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Tempke R, Musho T. Autonomous generation of single photon emitting materials. NANOSCALE 2024; 16:10239-10249. [PMID: 38726673 DOI: 10.1039/d3nr04944b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
The utilization of machine learning in Materials Science underscores the critical importance of the quality and quantity of data in training models effectively. Unlike fields such as image processing and natural language processing, there is limited availability of atomistic datasets, leading to biases in training data. Particularly in the domain of materials discovery, there exists an issue of continuity in atomistic datasets. Experimental data sourced from literature and patents is usually only available for favorable data, resulting in bias in the training dataset. This study focuses on developing a SMILES-based model for generating synthetic datasets of quantum materials using a variational autoencoder. This study centers on the generation of a synthetic dataset of quantum materials specifically for quantum sensing applications, with a focus on two-level quantum molecules that exhibit a dipole blockade. The proposed technique offers an improved sampling algorithm by incorporating newly generated data into the sampling algorithm to create a more normally distributed dataset. Through this technique, the study was able to generate over 1 000 000 candidate quantum materials from a small dataset of only 8000 materials. The generated dataset identified several iodine-containing molecules as promising single photon emitting materials for potential quantum sensing applications.
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Affiliation(s)
- Robert Tempke
- Department of Mechanical, Materials and Aerospace Engineering, West Virginia University, P.O. Box 6106, Morgantown, WV, USA.
| | - Terence Musho
- Department of Mechanical, Materials and Aerospace Engineering, West Virginia University, P.O. Box 6106, Morgantown, WV, USA.
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2
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Lebedeva IV, Jornet-Somoza J. Optical properties and exciton transfer between N-heterocyclic carbene iridium(III) complexes for blue light-emitting diode applications from first principles. J Chem Phys 2024; 160:084107. [PMID: 38391015 DOI: 10.1063/5.0193161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 02/05/2024] [Indexed: 02/24/2024] Open
Abstract
N-heterocyclic carbene (NHC) iridium(III) complexes are considered as promising candidates for blue emitters in organic light-emitting diodes. They can play the roles of the emitter as well as of electron and hole transporters in the same emission layer. We investigate optical transitions in such complexes with account of geometry and electronic structure changes upon excitation or charging and exciton transfer between the complexes from first principles. It is shown that excitation of NHC iridium complexes is accompanied by a large reorganization energy ∼0.7 eV and a significant loss in the oscillator strength, which should lead to low exciton diffusion. Calculations with account of spin-orbit coupling reveal a small singlet-triplet splitting ∼0.1 eV, whereas the oscillator strength for triplet excitations is found to be an order of magnitude smaller than for the singlet ones. The contributions of the Förster and Dexter mechanisms are analyzed via the explicit integration of transition densities. It is shown that for typical distances between emitter complexes in the emission layer, the contribution of the Dexter mechanism should be negligible compared to the Förster mechanism. At the same time, the ideal dipole approximation, although giving the correct order of the exciton coupling, fails to reproduce the result taking into account spatial distribution of the transition density. For charged NHC complexes, we find a number of optical transitions close to the emission peak of the blue emitter with high exciton transfer rates that can be responsible for exciton-polaron quenching. The nature of these transitions is analyzed.
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Affiliation(s)
- Irina V Lebedeva
- Nano-Bio Spectroscopy Group and ETSF, Universidad del País Vasco, CFM CSIC-UPV/EHU, 20018 San Sebastián, Spain
| | - Joaquim Jornet-Somoza
- Nano-Bio Spectroscopy Group and ETSF, Universidad del País Vasco, CFM CSIC-UPV/EHU, 20018 San Sebastián, Spain
- Max Planck Institute for the Structure and Dynamics of Matter and Center for Free-Electron Laser Science, Luruper Chaussee 149, 22761 Hamburg, Germany
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3
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Montserrat R, Oliveira RR, Rocha AB. Total absorption spectrum of benzene aggregates obtained from two different approaches. J Mol Model 2024; 30:66. [PMID: 38345753 DOI: 10.1007/s00894-024-05859-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 01/29/2024] [Indexed: 03/16/2024]
Abstract
CONTEXT The study of molecular aggregation effects on the electronic spectrum is essential for the development of optoelectronic devices. However, investigating the entire valence absorption spectrum of aggregates using quantum mechanical methods is a challenging task. In this work, we perform systematic simulations of the absorption spectrum of benzene molecular clusters up to 35 eV applying two approaches based on time-dependent density functional theory. The results show that depending on the dimer packing, different energy shifts occur for the symmetry allowed [Formula: see text] transition, in comparison to the monomer. The transition intensity increases for the band around 6 eV for larger aggregates from the monomer to dimers and tetramer, indicating the occurrence of the symmetry forbidden (in [Formula: see text] point group) [Formula: see text] [Formula: see text] transition. The benzene crystal exhibits a large redshift following the experimental spectrum. Also, the continuum regions of all spectra show a good agreement with the experiments both in gas and solid phases. METHODS Geometry optimization of the monomer was carried out with Gaussian 09 software using the PBE0/def2-TZVP level of theory. We used dimers and tetramer molecular geometries extracted from the experimental crystal structure. The absorption spectra were directly obtained by the Liouville-Lanczos TDDFT approach with plane waves basis set or indirectly by TDDFT pseudo-spectra calculated in a [Formula: see text] basis followed by analytic continuation procedure to obtain complex polarizability. The former is available at Quantum ESPRESSO, and the latter was calculated using Gaussian 09 with the post-processing performed with a code previously developed in our group.
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Affiliation(s)
- Ricardo Montserrat
- Departamento de Físico-Química, Universidade Federal do Rio de Janeiro, Avenida Athos da Silveira Ramos, 149, Rio de Janeiro, 21941-909, Rio de Janeiro, Brazil
| | - Ricardo R Oliveira
- Departamento de Físico-Química, Universidade Federal do Rio de Janeiro, Avenida Athos da Silveira Ramos, 149, Rio de Janeiro, 21941-909, Rio de Janeiro, Brazil.
| | - Alexandre B Rocha
- Departamento de Físico-Química, Universidade Federal do Rio de Janeiro, Avenida Athos da Silveira Ramos, 149, Rio de Janeiro, 21941-909, Rio de Janeiro, Brazil.
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4
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Zahid Nasim S, Sarfaraz S, Jan F, Yar M, Ur Rehaman A. Computational insights of excited state intramolecular proton transfer (ESIPT) based fluorescent detection and imaging of γ-glutamytranspeptidase activity. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 299:122814. [PMID: 37201329 DOI: 10.1016/j.saa.2023.122814] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/15/2023] [Accepted: 04/29/2023] [Indexed: 05/20/2023]
Abstract
γ-Glutamytranspeptidase (GGT) is an important tumor biomarker that widely appears in the tumor cells. Therefore, accurate imaging and detection of GGT activity in live cells, serum and pathological cells grasp great importance for the diagnosis, management, and treatment of cancer. Herein, 2-(2-hydroxyl-phenyl)-6-chloro-4-(3H)-quinazolinone (HPQ) is considered as the fluorophore probe for the detection of GGT activity, which is known for the typical mechanism of excited-state intramolecular proton transfer (ESIPT). All the simulations adopted to evaluate the sensing mechanism were carried out via DFT and TDDFT calculations at CAM-B3LYP/TZVP level of theory. The emission properties of HPQ and HPQ-TD are thoroughly studied to understand the photoinduced electron transfer (PET) and excited state intramolecular proton transfer (ESIPT) process. The results reveal that the fluorescence quenching of HPQ (enol form) is assigned to the PET process, whereas the large Stokes shift in fluorescence emission of HPQ (keto form) is related with ESIPT mechanism. The obtained results are further cross validated by frontier molecular orbital (FMO) analysis, geometric analysis, and potential energy curve (PEC) scanning. Our calculations provide powerful evidence for the ESIPT based sensing mechanism of HPQ (keto-enol form) for GGT activity.
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Affiliation(s)
- Sayed Zahid Nasim
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Sehrish Sarfaraz
- Department of Chemistry, COMSATS University, Abbottabad Campus, Abbottabad 22060, Pakistan
| | - Faheem Jan
- Shenyang National Laboratory for Materials Science, Institute of Metal Research, Chinese Academy of Sciences, Shenyang 110016, Liaoning, China; School of Materials Science and Engineering, University of Science and Technology of China, Shenyang 110016, Liaoning, China.
| | - Muhammad Yar
- Department of Chemistry, COMSATS University, Abbottabad Campus, Abbottabad 22060, Pakistan.
| | - Attiq Ur Rehaman
- Department of Chemistry, COMSATS University, Abbottabad Campus, Abbottabad 22060, Pakistan
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5
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Titov E, Beqiraj A. Exciton States of Azobenzene Aggregates: A First‐Principles Study. ADVANCED THEORY AND SIMULATIONS 2023. [DOI: 10.1002/adts.202200907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/22/2023]
Affiliation(s)
- Evgenii Titov
- University of Potsdam, Institute of Chemistry, Theoretical Chemistry Karl‐Liebknecht‐Straße 24‐25 14476 Potsdam Germany
| | - Alkit Beqiraj
- University of Potsdam, Institute of Chemistry, Theoretical Chemistry Karl‐Liebknecht‐Straße 24‐25 14476 Potsdam Germany
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6
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Trepl T, Schelter I, Kümmel S. Analyzing Excitation-Energy Transfer Based on the Time-Dependent Density Functional Theory in Real Time. J Chem Theory Comput 2022; 18:6577-6587. [PMID: 36268773 DOI: 10.1021/acs.jctc.2c00600] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Excitation-energy transfer is a key step in processes such as photosynthesis that convert light into other forms of energy. Time-dependent density functional theory (DFT) in real time is ideal for the first-principles simulation of such processes due to its computational efficiency. We here demonstrate how real-time DFT can be used for analyzing excitation-energy transfer from first-principles. We discuss several measures of energy transfer that are based solely on the time-dependent density, are well founded in the DFT framework, allow for intuitive understanding and visualization, and reproduce important limiting cases of an analytical model. We demonstrate their usefulness in calculations for model systems, both with static nuclei and in the context of DFT-based Ehrenfest dynamics.
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Affiliation(s)
- T Trepl
- Theoretical Physics IV, University of Bayreuth, Bayreuth95440, Germany
| | - I Schelter
- Theoretical Physics IV, University of Bayreuth, Bayreuth95440, Germany
| | - S Kümmel
- Theoretical Physics IV, University of Bayreuth, Bayreuth95440, Germany
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7
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Mattiat J, Luber S. Comparison of Length, Velocity, and Symmetric Gauges for the Calculation of Absorption and Electric Circular Dichroism Spectra with Real-Time Time-Dependent Density Functional Theory. J Chem Theory Comput 2022; 18:5513-5526. [PMID: 36041170 DOI: 10.1021/acs.jctc.2c00644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A velocity and symmetric gauge implementation for real-time time-dependent density functional theory (RT-TDDFT) in the CP2K package using a Gaussian and plane wave approach is presented, including the explicit gauge-transformed contributions due to the nonlocal part of pseudopotentials. Absorption spectra of gas-phase α-pinene are calculated in length and velocity gauges in the long-wavelength approximation for the application of a δ pulse in linear and full order. The velocity gauge implementation is also applied to a solvated uracil molecule to showcase its use within periodic boundary conditions (PBC). For the calculation of the expectation value of the electric dipole moment in PBC, both the velocity representation and the modern theory of polarization give equivalent absorption spectra if a distributed reference point is used for the nonlocal term of the velocity operator. The discussion of linear response theory takes place in a unified framework in terms of linear response functions in propagator notation, distinguishing the parts of the linear response functions associated with perturbation and response. To further investigate gauge dependence, electric circular dichroism (ECD) spectra of α-pinene were calculated either as magnetic response to an electric field perturbation, in length or velocity gauge, or as electric response to a magnetic field perturbation in the symmetric gauge. Both approaches, electric and magnetic perturbations, have been found to yield equivalent ECD spectra.
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Affiliation(s)
- Johann Mattiat
- Department of Chemistry, University of Zurich, Zurich 8057, Switzerland
| | - Sandra Luber
- Department of Chemistry, University of Zurich, Zurich 8057, Switzerland
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De Santis M, Vallet V, Gomes ASP. Environment Effects on X-Ray Absorption Spectra With Quantum Embedded Real-Time Time-Dependent Density Functional Theory Approaches. Front Chem 2022; 10:823246. [PMID: 35295974 PMCID: PMC8919347 DOI: 10.3389/fchem.2022.823246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 02/04/2022] [Indexed: 11/13/2022] Open
Abstract
In this work we implement the real-time time-dependent block-orthogonalized Manby-Miller embedding (rt-BOMME) approach alongside our previously developed real-time frozen density embedding time-dependent density functional theory (rt-TDDFT-in-DFT FDE) code, and investigate these methods’ performance in reproducing X-ray absorption spectra (XAS) obtained with standard rt-TDDFT simulations, for model systems comprised of solvated fluoride and chloride ions ([X@(H2O)8−, X = F, Cl). We observe that for ground-state quantities such as core orbital energies, the BOMME approach shows significantly better agreement with supermolecular results than FDE for the strongly interacting fluoride system, while for chloride the two embedding approaches show more similar results. For the excited states, we see that while FDE (constrained not to have the environment densities relaxed in the ground state) is in good agreement with the reference calculations for the region around the K and L1 edges, and is capable of reproducing the splitting of the 1s1 (n + 1)p1 final states (n + 1 being the lowest virtual p orbital of the halides), it by and large fails to properly reproduce the 1s1 (n + 2)p1 states and misses the electronic states arising from excitation to orbitals with important contributions from the solvent. The BOMME results, on the other hand, provide a faithful qualitative representation of the spectra in all energy regions considered, though its intrinsic approximation of employing a lower-accuracy exchange-correlation functional for the environment induces non-negligible shifts in peak positions for the excitations from the halide to the environment. Our results thus confirm that QM/QM embedding approaches are viable alternatives to standard real-time simulations of X-ray absorption spectra of species in complex or confined environments.
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9
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Bertoni AI, Fogarty RM, Sánchez CG, Horsfield AP. QM/MM optimization with quantum coupling: Host–guest interactions in a pentacene-doped p-terphenyl crystal. J Chem Phys 2022; 156:044110. [DOI: 10.1063/5.0079788] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Andrés I. Bertoni
- Instituto Interdisciplinario de Ciencias Básicas (ICB-CONICET), Universidad Nacional de Cuyo, Padre Jorge Contreras 1300, Mendoza 5502, Argentina
| | - Richard M. Fogarty
- Department of Materials and Thomas Young Centre, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Cristián G. Sánchez
- Instituto Interdisciplinario de Ciencias Básicas (ICB-CONICET), Universidad Nacional de Cuyo, Padre Jorge Contreras 1300, Mendoza 5502, Argentina
| | - Andrew P. Horsfield
- Department of Materials and Thomas Young Centre, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
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10
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Mattiat J, Luber S. Recent Progress in the Simulation of Chiral Systems with Real Time Propagation Methods. Helv Chim Acta 2021. [DOI: 10.1002/hlca.202100154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Johann Mattiat
- Department of Chemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich Switzerland
| | - Sandra Luber
- Department of Chemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich Switzerland
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11
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Hekele J, Yao Y, Kanai Y, Blum V, Kratzer P. All-electron real-time and imaginary-time time-dependent density functional theory within a numeric atom-centered basis function framework. J Chem Phys 2021; 155:154801. [PMID: 34686041 DOI: 10.1063/5.0066753] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Real-time time-dependent density functional theory (RT-TDDFT) is an attractive tool to model quantum dynamics by real-time propagation without the linear response approximation. Sharing the same technical framework of RT-TDDFT, imaginary-time time-dependent density functional theory (it-TDDFT) is a recently developed robust-convergence ground state method. Presented here are high-precision all-electron RT-TDDFT and it-TDDFT implementations within a numerical atom-centered orbital (NAO) basis function framework in the FHI-aims code. We discuss the theoretical background and technical choices in our implementation. First, RT-TDDFT results are validated against linear-response TDDFT results. Specifically, we analyze the NAO basis sets' convergence for Thiel's test set of small molecules and confirm the importance of the augmentation basis functions for adequate convergence. Adopting a velocity-gauge formalism, we next demonstrate applications for systems with periodic boundary conditions. Taking advantage of the all-electron full-potential implementation, we present applications for core level spectra. For it-TDDFT, we confirm that within the all-electron NAO formalism, it-TDDFT can successfully converge systems that are difficult to converge in the standard self-consistent field method. We finally benchmark our implementation for systems up to ∼500 atoms. The implementation exhibits almost linear weak and strong scaling behavior.
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Affiliation(s)
- Joscha Hekele
- Faculty of Physics, University of Duisburg-Essen, Lotharstr. 1, 47057 Duisburg, Germany
| | - Yi Yao
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, USA
| | - Yosuke Kanai
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Volker Blum
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, USA
| | - Peter Kratzer
- Faculty of Physics, University of Duisburg-Essen, Lotharstr. 1, 47057 Duisburg, Germany
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12
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Grobas Illobre P, Marsili M, Corni S, Stener M, Toffoli D, Coccia E. Time-Resolved Excited-State Analysis of Molecular Electron Dynamics by TDDFT and Bethe-Salpeter Equation Formalisms. J Chem Theory Comput 2021; 17:6314-6329. [PMID: 34486881 PMCID: PMC8515806 DOI: 10.1021/acs.jctc.1c00211] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Indexed: 12/16/2022]
Abstract
In this work, a theoretical and computational set of tools to study and analyze time-resolved electron dynamics in molecules, under the influence of one or more external pulses, is presented. By coupling electronic-structure methods with the resolution of the time-dependent Schrödinger equation, we developed and implemented the time-resolved induced density of the electronic wavepacket, the time-resolved formulation of the differential projection density of states (ΔPDOS), and of transition contribution map (TCM) to look at the single-electron orbital occupation and localization change in time. Moreover, to further quantify the possible charge transfer, we also defined the energy-integrated ΔPDOS and the fragment-projected TCM. We have used time-dependent density-functional theory (TDDFT), as implemented in ADF software, and the Bethe-Salpeter equation, as provided by MolGW package, for the description of the electronic excited states. This suite of postprocessing tools also provides the time evolution of the electronic states of the system of interest. To illustrate the usefulness of these postprocessing tools, excited-state populations have been computed for HBDI (the chromophore of GFP) and DNQDI molecules interacting with a sequence of two pulses. Time-resolved descriptors have been applied to study the time-resolved electron dynamics of HBDI, DNQDI, LiCN (being a model system for dipole switching upon highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) electronic excitation), and Ag22. The computational analysis tools presented in this article can be employed to help the interpretation of fast and ultrafast spectroscopies on molecular, supramolecular, and composite systems.
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Affiliation(s)
- P. Grobas Illobre
- Dipartimento
di Scienze Chimiche e Farmaceutiche, Universitá
di Trieste, via L. Giorgieri 1, Trieste 34127, Italy
| | - M. Marsili
- Dipartimento
di Scienze Chimiche, Universitá di
Padova, via Marzolo 1, Padova 35131, Italy
| | - S. Corni
- Dipartimento
di Scienze Chimiche, Universitá di
Padova, via Marzolo 1, Padova 35131, Italy
- CNR
Istituto di Nanoscienze, via Campi 213/A, Modena 41125, Italy
| | - M. Stener
- Dipartimento
di Scienze Chimiche e Farmaceutiche, Universitá
di Trieste, via L. Giorgieri 1, Trieste 34127, Italy
| | - D. Toffoli
- Dipartimento
di Scienze Chimiche e Farmaceutiche, Universitá
di Trieste, via L. Giorgieri 1, Trieste 34127, Italy
| | - E. Coccia
- Dipartimento
di Scienze Chimiche e Farmaceutiche, Universitá
di Trieste, via L. Giorgieri 1, Trieste 34127, Italy
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Sorour MI, Kistler KA, Marcus AH, Matsika S. Accurate Modeling of Excitonic Coupling in Cyanine Dye Cy3. J Phys Chem A 2021; 125:7852-7866. [PMID: 34494437 DOI: 10.1021/acs.jpca.1c05556] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Accurate modeling of excitonic coupling in molecules is of great importance for inferring the structures and dynamics of coupled systems. Cy3 is a cyanine dye that is widely used in molecular spectroscopy. Its well-separated excitation bands, high sensitivity to the surroundings, and the high energy transfer efficiency make it a perfect choice for excitonic coupling experiments. Many methods have been used to model the excitonic coupling in molecules with varying degrees of accuracy. The atomic transition charge model offers a high-accuracy and cost-effective way to calculating the excitonic coupling. The main focus of this work is to generate high-quality atomic transition charges that can accurately model the Cy3 dye's transition density. The transition density of the excitation of the ground to first excited state is calculated using configuration-interaction singles and time-dependent density functional theory and is benchmarked against the algebraic diagrammatic construction method. Using the transition density we derived the atomic transition charges using two approaches: Mulliken population analysis and charges fitted to the transition electrostatic potential. The quality of the charges is examined, and their ability to accurately calculate the excitonic coupling is assessed via comparison to experimental data of an artificial biscyanine construct. Theoretical comparisons to the supermolecule ab initio couplings and the widely used point-dipole approximation are also made. Results show that using the transition electrostatic potential is a reliable approach for generating the transition atomic charges. A high-quality set of charges, that can be used to model the Cy3 dye dimer excitonic coupling with high-accuracy and a reasonable computational cost, is obtained.
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Affiliation(s)
- Mohammed I Sorour
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Kurt A Kistler
- Department of Chemistry, Brandywine Campus, The Pennsylvania State University, Media, Pennsylvania 19063, United States
| | - Andrew H Marcus
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403, United States
| | - Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
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14
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Ren Y, Li MY, Song YX, Sui MY, Sun GY, Qu XC, Xie P, Lu JL. Refined standards for simulating UV–vis absorption spectra of acceptors in organic solar cells by TD-DFT. J Photochem Photobiol A Chem 2021. [DOI: 10.1016/j.jphotochem.2020.113087] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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15
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Osella S. Artificial Photosynthesis: Is Computation Ready for the Challenge Ahead? NANOMATERIALS 2021; 11:nano11020299. [PMID: 33498961 PMCID: PMC7911014 DOI: 10.3390/nano11020299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 12/13/2022]
Abstract
A tremendous effort is currently devoted to the generation of novel hybrid materials with enhanced electronic properties for the creation of artificial photosynthetic systems. This compelling and challenging problem is well-defined from an experimental point of view, as the design of such materials relies on combining organic materials or metals with biological systems like light harvesting and redox-active proteins. Such hybrid systems can be used, e.g., as bio-sensors, bio-fuel cells, biohybrid photoelectrochemical cells, and nanostructured photoelectronic devices. Despite these efforts, the main bottleneck is the formation of efficient interfaces between the biological and the organic/metal counterparts for efficient electron transfer (ET). It is within this aspect that computation can make the difference and improve the current understanding of the mechanisms underneath the interface formation and the charge transfer efficiency. Yet, the systems considered (i.e., light harvesting protein, self-assembly monolayer and surface assembly) are more and more complex, reaching (and often passing) the limit of current computation power. In this review, recent developments in computational methods for studying complex interfaces for artificial photosynthesis will be provided and selected cases discussed, to assess the inherent ability of computation to leave a mark in this field of research.
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Affiliation(s)
- Silvio Osella
- Chemical and Biological Systems Simulation Lab, Center of New Technologies, University of Warsaw, Banacha 2C, 02-097 Warsaw, Poland
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16
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Takenaka M, Taketsugu T, Iwasa T. Theoretical method for near-field Raman spectroscopy with multipolar Hamiltonian and real-time-TDDFT: Application to on- and off-resonance tip-enhanced Raman spectroscopy. J Chem Phys 2021; 154:024104. [PMID: 33445901 DOI: 10.1063/5.0034933] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Tip-enhanced Raman spectroscopy in combination with scanning tunneling microscopy could produce ultrahigh-resolution Raman spectra and images for single-molecule vibrations. Furthermore, a recent experimental study successfully decoupled the interaction between the molecule and the substrate/tip to investigate the intrinsic properties of molecules and their near-field interactions by Raman spectroscopy. In such a circumstance, more explicit treatments of the near field and molecular interactions beyond the dipole approximation would be desirable. Here, we propose a theoretical method based on the multipolar Hamiltonian that considers full spatial distribution of the electric field under the framework of real-time time-dependent density functional theory. This approach allows us to treat the on- and off-resonance Raman phenomena on the same footing. For demonstration, a model for the on- and off-resonance tip-enhanced Raman process in benzene was constructed. The obtained Raman spectra are well understood by considering both the spatial structure of the near field and the molecular vibration in the off-resonance condition. For the on-resonance condition, the Raman spectra are governed by the transition moment, in addition to the selection rule of off-resonance Raman. Interestingly, on-resonance Raman can be activated even when the near field forbids the π-π* transition at equilibrium geometry due to vibronic couplings originating from structural distortions.
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Affiliation(s)
- Masato Takenaka
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-0810, Japan
| | - Tetsuya Taketsugu
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Takeshi Iwasa
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
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17
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Yang J, Pei Z, Deng J, Mao Y, Wu Q, Yang Z, Wang B, Aikens CM, Liang W, Shao Y. Analysis and visualization of energy densities. I. Insights from real-time time-dependent density functional theory simulations. Phys Chem Chem Phys 2020; 22:26838-26851. [PMID: 33170198 PMCID: PMC7722154 DOI: 10.1039/d0cp04206d] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this article, we report a scheme to analyze and visualize the energy density fluctuations during the real-time time-dependent density functional theory (RT-TDDFT) simulations. Using Ag4-N2 complexes as examples, it is shown that the grid-based Kohn-Sham energy density can be computed at each time step using a procedure from Nakai and coworkers. Then the instantaneous energy of each molecular fragment (such as Ag4 and N2) can be obtained by partitioning the Kohn-Sham energy densities using Becke or fragment-based Hirshfeld (FBH) scheme. A strong orientation-dependence is observed for the energy flow between the Ag4 cluster and a nearby N2 molecule in the RT-TDDFT simulations. Future applications of such an energy density analysis in electron dynamics simulations are discussed.
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Affiliation(s)
- Junjie Yang
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Pkwy, Norman, OK 73019, USA.
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18
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Wang LW. Natural Orbital Branching Scheme for Time-Dependent Density Functional Theory Nonadiabatic Simulations. J Phys Chem A 2020; 124:9075-9087. [DOI: 10.1021/acs.jpca.0c06367] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Lin-Wang Wang
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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19
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Kehrer J, Richter R, Foerster JM, Schelter I, Kümmel S. Self-interaction correction, electrostatic, and structural influences on time-dependent density functional theory excitations of bacteriochlorophylls from the light-harvesting complex 2. J Chem Phys 2020; 153:144114. [PMID: 33086803 DOI: 10.1063/5.0014938] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
First-principles calculations offer the chance to obtain a microscopic understanding of light-harvesting processes. Time-dependent density functional theory can have the computational efficiency to allow for such calculations. However, the (semi-)local exchange-correlation approximations that are computationally most efficient fail to describe charge-transfer excitations reliably. We here investigate whether the inexpensive average density self-interaction correction (ADSIC) remedies the problem. For the systems that we study, ADSIC is even more prone to the charge-transfer problem than the local density approximation. We further explore the recently reported finding that the electrostatic potential associated with the chromophores' protein environment in the light-harvesting complex 2 beneficially shifts spurious excitations. We find a great sensitivity on the chromophores' atomistic structure in this problem. Geometries obtained from classical molecular dynamics are more strongly affected by the spurious charge-transfer problem than the ones obtained from crystallography or density functional theory. For crystal structure geometries and density-functional theory optimized ones, our calculations confirm that the electrostatic potential shifts the spurious excitations out of the energetic range that is most relevant for electronic coupling.
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Affiliation(s)
- Juliana Kehrer
- Theoretical Physics IV, University of Bayreuth, D-95440 Bayreuth, Germany
| | - Rian Richter
- Theoretical Physics IV, University of Bayreuth, D-95440 Bayreuth, Germany
| | | | - Ingo Schelter
- Theoretical Physics IV, University of Bayreuth, D-95440 Bayreuth, Germany
| | - Stephan Kümmel
- Theoretical Physics IV, University of Bayreuth, D-95440 Bayreuth, Germany
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20
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Hofmann F, Kümmel S. Molecular excitations from meta-generalized gradient approximations in the Kohn-Sham scheme. J Chem Phys 2020; 153:114106. [PMID: 32962375 DOI: 10.1063/5.0023657] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Meta-Generalized Gradient Approximations (meta-GGAs) can, in principle, include spatial and temporal nonlocality in time-dependent density functional theory at a much lower computational cost than functionals that use exact exchange. We here test whether a meta-GGA that has recently been developed with a focus on capturing nonlocal response properties and the particle number discontinuity can realize such features in practice. To this end, we extended the frequency-dependent Sternheimer formalism to the meta-GGA case. Using the Krieger-Li-Iafrate (KLI) approximation, we calculate the optical response for the selected paradigm molecular systems and compare the meta-GGA Kohn-Sham response to the one found with exact exchange and conventional (semi-)local functionals. We find that the new meta-GGA captures important properties of the nonlocal exchange response. The KLI approximation, however, emerges as a limiting factor in the evaluation of charge-transfer excitations.
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Affiliation(s)
- Fabian Hofmann
- Theoretical Physics IV, University of Bayreuth, D-95440 Bayreuth, Germany
| | - Stephan Kümmel
- Theoretical Physics IV, University of Bayreuth, D-95440 Bayreuth, Germany
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21
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Ding S, Xu A, Sun A, Xia Y, Liu Y. An Excited State Intramolecular Proton Transfer-Based Fluorescent Probe with a Large Stokes Shift for the Turn-on Detection of Cysteine: A Detailed Theoretical Exploration. ACS OMEGA 2020; 5:19695-19701. [PMID: 32803064 PMCID: PMC7424714 DOI: 10.1021/acsomega.0c02393] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 07/17/2020] [Indexed: 05/29/2023]
Abstract
DFT and TDDFT calculations are adopted to study the sensing mechanism of a turn-on-type cysteine fluorescent probe (2-(1-phenyl-imidazo[1,5-α]pyridine-3-yl)phenyl acrylate, denoted as MZC-AC). The photoinduced electron transfer (PET) process of MZC-AC and the excited state intramolecular proton transfer (ESIPT) process of MZC have been investigated in detail. We demonstrate that the fluorescence quenching of MZC-AC is ascribed to the PET mechanism and the large Stokes shift fluorescence emission of MZC is the result of the ESIPT mechanism. The results have been cross-validated by geometries, frontier molecular orbital analysis, and potential energy curve scanning. As a result, our calculations completely reproduce the experimental results and give powerful evidence for the sensing mechanism of MZC-AC for cysteine.
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Affiliation(s)
- Sha Ding
- School
of Packaging and Materials Engineering, Hunan University of Technology, Zhuzhou 412007, PR China
- Hunan
Key Laboratory of Biomass Fiber Functional Materials, Hunan University of Technology, Zhuzhou 412007, PR China
| | - Aixiang Xu
- School
of Civil Engineering, Hunan University of
Technology, Zhuzhou 412007, China
| | - Aokui Sun
- School
of Packaging and Materials Engineering, Hunan University of Technology, Zhuzhou 412007, PR China
| | - Yong Xia
- School
of Packaging and Materials Engineering, Hunan University of Technology, Zhuzhou 412007, PR China
- College
of Chemistry and Chemical Engineering, Central
South University, Changsha 410083, China
| | - Yuejun Liu
- School
of Packaging and Materials Engineering, Hunan University of Technology, Zhuzhou 412007, PR China
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22
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Tancogne-Dejean N, Oliveira MJT, Andrade X, Appel H, Borca CH, Le Breton G, Buchholz F, Castro A, Corni S, Correa AA, De Giovannini U, Delgado A, Eich FG, Flick J, Gil G, Gomez A, Helbig N, Hübener H, Jestädt R, Jornet-Somoza J, Larsen AH, Lebedeva IV, Lüders M, Marques MAL, Ohlmann ST, Pipolo S, Rampp M, Rozzi CA, Strubbe DA, Sato SA, Schäfer C, Theophilou I, Welden A, Rubio A. Octopus, a computational framework for exploring light-driven phenomena and quantum dynamics in extended and finite systems. J Chem Phys 2020; 152:124119. [PMID: 32241132 DOI: 10.1063/1.5142502] [Citation(s) in RCA: 114] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Over the last few years, extraordinary advances in experimental and theoretical tools have allowed us to monitor and control matter at short time and atomic scales with a high degree of precision. An appealing and challenging route toward engineering materials with tailored properties is to find ways to design or selectively manipulate materials, especially at the quantum level. To this end, having a state-of-the-art ab initio computer simulation tool that enables a reliable and accurate simulation of light-induced changes in the physical and chemical properties of complex systems is of utmost importance. The first principles real-space-based Octopus project was born with that idea in mind, i.e., to provide a unique framework that allows us to describe non-equilibrium phenomena in molecular complexes, low dimensional materials, and extended systems by accounting for electronic, ionic, and photon quantum mechanical effects within a generalized time-dependent density functional theory. This article aims to present the new features that have been implemented over the last few years, including technical developments related to performance and massive parallelism. We also describe the major theoretical developments to address ultrafast light-driven processes, such as the new theoretical framework of quantum electrodynamics density-functional formalism for the description of novel light-matter hybrid states. Those advances, and others being released soon as part of the Octopus package, will allow the scientific community to simulate and characterize spatial and time-resolved spectroscopies, ultrafast phenomena in molecules and materials, and new emergent states of matter (quantum electrodynamical-materials).
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Affiliation(s)
- Nicolas Tancogne-Dejean
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, D-22761 Hamburg, Germany
| | - Micael J T Oliveira
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, D-22761 Hamburg, Germany
| | - Xavier Andrade
- Quantum Simulations Group, Lawrence Livermore National Laboratory, Livermore, California 94551, USA
| | - Heiko Appel
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, D-22761 Hamburg, Germany
| | - Carlos H Borca
- Quantum Simulations Group, Lawrence Livermore National Laboratory, Livermore, California 94551, USA
| | - Guillaume Le Breton
- Département de Physique, École Normale Supérieure de Lyon, 46 Allée d'Italie, Lyon Cedex 07, France
| | - Florian Buchholz
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, D-22761 Hamburg, Germany
| | - Alberto Castro
- Institute for Biocomputation and Physics of Complex Systems, University of Zaragoza, Calle Mariano Esquillor, 50018 Zaragoza, Spain
| | - Stefano Corni
- Dipartimento di Scienze Chimiche, Università degli studi di Padova, via F. Marzolo 1, 35131 Padova, Italy
| | - Alfredo A Correa
- Quantum Simulations Group, Lawrence Livermore National Laboratory, Livermore, California 94551, USA
| | - Umberto De Giovannini
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, D-22761 Hamburg, Germany
| | - Alain Delgado
- Xanadu, 777 Bay Street, Toronto, Ontario M5G 2C8, Canada
| | - Florian G Eich
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, D-22761 Hamburg, Germany
| | - Johannes Flick
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Gabriel Gil
- Dipartimento di Scienze Chimiche, Università degli studi di Padova, via F. Marzolo 1, 35131 Padova, Italy
| | - Adrián Gomez
- Institute for Biocomputation and Physics of Complex Systems, University of Zaragoza, Calle Mariano Esquillor, 50018 Zaragoza, Spain
| | - Nicole Helbig
- Nanomat/Qmat/CESAM and ETSF, Université de Liège, B-4000 Sart-Tilman, Belgium
| | - Hannes Hübener
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, D-22761 Hamburg, Germany
| | - René Jestädt
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, D-22761 Hamburg, Germany
| | - Joaquim Jornet-Somoza
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, D-22761 Hamburg, Germany
| | - Ask H Larsen
- Nano-Bio Spectroscopy Group and ETSF, Universidad del País Vasco, 20018 San Sebastián, Spain
| | - Irina V Lebedeva
- Nano-Bio Spectroscopy Group and ETSF, Universidad del País Vasco, 20018 San Sebastián, Spain
| | - Martin Lüders
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, D-22761 Hamburg, Germany
| | - Miguel A L Marques
- Institut für Physik, Martin-Luther-Universität Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Sebastian T Ohlmann
- Max Planck Computing and Data Facility, Gießenbachstraße 2, 85741 Garching, Germany
| | - Silvio Pipolo
- Université de Lille, CNRS, Centrale Lille, ENSCL, Université d' Artois UMR 8181-UCCS Unité de Catalyse et Chimie du Solide, F-59000 Lille, France
| | - Markus Rampp
- Max Planck Computing and Data Facility, Gießenbachstraße 2, 85741 Garching, Germany
| | - Carlo A Rozzi
- CNR - Istituto Nanoscienze, via Campi 213a, 41125 Modena, Italy
| | - David A Strubbe
- Department of Physics, School of Natural Sciences, University of California, Merced, California 95343, USA
| | - Shunsuke A Sato
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, D-22761 Hamburg, Germany
| | - Christian Schäfer
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, D-22761 Hamburg, Germany
| | - Iris Theophilou
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, D-22761 Hamburg, Germany
| | - Alicia Welden
- Quantum Simulations Group, Lawrence Livermore National Laboratory, Livermore, California 94551, USA
| | - Angel Rubio
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, D-22761 Hamburg, Germany
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23
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Schelter I, Foerster JM, Gardiner AT, Roszak AW, Cogdell RJ, Ullmann GM, de Queiroz TB, Kümmel S. Assessing density functional theory in real-time and real-space as a tool for studying bacteriochlorophylls and the light-harvesting complex 2. J Chem Phys 2019; 151:134114. [DOI: 10.1063/1.5116779] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Affiliation(s)
- Ingo Schelter
- Theoretical Physics IV, University of Bayreuth, Bayreuth, Germany
| | - Johannes M. Foerster
- Theoretical Physics IV and Computational Biochemistry, University of Bayreuth, Bayreuth, Germany
| | | | - Aleksander W. Roszak
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, United Kingdom
| | - Richard J. Cogdell
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, United Kingdom
| | | | | | - Stephan Kümmel
- Theoretical Physics IV, University of Bayreuth, Bayreuth, Germany
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