Rhodopsins can modulate the optical properties of their chromophores over a wide range wavelengths. The mechanism for this spectral tuning is based on response retinal chromophore to external stress and interaction with charged, polar, polarizable amino acids protein environment connected its large change in dipole moment upon excitation, electronic polarizability, structural flexibility. In work, we investigate accuracy computational approaches modeling changes absorption energies respect...

The mechanism of color tuning in the rhodopsin family proteins has been studied by comparing optical properties light-driven proton pump bacteriorhodopsin (bR) and light detector sensory II (sRII). Despite a high structural similarity, maximal absorption is blue-shifted from 568 nm bR to 497 sRII. molecular this shift still matter debate, its clarification sheds onto general mechanisms retinal proteins. calculations employ combined quantum mechanical/molecular mechanical (QM/MM) technique,...

This work investigates the capability of time-dependent density functional response theory to describe excited state potential energy surfaces conjugated organic molecules. Applications linear polyenes, aromatic systems, and protonated Schiff base retinal demonstrate scope currently used exchange-correlation functionals as local, adiabatic approximations Kohn-Sham theory. The results are compared experimental ab initio data various kinds attain a critical analysis common problems concerning...

In the present work, we perform a benchmark study on both isolated chromophores retinal and BChl as well biological systems, to determine accuracy of LC-TD-DFT LC-TD-DFTB for describing color-tuning effects.

Recently the novel system of linear carbon chains inside double-walled nanotubes has extended length $s{p}^{1}$ hybridized from 44 to thousands atoms [Shi et al., Nat. Mater. 15, 634 (2016)]. The optoelectronic properties these ultralong are poorly described by current theoretical models, which based on short chain experimental data and assume a constant environment. As such, physical understanding in terms charge transfer van der Waals interactions is widely missing. We provide reference...

The optical and IR-spectroscopic properties of the protonated Schiff base retinal are highly sensitive to electrostatic environment. This feature makes a useful probe study structural differences changes in rhodopsins. It also raises an interest theoretically predict spectroscopic response mutation evolution. Computational models appropriate for this purpose usually combine sophisticated quantum mechanical (QM) methods with molecular mechanics (MM) force fields. In effort test improve...

Ultra long linear carbon chains of more than 6000 atoms have recently been synthesized within double-walled nanotubes, and they show a promising new route to one--atom--wide semiconductors with direct band gap. Theoretical studies predicted that this gap can be tuned by the length chains, end groups, their interactions environment. However, different density functionals lead very values infinitely carbyne. In work, we applied resonant Raman excitation spectroscopy 50 laser wavelengths...

The potential energy surfaces and non-adiabatic dynamics of the C5H6NH 2 + protonated Schiff base (PSB3) have been investigated using OM2 semiempirical Hamiltonian with GUGA configuration interaction. Three approaches to selecting GUGA-CI active space are evaluated closed-shell open-shell molecular orbitals. Energy minima minimum crossing points (MECPs) compared ab initio CASSCF CASPT2 results. Only calculations give a qualitatively correct MECP. Minimum path (MEP) demonstrate that minimal...

The explicit treatment of polarization as a many-body interaction in condensed-phase systems represents current problem empirical force-field development. Although variety efficient models for molecular have been suggested, polarizable force fields are still far from common use nowadays. In this work, we consider interactive employing Thole's short-range damping scheme and assess them application on polypeptides. Despite the simplicity model, find mean polarizabilities anisotropies amino...

The structure and spectroscopy of rhodopsin have been intensely studied in the past decade both experimentally theoretically; however, important issues still remain unresolved. Of central interest is protonation state Glu181, where controversial contradictory experimental evidence has appeared. While FTIR measurements indicate this residue to be unprotonated, preresonance Raman UV-vis spectra interpreted favor a protonated Glu181. Previous computational approaches were not able resolve...

Abstract An analytical formulation for the geometrical derivatives of excitation energies within time‐dependent density‐functional tight‐binding (TD‐DFTB) method is presented. The derivation based on auxiliary functional approach proposed in [Furche and Ahlrichs, J Chem Phys 2002, 117, 7433]. To validate quality potential energy surfaces provided by method, adiabatic energies, excited state geometries, harmonic vibrational frequencies were calculated a test set molecules states different...

Abstract The complex photophysical properties of fluorescent proteins give rise to a wide field applications as markers in molecular biology. Understanding these is essential for rational genetic engineering new proteins. Here, theoretical models are required support the interpretation structural and spectroscopic experimental data. This requires accurate reliable prediction excited‐state features chromophore its interactions with protein matrix. we compare calculations absorption emission...

Charge-transfer excitations highly depend on the electronic coupling between donor and acceptor groups. Nitrophenolates are simple examples of charge-transfer systems where degree differs ortho, meta para isomers. Here we report absorption spectra isolated anions in vacuo to avoid complications solvent effects. Gas-phase action spectroscopy was done with two different setups, an electrostatic ion storage ring accelerator mass spectrometer. The results interpreted basis CC2 quantum chemical...

From blue to red: While four pi-conjugated nitrophenolates absorb within a relatively narrow region in solution, they cover the entire visible spectrum when isolated vacuo [picture: see text]. The work combines gas- and solution-phase spectroscopy provides first benchmark of theoretical excitation energies for nitrophenolates.

Bacteriorhodopsin is a proton-pumping membrane protein found in the plasma of archaeon Halobacterium salinarium. Light-induced isomerization retinal chromophore from all-trans to 13-cis leads sequence five conformation-coupled proton transfer steps and net transport one cytoplasmic extracellular side membrane. The mechanism long-distance primary acceptor Asp85 release group during O → bR poorly understood. Experiments suggest that this could involve transient state [O] which resides on...

Many biochromophore anions located within protein pockets display charge-transfer (CT) transitions that are perturbed by the nearby environment, such as water or amino acid residues. These often contain phenolate moiety electron donor and an acceptor group couples to via a π-conjugated system. Here we show using action spectroscopy single molecules of water, methanol, acetonitrile cause blue shifts in electronic transition energy bare m-nitrophenolate anion 0.22, 0.12 eV, respectively...

The search for new near-infrared probes fluorescence imaging applications is a rapidly growing field of research. Monomeric fluorescent proteins that autocatalyze their chromophore are the most versatile markers in vivo applications, but development bright far-red (RFPs) has proven difficult. In this contribution, we theoretical limit red shift and how it can be reached without sacrificing quantum yield. Through extensive excited-state pathway calculations, molecular dynamics sampling,...

Double vs triple: How is the electronic coupling between donor and acceptor affected by alkene alkyne bridges? To address this question authors have elucidated intrinsic optical properties of p-nitrophenolates using state-of-the-art gas-phase spectroscopy (see picture) excited-state calculations. Detailed facts importance to specialist readers are published as ”Supporting Information”. Such documents peer-reviewed, but not copy-edited or typeset. They made available submitted authors. Please...

The relationship between conformational changes of suberate dianions in water clusters and the corresponding spectroscopic characteristics were studied theoretically by IR spectroscopy (see picture for charge displacement associated with excitation carboxylate symmetric stretching modes). Folded structures are stabilized formation additional hydrogen bonds solvated dianion H2O molecules should thus be retained larger, microhydrated clusters. Detailed facts importance to specialist readers...

Many photoactive biomolecules are anions and exhibit ππ* optical transitions but with a degree of charge transfer (CT) character determined by the local environment. The phenolate moiety is common structural motif among biochromophores luminophores, nitrophenolates good model systems because nitro substituent allows for CT-like transitions. Here we report gas-phase absorption spectra o- p-nitrophenolate·H2O complexes to decipher effect just one H2O compare them ab initio calculations...

Understanding the mechanism of color tuning retinal chromophore by its host protein became one key issues in research on rhodopsins. While early mutation studies addressed genetic origin, recent advanced to investigate structural based X-ray crystallographic structures. For human cone pigments, no crystal structures have been produced, and homology models were employed elucidate origin blue-shifted absorption. In this theoretical study, we take a different route establish model for blue....

Abstract The influence of cross‐conjugation vs. linear conjugation on the electronic communication between donor and acceptor groups in phenol(ate)–bridge–nitrobenzene chromophores was investigated by solution gas‐phase absorption spectroscopy, fluorescence quantum chemical calculations. compounds studied include, among others, geminally trans ‐substituted diethynylethenes prepared stepwise Sonogashira cross‐coupling reactions, cross‐conjugated analogue stilbene. A butadiyne‐bridged...

We combine infrared photodissociation spectroscopy with quantum chemical calculations to characterize the hydration behavior of microsolvated dicarboxylate dianions, (CH2)m(COO−)2·(H2O)n, as a function aliphatic chain length m. find evidence for solvent-mediated folding transitions, signaled by intensity quenching symmetric carboxylate stretching modes, all three species studied (m = 2, 4, 8). The number water molecules required induce increases monotonically and is n 9–12, 13, 18–19...