Publications

Publication:Journal of Computational Chemistry
Authors:Dr. Shuai Liu, Dr. Mingjun Yang et al.
Date:Nov. 13, 2019

Optimal Designs for Pairwise Calculation: an Application to Free Energy Perturbation in Minimizing Prediction Variability

J. Comput. Chem. 2019, 9999, 1–11

Pairwise‐based methods such as the free energy perturbation (FEP) method have been widely deployed to compute the binding free energy differences between two similar host–guest complexes. The calculated pairwise free energy difference is either directly adopted or transformed to absolute…

Publication:Crystal Growth Design
Authors:Dr. Yuriy Abramov, Dr. Guangxu Sun
Date:Oct. 17, 2019

Solid-form Transition Temperature Prediction from a Virtual Polymorph Screening:A Reality Check

Cryst. Growth Des. 2019, 19, 7132−7137

The focus of this study is an estimation of uncertainty of solid-form transition temperature (Ttr) prediction based on modern virtual polymorph screening calculations. That was done through error propagation, utilizing estimated uncertainties of the relative free energy predictions at 0 K as well as of finite-temperature contribution to the polymorphic relative free energy…

Publication:The Journal of Chemical Physics
Authors:Dr. M. A. Bellucci et al.
Date:March 5, 2019

Solubility of Paracetamol in Ethanol by Molecular Dynamics Using the Extended Einstein Crystal Method and Experiments

J. Chem. Phys. 150, 094107 (2019)

Li and co-workers [Li et al., J. Chem. Phys. 146, 214110 (2017)] have recently proposed a methodology to compute the solubility of molecular compounds from first principles, using molecular dynamics simulations. We revise and further explore their methodology that was originally applied to nap…

Publication:The Journal of Chemical Physics
Authors:Dr. Huimin Cheng, Dr. Dong Fang, Dr Mingjun Yang et al.
Date:Jan. 31, 2019

Enhanced QM/MM sampling for free energy calculation of chemical reactions: A case study of double proton transfer

J. Chem. Phys. 150, 044111 (2019)

Free energy calculations for chemical reactions with a steep energy barrier require well defined reaction coordinates (RCs). However, when multiple parallel channels exist along selected RC, the application of conventional enhanced samplings is difficult to generate correct sampling within li…

Publication:Catalysis Science & Technology
Authors:Dr. Mingjun Yang et al.
Date:Dec. 6, 2018

Understanding the entropic effect in chorismate mutase reaction catalyzed by isochorismate-pyruvate lyase from Pseudomonas aeruginosa (PchB)

Catal. Sci. Technol., 2019,9, 957-965

Elucidation of the role of entropy in enzymatic reactions can be utilized in the de novo design of enzymes or protein engineering. Recently, the change in entropy in the enzyme-catalyzed chorismate mutase reaction brought about uncertainty as a result of an experiment using PchB, in …

Publication:Crystal Growth Design
Authors:Dr. Peiyu Zhang et al.
Date:Nov. 18, 2018

Harnessing Cloud Architecture for Crystal Structure Prediction Calculations

Cryst. Growth Des. 2018, 18, 11, 6891-6900

Accurate and rapid crystal structure predictions have the potential to transform the development of new materials, particularly in fields with highly complex molecular structures (such as in drug development). In this work we present a novel cloud-computing crystal structure prediction (CSP) platform with the capability of scheduling hundreds of thousands CPU cores and integrating cutting-edge computational chemistry algorithms.…