Direct approximation of the long- and short-range components of the exchange-correlation Kohn-Sham potential

An approximation scheme was developed for the Kohn-Sham exchange-correlation potential v_xcσ, making use of a partitioning of v_xcσ into a long-range screening v_scrσ and a short-range response v_resp component. For the response part, a model v^mod_respσ was used, which represents v_resp as weighted orbital density contributions, the weights being determined by the orbital energies. v^mod_respσ possesses the proper short-range behavior and the atomic-shell stepped structure characteristic for v_resp. For the screening part, two model potentials v^mod_scrσ were used, one with the accurate Slater potential; the other one with the generalized gradient approximation (GGA) for the exchange part. Both use the GGA for the Coulomb correlation contribution to v_scrσ. The scheme provides an adequate approximation to v_xcσ in the outer-valence region with both the proper asymptotics and a rather accurate estimate of the ionization potential from the highest one-electron energy and a reasonable estimate of atomic E_xc and total energies E_tot. © 1997 John Wiley & Sons, Inc.     

Atmospheric chemistry of di-tert-butyl ether: Rates and products of the reactions with chlorine atoms,hydroxyl radicals,and nitrate radicals

The rate constants for the gas-phase reactions of di-tert-butyl ether (DTBE) with chlorine atoms, hydroxyl radicals, and nitrate radicals have been determined in relative rate experiments using FTIR spectroscopy. Values of k_(DTBE+CI) = (1.4 ± 0.2) × 10⁻¹⁰,k_(DTBE+OH) = (3.7 ± 0.7) × 10⁻¹², and k_(DTBE+N03) = (2.8 ± 0.9) × 10⁻¹⁶ cm³ molecule⁻¹ s⁻¹ were obtained. Tert-butyl acetate was identified as the major product of both Cl atom and OH radical initiated oxidation of DTBE in air in the presence of NO_x. The molar tert-butyl acetate yield was 0.85 ± 0.11 in the Cl atom experiments and 0.84 ± 0.11 in OH radical experiments. As part of this work the rate constant for reaction of Cl atoms with tert-butyl acetate at 295 K was determined to be (1.6 ± 0.3) × 10⁻¹¹ cm³ molecule⁻¹ s⁻¹. The stated errors are two standard deviations (2σ). © 1996 John Wiley & Sons, Inc.     

Structure of the optimized effective Kohn—Sham exchange potential and its gradient approximations

An analysis of the structure of the optimized effective Kohn-Sham exchange potential v_x and its gradient approximations is presented. The potential is decomposed into the Slater potential v_s and the response of v_s to density variations, v_resp. The latter exhibits peaks that reflect the atomic shell structure. Kohn—Sham exchange potentials derived from current gradient approaches for the exchange energy are shown to be quite reasonable for the Slater potential, but they fail to approximate the response part, which leads to poor overall potentials. Improved potentials are constructed by a direct fit of v_x with a gradient-dependent Padé approximant form. The potentials obtained possess proper asymptotic and scaling properties and reproduce the shell structure of the exact v_x. © 1996 John Wiley & Sons, Inc.     

Hydrogen bonding in mimics of Watson-Crick base pairs involving C-H proton donor and F proton acceptor groups: a theoretical study.

We have theoretically analyzed mimics of Watson-Crick adenine-thymine (AT) and guanine-cytosine (GC) base pairs in which N-H...O and N...H-N hydrogen bonds are replaced by N-H...F and N...H-C, respectively, by using the generalized gradient approximation of density functional theory at BP86/TZ2P. The general effect of the above substitutions is an elongation and weakening of the hydrogen bonds that hold together the base pairs. However, the precise effects depend on how many and, in particular, on which hydrogen bonds are substituted in AT and GC. Another purpose of this work is to clarify the relative importance of electrostatic attraction versus orbital interaction in the weak hydrogen bonds involved in the mimics, by using a quantitative bond-energy decomposition scheme. At variance with widespread believe, the orbital interaction component in these weak hydrogen bonds is found to contribute 34-42% of the attractive interactions and is thus of the same order of magnitude as the electrostatic component, which provides the remaining attraction component.     

Precisely Tailoring Upconversion Dynamics via Energy Migration in Core–Shell Nanostructures

Upconversion emission dynamics have long been believed to be determined by the activator and its interaction with neighboring sensitizers. Herein this assumption is, however, shown to be invalid for nanostructures. We demonstrate that excitation energy migration greatly affects upconversion emission dynamics. “Dopant ions’ spatial separation” nanostructures are designed as model systems and the intimate link between the random nature of energy migration and upconversion emission time behavior is unraveled by theoretical modelling and confirmed spectroscopically. Based on this new fundamental insight, we have successfully realized fine control of upconversion emission time behavior (either rise or decay process) by tuning the energy migration paths in various specifically designed nanostructures. This result is significant for applications of this type of materials in super resolution spectroscopy, high‐density data storage, anti‐counterfeiting, and biological imaging.     

Chemical Proteomic Discovery of Isotype-Selective Covalent Inhibitors of the RNA Methyltransferase NSUN2

5-Methylcytosine (m⁵C) is an RNA modification prevalent on tRNAs, where it can protect tRNAs from endonucleolytic cleavage to maintain protein synthesis. The NSUN family (NSUN1-7 in humans) of RNA methyltransferases are capable of installing the methyl group onto the C⁵ position of cytosines in RNA. NSUNs are implicated in a wide range of (patho)physiological processes, but selective and cell-active inhibitors of these enzymes are lacking. Here, we use cysteine-directed activity-based protein profiling (ABPP) to discover azetidine acrylamides that act as stereoselective covalent inhibitors of human NSUN2. Despite targeting a conserved catalytic cysteine in the NSUN family, the NSUN2 inhibitors show negligible cross-reactivity with other human NSUNs and exhibit good proteome-wide selectivity. We verify that the azetidine acrylamides inhibit the catalytic activity of recombinant NSUN2, but not NSUN6, and demonstrate that these compounds stereoselectively disrupt NSUN2-tRNA interactions in cancer cells, leading to a global reduction in tRNA m⁵C content. Our findings thus highlight the potential to create isotype-selective and cell-active inhibitors of NSUN2 with covalent chemistry targeting a conserved catalytic cysteine.     

A new mechanism for methane production from methyl-coenzyme M reductase as derived from density functional calculations

We propose a new DFT-based mechanism for methane production using the full F430 cofactor of MCR (methyl-coenzyme M reductase) along with a coordinated O=CH2CH2C(H)NH2C(H)O (surrogate for glutamine) as a model of the active site for conversion of CH3SCoM(-) (CH3SCH2CH2SO3(-)) + HSCoB to methane plus the corresponding heterodisulfide. The cycle begins with the protonation of F430, either on Ni or on the C-ring nitrogen of the tetrapyrrole ring, both of which are nearly equally favorable. The C-ring protonated form is predicted to oxidatively add CH3SCoM(-) to give a 4-coordinate Ni center where the Ni moves out of the plane of the four ring nitrogens. The movement of Ni (and the attached CH3 and SCH2CH2SO3(2-) ligands) toward the SCoB(-) (deprotonated HSCoB) cofactor allows a 2c-3e interaction to form between the two sulfur atoms. The release of the heterodisulfide yields a Ni(III) center with a methyl group attached. The concerted elimination of methane, where the methyl group coordinated to Ni abstracts the proton from the C-ring nitrogen, has a very small calculated activation barrier (5.4 kcal/mol). The NPA charge on Ni for the various reaction steps indicates that the oxidation state changes occur largely on the attached ligands.     

Solvation of p-coumaric acid in water

The photoactive yellow protein (PYP) is an important model protein for many (photoactive) signaling proteins. Key steps in the PYP photocycle are the isomerization and protonation of its chromophore, p-coumaric acid (pCA). In the ground state of the protein, this chromophore is in the trans configuration with its phenolic oxygen deprotonated. For this paper, we studied four different configurations of pCA solvated in water with ab initio molecular dynamics simulations as implemented in CP2K/Quickstep. We researched the influence of the protonation and isomerization state of pCA on its hydrogen-bonding properties and on the Mulliken charges of the atoms in the simulation. The chromophore isomerization state influenced the hydrogen-bonding less than its protonation state. In general, more charge yielded a higher hydrogen-bond coordination number. Where deprotonation increases both the coordination number and the residence time of the water molecules around the chromophore, protonation showed a somewhat lower coordination number on two of the three pCA oxygens but much higher residence times on all of them. This could be explained by the increased polarization of the OH groups of the molecule. The presence of the chromophore also influenced the charge and polarization of the water molecules around it. This effect was different in the four systems studied and mainly localized in the first solvation shell. We also performed a proton-transfer reaction from hydronium through various other water molecules to the chromophore. In this small charge-separated system, the protonation occurred within 6.5 ps. We identified the transition state for the final step in this protonation series.