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Thøgersen J, Chatterley AS, Weidner T, Jensen F. Peptide Bond of Aqueous Dipeptides Is Resilient to Deep Ultraviolet Irradiation. J Am Chem Soc 2023; 145:9777-9785. [PMID: 37075197 DOI: 10.1021/jacs.3c01469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2023]
Abstract
The susceptibility of aqueous dipeptides to photodissociation by deep ultraviolet irradiation is studied by femtosecond spectroscopy supported by density functional theory calculations. The primary photodynamics of the aqueous dipeptides of glycyl-glycine (gly-gly), alalyl-alanine (ala-ala), and glycyl-alanine (gly-ala) show that upon photoexcitation at a wavelength of 200 nm, about 10% of the excited dipeptides dissociate by decarboxylation within 100 ps, while the rest of the dipeptides return to their native ground state. Accordingly, the vast majority of the excited dipeptides withstand the deep ultraviolet excitation. In those relatively few cases, where excitation leads to dissociation, the measurements show that deep ultraviolet irradiation breaks the Cα-C bond rather than the peptide bond. The peptide bond is thereby left intact, and the decarboxylated dipeptide moiety is open to subsequent reactions. The experiments indicate that the low photodissociation yield and in particular the resilience of the peptide bond to dissociation are due to rapid internal conversion from the excited state to the ground state, followed by efficient vibrational relaxation facilitated by intramolecular coupling among the carbonate and amide modes. Thus, the entire process of internal conversion and vibrational relaxation to thermal equilibrium on the dipeptide ground state occurs on a time scale of less than 2 ps.
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Affiliation(s)
- Jan Thøgersen
- Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
| | - Adam S Chatterley
- Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
| | - Tobias Weidner
- Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
| | - Frank Jensen
- Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
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2
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ThOgersen J, Weidner T, Jensen F. The primary photo-dissociation dynamics of aqueous formamide and dimethylformamide. Phys Chem Chem Phys 2022; 24:24695-24705. [DOI: 10.1039/d2cp03166c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We study the primary dissociation dynamics of aqueous formamide (HCONH2) and dimethylformamide (HCON(CH3)2) induced by photo-excitation at λ = 200 nm. The photolysis is recorded with sub-picosecond time resolution by...
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3
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Duchemin I, Guido CA, Jacquemin D, Blase X. The Bethe-Salpeter formalism with polarisable continuum embedding: reconciling linear-response and state-specific features. Chem Sci 2018; 9:4430-4443. [PMID: 29896384 PMCID: PMC5956976 DOI: 10.1039/c8sc00529j] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 04/02/2018] [Indexed: 11/25/2022] Open
Abstract
The Bethe-Salpeter equation (BSE) formalism has been recently shown to be a valuable alternative to time-dependent density functional theory (TD-DFT) with the same computing time scaling with system size. In particular, problematic transitions for TD-DFT such as charge-transfer, Rydberg and cyanine-like excitations were shown to be accurately described with BSE. We demonstrate here that combining the BSE formalism with the polarisable continuum model (PCM) allows us to include simultaneously linear-response and state-specific contributions to solvatochromism. This is confirmed by exploring transitions of various natures (local, charge-transfer, etc.) in a series of solvated molecules (acrolein, indigo, p-nitro-aniline, donor-acceptor complexes, etc.) for which we compare BSE solvatochromic shifts to those obtained by linear-response and state-specific TD-DFT implementations. Such a remarkable and unique feature is particularly valuable for the study of solvent effects on excitations presenting a hybrid localised/charge-transfer character.
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Affiliation(s)
- Ivan Duchemin
- Univ. Grenobles Alpes , CEA, INAC-MEM, L_Sim , F-38000 Grenoble , France . ;
| | - Ciro A Guido
- Laboratoire CEISAM - UMR CNR 6230 , Université de Nantes , 2 Rue de la Houssinière, BP 92208 , 44322 Nantes Cedex 3 , France
- Laboratoire MOLTECH - UMR CNRS 6200 , Université de Angers , 2 Bd Lavoisier , 49045 Angers Cedex , France
| | - Denis Jacquemin
- Laboratoire CEISAM - UMR CNR 6230 , Université de Nantes , 2 Rue de la Houssinière, BP 92208 , 44322 Nantes Cedex 3 , France
| | - Xavier Blase
- Univ. Grenobles Alpes , CNRS , Institut Néel , F-38042 Grenoble , France
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4
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Hršak D, Nørby MS, Coriani S, Kongsted J. One-Photon Absorption Properties from a Hybrid Polarizable Density Embedding/Complex Polarization Propagator Approach for Polarizable Solutions. J Chem Theory Comput 2018; 14:2145-2154. [DOI: 10.1021/acs.jctc.8b00155] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Dalibor Hršak
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Morten Steen Nørby
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Sonia Coriani
- Department of Chemistry, Technical University of Denmark, Kemitorvet Building 207, 2800 Kongens Lyngby, Denmark
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
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5
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Hršak D, Olsen JMH, Kongsted J. Polarizable Density Embedding Coupled Cluster Method. J Chem Theory Comput 2018; 14:1351-1360. [DOI: 10.1021/acs.jctc.7b01153] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Dalibor Hršak
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Jógvan Magnus Haugaard Olsen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
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6
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Bennie SJ, Curchod BFE, Manby FR, Glowacki DR. Pushing the Limits of EOM-CCSD with Projector-Based Embedding for Excitation Energies. J Phys Chem Lett 2017; 8:5559-5565. [PMID: 29076727 DOI: 10.1021/acs.jpclett.7b02500] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The calculation of accurate excitation energies using ab initio electronic structure methods such as standard equation of motion coupled cluster singles and doubles (EOM-CCSD) has been cost prohibitive for large systems. In this work, we use a simple projector-based embedding scheme to calculate the EOM-CCSD excitation energies of acrolein solvated in water molecules modeled using density functional theory (DFT). We demonstrate the accuracy of this approach gives excitation energies within 0.01 eV of full EOM-CCSD, but with significantly reduced computational cost. This approach is also shown to be relatively invariant to the choice of functional used in the environment and allows for the description of systems with large numbers of basis functions (>1000) to be treated using state-of-the-art wave function methods. The flexibility of embedding to select orbitals to add to the excited-state method provides insights into the origins of the excitations and can reduce artifacts that could arise in traditional linear response time-dependent DFT (LR-TDDFT).
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Affiliation(s)
- Simon J Bennie
- Centre for Computational Chemistry, School of Chemistry, University of Bristol , Bristol, BS8 1TH, United Kingdom
| | - Basile F E Curchod
- Centre for Computational Chemistry, School of Chemistry, University of Bristol , Bristol, BS8 1TH, United Kingdom
| | - Frederick R Manby
- Centre for Computational Chemistry, School of Chemistry, University of Bristol , Bristol, BS8 1TH, United Kingdom
| | - David R Glowacki
- Centre for Computational Chemistry, School of Chemistry, University of Bristol , Bristol, BS8 1TH, United Kingdom
- Department of Computer Science, University of Bristol , Bristol, BS8 1UB, United Kingdom
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7
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List NH, Olsen JMH, Kongsted J. Excited states in large molecular systems through polarizable embedding. Phys Chem Chem Phys 2016; 18:20234-50. [DOI: 10.1039/c6cp03834d] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Using the polarizable embedding model enables rational design of light-sensitive functional biological materials.
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Affiliation(s)
- Nanna Holmgaard List
- Department of Physics, Chemistry and Pharmacy
- University of Southern Denmark
- 5230 Odense M
- Denmark
| | | | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy
- University of Southern Denmark
- 5230 Odense M
- Denmark
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8
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Solvent effect on UV/Vis absorption and emission spectra in aqueous solution based on a modified form of solvent reorganization energy. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.07.079] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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De Silva N, Willow SY, Gordon MS. Solvent induced shifts in the UV spectrum of amides. J Phys Chem A 2013; 117:11847-55. [PMID: 23758065 DOI: 10.1021/jp402999p] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Solvent effects on the electronic spectra of formamide and trans-N-methylacetamide are studied using four different levels of theory: singly excited configuration interaction (CIS), equations of motion coupled-cluster theory with singles and doubles (EOM-CCSD), completely renormalized coupled-cluster theory with singles and doubles with perturbative triple excitations (CR-EOM-CCSD(T)), and time-dependent density functional theory (TDDFT), employing small clusters of water molecules. The simulated electronic spectrum is obtained via molecular dynamics simulations with 100 waters modeled with the effective fragment potential method and exhibits a blue-shift and red-shift, respectively, for the n → π* and πnb → π* vertical excitation energies, in good agreement with the experimental electronic spectra of amides.
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Affiliation(s)
- Nuwan De Silva
- Department of Chemistry, Iowa State University , Ames, Iowa 50011, United States
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10
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Lunkenheimer B, Köhn A. Solvent Effects on Electronically Excited States Using the Conductor-Like Screening Model and the Second-Order Correlated Method ADC(2). J Chem Theory Comput 2012; 9:977-94. [DOI: 10.1021/ct300763v] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bernd Lunkenheimer
- Institut für Physikalische
Chemie, Johannes Gutenberg-Universität, 55099 Mainz,
Germany
| | - Andreas Köhn
- Institut für Physikalische
Chemie, Johannes Gutenberg-Universität, 55099 Mainz,
Germany
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11
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Schwabe T, Sneskov K, Haugaard Olsen JM, Kongsted J, Christiansen O, Hättig C. PERI–CC2: A Polarizable Embedded RI-CC2 Method. J Chem Theory Comput 2012; 8:3274-83. [DOI: 10.1021/ct3003749] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tobias Schwabe
- Center for Bioinformatics and
Institute of Physical Chemistry, University of Hamburg, Bundesstraße
43, D-20146 Hamburg, Germany
| | - Kristian Sneskov
- Center for Oxygen Microscopy
and Imaging, Department of Chemistry, Aarhus University, Langelandsgade
140, DK-8000 Aarhus C, Denmark
- The Lundbeck Foundation Center
for Theoretical Chemistry, Department of Chemistry, Aarhus University,
Langelandsgade 140, DK-8000 Aarhus C, Denmark
| | - Jógvan Magnus Haugaard Olsen
- Department of Physics, Chemistry
and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230
Odense M, Denmark
| | - Jacob Kongsted
- Department of Physics, Chemistry
and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230
Odense M, Denmark
| | - Ove Christiansen
- Center for Oxygen Microscopy
and Imaging, Department of Chemistry, Aarhus University, Langelandsgade
140, DK-8000 Aarhus C, Denmark
- The Lundbeck Foundation Center
for Theoretical Chemistry, Department of Chemistry, Aarhus University,
Langelandsgade 140, DK-8000 Aarhus C, Denmark
| | - Christof Hättig
- Lehrstuhl
für Theoretische
Chemie, Ruhr-Universität Bochum, 44801 Bochum, Germany
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12
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Helgaker T, Coriani S, Jørgensen P, Kristensen K, Olsen J, Ruud K. Recent Advances in Wave Function-Based Methods of Molecular-Property Calculations. Chem Rev 2012; 112:543-631. [DOI: 10.1021/cr2002239] [Citation(s) in RCA: 463] [Impact Index Per Article: 38.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Trygve Helgaker
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, N-0315 Oslo, Norway
| | - Sonia Coriani
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Trieste, Via Giorgieri 1, I-34127 Trieste, Italy
| | - Poul Jørgensen
- Lundbeck Center for Theoretical Chemistry, Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
| | - Kasper Kristensen
- Lundbeck Center for Theoretical Chemistry, Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
| | - Jeppe Olsen
- Lundbeck Center for Theoretical Chemistry, Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
| | - Kenneth Ruud
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø, N-9037 Tromsø, Norway
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13
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Kjaer H, Sauer SPA, Kongsted J. The coupling constant polarizability and hyperpolarizabilty of 1J(NH) in N-methylacetamide, and its application for the multipole spin-spin coupling constant polarizability/reaction field approach to solvation. J Comput Chem 2011; 32:3168-74. [PMID: 21953553 DOI: 10.1002/jcc.21897] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Revised: 06/27/2011] [Accepted: 06/29/2011] [Indexed: 12/29/2022]
Abstract
We present a benchmark study of a combined multipole spin-spin coupling constant (SSCC) polarizability/reaction field (MJP/RF) approach to the calculation of both specific and bulk solvation effects on SSCCs of solvated molecules. The MJP/RF scheme is defined by an expansion of the SSCCs of the solvated molecule in terms of coupling constant dipole and quadrupole polarizabilities and hyperpolarizabilities derived from single molecule ab initio calculations. The solvent electric field and electric field gradient are calculated based on data derived from molecular dynamics (MD) simulations thereby accounting for solute-solvent dynamical effects. The MJP/RF method is benchmarked against polarizable QM/MM calculations for the one-bond N-H coupling constant in N-methylacetamide. The best agreement between the MJP/RF and QM/MM approaches is found by truncating the electric field expansion in the MJP/RF approach at the linear electric field level. In addition, we investigate the sensitivity of the results due to the choice of one-electron basis set in the ab initio calculations of the coupling constant (hyper-)polarizabilities and find that they are affected by the basis set in a way similar to the coupling constants themselves.
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Affiliation(s)
- Hanna Kjaer
- Department of Chemistry, University of Copenhagen, Copenhagen Ø, Denmark.
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14
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Sneskov K, Christiansen O. Excited state coupled cluster methods. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.99] [Citation(s) in RCA: 123] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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15
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Sneskov K, Schwabe T, Christiansen O, Kongsted J. Scrutinizing the effects of polarization in QM/MM excited state calculations. Phys Chem Chem Phys 2011; 13:18551-60. [PMID: 21947164 DOI: 10.1039/c1cp22067e] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this paper we demonstrate the importance of including polarization-especially in a fully self-consistent-field manner-when calculating excited states within linear response QM/MM methods based on correlated electronic structure methods. We perform a systematic investigation of solvent polarization effects by identifying lower order polarization reaction fields as compared to the full treatment. In the process we highlight the different nature of static and dynamic reaction fields and demonstrate-by method of example on both solvated systems as well as on biomolecules-that inclusion of both of these is mandatory for an accurate description of excited states. Ultimately, these findings reflect the importance of the change in the solvent reaction field upon electronic excitations. In light of the recent increasing interest in excited state QM/MM methods incorporating mutual polarization between subsystems as a method for treating large molecular systems, the reported investigation constitutes an important step towards dissecting the accuracy of such calculations.
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Affiliation(s)
- Kristian Sneskov
- The Lundbeck Foundation Center for Theoretical Chemistry, Department of Chemistry, University of Aarhus, Langelandsgade 140, DK-8000 Aarhus C, Denmark.
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Fukuda R, Ehara M, Nakatsuji H, Cammi R. Nonequilibrium solvation for vertical photoemission and photoabsorption processes using the symmetry-adapted cluster–configuration interaction method in the polarizable continuum model. J Chem Phys 2011; 134:104109. [DOI: 10.1063/1.3562211] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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17
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Sneskov K, Schwabe T, Kongsted J, Christiansen O. The polarizable embedding coupled cluster method. J Chem Phys 2011; 134:104108. [DOI: 10.1063/1.3560034] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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18
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Kjær H, Sauer SPA, Kongsted J. Benchmarking the multipole shielding polarizability/reaction field approach to solvation against QM/MM: Applications to the shielding constants of N-methylacetamide. J Chem Phys 2011; 134:044514. [DOI: 10.1063/1.3546033] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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19
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Olsen JM, Aidas K, Kongsted J. Excited States in Solution through Polarizable Embedding. J Chem Theory Comput 2010. [DOI: 10.1021/ct1003803] [Citation(s) in RCA: 264] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jógvan Magnus Olsen
- Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark, and Department of Chemistry, H. C. Ørsted Institute, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | - Kęstutis Aidas
- Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark, and Department of Chemistry, H. C. Ørsted Institute, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | - Jacob Kongsted
- Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark, and Department of Chemistry, H. C. Ørsted Institute, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
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Cammi R, Fukuda R, Ehara M, Nakatsuji H. Symmetry-adapted cluster and symmetry-adapted cluster-configuration interaction method in the polarizable continuum model: Theory of the solvent effect on the electronic excitation of molecules in solution. J Chem Phys 2010; 133:024104. [DOI: 10.1063/1.3456540] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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