Spectral tuning in visual pigments: an ONIOM(QM:MM) study on bovine rhodopsin and its mutants

We have investigated geometries and excitation energies of bovine rhodopsin and some of its mutants by hybrid quantum mechanical/molecular mechanical (QM/MM) calculations in ONIOM scheme, employing B3LYP and BLYP density functionals as well as DFTB method for the QM part and AMBER force field for the MM part. QM/MM geometries of the protonated Schiff-base 11- cis-retinal with B3LYP and DFTB are very similar to each other. TD-B3LYP/MM excitation energy calculations reproduce the experimental absorption maximum of 500 nm in the presence of native rhodopsin environment and predict spectral shifts due to mutations within 10 nm, whereas TD-BLYP/MM excitation energies have red-shift error of at least 50 nm. In the wild-type rhodopsin, Glu113 shifts the first excitation energy to blue and accounts for most of the shift found. Other amino acids individually contribute to the first excitation energy but their net effect is small. The electronic polarization effect is essential for reproducing experimental bond length alternation along the polyene chain in protonated Schiff-base retinal, which correlates with the computed first excitation energy. It also corrects the excitation energies and spectral shifts in mutants, more effectively for deprotonated Schiff-base retinal than for the protonated form. The protonation state and conformation of mutated residues affect electronic spectrum significantly. The present QM/MM calculations estimate not only the experimental excitation energies but also the source of spectral shifts in mutants.     

Influence of Arrestin on the Photodecay of Bovine Rhodopsin

Continued activation of the photocycle of the dim‐light receptor rhodopsin leads to the accumulation of all‐trans‐retinal in the rod outer segments (ROS). This accumulation can damage the photoreceptor cell. For retinal homeostasis, deactivation processes are initiated in which the release of retinal is delayed. One of these processes involves the binding of arrestin to rhodopsin. Here, the interaction of pre‐activated truncated bovine visual arrestin (Arr^Tr) with rhodopsin in 1,2‐diheptanoyl‐sn‐glycero‐3‐phosphocholine (DHPC) micelles is investigated by solution NMR techniques and flash photolysis spectroscopy. Our results show that formation of the rhodopsin–arrestin complex markedly influences partitioning in the decay kinetics of rhodopsin, which involves the simultaneous formation of a meta II and a meta III state from the meta I state. Binding of Arr^Tr leads to an increase in the population of the meta III state and consequently to an approximately twofold slower release of all‐trans‐retinal from rhodopsin.     

Relationship between orbital energy gaps and excitation energies for long‐chain systems

The difference between the excitation energies and corresponding orbital energy gaps, the exciton binding energy, is investigated based on time‐dependent (TD) density functional theory (DFT) for long‐chain systems: all‐trans polyacetylenes and linear oligoacenes. The optimized geometries of these systems indicate that bond length alternations significantly depend on long‐range exchange interactions. In TDDFT formalism, the exciton binding energy comes from the two‐electron interactions between occupied and unoccupied orbitals through the Coulomb‐exchange‐correlation integral kernels. TDDFT calculations show that the exciton binding energy is significant when long‐range exchange interactions are involved. Spin‐flip (SF) TDDFT calculations are then carried out to clarify double‐excitation effects in these excitation energies. The calculated SF‐TDDFT results indicate that double‐excitation effects significantly contribute to the excitations of long‐chain systems. The discrepancies between the vertical ionization potential minus electron affinity (IP–EA) values and the HOMO–LUMO excitation energies are also evaluated for the infinitely long polyacetylene and oligoacene using the least‐square fits to estimate the exciton binding energy of infinitely long systems. It is found that long‐range exchange interactions are required to give the exciton binding energy of the infinitely long systems. Consequently, it is concluded that long‐range exchange interactions neglected in many DFT calculations play a crucial role in the exciton binding energies of long‐chain systems, while double‐excitation correlation effects are also significant to hold the energy balance of the excitations. © 2016 Wiley Periodicals, Inc.     

Comparison of ground and excited state polarizabilities of thiophene,cyclopentadiene, and fulvene oligomers and their cyano substituted derivatives—Ab initio study

Ab Initio study of the ground and excited state polarizabilities of thiophene, fulvene, and cyclopentadiene based conducting oligomers and their cyano derivatives have been performed using the restricted Hartree–Fock (RHF) and the configuration interaction singles (CIS) approaches, respectively, with 3‐21G* basis set. For comparison purposes, for some small oligomers (monomers and dimers), higher basis sets (6‐31G*, 6‐31+G*, aug‐cc‐pVTZ) were also employed in the computations of polarizabilities. The trends in polarizability as a function of oligomer length were investigated. For all systems, the RHF polarizability increases as n^1.2–1.3 as n gets larger and the CIS polarizability increases as n^1.4–1.6 for n less than seven or eight rings and then increases approximately linearly with n for larger n. For the thiophene based systems the dependence of the polarizability on bond length alternation (BLA) along the backbone of the oligomers was also investigated using the RHF, density functional (DFT), and CIS theories (with 3‐21G* basis set). For thiophene dimer, we also performed RHF/aug‐cc‐pVTZ calculations of polarizabilities versus BLA. We found that the polarizability is largest when BLA is near zero (for both ground and excited states), which correlates with the lowest excitation energy. Comparison with experimental results has been made where possible. © 2007 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 45: 1983–1995, 2007     

pH‐dependent Interaction of Rhodopsin with Cyanidin‐3‐glucoside. 2. Functional Aspects†

Anthocyanins are a class of phytochemicals that confer color to flowers, fruits, vegetables and leaves. They are part of our regular diet and serve as dietary supplements because of numerous health benefits, including improved vision. Recent studies have shown that the anthocyanin cyanidin‐3‐O‐glucoside (C3G) increased regeneration of the dim‐light photoreceptor rhodopsin (Matsumoto et al. [2003] J. Agric. Food Chem., 51 , 3560–3563). In an accompanying study (Yanamala et al. [2009] Photochem. Photobiol.), we show that C3G directly binds to rhodopsin in a pH‐dependent manner. In this study, we investigated the functional consequences of C3G binding to rhodopsin. As observed previously in rod outer segments, regeneration of purified rhodopsin in detergent micelles is also accelerated in the presence of C3G. Thermal denaturation and stability studies using circular dichroism, fluorescence and UV/visible absorbance spectroscopy show that C3G exerts a destabilizing effect on rhodopsin structure while it only modestly alters G‐protein activation and the rates at which the light‐activated Metarhodopsin II state decays to opsin and free retinal. These results indicate that the mechanism of C3G‐enhanced regeneration may be based on changes in opsin structure promoting access to the retinal binding pocket.     

Substituent Effects in the Absorption Spectra of Phenol Radical Species: Origin of the Redshift Caused by 3,5‐Dimethoxyl Substitution

The ground‐state equilibrium geometries, electronic structures and vertical excitation energies of methyl‐ and methoxyl‐substituted phenol radical cations and phenoxyl radicals have been investigated using time‐dependent density‐functional theory (namely TD‐B3LYP) and complete‐active‐space second‐order perturbation theory (CASPT2). The “anomalous” large redshifts of the absorption maxima of the phenol radical species observed in the ultraviolet–visible spectral region upon di‐meta‐methoxyl substitution are reproduced by the calculations. Furthermore, these “anomalous” shifts which were unexplained to date can be rationalized on the basis of a qualitative molecular orbital perturbation analysis.     

Is the choice of a standard zeroth‐order hamiltonian in CASPT2 ansatz optimal in calculations of excitation energies in protonated and unprotonated schiff bases of retinal?

To account for systematic error of CASPT2 method empirical modification of the zeroth‐order Hamiltonian with Ionization Potential‐Electron Affinity (IPEA) shift was introduced. The optimized IPEA value (0.25 a.u.), called standard IPEA (S‐IPEA), was recommended but due to its unsatisfactory performance in multiple metallic and organic compounds it has been questioned lately as a general parameter working properly for all molecules under CASPT2 study. As we are interested in Schiff bases of retinal, an important question emerging from this conflict of choice, to use or not to use S‐IPEA, is whether the introduction of the modified zeroth‐order Hamiltonian into CASPT2 ansatz does really improve their energetics. To achieve this goal, we assessed an impact of the IPEA shift value, in a range of 0–0.35 a.u., on vertical excitation energies to low‐lying singlet states of two protonated (RPSBs) and two unprotonated (RSBs) Schiff bases of retinal for which experimental data in gas phase are available. In addition, an effect of geometry, basis set, and active space on computed VEEs is also reported. We find, that for these systems, the choice of S‐IPEA significantly overestimates both S₀→S₁ and S₀→S₂ energies and the best theoretical estimate, in reference to the experimental data, is provided with either unmodified zeroth‐order Hamiltonian or small value of the IPEA shift in a range of 0.05–0.15 a.u., depending on active space and basis set size, equilibrium geometry, and character of the excited state. © 2018 Wiley Periodicals, Inc.     

Quantum chemical comparison of vertical,adiabatic, and 0‐0 excitation energies: The PYP and GFP chromophores

A number of benchmark studies investigating the performance of quantum chemical methods for calculating vertical excitation energies are today available in the literature. However, less established is the variation between methods in their estimates of the differences between vertical, adiabatic, and 0‐0 excitation energies. To this end, such excitation energies are here calculated for the bright S₁ states of the anionic chromophores of the photoactive yellow protein (PYP) and the green fluorescent protein (GFP) in the gas phase using configuration interaction singles, complete active space self‐consistent field, coupled‐cluster singles and doubles, and time‐dependent density functional theory methods. Although the estimates of the excitation energies vary by more than 1 eV between the methods, the differences between the different types of excitation energies are found to be relatively method‐insensitive, varying by ～0.1 eV only for these particular chromophores. Specifically, the adiabatic energies are uniformly 0.10–0.17 (PYP) and 0.06–0.17 eV (GFP) lower than the vertical energies, and the 0‐0 energies are similarly 0.09–0.14 (PYP) and 0.07–0.17 eV (GFP) lower than the adiabatic energies. © 2012 Wiley Periodicals, Inc.     

The Photocycle of Channelrhodopsin‐2: Ultrafast Reaction Dynamics and Subsequent Reaction Steps

The photocycle of channelrhodopsin‐2 is investigated in a comprehensive study by ultrafast absorption and fluorescence spectroscopy as well as flash photolysis in the visible spectral range. The ultrafast techniques reveal an excited‐state decay mechanism analogous to that of the archaeal bacteriorhodopsin and sensory rhodopsin II from Natronomonas pharaonis. After a fast vibrational relaxation of the excited‐state population with 150 fs its decay with mainly 400 fs is observed. Hereby, both the initial all‐trans retinal ground state and the 13‐cis‐retinal K photoproduct are populated. The reaction proceeds with a 2.7 ps component assigned to cooling processes. Small spectral shifts are observed on a 200 ps timescale. They are attributed to conformational rearrangements in the retinal binding pocket. The subsequent dynamics progresses with the formation of an M‐like intermediate (7 and 120 μs), which decays into red‐shifted states within 3 ms. Ground‐state recovery including channel closing and reisomerization of the retinal chromophore occurs in a triexponential manner (6 ms, 33 ms, 3.4 s). To learn more about the energy barriers between the different photocycle intermediates, temperature‐dependent flash photolysis measurements are performed between 10 and 30 °C. The first five time constants decrease with increasing temperature. The calculated thermodynamic parameters indicate that the closing mechanism is controlled by large negative entropy changes. The last time constant is temperature independent, which demonstrates that the photocycle is most likely completed by a series of individual steps recovering the initial structure.     

Theoretical studies on structures and electronic spectra of linear carbon chains C2nH+ (n = 1−5)

The density functional theory (DFT) and the complete active space self‐consistent‐field (CASSCF) method have been used for full geometry optimization of carbon chains C_2nH⁺ (n = 1–5) in their ground states and selected excited states, respectively. Calculations show that C_2nH⁺ (n = 1–5) have stable linear structures with the ground state of X³Π for C₂H⁺ or X³Σ^? for other species. The excited‐state properties of C_2nH⁺ have been investigated by the multiconfigurational second‐order perturbation theory (CASPT2), and predicted vertical excitation energies show good agreement with the available experimental values. On the basis of our calculations, the unsolved observed bands in previous experiments have been interpreted. CASSCF/CASPT2 calculations also have been used to explore the vertical emission energy of selected low‐lying states in C_2nH⁺ (n = 1–5). Present results indicate that the predicted vertical excitation and emission energies of C_2nH⁺ have similar size dependences, and they gradually decrease as the chain size increases. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Influence of the Delocalization Error and Applicability of Optimal Functional Tuning in Density Functional Calculations of Nonlinear Optical Properties of Organic Donor–Acceptor Chromophores

Nonempirically tuned hybrid density functionals with range‐separated exchange are applied to calculations of the first hyperpolarizability (β_∥) and charge‐transfer (CT) excitations of linear “push–pull” donor–acceptor‐substituted organic molecules with extended π‐conjugated bridges. An unphysical delocalization with increasing chain length in density functional calculations can be reduced significantly by enforcing an asymptotically correct exchange‐correlation potential adjusted to give frontier orbital energies representing ionization potentials. The delocalization error for a number of donor–acceptor systems is quantified by calculations with fractional electron numbers and from orbital localizations. Optimally tuned hybrid variants of the PBE functional incorporating range‐separated exchange can produce similar magnitudes for β_∥ as Møller–Plesset second‐order perturbation (MP2) correlated calculations. Improvements are also found for CT excitation energies, with results similar to an approximate coupled‐cluster model (CC2).     

Structural and electronic properties of polyacetylene and polyyne from hybrid and Coulomb-attenuated density functionals

The bond length alternation (BLA), the highest-occupied-lowest-unoccupied (HO-LU) orbital energy gap, and the corresponding excitation energy are determined for trans-polyacetylene (PA) and polyyne (PY) using density functional theory. Results from the Coulomb-attenuated CAM-B3LYP functional are compared with those from the conventional BHHLYP and B3LYP hybrid functionals. BLA values and HO-LU gaps are determined using both finite oligomer and infinite chain calculations, subject to periodic boundary conditions. TDDFT excitation energies are determined for the oligomers. The oligomer excitation energies and HO-LU gaps are then used, in conjunction with the infinite chain HO-LU gap, to estimate the infinite chain excitation energy. Overall, BHHLYP and CAM-B3LYP give BLA values and excitation energies that are larger and more accurate than those obtained using B3LYP. The results highlight the degree to which excitation energies can be approximated using the HO-LU gaps-at the infinite limit, this approximation works well for B3LYP, but not for the other functionals, where the HO-LU gap is significantly larger. The study provides further evidence for the high-quality theoretical predictions that can be obtained from the CAM-B3LYP functional.     

Retinal Conformation and Dynamics in Activation of Rhodopsin Illuminated by Solid‐state 2H NMR Spectroscopy†

Solid‐state NMR spectroscopy gives a powerful avenue for investigating G protein‐coupled receptors and other integral membrane proteins in a native‐like environment. This article reviews the use of solid‐state ²H NMR to study the retinal cofactor of rhodopsin in the dark state as well as the meta I and meta II photointermediates. Site‐specific ²H NMR labels have been introduced into three regions (methyl groups) of retinal that are crucially important for the photochemical function of rhodopsin. Despite its phenomenal stability ²H NMR spectroscopy indicates retinal undergoes rapid fluctuations within the protein binding cavity. The spectral lineshapes reveal the methyl groups spin rapidly about their three‐fold (C₃) axes with an order parameter for the off‐axial motion of For the dark state, the ²H NMR structure of 11‐cis‐retinal manifests torsional twisting of both the polyene chain and the β‐ionone ring due to steric interactions of the ligand and the protein. Retinal is accommodated within the rhodopsin binding pocket with a negative pretwist about the C11=C12 double bond. Conformational distortion explains its rapid photochemistry and reveals the trajectory of the 11‐cis to trans isomerization. In addition, ²H NMR has been applied to study the retinylidene dynamics in the dark and light‐activated states. Upon isomerization there are drastic changes in the mobility of all three methyl groups. The relaxation data support an activation mechanism whereby the β‐ionone ring of retinal stays in nearly the same environment, without a large displacement of the ligand. Interactions of the β‐ionone ring and the retinylidene Schiff base with the protein transmit the force of the retinal isomerization. Solid‐state ²H NMR thus provides information about the flow of energy that triggers changes in hydrogen‐bonding networks and helix movements in the activation mechanism of the photoreceptor.     

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     

A high‐accuracy theoretical study of the CHnP Systems n = 1–3

We have performed high‐level electronic structure computations on the most important species of the CH_nP systems n = 1–3 to characterize them and provide reliable information about the equilibrium and vibrationally averaged molecular structures, rotational constants, vibrational frequencies (harmonic and anharmonic), formation enthalpies, and vertical excitation energies. Those chemical systems are intermediates for several important reactions and also prototypical phosphorus‐carbon compounds; however, they are often elusive to experimental detection. The present results significantly complement their knowledge and can be used as an assessment of the experimental information when available. The explicitly correlated coupled‐cluster RCCSD(T)‐F12 method has been used for geometry optimizations and vibrational frequency calculations. Vibrational configuration interaction theory has been used to account for anharmonicity effects. Basis‐set limit extrapolations have been carried out to determine accurate thermochemical quantities. Electronic excited states have been calculated with coupled‐cluster approaches and also by means of the multireference configuration interaction method. © 2013 Wiley Periodicals, Inc.     

线性BC2nB (n＝1～12)的结构特征和电子光谱的理论研究

应用密度泛函理论, 在B3LYP/6-31G^*水平上优化得到了线性簇合物BC_2nB (n＝1～12, D_(h)的平衡几何构型, 并计算了它们的谐振动频率. 在优化平衡几何构型下, 通过TD-B3LYP/cc-pvDZ和TD-B3LYP/cc-pvTZ计算, 分别得到了n＝1～12和n＝1～7的电子跃迁的垂直激发能和对应的振子强度. 在B3LYP/6-311＋G^*水平上计算得到了簇合物BC_2nB (n＝1～12, D_(h)的电离能. 基于计算结果, 导出了BC_2nB体系电子跃迁能以及第一电离能与体系大小n的解析表达式.     

Light Dynamics of the Retinal‐Disease‐Relevant G90D Bovine Rhodopsin Mutant

The RHO gene encodes the G‐protein‐coupled receptor (GPCR) rhodopsin. Numerous mutations associated with impaired visual cycle have been reported; the G90D mutation leads to a constitutively active mutant form of rhodopsin that causes CSNB disease. We report on the structural investigation of the retinal configuration and conformation in the binding pocket in the dark and light‐activated state by solution and MAS‐NMR spectroscopy. We found two long‐lived dark states for the G90D mutant with the 11‐cis retinal bound as Schiff base in both populations. The second minor population in the dark state is attributed to a slight shift in conformation of the covalently bound 11‐cis retinal caused by the mutation‐induced distortion on the salt bridge formation in the binding pocket. Time‐resolved UV/Vis spectroscopy was used to monitor the functional dynamics of the G90D mutant rhodopsin for all relevant time scales of the photocycle. The G90D mutant retains its conformational heterogeneity during the photocycle.     

Studies on metabolites and metabolic pathways of bulleyaconitine A in rat liver microsomes using LC‐MSn combined with specific inhibitors

Bulleyaconitine A (BLA) from Aconitum bulleyanum plants is usually used as anti‐inflammatory drug in some Asian countries. It has a variety of bioactivities, and at the same time some toxicities. Since the bioactivities and toxicities of BLA are closely related to its metabolism, the metabolites and the metabolic pathways of BLA in rat liver microsomes were investigated by HPLC–MSⁿ. In this research, the 12 metabolites of BLA were identified according to the results of HPLC‐MSⁿ data and the relevant literature. The results showed that there are multiple metabolites of BLA in rat liver microsomes, including demethylation, deacetylation, dehydrogenation deacetylation and hydroxylation. The major metabolic pathways of BLA in rat liver microsomes were clarified by HPLC‐MS combined with specific inhibitors of CYP450 isoforms. As a result, CYP3A and 2C were found to be the principal CYP isoforms contributing to the metabolism of BLA. Moreover, CYP2D6 and 2E1 are also more important CYP isoforms for the metabolism of BLA. While CYP1A2 only affected the formation rate of M11, its effect on the metabolism of BLA is very small. Copyright © 2014 John Wiley & Sons, Ltd.     

The sensing mechanism of fluoride anion for a novel molecule D2: Desilylation and intramolecular charge transfer

In this work, the sensing mechanism of a new fluoride chemosensor 12‐([tert‐butyldiphenylsilyl]oxy)‐8a,13a‐dihydro‐7H‐benzo[de]benzo[4,5]imidazo[2,1‐a]‐isoquinolin‐7‐one (abbreviated as D2) is investigated using density functional theory (DFT) and time‐dependent DFT (TDDFT) methods. The theoretical electronic spectra (vertical excitation energies and fluorescence peak) reproduced previous experimental results (D. Li et al., Spectrochim. Acta A Mol. Biomol. Spectrosc. 2017 , 185, 173), which confirms the rationality of the theoretical level used in this work. The constructed potential energy curve of the desilylation process suggests that the low barrier could be responsible for the rapid response to fluoride anions. Analyses of the binding energies show that only fluoride anion can be detected by D2 chemosensor in dimethylsulfoxide (DMSO). In view of the excitation process, the strong intramolecular charge transfer (ICT) process of the S₀ → S₁ transition explains the red shift of the absorption peak of the D2 sensor with the addition of fluoride anions. This work not only presents a straightforward sensing mechanism of sensing of the fluoride anion by the D2 chemosensor but should also play an important role in the synthesis and design of fluorescent sensors in future.