News

Chemical Science, the flagship journal of the Royal Society of Chemistry, announced today that the article

“Density Matrix Renormalization Group Pair-Density Functional Theory (DMRG-PDFT): Singlet-Triplet Gaps in Polyacenes and Polyacetylenes,” P. Sharma, V. Bernales, S. Knecht, D. G. Truhlar, and L. Gagliardi, Chemical Science 10, 1716-1723 (2019). doi.org/10.1039/C8SC03569E   

has been selected for the themed collection Most Popular 2018-2019 Physical and Theoretical Chemistry Articles: 

https://pubs.rsc.org/en/journals/articlecollectionlanding?sercode=sc&themeid=02ec2dec-e7e7-4d78-8411-7afb634a771a

     The density matrix renormalization group (DMRG) [White and Martin 1999; Chan and Head-Gordon 2002; Ma, Knecht, Keller, and Reiher 2017] is a variational electronic structure method converging in principle to full configuration interaction (as one increases the bond dimension M) by using a sweep algorithm to optimize a matrix-product-state representation of the wave function. It allows one to use active spaces about six times larger than conventional CASSCF. But DMRG (like conventional CASSCF) is energetically unreliable without a post-SCF calculation of external correlation. In this paper we presented an inexpensive way to calculate dynamic correlation energy starting from a DMRG wave function by using pair-density functional theory (PDFT).

     In the Chemical Science paper, we applied this new approach, called DMRG-PDFT, to study singlet–triplet gaps in polyacenes and polyacetylenes that require active spaces larger than the feasibility limit of the conventional CASSCF method. The results matched reasonably well with the most reliable literature values, and they have only a moderate dependence on the compression of the initial DMRG wave function. Furthermore, DMRG-PDFT is significantly more affordable than other commonly applied way of adding additional correlation to DMRG, such as DMRG followed by multireference perturbation theory.

Structure of n-acenes and n-polyacetylene

(a) n-acenes, (b) n-polyacetylene

     More recently, our group has applied the DMRG-PDFT method to free-base iron porphyrin, Fe(P):

“Multiconfiguration Pair-Density Functional Theory for Iron Porphyrin with CAS, RAS, and DMRG Active Spaces,” C. Zhou, L. Gagliardi, and D. G. Truhlar, Journal of Physical Chemistry A 123, 3389-3394 (2019).  doi.org/10.1021/acs.jpca.8b12479

In this paper, we used MC-PDFT to calculate the energetic order of four states of Fe(P) with active spaces ranging from 8 active electrons in  6 active orbitals to 34 active electrons in  35 active orbitals, and the largest active space is only affordable for DMRG-PDFT. DMRG-PDFT gives the correct ground state, regardless of the selection of active space, and it provides an efficient and accurate approach to treat electron correlation in large molecules like for iron porphyrin.

     A third application of DMRG-PDFT will be published shortly:

“Magnetic Coupling in a Tris-hydroxobridged Chromium Dimer Occurs Through Ligand-Mediated Superexchange in Conjunction with Through-Space Coupling,” by P. Sharma, D. G. Truhlar, and L. Gagliardi, to be published.

     DMRG-PDFT calculations are performed with the OpenMolcas 8.3 software package using an implementation based on the QCMaquis software suite in OpenMolcas 8.3. To carry out the calculations, one has to enable the DMRG function while compiling. When one installs OpenMolcas and enables DMRG, one automatically downloads the source files and necessary libraries of QCMaquis.

 

August 5, 2020

Yinan Shu

Link to the Department of Chemistry News

We are pleased to congratulate Dr. Yinan Shu, a postdoctoral associate in our group, who has just been awarded the Robin Hochstrasser Young Investigator Award. The Robin Hochstrasser Young Investigator Award was created by Elsevier Publishing to honor Robin Hochstrasser and support young scientists; it is given each year to a scientist working in chemical physics and younger than 40 years of age who does not have permanent professorship. The winner is selected by an international committee of scientists consisting of five members of the editorial board of Chemical Physics. Professor Robin Hochstrasser was the Editor of Chemical Physics for almost four decades; he was a pioneer in the application of lasers in chemical and biomedical research and among his students was Nobel Laureate Ahmed Zewail.

Yinan Shu was born in Hangzhou, China and obtained his BS degrees in Chemistry and Biological Science from Wuhan University in 2011. In our group he has worked on density functional electronic structure theory, especially for excited electronic states, on understanding complex photochemical and photophysical processes, on nonadiabatic dynamics algorithms, and on machine learning via deep neural networks.  His Google Scholar page is

     https://scholar.google.com/citations?user=UtZEpfMAAAAJ&hl=en&oi=ao

Yinan won the ACS Physical Chemistry Division Young Investigator Award in April so this is his second major award in a very short period of time.

July 22, 2020

Yinan ShuYinan Shu, Ph.D., a post-doctoral associate working with Regents Professor Donald Truhlar, has received the American Chemical Society Division of Physical Chemistry's 2020 Young Investigator Award. He was one of four researchers selected to receive this award and will present his research at a future PHYS symposium. 

Yinan earned his bachelor's degrees in chemistry and biological science from Wuhan University in China, and his doctorate from Michigan State University. His thesis focused on, "Understanding Non-Radiative Recombination Processes of the Optoelectronic Materials from First Principles." His research work with Professor Truhlar focuses on understanding complex behaviors of molecules and materials upon excitations and employ machine learning to solve theoretical chemistry problems. 

This news article was written by Eileen Harvala for the Department of Chemistry News.

April 16 2020

We are pleased to congratulate two group alumni on new positions that they will assume starting in academic year 2020-2021.  Junwei Lucas Bao, who was a graduate student in our group from 2014 to 2018 and who is now a postdoctoral associate with Emily Carter at Princeton, has accepted a position as assistant professor in the Department of Chemistry at Boston College in Chestnut Hill, MA. Dr. Sijia Dong, who was a postdoctoral associate in our group  from 2017 to 2019 and who is now a postdoctoral associate in the group of Guilia Galli at the University of Chicago, has accepted an assistant professor position in the Department of Chemistry and Chemical Biology at Northeastern University in Boston, MA. We wish them both well, and we are confident they will excel in their new positions!

Junwei Lucas Bao

Junwei Lucas Bao

 

Sijia Dong

Sijia Dong

 

March 24, 2020

The Journal of Chemical theory and Computation has published a virtual issue honoring the work of the Truhlar group and collaborators:

https://pubs.acs.org/page/jctcce/vi/truhlar.html

The coauthors honored in this virtual issue are Ahren Jasper, Alek Marenich, Andy Luo, Antonio Fernández-Ramos, Becky Carlson, Ben Janesko, Bo Wang, Chao Zhu, Chris Cramer, Dongxia Ma, Erin (Dahlke) Speetzen, Ewa Papajak, Giovanni Li Manni, Giovanni Scalmani, Hannah Leverentz, Haoyu Yu, Jeppe Olsen, Jingjing Zheng, John Alecu, Kaining Duanmu, Ke Yang, Laura Gagliardi, Lucas Bao, Mike Frisch, Pragya Verma, Rubén Meana-Pañeda, Samuel Odoh, Shaohong L. Li, Steve Jerome, Xiao He, Xuefei Xu, Yan Zhao, and Ying Wang.

Feb. 6, 2020

Our group recently welcomed postdoctoral associate Dihua Wu and visiting student Shuhong Li to the group.  The montage photo that accompanies this news item shows all the Nankai University members and past members of the group. At the upper left is Professor Ruifang Li of Nankai University, who first entered Nankai in 1999 and who was the first Nankai University participant in the Truhlar group, starting in 2009. At the upper right is Benchen (Kevin) Huang, now a graduate student at the University of Chicago, who entered Nankai in 2015 and was in our group as a visiting student in 2018-2019. In front of the bookcase are current group members, Dihua Wu (first left, entered Nankai in 2008), Jiaxin Ning (second left, entered Nankai in 2014, now a graduate student in the group), Don Truhlar (middle), Shuhang Li (second right, entered Nankai in 2016), and Jie Bao (first right, entered Nankai in 2010, now a graduate student in the group).

Nankai Alumni

 

September 11, 2019

The Royal Society of Chemistry has informed us that three papers from our group are all in the top 5% of highly cited papers in their General chemistry portfolio of journals. The successful articles are as follows:

 

Article

Times cited in 2018

1

doi.org/10.1039/C6SC00705h 

“MN15: A Kohn-Sham Global-Hybrid Exchange-Correlation Density Functional with Broad Accuracy for Multi-Reference and Single-Reference Systems and Noncovalent Interactions,” H. S. Yu, X. He, S. L. Li, and D. G. Truhlar, Chemical Science 7, 5032-5051 (2016).

                    

59

  2

doi.org/10.1039/C7CS00602K

“Variational Transition State Theory: Theoretical Framework and Recent Developments,” J. L. Bao and D. G. Truhlar, Chemical Society Reviews 46, 7548-7596 (2017).

 

23

3

doi.org/10.1039/C6SC05036K

“Generalized-Active-Space Pair-Density Functional Theory: An Efficient Method to Study Large, Strongly Correlated, Conjugated Systems,” S. Ghosh, C. J. Cramer, D. G. Truhlar, L. Gagliardi, Chemical Science 8, 2741-2750 (2017).

                    

14

 

July 31, 2019

umIn June, our group was pleased to welcome Lyuben Borislavov from the University of Sophia in Sophia, Bulgaria, where he was recommended by Professors Alia Tadjer and Todor Dudev, and Erica Mitchell from Taylor University in Upland Indiana, where she was recommended by Professor T. Brandon Magers. Erica  worked on the multi-configuration pair-density functional theory of Diels-Alder reactions and the speedup of MC-PDFT analytic gradients, co-supervised by Professor Laura Gagliardi and also aided by Thais Scott, Jie Bao, and Matt Hermes. Lyuben worked on machine learning of molecular dynamics trajectories for the photodissociation of thioanisole, aided by Kelsey Parker and Yinan Shu. Both students presented their work at the 2019 Summer Undergraduate Research Fellowship Symposium (SURF Symposium) of CTC on August 6: The speakers were 

  Lyuben Borislavov from Sofia University (Bulgaria), Don Truhlar group 

  Janey Lin from Mount Holyoke College, Massachusetts, Laura Gagliardi group

  Maria Mikhailenko from ITMO University (Russia), Jason Goodpaster group

  Erica Mitchell from Taylor University, Indiana, groups of Gagliardi and Truhlar

  Claire Shugart from Carlton College, Minnesota, Gagliardi group

  Samuel Powell from Ohio Northern University, Gagliardi group

  Victoria Vernadskaia from ITMO University (Russia), Ilja Siepmann group

  Peiyao Wu from Emory University, Georgia, Siepmann group

After the symposium the picture at the right was taken of all the summer researchers in the CTC SURF program, along with the participating mentors and advisers.

 

August 7, 2019

Postdoctroal assoicate Jingyun Ye will begin as assistant professor of Chemistry at Clarkson University in Potsdam, New York in January 2020. Here is a list of her publications so far in the Truhlar group:

jacs1“Bridging Zirconia Nodes within a Metal–Organic Framework via Catalytic Ni-hydroxo Clusters to Form Hetero-Bimetallic Nanowires," A. E. Platero-Prats, A. B. League, V. Bernales, L C. Gallington, A. Vjunov, N. M. Schweitzer, J. Ye, J. Zheng, B. L Mehdi, Z. Li, A. J. Stevens, O. K. Farha, J. T. Hupp, N. D. Browning, D. G. Truhlar, J. L. Fulton,  J. A. Lercher, D. M. Camaioni, L. Gagliardi, C. J. Cramer, K. W. Chapman, Journal of the American Chemical Society 139, 10410-10418 (2017). 

doi.org/10.1021/jacs.7b04997

 

jcatal1“Single Ni Atoms and Ni4 Clusters Have Similar Catalytic Activity for Ethylene Dimerization,” J. Ye, L. Gagliardi, C. J Cramer, and D. G Truhlar, Journal of Catalysis 354, 278–286 (2017). 

doi.org/10.1016/j.jcat.2017.08.011

 

 

 jcatal2“Computational Screening of MOF-Supported Transition Metal Catalysts for Activity and Selectivity in Ethylene Dimerization,” J. Ye, L. Gagliardi, C. J. Cramer, and D. G. Truhlar, Journal of Catalysis 360, 160-167 (2018). 

doi.org/10.1016/j.jcat.2017.12.007

 

 

acscatal“Rationalizing the Reactivity of Bimetallic Molecular Catalysts for CO2 Hydrogenation,” J. Ye, R. C. Cammarota, J. Xie, M. V. Vollmer, D. G. Truhlar, C. J. Cramer, C. C. Lu, and L. Gagliardi, ACS Catalysis 8, 4955-4968 (2018).

 doi.org/10.1021/acscatal.8b00803

 

 

jacs2“Beyond the Active Site: Tuning the Activity and Selectivity of a Metal−Organic Framework-Supported Ni Catalyst for Ethylene Dimerization,” J. Liu, J. Ye, Z. Li, K. i. Otake, Y.  Liao, A.  Peters, H. Noh, D. G. Truhlar, L. Gagliardi, C. J. Cramer, O. Farha, and J. Hupp, Journal of the American Chemical Society 140, 11174-11178 (2018). 

doi.org/10.1021/jacs.8b06006

 

jpcc1“Organic Linker Effect on the Growth and Diffusion of Cu Clusters in a Metal-Organic Framework,” J. Ye, C. J Cramer, and D. G. Truhlar, Journal of Physical Chemistry C 122, 26987-26997 (2018).

doi.og/ 10.1021/acs.jpcc.8b09178

 

February 17, 2019

The editors of PCCP (the physical chemistry journal of the Royal Society of Chemistry) have selected the paper 

        “Extended Hamiltonian Molecular Dynamics: Semiclassical Trajectories with Improved Maintenance of Zero Point Energy,” Yinan Shu, Sijia S. Dong, Kelsey A. Parker, J. Lucas Bao, Linzao Zhang, and Don Truhlar, Physical Chemistry Chemical Physics 20, 30209-30218 (2018). doi.org/10.1039/C8CP04914A

for the  the themed collection "2018 PCCP HOT Articles”.

Classical molecular dynamics is one of the most widely employed simulation tools in physical chemistry. A long-standing problem in classical molecular dynamics simulations is the inability of classical mechanics to maintain zero point energy in the vibrational modes.  There have been many attempts to overcome this deficiency, but no practical and completely satisfactory method has emerged. This article shows how the problem can be tamed by presenting a very simple extended Hamiltonian goes a long way toward solving the problem. The paper is of broad interest because the method can be applied even to the most complex problems for which classical simulations are currently employed. 

yinan

February 6, 2019 

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