Chemistry¶

2024¶
	Title	Authors/Co-Authors
1	Ionic Covalent Organic Framework as a Dual Functional Sensor for Temperature and Humidity	Serdal Kirmizialtin
2	Unveiling the topology of partially disordered micro-crystalline nitro-perylenediimide with X-aggregate stacking: an integrated approach	Brijith Thomas

2023¶
	Title	Authors/Co-Authors
1	Light-driven self-assembly of spiropyran-functionalized covalent organic framework	Serdal Kirmizialtin
2	A primer to polarizing agent design: Quantum mechanical understanding of cross effect magic-angle spinning Dynamic Nuclear Polarization	Asif Equbal
3	An exploration of machine learning models for the determination of reaction coordinates associated with conformational transitions	Serdal Kirmizialtin
4	Dynamic Nuclear Polarization-Enabled Quantum Sensing for Investigating Peptide Configurations	Asif Equbal
5	Direct Sensing of Remote Nuclei: Expanding the Reach of Cross-Effect Dynamic Nuclear Polarization	Asif Equbal
6	Atomistic structure of the SARS-CoV-2 pseudoknot in solution from SAXS-driven molecular dynamics	Serdal Kirmizialtin
7	Nucleic Acid Structure and Interactions Revealed by Computer Simulations	Weiwei He

2022¶
	Title	Authors/Co-Authors
1	Substrate specificity and proposed structure of the proofreading complex of T7 DNA polymerase	Serdal Kirmizialtin
2	Visualizing RNA Structures by SAXS-Driven MD Simulations	Serdal Kirmizialtin
3	Insights into the structural stability of major groove RNA triplexes by WAXS-guided MD simulations Author links open overlay panel	Serdal Kirmizialtin
4	Complete resonance assignment of a pharmaceutical drug at natural isotopic abundance from DNP-Enhanced solid-state NMR	Lydia Gkoura
5	Refining the RNA Force Field with Small-Angle X-ray Scattering of Helix–Junction–Helix RNA	Serdal Kirmizialtin
6	Covalent Organic Framework Based on Azacalix [4] arene for the Efficient Capture of Dialysis Waste Products	Nawavi Naleem
7	Differences in ion-RNA binding modes due to charge density variations explain the stability of RNA in monovalent salts	Serdal Kirmizialtin

2021¶
	Title	Authors/Co-Authors
1	Taming the Topology of Calix[4]arene-Based 2D-Covalent Organic Frameworks: Interpenetrated vs Noninterpenetrated Frameworks and Their Selective Removal of Cationic Dyes	Serdal Kirmizialtin
2	Bridging Theories and Experiments: Modeling Solution X-Ray Scattering of Small RNA Molecules	Yen-Lin Chen
3	The structural plasticity of nucleic acid duplexes revealed by WAXS and MD	Serdal Kirmizialtin
4	Conformational dynamics during misincorporation and mismatch extension defined using a DNA polymerase with a fluorescent artificial amino acid	Serdal Kirmizialtin

2020¶
	Title	Authors/Co-Authors
1	Identifying Aspirin Polymorphs from Combined DFT‐Based Crystal Structure Prediction and Solid‐State NMR	Maria Baias
2	Designed cell-penetrating peptide inhibitors of amyloid-beta aggregation and cytotoxicity	Serdal Kirmizialtin
3	Structure-guided DNA-DNA attraction mediated by divalent cations	Serdal Kirmizialtin
4	From Mechanical Effects to Mechanochemistry: Softening and Depression of the Melting Point of Deformed Plastic Crystals	Pance Naumov
5	Loss of 𝜷-Actin Leads to Accelerated Mineralization and Dysregulation of Osteoblast-Differentiation Genes during Osteogenic Reprogramming	Pance Naumov
6	Exploring Cation Mediated DNA Interactions Using Computer Simulations	Serdal Kirmizialtin
7	Rapid and Efficient Removal of Perfluorooctanoic Acid from Water with Fluorine-Rich Calixarene-Based Porous Polymers	Serdal Kirmizialtin
8	Kinetic and thermodynamic analysis defines roles for two metal ions in DNA polymerase nucleotide specificity and catalysis	Serdal Kirmizialtin
9	Dramatic shape changes occur as Cytochrome c folds	Serdal Kirmizialtin

2019¶
	Title	Authors/Co-Authors
1	Thermochemiluminescent peroxide crystals	Panče Naumov
2	A polyrotaxanated covalent organic network based on viologen and cucurbit [7] uril	Serdal Kirmizialtin
3	Reversible Multicolor Photochromism of Dihydroazulene Crystals	Panče Naumov
4	Cryo_fit: Democratization of flexible fitting for cryo-EM	Serdal Kirmizialtin

2018¶
	Title	Authors/Co-Authors
1	Redox‐Responsive Covalent Organic Nanosheets from Viologens and Calix [4] arene for Iodine and Toxic Dye Capture	Serdal Kirmizialtin
2	The catalytic inactivation of the N-half of human hexokinase 2 and structural and biochemical characterization of its mitochondrial conformation	Wael M. Rabeh
3	Calix[4]arene-based Porous Organic Nanosheets	Serdal Kirmizialtin
4	Revealing the distinct folding phases of an RNA three-helix junction	Serdal Kirmizialtin
5	Comparative Computational Approach To Study Enzyme Reactions Using QM and QM-MM Methods	Serdal Kirmizialtin

Pre 2018¶
	Title	Authors/Co-Authors
1	A DFT-based mechanistic study on the formation of oximes	Serdal Kirmizialtin
2	Pushing to the low limits: tetraa zaanthracenes with very low-lying LUMO levels and near-infrared absorption	Panče Naumov
3	Probing Structural Perturbation in a Bent Molecular Crystal with Synchrotron Infrared Microspectroscopy and Periodic Density Functional Theory Calculations	Panče Naumov
4	Computational insight into the interaction of methylated lysine A with aromatic amino acid cages	Ibrahim Yildiz
5	A Chemicas Template for Synthesis of Molecular Sheets of Calcium Carbonate	Serdal Kirmizialtin
6	A DFT Approach to the Mechanistic Study of Hydrozone Hydrolysis	Ibrahim Yildiz
7	Vibrational Spectra of Chemical and Isotopic Variants of Oxyluciferin, the Light Emitter of Firefly Bioluminescence	Panče Naumov
8	Colossal positive and negative thermal expansion and thermosalient effect in a pentamorphic organometallic martensite	Panče Naumov
9	Efficient Calculation of Free Energy Differers Associated with Isotopic Substitution Using Path-Integral Molecular Dynamics	Mark E Teckerman
10	Dynamic Void Distribution in Myoglobin and five Mutants	Serdal Kirmizialtin
11	Integrating Molecular Dynamics Simulations with Chemical Probing Experiments Using SHAPE-FIT	Serdal Kirmizialtin
12	Using Molecular Simulation to Model High-Resolution Cryo-EM Reconstructions	Serdal Kirmizialtin
13	The In Vitro Selection World	Serdal Kirmizialtin
14	Nanoscale Biological Materials	Serdal Kirmizialtin
15	A Chemical Template for Synthesis of Molecular Sheets of Calcium Carbonate	Serdal Kirmizialtin
16	Tracking fluctuation hotspots on the yeast ribosome through the elongation cycle	Serdal Kirmizialtin
17	Enzyme Selectivity of HIV Reverse Transcriptase: Conformations, Ligands, and Free Energy Partition	Serdal Kirmizialtin