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Thomas James Penfold

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Related publications (35)

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Pushing the Frontiers of First-Principles Based Computer Simulations of Chemical and Biological Systems

Ursula Röthlisberger, Ivano Tavernelli, Basile Curchod, Marilisa Neri, Pablo Campomanes Ramos, Stefano Vanni, Elizabeth Claire Brunk, Manuel Dömer, Andrey Laktionov, Negar Ashari Astani, Polydefkis Diamantis, Thomas James Penfold, Giulia Palermo

The Laboratory of Computational Chemistry and Biochemistry is active in the development and application of first-principles based simulations of complex chemical and biochemical phenomena. Here, we review some of our recent efforts in extending these metho ...

2011

Probing the electronic and geometric structure of ferric and ferrous myoglobins in physiological solutions by Fe K-edge absorption spectroscopy

Majed Chergui, Ursula Röthlisberger, Ivano Tavernelli, Frederico Alves Lima, Marco Eli Reinhard, Thomas James Penfold

We present an iron K-edge X-ray absorption study of carboxymyoglobin (MbCO), nitrosylmyoglobin (MbNO), oxymyoglobin (MbO(2)), cyanomyoglobin (MbCN), aquomet myoglobin (metMb) and unligated myoglobin (deoxyMb) in physiological media. The analysis of the XAN ...

2014

Solvent Induced Luminescence Quenching: Static and Time-Resolved X-Ray Absorption Spectroscopy of a Copper(I) Phenanthroline Complex

Majed Chergui, Olivier Christian Bräm, Ursula Röthlisberger, Ivano Tavernelli, Frederico Alves Lima, Marco Eli Reinhard, Mercedes Hannelore Rittmann-Frank, Thomas James Penfold, Lotta Susanne Karlsson, Jochen Rittmann, Gloria Capano

We present a static and picosecond X-ray absorption study at the Cu K-edge of bis(2,9-dimethyl-1,10-phenanthroline)copper(I) (Cu(dmp)(2); dmp = 2,9-dimethyl-1,10-phenanthroline) dissolved in acetonitrile and dichloromethane. The steady-state photolumi ...

Amer Chemical Soc2013

Evidence for a Peierls phase-transition in a three-dimensional multiple charge-density waves solid

Majed Chergui, Mathieu Julien Gino Cottet, Fabrizio Carbone, Thomas James Penfold

The effect of dimensionality on materials properties has become strikingly evident with the recent discovery of graphene. Charge ordering phenomena can be induced in one dimension by periodic distortions of a material's crystal structure, termed Peierls or ...

National Academy of Sciences2012

A wavelet analysis for the X-ray absorption spectra of molecules

Majed Chergui, Ursula Röthlisberger, Ivano Tavernelli, Amal El Nahhas, Marco Eli Reinhard, Thomas James Penfold

We present a Wavelet transform analysis for the X-ray absorption spectra of molecules. In contrast to the traditionally used Fourier transform approach, this analysis yields a 2D correlation plot in both R- and k-space. As a consequence, it is possible to ...

American Institute of Physics2013

Quantum dynamics study of the competing ultrafast intersystem crossing and internal conversion in the "channel 3" region of benzene

Thomas James Penfold

Time-resolved photoelectron spectroscopy can obtain detailed information about the dynamics of a chemical process on the femtosecond timescale. The resulting signal from such detailed experiments is often difficult to analyze and therefore theoretical calc ...

American Institute of Physics2012

Ultrafast anisotropic x-ray scattering in the condensed phase

Majed Chergui, Ursula Röthlisberger, Ivano Tavernelli, Thomas James Penfold

The advent of x-ray free electron lasers offers new opportunities for x-ray scattering (XRS) studies of ultrafast molecular dynamics in liquids, which have so far been limited to the 100 ps resolution of synchrotrons. In particular, anisotropic XRS induced ...

Institute of Physics (IoP) and Deutsche Physikalische Gesellschaft2012

Hydrophobicity with atomic resolution: Steady-state and ultrafast X-ray absorption and molecular dynamics studies

Majed Chergui, Ivano Tavernelli, Thomas James Penfold

Static and time-resolved X-ray absorption spectroscopy (XAS) is used to probe the solvent shell structure around iodide and iodine. In particular, we characterize the changes ob served upon electron abstraction of aqueous iodide, which reflects the transit ...

De Gruyter2013

Characterizing the Structure and Defect Concentration of ZnO Nanoparticles in a Colloidal Solution

Majed Chergui, Marco Eli Reinhard, Mercedes Hannelore Rittmann-Frank, Thomas James Penfold, Jochen Rittmann, Thomas Charles Henry Rossi

The structure and defect concentration of colloidal solutions of ZnO nanoparticles, synthesized by a sol gel procedure (SG-NP), as well as commercially available ZnO nanoparticles (SA-NP) are investigated by UV-vis absorption spectroscopy, transmission ele ...

Amer Chemical Soc2014

Solvent rearrangements during the transition from hydrophilic to hydrophobic solvation

Majed Chergui, Ursula Röthlisberger, Ivano Tavernelli, Manuel Dömer, Thomas James Penfold

We present an ab initio Born-Oppenheimer molecular dynamics study of the early time solvent dynamics after electron abstraction from aqueous iodide. An initial response occurs within ∼75 fs, corresponding to a water molecule sharing almost one electron wit ...

Elsevier2013

Local Control Theory in Trajectory Surface Hopping Dynamics Applied to the Excited-State Proton Transfer of 4-Hydroxyacridine

Ursula Röthlisberger, Ivano Tavernelli, Basile Curchod, Thomas James Penfold

The application of local control theory combined with nonadiabatic ab initio molecular dynamics to study the photoinduced intramolecular proton transfer reaction in 4-hydroxyacridine was investigated. All calculations were performed within the framework of ...

2015

Photoaquation Mechanism of Hexacyanoferrate(II) Ions: Ultrafast 2D UV and Transient Visible and IR Spectroscopies

Majed Chergui, Gerald Auböck, Marco Eli Reinhard, Thomas James Penfold

Ferrous iron(II) hexacyanide in aqueous solutions is known to undergo photoionization and photoaquation reactions depending on the excitation wavelength. To investigate this wavelength dependence, we implemented ultrafast two-dimensional UV transient absor ...

American Chemical Society2017

Photophysics of a copper phenanthroline elucidated by trajectory and wavepacket-based quantum dynamics: a synergetic approach

Majed Chergui, Ivano Tavernelli, Thomas James Penfold, Gloria Capano

On-the-fly excited state molecular dynamics is a valuable method for studying non-equilibrium processes in excited states and is beginning to emerge as a mature approach much like its ground state counterparts. In contrast to quantum wavepacket dynamics me ...

Royal Society of Chemistry2017

A femtosecond fluorescence study of vibrational relaxation and cooling dynamics of UV dyes

Majed Chergui, Olivier Christian Bräm, Andrea Cannizzo, Thomas James Penfold

We present a femtosecond broad-band fluorescence up-conversion study of the vibrational relaxation dynamics of two UV chromophores, 2,5-diphenyloxazole (PPO) and para-terphenyl (pTP), pumped with a large excess of vibrational energy (>2000 cm(-1)). The ban ...

2012

Probing the Transition from Hydrophilic to Hydrophobic Solvation with Atomic Scale Resolution

Majed Chergui, Ivano Tavernelli, Amal El Nahhas, Van Thai Pham, Renske Marjan van der Veen, Frederico Alves Lima, Thomas James Penfold

Picosecond and femtosecond X-ray absorption spectroscopy is used to probe the changes of the solvent shell structure upon electron abstraction of aqueous iodide using an ultrashort laser pulse. The transient L-1,L-3 edge EXAFS at 50 ps time delay points to ...

2011

Simulations of X-ray absorption spectra: the effect of the solvent

Majed Chergui, Ursula Röthlisberger, Ivano Tavernelli, Basile Curchod, Thomas James Penfold

We perform quantum mechanics/molecular mechanics molecular dynamics simulations on the Pt-2(P2O5H2)(4) (abbreviated PtPOP) complex; in water, dimethylformamide and ethanol. These are used to calculate the ground state X-ray absorption spectrum of the ...

2012

Recent experimental and theoretical developments in time-resolved X-ray spectroscopies

Majed Chergui, Thomas James Penfold

Capturing the evolving geometric and electronic structure in the course of a chemical reaction or biological process is the principal aim of time-resolved X-ray spectroscopies. Recent technological and methodological improvements, such as high repetition r ...

Elsevier2014

Derivation of spin-orbit couplings in collinear linear-response TDDFT: A rigorous formulation

Ivano Tavernelli, Basile Curchod, Thomas James Penfold

Using an approach based upon a set of auxiliary many-electron wavefunctions we present a rigorous derivation of spin-orbit coupling (SOC) within the framework of linear-response time-dependent density functional theory (LR-TDDFT). Our method is based on a ...

2014

A Vibronic Coupling Hamiltonian to Describe the Ultrafast Excited State Dynamics of a Cu(I)-Phenanthroline Complex

Ursula Röthlisberger, Ivano Tavernelli, Thomas James Penfold, Gloria Capano

We present a model Hamiltonian to study the nonadiabatic dynamics of photoexcited Cu(dmp)(2), (dmp = 2,9-dimethyl-1,10-phenanthroline). The relevant normal modes, identified by the magnitude of the first order coupling constants, correspond closely to ...

2014

Mapping of the Photoinduced Electron Traps in TiO2 by Picosecond X-ray Absorption Spectroscopy

Majed Chergui, Marco Eli Reinhard, Mercedes Hannelore Rittmann-Frank, Thomas James Penfold, Jochen Rittmann

Titanium dioxide (TiO2) is the most popular material for applications in solar-energy conversion and photocatalysis, both of which rely on the creation, transport, and trapping of charges (holes and electrons). The nature and lifetime of electron traps at ...

Wiley-Blackwell2014