Characterization of the monovalent ion position and hydrogen-bond network in guanine quartets by DFT calculations of NMR parameters

Conformational stability of G-quartets found in telomeric DNA quadruplex structures requires the coordination of monovalent ions. Here, an extensive Hartree-Fock and density functional theory analysis of the energetically favored position of Li+, Na+, and K+ ions is presented. The calculations show that at quartet-quartet distances observed in DNA quadruplex structures (3.3 A), the Li+ and Na+ ions favor positions of 0.55 and 0.95 A outside the plane of the G-quartet, respectively. The larger K+ ion prefers a central position between successive G-quartets. The energy barrier separating the minima in the quartet-ion-quartet model are much smaller for the Li+ and Na+ ions compared with the K+ ion; this suggests that K+ ions will not move as freely through the central channel of the DNA quadruplex. Spin-spin coupling constants and isotropic chemical shifts in G-quartets extracted from crystal structures of K+- and Na+-coordinated DNA quadruplexes were calculated with B3LYP/6-311G(d). The results show that the sizes of the trans-hydrogen-bond couplings are influenced primarily by the hydrogen bond geometry and only slightly by the presence of the ion. The calculations show that the R(N2N7) distance of the N2-H2...N7 hydrogen bond is characterized by strong correlations to both the chemical shifts of the donor group atoms and the (h2)J(N2N7) couplings. In contrast, weaker correlations between the (h3)J(N1C6') couplings and single geometric factors related to the N1-H1...O6=C6 hydrogen bond are observed. As such, deriving geometric information on the hydrogen bond through the use of trans-hydrogen-bond couplings and chemical shifts is more complex for the N1-H1...O6=C6 hydrogen bond than for the N2-H2...N7 moiety. The computed trans-hydrogen-bond couplings are shown to correlate with the experimentally determined couplings. However, the experimental values do not show such strong geometric dependencies.     

Interference between the hydrogen bonds to the two rings of nicotine

The biochemical transport and binding of nicotine depends on the hydrogen bonding between water and binding site residues to the pyridine ring and the protonated pyrrolidinium ring. To test the independence of these two moderately separated hydrogen-bonding sites, we have calculated the structures of clusters of protonated nicotine with water and a bicarbonate anion, benzene, indole, or a second water molecule. Unprotonated nicotine-water clusters have also been studied for contrast. The potential energy surfaces are first explored with an intermolecular anisotropic atom-atom model potential. Full geometry optimizations are then carried out using density functional theory to include nonadditive terms in the interaction energies. The presence of the charge on the pyrrolidine nitrogen removes the conventional hydrogen-bonding site on the pyridine ring. The hydrogen-bond ability of this site is nearly recovered when the protonated pyrrolidinium ring is bound to a bicarbonate anion, whereas its interaction with benzene shows a much smaller effect. Indole appears to partially restore the hydrogen-bond ability of the pyridine nitrogen, although indole and benzene both pi-bond to the pyrrolidinium ring. A second hydrogen-bonding water produces a significant conformational distortion of the nicotine. This demonstrates the limitations of the conventional qualitative predictions of hydrogen bonding based on the independence of molecular fragments. It also provides benchmarks for the development of atomistic modeling of biochemical systems.     

Solvable lattice gas models of random heteropolymers at finite density: II. Dynamics and transitions to compact states

The European Physical Journal E - In this paper we analyse both the dynamics and the high density physics of the infinite dimensional lattice gas model for random heteropolymers recently introduced...     

DFT study of polymorphism of the DNA double helix at the level of dinucleoside monophosphates

We apply DFT calculations to deoxydinucleoside monophosphates (dDMPs) which represent minimal fragments of the DNA chain to study the molecular basis of stability of the DNA duplex, the origin of its polymorphism and conformational heterogeneity. In this work, we continue our previous studies of dDMPs where we detected internal energy minima corresponding to the “classical” B conformation (BI‐form), which is the dominant form in the crystals of oligonucleotide duplexes. We obtained BI local energy minima for all existing base sequences of dDMPs. In the present study, we extend our analysis to other families of DNA conformations, successfully identifying A, BI, and BII energy minima for all dDMP sequences. These conformations demonstrate distinct differences in sugar ring puckering, but similar sequence‐dependent base arrangements. Internal energies of BI and BII conformers are close to each other for nearly all the base sequences. The dGpdG, dTpdG, and dCpdA dDMPs slightly favor the BII conformation, which agrees with these sequences being more frequently experimentally encountered in the BII form. We have found BII‐like structures of dDMPs for the base sequences both existing in crystals in BII conformation and those not yet encountered in crystals till now. On the other hand, we failed to obtain dDMP energy minima corresponding to the Z family of DNA conformations, thus giving us the ground to conclude that these conformations are stabilized in both crystals and solutions by external factors, presumably by interactions with various components of the media. Overall the accumulated computational data demonstrate that the A, BI, and BII families of DNA conformations originate from the corresponding local energy minimum conformations of dDMPs, thus determining structural stability of a single DNA strand during the processes of unwinding and rewinding of DNA. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem 110:2548–2559, 2010     

Light-induced spin crossover in Fe(II)-based complexes: The full photocycle unraveled by ultrafast optical and X-ray spectroscopies

The light-induced spin and structure changes upon excitation of the singlet metal-to-ligand charge transfer (¹MLCT) state of Fe(II)-polypyridine complexes are investigated in detail in the case of aqueous iron(II)-tris-bipyridine ([Fe^II(bpy)₃]²⁺) by a combination of ultrafast optical and X-ray spectroscopies. Polychromatic femtosecond fluorescence up-conversion, transient absorption studies in the 290–600 nm region and femtosecond X-ray absorption spectroscopy allow us to retrieve the entire photocycle upon excitation of the ¹MLCT state from the singlet low-spin ground state (¹GS) as the following sequence: ^1,3MLCT → ⁵T → ¹GS, which does not involve intermediate singlet and triplet ligand-field states. The population time of the HS state is found to be ～150 fs, leaving it in a vibrationally hot state that relaxes in 2–3 ps, before decaying to the ground state in 650 ps. We also determine the structure of the high-spin quintet excited state by picosecond X-ray absorption spectroscopy at the K-edge of Fe. We argue that given the many common electronic (ordering of electronic states) and structural (Fe–N bond elongation in the high-spin state, Fe–N mode frequencies, etc.) similarities between all Fe(II)-polypyridine complexes, the results on the electronic relaxation processes reported in the case of [Fe^II(bpy)₃]²⁺ are of general validity to the entire family of Fe(II)-polypyridine complexes.     

Swollen-collapsed transition in random hetero-polymers

A lattice model of a hetero-polymer with random hydrophilic-hydrophobic charges interacting with the solvent is introduced, whose continuum counterpart has been proposed by Garel, Leibler and Orland [#!GLO!#]. The transfer matrix technique is used to study various constrained annealed systems which approximate at various degrees of accuracy the original quenched model. For highly hydrophobic chains an ordinary -point transition is found from a high temperature swollen phase to a low temperature compact phase. Depending on the type of constrained averages, at very low temperatures a swollen phase or a coexistence between compact and swollen phases are found. The results are carefully compared with the corresponding ones obtained in the continuum limit, and various improvements in the original calculations are discussed. Received: 10 April 1998 / Revised: 4 June 1998 / Accepted: 1st July 1998     

Aqueous solvation dynamics at metal oxide surfaces

Broadband transient absorption (TA) spectroscopy, three-pulse photon echo peak shift (3PEPS), and anisotropy decay measurements were used to study the solvation dynamics in bulk water and interfacial water at ZrO(2) surfaces, using Eosin Y as a probe. The 3PEPS results show a multiexponential behavior with two subpicosecond components that are similar in bulk and interfacial water, while a third component of several picoseconds is significantly lengthened at the interface. The bandwidth correlation function from TA spectra exhibits the same behavior, and the TA spectra are well reproduced using the doorway-window picture with the time constants from PEPS. Our results suggest that interfacial water is restricted to a thickness of less than 5 A. Also the high-frequency collective dynamics of water does not seem to be affected by the interface. On the other hand, the increase of the third component may point to a slowing down of diffusional motion at the interface, although other effects, may play a role, which are discussed.     

Benchmark calculations with correlated molecular wavefunctions. XIII. Potential energy curves for He2, Ne2 and Ar2 using correlation consistent basis sets through augmented sextuple zeta

The potential energy curves of the rare gas dimers He2, Ne2, and Ar2 have been computed using correlation consistent basis sets ranging from singly augmented aug-cc-pVDZ sets through triply augmented t-aug-cc-pV6Z sets, with the augmented sextuple basis sets being reported herein. Several methods for including electron correlation were investigated, namely Møller—Plesset perturbation theory (MP2, MP3 and MP4) and coupled cluster theory [CCSD and CCSD(T)]. For He2 CCSD(T)/d-aug-cc-pV6Z calculations yield a well depth of 7.35 cm-1 (10.58 K), with an estimated complete basis set (CBS) limit of 7.40 cm-1 (10.65 K). The latter is smaller than the 'exact' well depth (Aziz, R. A., Janzen, A. R., and Moldover, M. R., 1995, Phys. Rev. Lett., 74, 1586) by about 0.2 cm-1 (0.35 K). The Ne2 well depth, computed with the CCSD(T)/d-aug-cc-pV6Z method, is 28.31 cm-1 and the estimated CBS limit is 28.4 cm-1, approximately 1 cm-1 smaller than the empirical potential of Aziz, R. A., and Slaman, M., J., 1989, Chem. Phys., 130, 187. Inclusion of core and core—valence correlation effects has a negligible effect on the Ne2 well depth, decreasing it by only 0.04 cm-1. For Ar2, CCSD(T)/d-aug-cc-pV6Z calculations yield a well depth of 96.2 cm-1. The corresponding HFDID potential of Aziz, R. A., 1993, J. chem. Phys., 99, 4518 predicts of De of 99.7 cm-1. Inclusion of core and core-valence effects in Ar2 increases the well depth and decreases the discrepancy by approximately 1 cm-1.     

Ultrafast UV photon echo peak shift and fluorescence up conversion studies of non-polar solvation dynamics

We present photon echo peak shift and femtosecond fluorescence up-conversion studies of non-polar solvation dynamics of a simple non-polar dye p-terphenyl in ethanol and cyclohexane, using excitation in the UV range at 290 nm. The UV fluorescence up-conversion experiments were combined with a polychromatic detection and the results highlight the high sensitivity of this approach to fully characterize the excited state dynamics of the dye. We also demonstrate the feasibility of UV photon echo and transient grating and its sensitivity for the detection of non-polar solvation dynamics by measuring the frequency correlation function of the dye in the ground state. While solvation dynamics in the picosecond regime is observed in ethanol, electronic coherence dephasing occurs on timescales faster than 100 fs in ethanol as well as in the non-polar solvent cyclohexane.