Publications

Highlights

(For a full list see below or go to Google Scholar)

Stable excited dication: trapping on the S1 state of formaldehyde dication after strong field ionization

Combined theoretical and experimental work examines the dynamics of dication formaldehyde produced by strong field ionization. Trajectory surface hopping dynamics on the first several singlet electronic states of the formaldehyde dication are used to examine the relaxation pathways and dissociation channels, while kinetic energy distributions after strong field ionization of formaldehyde and deuterated formaldehyde are used to confirm the theoretical predictions. We find that the first excited state of the formaldehyde dication is stable, neither decays to the ground state nor dissociates, even though the ground state and higher lying states are directly dissociative. The stability of the first excited state is explained by its symmetry which does not allow for radiative or nonradiative transitions to the ground state and by large barriers to dissociate on the excited state surface.

V. Singh, C. Cheng, T. Weinacht and S Matsika

Phys. Chem. Chem. Phys., 24, 20701-20708 (2022)

Modeling the Electronic Absorption Spectra of the Indocarbocyanine Cy3

Accurate modeling of optical spectra requires careful treatment of the molecular structures and vibronic, environmental, and thermal contributions. The accuracy of the computational methods used to simulate absorption spectra is limited by their ability to account for all the factors that affect the spectral shapes and energetics. The ensemble-based approaches are widely used to model the absorption spectra of molecules in the condensed-phase, and their performance is system dependent. The Franck–Condon approach is suitable for simulating high resolution spectra of rigid systems, and its accuracy is limited mainly by the harmonic approximation. In this work, the absorption spectrum of the widely used cyanine Cy3 is simulated using the ensemble approach via classical and quantum sampling, as well as, the Franck–Condon approach. The factors limiting the ensemble approaches, including the sampling and force field effects, are tested, while the vertical and adiabatic harmonic approximations of the Franck–Condon approach are also systematically examined. Our results show that all the vertical methods, including the ensemble approach, are not suitable to model the absorption spectrum of Cy3, and recommend the adiabatic methods as suitable approaches for the modeling of spectra with strong vibronic contributions. We find that the thermal effects, the low frequency modes, and the simultaneous vibrational excitations have prominent contributions to the Cy3 spectrum. The inclusion of the solvent stabilizes the energetics significantly, while its negligible effect on the spectral shapes aligns well with the experimental observations.

MI Sorour, AH Marcus and S Matsika

Molecules, 27, 4062 (2022)

A unique QP-partitioning and Siegert width using real-valued continuum remover potential

A simple, practical quantum chemical procedure is presented for computing the energy position and the decay width of autoionization resonances. It combines the L2-stabilized resonance wave function obtained using the real-valued continuum-remover (CR) potential [Y. Sajeev Chem. Phys. Lett. 2013, 587, 105–112] and the Feshbach projection operator (FPO) partitioning technique. Unlike the conventional FPO partitioning of the total wave function into its resonant Q space and background P space components, an explicit partitioning of the total wave function into its interaction region and noninteraction region components is obtained with the help of real-valued continuum-remover potential. The molecular system is initially confined inside a CR potential which removes the electronic continuum of the molecular system in which its resonance state is embedded and, thus, unravels the Q space component of the resonance wave function as a bound, localized eigenstate of the confined system. The eigenfunctions of the molecular Hamiltonian represented in the {1-Q} space constitute a complementary, P orthogonal space. A unique QP partition is obtained when the level-shift of the Q space function due to its coupling with the P space is zero, and the resonance width is computed using these unique partitioned spaces.

Y Sajeev, M Thodika and S Matsika

J. Chem. Theory Comput., 18, 2863 (2022)

Time Resolved Photoelectron Spectroscopy as a Test of Electronic Structure and Nonadiabatic Dynamics

We compare different levels of theory for simulating excited state molecular dynamics and use time-resolved photoelectron spectroscopy measurements to benchmark the theory. We perform trajectory surface hopping simulations for uracil excited to the first bright state (ππ*) using three different levels of theory (CASSCF, MRCIS, and XMS-CASPT2) in order to understand the role of dynamical correlation in determining the excited state dynamics, with a focus on the coupling between different electronic states and internal conversion back to the ground state. These dynamics calculations are used to simulate the time-resolved photoelectron spectra. The comparison of the calculated and measured spectra allows us to draw conclusions regarding the relative insights and quantitative accuracy of the calculations at the three different levels of theory, demonstrating that detailed quantitative comparisons of time-resolved photoelectron spectra can be used to benchmark methodology.

P Chakraborty, Y Liu, S McClung, T Weinacht, S Matsika

J. Phys. Chem. Lett. 12, 21, 5099–5104 (2021)

Electronic structure methods for the description of nonadiabatic effects and conical intersections

Nonadiabatic effects are ubiquitous in photophysics and photochemistry, and therefore, many theoretical developments have been made to properly describe them. Conical intersections are central in nonadiabatic processes, as they promote efficient and ultrafast nonadiabatic transitions between electronic states. A proper theoretical description requires developments in electronic structure and specifically in methods that describe conical intersections between states and nonadiabatic coupling terms. This review focuses on the electronic structure aspects of nonadiabatic processes. We discuss the requirements of electronic structure methods to describe conical intersections and nonadiabatic couplings, how the most common excited state methods perform in describing these effects, and what the recent developments are in expanding the methodology and implementing nonadiabatic couplings.

Spiridoula Matsika

Chem. Rev., 121, 9407–9449 (2021)

Understanding the Interplay Between the Non-Valence and Valence State of the Uracil Anion Upon Mono-Hydration

In this work we present an ab initio investigation into the effect of monohydration on the interaction of uracil with low energy electrons. Electron attachment and photodetachment experimental studies have previously shown dramatic changes in uracil upon solvation with even a single water molecule, due to an inversion of the character of the ground state of the anion. Here we explore the interplay between the nonvalence and valence states of the uracil anion, as a function of geometry and site of solvation. Our model provides unambiguous interpretation of previous photoelectron studies, reproducing the binding energies and photoelectron images for bare uracil and a single isomer of the U•(H2O)1 cluster. The results of this study provide insight into how electrons may attach to hydrated nucleobases. These results lay the foundations for further investigations into the effect of microhydration on the electronic structure and electron capture dynamics of nucleobases.

Cate S. Anstöter and Spiridoula Matsika

J. Phys. Chem. A, 124, 9237 (2020)

 

Full List

Nonadiabatic Excited State Dynamics of Organic Chromophores: Take-Home Messages
P. Chakraborty, Y. Liu, S. McClung, T. Weinacht and S Matsika
J. Phys. Chem. A, 126, 6021-6031 (2022)

Stable excited dication: trapping on the S1 state of formaldehyde dication after strong field ionization
V. Singh, C. Cheng, T. Weinacht and S Matsika
Phys. Chem. Chem. Phys., 24, 20701-20708 (2022)

Modeling the Electronic Absorption Spectra of the Indocarbocyanine Cy3
MI Sorour, AH Marcus and S Matsika
Molecules, 27, 4062 (2022)

Conformer-Specific Dissociation Dynamics in Dimethyl Methylphosphonate Radical Cation
V Singh, HAL Peña, JM Shusterman, PV Zandbergen, KM Tibbetts and S Matsika
Molecules, 27, 2269 (2022)

Projected Complex Absorbing Potential Multi-Reference Configuration Interaction for Shape and Feshbach Resonances
M Thodika and S Matsika
J. Chem. Theory Comput., 18, 3377-3390 (2022)

A unique QP-partitioning and Siegert width using real-valued continuum remover potential
Y Sajeev, M Thodika and S Matsika
J. Chem. Theory Comput., 18, 2863 (2022)

Accurate Modeling of Excitonic Coupling in Cyanine Dye Cy3
MI Sorour, KA Kistler, AH Marcus, S Matsika
J. Phys. Chem. A 125, 36, 7852–7866 (2021)

Modeling the Ultrafast Electron Attachment Dynamics of Solvated Uracil
CS Anstöter, M DelloStritto, ML Klein, S Matsika
J. Phys. Chem. A 125, 32, 6995–7003 (2021)

Time Resolved Photoelectron Spectroscopy as a Test of Electronic Structure and Nonadiabatic Dynamics
P Chakraborty, Y Liu, S McClung, T Weinacht, S Matsika
J. Phys. Chem. Lett. 12, 21, 5099–5104 (2021)

Electronic structure methods for the description of nonadiabatic effects and conical intersections
Spiridoula Matsika
Chem. Rev., 121, 9407–9449 (2021)

Modeling Solvation Effects on Absorption and Fluorescence Spectra of Indole in Aqueous Solution
Salsa Abou-Hatab, Vincenzo Carnevale and Spiridoula Matsika
J. Chem. Phys., 154, 064104 (2021)

Benchmarking Quantum Mechanical Methods for the Description of Charge-Transfer States in π Stacked Nucleobases
Camilo Zuluaga, Vince Spata and Spiridoula Matsika
J. Chem. Theory Comput.,17, 376-387, (2021)

Effect of Dynamic Correlation on the Ultrafast Relaxation of Uracil in the Gas Phase
Pratip Chakraborty, Yusong Liu, Thomas Weinacht and Spiridoula Matsika
Faraday Discuss., 228, 226 (2020)

Description of Two-particle One-hole Electronic Resonances using Orbital Stabilization Methods
Mushir Thodika, Nathan Mackouse and Spiridoula Matsika
J. Phys. Chem. A, 124, 9011 (2020)

Understanding the Interplay Between the Non-Valence and Valence State of the Uracil Anion Upon Mono-Hydration
Cate S. Anstöter and Spiridoula Matsika
J. Phys. Chem. A, 124, 9237 (2020)

Stabilization of triplet biradical intermediate of 5-methylcytosine enhances cyclobutane pyrimidine dimer (CPD) formation in DNA
Wook Lee and Spiridoula Matsika
Chem. Eur. J., 26, 14181-14186 (2020)

Excited State Dynamics of cis,cis-1,3-Cyclooctadiene: UV Pump VUV Probe Time Resolved Photoelectron Spectroscopy
Yusong Liu, Pratip Chakraborty, Spiridoula Matsika and Thomas Weinacht
J. Chem. Phys., 153, 074301 (2020)

Excited State Dynamics of cis,cis-1,3-Cyclooctadiene: Non-adiabatic Trajectory Surface Hopping
Pratip Chakraborty, Yusong Liu, Thomas Weinacht, and Spiridoula Matsika
J. Chem. Phys., 152, 174302 (2020)

The Generality of the GUGA MRCI Approach in COLUMBUS for Treating Complex Quantum Chemistry
Hans Lischka, Ron Shepard, Thomas Muller, Peter G. Szalay, Russel M. Pitzer, Adelia J. A. Aquino, Mayzza M. Araujo do Nascimento, Mario Barbatti, Lachlan T. Belcher, Itamar Borges Jr., Scott R. Brozell, Anita Das, Silmar A. do Monte, Leticia Gonzalez, William L. Hase, Gary Kedziora, Fabris Kossoski, Francisco B. C. Machado, Spiridoula Matsika, Dana Nachtigallova, Reed Nieman, Markus Oppel, Felix Plasser, Rene F. K. Spada, Eric A. Stahlberg, Elizete Ventura, David R. Yarkony
J. Chem. Phys., 152, 134110 (2020)

Comparative study of methodologies for calculating metastable states of small to medium-sized molecules
Mushir Thodika, Mark Fennimore, Tolga N.V. Karsili and Spiridoula Matsika
J. Chem. Phys., 151, 244104 (2019)

Electron correlation in channel resolved strong field molecular double ionization
Chuan Cheng, Patricia Vindel Zandbergen, Spiridoula Matsika, and Thomas Weinacht
Phys. Rev. A, 100, 053405 (2019)

Theoretical Investigation of Positional Substitution and Solvent Effects on n-Cyanoindole Fluorescent Probes
Salsabil Abou-Hatab and Spiridoula Mastika
J. Phys. Chem. B, 123, 7424 - 7435 (2019)

Role of charge transfer states into the formation of cyclobutane pyrimidine dimers in DNA
Wook Lee and Spiridoula Matsika
Faraday Discussions, 216, 507-519 (2018)

Intersystem crossing in the exit channel
Hongwei Li, Alexander Kamasah, Spiridoula Matsika, Arthur G. Suits
Nature Chem 11, 123–128 (2019)

Strong and Weak-Field Ionization in Pump-Probe Spectroscopy
Spencer L. Horton, Yusong Liu, Pratip Chakraborty, Philipp Marquetand, Tamas Rozgonyi, Spiridoula Matsika and Thomas Weinacht
Phys. Rev. A, 98, 053416, (2018)

Ultrafast Photoinduced Processes in Polyatomic Molecules: Electronic Structure, Dynamics and Spectroscopy dedicated to Prof. Wolfgang Domcke on the occasion of his 70th birthday
Maxim F. Gelin, Spiridoula Matsika, Andrzej Sobolewski and Yoshitaka Tanimura
Chem. Phys., 515, 1-2, (2018)

Introduction: Theoretical Modeling of Excited State Processes
Spiridoula Matsika and Anna Krylov
Chem. Rev. , 118, 6925-6926, (2018)

The Origin of Fluorescence in DNA Thio-Analogues
Tolga N. V. Karsili, Mushir Thodika, Linh Nguyen, Spiridoula Matsika
Chem. Phys. 515, 434-440 (2018)

Electron-induced origins of prebiotic sugars: self-reactions of methanol anion clusters
Tolga N.V. Karsili, Mark A. Fennimore and Spiridoula Matsika
Phys. Chem. Chem. Phys., 20, 12599 - 12607, (2018)

Electronic Resonances of Nucleobases Using Stabilization Methods
Mark A. Fennimore, and Spiridoula Matsika
J. Phys. Chem. A, 122, 4048-4057, (2018)

Quadruple coincidence measurement of electron correlation in strong field molecular double ionization
Arthur Zhao, Chuan Cheng, Spiridoula Matsika and Thomas Weinacht
Phys. Rev. A, 97, 043412, (2018)

Photochemical Formation of Cyclobutane Pyrimidine Dimers in DNA through Electron Transfer from a Flanking Base
Wook Lee and Spiridoula Matsika
Chem. Phys. Chem. 19, 1568-1571 (2018)

Mechanistic insights into photoinduced damage of DNA and RNA nucleobases in the gas phase and in bulk solution
Pratip Chakraborty, Tolga N.V. Karsili, Barbara Marchetti, and Spiridoula Matsika
Faraday Discussions, 207, 329 - 350, (2018)

Origins of Photodamage in Pheomelanin Constituents: Photochemistry of 4-Hydroxybenzothiazole
Tolga N.V. Karsili, Barbara Marchetti, and Spiridoula Matsika
J. Phys. Chem. A, 122, 1986-1993 (2018)

Calculations of non-adiabatic couplings within equation-of-motion coupled-cluster framework: Theory, implementation, and validation against multi-reference methods
Shirin Faraji, Spiridoula Matsika, and Anna I. Krylov
Chem. Phys, 148 , 044103, (2018)

Vibrationally Assisted Below Threshold Ionization
Spencer L. Horton, Yusong Liu, Pratip Chakraborty, Spiridoula Matsika, and Thomas Weinacht
Phys. Rev. A, 95, 063413, (2017)

Mechanisms of H and CO Loss from the Uracil Anion Following Low Energy Electron Irradiation
Mark A. Fennimore, Tolga N. V. Karsili and Spiridoula Matsika
Phys.Chem.Chem.Phys., 19, 17233 - 17241, (2017)

Controlling Photorelaxation in Uracil with Shaped Laser Pulses: A Theoretical Assessment
Daniel Keefer, Sebastian Thallmair, Spiridoula Matsika and Regina de Vivie-Riedle
J.Am. Chem. Soc., 139, 5061 - 5066, (2017)

Ultrafast Internal Conversion Dynamics of Highly Excited Pyrrole Studied with VUV/UV Pump Probe Spectroscopy
Spencer L. Horton, Yusong Liu, Pratip Chakraborty, Spiridoula Matsika, and Thomas Weinacht
J. Chem. Phys., 146, 064306, (2017)

Substituent Effects on the Absorption and Fluorescence Properties of Anthracene
Salsabil Abou-Hatab, Vincent A. Spata, Spiridoula Matsika
J. Phys. Chem. A, 121, 1213-1222, (2017)

Conformational and electronic effects on the formation of anti cyclobutane pyrimidine dimer in G-quadruplex structure
Wook Lee and Spiridoula Matsika
Phys. Chem. Chem. Phys. , 19, 3325-3336, (2017)

Core-Excited and Shape Resonance of Uracil
Mark A. Fennimore and Spiridoula Matsika
Phys.Chem.Chem.Phys., 18, 30536 - 30545, (2016)

Coexistence of different electron transfer mechanisms in the DNA repair process by photolyase
Wook Lee, Goutham Kodali, Robert J. Stanley, Spiridoula Matsika
Chemistry-A European Journal, 22, 11371-11381, (2016)

Photophysical Properties of Pyrrolocytosine, a Cytosine Fluorescent Base Analogue
Quynh Nguyen, Vincent A. Spata, Spiridoula Matsika
Phys.Chem.Chem.Phys., 18, 20189-20198, (2016)

Molecular Double Ionization Using Field Few Cycle Laser Pulses
Arthur Zhao, Peter Sandor, Vincent Tagliamonti, Thomas Weinacht, and Spiridoula Matsika
J. Phys. Chem. A , 120, 3233–3240, (2016)

Excimers and Exciplexes in Photoinitiated Processes of Oligonucleotides
Vincent A. Spata, Wook Lee and Spiridoula Matsika
J. Phys. Chem. Lett., invited perspective, 7, 976-984, (2016)

Surface hopping investigation of the relaxation dynamics in radical cations
Mariana Assmann, Thomas Weinacht, and Spiridoula Matsika
J. Chem. Phys., 144, 034301 (2016)

Photophysical Deactivation Pathways in Adenine Oligonucleotides
Vincent A. Spata and Spiridoula Matsika
Phys.Chem.Chem.Phys., 17, 31073 (2015)

Controlling the Dissociation Dynamics of Acetophenone Radical Cation Through Excitation of Ground and Excited State Wavepackets
Katherine Moore Tibbetts, Maryam Tarazkar, Timothy Bohinski, Dmitri Romanov, Spiridoula Matsika and Robert Levis
Journal of Physics B Atomic, Molecular and Optical Physics, 48, 164002, (2015)

Excited state relaxation of neutral and basic 8-Oxoguanine
Zhen Lu, Ashley Beckstead, Bern Kohler, Spiridoula Matsika
J. Phys. Chem. B, 119, 8293 - 8301, (2015)

QM/MM studies reveal pathways leading to the quenching of the formation of thymine dimer photoproduct by flanking bases
Wook Lee and Spiridoula Matsika
Phys. Chem. Chem. Phys. 17, 9927-9935, (2015)

Photoelectron spectrum and dynamics of the uracil cation
Mariana Assmann, Horst Köppel and Spiridoula Matsika
J. Phys. Chem. A, 119, 866-875, (2015)

Modified Nucleobases
S. Matsika
Topics in Current Chemistry - Photoinduced Phenomena in Nucleic Acids 355, 209-243, (2015)

Strong Field Adiabatic Ionization Prepares a Launch State for Coherent Control
Timothy Bohinski, Katharine Moore Tibbetts, Maryam Tarazkar, Dmitri Romanov, Spiridoula Matsika and Robert Levis
J. Phys. Chem. Lett., 5, 4305-4309, (2014)

Tribute to David R. Yarkony
Spiridoula Matsika, Henry F. Schaefer, III, and Michael S. Schuurman
J. Phys. Chem. A, 118, 11837-11837, (2014)

What We Can Learn from the Norms of One-particle Density Matrices, and What We Can’t
Spiridoula Matsika, Xintian Feng, Anatoly Luzanov, Anna Krylov
J. Phys. Chem. A, 118, 11943-11955, (2014)

Role of Excitonic Coupling and Charge-Transfer States in the Absorption and CD Spectra of Adenine-Based Oligonucleotides Investigated through QM/MM Simulations
Vincent Spata and Spiridoula Matsika
J. Phys. Chem. A, 118, 12021-12030, (2014)

Theoretical Studies of the Excited States of p-Cyanophenylalanine and Comparisons with the Natural Amino Acids Phenylalanine and Tyrosine
Stephen Meloni and Spiridoula Matsika
Theoretical Chemistry Accounts, 133, 1497, (2014)

Radical Cation Spectroscopy of Substituted Alkyl Phenyl Ketones via Tunnel Ionization
Timothy Bohinski, Katharine Moore Tibbetts, Kristin Munkerup, Maryam Tarazkar, Dmitri Romanov, Spiridoula Matsika and Robert Levis
Chemical Physics, 442, 81-85, (2014)

Ultrafast Excited-State Dynamics and Vibrational Cooling of 8-oxo-7,8-dihydro-2-deoxyguanosine in D2O
Yuyuan Zhang, Jordan Dood, Ashley Beckstead, Jinquan Chen, Xi-Bo Li, Cynthia J. Burrows, Zhen Lu, Spiridoula Matsika, and Bern Kohler
J. Phys. Chem. A, 117, 48, 12851-12857, (2013)

Measurement of Ionic Resonances in Alkyl Phenyl Ketone Cations via Infrared Strong Field Mass Spectrometry
Timothy Bohinski, Katharine Moore Tibbetts, Maryam Tarazkar, Dmitri Romanov, Spiridoula Matsika, and Robert Levis
J. Phys. Chem. A, 117, 47, 12374-12381, (2013)

Ultrafast Relaxation Dynamics of Uracil Probed via Strong Field Dissociative Ionization
Spiridoula Matsika, Michael Spanner, Marija Kotur, and Thomas C. Weinacht
J. Phys. Chem. A, 117, 48, 12796-12801, (2013)

Excited-State Tautomerization of Gas-Phase Cytosine
Catherine G. Triandafillou and Spiridoula Matsika
J. Phys. Chem. A, 117, 46, 12165-12174,(2013)

Dissociative electron attachment to carbon dioxide via the 2Πu shape resonance
A. Moradmand, D. S. Slaughter, D. J. Haxton, T. N. Rescigno, C. W. McCurdy, Th. Weber, S. Matsika, A. L. Landers, A. Belkacem, and M. Fogle
Phys. Rev. A, 88, 032703, (2013)

Measurement of an Electronic Resonance in Ground State, Gas Phase Acetophenone Cation via Strong Field Mass Spectrometry
Timothy Bohinski, Katharine Moore Tibbetts, Maryam Tarazkar, Dmitri Romanov, Spiridoula Matsika, Robert J. Levis
J. Phys. Chem. Lett., 4, 10, 1587-1591, (2013)

High-Multiplicity Natural Orbitals in Multireference Configuration Interaction for Excited State Potential Energy Surfaces
Zhen Lu and Spiridoula Matsika
J. Phys. Chem. A, 117, 32, 7421-7430, (2013)

Exciplexes and conical intersections lead to fluorescence quenching in pi-stacked dimers of 2-aminopurine with nucleobases
JingXin Liang, Quynh L. Nguyen, and Spiridoula Matsika
Photochem. Photobiol. Sci.,12, 1387-1400, (2013)

Contrasting Photophysical Behaviors of Star-shaped vs Linear Chromophores
Christopher M. Pochas, Kurt A. Kistler, Hajime Yamagata, Spiridoula Matsika, Frank C. Spano
J. Am. Chem. Soc., 135, 8, 3056-3066, (2013)

A Benchmark of Excitonic Couplings Derived from Atomic Transition Charges
Kurt A. Kistler, Francis C. Spano, and Spiridoula Matsika
J. Phys. Chem. B, 117, 7, 2032-2044, (2013)

Angle-Resolved Strong Field Ionization of Polyatomic Molecules: More than the Orbitals Matters
Oumarou Njoya, Spiridoula Matsika, and Thomas Weinacht
ChemPhysChem, 14, 1451-1455, (2013)

Ultrafast Excited State Dynamics of Allopurinol, a Modified DNA Base
Juan P. Villabona-Monsalve, Rosa E. Islas, William Rodriguez-Cordoba, Spiridoula Matsika and Jorge Peon
J. Phys. Chem. A, 117, 5, 898-904, (2013)

Neutral Ionic Correlations in Strong Field Molecular Ionization
Marija Kotur, Congyi Zhou, Spiridoula Matsika, Serguei Patchkovskii, Michael Spanner, and Thomas C. Weinacht
Phys. Rev. Lett., 109, 203007, (2012)

Dyson Norms in XUV and Strong-field Ionization of Polyatomics: Cytosine and uracil
Michael Spanner, Serguei Patchkovskii, Congyi Zhou, Spiridoula Matsika, Marija Kotur, and Thomas C. Weinacht
Phys. Rev. A, 86, 053406, (2012)

Fragmentation Pathways in the Uracil Radical Cation
Congyi Zhou, Spiridoula Matsika, Marija Kotur, and Thomas C. Weinacht
J. Phys. Chem. A, 116, 9217-9227, (2012)

Correction to Pathways for Fluorescence Quenching in 2-Aminopurine pi-Stacked with Pyrimidine Nucleobases
JingXin Liang, and Spiridoula Matsika
J. Amer. Chem. Soc., 134, 10713 - 10714, (2012)

Two Dimensional Fourier-Transform Spectroscopy of Adenine and Uracil Using Shaped Ultrafast Laser Pulses in the Deep UV
Chien-hung Tseng, Peter Sandor, Marija Kotur, Thomas C. Weinacht and Spiridoula Matsika
J. Chem. Phys., 137, 22A537, (2012)

On the Accessibility to Conical Intersections in Purines: Hypoxanthine and its Singly Protonated and Deprotonated Forms
Juan Villabona-Monsalve, Raquel Noria, Spiridoula Matsika, and Jorge Peon
J. Am. Chem. Soc., 134, 7820 - 7829. (2012)

High-multiplicity natural orbitals in multireference configuration interaction for excited states
Zhen Lu, and Spiridoula Matsika
J. Chem. Theory Comput., 8, 509-517, (2012)

Absorption, Circular Dichroism and Photoluminescence in Perylene Diimide Bichromophores: Polarization Dependent H- and J-aggregate Behavior
K. A. Kistler, C. M. Pochas, H. Yamagata, S. Matsika and F.C. Spano
J. Phys. Chem. B, 116, 77 - 86, (2012)

Nuclear Dynamics on a Three-state Jahn-Teller Model System
Pascal Krause and Spiridoula Matsika
J. Chem. Phys., 136, 034110 (2012)

Following Ultrafast Radiationless Relaxation Dynamics With Strong Field Dissociative Ionization: A Comparison Between Adenine, Uracil, and Cytosine
Marija Kotur, Thomas C. Weinacht, Congyi Zhou, and Spiridoula Matsika
IEEE Journal of selected topics in Quantum Electronics, 18, 187-194, (2012)

Three-state conical intersections
Spiridoula Matsika
Chapter in Conical Intersections: Theory, Computation and Experiment, Advanced Series in Physical Chemistry - Vol 17, 83-116, World Scientific Publishing Company, 2011

Strong Field Molecular Ionization from Multiple Orbitals
Marija Kotur, Thomas C. Weinacht, Congyi Zhou, and Spiridoula Matsika
Phys. Rev. X, 1, 021010, (2011)

Combining dissociative ionization pump probe spectroscopy and ab initio calculations to explore excited state dynamics involving conical intersections
Spiridoula Matsika, Congyi Zhou, Marija Kotur, and Thomas C. Weinacht
Faraday Discussions, 153, 247 - 260, (2011)

Distinguishing Between Relaxation Pathways by Combining Dissociative Ionization Pump Probe Spectroscopy and ab initio Calculations: A Case Study of Cytosine
Marija Kotur, Thomas C. Weinacht, Congyi Zhou, Kurt A. Kistler, and Spiridoula Matsika
J. Chem. Phys., 134, 184309, (2011)

Pathways for fluorescence quenching in 2-aminopurine pi-stacked with pyrimidine nucleobases
JingXin Liang, and Spiridoula Matsika
J. Amer. Chem. Soc., 133 , 6799-6808, (2011)

Nonadiabatic Events and Conical Intersections
Spiridoula Matsika, and Pascal Krause
Annu. Rev. Phys. Chem., 62, 621 - 643, (2011)

Photophysical pathways of cytosine in aqueous solution
Kurt A. Kistler and Spiridoula Matsika
Phys. Chem. Chem. Phys., 12, 5024-5031, (2010)

Excited State Energies and Electronic Couplings of DNA Base Dimers
Christopher R. Kozak, Kurt A. Kistler, Zhen Lu, and Spiridoula Matsika
J. Phys. Chem. B, 114, 4, 1674-1683, (2010)

Change in Electronic Structure upon Optical Excitation of 8-Vinyladenosine: An Experimental and Theoretical Study
Goutham Kodali, Kurt A. Kistler, Madhavan Narayanan, Spiridoula Matsika, and Robert J. Stanley
J. Phys. Chem. A, 114, 1, 256-267, (2010)

An Ab Initio Study of Substituent Effects on the Excited States of Purine Derivatives
Elizabeth Mburu and Spiridoula Matsika
J. Phys. Chem. A, 112, 48, 12485-12491,(2008)

On the Electronically Excited States of Uracil
Evgeny Epifanovsky, Karol Kowalski, Peng-Dong Fan, Marat Valiev, Spiridoula Matsika, and Anna I. Krylov
J. Phys. Chem. A, 112, 40, 9983-9992, (2008)

Three-State Conical Intersections in Cytosine and Pyrimidinone Bases
Kurt A. Kistler and Spiridoula Matsika
J. Chem. Phys. 128, 215102 (2008)

Interpreting Ultrafast Molecular Fragmentation Dynamics with ab initio Calculations
Carlos Trallero, Brett J. Pearson, Thomas Weinacht, Kandis Gilliard, and Spiridoula Matsika
J. Chem. Phys. 128, 124107 (2008)

Two and three state conical intersections in uracil cation radical
Spiridoula Matsika
Chem. Phys., 349, 356-362, (2008)

2-Aminopurine Excited State Electronic Structure Measure by Stark Spectroscopy
Goutham Kodali, Kurt A. Kistler, Spiridoula Matsika, and Robert J. Stanley
J. Phys. Chem. B, 112, 6, 1789-1795, (2008)

Excited Electronic States and Photophysics of Uracil-Water Complexes
Akihiko Yoshikawa and Spiridoula Matsika
Chem. Phys., 347, 393-404, (2008)

Inclusion of Second-order Correlation Effects for the Ground and Singly Excited States Suitable for the Study of Conical Intersections: the CIS(2) Model
Dimitri Laikov and Spiridoula Matsika
Chem. Phys. Lett., 448, 132-137, (2007)

Cytosine in Context: A Theoretical Study of Substituent Effects on the Excitation Energies of 2-Pyrimidinone Derivatives
Kurt A. Kistler and Spiridoula Matsika
J. Phys. Chem. A, 111, 35, 8708-8716, (2017)

6MAP, a fluorescent adenine analogue, is a probe of base flipping by DNA photolyase
Kongsheng Yang, Spiridoula Matsika, and Robert J. Stanley
J. Phys. Chem. B, 111, 35, 10615-10625, (2017)

Radiationless Decay Mechanism of Cytosine: An Ab Initio Study with Comparisons to the Fluorescent Analogue 5-Methyl-2-Pyrimidinone
Kurt A. Kistler and Spiridoula Matsika
J. Phys. Chem. A, 111, 14, 2650-2661, (2007)

The Fluorescence Mechanism of 5-Methyl-2-Pyrimidinone: An Ab Initio Study of a Fluorescent Pyrimidine Analog
Kurt A. Kistler and Spiridoula Matsika
Photochemistry and Photobiology , 83, 611-624, (2007)

Conical intersections in Molecular Systems
Spiridoula Matsika
Rev. Comp. Chem. 23 , 83, (2007)

A Combined Multireference Configuration Interaction/Molecular Dynamics Approach for Calculating Solvatochromic Shifts- Application to the nO -> pi* Electronic Transition in Formaldehyde
ZongRong Xu and Spiridoula Matsika
J. Phys. Chem. A, 110, 43, 12035-12043, (2006)

Excited Electronic States of the Cyclic Isomers of O3 and SO2
Ruth Elliott, Ryan Compton, Robert Levis, and Spiridoula Matsika
J. Phys. Chem. A, 109, 49, 11304 - 11311, (2005)

Three-state Conical Intersections in Nucleic Acid Bases
Spiridoula Matsika
J. Phys. Chem. A., 109, 33, 7538-7545, (2005)

Radiationless Decay of Excited States of Uracil through Conical Intersections
Spiridoula Matsika
J. Phys. Chem. A 2004, 108, 37, 7584-7590, (2004)

Quantitative Detection of Singlet O2 via Cavity Enhanced Absorption
Skip Williams, Manish Gupta, Thomas Owano, Douglas S. Baer, Anthony O’Keefe, David R. Yarkony, and Spiridoula Matsika
Opt. Lett. 29, 1066-1068, (2004)

Conical Intersections of Three Electronic States Affect the Ground State of Radical Species with Little or No Symmetry: Pyrazolyl
Spiridoula Matsika and David R. Yarkony
J. Am. Chem. Soc. 2003, 125, 41, 12428-12429, (2003)

Beyond Two-State Conical Intersections. Three-State Conical Intersections in Low Symmetry Molecules: the Allyl Radical
Spiridoula Matsika and David R. Yarkony
J. Am. Chem. Soc. 2003, 125, 35, 10672-10676, (2003)

Photodissociation of the Vinoxy Radical through Conical, and Avoided, Intersections
Spiridoula Matsika and David R. Yarkony
J. Chem. Phys. 117, 7198, (2002)

Accidental Conical Intersections of Three States of the Same Symmetry. I. Location and Relevance
Spiridoula Matsika and David R. Yarkony
J. Chem. Phys. 117, 6907, (2002)

Spin-Orbit Coupling and Conical Intersections . IV. A Perturbative Determination of the Electronic Energies, Derivative Couplings and a Rigorous Diabatic Representation near a Conical Intersection. The General Case
Spiridoula Matsika and David R. Yarkony
J. Phys. Chem. B 2002, 106, 33, 8108-8116, (2002)

Conical Intersections and the Nonadiabatic Reactions H2O+O(3P) -> OH(A)+OH(X)
Spiridoula Matsika and David R. Yarkony
J. Chem. Phys. 117, 3733, (2002)

Conical Intersections and the Spin-Orbit Interaction
Spiridoula Matsika and David R. Yarkony
The Role of Degenerate States in Chemistry: A Special Volume of Advances in Chemical Physics, 124, 557-581, (2002)

Intersecting Conical Intersection Seams: their Location, Representation, and Effect on Local Topography
Spiridoula Matsika and David R. Yarkony
J. Phys. Chem. A 2002, 106, 11, 2580-2591, (2002)

Spin-Orbit Coupling and Conical Intersections in Molecules with an Odd Number of Electrons. III. A Perturbative Determination of the Electronic Energies, Derivative Couplings and a Rigorous Diabatic Representation near a Conical Intersection
Spiridoula Matsika and David R. Yarkony
J. Chem. Phys. 116, 2825, (2002)

On the Effects of Spin-Orbit Coupling on Conical Intersection Seams in Molecules with an Odd Number of Electrons. II. Characterizing the Local Topography of the Seam
Spiridoula Matsika and David R. Yarkony
J. Chem. Phys. 115, 5066, (2001)

On the Effects of Spin-Orbit Coupling on Conical Intersection Seams in Molecules with an Odd Number of Electrons. I. Locating the Seam
Spiridoula Matsika and David R. Yarkony
J. Chem. Phys. 115, 2038, (2001)

Electronic Structure and Spectra of Actinyl Ions
S. Matsika, Z. Zhang, S. R. Brozell, J.-P. Blaudeau, Q. Wang, R. M. Pitzer
J. Phys. Chem. A 2001, 105, 15, 3825-3828, (2001)

Actinyl Ions in Cs2UO2Cl4
S. Matsika and R. M. Pitzer
J. Phys. Chem. A 2001, 105, 3, 637-645, (2001)

Intensities in the Spectra of Actinyl Ions
S. Matsika, R. M. Pitzer
J. Phys. Chem. A 2000, 104, 51, 11983-11992, (2000)

The Electronic Spectrum of the NpO22+ and NpO2+ Ions
S. Matsika and R. M. Pitzer
J. Phys. Chem. A 2000, 104, 17, 4064-4068, (2000)

Atomic Orbital Basis Sets for Use with Effective Core Potentials
J.-P. Blaudeau, S. R. Brozell, S. Matsika, Z. Zhang and R. M. Pitzer
Int. J. Quantum Chem., 77, 516-520, (2000)

Spin-Orbit Splittings in Mg+-Neutral Complexes
S. Matsika and R. M. Pitzer
J. Phys. Chem. A 1998, 102, 9, 1652-1656, (1998)

Ab Initio Study of the Ground and Several Excited States of the NLi System
S. Matsika, A. Papakondylis and A. Mavridis
Chem. Phys. Lett., 250, 409-414, (1996)