1
|
de Wergifosse M, Beaujean P, Grimme S. Ultrafast Evaluation of Two-Photon Absorption with Simplified Time-Dependent Density Functional Theory. J Phys Chem A 2022; 126:7534-7547. [PMID: 36201255 DOI: 10.1021/acs.jpca.2c02395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This work presents the theoretical background to evaluate two-photon absorption (2PA) cross-sections in the framework of simplified time-dependent density functional theory (sTD-DFT). Our new implementation allows the ultrafast evaluation of 2PA cross-sections for large molecules based on a regular DFT ground-state determinant as well as a variant employing our tight-binding sTD-DFT-xTX flavor for very large systems. The method is benchmarked against higher-level calculations for trans-stilbene and typical fluorescent protein chromophores. For eGFP, a quadrupolar chromophore and its branched version, the flavine mono-nucleotide, and the iLOV protein, we compare sTD-DFT 2PA spectra to experimental ones. This includes extension and testing of our all-atom quantum chemistry methodology for the evaluation of 2PA for a system of ∼2000 atoms, providing striking agreement with the experimental spectrum.
Collapse
Affiliation(s)
- Marc de Wergifosse
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Universität Bonn, Beringstr. 4, D-53115Bonn, Germany
| | - Pierre Beaujean
- Laboratory of Theoretical Chemistry, Unit of Theoretical and Structural Physical Chemistry, Namur Institute of Structured Matter, University of Namur, Rue de Bruxelles 61, B-5000Namur, Belgium
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Universität Bonn, Beringstr. 4, D-53115Bonn, Germany
| |
Collapse
|
2
|
Ajami A, Husinsky W, Ovsianikov A, Liska R. Dispersive white light continuum single Z-scan for rapid determination of degenerate two-photon absorption spectra. APPLIED PHYSICS. B, LASERS AND OPTICS 2018; 124:142. [PMID: 30996529 PMCID: PMC6435023 DOI: 10.1007/s00340-018-7011-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 06/13/2018] [Indexed: 06/09/2023]
Abstract
We present an experimental technique to determine the degenerate two-photon absorption (2PA) spectra by performing a single Z-scan using a high-spectral-irradiance white light continuum (WLC) generated by a hollow core fiber. The hollow fiber was filled with Argon (Ar) gas at a pressure of 0.6 bar and was pumped with 500 mJ, 30 fs, and 800 nm pulses. The broadband WLC pulses with 350 nm bandwidth in the range of 600-950 nm were compressed to sub-8 fs pulses. To characterize and interpret the data obtained from this method, the spectral, temporal and spatial characteristics of the WLC were first analyzed. The WLC emerging from the compressor was dispersed using a prism pair and then focused into the sample by a cylindrical lens. Since different spectral components are spatially separated, any part of the sample in the beam cross section is irradiated with almost single wavelength pulses leading to only a degenerate 2PA process. The nonlinear transmittance was then measured by a charge-coupled-device (CCD) line camera as a function of the sample position while the sample was moved along the beam direction by a motorized translation stage. In this way the Z-scans at different wavelengths in the WLC spectral range can be measured and thus the wavelength-resolved degenerate 2PA spectra can be obtained by performing a single scan using dispersive WLC. This method was verified on a well-characterized dye Rhodamine B and yield a reasonable agreement with the data found in the literature. We used this method to determine the 2PA spectra of some two-photon initiators (2PIs) developed for two-photon polymerization (2PP) based 3D micro-structuring.
Collapse
Affiliation(s)
- Aliasghar Ajami
- Faculty of Physics, Semnan University, P. O. Box 35195-363, Semnan, Iran
| | - Wolfgang Husinsky
- Institute of Applied Physics, TU Wien (Technische Universitat Wien), Wiedner Hauptstrasse. 8, 1060 Vienna, Austria
| | - Aleksandr Ovsianikov
- Institute of Materials Science and Technology (E308), TU Wien (Technische Universitat Wien), Getreidemarkt 9, 1060 Vienna, Austria
| | - Robert Liska
- Institute of Applied Synthetic Chemistry, TU Wien (Technische Universitat Wien), Getreidemarkt 9, 1060 Vienna, Austria
| |
Collapse
|
3
|
Salem MA, Twelves I, Brown A. Prediction of two-photon absorption enhancement in red fluorescent protein chromophores made from non-canonical amino acids. Phys Chem Chem Phys 2016; 18:24408-16. [PMID: 27534378 DOI: 10.1039/c6cp03865d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Two-photon spectroscopy of fluorescent proteins is a powerful bio-imaging tool known for deep tissue penetration and little cellular damage. Being less sensitive than the one-photon microscopy alternatives, a protein with a large two-photon absorption (TPA) cross-section is needed. Here, we use time-dependent density functional theory (TD-DFT) at the B3LYP and CAM-B3LYP/6-31+G(d,p) levels of theory to screen twenty-two possible chromophores that can be formed upon replacing the amino-acid Tyr66 that forms the red fluorescent protein (RFP) chromophore with a non-canonical amino acid. The two-level model for TPA was used to assess the properties (i.e., transition dipole moment, permanent dipole moment difference, and the angle between them) leading to the TPA cross-sections determined via response theory. Computing TPA cross-sections with B3LYP and CAM-B3LYP yields similar overall trends. Results using both functionals agree that the RFP-derived model of the Gold Fluorescent Protein chromophore (Model 20) has the largest intrinsic TPA cross-section at the optimized geometry. TPA was further computed for selected chromophores following conformational changes: variation of both the dihedral angle of the acylimine moiety and the tilt and twist angles between the rings of the chromophore. The TPA cross-section assumed an oscillatory trend with the rotation of the acylimine dihedral, and the TPA is maximized in the planar conformation for almost all models. Model 21 (a hydroxyquinoline derivative) is shown to be comparable to Model 20 in terms of TPA cross-section. The conformational study on Model 21 shows that the acylimine angle has a much stronger effect on the TPA than its tilt and twist angles. Having an intrinsic TPA ability that is more than 7 times that of the native RFP chromophore, Models 20 and 21 appear to be very promising for future experimental investigation.
Collapse
Affiliation(s)
- M Alaraby Salem
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada.
| | | | | |
Collapse
|
4
|
Nanda KD, Krylov AI. Two-photon absorption cross sections within equation-of-motion coupled-cluster formalism using resolution-of-the-identity and Cholesky decomposition representations: Theory, implementation, and benchmarks. J Chem Phys 2015; 142:064118. [PMID: 25681898 DOI: 10.1063/1.4907715] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The equation-of-motion coupled-cluster (EOM-CC) methods provide a robust description of electronically excited states and their properties. Here, we present a formalism for two-photon absorption (2PA) cross sections for the equation-of-motion for excitation energies CC with single and double substitutions (EOM-CC for electronically excited states with single and double substitutions) wave functions. Rather than the response theory formulation, we employ the expectation-value approach which is commonly used within EOM-CC, configuration interaction, and algebraic diagrammatic construction frameworks. In addition to canonical implementation, we also exploit resolution-of-the-identity (RI) and Cholesky decomposition (CD) for the electron-repulsion integrals to reduce memory requirements and to increase parallel efficiency. The new methods are benchmarked against the CCSD and CC3 response theories for several small molecules. We found that the expectation-value 2PA cross sections are within 5% from the quadratic response CCSD values. The RI and CD approximations lead to small errors relative to the canonical implementation (less than 4%) while affording computational savings. RI/CD successfully address the well-known issue of large basis set requirements for 2PA cross sections calculations. The capabilities of the new code are illustrated by calculations of the 2PA cross sections for model chromophores of the photoactive yellow and green fluorescent proteins.
Collapse
Affiliation(s)
- Kaushik D Nanda
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, USA
| | - Anna I Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, USA
| |
Collapse
|
5
|
Abstract
Optogenetics is an innovative technique for optical control of cells. This field has exploded over the past decade or so and has given rise to great advances in neuroscience. A variety of applications both from the basic and applied research have emerged, turning the early ideas into a powerful paradigm for cell biology, neuroscience and medical research. This review aims at highlighting the basic concepts that are essential for a comprehensive understanding of optogenetics and some important biological/biomedical applications. Further, emphasis is placed on advancement in optogenetics-associated light-based methods for controlling gene expression, spatially-controlled optogenetic stimulation and detection of cellular activities.
Collapse
Affiliation(s)
- Samarendra K. Mohanty
- Biophysics and Physiology Group, Department of Physics, The University of Texas at Arlington, USA. Tel. 817-272-1177, Fax: +1-817-272-3637
| | - Vasudevan Lakshminarayananan
- School of Optometry and Vision Science, Departments of Physics and Electrical and Computer Engineering, University of Waterloo, Waterloo, ON Canada. Department of Physics, Unviersity of Michigan, Ann Arbor, USA
| |
Collapse
|
6
|
Vivas MG, Siqueira JP, Silva DL, de Boni L, Mendonca CR. Investigation of the nonlinear absorption spectrum of all-trans retinoic acid by using the steady and transient two-photon absorption spectroscopy. RSC Adv 2015. [DOI: 10.1039/c5ra10719a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
This paper reports for the first time a complete study on the steady and transient excited state dynamics induced by 2PA for ATRA.
Collapse
Affiliation(s)
- M. G. Vivas
- Instituto de Física de São Carlos
- Universidade de São Paulo
- 13560-970 São Carlos
- Brazil
- Instituto de Ciência de Tecnologia
| | - J. P. Siqueira
- Instituto de Física de São Carlos
- Universidade de São Paulo
- 13560-970 São Carlos
- Brazil
| | - D. L. Silva
- Departamento de Ciências da Natureza
- Matemática e Educação
- Universidade Federal de São Carlos
- 13600-970 Araras
- Brazil
| | - L. de Boni
- Instituto de Física de São Carlos
- Universidade de São Paulo
- 13560-970 São Carlos
- Brazil
| | - C. R. Mendonca
- Instituto de Física de São Carlos
- Universidade de São Paulo
- 13560-970 São Carlos
- Brazil
| |
Collapse
|
7
|
Dhakal KR, Gu L, Shivalingaiah S, Dennis TS, Morris-Bobzean SA, Li T, Perrotti LI, Mohanty SK. Non-scanning fiber-optic near-infrared beam led to two-photon optogenetic stimulation in-vivo. PLoS One 2014; 9:e111488. [PMID: 25383687 PMCID: PMC4226470 DOI: 10.1371/journal.pone.0111488] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 09/24/2014] [Indexed: 11/18/2022] Open
Abstract
Stimulation of specific neurons expressing opsins in a targeted region to manipulate brain function has proved to be a powerful tool in neuroscience. However, the use of visible light for optogenetic stimulation is invasive due to low penetration depth and tissue damage owing to larger absorption and scattering. Here, we report, for the first time, in-depth non-scanning fiber-optic two-photon optogenetic stimulation (FO-TPOS) of neurons in-vivo in transgenic mouse models. In order to optimize the deep-brain stimulation strategy, we characterized two-photon activation efficacy at different near-infrared laser parameters. The significantly-enhanced in-depth stimulation efficiency of FO-TPOS as compared to conventional single-photon beam was demonstrated both by experiments and Monte Carlo simulation. The non-scanning FO-TPOS technology will lead to better understanding of the in-vivo neural circuitry because this technology permits more precise and less invasive anatomical delivery of stimulation.
Collapse
Affiliation(s)
- Kamal R. Dhakal
- Biophysics and Physiology Lab, Department of Physics, The University of Texas at Arlington, Arlington, Texas, United States of America
| | - Ling Gu
- Biophysics and Physiology Lab, Department of Physics, The University of Texas at Arlington, Arlington, Texas, United States of America
| | - Shivaranjani Shivalingaiah
- Biophysics and Physiology Lab, Department of Physics, The University of Texas at Arlington, Arlington, Texas, United States of America
| | - Torry S. Dennis
- Department of Psychology, The University of Texas at Arlington, Arlington, Texas, United States of America
| | - Samara A. Morris-Bobzean
- Department of Psychology, The University of Texas at Arlington, Arlington, Texas, United States of America
| | - Ting Li
- Key lab for Neuroinformatics of Ministry of Education, University of Electronic Science & Technology of China, Chengdu, Sichuan, China
| | - Linda I. Perrotti
- Department of Psychology, The University of Texas at Arlington, Arlington, Texas, United States of America
| | - Samarendra K. Mohanty
- Biophysics and Physiology Lab, Department of Physics, The University of Texas at Arlington, Arlington, Texas, United States of America
| |
Collapse
|
8
|
Dhakal K, Gu L, Black B, Mohanty SK. Fiber-optic two-photon optogenetic stimulation. OPTICS LETTERS 2013; 38:1927-9. [PMID: 23722792 DOI: 10.1364/ol.38.001927] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Optogenetic stimulation of genetically targeted cells is proving to be a powerful tool in the study of cellular systems, both in vitro and in vivo. However, most opsins are activated in the visible spectrum, where significant absorption and scattering of stimulating light occurs, leading to low penetration depth and less precise stimulation. Since we first (to the best of our knowledge) demonstrated two-photon optogenetic stimulation (TPOS), it has gained considerable interest in the probing of cellular circuitry by precise spatial modulation. However, all existing methods use microscope objectives and complex scanning beam geometries. Here, we report a nonscanning method based on multimode fiber to accomplish fiber-optic TPOS of cells.
Collapse
Affiliation(s)
- K Dhakal
- Biophysics and Physiology Laboratory, Department of Physics, University of Texas-Arlington, Texas 76019, USA
| | | | | | | |
Collapse
|
9
|
Kirkus M, Knippenberg S, Beljonne D, Cornil J, Janssen RAJ, Meskers SCJ. Synthesis and Optical Properties of Pyrrolo[3,2-b]pyrrole-2,5(1H,4H)-dione (iDPP)-Based Molecules. J Phys Chem A 2013; 117:2782-9. [DOI: 10.1021/jp400256s] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Mindaugas Kirkus
- Molecular Materials and Nanosystems, Eindhoven University of Technology, P.O. Box 513, 5600
MB Eindhoven, The Netherlands
| | - Stefan Knippenberg
- Laboratory for Chemistry of
Novel Materials, University of Mons, Place
du Parc 20, B-7000 Mons, Belgium
| | - David Beljonne
- Laboratory for Chemistry of
Novel Materials, University of Mons, Place
du Parc 20, B-7000 Mons, Belgium
| | - Jérôme Cornil
- Laboratory for Chemistry of
Novel Materials, University of Mons, Place
du Parc 20, B-7000 Mons, Belgium
| | - René A. J. Janssen
- Molecular Materials and Nanosystems, Eindhoven University of Technology, P.O. Box 513, 5600
MB Eindhoven, The Netherlands
| | - Stefan C. J. Meskers
- Molecular Materials and Nanosystems, Eindhoven University of Technology, P.O. Box 513, 5600
MB Eindhoven, The Netherlands
| |
Collapse
|
10
|
Vivas MG, Silva DL, De Boni L, Bretonniere Y, Andraud C, Laibe-Darbour F, Mulatier JC, Zaleśny R, Bartkowiak W, Canuto S, Mendonca CR. Experimental and Theoretical Study on the One- and Two-Photon Absorption Properties of Novel Organic Molecules Based on Phenylacetylene and Azoaromatic Moieties. J Phys Chem B 2012; 116:14677-88. [DOI: 10.1021/jp310731t] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marcelo G Vivas
- Instituto de Física de São Carlos, Universidade de São Paulo, Caixa Postal 369, 13560-970 São Carlos, SP, Brazil.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
11
|
Vivas MG, Mendonca CR. Temperature Effect on the Two-Photon Absorption Spectrum of All-trans-β-carotene. J Phys Chem A 2012; 116:7033-8. [DOI: 10.1021/jp303789s] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- M. G. Vivas
- Instituto de Física de São
Carlos, Universidade de São Paulo, Caixa Postal 369, 13560-970 São Carlos, São Paulo,
Brazil
| | - C. R. Mendonca
- Instituto de Física de São
Carlos, Universidade de São Paulo, Caixa Postal 369, 13560-970 São Carlos, São Paulo,
Brazil
| |
Collapse
|