Publications
59 results found
Cuéllar-Zuquin J, Pepino AJ, Fdez Galván I, et al., 2023, Characterizing Conical Intersections in DNA/RNA Nucleobases with Multiconfigurational Wave Functions of Varying Active Space Size., J Chem Theory Comput, Vol: 19, Pages: 8258-8272
We characterize the photochemically relevant conical intersections between the lowest-lying accessible electronic excited states of the different DNA/RNA nucleobases using Cholesky decomposition-based complete active space self-consistent field (CASSCF) algorithms. We benchmark two different basis set contractions and several active spaces for each nucleobase and conical intersection type, measuring for the first time how active space size affects conical intersection topographies in these systems and the potential implications these may have toward their description of photoinduced phenomena. Our results show that conical intersection topographies are highly sensitive to the electron correlation included in the model: by changing the amount (and type) of correlated orbitals, conical intersection topographies vastly change, and the changes observed do not follow any converging pattern toward the topographies obtained with the largest and most correlated active spaces. Comparison across systems shows analogous topographies for almost all intersections mediating population transfer to the dark 1nO/Nπ* states, while no similarities are observed for the "ethylene-like" conical intersection ascribed to mediate the ultrafast decay component to the ground state in all DNA/RNA nucleobases. Basis set size seems to have a minor effect, appearing to be relevant only for purine-based derivatives. We rule out structural changes as a key factor in classifying the different conical intersections, which display almost identical geometries across active space and basis set change, and we highlight instead the importance of correctly describing the electronic states involved at these crossing points. Our work shows that careful active space selection is essential to accurately describe conical intersection topographies and therefore to adequately account for their active role in molecular photochemistry.
Segarra-Marti J, Tran T, Bearpark MJ, 2022, 3-Methylation alters excited state decay in photoionised uracil, PHYSICAL CHEMISTRY CHEMICAL PHYSICS, Vol: 24, Pages: 27038-27046, ISSN: 1463-9076
Chan HHS, Fitzpatrick N, Segarra-Marti J, et al., 2021, Molecular excited state calculations with adaptive wavefunctions on a quantum eigensolver emulation: reducing circuit depth and separating spin states, Physical Chemistry Chemical Physics, Vol: 23, Pages: 26438-26450, ISSN: 1463-9076
Ab initio electronic excited state calculations are necessary for the quantitative study of photochemical reactions, but their accurate computation on classical computers is plagued by prohibitive resource scaling. The Variational Quantum Deflation (VQD) is an extension of the quantum-classical Variational Quantum Eigensolver (VQE) algorithm for calculating electronic excited state energies, and has the potential to address some of these scaling challenges using quantum computers. However, quantum computers available in the near term can only support a limited number of quantum circuit operations, so reducing the quantum computational cost in VQD methods is critical to their realisation. In this work, we investigate the use of adaptive quantum circuit growth (ADAPT-VQE) in excited state VQD calculations, a strategy that has been successful previously in reducing the resources required for ground state energy VQE calculations. We also invoke spin restrictions to separate the recovery of eigenstates with different spin symmetry to reduce the number of calculations and accumulation of errors in computing excited states. We created a quantum eigensolver emulation package - Quantum Eigensolver Building on Achievements of Both quantum computing and quantum chemistry (QEBAB) – for testing the proposed adaptive procedure against two existing VQD methods that use fixed-length quantum circuits: UCCGSD-VQD and k-UpCCGSD-VQD. For a lithium hydride test case we found that the spin-restricted adaptive growth variant of VQD uses the most compact circuits out of the tested methods by far, consistently recovers adequate electron correlation energy for different nuclear geometries and eigenstates while isolating the singlet and triplet manifold. This work is a further step towards developing techniques which improve the efficiency of hybrid quantum algorithms for excited state quantum chemistry, opening up the possibility of exploiting real quantum computers for electronic exci
Segarra-Martí J, Bearpark MJ, 2021, Modelling Photoionisation in Isocytosine: Potential Formation of Longer-Lived Excited State Cations in its Keto Form., Chemphyschem, Vol: 22
The front cover artwork is provided by Dr. Javier Segarra-Martí (University of Valencia, Spain) and Prof. Michael J. Bearpark (Imperial College London, UK). The image shows the ultrafast photoionisation of DNA canonical nucleobase cytosine and the slower ionization process in non-canonical base isocytosine embedded within a DNA backbone. Read the full text of the Article at 10.1002/cphc.202100402.
SegarraMartí J, Bearpark MJ, 2021, Front Cover: Modelling Photoionisation in Isocytosine: Potential Formation of Longer‐Lived Excited State Cations in its Keto Form (ChemPhysChem 21/2021), ChemPhysChem, Vol: 22, Pages: 2138-2138, ISSN: 1439-4235
Segarra-Martí J, Bearpark MJ, 2021, Modelling photoionisation in isocytosine: potential formation of longer-lived excited state cations in its keto form., ChemPhysChem: a European journal of chemical physics and physical chemistry, Vol: 22, Pages: 2172-2181, ISSN: 1439-4235
Studying the effects of UV and VUV radiation on non-canonical DNA/RNA nucleobases allows us to compare how they release excess energy following absorption with respect to their canonical counterparts. This has attracted much research attention in recent years because of its likely influence on the origin of our genetic lexicon in prebiotic times. Here we present a CASSCF and XMS-CASPT2 theoretical study of the photoionisation of non-canonical pyrimidine nucleobase isocytosine in both its keto and enol tautomeric forms. We analyse their lowest energy cationic excited states including 2 π + , 2 n O + and 2 n N + and compare these to the corresponding electronic states in cytosine. Investigating lower-energy decay pathways we find - unexpectedly - that keto-isocytosine + presents a sizeable energy barrier potentially inhibiting decay to its cationic ground state, whereas enol-isocytosine + features a barrierless and consequently ultrafast pathway analogous to the one previously found for the canonical (keto) form of cytosine + . Dynamic electron correlation reduces the energy barrier in the keto form substantially (by ~1 eV) but it is nevertheless still present. We additionally compute UV/Vis absorption signals of the structures encountered along these decay channels to provide spectroscopic fingerprints to assist future experiments in monitoring these intricate photo-processes.
Segarra-Martí J, Nouri SM, Bearpark MJ, 2021, Modelling photoionisations in tautomeric DNA nucleobase derivatives 7H-adenine and 7H-Guanine: ultrafast decay and photostability, Photochem, Vol: 1, Pages: 287-301, ISSN: 2673-7256
The study of radiation effects in DNA is a multidisciplinary endeavour, connecting the physical, chemical and biological sciences. Despite being mostly filtered by the ozone layer, sunlight radiation is still expected to (photo)ionise DNA in sizeable yields, triggering an electron removal process and the formation of potentially reactive cationic species. In this manuscript, photoionisation decay channels of important DNA tautomeric derivatives, 7H-adenine and 7H-guanine, are characterised with accurate CASSCF/XMS-CASPT2 theoretical methods. These simulation techniques place the onset of ionisation for 7H-adenine and 7H-guanine on average at 8.98 and 8.43 eV, in line with recorded experimental evidence when available. Cationic excited state decays are analysed next, uncovering effective barrierless deactivation routes for both species that are expected to decay to their (cationic) ground state on ultrafast timescales. Conical intersection topographies reveal that these photoionisation processes are facilitated by sloped single-path crossings, known to foster photostability, and which are predicted to enable the (VUV) photo-protection mechanisms present in these DNA tautomeric species.
Roca-Sanjuán D, Carmona-García J, Ding BW, et al., 2021, Photochemistry, chemiluminescence and dark photochemistry: Computational advances (2018-2019), Photochemistry, Pages: 24-70, ISBN: 9781839161407
Recent progress (2018-2019) in the field of quantum chemistry applied to the excited electronic state are presented in this book chapter. General developments of methods and theory are described first, followed by applications organised in three main topics, (i) photo-induced chemistry (photochemistry), (ii) chemically induced light emission (chemiluminescence) and (iii) chemically induced excited-state chemistry (dark photochemistry). We shall highlight in this occasion developments of machine learning, GPU and quantum computing algorithms for excited states, non-adiabatic new methodological approaches, sunlight chemistry of atmospheric mercury compounds, boranes and stilbenoids photochemistry, DNA spectroscopy and excited-state chemistry, the bio/chemiluminescence mechanism of luminol and distinct luciferin-luciferase complexes and retinal activation in the dark.
Jaiswal VK, Segarra-Marti J, Marazzi M, et al., 2020, First-principles characterization of the singlet excited state manifold in DNA/RNA nucleobases, PHYSICAL CHEMISTRY CHEMICAL PHYSICS, Vol: 22, Pages: 15496-15508, ISSN: 1463-9076
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- Citations: 12
Aquilante F, Autschbach J, Baiardi A, et al., 2020, Modern quantum chemistry with [Open]Molcas, JOURNAL OF CHEMICAL PHYSICS, Vol: 152, ISSN: 0021-9606
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- Citations: 223
Alvertis AM, Barford W, Bourne Worster S, et al., 2020, Spectroscopic signatures of quantum effects: general discussion, FARADAY DISCUSSIONS, Vol: 221, Pages: 322-349, ISSN: 1359-6640
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- Citations: 2
Segarra-Martí J, Segatta F, Mackenzie TA, et al., 2020, Modeling multidimensional spectral lineshapes from first principles: Application to water-solvated adenine, Faraday Discussions, Vol: 221, Pages: 219-244, ISSN: 1359-6640
In this discussion we present a methodology to describe spectral lineshape from first principles, providing insight into the solvent-solute molecular interactions in terms of static and dynamic disorder and how these shape the signals recorded experimentally in linear and nonlinear optical spectroscopies, including two-dimensional electronic spectroscopy (2DES). Two different strategies for simulating the lineshape are compared, in which both the coupling to the intra-molecular vibrations and the influence exerted by the different water distributions attained along a molecular dynamics (MD) simulation are accurately described. The first method accounts for such water arrangements as first order perturbations on the adenine energies computed for a single reference (gas phase) quantum calculation. The second method requires to compute the manifold of excited states explicitly at each simulation snapshot, employing a hybrid quantum mechanics/molecular mechanics (QM/MM) scheme. Both approaches are applied to a large number of states of the adenine singlet excited manifold (chosen because of its biological role), and compared with available experimental data. They give comparable results but the first approach is two orders of magnitude faster. We show how the various contributions (static/dynamic disorder, intra-/inter-molecular interactions) sum up to build the total broadening observed in experiments.
Alvertis AM, Barford W, Worster SB, et al., 2020, Quantum coherence in complex environments: general discussion, FARADAY DISCUSSIONS, Vol: 221, Pages: 168-201, ISSN: 1359-6640
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- Citations: 4
Martinez-Fernandez L, Gavvala K, Sharma R, et al., 2019, Excited-State Dynamics of Thienoguanosine, an Isomorphic Highly Fluorescent Analogue of Guanosine (vol 25, pg 7375, 2019), CHEMISTRY-A EUROPEAN JOURNAL, Vol: 25, Pages: 13648-13648, ISSN: 0947-6539
Navarrete-Miguel M, Segarra Marti J, Francés-Monerris A, et al., 2019, Quantum chemistry of the excited state: recent trends in methods developments and applications, Photochemistry: Volume 46, Editors: Albini, Protti, Publisher: Royal Society of Chemistry, Pages: 28-77, ISBN: 9781788013369
Advances (2016–2017) in Quantum Chemistry of the Excited State (QCEX) are presentedin this book chapter focusing firstly on developments of methodology and excited-statereaction-path computational strategies and secondly on the applications of QCEX tostudy light–matter interaction in distinct fields of biology, (nano)-technology, medicineand the environment. We highlight in this contribution developments of static anddynamic electron-correlation methods and methodological approaches to determinedynamical properties, recent examples of the roles of conical intersections, novel DNAspectroscopy and photochemistry findings, photo-sensitisation mechanisms in biologicalstructures and the current knowledge on chemi-excitation mechanisms that give rise tolight emission (in the chemiluminescence and bioluminescence phenomena).
Segarra-Marti J, Tran T, Bearpark M, 2019, Computing the ultrafast and radiationless electronic excited state decay of cytosine and 5‐methyl‐cytosine cations: uncovering the role of dynamic electron correlation, ChemPhotoChem, Vol: 3, Pages: 856-865, ISSN: 2367-0932
Photoionisation in DNA, i.e. the process of photoinduced electron removal from the chromophoric species − the nucleobases − leading to their cationic form, has been scarcely studied despite being considered to be responsible for significant damaging instances in our genetic material. In this contribution we theoretically characterise the electronic ground and excited state decay pathways of cationic DNA nucleobase cytosine+ and its epigenetic derivative 5‐methyl‐cytosine+, including the effects of dynamic electron correlation on energies and geometries of minima and conical intersections. We do this by comparing the results of XMS‐CASPT2 calculations with CASSCF estimates and we find some significant differences between the results of these two methods. In particular, including dynamic electron correlation is found to significantly reduce the barrier to access the (D1/D0) conical intersection. We find notable similarities in both cytosine and 5‐methyl‐cytosine cations, accessible conical intersections in the vicinity of the Franck‐Condon region are found. This points towards an ultrafast depopulation of their electronic excited states. Moreover, the shape of the ground state potential energy surface strongly directs the decaying excited state population towards the cationic ground state minimum on ultrafast timescales, preventing photofragmentation and thus explaining their photostability.
Segarra-Marti J, Tran T, Mackenzie T, et al., 2019, Simulating photoionisation phenomena in DNA/RNA pyrimidine nucleobases, ACS Fall National Meeting and Exposition, Publisher: AMER CHEMICAL SOC, ISSN: 0065-7727
Segarra-Marti J, Segatta F, Mackenzie T, et al., 2019, Characterising spectral lineshapes in water-solvated adenine from first-principles, Fall National Meeting and Exposition of the American-Chemical-Society (ACS), Publisher: AMER CHEMICAL SOC, ISSN: 0065-7727
Tran T, Segarra-Martí J, Bearpark M, et al., 2019, Molecular vertical excitation energies studied with first-order RASSCF (RAS[1,1]): balancing covalent and ionic excited states, Journal of Physical Chemistry A, Vol: 123, Pages: 5223-5230, ISSN: 1089-5639
RASSCF calculations of vertical excitation energies were carried out on a benchmark set of 19 organic molecules studied by Thiel and co-workers [ J. Chem. Phys. 2008, 128, 134110]. The best results, in comparison with the MS-CASPT2 results of Thiel, were obtained using a RASSCF space that contains at most one hole and one particle in the RAS1 and RAS3 spaces, respectively, which we denote as RAS[1,1]. This subset of configurations recovers mainly the effect of polarization and semi-internal electronic correlation that is only included in CASSCF in an averaged way. Adding all-external correlation by allowing double excitations from RAS1 and RAS2 into RAS3 did not improve the results, and indeed, they were slightly worse. The accuracy of the first-order RASSCF computations is demonstrated to be a function of whether the state of interest can be classified as covalent or ionic in the space of configurations built from orbitals localized onto atomic sites. For covalent states, polarization and semi-internal correlation effects are negligible (RAS[1,1]), while for ionic states, these effects are large (because of inherent diffusiveness of these states compared to the covalent states) and, thus, an acceptable agreement with MS-CASPT2 can be obtained using first-order RASSCF with the extra basis set involving 3p orbitals in most cases. However, for those ionic states that are quasi-degenerate with a Rydberg state or for nonlocal nπ* states, there remains a significant error resulting from all external correlation effects.
Martinez-Fernandez L, Gavvala K, Sharma R, et al., 2019, Excited-State Dynamics of Thienoguanosine, an Isomorphic Highly Fluorescent Analogue of Guanosine, CHEMISTRY-A EUROPEAN JOURNAL, Vol: 25, Pages: 7375-7386, ISSN: 0947-6539
Segarra-Martí J, Tran T, Bearpark MJ, 2019, Ultrafast and radiationless electronic excited state decay of uracil and thymine cations: computing the effects of dynamic electron correlation, Physical Chemistry Chemical Physics, Vol: 21, Pages: 14322-14330, ISSN: 1463-9076
In this article we characterise the radiationless decay of the first few electronic excited states of the cations of DNA/RNA nucleobases uracil and thymine, including the effects of dynamic electron correlation on energies and geometries (optimised with XMS-CASPT2). In both systems, we find that one state of 2n+O and another two of 2π+ character can be populated following photoionisation, and their different minima and interstate crossings are located. We find strong similarities between uracil and thymine cations: with accessible conical intersections suggesting that depopulation of their electronic excited states takes place on ultrafast timescales in both systems, suggesting that they are photostable in agreement with previous theoretical (uracil+) evidence. We find that dynamic electron correlation separates the energy levels of the "3-state" conical intersection (D2/D1/D0)CI previously located with CASSCF for uracil+, which will therefore have a different geometry and higher energy. Simulating the electronic and vibrational absorptions allows us to characterise spectral fingerprints that could be used to monitor these cation photo-processes experimentally.
Weingart O, Nenov A, Altoe P, et al., 2018, COBRAMM 2.0 A software interface for tailoring molecular electronic structure calculations and running nanoscale (QM/MM) simulations, Journal of Molecular Modeling, Vol: 24, Pages: 1-30, ISSN: 0948-5023
We present a new version of the simulation software COBRAMM, a program package interfacing widely known commercial and academic software for molecular modeling. It allows a problem-driven tailoring of computational chemistry simulations with effortless ground and excited-state electronic structure computations. Calculations can be executed within a pure QM or combined quantum mechanical/molecular mechanical (QM/MM) framework, bridging from the atomistic to the nanoscale. The user can perform all necessary steps to simulate ground state and photoreactions in vacuum, complex biopolymer, or solvent environments. Starting from ground-state optimization, reaction path computations, initial conditions sampling, spectroscopy simulation, and photodynamics with deactivation events, COBRAMM is designed to assist in characterization and analysis of complex molecular materials and their properties. Interpretation of recorded spectra range from steady-state to time-resolved measurements. Various tools help the user to set up the system of interest and analyze the results.
Segarra-Marti J, Mukamel S, Garavelli M, et al., 2018, Towards Accurate Simulation of Two-Dimensional Electronic Spectroscopy, TOPICS IN CURRENT CHEMISTRY, Vol: 376, ISSN: 2365-0869
We introduce the basic concepts of two-dimensional electronic spectroscopy (2DES) and a general theoretical framework adopted to calculate, from first principles, the nonlinear response of multi-chromophoric systems in realistic environments. Specifically, we focus on UV-active chromophores representing the building blocks of biological systems, from proteins to nucleic acids, describing our progress in developing computational tools and protocols for accurate simulation of their 2DUV spectra. The roadmap for accurate 2DUV spectroscopy simulations is illustrated starting with benchmarking of the excited-state manifold of the chromophoric units in a vacuum, which can be used for building exciton Hamiltonians for large-scale applications or as a reference for first-principles simulations with reduced computational cost, enabling treatment of minimal (still realistic) multi-chromophoric model systems. By adopting a static approximation that neglects dynamic processes such as spectral diffusion and population transfer, we show how 2DUV is able to characterize the ground-state conformational space of dinucleosides and small peptides comprising dimeric chromophoric units (in their native environment) by tracking inter-chromophoric electronic couplings. Recovering the excited-state coherent vibrational dynamics and population transfers, we observe a remarkable agreement between the predicted 2DUV spectra of the pyrene molecule and the experimental results. These results further led to theoretical studies of the excited-state dynamics in a solvated dinucleoside system, showing that spectroscopic fingerprints of long-lived excited-state minima along the complex photoinduced decay pathways of DNA/RNA model systems can be simulated at a reasonable computational cost. Our results exemplify the impact of accurate simulation of 2DES spectra in revealing complex physicochemical properties of fundamental biological systems and should trigger further theoretical developments as well
Segarra-Martí J, Zvereva EE, Marazzi M, et al., 2018, Resolving the singlet excited states manifold of benzophenone by first-principles simulations and ultrafast spectroscopy, Journal of Chemical Theory and Computation, Vol: 14, Pages: 2570-2585, ISSN: 1549-9618
Accurate characterization of the high-lying excited state manifolds of organic molecules is of fundamental importance for the interpretation of the rich response detected in time-resolved nonlinear electronic spectroscopies. Here, we have characterized the singlet excited states manifold of benzophenone (BP), a versatile organic photoinitiator and a well-known DNA photosensitizer. Benchmarks of various multiconfigurational/multireference (RASSCF/PT2) and time-dependent density functional theory (TD-DFT) approaches allowed assignments of experimental linear absorption signals of BP in the ultraviolet (UV) region, with unprecedented characterization of ground state absorptions in the far UV. Experimental transient absorption spectra obtained by UV-Vis pump-probe spectroscopy at very short time-delays are shown to be directly comparable to theoretical estimates of excited state absorptions (from the low-lying nOπ* and ππ* singlet states) in the Franck-Condon region. Multireference computations provided reliable interpretation of the PP spectra, with TD-DFT results yielding a fair agreement as long as electronic transitions featuring double excitations contributions are not involved. These results lay the groundwork for further computational studies and interpretation of experimental nonlinear electronic spectra of benzophenone in more complex systems, such as BP/DNA adducts.
Segarra-Marti J, Ramakrishnan R, Vinals J, et al., 2018, Highlights from the Faraday discussion on photoinduced processes in nucleic acids and proteins, CHEMICAL COMMUNICATIONS, Vol: 54, Pages: 4207-4215, ISSN: 1359-7345
Bhat V, Cogdell R, Crespo-Hernández CE, et al., 2018, Photocrosslinking between nucleic acids and proteins: general discussion., Faraday Discuss, ISSN: 1359-6640
Chandra A, Cogdell R, Crespo-Hernández CE, et al., 2018, Light induced damage and repair in nucleic acids and proteins: general discussion., Faraday Discuss, ISSN: 1359-6640
Chattopadhyay A, Cogdell R, Crespo-Hernandez CE, et al., 2018, Light induced charge and energy transport in nucleic acids and proteins: general discussion, FARADAY DISCUSSIONS, Vol: 207, Pages: 153-180, ISSN: 1359-6640
Nenov A, Borrego-Varillas R, Oriana A, et al., 2018, UV-Light-Induced Vibrational Coherences: The Key to Understand Kasha Rule Violation in trans-Azobenzene., Journal of Physical Chemistry Letters, Vol: 9, Pages: 1534-1541, ISSN: 1948-7185
We combine sub-20 fs transient absorption spectroscopy with state-of-the-art computations to study the ultrafast photoinduced dynamics of trans-azobenzene (AB). We are able to resolve the lifetime of the ππ* state, whose decay within ca. 50 fs is correlated to the buildup of the nπ* population and to the emergence of coherences in the dynamics, to date unobserved. Nonlinear spectroscopy simulations call for the CNN in-plane bendings as the active modes in the subps photoinduced coherent dynamics out of the ππ* state. Radiative to kinetic energy transfer into these modes drives the system to a high-energy planar nπ*/ground state conical intersection, inaccessible upon direct excitation of the nπ* state, that triggers an ultrafast (0.45 ps) nonproductive decay of the nπ* state and is thus responsible for the observed Kasha rule violation in UV excited trans-AB. On the other hand, cis-AB is built only after intramolecular vibrational energy redistribution and population of the NN torsional mode.
Segarra Marti J, Pepino AJ, Nenov A, et al., 2018, The highly excited-state manifold of guanine: calibration for nonlinear electronic spectroscopy simulations, Theoretical Chemistry Accounts: Theory, Computation, and Modeling, Vol: 137, ISSN: 1432-881X
A computational protocol based on the complete and restricted active space self-consistent field (CASSCF/RASSCF) methods and their second-order perturbation theory extensions (CASPT2/RASPT2) is employed to benchmark the highly excited-state manifold of the DNA/RNA canonical purine nucleobase guanine in vacuo. Several RASPT2 schemes are tested, displaying a steady convergence of electronic transition energies and dipole moments upon active space enlargement toward the reference values. The outcome allows calibrating and optimizing computational efforts by considering cheaper and more approximate RAS schemes that could enable the characterization of the excited-state manifolds of multi-chromophoric systems, such as DNA/RNA nucleobase dimers or multimers. Simulations of two-dimensional electronic spectra show similar trends to those observed on the other purine nucleobase adenine, deviating from this and other pyrimidine nucleobases in featuring its main excited-state absorption signal, embodied by sizable double HOMO to LUMO excitation contributions, in the UV probing window.
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