Elisa Pieri

All Publications

• TeraChem protocol buffers (TCPB): Accelerating QM and QM/MM simulations with a client–server model THE JOURNAL OF CHEMICAL PHYSICS Cruzeiro, V. D., Wang, Y., Pieri, E., Hohenstein, E. G., Martínez, T. J. 2023; 158 (044801)

  View details for DOI 10.1063/5.0130886

• CpHMD-Then-QM/MM Identification of the Amino Acids Responsible for the Anabaena Sensory Rhodopsin pH-Dependent Electronic Absorption Spectrum JOURNAL OF CHEMICAL THEORY AND COMPUTATION Pieri, E., Ledentu, V., Sahlin, M., Dehez, F., Olivucci, M., Ferre, N. 2019; 15 (8): 4535–46

  Abstract

  Anabaena Sensory Rhodopsin (ASR), a microbial photoactive protein featuring the retinal chromophore in two different conformations, exhibits a pH-dependent electronic absorption spectrum. Using the recently developed CpHMD-then-QM/MM multiscale protocol applied to ASR embedded in a membrane model, the pH-induced changes in its maximum absorption wavelength have been reproduced and analyzed. While the acidic tiny red-shift is essentially correlated with the deprotonation of an aspartic acid located on the ASR extracellular side, the larger blue-shift experimentally reported at pH values larger than 5 involves a cluster of titrating residues sitting on the cytoplasmic side. The ASR pH-dependent spectrum is the consequence of the competitive stabilization of retinal ground and excited states by the protein electrostatic potential.

  View details for DOI 10.1021/acs.jctc.9b00221

  View details for Web of Science ID 000480826800023

  View details for PubMedID 31264415

• Relaxation Dynamics of Hydrated Thymine, Thymidine, and Thymidine Monophosphate Probed by Liquid Jet Time-Resolved Photoelectron Spectroscopy. The journal of physical chemistry. A Erickson, B. A., Heim, Z. N., Pieri, E. n., Liu, E. n., Martinez, T. J., Neumark, D. M. 2019

  Abstract

  The relaxation dynamics of thymine and its derivatives thymidine and thymidine monophosphate are studied using time-resolved photoelectron spectroscopy applied to a water microjet. Two absorption bands are studied; the first is a bright ππ* state which is populated using tunable-ultraviolet light in the range 4.74-5.17 eV and probed using a 6.20 eV probe pulse. By reversing the order of these pulses, a band containing multiple ππ* states is populated by the 6.20 eV pulse and the lower energy pulse serves as the probe. The lower lying ππ* state is found to decay in ∼400 fs in both thymine and thymidine independent of pump photon energy, while thymidine monophosphate decays vary from 670 to 840 fs with some pump energy dependence. The application of a computational quantum mechanical/molecular mechanical scheme at the XMS-CASPT2//CASSCF/AMBER level of theory suggests that conformational differences existing between thymidine and thymidine monophosphate in solution account for this difference. The higher lying ππ* band is found to decay in ∼600 fs in all three cases, but it is only able to be characterized when the 5.17 eV probe pulse is used. Notably, no long-lived signal from an nπ* state can be identified in either experiment on any of the three molecules.

  View details for DOI 10.1021/acs.jpca.9b08258

  View details for PubMedID 31756106