Irradiation-driven molecular dynamics: a review

Eur. Phys. J. D (2021) 75 :213 https://doi.org/10.1140/epjd/s10053-021-00223-3 THE EUROPEAN PHYSICAL JOURNAL D Topical Review - Atomic and Molecular Collisions Irradiation-driven molecular dynamics: a review Alexey V. Verkhovtsev1,3,a , Ilia A. Solov’yov2,3 , and Andrey V. Solov’yov1,3 1 MBN Research Center, Altenhöferallee 3, 60438 Frankfurt am Main, Germany Department of Physics, Carl von Ossietzky Universität Oldenburg, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany 3 On leave from Ioffe Institute, Polytekhnicheskaya 26, St. Petersburg, Russia 194021 2 Received 7 April 2021 / Accepted 6 July 2021 / Published online 23 July 2021 © The Author(s) 2021 Abstract. This paper reviews Irradiation-Driven Molecular Dynamics (IDMD)—a novel computational methodology for atomistic simulations of the irradiation-driven transformations of complex molecular systems implemented in the MBN Explorer software package. Within the IDMD framework, various quantum processes occurring in irradiated systems are treated as random, fast and local transformations incorporated into the classical MD framework in a stochastic manner with the probabilities elaborated on the basis of quantum mechanics. Major transformations of irradiated molecular systems (such as topological changes, redistribution of atomic partial charges, alteration of interatomic interactions) and possible paths of their further reactive transformations can be simulated by means of MD with reactive force fields, in particular with the reactive CHARMM (rCHARMM) force field implemented in MBN Explorer. This paper reviews the general concept of the IDMD methodology and the rCHARMM force field and provides several exemplary case studies illustrating the utilization of these methods. 1 Introduction There are numerous examples of chemical transformations of complex molecular systems driven by irradiation. Particular examples include (i) inactivation of living cells by ionizing radiation due to the induced complex DNA strand breaks [1–3]; (ii) the formation and composition of cosmic ices in the interstellar medium and planetary atmospheres due to the interplay of the molecular surface adsorption and surface irradiation [4]; (iii) the formation of biologically relevant molecules under extreme conditions involving irradiation [5], and many more. Irradiation-driven chemistry (IDC) is nowadays utilized in modern nanotechnologies, such as focused electron beam-induced deposition (FEBID) [6–8] and extreme ultraviolet (EUV) lithography [9,10]. FEBID and EUV belong to the next generation of nanofabrication techniques allowing the controlled creation of complex three-dimensional nanostructures with nanometer resolution. Fabrication of increasingly smaller structures has been the goal of the electronics industry for more than three decades and remains one of this industry’s biggest challenges. Furthermore, IDC is a key element in nuclear waste decomposition technologies [11] and medical radiotherapies [1,3,12]. IDC studies transformations of molecular systems induced by their irradiation with photon, neutron or a e-mail: (corresponding author) charged-particle beams. IDC is also relevant for molecular systems exposed to external fields, mechanical stress, or plasma environment. A rigorous quantummechanical description of the irradiation-driven molecular processes, e.g., within time-dependent density functional theory (TDDFT) is feasible but only for relatively small molecular systems containing, at most, a few hundred atoms [13–16]. This strong limitation makes TDDFT of limited use for the description of the IDC of complex molecular systems. Classical molecular dynamics (MD) represents an alternative theoretical framework for modeling complex molecular systems. For instance, the classical molecular mechanics approach permits studying the structure and dynamics of molecular systems containing millions of atoms [17,18] and evolving on time scales up to hundreds of nanoseconds [19–21]. In the molecular mechanics approach, the molecular system is treated classically, i.e., the atoms of the system interact with each other through a parametric phenomenological potential that relies on the network of chemical bonds in the system. This network defines the so-called molecular topology, i.e., a set of rules that impose constraints on the system and permit maintaining its natural shape, as well as its mechanical and thermodynamical properties. The molecular mechanics method has been widely used throughout the past decades and has been implemented, for instance, in the well-established computational packages CHARMM [22], AMBER [23], GROMACS [24], NAMD [25] and MBN Explorer [26]. 123 213 Page 2 of 12 Despite the numerous advantages, standard classical MD cannot simulate irradiation-driven processes. It typically does not account for the coupling of the system to incident radiation, nor does it describe quantum transformations in the molecular system induced by the irradiation. These deficiencies have been overcome recently by introducing Irradiation-Driven Molecular Dynamics (IDMD) [27], a new methodology allowing atomistic simulation of IDC in complex molecular systems. The IDMD approach has been implemented in MBN Explorer [26], the advanced software package for multiscale simulations of complex biomolecular, nano- and mesoscopic systems [28–30]. The IDMD methodology is applicable to any molecular system exposed to radiation. It accounts for the major dissociative transformations of irradiated molecular systems (topological changes, redistribution of atomic partial charges, atomic valences, bond multiplicities, interatomic interactions) and possible paths of their further reactive transformations [27]. Such transformations can be simulated by means of MD with reactive force fields, particularly with the reactive CHARMM (rCHARMM) force field [31] implemented in MBN Explorer. This paper provides an overview of the IDMD methodology exploiting the rCHARMM force field and complements it with several illustrative examples published previously [27,32,33]. 2 Irradiation-driven molecular dynamics This section describes the key principles of the IDMD methodology. Within the framework of IDMD various quantum collision processes (e.g., ionization, electronic excitation, bond dissociation via electron attachment or charge transfer) are treated as random, fast and local transformations incorporated into the classical MD framework in a stochastic manner with the probabilities elaborated on the basis of quantum mechanics. This can be achieved because the aforementioned quantum processes happen on the sub-femto- to femtosecond time scales (i.e., during the periods comparable or smaller than a typical single time step of MD simulations) and typically involve a relatively small number of atoms. The probability of each quantum process is equal to the product of the process cross section and the flux density of incident particles [34]. The cross sections of c (...truncated)