Izmaylov Research Group


    The main efforts of our group are directed toward developing electronic structure and quantum dynamics  methods to obtain detailed understanding of processes involving simultaneous changes in electronic and nuclear states. Such processes constitute crucial steps in many areas of fundamental and technological importance: solar energy conversion, UV-light DNA damage and repair, operation of MRI contrast agents, catalysis at surfaces, and general surface chemistry.

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Ongoing projects

    When two or more electronic surfaces approach each other the Born-Oppenheimer approximation breaks down and description of nuclear dynamics needs to account for possible switching between multiple electronic surfaces. In molecules that have more than 2 atoms, very often electronic surfaces cross forming energy degenerate regions. One of the most common intersection motifs is a so-called conical intersection.
Conical intersections are very common participants of photochemical processes, one of the most well known is a vision process that starts from photo-isomerization of the retinal chromophore in the rhodopsin protein.

    Interestingly, conical intersections not only create efficient channels between electronic surfaces but also impose special boundary conditions on electronic and nuclear wave-functions: a simple example is that if we go around the conical intersection both wave-functions must change their signs. In this series of projects we have two main themes:  First, what are the consequences of this
special boundary conditions for nuclear dynamics? Second, how to implement these boundary conditions efficiently in numerical simulations of chemical systems? Following the first theme we found that conical intersections can significantly slow down and even completely quench tunneling dynamics due to destructive interference. Further exploration of consequences of boundary conditions on nuclear dynamics as well as finding efficient techniques to account for them is an active area of research in our group.  

Representative publications:

  1. 1)I. G. Ryabinkin and A. F. Izmaylov, Geometric phase effects in dynamics near conical intersections: Symmetry breaking and spatial localizationPhys. Rev. Lett., 111, 220406 (2013)

  2. 2)I. G. Ryabinkin, L. Joubert-Doriol, and A. F. Izmaylov When do we need to account for the geometric phase in excited state dynamics? J. Chem. Phys. 140, 214116 (2014)

  3. 3)R. Gherib, I. G. Ryabinkin, and A. F. Izmaylov Why do mixed quantum-classical methods describe short-time dynamics through conical intersections so well? Analysis of geometric phase effects, J. Chem. Theory Comp., 11, 1375 (2015)

  4. 4)A. F. Izmaylov, J. Li, and  L. Joubert-Doriol, Diabatic definition of geometric phase effects, J. Chem. Theory Comp. 12, 5278 (2016)

  5. 5)L. Joubert-Doriol, J. Sivasubramanium, I. G. Ryabinkin, and  A. F. Izmaylov, Topologically correct quantum nonadiabatic formalism for on-the-fly dynamics, J. Phys. Chem. Lett. 8, 452 (2017)

YouTube videos:

  1. 1)Introduction to Geometric Phase Effects

  2. 2)Geometric Phase Effects in Low-energy Dynamics

  3. 3)Geometric Phase Effects in Radiationless Transitions


1. Geometric phase effects in nonadiabatic dynamics

2. Method development for energy and charge transfer in organic molecules

Charge and energy transfers are at the heart of efficient solar energy harvesting and utilization. They also involve non-adiabatic dynamics involving several electronic states. In this project we develop new methods to model and understand these processes in middle size organic molecules
that can be seen as potential dye components of semiconductor cells or building blocks for organic photovoltaics. There are three main
development branches: 1) perturbative non-equilibrium methods that start with diabatic model Hamiltonians built from first-principles electronic structure calculations [1], 2) on-the-fly wave-packet simulations with the perturbative spawning technique [2], 3) quantum-classical dynamics with the local energy operator approach [3].

Representative publications:

  1. 1)A. F. Izmaylov, Perturbative Wave-packet Spawning Procedure for Non-adiabatic Dynamics in Diabatic Representation, J. Chem. Phys., 138, 104115 (2013)

  2. 2)L. Joubert-Doriol, I. G. Ryabinkin, and A. F. Izmaylov Non-stochastic matrix Schrödinger equation for open systems, J. Chem. Phys. 141, 234112 (2014)

  3. 3)J. Nagesh, A. F. Izmaylov, and P. Brumer An efficient implementation of the localized operator partitioning method for electronic energy transfer, J. Chem. Phys. 142, 084114 (2015)

  4. 4)J. Nagesh, M. J. Frisch, P. Brumer, and A. F. Izmaylov, Localized operator partitioning method for electronic excitation energies in the time-dependent density functional formalism, J. Chem. Phys. 145, 244111 (2016)

  5. 5)A. F. Izmaylov and L. Joubert-Doriol, Quantum Nonadiabatic Cloning of Entangled Coherent States, J. Phys. Chem. Lett. 8, 1793 (2017)


4. DNA photo-damage repair by photolyases

    Photolyases are natural proteins that by absorbing sunlight can repair human DNA photo-damage caused by UV light. In spite of great potential for use of this natural photo-repair machine in future sunscreen techniques for skin cancer prevention, the detailed mechanism of the photolyase repair still has not been fully established. In this project we aim to unravel the mechanism of the DNA damage photo-repair catalyzed by photolyases in atomistic details. To deliver upon this promise, it is necessary to accurately predict not only electronic states of isolated active centers (see Figs),
but also their nuclear dynamics after photo-excitation, and how this behavior is changed through the interaction of the active centers with the protein environment. The objectives of the current project are to go beyond the individual molecule static picture, and advance our knowledge on the dynamics of photochemical processes and the effects of an environment upon them, also to consolidate methodology and procedures that allow predictability and transferability of simulation results. This is done by systematic comparison and assessment of different combinations of high level electronic structure calculations and state of the art dynamics simulation methods developed in the previous project.

Representative publications:

  1. 1)J. S. Endicott, L. Joubert-Doriol, and A. F. Izmaylov A perturbative formalism for electronic transitions through conical intersections in a fully quadratic vibronic model, J. Chem. Phys. 141, 034104 (2014)

  2. 2)L. Joubert-Doriol and A. F. Izmaylov Problem-free time-dependent variational principle for open systems, J. Chem. Phys. 142, 134107 (2015) 

  3. 3)L. Joubert-Doriol, T. Domratcheva, M. Olivucci, and  A. F. Izmaylov, Nuclear dynamics investigation of the initial electron transfer in the cyclobutane pyrimidine dimer lesion repair process by photolyases, submitted

  Metallic surfaces provide unprecedented capabilities for
supporting, assembling, investigating, controlling molecular structures and chemical reactions. They are perfect for manipulation of matter on an atomic and molecular scale to build more efficient
molecular-based devices (e.g., transistors, diodes, nanocircuits), nanoparticle heterogeneous catalysts, and metamaterials. In this project we develop new computational techniques and apply standard tools (mainly density functional theory) to do first principle modeling of molecules adsorbed on nanoparticles of different shapes (e.g., Pd) and Scanning Tunneling Microscope (STM) induced chemical reactions on surfaces of regular metals (e.g., Cu(110)).  The main questions which are addressed: 1) What is a minimal adequate representation of electronic states of a molecule on a metallic surface? 2) What is the interplay between electronic and nuclear subsystems? 3) How does surface structure affect chemical reactions on metallic surfaces?

    Representative publications:

  1. 1)A. Klinkova, P.V. Cherepanov, I. G. Ryabinkin, M. Ho, M. Ashokkumar, A. F. Izmaylov, D. V. Andreeva, E. Kumacheva, Shape-dependent Interactions of Palladium Nanocrystals with Hydrogen, Small, 12, 2450 (2016)

  2. 2)I. G. Ryabinkin and  A. F. Izmaylov, Mixed quantum-classical dynamics using collective electronic variables: A better alternative to electronic friction theories, J. Phys. Chem. Lett. 8, 440 (2017)


3. Modeling Chemical Reactions on Metallic Surfaces and Nanostructures