Akshaya Kumar Das

Charge migration and charge transfer in molecular systems

The transfer of charge at the molecular level plays a fundamental role in many areas of chemistry, physics, biology and materials science. Today, more than 60 years after the seminal work of R. A. Marcus, charge transfer is still a very active field of research. An important recent impetus comes from the ability to resolve ever faster temporal events, down to the attosecond time scale. Such a high temporal resolution now offers the possibility to unravel the most elementary quantum dynamics of both electrons and nuclei that participate in the complex process of charge transfer. This review covers recent research that addresses the following questions. Can we reconstruct the migration of charge across a molecule on the atomic length and electronic time scales? Can we use strong laser fields to control charge migration? Can we temporally resolve and understand intramolecular charge transfer in dissociative ionization of small molecules, in transition-metal complexes and in conjugated polymers? Can we tailor molecular systems towards specific charge-transfer processes? What are the time scales of the elementary steps of charge transfer in liquids and nanoparticles? Important new insights into each of these topics, obtained from state-of-the-art ultrafast spectroscopy and/or theoretical methods, are summarized in this review.

Copper Oxidation/Reduction in Water and Protein: Studies with DFTB3/MM and VALBOND Molecular Dynamics Simulations

We apply two recently developed computational methods, DFTB3 and VALBOND, to study copper oxidation/reduction processes in solution and protein. The properties of interest include the coordination structure of copper in different oxidation states in water or in a protein (plastocyanin) active site, the reduction potential of the copper ion in different environments, and the environmental response to copper oxidation. The DFTB3/MM and VALBOND simulation results are compared to DFT/MM simulations and experimental results whenever possible. For a copper ion in aqueous solution, DFTB3/MM results are generally close to B3LYP/MM with a medium basis, including both solvation structure and reduction potential for Cu(II); for Cu(I), however, DFTB3/MM finds a two-water coordination, similar to previous Born-Oppenheimer molecular dynamics simulations using BLYP and HSE, whereas B3LYP/MM leads to a tetrahedron coordination. For a tetraammonia copper complex in aqueous solution, VALBOND and DFTB3/MM are consistent in terms of both structural and dynamical properties of solvent near copper for both oxidation states. For copper reduction in plastocyanin, DFTB3/MM simulations capture the key properties of the active site, and the computed reduction potential and reorganization energy are in fair agreement with experiment, especially when the periodic boundary condition is used. Overall, the study supports the value of VALBOND and DFTB3(/MM) for the analysis of fundamental copper redox chemistry in water and protein, and the results also help highlight areas where further improvements in these methods are desirable.

Inner-Shell Water Rearrangement Following Photoexcitation of Tris(2,2′-bipyridine)iron(II)

The solvent dynamics in Fe-tris-bipyridine [Fe(bpy)3](2+) upon electronic excitation (oxidation) and subsequent relaxation is followed on the picosecond time scale by using atomistic simulations. Starting from the low spin (LS) Fe(II)LS state the transition to the excited Fe(III) (1,3)MLCT (metal-to-ligand charge transfer) state decreases the water coordination in immediate proximity of the central iron atom. This readjustment of the solvent shell occurs on the subpicosecond time scale. Full relaxation of the water environment would occur on the 10 ps time scale which is, however, never reached as the lifetime of the (1,3)MLCT state is only 200 fs. Further relaxation toward the long-lived (665 ps) [Fe(II)HS(bpy)3] high spin (HS) state does not change the degree of solvation. The results support a model in which the change in the degree of solvation is driven by electronic effects (charge redistribution) and not by structural changes (change in bond lengths). Furthermore, the results are consistent with recent combined X-ray emission (XES) and X-ray diffusion (XDS) scattering experiments which provided evidence for a reduced solvent density upon excitation of the [Fe(II)LS(bpy)3] initial state. However, the time scale for water exchange dynamics is faster than that found in the experiments.

Solvation of fluoro-acetonitrile in water by 2D-IR spectroscopy: A combined experimental-computational study

The solvent dynamics around fluorinated acetonitrile is characterized by 2-dimensional infrared spectroscopy and atomistic simulations. The lineshape of the linear infrared spectrum is better captured by semiempirical (density functional tight binding) mixed quantum mechanical/molecular mechanics simulations, whereas force field simulations with multipolar interactions yield lineshapes that are significantly too narrow. For the solvent dynamics, a relatively slow time scale of 2 ps is found from the experiments and supported by the mixed quantum mechanical/molecular mechanics simulations. With multipolar force fields fitted to the available thermodynamical data, the time scale is considerably faster--on the 0.5 ps time scale. The simulations provide evidence for a well established CF-HOH hydrogen bond (population of 25%) which is found from the radial distribution function g(r) from both, force field and quantum mechanics/molecular mechanics simulations.

Multi-State VALBOND for Atomistic Simulations of Hypervalent Molecules, Metal Complexes, and Reactions

The implementation, validation, and application of the multi-state VALBOND method for transition-metal-containing and hypervalent molecules are presented. This approach is particularly suited for molecules with unusual shapes and systems that need to be described by a superposition of resonance structures, each of which satisfies the octet rule. The implementation is based on the original VALBOND force field and allows us to smoothly switch between resonance structures, each of which can be characterized by its own force field, including varying charge distributions and coupling terms between the states. The implementation conserves total energy for simulations in the gas phase and in solution and is applied to a number of topical systems. For the small hypervalent molecule ClF3, the barrier for pseudorotation is found to be 4.3 kcal/mol, which compares favorably with the experimentally measured value of 4.8 kcal/mol. A transition-metal-containing complex, cisplatin, is characterized by six resonance states, for which the vibrational spectrum is found to be in good agreement with experiment. Finally, umbrella sampling simulations of the SN2 reaction BrMe + Cl- → Br- + MeCl in solution yield a barrier height of 24.6 kcal/mol, in good agreement with experiment (24.7 kcal/mol).

Kinetic Analysis and Structural Interpretation of Competitive Ligand Binding for NO Dioxygenation in Truncated Hemoglobin N

The conversion of nitric oxide (NO) into nitrate (NO3- ) by dioxygenation protects cells from lethal NO. Starting from NO-bound heme, the first step in converting NO into benign NO3- is the ligand exchange reaction FeNO+O2 →FeO2 +NO, which is still poorly understood at a molecular level. For wild-type (WT) truncated hemoglobin N (trHbN) and its Y33A mutant, the calculated barriers for the exchange reaction differ by 1.5 kcal mol-1 , compared with 1.7 kcal mol-1 from experiment. It is directly confirmed that the ligand exchange reaction is rate-limiting in trHbN and that entropic contributions account for 75 % of the difference between the WT and the mutant. Residues Tyr 33, Phe 46, Val 80, His 81, and Gln 82 surrounding the active site are expected to control the reaction path. By comparison with electronic structure calculations, the transition state separating the two ligand-bound states was assigned to a 2 A state.

Hydration Control Through Intramolecular Degrees of Freedom: Molecular Dynamics of [Cu(II)(Imidazole)4]

Structural characterization of the copper-coordination shell is important in catalysis and biology. Cu-containing domains are prevalent in biological systems and play important roles in oxidation and electron transport process. Here, the solution structure, solvent organization, and dynamics around aqueous [Cu(II)(Imidazole)4] were characterized using atomistic simulations. Asymmetric axial water coordination around the metal atom was found which agrees with results from Minuit X-ray absorption near-edge structure (MXAN) experiments. The simulations reveal that exchange of the axial water occurs on the 25 to 50 ps time scale and is facilitated by and coupled to the flexibility of the copper-out of plane motion relative to the nitrogen atoms. Both concerted and stepwise water exchange of the two axially coordinated water molecules with first-shell water molecules are observed. The results suggest that axial access of a copper center can be fine-tuned by the degree of flexibility of its first coordination sphere.

Empirical Force Fields for Mechanistic Studies of Chemical Reactions in Proteins

Following chemical reactions in atomistic detail is one of the most challenging aspects of current computational approaches to chemistry. In this chapter the application of adiabatic reactive MD (ARMD) and its multistate version (MS-ARMD) are discussed. Both methods allow to study bond-breaking and bond-forming processes in chemical and biological processes. Particular emphasis is put on practical aspects for applying the methods to investigate the dynamics of chemical reactions. The chapter closes with an outlook of possible generalizations of the methods discussed.