Full Color Modulation of Firefly Luciferase through Engineering with Unified Stark Effect

The firefly luciferase has been a unique marking tool used in various bioimaging techniques. Extensive color modulation is strongly required to meet special marking demands; however, intentional and accurate wavelength tuning has yet to be achieved. Here, we demonstrate that the color shift of the firefly chromophore (OxyLH₂-1) by internal and external fields can be described as a unified Stark shift. Electrostatic microenvironmental effects on fluorescent spectroscopy are modeled in vacuo through effective electric fields by using time-dependent density functional theory. A complete visible fluorescence spectrum of firefly chromophore is depicted, which enables one to control the emission in a specific color. As an application, the widely observed pH-correlated color shift is proved to be associated with the local Stark field generated by the trace water–ions (vicinal hydronium and hydroxide ions) at active sites close to the OxyLH₂-1

Optimized Exchange and Correlation Semilocal Functional for the Calculation of Energies of Formation

We present a semiempirical exchange-correlation functional for density functional theory tailored to calculate energies of formation of solids. It has the same form of a Perdew–Burke–Ernzerhof functional, but three parameters have been fitted to reproduce experimental energies of formation of a representative set of binaries. The quality of the obtained functional has then been assessed for a control set of binary and ternary compounds. Our functional succeeds in reducing the error of the Perdew–Burke–Ernzerhof generalized gradient approximation for energies of formation by a factor of 2. Furthermore, this result is achieved preserving the quality of the optimized geometry

Optimized Exchange and Correlation Semilocal Functional for the Calculation of Energies of Formation

We present a semiempirical exchange-correlation functional for density functional theory tailored to calculate energies of formation of solids. It has the same form of a Perdew–Burke–Ernzerhof functional, but three parameters have been fitted to reproduce experimental energies of formation of a representative set of binaries. The quality of the obtained functional has then been assessed for a control set of binary and ternary compounds. Our functional succeeds in reducing the error of the Perdew–Burke–Ernzerhof generalized gradient approximation for energies of formation by a factor of 2. Furthermore, this result is achieved preserving the quality of the optimized geometry

Benchmarking the AK13 Exchange Functional: Ionization Potentials and Electron Affinities

We perform benchmark calculations for the ionization potential and electronic affinity of atoms and small molecules using several semilocal exchange-correlation functionals of density-functional theory with improved asymptotic behavior. We are particularly interested in a new generalized-gradient approximation for exchange [Armiento and Kümmel, <i>Phys. Rev. Lett.</i> <b>2013</b>, <i>111</i>, 036402] that provides an energy functional whose functional derivative yields a potential with better decay behavior. We find that it yields energies that are worse than traditional energy functionals and potentials that are less accurate than functionals that model directly the exchange-correlation potential. However, we find that this functional offers a excellent balance between the quality of the energy and of the potential and is therefore a good compromise for applications that require at the same time reasonable energies and good potentials

Bioheterojunction Effect on Fluorescence Origin and Efficiency Improvement of Firefly Chromophores

We propose the heterojunction effect in the analysis of the fluorescence mechanism of the firefly chromophore. Following this analysis, and with respect to the HOMO−LUMO gap alignment between the chromophore’s functional fragments, three main heterojunction types (I, II, and I*) are identified. Time-dependent density functional theory optical absorption calculations for the firefly chromophore show that the strongest excitation appears in the deprotonated anion state of the keto form. This can be explained by its high HOMO−LUMO overlap due to strong bioheterojunction confinement. It is also found that the nitrogen atom in the thiazolyl rings, due to its larger electronegativity, plays a key role in the emission process, its importance growing when the HOMO and LUMO overlap at its location. This principle is applied to enhance the chromophore’s fluorescence efficiency and to guide the functionalization of molecular optoelectronic devices

Efficient Automatized Density-Functional Tight-Binding Parametrizations: Application to Group IV Elements

Density-functional tight-binding methods stand out as a very good compromise between accuracy and computational efficiency. These methods rely on parameter sets that have to be determined and tabulated for every pair of chemical elements. We describe an efficient, and to a large extent automatic, procedure to build such parameter sets. This procedure includes the generation of unbiased training sets and subsequent optimization of the parameters using a pattern search method. As target for the optimization we ask that the formation energy and the forces on the atoms calculated within tight-binding reproduce the ones obtained using density-functional theory. We then use this approach to calculate parameter sets for group IV elements and their binaries. These turn out to yield substantially better results than previously available parameters, especially in what concerns energies and forces

Efficient Automatized Density-Functional Tight-Binding Parametrizations: Application to Group IV Elements

Density-functional tight-binding methods stand out as a very good compromise between accuracy and computational efficiency. These methods rely on parameter sets that have to be determined and tabulated for every pair of chemical elements. We describe an efficient, and to a large extent automatic, procedure to build such parameter sets. This procedure includes the generation of unbiased training sets and subsequent optimization of the parameters using a pattern search method. As target for the optimization we ask that the formation energy and the forces on the atoms calculated within tight-binding reproduce the ones obtained using density-functional theory. We then use this approach to calculate parameter sets for group IV elements and their binaries. These turn out to yield substantially better results than previously available parameters, especially in what concerns energies and forces

Prediction of Stable Nitride Perovskites

Perovskites are one of the most studied classes of materials, with a variety of applications in diverse fields of science and technology. Their basic composition is ABX₃, where X is a nonmetal normally from the VIA or VIIA group. In this article we investigate the possibility of the existence of perovskites with X<i> = </i>N. Our approach is based on a combination of high-throughput techniques and global structural prediction methods. We find 21 new compositions of the form ABN₃ that are thermodynamically stable (considering all possible decomposition channels) and that have therefore excellent chances of being experimentally accessible. Most of these materials crystallize in monoclinic phases, but three compounds, namely, LaReN₃, LaWN₃, and YReN₃, are predicted to have distorted perovskite structures in their ground state. In particular, LaWN₃ is a semiconductor and displays a large ferroelectric polarization. The addition of nitride compounds to the perovskite family poses numerous questions related to the chemistry of this interesting family of materials

Efficient Automatized Density-Functional Tight-Binding Parametrizations: Application to Group IV Elements

Density-functional tight-binding methods stand out as a very good compromise between accuracy and computational efficiency. These methods rely on parameter sets that have to be determined and tabulated for every pair of chemical elements. We describe an efficient, and to a large extent automatic, procedure to build such parameter sets. This procedure includes the generation of unbiased training sets and subsequent optimization of the parameters using a pattern search method. As target for the optimization we ask that the formation energy and the forces on the atoms calculated within tight-binding reproduce the ones obtained using density-functional theory. We then use this approach to calculate parameter sets for group IV elements and their binaries. These turn out to yield substantially better results than previously available parameters, especially in what concerns energies and forces

Correction to Prediction of Stable Nitride Perovskites

Correction to Prediction of Stable Nitride Perovskite