Imperial College London

DrJoao PedroMalhado

Faculty of Natural SciencesDepartment of Chemistry

Senior Teaching Fellow







ChemistrySouth Kensington Campus





Publication Type

11 results found

Austin D, Johnson A, McGrath F, Wood D, Miseikis L, Siegel T, Hawkins P, Harvey A, Mašín Z, Patchkovskii S, Vacher M, Malhado JP, Ivanov M, Smirnova O, Marangos Jet al., 2021, Extracting sub-cycle electronic and nuclear dynamics from high harmonic spectra, Scientific Reports, Vol: 11, ISSN: 2045-2322

We present a new methodology for measuring few-femtosecond electronic and nuclear dynamics in both atoms and polyatomic molecules using multidimensional high harmonic generation (HHG) spectroscopy measurements, in which the spectra are recorded as a function of the laser intensity to form a two-dimensional data set. The method is applied to xenon atoms and to benzene molecules, the latter exhibiting significant fast nuclear dynamics following ionization. We uncover the signature of the sub-cycle evolution of the returning electron flux in strong-field ionized xenon atoms, implicit in the strong field approximation but not previously observed directly. We furthermore extract the nuclear autocorrelation function in strong field ionized benzene cations, which is determined to have a decay of τ0=4±1 fs, in good agreement with the τ0=3.5 fs obtained from direct dynamics variational multi-configuration Gaussian calculations. Our method requires minimal assumptions about the system, and is applicable even to un-aligned polyatomic molecules.

Journal article

Fernández Galván I, Vacher M, Alavi A, Angeli C, Aquilante F, Autschbach J, Bao JJ, Bokarev SI, Bogdanov NA, Carlson RK, Chibotaru LF, Creutzberg J, Dattani N, Delcey MG, Dong SS, Dreuw A, Freitag L, Frutos LM, Gagliardi L, Gendron F, Giussani A, Gonzalez L, Grell G, Guo M, Hoyer CE, Johansson M, Keller S, Knecht S, Kovačević G, Källman E, Li Manni G, Lundberg M, Ma Y, Mai S, Malhado JP, Malmqvist PA, Marquetand P, Mewes SA, Norell J, Olivucci M, Oppel M, Phung QM, Pierloot K, Plasser F, Reiher M, Sand AM, Schapiro I, Sharma P, Stein CJ, Sørensen LK, Truhlar DG, Ugandi M, Ungur L, Valentini A, Vancoillie S, Veryazov V, Weser O, Wesolowski TA, Widmark P-O, Wouters S, Zech A, Zobel JP, Lindh Ret al., 2019, OpenMolcas: From source code to insight, Journal of Chemical Theory and Computation, Vol: 15, Pages: 5925-5964, ISSN: 1549-9618

In this article we describe the OpenMolcas environment and invite the computational chemistry community to collaborate. The open-source project already includes a large number of new developments realized during the transition from the commercial MOLCAS product to the open-source platform. The paper initially describes the technical details of the new software development platform. This is followed by brief presentations of many new methods, implementations, and features of the OpenMolcas program suite. These developments include novel wave function methods such as stochastic complete active space self-consistent field, density matrix renormalization group (DMRG) methods, and hybrid multiconfigurational wave function and density functional theory models. Some of these implementations include an array of additional options and functionalities. The paper proceeds and describes developments related to explorations of potential energy surfaces. Here we present methods for the optimization of conical intersections, the simulation of adiabatic and nonadiabatic molecular dynamics and interfaces to tools for semiclassical and quantum mechanical nuclear dynamics. Furthermore, the article describes features unique to simulations of spectroscopic and magnetic phenomena such as the exact semiclassical description of the interaction between light and matter, various X-ray processes, magnetic circular dichroism and properties. Finally, the paper describes a number of built-in and add-on features to support the OpenMolcas platform with post calculation analysis and visualization, a multiscale simulation option using frozen-density embedding theory and new electronic and muonic basis sets.

Journal article

Vacher M, Bearpark M, Robb MA, Malhado JPet al., 2017, Electron dynamics upon ionisation of polyatomic molecules: Coupling to quantum nuclear motion and decoherence, Physical Review Letters, Vol: 118, Pages: 1-5, ISSN: 1079-7114

Knowledge about the electronic motion in molecules is essential for our understanding of chemicalreactions and biological processes. The advent of attosecond techniques opens up the possibility toinduce electronic motion, observe it in real time and potentially steer it. A fundamental questionremains the factors influencing electronic decoherence and the role played by nuclear motion in thisprocess. Here, we simulate the dynamics upon ionisation of the polyatomic molecules para-xyleneand modified bismethylene-adamantane, with a quantum mechanical treatment of both electron andnuclear dynamics using the direct dynamics variational multi-configuration Gaussian method. Oursimulations give new important physical insights about the expected decoherence process. We haveshown that the decoherence of electron dynamics happens on the time scale of a few femtoseconds,with the interplay of different mechanisms: thedephasingis responsible for the fast decoherencewhile thenuclear overlap decaymay actually help maintaining it and is responsible for small revivals.

Journal article

Malhado JP, Hynes JT, 2016, Non-adiabatic transition probability dependence on conical intersection topography, Journal of Chemical Physics, Vol: 145, ISSN: 1089-7690

We derive a closed form analytical expression for the non-adiabatic transition probability for a distribution of trajectories passing through a generic conical intersection (CI), based on the Landau-Zener equation for the non-adiabatic transition probability for a single straight-line trajectory in the CI's vicinity. We investigate the non-adiabatic transition probability's variation with topographical features and find, for the same crossing velocity, no intrinsic difference in efficiency at promoting non-adiabatic decay between peaked and sloped CIs, a result in contrast to the commonly held view. Any increased efficiency of peaked over sloped CIs is thus due to dynamical effects rather than to any increased transition probability of topographical origin. It is also shown that the transition probability depends in general on the direction of approach to the CI, and that the coordinates' reduced mass can affect the transition probability via its influence on the CI topography in mass-scaled coordinates. The resulting predictions compare well with surface hopping simulation results.

Journal article

Santolini V, Malhado JP, Robb MA, Garavelli M, Bearpark MJet al., 2015, Photochemical reaction paths of cis-dienes studied with RASSCF: the changing balance between ionic and covalent excited states, Molecular Physics, Vol: 113, Pages: 1978-1990, ISSN: 1362-3028

The balanced description of ionic and covalent molecular excited electronic states still presents a challenge for currentelectronic structure methods. In this contribution, we show how the restricted active space self-consistent field (RASSCF)method can be used to address this problem, applied to two dienes in the cis conformation. As with the closely relatedcomplete active space self-consistent field (CASSCF) method, the construction of the orbital active space in the RASSCFmethodology requires the a priori formulation of a physical or theoretical model of the system being studied. In this article,we discuss how the active space can be constructed in a guided and systematic way, using pairs of natural bond orbitalsas correlating partner orbitals (oscillator orbitals) and semi-internal correlation. The resulting balanced description of thecovalent and ionic valence excited states – with the ionic state correctly lower in energy at the Franck–Condon geometry –is suitable to study the photochemistry of these and other molecules.

Journal article

Malhado JP, Bearpark MJ, Hynes JT, 2014, Non-adiabatic dynamics close to conical intersections and the surface hopping perspective., Frontiers in Chemistry, Vol: 2, ISSN: 2296-2646

Conical intersections play a major role in the current understanding of electronic de-excitation in polyatomic molecules, and thus in the description of photochemistry and photophysics of molecular systems. This article reviews aspects of the basic theory underlying the description of non-adiabatic transitions at conical intersections, with particular emphasis on the important case when the dynamics of the nuclei are treated classically. Within this classical nuclear motion framework, the main aspects of the surface hopping methodology in the conical intersection context are presented. The emerging picture from this treatment is that of electronic transitions around conical intersections dominated by the interplay of the nuclear velocity and the derivative non-adiabatic coupling vector field.

Journal article

Malhado JP, Spezia R, Hynes JT, 2013, Conical intersection structure and dynamics for a model protonated schiff base photoisomerization in solution, INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Vol: 113, Pages: 296-305, ISSN: 0020-7608

Journal article

Malhado JP, Hynes JT, 2012, Photoisomerization for a model protonated Schiff base in solution: Sloped/peaked conical intersection perspective, JOURNAL OF CHEMICAL PHYSICS, Vol: 137, ISSN: 0021-9606

Journal article

Malhado JP, Spezia R, Hynes JT, 2011, Dynamical Friction Effects on the Photoisomerization of a Model Protonated Schiff Base in Solution, JOURNAL OF PHYSICAL CHEMISTRY A, Vol: 115, Pages: 3720-3735, ISSN: 1089-5639

Journal article

Malhado JP, Hynes JT, 2008, On the Landau-Zener approach to nonadiabatic transitions for a vertical conical intersection, CHEMICAL PHYSICS, Vol: 347, Pages: 39-45, ISSN: 0301-0104

Journal article

Malhado JBC, Tavares M, Berberan-Santos MN, 2003, Study of a Reversible Gas Phase Reaction: An Integrated Physical Chemistry Project, Chemical Educator, Vol: 9, Pages: 32-38

Journal article

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