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SUMMARY:Making the inaccessible, accessible: Novel Techniques for Obtaining
  Accurate QM/MM Free Energies at Affordable Costs
LOCATION:Chemistry A101
TZID:America/Denver
DTSTART:20230217T160000
UID:2026-04-30-21-11-59@natsci.colostate.edu
DTSTAMP:20260430T211159
Description:About the Seminar\n\nThe use of the most accurate (i.e.\, QM or
  QM/MM) levels of theory for free energy simulations (FES) is typically no
 t possible. Primarily\, this is because the computational cost associated 
 with the extensive configurational sampling needed for converging FES is p
 rohibitive. To ensure the feasibility of QM-based FES\, the \"indirect\" a
 pproach is generally taken\, i.e.\, necessitating the computation of ΔA(M
 M➝QM). Ideally\, this step is performed with standard Free Energy Pertur
 bation (FEP) as it only requires simulations to be carried out at the low 
 level of theory\, however\, work from several groups over the past few yea
 rs has conclusively shown that FEP is ill-suited to this task. As such\, s
 everal alternative strategies and approximations have arisen to mitigate d
 ifficulties with FEP. In this presentation\, I will discuss our recent dev
 elopments to this end with particular emphasis on (1) using more robust te
 chniques to compute ΔA(MM➝QM)\, (2) improving MM descriptions of QM sys
 tems via machine learning techniques\, and (3) developing new techniques f
 or modeling protein-ligand binding with full flexibility.\n\nAbout the Spe
 aker \n\nHello\, my name is H. Lee Woodcock. I completed a B.S. in Chemis
 try with a minor in Biology at Appalachian State University. Here is where
  I first learned about the exciting possibilities of actually performing c
 hemistry research via computer modeling. After briefly flirting with pharm
 acy school\, I decided graduate school in computational chemistry was my t
 op interest. My dissertation research was done under the direction of Prof
 essor Henry F. Schaefer and I completed my Ph.D. in computational quantum 
 chemistry in 2003. The major focus of my graduate research was physical or
 ganic chemistry\; here I supplemented my education by working and publishi
 ng with world leaders in the field such as Prof. Paul von Ragué Schleyer 
 and Prof. Peter R. Schreiner.\nAfter finishing at UGA\, I was awarded a fe
 llowship for post-doctoral studies at the National Institutes of Health. W
 hile at NIH\, I worked with Dr. Bernard Brooks on the development and appl
 ication of general multi-scale methods with a particular focus on hybrid q
 uantum mechanical/molecular mechanical (QM/MM) techniques to study reactio
 n mechanisms and their associated free energies. This work led to numerous
  publications and awards (e.g.\, Career Transition Award). Upon leaving NI
 H I accepted an assistant professorship at the University of South Florida
  (USF\, Tampa\, FL).\n\nSince arriving at USF\, I have not only continued 
 to focus on developing methods for efficiently calculating QM/MM free ener
 gies\, but have also focused on developing and applying techniques for com
 puter-aided drug design (CADD) and characterizing protein structure-functi
 on relationships via computational techniques. These efforts have resulted
  in numerous high-profile publications (i.e.\, in Altmetric’s top 100 pa
 pers of 2018 and 2020) and several new techniques which have been implemen
 ted in two major software packages\; the CHARMM biomolecular simulation pa
 ckage and the quantum chemistry package Q-Chem. I have also been successfu
 l obtaining funding from a variety of locations including: NIH (Career Tra
 nsition Award (K22)\, 4 R01s)\, NSF (single-PI grant)\, and DOE (Phase I a
 nd Phase II SBIR).\nI have also been an active member of the ACS Computers
  in Chemistry (COMP) division for over 20 years. During the past 10+ years
 \, I have been serving in various capacities for COMP with the majority of
  my efforts focused on programming. During this time I (along with my co-c
 hairs) have worked diligently to improve the quality\, opportunities\, and
  diversity of ACS COMP programming. These accomplishments have contributed
  to an ~25% increase in ACS COMP member participation at ACS national meet
 ings since I have taken over as program chair in 2015. 4:00 pm
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