Computation

Ligands with Pi Acceptor Character and Resonance Stabilize the Fe-ONS- Bond

cnguye18 CURE Projects, Spring 2021 , , ,

This poster displays the five ligands we examined in our experiment ranked in order of how well they stabilized an (SNO)- ligand, and a summary of our main findings.

Class: CHEM 0500 – Inorganic Chemistry Lab

Instructor(s): Dr. Eric Victor

Student(s): Rebecca Kim ’23, Emma Hansen, Fasika Petros, Oren Lederberg, Shawn Avidan (Chemistry ’22)

Description:

Our objective was to find a ligand that best stabilized an (SNO)- ligand coordinated to an iron center upon computational modeling. Computational optimizations included those for geometry, vibrational spectroscopy, UV-Visible spectroscopy, and molecular orbitals.

Using Fe-O bond length as a proxy to track stability, we discovered that a ligand with a 1) high degree of aromaticity and 2) pi-accepting character was best for stabilizing (SNO)-.

“CURE has increased my confidence about participating in research at Brown.”

-Student

I hadn’t really heard about CURE until taking this class. I appreciate the way CURE challenged me and I think CURE has increased my confidence about participating in research at Brown. It was a different experience from the typical lab portions of the class. I think there are advantages and disadvantages, it was unique and interesting and taught team building.

Binding of SNO- Ligand to High Spin Fe2+ Metal Complexes

cnguye18 CURE Projects, Spring 2021 , , ,
Project Poster
This poster examines the binding of the SNOˉ ligand to high spin Fe2+ metal complexes. We examined the SOMOS, trends, and IR and UV-vis spectra that resulted from each of the ligands that were investigated.

Class: CHEM 0500 – Inorganic Chemistry Lab

Instructor(s): Dr. Eric Victor

Student(s): Ahjeetha Shankar (Neuroscience and Hispanic Literatures & Culture, ‘22) Shakson Isaac, Harrison Judd, Jonah Boardman

Description:

Our project worked to address the question of how the transition metal and the ligand environment influence the reactivity with SNOˉ. We used computational modeling to understand the electronic structure of various metal complexes and then explore their binding to SNOˉ. We examined the SOMOS, trends, and IR and UV-vis spectra that resulted from each of the ligands that were investigated.

“The CURE course has definitely strengthened our abilities as researchers, making us excited to continue conducting research in the future.”

-Student

Having CHEM 0500 be a CURE course has allowed us to engage in authentic chemistry research and learn more about various computational techniques. Despite the pandemic, we have enjoyed virtually collaborating with each other and sharing our findings in order to discover some really interesting trends and conclusions. Moreover, we have been able to hone our skills in communicating scientific research through presenting our work at weekly virtual lab meetings, writing lab reports, and creating research posters. The CURE course has definitely strengthened our abilities as researchers, making us excited to continue conducting research in the future.

A Proposed Ligand to Increase the Binding of SNO- in an Iron (II) Complex

cnguye18 CURE Projects, Spring 2021 , , ,
CHEM 500L CURE Poster - Logan Chin
A brief infographic that conveys the project we worked on this semester, written in an approachable style.

Class: CHEM 0500 – Inorganic Chemistry Lab

Instructor(s): Dr. Eric Victor

Student(s): Logan Chin (Biochemistry and Molecular Biology, ’23), Matthew Shinkar, Noah Feng, Casey Chan

“This CURE has been special because of the unique accessibility, as this lab was done completely remotely, using computers and math in order to simulate chemistry.”

-Logan Chin

Description:

Our project investigated how we could enhance the binding of a ligand, SNO-, through its sulfur to an iron ion through other ligands bound to the ion. We used Brown’s supercomputer cluster, OSCAR, to do computational chemistry to see how various ligands affected the SNO- binding, and then we took all the best parts of each ligand that we “made” and combined them into one.

This CURE has been special because of the unique accessibility, as when one thinks about a chemistry lab, it’s usually wet lab chemistry where the contents of various beakers are mixed together- however, this lab was done completely remotely, using computers and math in order to simulate chemistry.

Computational modelling of SNO- binding Iron(II) Complexes

cnguye18 CURE Projects, Spring 2021 , , ,

Project Poster

Class: CHEM 0500 – Inorganic Chemistry Lab

Instructor(s): Dr. Eric Victor

Student(s): Masha Glik (Biochemistry and Molecular Biology ‘21.5), Dominic Covelli, Janavi Sethurathnam, Jolie Ren, Amit Chakrabarti

“Research at Brown is a very accessible and exciting opportunity that students should definitely participate in.”

-Masha Glik

Description:

In order to advance our understanding of the transport of H2S and NO gasotransmitters, novel benzothiazole iron(II) complexes conjugated to SNO- were developed utilizing computational methods. The structural, electronic, and spectral characteristics of these molecules were analyzed. We found that complexes differ by the benzothiazole ligand which affects the bond strength, bond angle, and energetic properties of the SNO- ligand.

We had heard about CURE from Prof. Eric Victor, who has been very supportive, provided a lot of guidance at every stage, making our research experience very fun. Research at Brown is a very accessible and exciting opportunity that students should definitely participate in.

How Can We Computationally Characterize the Properties of and Compare/Contrast a Ruthenium Complex with H, Cl, Br, and I Substituted Ligands?

jpark189 CURE Projects, Spring 2020 , , , ,

 

Class: CHEM 0500 – Inorganic Chemistry

Instructor(s): Dr. Eric Victor

Student(s): Vivian Dong (Biochemistry & Molecular Biology, ’21), Charles Bui, Eashan Das, Javier Syquia

Description: 

We wanted to computationally characterize the electronic and molecular properties of different halide-substituted ligands.

Differential Gene Expression of Stressed and Unstressed Cultivars of Solanum lycopersicum

jpark189 CURE Projects, Spring 2020 , , ,

Class: BIOL 0440 – Inquiry in Plant Biology: Analysis of Plant Growth, Reproduction and Adaptive Responses

Instructor(s): Dr. Alison DeLong, Dr. Mark A Johnson

Student(s): Thomas Murphy, Paige Lind, Ryan Chaffee

Affiliated Faculty and Collaborators: Ann Loraine (UNC-Charlotte), Kelly Pan, Sorel Ouonkap Yimga

“We learned that genes could themselves be different while doing the same thing, and example of convergent evolution.”

-Student 

Description: 

What do the patterns of differential gene expression between heat unstressed and stressed conditions for thermosensitive and thermotolerant cultivars of Solanum lycopersicum reveal about their heat stress responses? Using R code developed by thermotolerance Ann Loraine and with help from other collaborator, a list was generated of genes demonstrating significant differential expression between the control and heat stress groups for each cultivar. There is a high degree of overlap between the Malintka and Tamaulipas cultivars and less overlap for the Nagcarlang group with either of the other thermotolerant cultivars. Transport regulation, protein refolding, and potentially transcription are aspects of Nagcarlang’s unique response to heat stress. “Unique” in this context does not necessarily refer to the molecular mechanisms as being chemically dissimilar, but rather, that the expressed loci employed to produce these responses are different from Malintka and Tamaulipas.

Formation of Ru Metal Complexes From (-)-1,2-Bis{(s)-4-isopropyl-4,5-dihydro-oxazol-2-yl]benzene ligand varieties: A Computational Approach

jpark189 CURE Projects, Spring 2020 , , , ,

Class: CHEM 0500 – Inorganic Chemistry 

Instructor(s): Dr. Eric Victor

Student(s): Keerthi Sreenivasan (Chemistry ’21), Sophia Zheng, Laura Perlmutter, Allison Lin, Veronica Gordon

“This poster includes generated data calculations and analysis of the notable properties of the ligands as they change after bonding to the Ru metal center.”

–Keerthi Sreenivasan

Description: 

Based on an existing protocol for synthesizing 2,6-bis[(S)-isopropyl-4,5-dihydro-oxazol-2-yl]- thiobenzene by Peer et. al, we tested a novel microwave synthesis protocol aimed at shortening the 3-5 day synthesis time. After two rounds of testing microwave synthesis, characterization of the product using GC-MS was inconclusive, and future refinement of the microwave synthesis protocol is necessary. Due to the transition to remote work, we then moved to computational work on the ligand and two modified versions. Calculations were performed to determine structural parameters of the ligands, simulations of spectroscopy and orbital images. A second round of calculations was done while binding the ligands in a tridentate fashion to a ruthenium metal complex. Reactive nitrogen oxide species have been shown to play a significant role in biological processes, and various metal complexes show reactivity with SNO and SSNO anions. In this CURE project, we were able to learn how to perform novel synthetic methods for a ruthenium complex using published ligands and characterize them using computational software.

Remote-Learning Ruthenium (II) Complexes

jpark189 CURE Projects, Spring 2020 , , , ,

 

Class: CHEM 0500 – Inorganic Chemistry 

Instructor(s): Dr. Eric Victor 

Student(s): Jon Mallen (Biophysics Sc.B. ’22), Yolanda Candler, Myung Joo Lee, Nicholas Moreno, Vivian Yuen

”My opinion about research at Brown has only been improved. Learning about bacteriophages in my first year and discovering my own, and now taking part in the Inorganic Chemistry CURE last semester, has confirmed my affinity for laboratory research, and also allowed me to better pinpoint my interests, skills, and weaknesses.”

–John Mallen

Description: 

We computationally developed, optimized, and extracted energetic and physical parameters for the structures of eight novel benzothiazole alkimazole ruthenium (II) complexes through the Avogadro and ORCA software packages. Four complexes employed a benzothiazole methimazole ligand that was bound to the ruthenium (II) with either syn or anti sulfur-sulfur coordination in either the fac or mer geometry, and the other four employed a benzothiazole isopropimazole with the same syn/anti and fac/mer variation as its methimazole counterpart. There is no clear preference for coordination site and geometry among the different methimazole and isopropimazole in each of their four comparitive structures. However, the small difference in alkyl side-chain between the methimazole and isopropimazole has a significant effect on the resulting energetics of the involved complexes, with the isopropimazole variants uniformly more lower in energy than the methimazole complexes. This is evidence of greater trends in the complexation of ruthenium (II) with benzothiazole alkimazole ligands and is thus a part of the empirical data that will contribute to the future design of chemical routes employing this class of molecules.