Dynamics of 5R-Tg Base Flipping in DNA Duplexes Based on Simulations─Agreement with Experiments and Beyond.

Damaged or mismatched DNA bases are normally thought to be able to flip out of the helical stack, providing enzymes with access to the faulty genetic information otherwise hidden inside the helix. Thymine glycol (Tg) is one of the most common products of nucleic acid damage. However, the static and dynamic structures of DNA duplexes affected by 5R-Tg epimers are still not clearly understood, including the ability of these to undergo spontaneous base flipping.

Structures and dynamic properties of the LiPF electrolytic solution under electric fields - a theoretical study.

Fluorinated carbonates have attracted increasing attention in high-voltage lithium ion battery applications. Under free and electric fields, their structure-related solvent dynamic properties such as charge and discharge rate, however, are rarely reported. Herein, solutions including linear fluorinated carbonates have been simulated using joint MD/DFT calculations.

Theoretical Insights on the Inefficiency of RNA Oxidative Damage under Aerobic Conditions.

Oxidative damage to RNA has been linked to change or loss of RNA function and development of many human age-related diseases. However, knowledge on the nature of RNA oxidative damage is relatively limited. In this study, oxidative damage to RNA is investigated under anaerobic and aerobic conditions by exploring the properties and reactions of 5-hydroxyl-2'-uridin-6-yl and its peroxyl diastereoisomers in the RNA strand, respectively.

Joint experimental and theoretical studies of the surprising stability of the aryl pentazole upon noncovalent binding to β-cyclodextrin.

Herein, binding of the β-cyclodextrin (β-CD) host to the unstable aryl pentazole guest has been confirmed experimentally and theoretically. After the confinement of aryl pentazole, electron density reorganization was studied by M06-2X dispersion-corrected DFT and further reflected in the characteristic shift in the NMR spectra. Among the host-guest complexes, the inclusion complex is favored with the phenyl ring expectedly encapsulated within the cavity through noncovalent interactions such as hydrogen bonding, C-Hπ, and the special C-HH-C bonding discovered by the NBO, QTAIM, and NCI-RDG theories.

A new understanding towards the reactivity of DNA peroxy radicals.

The reactivity of thymine peroxy radicals in DNA and their fate are studied using the reliable DFT methods. The most accessible H1' abstraction by the C6-peroxyl once reported experimentally is effectively competitive to the crosslinking reaction between the C6-peroxyl and the C5 or C6 on the 5'-adjacent thymine base. The rare transfer of the ObH1' group to the C1' radical from the formed hydroperoxide happens with a very strong heat release.

Solid-state Reaction of Azolium Hydrohalogen Salts with Silver Dicyanamide--Unexpected Formation of Cyanoguanidine-azoles, Reaction Mechanism and Their Hypergolic Properties.

Cyanoguanidines as well as azoles are important bioactive groups, which play an important role in the medical application; meanwhile, the high nitrogen content makes them excellent backbones for energetic materials. A Novel and simple method that combined these two fragments into one molecular compound was developed through the transformation of dicyanamide ionic salts. In return, compounds 4-11 were synthesized, and fully characterized by IR, MS, NMR and elemental analysis.

A theoretical rationale for why azetidine has a faster rate of formation than oxetane in TC(6-4) photoproducts.

The mechanism of formation of azetidine and oxetane in (6-4) photoproducts between thymine and imine-type cytosine is studied using the MPWB1K and B3LYP functionals together with the 6-31G(d,p) and 6-311++G(d,p) basis sets, in vacuum and bulk solvent. The photoinduced cycloaddition displays favorable energy barriers in the triplet excited state for formation of both azetidine and oxetane. The stepwise cycloaddition in the triplet excited state involves the initial formation of a diradical followed by ring closure via singlet-triplet interaction.

Theoretical investigation of 4,4',6,6'-tetra(azido)azo-1,3,5-triazine-N-oxides and the effects of N→O bonding on organic azides.

A family of 4,4',6,6'-tetra(azido)azo-1,3,5-triazine-N-oxides was designed and investigated by theoretical method. The effects of the N→O bond on the properties of TAAT-N-oxides, such as density, heat of formation, and detonation performance, were discussed. By comparison with the bond-dissociation energy of the weakest bond and the electrostatic potentials, the effects of the N→O bond on the stability and impact sensitivity of organic azides were also discussed.

A triplet mechanism for the formation of thymine-thymine (6-4) dimers in UV-irradiated DNA.

The reaction pathway for the photochemical formation of thymine-thymine (6-4) dimers in DNA is explored using hybrid density functional theory techniques in gas and in bulk solvent. It is concluded that the photo-induced cycloaddition displays favorable energy barriers in the triplet excited state. The stepwise cycloaddition in the triplet excited state involves the initial formation of a diradical followed by ring closure via singlet-triplet interaction.

The fate of H atom adducts to 3'-uridine monophosphate.

The stabilities of the adducts deriving from H free radical addition to the O2, O4, and C5 positions of 3'-uridine monophosphate (3'UMP) are studied by the hybrid density functional B3LYP approach. Upon H atom addition at the O2 position, a concerted low-barrier proton-transfer process will initially occur, followed by the potential ruptures of the N-glycosidic or beta-phosphate bonds. The rupture barriers are strongly influenced by the rotational configuration of the phosphate group at the 3' terminal, and are influenced by bulk solvation effects.

Theoretical study on conformational preferences of ribose in 2-thiouridine--the role of the 2'OH group.

Conformational changes in ribose are well-known to play a significant role in biomolecular identification. The mechanism of selectivity towards C3'-endo conformation (conformer b) in ribose of 2-thiouridine has been studied using DFT (B3LYP) and MP2 methodology, together with 6-31+G(d,p) basis set. The polarity of the C2S2 bond is enhanced due to the orientation of H2' towards the S2 atoms, which leads to a difference in the corresponding bond lengths, the atomic charges and the vO2'H2' stretch vibrations in all the conformers.

Schisanlactone H and sphenanthin A, new metabolites from Schisandra sphenanthera.

From the fruits of Schisandra sphenanthera (Schisandraceae), a new 3,4-seco-lanostane triterpenoid, schisanlactone H (1), and a new monocyclofarnesane sesquiterpenoid, sphenanthin A (2), were isolated. Their structures were elucidated by spectroscopic methods including extensive 1D and 2D NMR techniques.

Distinct hydroxy-radical-induced damage of 3'-uridine monophosphate in RNA: a theoretical study.

RNA strand scission and base release in 3'-uridine monophosphate (UMP), induced by OH radical addition to uracil, is studied at the DFT B3LYP/6-31+G(d,p) level in the gas phase and in solution. In particular, the mechanism of hydrogen-atom transfer subsequent to radical formation, from C2' on the sugar to the C6 site on the base, is explored. The barriers of (C2'-)H2'(a) abstraction by the C6 radical site range from 11.

Theoretical studies of damage to 3'-uridine monophosphate induced by electron attachment.

Low-energy electrons (LEE) are well known to induce nucleic acid damage. However, the damage mechanisms related to charge state and structural features remain to be explored in detail. In the present work, we have investigated the N1-glycosidic and C3'-O(P) bond ruptures of 3'-UMP (UMP=uridine monophosphate) and the protonated form 3'-UMPH with -1 and zero charge, respectively, based on hybrid density functional theory (DFT) B3 LYP together with the 6-31+G(d,p) basis set.

Hydrogen abstraction from deoxyribose by a neighbouring uracil-5-yl radical.

Hydrogen abstraction from the C1' and C2' positions of deoxyadenosine by a neighbouring uracil-5-yl radical in the 5'-AU*-3' DNA sequence is explored using DFT. This hydrogen abstraction is the first step in a sequence leading to single or double strand break in DNA. The uracil-5-yl radical can be the result of photolysis or low-energy electron (LEE) attachment.

Radical-Induced Damage in 3'dTMP [Formula: see text] Insights into a Mechanism for DNA Strand Cleavage.

DNA strand scission and base release in 3'dTMP, induced by H and OH radical addition to thymine, is studied at the DFT B3LYP/6-31+G(d,p) level in the gas phase and in solution. In particular the mechanism of H atom transfer subsequent to radical formation, from C2' on the sugar to the C6 site on the base, is explored. Bulk solvation is found to lower the barrier by up to 5 kcal mol(-1) and the reaction energy by up to 12 kcal mol(-1) for the hydroxyl radical adducts.

The role of nucleobase carboradical and carbanion on DNA lesions: a theoretical study.

DNA base release induced by H and OH radical addition to thymine and their corresponding electron adducts is studied at the DFT B3LYP/6-31+G(d,p) level in gas phase and in solution. H atom transfer after radical formation from C2' on the sugar to the C6 site on the base is shown to be prohibited for the radical species. Their corresponding electron adducts, albeit minor events in cellular systems, show excellent capabilities to proton transfer from C2' on the sugar to the C6 site on the base.

Hydrogen bonding to pi-systems of indole and 1-methylindole: is there any OH...phenyl bond?

The weak hydrogen-bonded complexes between proton donors and the pi-cloud of indole and 1-methylindole (MI) are investigated theoretically by three different methods: DFT/B3LYP, MPW1B95, and MP2. This study addresses the question as to whether the 1:1 complex can only form between the proton and the pi-cloud of the pyrrole part of indole or if there also exists a 1:1 complex between the proton and the pi-cloud of the phenyl ring. For the water-indole system, the more elaborate MP2 and MPW1B95 methods yield only one minimum with a hydrogen bond to the pyrrole part and weak secondary interactions to the phenyl ring, in agreement with a recent criticism by Van Mourik (Chem.

A triplet mechanism for the formation of cyclobutane pyrimidine dimers in UV-irradiated DNA.

The reaction pathways for the photochemical formation of cyclobutane thymine dimers in DNA are explored using hybrid density functional theory techniques. It is concluded that the thymine-thymine [2 + 2] cycloaddition displays favorable energy barriers and reaction energies in both the triplet and the singlet excited states. The stepwise cycloaddition in the triplet excited state involves the initial formation of a diradical followed by ring closure via singlet-triplet interaction.

Theoretical studies on the mechanism of primary electron transfer in the photosynthetic reaction center of Rhodobacter sphaeroides.

The mechanism of the primary electron transfer (ET) process in the photosynthetic reaction center (PRC) of Rhodobacter sphaeroides has been studied with quantum chemistry method of ab initio density functional theory (DFT) (B3LYP/6-31G) based on the optimized X-ray crystallographic structure. The calculation was carried out on different structural levels. The electronic structure of pigment molecules was first studied, and then the influence of the neighboring protein was taken into account at three approximation levels: (a) the surrounding proteins were treated as a homogeneous medium with a uniform dielectric constant (SCRF); (b) both the influence of axial coordination of His to the special pair P and ABChl as, and the hydrogen bonds between related residues and P and also BPhas were included; and (c) the influence of the electronic structure of the protein subunit chains as a whole was studied.