Characterizing the protonation states of the catalytic residues in apo and substrate-bound human T-cell leukemia virus type 1 protease

Human T-cell leukemia virus type 1 (HTLV-1) protease is an attractive target when developing inhibitors to treat HTLV-1 associated diseases. To study the catalytic mechanism and design novel HTLV-1 protease inhibitors, the protonation states of the two catalytic aspartic acid residues must be determined. Free energy simulations have been conducted to study the proton transfer reaction between the catalytic residues of HTLV-1 protease using a combined quantum mechanical and molecular mechanical (QM/MM) molecular dynamics simulation. The free energy profiles for the reaction in the apo-enzyme and in an enzyme – substrate complex have been obtained. In the apo-enzyme, the two catalytic residues are chemically equivalent and are expected to be both unprotonated. Upon substrate binding, the catalytic residues of HTLV-1 protease evolve to a singly protonated state, in which the OD1 of Asp32 is protonated and forms a hydrogen bond with the OD1 of Asp32′, which is unprotonated. The HTLV-1 protease–substrate complex structure obtained from this simulation can serve as the Michaelis complex structure for further mechanistic studies of HTLV-1 protease while providing a receptor structure with the correct protonation states for the active site residues toward the design of novel HTLV-1 protease inhibitors through virtual screening.     

Multiple Reaction Pathways Operating in the Mechanism of Vinylogous Mannich‐Type Reaction Activated by a Water Molecule

A systematic search for reaction pathways for the vinylogous Mannich‐type reaction was performed by the artificial force induced reaction method. This reaction affords δ‐amino‐γ‐butenolide in one pot by mixing 2‐trimethylsiloxyfuran, imine, and water under solvent‐free conditions. Surprisingly, the search identified as many as five working pathways. Among them, two concertedly produce anti and syn isomers of the product. Another two give an intermediate, which is a regioisomer of the main product. This intermediate can undergo a retro‐Mannich reaction to give a pair of intermediates: an imine and 2‐furanol. The remaining pathway directly generates this intermediate pair. The imine and 2‐furanol easily react with each other to afford the product. Thus, all of these stepwise pathways finally converge to give the main product. The rate‐determining step of all five (two concerted and three stepwise) pathways have a common mechanism: concerted Si? O bond formation through the nucleophilic attack of a water molecule on the silicon atom followed by proton transfer from the water molecule to the imine. Therefore, these five pathways have comparable barriers and compete with each other.     

Contribution of Cytosine‐Containing Cyclobutane Dimers to DNA Damage Produced by Photosensitized Triplet–Triplet Energy Transfer

Mutagenic cyclobutane pyrimidine dimers (CPDs) can be induced in DNA through either direct excitation or photosensitized triplet–triplet energy transfer (TTET). In the latter pathway, thymines are expected to receive the excitation energy from the photosensitizer and react with adjacent pyrimidines. By using state‐of‐the art analytical tools, we provide herein additional information on the formation of cytosine‐containing CPDs. We thus determined the yield of all possible CPDs upon TTET in a series of natural DNAs with various base compositions. We show that the distribution of CPDs cannot be explained only by excitation of individual thymines. We propose that the mechanism for TTET involves at least dinucleotides as the minimal targets. The observation of the formation of cytosine–cytosine CPDs also suggests that additional pathways are involved in this photosensitized reaction.     

Ionization thresholds and positions of avoided crossing of potassium Stark Rydberg states: a Stark-adapted quantum defect orbital treatment

We have calculated the positions of the avoided level crossings between (n+2)s, np states and nd, k Stark states in the Rydberg Stark states of the potassium atom with principal quantum number n comprised between 12 and 17. We have also studied the adiabatic electric field ionization thresholds for the above Rydberg states. Both the ionization thresholds and the positions of avoided crossings have been calculated using the recently developed Stark-adapted quantum defect orbital (SQDO) formalism. The presently reported values appear to be in very good agreement with the available theoretical and experimental data.     

An Energy Interconversion Principle Applied in Reaction dynamics for the determination of equilibrium standard states

Chemical and other reaction theories involving thermodynamical equilibrium states utilize statistical mechanical equilibrium density distributions. Here, a definition of heat-work transformation termed thermo-mechanical coherence is first made, and it is conjectured that most molecular bonds have the above heat-work transformation property, which models a chemical bond as a “centrifugal heat engine”, where the internal energy state need not correspond to any of the standard equilibrium densities. Expressions are derived for the standard Gibbs free energy, enthalpy, and entropy where the bond coordinates need not conform to a non-degenerate Boltzmann state, since bond breakdown and formation are processes that have direction, whereas equilibrium distributions are derived when the Hamiltonian is of fixed form, which is not the case for chemical reactions using localized Hamiltonians. The empirically determined Gibbs free energy from a known molecular dynamics simulation of a dimer reaction , accords rather well with the theoretical estimate. A relation connecting the rate of reaction with the equilibrium constant and other kinetic parameters is derived and could place the commonly observed linear relationship between the logarithms of the rate constant and equilibrium constant on a firmer theoretical footing. These relationships could include analogues of the Hammett correlations used extensively in physical organic chemistry, as well as others which are temperature dependent. One prediction of the principles developed here is that the equilibrium standard reaction free energy is more dependent on the height of the intermolecular potential than its depth, so that the sign of the ΔG ^θ can change for varying barrier height with fixed well depth, which may appear counter-intuitive. All the above developments can be tested directly in simulations and therefore provides a fertile ground for further research with significant implications on how standard states are determined in relation to the direction of chemical reaction.This work treats the molecular bond using standard thermodynamics as if it were a system, and it is anticipated that with the advent of single-molecule science and experiment, that might be one direction in which molecular statistical thermodynamics would develop.     

Theoretical study on the spectroscopic properties and electronic structures of heteroleptic phosphorescent Ir(III) complexes

The geometries, spectroscopic and electronic structures properties of a series of heteroleptic phosphorescent Ir(III) complexes including N981, N982, N983, N984 have been characterized by density functional theory calculations. The excited‐state properties of the Ir(III) complexes have been characterized by CIS method. The ground‐ and excited‐state geometries were optimized at the B3LYP/LANL2DZ and CIS/LANL2DZ levels, respectively. By using the time‐dependent density functional theory method, the absorption and phosphorescence spectra were calculated based on the optimized ground‐ and excited‐state geometries, respectively. The results show that the absorption and emission data agree well with the corresponding experimental results. The calculated results also revealed that the nature of the substituent at the 4‐position of the pyridyl moiety can influence the distributions of HOMO and LUMO and their energies. In addition, the charge transport quality has been estimated approximately by the calculated reorganization energy (λ). Our result also indicates that the positions of the substitute groups not only change the transition characters but also affect the charge transfer rate and balance, and complex N982 is a very good charge transfer material for green OLEDs. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Theoretical studies on structures and electronic spectra of linear carbon chains C2nH+ (n = 1−5)

The density functional theory (DFT) and the complete active space self‐consistent‐field (CASSCF) method have been used for full geometry optimization of carbon chains C_2nH⁺ (n = 1–5) in their ground states and selected excited states, respectively. Calculations show that C_2nH⁺ (n = 1–5) have stable linear structures with the ground state of X³Π for C₂H⁺ or X³Σ^? for other species. The excited‐state properties of C_2nH⁺ have been investigated by the multiconfigurational second‐order perturbation theory (CASPT2), and predicted vertical excitation energies show good agreement with the available experimental values. On the basis of our calculations, the unsolved observed bands in previous experiments have been interpreted. CASSCF/CASPT2 calculations also have been used to explore the vertical emission energy of selected low‐lying states in C_2nH⁺ (n = 1–5). Present results indicate that the predicted vertical excitation and emission energies of C_2nH⁺ have similar size dependences, and they gradually decrease as the chain size increases. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009