The extreme instability and strong chemical activity of carbyne, the infinite sp 1 hybridized carbon chain, are responsible for its low possibility to survive at ambient conditions. Therefore, much less has been possible to explore about carbyne as compared to other novel carbon allotropes like fullerenes, nanotubes and graphene. Although end-capping groups can be used to stabilize a carbon chain, length limitation is still a barrier for its actual production, and even more for applications. Here, we report on a novel route for bulk production of record long acethylenic linear carbon chains protected by thin double-walled carbon nanotubes. A corresponding extremely high Raman band is the first proof of a truly bulk yield formation of very long arrangements, which is unambiguously confirmed by transmission electron microscopy. Our production establishes a way to exceptionally long stable carbon chains, and an elegant forerunner towards the final goal of a bulk production of essentially infinite carbyne.Different kinds of allotropes can be formed from elemental carbon due to its sp n hybridization 1 . 1 arXiv:1507.04896v2 [cond-mat.mtrl-sci]

Rhodopsins can modulate the optical properties of their chromophores over a wide range of wavelengths. The mechanism for this spectral tuning is based on the response of the retinal chromophore to external stress and the interaction with the charged, polar, and polarizable amino acids of the protein environment and is connected to its large change in dipole moment upon excitation, its large electronic polarizability, and its structural flexibility. In this work, we investigate the accuracy of computational approaches for modeling changes in absorption energies with respect to changes in geometry and applied external electric fields. We illustrate the high sensitivity of absorption energies on the ground-state structure of retinal, which varies significantly with the computational method used for geometry optimization. The response to external fields, in particular to point charges which model the protein environment in combined quantum mechanical/molecular mechanical (QM/MM) applications, is a crucial feature, which is not properly represented by previously used methods, such as time-dependent density functional theory (TDDFT), complete active space self-consistent field (CASSCF), and Hartree-Fock (HF) or semiempirical configuration interaction singles (CIS). This is discussed in detail for bacteriorhodopsin (bR), a protein which blue-shifts retinal gas-phase excitation energy by about 0.5 eV. As a result of this study, we propose a procedure which combines structure optimization or molecular dynamics simulation using DFT methods with a semiempirical or ab initio multireference configuration interaction treatment of the excitation energies. Using a conventional QM/MM point charge representation of the protein environment, we obtain an absorption energy for bR of 2.34 eV. This result is already close to the experimental value of 2.18 eV, even without considering the effects of protein polarization, differential dispersion, and conformational sampling.

The mechanism of color tuning in the rhodopsin family of proteins has been studied by comparing the optical properties of the light-driven proton pump bacteriorhodopsin (bR) and the light detector sensory rhodopsin II (sRII). Despite a high structural similarity, the maximal absorption is blue-shifted from 568 nm in bR to 497 nm in sRII. The molecular mechanism of this shift is still a matter of debate, and its clarification sheds light onto the general mechanisms of color tuning in retinal proteins. The calculations employ a combined quantum mechanical/molecular mechanical (QM/MM) technique, using a DFT-based method for ground state properties and the semiempirical OM2/MRCI method and ab initio SORCI method for excited state calculations. The high efficiency of the methodology has allowed us to study a wide variety of aspects including dynamical effects. The absorption shift as well as various mutation experiments and vibrational properties have been successfully reproduced. Our results indicate that several sources contribute to the spectral shift between bR and sRII. The main factors are the counterion region at the extracellular side of retinal and the amino acid composition of the binding pocket. Our analysis allows a distinction and identification of the different effects in detail and leads to a clear picture of the mechanism of color tuning, which is in good agreement with available experimental data.

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

Ultra long linear carbon chains of more than 6000 carbon atoms have recently been synthesized within doublewalled carbon nanotubes, and they show a promising new route to one-atom-wide semiconductors with a direct band gap. Theoretical studies predicted that this band gap can be tuned by the length of the chains, the end groups, and their interactions with the environment. However, different density functionals lead to very different values of the band gap of infinitely long carbyne. In this work, we applied resonant Raman excitation spectroscopy with more than 50 laser wavelengths to determine for the first time the band gap of long carbon chains encapsulated inside DWCNTs. The experimentally determined band gaps ranging from 2.253 to 1.848 eV follow a linear relation with Raman frequency. This lower bound is the smallest band gap of linear carbon chains observed so far. The comparison with experimental data obtained for short chains in gas phase or in solution demonstrates the effect of the DWCNT encapsulation, leading to an essential downshift of the band gap. This is explained by the interaction between the carbon chain and the host tube, which greatly modifies the chain's bond length alternation. arXiv:1705.02259v2 [cond-mat.mtrl-sci]

The optical and IR-spectroscopic properties of the protonated Schiff base of retinal are highly sensitive to the electrostatic environment. This feature makes retinal a useful probe to study structural differences and changes in rhodopsins. It also raises an interest to theoretically predict the spectroscopic response to mutation and structural evolution. Computational models appropriate for this purpose usually combine sophisticated quantum mechanical (QM) methods with molecular mechanics (MM) force fields. In an effort to test and improve the accuracy of these QM/MM models, we consider in this article the effects of polarization and inter-residual charge transfer within the binding pocket of bacteriorhodopsin (bR) and pharaonis sensory rhodopsin II (psRII, also called pharaonis phoborhodopsin, ppR) on the excitation energy using an ab initio QM/QM/MM approach. The results will serve as reference for assessing empirical polarization models in a consecutive article.

The potential energy surfaces and non-adiabatic dynamics of the C 5 H 6 NH 2 ? protonated Schiff base (PSB3) have been investigated using the OM2 semiempirical Hamiltonian with GUGA configuration interaction. Three approaches to selecting the GUGA-CI active space are evaluated using closed-shell and open-shell molecular orbitals. Energy minima and minimum energy crossing points (MECPs) have been compared with ab initio CASSCF and CASPT2 results. Only the open-shell calculations give a qualitatively correct MECP. Minimum energy path (MEP) calculations demonstrate that a minimal active space gives a barrierless path from the planar S 1 minimum to the ground state, whereas larger active spaces result in a small barrier to torsional motion. Surface hopping dynamics calculations indicate that this barrier induces bi-exponential dynamics. The comparable CAS-SCF S 1 energy surface is barrierless, but the CASPT2 surface features an energy plateau, which may also lead to more complex dynamics.

Recently the novel system of linear carbon chains inside double-walled carbon nanotubes has extended the length of sp1 hybridized carbon chains from 44 to thousands of atoms [Shi et al., Nat. Mater. 15, 634 (2016)]. The optoelectronic properties of these ultralong chains are poorly described by current theoretical models, which are based on short chain experimental data and assume a constant environment. As such, a physical understanding of the system in terms of charge transfer and van der Waals interactions is widely missing. We provide a reference for the intrinsic Raman frequency of polyynes in vacuo and explicitly describe the interactions between polyynes and carbon nanotubes. We find that van der Waals interactions strongly shift this frequency, which has been neither expected nor described for other intramolecular C-C stretching vibrations. As a consequence of charge transfer from the tube to the chain, the Raman response of long chains is qualitatively different from the known phonon dispersion of polymers close to the Γ point. Based on these findings we show how to correctly interpret the Raman data, considering the nanotube's properties. This is essential for its use as an analytical tool to optimize the growth process for future applications