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1. G4 accuracy at DFT cost: unlocking accurate redox potentials for organic molecules using systematic error cancellation

   https://doi.org/10.1039/c9cp06622e  

   Maier, Sarah; Thapa, Bishnu; Raghavachari, Krishnan (February 2020, Physical Chemistry Chemical Physics)

   The redox potential is a powerful thermodynamic and kinetic tool used to predict numerous chemical and biochemical mechanisms. However, despite the improving predictive power of density functional theory (DFT), chemically accurate theoretical redox potentials are often difficult to achieve with DFT. For example, calculated redox potentials are sensitive to density functional choice and often fall short of the desired accuracy. Thus, ranges of errors for computed redox potentials between different density functionals can become quite large. The current study presents a cost-effective protocol that utilizes effective error cancellation schemes in order to accurately predict the redox potentials of a wide range of organic molecules. This computational protocol, called CBH-Redox, is an extension of the connectivity-based hierarchy (CBH) method, and produces thermochemical data with near-G4 accuracy. Herein, we test the CBH-Redox protocol against both experimental and G4 reference values and compare these results to DFT alone. Considering 46 C, O, N, F, Cl, and S atom-containing molecules, when using the CBH-Redox correction scheme, the MAEs for all eight density functionals tested are within the 0.09 V target accuracy versus both experiment and G4. Moreover, CBH-Redox achieves an impressive accuracy, with a MAE of 0.05 V or below when compared to G4 for six of the eight density functionals tested. In addition, when the CBH correction is applied, the error range across all functionals tested decreases from 0.12 V to about 0.05 V versus G4, and from 0.13 V to 0.04 V versus experiment. 

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2. Domain‐based local pair natural orbital methods within the correlation consistent composite approach

   https://doi.org/10.1002/jcc.26129  

   Patel, Prajay; Wilson, Angela K. (December 2019, Journal of Computational Chemistry)

   Ab initio composite approaches have been utilized to model and predict main group thermochemistry within 1 kcal mol⁻¹, on average, from well‐established reliable experiments, primarily for molecules with less than 30 atoms. For molecules of increasing size and complexity, such as biomolecular complexes, composite methodologies have been limited in their application. Therefore, the domain‐based local pair natural orbital (DLPNO) methods have been implemented within the correlation consistent composite approach (ccCA) framework, namely DLPNO‐ccCA, to reduce the computational cost (disk space, CPU (central processing unit) time, memory) and predict energetic properties such as enthalpies of formation, noncovalent interactions, and conformation energies for organic biomolecular complexes including one of the largest molecules examined via composite strategies, within 1 kcal mol⁻¹, after calibration with 119 molecules and a set of linear alkanes. © 2019 Wiley Periodicals, Inc. 

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3. Thermochemistry and mechanisms of the Pt ⁺ + SO ₂ reaction from guided ion beam tandem mass spectrometry and theory

   https://doi.org/10.1063/5.0091510  

   Armentrout, P. B. (May 2022, The Journal of Chemical Physics)

   The kinetic energy dependences of the reactions of Pt + ( 2 D 5/2 ) with SO 2 were studied using a guided ion beam tandem mass spectrometer and theory. The observed cationic products are PtO + and PtSO + , with small amounts of PtS + , all formed in endothermic reactions. Modeling the kinetic energy dependent product cross sections allows determination of the product bond dissociation energies (BDEs): D 0 (Pt + –O) = 3.14 ± 0.11 eV, D 0 (Pt + –S) = 3.68 ± 0.31 eV, and D 0 (Pt + –SO) = 3.03 ± 0.12 eV. The oxide BDE agrees well with more precise literature values, whereas the latter two results are the first such measurements. Quantum mechanical calculations were performed for PtO + , PtS + , PtO 2 + , and PtSO + at the B3LYP and coupled-cluster with single, double, and perturbative triple [CCSD(T)] levels of theory using the def2-XZVPPD (X = T, Q) and aug-cc-pVXZ (X = T, Q, 5) basis sets and complete basis set extrapolations. These theoretical BDEs agree well with the experimental values. After including empirical spin–orbit corrections, the product ground states are determined as PtO + ( 4 Σ 3/2 ), PtS + ( 4 Σ 3/2 ), PtO 2 + ( 2 Σ g + ), and PtSO + ( 2 A′). Potential energy profiles including intermediates and transition states for each reaction were also calculated at the B3LYP/def2-TZVPPD level. Periodic trends in the thermochemistry of the group 9 metal chalcogenide cations are compared, and the formation of PtO + from the Pt + + SO 2 reaction is compared with those from the Pt + + O 2 , CO 2 , CO, and NO reactions. 

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4. Long G4-rich enhancers target promoters via a G4 DNA-based mechanism

   https://doi.org/10.1093/nar/gkae1180  

   DeMeis, Jeffrey D.; Roberts, Justin T.; Delcher, Haley A.; Godang, Noel L.; Coley, Alexander B.; Brown, Cana L.; Shaw, Michael H.; Naaz, Sayema; Dahal, Ayush; Alqudah, Shahem Y.; et al (December 2024, Nucleic Acids Research)

   Abstract Several studies have now described instances where G-rich sequences in promoters and enhancers regulate gene expression through forming G-quadruplex (G4) structures. Relatedly, our group recently identified 301 long genomic stretches significantly enriched for minimal G4 motifs (LG4s) in humans and found the majority of these overlap annotated enhancers, and furthermore, that the promoters regulated by these LG4 enhancers are similarly enriched with G4-capable sequences. While the generally accepted model for enhancer:promoter specificity maintains that interactions are dictated by enhancer- and promoter-bound transcriptional activator proteins, the current study tested an alternative hypothesis: that LG4 enhancers interact with cognate promoters via a direct G4:G4 DNA-based mechanism. This work establishes the nuclear proximity of LG4 enhancer:promoter pairs, biochemically demonstrates the ability of individual LG4 single-stranded DNAs (ssDNAs) to directly interact target promoter ssDNAs, and confirms that these interactions, as well as the ability of LG4 enhancers to activate target promoters in culture, are mediated by G4 DNA. 

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5. “Anti-electrostatic” halogen bonding in solution

   https://doi.org/10.1039/d1sc01863a  

   Loy, Cody; Holthoff, Jana M.; Weiss, Robert; Huber, Stefan M.; Rosokha, Sergiy V. (June 2021, Chemical Science)

   null (Ed.)

   Halogen-bonded (XB) complexes between halide anions and a cyclopropenylium-based anionic XB donor were characterized in solution for the first time. Spontaneous formation of such complexes confirms that halogen bonding is sufficiently strong to overcome electrostatic repulsion between two anions. The formation constants of such “anti-electrostatic” associations are comparable to those formed by halides with neutral halogenated electrophiles. However, while the latter usually show charge-transfer absorption bands, the UV-Vis spectra of the anion–anion complexes examined herein are determined by the electronic excitations within the XB donor. The identification of XB anion–anion complexes substantially extends the range of the feasible XB systems, and it provides vital information for the discussion of the nature of this interaction. 

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