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Article ; Online: Modeling molecular J and H aggregates using multiple-Davydov D2 ansatz.

Jakučionis, Mantas / Žukas, Agnius / Abramavičius, Darius

Physical chemistry chemical physics : PCCP

2022 Volume 24, Issue 29, Page(s) 17665–17672

Abstract: The linear absorption spectrum of J and H molecular aggregates is studied using the time-dependent Dirac-Frenkel variational principle (TDVP) with the multi-Davydov ... ...

Abstract	The linear absorption spectrum of J and H molecular aggregates is studied using the time-dependent Dirac-Frenkel variational principle (TDVP) with the multi-Davydov D
Language	English
Publishing date	2022-07-27
Publishing country	England
Document type	Journal Article
ZDB-ID	1476244-4
ISSN	1463-9084 ; 1463-9076
ISSN (online)	1463-9084
ISSN	1463-9076
DOI	10.1039/d2cp00819j
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Article ; Online: Two phases of

Karpicz, Renata / Kareivaite, Gabriele / Macernis, Mindaugas / Abramavicius, Darius / Valkunas, Leonas

Physical chemistry chemical physics : PCCP

2023 Volume 25, Issue 32, Page(s) 21183–21190

Abstract: Variability in the spectral properties of solid conformations of stilbene under various external conditions still remains obscure. The photophysical properties ... ...

Abstract	Variability in the spectral properties of solid conformations of stilbene under various external conditions still remains obscure. The photophysical properties of
Language	English
Publishing date	2023-08-16
Publishing country	England
Document type	Journal Article
ZDB-ID	1476244-4
ISSN	1463-9084 ; 1463-9076
ISSN (online)	1463-9084
ISSN	1463-9076
DOI	10.1039/d3cp03015f
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Article ; Online: Simulation of Ab Initio Optical Absorption Spectrum of β-Carotene with Fully Resolved

Jakučionis, Mantas / Gaižiu Nas, Ignas / Šulskus, Juozas / Abramavičius, Darius

The journal of physical chemistry. A

2022 Volume 126, Issue 2, Page(s) 180–189

Abstract: The electronic absorption spectrum of β-carotene (β-Car) is studied using quantum chemistry and quantum dynamics simulations. Vibrational normal modes were computed in optimized geometries of the electronic ground ... ...

Abstract	The electronic absorption spectrum of β-carotene (β-Car) is studied using quantum chemistry and quantum dynamics simulations. Vibrational normal modes were computed in optimized geometries of the electronic ground state
MeSH term(s)	Computer Simulation ; Quantum Theory ; Solvents ; Vibration ; beta Carotene
Chemical Substances	Solvents ; beta Carotene (01YAE03M7J)
Language	English
Publishing date	2022-01-05
Publishing country	United States
Document type	Journal Article
ISSN	1520-5215
ISSN (online)	1520-5215
DOI	10.1021/acs.jpca.1c06115
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Article ; Online: Modeling irreversible molecular internal conversion using the time-dependent variational approach with sD

Jakučionis, Mantas / Mancal, Tomas / Abramavičius, Darius

Physical chemistry chemical physics : PCCP

2020 Volume 22, Issue 16, Page(s) 8952–8962

Abstract: Effects of non-linear coupling between the system and the bath vibrational modes on the system internal conversion dynamics are investigated using the Dirac-Frenkel variational approach with a newly defined sD2 ansatz. It explicitly accounts for the ... ...

Abstract	Effects of non-linear coupling between the system and the bath vibrational modes on the system internal conversion dynamics are investigated using the Dirac-Frenkel variational approach with a newly defined sD2 ansatz. It explicitly accounts for the entangled system electron-vibrational states, while the bath quantum harmonic oscillator states are expanded in a superposition of quantum coherent states. Using a non-adiabatically coupled three-level model, we show that efficient irreversible internal conversion due to quadratic vibrational-bath coupling occurs when the initially populated system vibrational levels are in resonance with the vibrational levels of a lower energy electronic state, also, a non-Gaussian bath wavepacket representation is required. The quadratic system-bath couplings result in broadened and asymmetrically squeezed bath quantum harmonic oscillator wavepackets in the coordinate-momentum phase space.
Language	English
Publishing date	2020-04-15
Publishing country	England
Document type	Journal Article
ZDB-ID	1476244-4
ISSN	1463-9084 ; 1463-9076
ISSN (online)	1463-9084
ISSN	1463-9076
DOI	10.1039/d0cp01092h
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Article ; Online: Second harmonic generation theory for a helical macromolecule with high sensitivity to structural disorder.

Abramavicius, Darius / Krouglov, Serguei / Barzda, Virginijus

Physical chemistry chemical physics : PCCP

2021 Volume 23, Issue 36, Page(s) 20201–20217

Abstract: Microscopic theory for the second harmonic generation in a helical molecular system is developed in the minimal coupling representation including non-local interaction effects. At the second order to the field we find a compact expression which combines ... ...

Abstract	Microscopic theory for the second harmonic generation in a helical molecular system is developed in the minimal coupling representation including non-local interaction effects. At the second order to the field we find a compact expression which combines dipolar, quadrupolar and magnetic contributions. A detailed derivation of the response is performed to specifically isolate the quadratic coupling terms, which we denote as the
Language	English
Publishing date	2021-09-22
Publishing country	England
Document type	Journal Article
ZDB-ID	1476244-4
ISSN	1463-9084 ; 1463-9076
ISSN (online)	1463-9084
ISSN	1463-9076
DOI	10.1039/d1cp00694k
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Article ; Online: Vibration-mediated energy transport in bacterial reaction center: Simulation study.

Bubilaitis, Vytautas / Rancova, Olga / Abramavicius, Darius

The Journal of chemical physics

2021 Volume 154, Issue 21, Page(s) 214115

Abstract: Exciton energy relaxation in a bacterial Reaction Center (bRC) pigment-protein aggregate presumably involves emission of high energy vibrational quanta to cover wide energy gaps between excitons. Here, we assess this hypothesis utilizing vibronic two- ... ...

Abstract	Exciton energy relaxation in a bacterial Reaction Center (bRC) pigment-protein aggregate presumably involves emission of high energy vibrational quanta to cover wide energy gaps between excitons. Here, we assess this hypothesis utilizing vibronic two-particle theory in modeling of the excitation relaxation process in bRC. Specific high frequency molecular vibrational modes are included explicitly one at a time in order to check which high frequency vibrations are involved in the excitation relaxation process. The low frequency bath modes are treated perturbatively within Redfield relaxation theory. The analysis of the population relaxation rate data indicates energy flow pathways in bRC and suggests that specific vibrations may be responsible for the excitation relaxation process.
MeSH term(s)	Energy Transfer ; Molecular Dynamics Simulation ; Photosynthetic Reaction Center Complex Proteins/chemistry ; Photosynthetic Reaction Center Complex Proteins/metabolism ; Rhodobacter sphaeroides/chemistry ; Rhodobacter sphaeroides/metabolism ; Vibration
Chemical Substances	Photosynthetic Reaction Center Complex Proteins
Language	English
Publishing date	2021-07-09
Publishing country	United States
Document type	Journal Article
ZDB-ID	3113-6
ISSN	1089-7690 ; 0021-9606
ISSN (online)	1089-7690
ISSN	0021-9606
DOI	10.1063/5.0048815
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Article ; Online: Two-dimensional electronic spectroscopy of anharmonic molecular potentials.

Anda, André / Abramavičius, Darius / Hansen, Thorsten

Physical chemistry chemical physics : PCCP

2018 Volume 20, Issue 3, Page(s) 1642–1652

Abstract: Two-dimensional electronic spectroscopy (2DES) is a powerful tool in the study of coupled electron-phonon dynamics, yet very little is known about how nonlinearities in the electron-phonon coupling, arising from anharmonicities in the nuclear potentials, ...

Abstract	Two-dimensional electronic spectroscopy (2DES) is a powerful tool in the study of coupled electron-phonon dynamics, yet very little is known about how nonlinearities in the electron-phonon coupling, arising from anharmonicities in the nuclear potentials, affect the spectra. These become especially relevant when the coupling is strong. From the linear spectroscopies, anharmonicities are known to give structure to the zero-phonon line and to break mirror-symmetry between absorption and emission, but the 2D analogues of these effects have not been identified. Using a simple two-level model where the electronic states are described by (displaced) harmonic oscillators with differing curvatures or displaced Morse oscillators, we find that the zero-phonon line shape is essentially transferred to the diagonal in 2DES spectra, and that anharmonicities break a horizontal mirror-symmetry in the infinite waiting time limit. We also identify anharmonic effects that are only present in 2DES spectra: twisting of cross-peaks stemming from stimulated emission signals; and oscillation period mismatch between ground state bleach and stimulated emission (for harmonic oscillators with differing curvatures), or inherently chaotic oscillations (for Morse oscillators). Our findings will facilitate an improved understanding of 2DES spectra and aid the interpretation of signals that are more realistic than those arising from simple models.
Language	English
Publishing date	2018-01-17
Publishing country	England
Document type	Journal Article
ZDB-ID	1476244-4
ISSN	1463-9084 ; 1463-9076
ISSN (online)	1463-9084
ISSN	1463-9076
DOI	10.1039/c7cp06583c
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Article ; Online: Excitation transfer pathways in excitonic aggregates revealed by the stochastic Schrödinger equation.

Abramavicius, Vytautas / Abramavicius, Darius

The Journal of chemical physics

2014 Volume 140, Issue 6, Page(s) 65103

Abstract: We derive the stochastic Schrödinger equation for the system wave vector and use it to describe the excitation energy transfer dynamics in molecular aggregates. We suggest a quantum-measurement based method of estimating the excitation transfer time. ... ...

Abstract	We derive the stochastic Schrödinger equation for the system wave vector and use it to describe the excitation energy transfer dynamics in molecular aggregates. We suggest a quantum-measurement based method of estimating the excitation transfer time. Adequacy of the proposed approach is demonstrated by performing calculations on a model system. The theory is then applied to study the excitation transfer dynamics in a photosynthetic pigment-protein Fenna-Matthews-Olson (FMO) aggregate using both the Debye spectral density and the spectral density obtained from earlier molecular dynamics simulations containing strong vibrational high-frequency modes. The obtained results show that the excitation transfer times in the FMO system are affected by the presence of the vibrational modes; however, the transfer pathways remain the same.
MeSH term(s)	Bacterial Proteins/chemistry ; Chlorobi/chemistry ; Energy Transfer ; Light-Harvesting Protein Complexes/chemistry ; Models, Molecular ; Quantum Theory ; Stochastic Processes
Chemical Substances	Bacterial Proteins ; FMO bacteriochlorophyll protein, Bacteria ; Light-Harvesting Protein Complexes
Language	English
Publishing date	2014-02-14
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	3113-6
ISSN	1089-7690 ; 0021-9606
ISSN (online)	1089-7690
ISSN	0021-9606
DOI	10.1063/1.4863968
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Article ; Online: Two-dimensional electronic Stark spectroscopy of a photosynthetic dimer.

Nguyen, Hoang H / Loukianov, Anton D / Ogilvie, Jennifer P / Abramavicius, Darius

The Journal of chemical physics

2020 Volume 153, Issue 14, Page(s) 144203

Abstract: Stark spectroscopy, which measures changes in the linear absorption of a sample in the presence of an external DC electric field, is a powerful experimental tool for probing the existence of charge-transfer (CT) states in photosynthetic systems. CT ... ...

Abstract	Stark spectroscopy, which measures changes in the linear absorption of a sample in the presence of an external DC electric field, is a powerful experimental tool for probing the existence of charge-transfer (CT) states in photosynthetic systems. CT states often have small transition dipole moments, making them insensitive to other spectroscopic methods, but are particularly sensitive to Stark spectroscopy due to their large permanent dipole moment. In a previous study, we demonstrated a new experimental method, two-dimensional electronic Stark spectroscopy (2DESS), which combines two-dimensional electronic spectroscopy (2DES) and Stark spectroscopy. In order to understand how the presence of CT states manifest in 2DESS, here, we perform computational modeling and calculations of 2DESS as well as 2DES and Stark spectra, studying a photosynthetic dimer inspired by the photosystem II reaction center. We identify specific cases where qualitatively different sets of system parameters produce similar Stark and 2DES spectra but significantly different 2DESS spectra, showing the potential for 2DESS to aid in identifying CT states and their coupling to excitonic states.
MeSH term(s)	Chlorophyll A/chemistry ; Computer Simulation ; Dimerization ; Spectrum Analysis/methods ; Thermodynamics
Chemical Substances	Chlorophyll A (YF5Q9EJC8Y)
Language	English
Publishing date	2020-10-20
Publishing country	United States
Document type	Journal Article
ZDB-ID	3113-6
ISSN	1089-7690 ; 0021-9606
ISSN (online)	1089-7690
ISSN	0021-9606
DOI	10.1063/5.0021529
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Role of Bath Fluctuations in the Double-Excitation Manifold in Shaping the 2DES of Bacterial Reaction Centers at Low Temperature.

Rancova, Olga / Jankowiak, Ryszard / Abramavicius, Darius

The journal of physical chemistry. B

2018 Volume 122, Issue 4, Page(s) 1348–1366

Abstract: Spectroscopically relevant properties in photosynthetic reaction centers change during charge separation. In this paper, we focus on incorporation of the complete set of environmental fluctuations in the modeling of the nonlinear spectra of molecular ... ...

Abstract	Spectroscopically relevant properties in photosynthetic reaction centers change during charge separation. In this paper, we focus on incorporation of the complete set of environmental fluctuations in the modeling of the nonlinear spectra of molecular aggregates. The model is applied in simulations of two-dimensional electronic spectra of a photosynthetic reaction center at low temperature (5 K), where spectral lines are narrow, such that more features can be resolved. We show that vertical cross sections of the simulated two-dimensional spectra (with all populations in the lowest excited state) reveal transient hole-burned spectra excited resonantly within the B band in agreement with experiment, thus providing new insight into environmental fluctuation parameters of Rhodobacter sphaeroides at low temperatures. Correlated fluctuations of molecular parameters are found to be necessary to describe charge separated configurations of molecular excited states.
MeSH term(s)	Molecular Dynamics Simulation ; Photosynthetic Reaction Center Complex Proteins/chemistry ; Photosynthetic Reaction Center Complex Proteins/metabolism ; Protein Aggregates ; Rhodobacter sphaeroides/chemistry ; Rhodobacter sphaeroides/metabolism ; Spectrum Analysis ; Temperature
Chemical Substances	Photosynthetic Reaction Center Complex Proteins ; Protein Aggregates
Language	English
Publishing date	2018--01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	1520-5207
ISSN (online)	1520-5207
DOI	10.1021/acs.jpcb.7b08905
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