The Structure of LNA:DNA Hybrids from Molecular Dynamics Simulations: The Effect of Locked Nucleotides^†

Locked nucleic acids (LNAs) exhibit a modified sugar fragment that is restrained to the C3‘-endo conformation. LNA-containing duplexes are rather stable and have a more rigid structure than DNA duplexes, with a propensity for A-conformation of the double helix. To gain detailed insight into the local structure of LNA-modified DNA oligomers (as a foundation for subsequent exploration of the electron-transfer capabilities of such modified duplexes), we carried out molecular dynamics simulations on a set of LNA:DNA 9-mer duplexes and analyzed the resulting structures in terms of base step parameters and the conformations of the sugar residues. The perturbation introduced by a single locked nucleotide was found to be fairly localized, extending mostly to the first neighboring base pairs; such duplexes featured a B-type helix. With increasing degree of LNA modification the structure gradually changed; the duplex with one complete LNA strand assumed a typical A-DNA structure. The relative populations of the sugar conformations agreed very well with NMR data, lending credibility to the validity of the computational protocol

Solvent Reorganization Energies in A-DNA, B-DNA, and Rhodamine 6G−DNA Complexes from Molecular Dynamics Simulations with a Polarizable Force Field

We estimate solvent reorganization energies λs of electron transfer (ET) in DNA stacks between positively charged guanine (acceptor) and neutral guanine (donor), as well as in rhodamine 6G (R6G)−DNA complexes between R6G (acceptor) and neutral guanine (donor) from molecular dynamics simulations that used a polarizable force field in combination with a polarizable water model. We compare results from the polarizable scheme with those from a common nonpolarizable analogue. We also discuss the influence of charge sets, separate contributions of solute and solvent electronic polarizations, and partial contributions of different molecular groups to changes of λs due to electronic polarization. Independent of donor−acceptor distances, solvent reorganization energies of ET processes in DNA duplexes from a polarizable force field are about 30% smaller than the corresponding results from a nonpolarizable force field. The effective optical dielectric constant ε̃∞ = 1.5, extracted from pertinent scaling factors, is also independent of the donor−acceptor separation over a wide range of distances, from 3.4 to 50.0 Å. Reorganization energies calculated with the polarizable force field agree satisfactorily with experimental data for DNA duplexes. Comparison of results for A-DNA and B-DNA forms as well as for the conformational alignment of the dye relative to the duplex in R6G-DNA complexes demonstrates that the conformation of a duplex hardly affects λs. Among these DNA-related systems, the effective parameter ε̃∞ is remarkably constant over a broad range of donor−acceptor distances

Systematic Study of the Influence of Base-Step Parameters on the Electronic Coupling between Base-Pair Dimers: Comparison of A-DNA and B-DNA Forms

The electronic coupling is one of the key parameters governing electron hole transfer along DNA helices. In this study, we established the first comprehensive data base of electronic coupling elements, calculated at the ab initio level. The data set comprises all possible Watson−Crick base pair dimers, both in standard A-DNA and B-DNA geometries. We also quantified the sensitivity of the coupling elements with respect to geometry changes by varying each of the six standard base step parameters, which specify the relative orientation of neighboring base pairs. We compare the couplings in a systematic way by discussing variations in the coupling magnitude due to geometry or nucleotide sequence in the dimer, and we analyze how the structure affects the electronic coupling in terms of general and dimer-specific trends. Furthermore, we studied how the coupling changes when one introduces the chemically modified base 7-deazaguanine in the corresponding base-pair dimers. Finally, on the basis of the calculated coupling elements, we suggest a model duplex with an enhanced capacity for hole transfer

Study on the Heteroatom Influence in Pyridine-Based Nitronyl Nitroxide Biradicals with Phenylethynyl Spacers on the Molecular Ground State

Novel pyridine-based nitronyl nitroxide (NIT) biradicals, 3,5-bis[4-(1-oxyl-3-oxo-4,4,5,5-tetramethylimidazolin-2-yl)phenylethynyl)]pyridine (1) and 2,6-bis[4-(1-oxyl-3-oxo-4,4,5,5-tetramethylimidazolin-2-yl)phenylethynyl)]pyridine (2), and monoradicals, 4-(5-bromopyridine-3-ylethynyl)-1-(1-oxyl-3-oxo-4,4,5,5-tetramethylimidazolin-2-yl)benzene (3), 4-trimethylsilylethynyl-1-(1-oxyl-3-oxo-4,4,5,5-tetramethylimidazolin-2-yl)benzene (4), and 4-trimethylsilylethynyl-1-(1-oxyl-3-oxo-4,4,5,5-tetramethylimidazolin-2-yl)pyridine (5), were synthesized and investigated by ESR and UV−vis spectroscopy. The solution EPR measurements of the biradicals gave well-resolved, nine-line spectra with exact half line spacing as compared to monoradicals (giso = 2.0067) with isotropic line spacing |aN|= 7.36 G. This indicates strong, intramolecular exchange coupling (J ≫ 7 × 10-4 cm-1; J/aN ≫ 1) of the biradicals with in the limit of EPR. The temperature dependence on the Δms = ±2 signal intensity of biradicals follow Curie behavior down to 4 K ascertaining the triplet ground state or its near-degeneracy with the singlet state. UV−vis studies of 1−5 show characteristic differences in the extinctions of n−π* transitions around 600 nm. Both biradicals 1 and 2 were crystallized in monoclinic space groups C2/c and P21/a with the intraradical distances 1.54 and 1.47 nm, respectively. Computational studies of the biradicals 1, 2, and 1,3-bis[4-(1-oxyl-3-oxo-4,4,5,5-tetramethylimidazolin-2-yl)phenylethynyl)]benzene (T) were performed by the AM1/CAS(8,8) method to calculate the singlet−triplet (ΔEST) energy difference and the spin density distribution. Results show that the position of the pyridyl nitrogen in 1 and 2 in comparison with T does not alter the triplet ground-state spin multiplicities supporting the obtained experimental results

Estimation of the Mutual Orientation and Intermolecular Interaction of C₁₂E_<i>x</i> from Molecular Dynamics Simulations

Nonionic surfactants, such as poly­(ethylene glycol) alkyl ethers (abbreviated as CyEx) show a rich phase behavior in aqueous solution, i.e., they form micellar, lamellar, cubic, and so forth phases depending on experimental parameters such as the hydrophobic and hydrophilic chain lengths, temperature, or concentration. The aim of the present study is to determine the nature of the preaggregates, which are inferred to exist before the actual self-assembly process in aqueous solution, and to assess the aptitude to their formation. The target molecules are C12E3, C12E4 and C12E5, surfactants of moderate water solubility. Coarse-grained and all-atom molecular dynamics simulations (NPT/293 K) of two molecules of each species with explicit water in periodic boundary conditions are carried out to estimate the mutual orientation and the interaction between the surfactants in their dimers. The force fields are MARTINI and Amber99, the latter with self-derived parameters for the ether groups. The change in the orientation and distance between the molecules in the dimers are discussed based on different structural parameters. In addition, the interaction between the surfactants is evaluated from quantum chemistry calculations in terms of binding energy for the average structures from the cluster analysis. The solvent–solute interaction is quantified by the mean number of hydrogen bonds formed between them. On the basis of combined analysis, a series of different structures for subsequent study of the possible self-assembly patterns of C12E3, C12E4, and C12E5 is outlined

Magnetostructural Correlation for Rational Design of Mn(II) Hybrid-Spin Complexes

The magnetic properties of a series of manganese­(II) diacetylacetonate and dihexafluoroacetylacetonate hybrid-spin complexes with neutral pyridine-based organic radicals were characterized theoretically by DFT calculations. Three stable radicals, in which a radical group is bound in either para or meta position with respect to the pyridine nitrogen atom, were considered. The correct stable structures and multiplets of the complexes were obtained by full geometry optimization starting from an ideal structure. A total of three important geometry descriptors of the complexes were monitored and related to their magnetic characteristics. These structural parameters are (i) the torsion angle governing the conjugation of the organic radical <b><i>m</i>-PyNO</b> (anti versus gauche), (ii) the coordination geometry of the acetyl acetonate ligands around the metal ion (square versus rhombic), and (iii) the relative orientation of the organic radical with respect to the acetyl acetonate plane (parallel versus perpendicular). It was found that the magnetic properties are not sensitive to the orientation of the radicals with respect to the equatorial plane but do depend on the conformation of the organic radicals. Even a spin switch between the ferromagnetic (<i>S</i> = ⁷/₂) and antiferromagnetic (<i>S</i> = ³/₂) ground state was found to be feasible for one of the complexes upon variation of the organic radical geometry, namely, the dihedral angle between the organic radical moiety and the pyridine ring. The pattern of molecular orbital overlap was determined to be the key factor governing the exchange coupling in the modeled systems. Bonding π-type overlap provides antiferromagnetic coupling in all complexes of the para radicals. In the meta analogues, the spins are coupled through the σ orbitals. A low-spin ground state occurs whenever a continuous σ-overlap pathway is present in the complex. Ferromagnetic interaction requires σ–π orthogonality of the pyridine atomic orbitals and/or π-antibonding Mn–pyridine natural orbital overlap. Using an estimate of the donor–acceptor energy stabilization, the affinity of a given Mn­(II) d-orbital to mix with the sp² orbital from pyridine can be predicted

Structure of Rhodamine 6G−DNA Complexes from Molecular Dynamics Simulations

Chromophore−DNA complexes are useful for understanding charge transport along π-stacks once their structural properties have been clarified. We studied two rhodamine 6G semicapping complexes with 15-mer B-DNA duplexes to determine the preferred orientation of the dye with respect to the neighboring base pair. For each of these systems, two distinct chromophore alignments were identified and quantified in terms of base-step parameters. The obtained geometries agree well with those derived from an NMR structure refinement of similar complexes. Cross-correlation analysis of the base-step parameters shows that slide and twist are highly interdependent during the structural transition from one conformation to the other

Characteristics of a Folate Receptor‑α Anchored into a Multilipid Bilayer Obtained from Atomistic Molecular Dynamics Simulations

Thorough computational description of the properties of membrane-anchored protein receptors, which are important for example in the context of active targeting drug delivery, may be achieved by models representing as close as possible the immediate environment of these macromolecules. An all-atom bilayer, including 35 different lipid types asymmetrically distributed among the two monolayers, is suggested as a model neoplastic cell membrane. One molecule of folate receptor-α (FRα) is anchored into its outer leaflet, and the behavior of the system is explored by atomistic molecular dynamics simulations. The total number of atoms in the model is ∼185 000. Three 1-μs-long simulations are carried out, where physiological conditions (310 K and 1 bar) are maintained with three different pressure scaling schemes. To evaluate the structure and the phase state of the membrane, the density profiles of the system, the average area per lipid, and the deuterium order parameter of the lipid tails are calculated. The bilayer is in liquid ordered state, and the specific arrangement varies between the three trajectories. The changes in the structure of FRα are investigated and are found time- and ensemble-dependent. The volume of the ligand binding pocket fluctuates with time, but this variation remains independent of the more global structural alterations. The latter are mostly “waving” motions of the protein, which periodically approaches and retreats from the membrane. The semi-isotropic pressure scaling perturbs the receptor most significantly, while the isotropic algorithm induces rather slow changes. Maintaining constant nonzero surface tension leads to behavior closest to the experimentally observed one

Absorption Spectra of Model Single Chains of Conducting Polyaniline

The theoretical study addresses the type and nature of the transitions in the absorption spectra of octamers, dodecamers, and hexadecamers of the emeraldine saltthe conducting form of polyaniline. Each of the fully protonated oligomers is modeled in its lowest singlet (bipolaronic form) and highest possible multiplicity (polaronic form). Two configurations of the chloride counterions with respect to the oligomer chains are considered. All structures are optimized with BLYP/6-31G*/PCM, while the spectra are evaluated with CIS/6-31G*/PCM. The optical behavior of the bipolaronic and polaronic forms of the investigated systems is discussed and compared to relevant experimental data. The optical transitions at about 400 and 800 nm characteristic for the emeraldine salt are registered for all model structures. Weighed against experimental and earlier theoretical findings the results prove that CIS gives qualitatively correct electronic spectra of these conjugated species. While the two configurations have almost identical spectra in the highest multiplicity, the singlets’ absorption conduct turns out to be sensitive to the counterions position. In all cases the most intensive absorption is the longest wavelength one in the near-IR region, but the number and oscillator strengths of the polaronic and bipolaronic bands are noticeably dissimilar. The bands of the low-spin oligomers are grouped, while those of the high-spin species cover the entire visible region. Each extension of the chain with one elementary unit contributes systematically a set of new bands to the spectrum. The possibility for a solvatochromic effect is estimated