San Diego (spring 2016)

ACS Award for Computers in Chemical and Pharmaceutical Research: Warren Hehre

J. Phillip Bowen (Mercer University) and Alan Shusterman (Reed College)

From dynamics to function and back again: Adventures in simulating biomolecules

Jana Shen, Michael Feig, Hung Nguyen

Over the past three decades, significant advances have been made in the development of molecular dynamics based methods for predictive modeling of dynamical processes of proteins and nucleic acids. These advances, together with the development of spectroscopic techniques, have allowed novel and deeper understanding of fundamental and applied problems such as protein folding, enzyme catalysis and inhibition of pharmaceutical targets. To celebrate the achievements, this symposium brings together some of the pioneers as well as rising stars to inform the status and project the future of the field.

Advances in Computer-Aided Biologics Design

Melissa Landon (Schrodinger), David Pearlman (Schrodinger), and Sandor Vajda (Boston University)

Increasingly pharmaceutical and biotech companies are shifting focus from small molecule to biotherapeutics. This requires a concomitant shift in computational approaches. This symposium will cover algorithmic developments and real-world applications related to computational design and optimization of biotherapeutic agents, such as peptides, antibodies, and enzymes.

​From Synthesis to Design: Modeling Tools for Medicinal Chemists

Melissa Landon (Schrodinger)

​The role of the medicinal chemist is evolving. As contract synthesis has become more prevalent, many pharmaceutical companies are shifting their internal resources toward design. This session will explore the development of new technologies to address the increasing need for med chemist-friendly computational design tools

Measuring “Success” of Molecular Modeling Efforts

Andrew Rusinko (Merck & Co.) and Ed Sherer (Merck & Co.)

Evaluation of the performance of computational chemistry and cheminformatics efforts and tools/software can be a useful indicator of the impact these efforts have on drug discovery programs. Furthermore, analysis could potentially be used to point out technology gaps for companies to address. The purpose of this symposium is to provide timely and accurate insights into how to best perform these surveys and provide suggestions from the lessons learned to date. In part, the goals of this symposium are to determine pertinent questions to assess performance; determine impact of computational units on projects; provide examples and insights; a make recommendations for best practices and future needs. This is the second session of two which began during the Fall Meeting in Boston.

COMP Undergraduate Research Workshop

Ed Sherer (Merck & Co.) and Maria Nagan (Adelphi University)

Undergraduate research plays a key role in the field of computers in chemistry and undergraduate involvement at the ACS National Meeting level is of increasing importance for the COMP Division. This symposium will provide an opportunity for selected undergraduates to present a short overview (5 minutes) of their research via an oral presentation which will be an introduction to their posters presented later during the meeting poster sessions. The short presentations will be accompanied by an overview of the COMP programming for the Spring meeting as well as a general question and answer session with a round table of academic and industrial COMP members. Undergraduates that would like to apply for free registration and this workshop should click here.

Time-dependent Dynamics and Electronic Excited States

Bryan M Wong (University of California, Riverside)

While much effort in computational and theoretical chemistry has focused on ground-state properties, the prediction of molecules and large systems in electronic-excited states (in the presence of time-dependent fields) remains a challenging problem. Specifically, both theoretical and computational chemistry still lack a definitive and systematic approach that is capable of bridging the different spatial and time scales required for describing light-induced processes in nanostructures, biomolecules, and complex systems with predictive accuracy. New excited-state computational methods, especially time-dependent density-functional theory (TD-DFT), have begun to demonstrate their usefulness in addressing this enormous challenge of large spatial and long time scales. The use of TDDFT and other coarse-grained excited-state methods are now becoming the computational tools of choice to obtain reliable predictions of excited-state properties in chemistry, solid-state physics, and biophysics. In particular, the accurate computation of electronic excitations is crucial for understanding the photochemistry of molecular reactions, designing specific photocatalysts, optimizing thin film materials for devices, and tuning molecular energy levels for efficient electron transfer. Using computation to predict and control the electron dynamics underlying these charge transfer processes is key to advancing and improving these chemically-based energy technologies. It is the purpose of this symposium to bring to light some of the current capabilities and successes (as well as highlight limits and deficiencies) of using computation to predict the electron dynamics and excited-state properties in various chemical systems.

Peptide Modeling

Sookhee Ha (Merck & Co.)

Interests in the peptides as the therapeutic agents have increased for last decades due to their safety, efficacy, and shorter time to market. On the other hand, there are some challenges to overcome - such as instability, aggregation, short half-life and low membrane permeability that cause low oral bioavailability. There is a wealth of opportunities for computational chemists to facilitate the design of the peptides and to address the challenges in this field. The use of predictive computational tools for facilitating rational design is expected to increase exponentially. The aim of this session is twofold: to cover new sciences that address those issues and to connect/build/identify the opportunities for collaboration within the community of computational chemistry for the peptide discovery.

Computational Chemistry Across Catalysis (organized by CATL, co-sponsored via COMP)

Carine Michel (University of Lyon), Philippe Sautet (University of Lyon), Dionisios Vlachos (University of Delaware), Andreas Goetz (San Diego Super Computing)

This symposium aims at gathering researchers that share a common interest in the computational modeling of catalytic processes. The topics will span all domains of catalysis including homogeneous and heterogeneous catalysis, biocatalysis, photocatalysis, electrocatalysis and others. Depending on the considered context and scale, a wide variety of modeling methods can be employed, including ab initio electronic structure computations, kinetics simulations (mean field, KMC), molecular dynamics, non-adiabatic dynamics and free energy perturbations. The overarching objective of this symposium is to stimulate discussions among experts in the different fields, facilitate the transfer of computational strategies and methods from one domain to another, while underlining common concepts. This symposium will be organized around three challenges: (i) complex reaction networks (ii) towards chemical accuracy (iii) improving the models.

Structure, dynamics and reactivity at complex interfaces with relevance in renewable energy and environmental applications.

Vassiliki-Alexandra Glezakou (PNNL) and Roger Rousseau (PNNL)

The interface between a solid and a complex, multi-component liquid constitutes a unique reaction environment whose structure and composition can significantly deviate from either bulk or liquid phases. Additionally, it is poorly understood due the innate difficulty to obtain molecular level information. A large number of important chemical phenomena, relevant to catalysis (e.g. electrochemical and thermal catalysis), geochemistry and atmospheric/environmental phenomena happen at these interfaces. In all cases, critical scientific questions arise regarding what species are present at the surface proximal to the liquid boundary layer, the impact of the dynamics and structure of this layer on surface reconstruction and reactivity. Advances in computational methods have afforded us with the unique opportunity to address these issues at different length and time scales. The goal of the proposed session is to bring together world-leading computational scientists interested in these phenomena and engage them in spirited exchange of ideas, new methodological advances and forefront applications. Topics of particular interest are: ab initio molecular dynamics, enhanced sampling techniques and multi-scale approaches.

Computational Materials Chemistry

De­-en Jiang (University of California, Riverside)

Driven by the urgent need for materials discovery for renewable energy, clean environment, and biomedical applications, materials chemistry has been one of the fastest growing areas of chemical research in the past decade. Understanding structure-­property relationships is fundamental to the chemistry of materials and key to realizing materials’ functions. Advances in theoretical understanding, algorithms and computational power are enabling computational tools to play an increasing role in materials discovery, development and optimization. This symposium aims to bring together computational researchers working on focused topics of materials chemistry to exchange ideas and to stimulate discussion. Covered topics include: Structure prediction for novel materials,virtual screening, exploration of potential energy surface, advanced force fields, multiscale modeling of materials chemistry, modeling of materials for electric energy storage, and materials design for electro­ and photo­ catalysis.

Know Your Unknowns: Estimating the Reliability of Individual Activity and Property Predictions

Robert D. Clark (Simulations Plus, Inc.)

The literature devoted to evaluating the aggregate predictive performance of quantitative structure/activity (QSAR) and structure/property (QSPR) models is extensive. It is clear that not all individual predictions are equally reliable, however, and any prediction made without some attendant indication of its reliability can only be of limited use in making regulatory and drug development decisions. This symposium will deal with advances in generating quantitative estimates of how reliable QSAR and QSPR predictions for individual compounds are as well as why they are needed and how such estimates might best be used.