogen by both oxygen atoms and a concomitantly large redshift of the adiabatic excitation energy of approximately 1 eV relative to the vertical excitation energy. The combination of redshifts ensures that the electronic transition in the complex lies well outside the equivalent excitation in the hydroxyl radical monomer. The complex is approximately five times more strongly bound in the excited state than in the ground state.     

On the electronically excited states of uracil

Vertical excitation energies in uracil in the gas phase and in water solution are investigated by the equation-of-motion coupled-cluster and multireference configuration interaction methods. Basis set effects are found to be important for converged results. The analysis of electronic wave functions reveals that the lowest singlet states are predominantly of a singly excited character and are therefore well described by single-reference equation-of-motion methods augmented by a perturbative triples correction to account for dynamical correlation.Our best estimates for the vertical excitation energies for the lowest singlet n --> pi* and pi --> pi* are 5.0 +/- 0.1 eV and 5.3 +/- 0.1 eV, respectively. The solvent effects for these states are estimated to be +0.5 eV and +/- 0.1 eV, respectively. We attribute the difference between the computed vertical excitations and the maximum of the experimental absorption to strong vibronic interaction between the lowest A" and A' states leading to intensity borrowing by the forbidden transition.     

Analytical nuclear excited‐state gradients for the Tamm–Dancoff approximation using uncoupled frozen‐density embedding

We report the derivation and implementation of analytical nuclear gradients for excited states using time‐dependent density functional theory using the Tamm–Dancoff approximation combined with uncoupled frozen‐density embedding using density fitting. Explicit equations are presented and discussed. The implementation is able to treat singlet as well as triplet states and functionals using the local density approximation, the generalized gradient approximation, combinations with Hartree–Fock exchange (hybrids), and range‐separated functionals such as CAM‐B3LYP. The new method is benchmarked against supermolecule calculations in two case studies: The solvatochromic shift of the (vertical) fluorescence energy of 4‐aminophthalimide on solvation, and the first local excitation of the benzonitrile dimer. Whereas for the 4‐aminophthalimide–water complex deviations of about 0.2 eV are obtained to supermolecular calculations, for the benzonitrile dimer the maximum error for adiabatic excitation energies is below 0.01 eV due to a weak coupling of the subsystems. © 2017 Wiley Periodicals, Inc.     

Syntheses,Spectroscopic and DFT Studies of Two New D‐π‐A Compounds

Two novel 1,3‐dithiole‐2‐ylidene derivatives with a push–pull structures, 3‐(4,5‐dicarbomethoxy‐1,3‐dithiol‐2‐ylidene)naphthopyranone 1 and 3‐(4,5‐dimethylthio‐1,3‐dithiol‐2‐ylidene)naphthopyranone 2 , have been synthesized and characterized by ¹H NMR, IR, MS. The UV–vis spectra of 1 , 2 in CH₂Cl₂, the lowest‐energy absorption bands, are centered at 280, 316, and 430 nm for 1 and 284, 317, and 450 nm for 2 , respectively, which are caused by the HOMO → LUMO single electron promotion. Furthermore, the steady‐state fluorescence originating states of 1 , 2 from the excited charge‐transfer were observed. To estimate the position and energies of frontier orbitals for 1 , 2 , DFT calculations were performed using the Gaussian 03 program at the B3LYP/6‐31 G* level. The calculated vertical excitation energies are in good agreement with the experimental data. The high HOMO–LUMO gaps of 1 (3.08 eV) and 2 (3.00 eV) indicate high kinetic stability of the title compounds.     

Radiationless decay of excited states of tetrahydrocannabinol through the S 1–S 0 (conical) intersection

The ground and electronically excited singlet states of tetrahydrocannabinol have been studied theoretically using density functional and time-dependent density functional methods. The vertical excitation energies, the equilibrium geometries as well as the adiabatic excitation energies have been determined. Opening of the six-membered ring between the oxygen and carbon atoms has been considered as photochemical reaction path. This mechanism leads to a typical excited-state intramolecular hydrogen-transfer process and produces low-lying S ₀–S ₁ intersection (possible conical intersection, CI) which provides a channel for effective radiationless deactivation of the electronically excited state.