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Choudhury A, Santra S, Ghosh D. Understanding the Photoprocesses in Biological Systems: Need for Accurate Multireference Treatment. J Chem Theory Comput 2024; 20:4951-4964. [PMID: 38864715 DOI: 10.1021/acs.jctc.4c00027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2024]
Abstract
Light-matter interaction is crucial to life itself and revolves around many of the central processes in biology. The need for understanding these photochemical and photophysical processes cannot be overemphasized. Interaction of light with biological systems starts with the absorption of light and subsequent phenomena that occur in the excited states of the system. However, excited states are typically difficult to understand within the mean field approximation of quantum chemical methods. Therefore, suitable multireference methods and methodologies have been developed to understand these phenomena. In this Perspective, we will describe a few methods and methodologies suitable for these descriptions and discuss some persisting difficulties.
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Affiliation(s)
- Arpan Choudhury
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Supriyo Santra
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Debashree Ghosh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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2
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Huang H, Peng J, Zhang Y, Gu FL, Lan Z, Xu C. The development of the QM/MM interface and its application for the on-the-fly QM/MM nonadiabatic dynamics in JADE package: Theory, implementation, and applications. J Chem Phys 2024; 160:234101. [PMID: 38884395 DOI: 10.1063/5.0215036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 05/15/2024] [Indexed: 06/18/2024] Open
Abstract
Understanding the nonadiabatic dynamics of complex systems is a challenging task in computational photochemistry. Herein, we present an efficient and user-friendly quantum mechanics/molecular mechanics (QM/MM) interface to run on-the-fly nonadiabatic dynamics. Currently, this interface consists of an independent set of codes designed for general-purpose use. Herein, we demonstrate the ability and feasibility of the QM/MM interface by integrating it with our long-term developed JADE package. Tailored to handle nonadiabatic processes in various complex systems, especially condensed phases and protein environments, we delve into the theories, implementations, and applications of on-the-fly QM/MM nonadiabatic dynamics. The QM/MM approach is established within the framework of the additive QM/MM scheme, employing electrostatic embedding, link-atom inclusion, and charge-redistribution schemes to treat the QM/MM boundary. Trajectory surface-hopping dynamics are facilitated using the fewest switches algorithm, encompassing classical and quantum treatments for nuclear and electronic motions, respectively. Finally, we report simulations of nonadiabatic dynamics for two typical systems: azomethane in water and the retinal chromophore PSB3 in a protein environment. Our results not only illustrate the power of the QM/MM program but also reveal the important roles of environmental factors in nonadiabatic processes.
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Affiliation(s)
- Haiyi Huang
- MOE Key Laboratory of Environmental Theoretical Chemistry and Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou 510006, China
- Center for Advanced Materials Research, Beijing Normal University, Zhuhai 519087, China
- MOE Key Laboratory of Theoretical and Computational Photochemistry, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Jiawei Peng
- MOE Key Laboratory of Environmental Theoretical Chemistry and Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou 510006, China
| | - Yulin Zhang
- MOE Key Laboratory of Environmental Theoretical Chemistry and Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou 510006, China
| | - Feng Long Gu
- MOE Key Laboratory of Environmental Theoretical Chemistry and Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou 510006, China
| | - Zhenggang Lan
- MOE Key Laboratory of Environmental Theoretical Chemistry and Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou 510006, China
| | - Chao Xu
- MOE Key Laboratory of Environmental Theoretical Chemistry and Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou 510006, China
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3
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Geng X, Wang J, Liu Y, Yan W, Xu Z, Chen J, Zhao L. Theoretical Investigation on the Reversible Photoswitch Mechanism of Benzylidene-Oxazolone System. Chemphyschem 2024:e202400250. [PMID: 38820005 DOI: 10.1002/cphc.202400250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 05/31/2024] [Accepted: 05/31/2024] [Indexed: 06/02/2024]
Abstract
The design and application of molecular photoswitches have attracted much attention. Herein, we performed a detailed computational study on the photoswitch benzylidene-oxazolone system based on static electronic structure calculations and on-the-fly excited-state dynamic simulations. For the Z and E isomer, we located six and four minimum energy conical intersections (MECIs) between the first excited state (S1) and the ground state (S0), respectively. Among them, the relaxation pathway driven by ring-puckering motion is the most competitive channel with the photoisomeization process, leading to the low photoisomerization quantum yield. In the dynamic simulations, about 88 % and 66 % trajectories decay from S1 to S0 for Z and E isomer, respectively, within the total simulation time of ~2 ps. The photoisomeization quantum yields obtained in our study (0.20 for Z→E and 0.12 for E→Z) agree well with the experimental measured values (0.25 and 0.11), even though the number of trajectories is limited to 50. Our study sheds light on the complexity of the benzylidene-oxazolone system 's deactivation process and the competitive mechanisms among different reaction channels, which provides theoretical guidance for further design and development of benzylidene-oxazolone based molecular photoswitches.
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Affiliation(s)
- Xuehui Geng
- College of Science, China University of Petroleum (East China), Qingdao, 266580, Shandong, China
| | - Jiangyue Wang
- College of Science, China University of Petroleum (East China), Qingdao, 266580, Shandong, China
| | - Yuxuan Liu
- College of Science, China University of Petroleum (East China), Qingdao, 266580, Shandong, China
| | - Wenhui Yan
- College of Science, China University of Petroleum (East China), Qingdao, 266580, Shandong, China
| | - Zhijie Xu
- College of Science, China University of Petroleum (East China), Qingdao, 266580, Shandong, China
| | - Junsheng Chen
- Nano-Science Center & Department of Chemistry University of Copenhagen, Universitetsparken 5, 2100, KøbenhavnØ, Denmark
| | - Li Zhao
- College of Science, China University of Petroleum (East China), Qingdao, 266580, Shandong, China
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4
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Hamerla C, Mondal P, Hegger R, Burghardt I. Controlled destabilization of caged circularized DNA oligonucleotides predicted by replica exchange molecular dynamics simulations. Phys Chem Chem Phys 2023; 25:26132-26144. [PMID: 37740309 DOI: 10.1039/d3cp02961a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
Spatiotemporal control is a critical issue in the design of strategies for the photoregulation of oligonucleotide activity. Efficient uncaging, i.e., activation by removal of photolabile protecting groups (PPGs), often necessitates multiple PPGs. An alternative approach is based on circularization strategies, exemplified by intrasequential circularization, also denoted photo-tethering, as introduced in [Seyfried et al., Angew. Chem., Int. Ed., 2017, 56, 359]. Here, we develop a computational protocol, relying on replica exchange molecular dynamics (REMD), in order to characterize the destabilization of a series of circularized, caged DNA oligonucleotides addressed in the aforementioned study. For these medium-sized (32 nt) oligonucleotides, melting temperatures are computed, whose trend is in good agreement with experiment, exhibiting a large destabilization and, hence, reduction of the melting temperature of the order of ΔTm ∼ 30 K as compared with the native species. The analysis of free energy landscapes confirms the destabilization pattern experienced by the circularized oligonucleotides. The present study underscores that computational protocols that capture controlled destabilization and uncaging of oligonucleotides are promising as predictive tools in the tailored photocontrol of nucleic acids.
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Affiliation(s)
- Carsten Hamerla
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany.
| | - Padmabati Mondal
- Department of Chemistry and Center for Atomic, Molecular, and Optical Sciences and Technologies (CAMOST), Indian Institute of Science Education and Research (IISER) Tirupati, Panguru (G.P), Yerpedu Mandal, 517619 - Tirupati Dist., Andhra Pradesh, India
| | - Rainer Hegger
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany.
| | - Irene Burghardt
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany.
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5
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Osella S, Granucci G, Persico M, Knippenberg S. Dual photoisomerization mechanism of azobenzene embedded in a lipid membrane. J Mater Chem B 2023; 11:2518-2529. [PMID: 36852914 DOI: 10.1039/d2tb02767d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
The photoisomerization of chromophores embedded in biological environments is of high importance for biomedical applications, but it is still challenging to define the photoisomerization mechanism both experimentally and computationally. We present here a computational study of the azobenzene molecule embedded in a DPPC lipid membrane, and assess the photoisomerization mechanism by means of the quantum mechanics/molecular mechanics surface hopping (QM/MM-SH) method. We observe that while the trans-to-cis isomerization is a slow process governed by a torsional mechanism due to the strong interaction with the environment, the cis-to-trans mechanism is completed in sub-ps time scale and is governed by a pedal-like mechanism in which both weaker interactions with the environment and a different geometry of the potential energy surface play a key role.
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Affiliation(s)
- Silvio Osella
- Chemical and Biological Systems Simulation Lab, Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097 Warsaw, Poland. .,Materials and Process Simulation Center (MSC), California Institute of Technology, MC 139-74, Pasadena, CA, 91125, USA
| | - Giovanni Granucci
- Dipartimento di Chimica e Chimica Industriale, Universitá di Pisa, v. Moruzzi 13, I-56124 Pisa, Italy
| | - Maurizio Persico
- Dipartimento di Chimica e Chimica Industriale, Universitá di Pisa, v. Moruzzi 13, I-56124 Pisa, Italy
| | - Stefan Knippenberg
- Hasselt University, Theory Lab, Agoralaan Building D, 3590 Diepenbeek, Belgium.,Université Libre de Bruxelles, Spectroscopy, Quantum Chemistry and Atmospheric Remote Sensing (SQUARES), 50 Avenue F. Roosevelt, C.P. 160/09, B-1050 Brussels, Belgium.
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6
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Francés-Monerris A, Carmona-García J, Trabelsi T, Saiz-Lopez A, Lyons JR, Francisco JS, Roca-Sanjuán D. Photochemical and thermochemical pathways to S 2 and polysulfur formation in the atmosphere of Venus. Nat Commun 2022; 13:4425. [PMID: 35907911 PMCID: PMC9338966 DOI: 10.1038/s41467-022-32170-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 07/18/2022] [Indexed: 11/25/2022] Open
Abstract
Polysulfur species have been proposed to be the unknown near-UV absorber in the atmosphere of Venus. Recent work argues that photolysis of one of the (SO)2 isomers, cis-OSSO, directly yields S2 with a branching ratio of about 10%. If correct, this pathway dominates polysulfur formation by several orders of magnitude, and by addition reactions yields significant quantities of S3, S4, and S8. We report here the results of high-level ab-initio quantum-chemistry computations that demonstrate that S2 is not a product in cis-OSSO photolysis. Instead, we establish a novel mechanism in which S2 is formed in a two-step process. Firstly, the intermediate S2O is produced by the coupling between the S and Cl atmospheric chemistries (in particular, SO reaction with ClS) and in a lesser extension by O-abstraction reactions from cis-OSSO. Secondly, S2O reacts with SO. This modified chemistry yields S2 and subsequent polysulfur abundances comparable to the photolytic cis-OSSO mechanism through a more plausible pathway. Ab initio quantification of the photodissociations at play fills a critical data void in current atmospheric models of Venus. Polysulfur compounds have been ascribed as the unknown near-UV absorbers in Venusian atmosphere and play a key role in the sulfur chemical cycle of this planet. Here, authors establish their production from (SO)2 on the grounds of quantifications of photochemical and thermal pathways involved in the sulfur chemical cycle of the planet.
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Affiliation(s)
| | - Javier Carmona-García
- Institut de Ciència Molecular, Universitat de València, 46071, València, Spain.,Department of Atmospheric Chemistry and Climate, Institute of Physical Chemistry Rocasolano, CSIC, 28006, Madrid, Spain
| | - Tarek Trabelsi
- Department of Earth and Environmental Sciences and Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Alfonso Saiz-Lopez
- Department of Atmospheric Chemistry and Climate, Institute of Physical Chemistry Rocasolano, CSIC, 28006, Madrid, Spain
| | | | - Joseph S Francisco
- Department of Earth and Environmental Sciences and Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - Daniel Roca-Sanjuán
- Institut de Ciència Molecular, Universitat de València, 46071, València, Spain.
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7
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Liang R, Bakhtiiari A. Effects of Enzyme-Ligand Interactions on the Photoisomerization of a Light-Regulated Chemotherapeutic Drug. J Phys Chem B 2022; 126:2382-2393. [PMID: 35297246 DOI: 10.1021/acs.jpcb.1c10819] [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
Molecular photoswitches permit using light to control protein activity with high spatiotemporal resolutions, thereby alleviating the side effects of conventional chemotherapy. However, due to the challenges in probing ultrafast photoisomerization reactions in biological environments, it remains elusive how the protein influences the photochemistry of the photoswitches, which hampers the rational design of light-regulated therapeutics. To overcome this challenge, we employed first-principles nonadiabatic dynamics simulations to characterize the photodynamics of the phototrexate (PTX), a recently developed photoswitchable anticancer chemotherapeutic that reversibly inhibits its target enzyme dihydrofolate reductase (DHFR). Our simulations show that the protein environment impedes the trans to cis photoisomerization of the PTX. The confinement in the ligand-binding cavity slows down the isomerization kinetics and quantum yield of the photoswitch by reshaping its conical intersection, increasing its excited-state free-energy barrier and quenching its local density fluctuations. Also, the protein environment results in a suboptimal binding mode of the photoproduct that needs to undergo large structural rearrangement to effectively inhibit the enzyme. Therefore, we predict that the PTX's trans → cis photoisomerization in solution precedes its binding with the protein, despite the favorable binding energy of the trans isomer. Our findings highlight the importance of the protein environment on the photochemical reactions of the molecular photoswitches. As such, our work represents an important step toward the rational design of light-regulated drugs in photopharmacology.
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Affiliation(s)
- Ruibin Liang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Amirhossein Bakhtiiari
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
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8
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Barbosa N, Sagresti L, Brancato G. Photoinduced azobenzene-modified DNA dehybridization: insights into local and cooperativity effects from a molecular dynamics study. Phys Chem Chem Phys 2021; 23:25170-25179. [PMID: 34730143 DOI: 10.1039/d1cp04032d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photoresponsive azobenzene-modified DNA (RNA) has become a very fruitful material for nanotechnology due to the capability of switching on and off hybridization (i.e., duplex formation) in smart nanostructures. This nanomaterial exploits the well-known azobenzene trans/cis photo-isomerization. In fact, it has been found that DNA tethered with trans-azobenzene shows normal nucleic acid recognition and hybridization, while the cis form destabilizes the duplex configuration, eventually leading to DNA unzipping. However, while the working principle of the light-triggered DNA dehybridization is apparent, specific details of this mechanism still remain elusive to experiments. Previous in silico studies successfully addressed some aspects (e.g., local structural effects, thermal stability, and early events of azobenzene photoisomerization) of this challenging molecular process characterized by timescales spanning several orders of magnitude, from picoseconds (i.e., azobenzene photoisomerization) to micro- and milli-seconds (i.e., complete strand detachment). In this work, inspired by a recent report by Asanuma and coworkers, we focus on the local and cooperativity effects played by multiple azobenzene units on a 10-mer azobenzene-modified DNA duplex. Using molecular dynamics (MD) simulations, we investigated nine systems equipped with a variable number (from 1 to 7) of photoswitch units and different configurations, focusing our analysis on the initial events (from few ps to hundreds of ns) characterizing DNA destabilization upon trans-to-cis isomerization, such as hydrogen bonding breakage and base pair misalignment. Results highlight, on one hand, the local effects of single azobenzene units on DNA duplex structure and, on the other hand, the cooperative role that multiple photoswitches show in enhancing and accelerating DNA dehybridization following trans-to-cis conversion, in agreement with previously reported data and observations.
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Affiliation(s)
- Nuno Barbosa
- Scuola Normale Superiore and CSGI, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.
| | - Luca Sagresti
- Scuola Normale Superiore and CSGI, Piazza dei Cavalieri 7, I-56126 Pisa, Italy. .,Istituto Nazionale di Fisica Nucleare, Largo Pontecorvo 3, I-56100 Pisa, Italy
| | - Giuseppe Brancato
- Scuola Normale Superiore and CSGI, Piazza dei Cavalieri 7, I-56126 Pisa, Italy. .,Istituto Nazionale di Fisica Nucleare, Largo Pontecorvo 3, I-56100 Pisa, Italy
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9
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Carmona-García J, Francés-Monerris A, Cuevas CA, Trabelsi T, Saiz-Lopez A, Francisco JS, Roca-Sanjuán D. Photochemistry and Non-adiabatic Photodynamics of the HOSO Radical. J Am Chem Soc 2021; 143:10836-10841. [PMID: 34270223 DOI: 10.1021/jacs.1c05149] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Hydroxysulfinyl radical (HOSO) is important due to its involvement in climate geoengineering upon SO2 injection and generation of the highly hygroscopic H2SO4. Its photochemical behavior in the upper atmosphere is, however, uncertain. Here we present the ultraviolet-visible photochemistry and photodynamics of this species by simulating the atmospheric conditions with high-level quantum chemistry methods. Photocleavage to HO + SO arises as the major solar-induced channel, with a minor contribution of H + SO2 photoproducts. The efficient generation of SO is relevant due to its reactivity with O3 and the consequent depletion of ozone in the stratosphere.
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Affiliation(s)
- Javier Carmona-García
- Institut de Ciència Molecular, Universitat de València, València 46071, Spain.,Department of Atmospheric Chemistry and Climate, Institute of Physical Chemistry Rocasolano, CSIC, Madrid 28006, Spain
| | - Antonio Francés-Monerris
- Departament de Química Física, Universitat de València, 46100 Burjassot, Spain.,Université de Lorraine, CNRS, LPCT, F-54000 Nancy, France
| | - Carlos A Cuevas
- Department of Atmospheric Chemistry and Climate, Institute of Physical Chemistry Rocasolano, CSIC, Madrid 28006, Spain
| | - Tarek Trabelsi
- Department of Earth and Environmental Sciences and Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Alfonso Saiz-Lopez
- Department of Atmospheric Chemistry and Climate, Institute of Physical Chemistry Rocasolano, CSIC, Madrid 28006, Spain
| | - Joseph S Francisco
- Department of Earth and Environmental Sciences and Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Daniel Roca-Sanjuán
- Institut de Ciència Molecular, Universitat de València, València 46071, Spain
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10
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Gholamjani Moghaddam K, Giudetti G, Sipma W, Faraji S. Theoretical insights into the effect of size and substitution patterns of azobenzene derivatives on the DNA G-quadruplex. Phys Chem Chem Phys 2020; 22:26944-26954. [PMID: 33206064 DOI: 10.1039/d0cp04392c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Introducing photoswitches into the DNA G-quadruplex provides excellent opportunities to control folding and unfolding of these assemblies, demonstrating their potential in the development of novel nanodevices with medical and nanotechnology applications. Using a quantum mechanics/molecular mechanics (QM/MM) scheme, we carried out a series of simulations to identify the effect of the size and substitution patterns of three azobenzene derivatives (AZ1, AZ2 and AZ3) on the excitation energies of the two lowest excited states of the smallest photoswitchable G-quadruplex reported to date. We demonstrated that the size and the substitution pattern do not affect the ultrafast cis-trans photoiomerization mechanism of the azobenzene derivatives significantly, in agreement with the experiment. However, molecular dynamics simulations revealed that while AZ2 and AZ3 G-quadruplexes are structurally stable during the simulations, the AZ1 G-quadruplex undergoes larger structural changes and shows two ground state populations that differ in the azobenzene backbone adopting two different conformations. AZ1, with para-para substitution pattern, provides more flexibility to the whole G-quadruplex structure compared to AZ2 and AZ3, and can thus facilitate the photoisomerization reaction between a nonpolymorphic, stacked, tetramolecular G-quadruplex and an unstructured state after trans-cis isomerization occurring in a longer time dynamics, in agreement with the experimental findings. The QM/MM simulations of the absorption spectra indicated that the thermal fluctuation plays a more crucial role in the main absorption band of the azobenzene derivatives than the inclusion of the G-quadruplex, implying that the influence of the G-quadruplex environment is minimal. We propose that the latter is attributed to the position of the azobenzene linkers in the G-quadruplexes, i.e. the edgewise loops containing the azobenzene moieties that are located above the G-quartets, not being fully embedded inside or involved in the stacked structure. Our theoretical findings provide support to a recent study of the photoresponsive formation of photoswitchable G-quadruplex motifs.
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11
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Imperatore C, Varriale A, Rivieccio E, Pennacchio A, Staiano M, D’Auria S, Casertano M, Altucci C, Valadan M, Singh M, Menna M, Varra M. Spectroscopic Properties of Two 5'-(4-Dimethylamino)Azobenzene Conjugated G-Quadruplex Forming Oligonucleotides. Int J Mol Sci 2020; 21:E7103. [PMID: 32993097 PMCID: PMC7582650 DOI: 10.3390/ijms21197103] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/10/2020] [Accepted: 09/24/2020] [Indexed: 12/12/2022] Open
Abstract
The synthesis of two 5'-end (4-dimethylamino)azobenzene conjugated G-quadruplex forming aptamers, the thrombin binding aptamer (TBA) and the HIV-1 integrase aptamer (T30695), was performed. Their structural behavior was investigated by means of UV, CD, fluorescence spectroscopy, and gel electrophoresis techniques in K+-containing buffers and water-ethanol blends. Particularly, we observed that the presence of the 5'-(4-dimethylamino)azobenzene moiety leads TBA to form multimers instead of the typical monomolecular chair-like G-quadruplex and almost hampers T30695 G-quadruplex monomers to dimerize. Fluorescence studies evidenced that both the conjugated G-quadruplexes possess unique fluorescence features when excited at wavelengths corresponding to the UV absorption of the conjugated moiety. Furthermore, a preliminary investigation of the trans-cis conversion of the dye incorporated at the 5'-end of TBA and T30695 showed that, unlike the free dye, in K+-containing water-ethanol-triethylamine blend the trans-to-cis conversion was almost undetectable by means of a standard UV spectrophotometer.
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Affiliation(s)
- Concetta Imperatore
- Department of Pharmacy, School of Medicine, University of Naples “Federico II”, Via D. Montesano 49, 80131 Naples, Italy; (C.I.); (E.R.); (M.C.); (M.M.)
| | - Antonio Varriale
- Institute of Food Sciences, National Research Council of Italy, via Roma 64, 83100 Avellino, Italy; (A.V.); (A.P.); (M.S.); (S.D.)
| | - Elisa Rivieccio
- Department of Pharmacy, School of Medicine, University of Naples “Federico II”, Via D. Montesano 49, 80131 Naples, Italy; (C.I.); (E.R.); (M.C.); (M.M.)
| | - Angela Pennacchio
- Institute of Food Sciences, National Research Council of Italy, via Roma 64, 83100 Avellino, Italy; (A.V.); (A.P.); (M.S.); (S.D.)
| | - Maria Staiano
- Institute of Food Sciences, National Research Council of Italy, via Roma 64, 83100 Avellino, Italy; (A.V.); (A.P.); (M.S.); (S.D.)
| | - Sabato D’Auria
- Institute of Food Sciences, National Research Council of Italy, via Roma 64, 83100 Avellino, Italy; (A.V.); (A.P.); (M.S.); (S.D.)
| | - Marcello Casertano
- Department of Pharmacy, School of Medicine, University of Naples “Federico II”, Via D. Montesano 49, 80131 Naples, Italy; (C.I.); (E.R.); (M.C.); (M.M.)
| | - Carlo Altucci
- Department of Physics “Ettore Pancini”, University of Naples Federico II, Via Cinthia, 21—Building 6, 80126 Naples, Italy; (C.A.); (M.V.); (M.S.)
| | - Mohammadhassan Valadan
- Department of Physics “Ettore Pancini”, University of Naples Federico II, Via Cinthia, 21—Building 6, 80126 Naples, Italy; (C.A.); (M.V.); (M.S.)
| | - Manjot Singh
- Department of Physics “Ettore Pancini”, University of Naples Federico II, Via Cinthia, 21—Building 6, 80126 Naples, Italy; (C.A.); (M.V.); (M.S.)
| | - Marialuisa Menna
- Department of Pharmacy, School of Medicine, University of Naples “Federico II”, Via D. Montesano 49, 80131 Naples, Italy; (C.I.); (E.R.); (M.C.); (M.M.)
| | - Michela Varra
- Department of Pharmacy, School of Medicine, University of Naples “Federico II”, Via D. Montesano 49, 80131 Naples, Italy; (C.I.); (E.R.); (M.C.); (M.M.)
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12
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Xie Z, Duan S, Wang CK, Luo Y. Finding the true pathway for reversible isomerization of a single azobenzene molecule tumbling on Au(111) surface. NANOSCALE 2020; 12:10474-10479. [PMID: 32373867 DOI: 10.1039/d0nr01629b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Switchable trans-cis isomerization of azobenzene (AB) and its derivatives on metallic surfaces have offered rich possibilities to functionalize molecular devices. However, the lack of a good understanding of the isomerization pathway has severely limited our ability for rational design. One of the long-debated issues is the cis configuration of the parental AB on the Au(111) surface, for which the experimentally inferred structure differs from the theoretically predicted global minimum. Here, we theoretically identify a new in situ metastable configuration for cis-AB on Au(111) that can reproduce all the observations reported in the scanning tunneling microscopy experiments. It reveals that the bistability of AB on the Au(111) surface is attributed to the significantly increased kinetic stability of the newly discovered cis-AB isomer. A fascinating tumbling pathway that overcomes two energy barriers stimulated by tunneling electrons for the trans-cis AB isomerization on Au(111) has been verified, suggesting a new type of molecular motion based on the AB systems.
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Affiliation(s)
- Zhen Xie
- Shandong Province Key Laboratory of Medical Physics and Image Processing Technology, School of Physics and Electronics, Shandong Normal University, Jinan 250014, People's Republic of China
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Francés‐Monerris A, Carmona‐García J, Acuña AU, Dávalos JZ, Cuevas CA, Kinnison DE, Francisco JS, Saiz‐Lopez A, Roca‐Sanjuán D. Photodissociation Mechanisms of Major Mercury(II) Species in the Atmospheric Chemical Cycle of Mercury. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201915656] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Antonio Francés‐Monerris
- Université de LorraineCNRS, LPCT 54000 Nancy France
- Departamento de Química FísicaUniversitat de València 46100 Burjassot Spain
| | | | - A. Ulises Acuña
- Department of Atmospheric Chemistry and ClimateInstitute of Physical Chemistry RocasolanoCSIC 28006 Madrid Spain
| | - Juan Z. Dávalos
- Department of Atmospheric Chemistry and ClimateInstitute of Physical Chemistry RocasolanoCSIC 28006 Madrid Spain
| | - Carlos A. Cuevas
- Department of Atmospheric Chemistry and ClimateInstitute of Physical Chemistry RocasolanoCSIC 28006 Madrid Spain
| | | | - Joseph S. Francisco
- Department of Earth and Environmental Sciences and Department of ChemistryUniversity of Pennsylvania Philadelphia PA 19104 USA
| | - Alfonso Saiz‐Lopez
- Department of Atmospheric Chemistry and ClimateInstitute of Physical Chemistry RocasolanoCSIC 28006 Madrid Spain
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14
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Francés‐Monerris A, Carmona‐García J, Acuña AU, Dávalos JZ, Cuevas CA, Kinnison DE, Francisco JS, Saiz‐Lopez A, Roca‐Sanjuán D. Photodissociation Mechanisms of Major Mercury(II) Species in the Atmospheric Chemical Cycle of Mercury. Angew Chem Int Ed Engl 2020; 59:7605-7610. [DOI: 10.1002/anie.201915656] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Indexed: 12/23/2022]
Affiliation(s)
- Antonio Francés‐Monerris
- Université de LorraineCNRS, LPCT 54000 Nancy France
- Departamento de Química FísicaUniversitat de València 46100 Burjassot Spain
| | | | - A. Ulises Acuña
- Department of Atmospheric Chemistry and ClimateInstitute of Physical Chemistry RocasolanoCSIC 28006 Madrid Spain
| | - Juan Z. Dávalos
- Department of Atmospheric Chemistry and ClimateInstitute of Physical Chemistry RocasolanoCSIC 28006 Madrid Spain
| | - Carlos A. Cuevas
- Department of Atmospheric Chemistry and ClimateInstitute of Physical Chemistry RocasolanoCSIC 28006 Madrid Spain
| | | | - Joseph S. Francisco
- Department of Earth and Environmental Sciences and Department of ChemistryUniversity of Pennsylvania Philadelphia PA 19104 USA
| | - Alfonso Saiz‐Lopez
- Department of Atmospheric Chemistry and ClimateInstitute of Physical Chemistry RocasolanoCSIC 28006 Madrid Spain
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15
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Mai S, González L. Identification of important normal modes in nonadiabatic dynamics simulations by coherence, correlation, and frequency analyses. J Chem Phys 2019; 151:244115. [DOI: 10.1063/1.5129335] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Sebastian Mai
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 17, 1090 Vienna, Austria
| | - Leticia González
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Str. 17, 1090 Vienna, Austria
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16
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Zhang TS, Li ZW, Fang Q, Barbatti M, Fang WH, Cui G. Stereoselective Excited-State Isomerization and Decay Paths in cis-Cyclobiazobenzene. J Phys Chem A 2019; 123:6144-6151. [DOI: 10.1021/acs.jpca.9b04372] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Teng-Shuo Zhang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Zi-Wen Li
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Qiu Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | | | - Wei-Hai Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
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17
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Qu R, Liu Y, Zhang W, Li X, Feng L, Jiang L. Aminoazobenzene@Ag modified meshes with large extent photo-response: towards reversible oil/water removal from oil/water mixtures. Chem Sci 2019; 10:4089-4096. [PMID: 31049191 PMCID: PMC6469292 DOI: 10.1039/c9sc00020h] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 02/23/2019] [Indexed: 01/15/2023] Open
Abstract
A large-extent photo-responsive wettability transformation is realized by aminoazobenzene@Ag to selectively remove oil/water.
Photo-responsive materials with superwetting properties, especially in the azo-based class, have been used in water treatment because of their smart performance on wettability changes. However, their transformation extent in wettability has always troubled researchers. Here, we modified nano-Ag pine needles and aminoazobenzene (AABN) on polydopamine (PDA) pre-treated porous meshes, realizing a large-extent reversible photo-responsive wettability transformation from highly hydrophobic to highly hydrophilic. The contact angle is about 150.0° after being exposed to visible light, and is about 10.0° under 365 nm UV light. Accordingly, the modified mesh can achieve photo-responsive removal between oil and water from oil/water mixtures. This facile and universal approach based on trans–cis isomerization of AABN could be endowed to various commercial conductive meshes. Moreover, the modified meshes exhibit satisfactory removal efficiency, reusability and physical/chemical stability, which are more promising for practical applications such as fuel recycling, remote controlled oil/water separation and astronautical resource regeneration.
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Affiliation(s)
- Ruixiang Qu
- Department of Chemistry , Tsinghua University , Beijing 100084 , P. R. China .
| | - Yanan Liu
- Department of Chemistry , Tsinghua University , Beijing 100084 , P. R. China .
| | - Weifeng Zhang
- Department of Chemistry , Tsinghua University , Beijing 100084 , P. R. China .
| | - Xiangyu Li
- Department of Chemistry , Tsinghua University , Beijing 100084 , P. R. China .
| | - Lin Feng
- Department of Chemistry , Tsinghua University , Beijing 100084 , P. R. China .
| | - Lei Jiang
- Key Laboratory of Bio-inspired Smart Interface Sciences , Technical Institute of Physics and Chemistry , Chinese Academy of Sciences , Beijing , 100084 , P. R. China
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Segalina A, Francés-Monerris A, Pastore M, Leininger T, Evangelisti S, Monari A. Conical intersection properties unraveled by the position spread tensor. Theor Chem Acc 2018. [DOI: 10.1007/s00214-018-2377-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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