Twist‐dependent stacking energy of base‐pair steps in B‐DNA geometry: A density functional theory approach

Stacking energy of all the 10 unique DNA base‐pair steps (bp step) are calculated using density functional theory within the ultrasoft pseudopotential plane wave method and local density approximation for the exchange‐correlation functional. We have studied the dependence of stacking energy on twist angle, an aspect found difficult to explain using classical theory. We have found that the twist angle for different bp steps at stacking energy minimum matches extremely well with the values of average twist obtained from B‐DNA crystal structure data. This indicates that the use of a proper quantum chemical method to calculate the π‐π electronic interactions may explain stacking energy without incorporating hydrophobic interaction through solvent or effect of backbone through pseudobond. From the twist angle‐dependent stacking energy profile, we have also generated the probability distributions of twist for all the bp steps and calculated the variance of the distribution. Our calculated variances show similar trend to that of the experimental data for which sufficient numbers of data are available. The TA, AT, and CG doublets show large variances among the 10 possible bp steps, indicating their maximum flexibility. This might be the case of unusual deformation observed at the TATA‐box while binding to TBP protein. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Molecular dynamics of minimal B‐DNA

Stable and accurate molecular dynamics (MD) of B‐DNA duplexes can be obtained in inexpensive computational conditions where only the minor groove is filled with water while the bulk solvent is represented implicitly. This model system presents significant theoretical as well as practical interest because, due to its simplicity and exceptional computational performance, it can be employed in simulations of very long DNA fragments. To better understand its properties and clarify the physical background of the effects produced by the limited water shell, dynamics of several different DNA oligomers was studied. It is found that optimal simulation conditions are reached when the explicit water is confined within the minor groove while the major groove is cleaned periodically. The internal solvent mobility appears high enough to observe in the nanosecond time scale spontaneous formation of sequence‐specific hydration patterns known from experiments. It is shown that the model produces stable MD trajectories close to the B‐DNA form regardless of the base pair sequence and that, on the other hand, the dynamics are strongly sequence dependent. Independent observations suggest that B‐DNA with only minor groove hydrated resembles its natural thermodynamic state at low water concentration; therefore, this model system can be tentatively called “minimal B‐DNA.” © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 457–467, 2001     

DFT performance for the hole transfer parameters in DNA π stacks

Recently, we showed that unoccupied Kohn‐Sham (KS) orbitals stemming from DFT calculations of a neutral system can be used to derive accurate estimates of the free energy and electronic couplings for excess electron transfer in DNA (Félix and Voityuk, J Phys Chem A 2008, 112, 9043). In this article, we consider the propagation of radical cation states (hole transfer) through DNA π‐stacks and compare the performance of different exchange‐correlation functionals to estimate the hole transfer (HT) parameters. Two different approaches are used: (1) calculations that use occupied KS orbitals of neutral π stacks of nucleobases, and (2) the time‐dependent DFT method which is applied to the radical cation states of these stacks. Comparison of the calculated parameters with the reference data suggests that the best results are provided by the KS scheme with hybrid functionals (B3LYP, PBE0, and BH&HLYP). The TD DFT approach gives significantly less accurate values of the HT parameters. In agreement with high‐level ab initio results, the KS scheme predicts that the hole in π stacks is confined to a single nucleobase; in contrast, the spin‐unrestricted DFT method considerably overestimates the hole delocalization in the radical cations. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Structural characterization of the regioisomers of di(hydroxybutyl) ether by GC‐EI MS and theoretical calculations

Di(hydroxybutyl) ether (DHBE), a liver protecting drug, is composed of a mixture of three regioisomers: 4‐(3‐hydroxybutoxy)‐2‐butanol (1), 3‐(4‐hydroxy‐2‐butoxy)‐1‐butanol (2), and 3‐(3‐hydroxybutoxy)‐1‐butanol (3). Unequivocal differentiation of each regioisomer of DHBE was rapidly obtained without isolation of the single components, using GC‐MS with electron ionization (EI). The mass spectrum of 1 showed a rearrangement ion at m/z 118, characteristic of the 3‐hydroxybutyl chain, deriving from loss of acetaldehyde from the molecular ion, whereas 2 and 3 were characterized by the ion at m/z 117, expected from α‐cleavage of the 4‐hydroxy‐2‐butyl chain. The species at m/z 118, in turn, loses a water molecule via a mechanism involving both alcohol hydrogens, as shown by deuterium exchange experiments. Both this finding and theoretical calculations support a mechanism in which the loss of acetaldehyde in 1 occurs via a cyclic intermediate, stabilized by a strong hydrogen bond between the alcohol oxygen bearing the charge and the other alcohol oxygen, and involves initial hydrogen transfer from the former to the latter. The EI spectrum of 2, having two 4‐hydroxy‐2‐butyl chains, showed the fragmentations expected from classical fragmentation rules of aliphatic ethers and alcohols, whereas the EI spectrum of 3, bearing one 4‐hydroxy‐2‐butyl and one 3‐hydroxybutyl chain, showed essentially the characteristic fragments of both chains. Copyright © 2009 John Wiley & Sons, Ltd.     

Electron attachment to the DNA bases adenine and guanine and dehydrogenation of their anionic derivatives: Density functional study

Density functional theory (DFT) calculations have been used to explore electron attachment to the purines adenine and guanine and their hydrogen atom loss. Calculations show that the dehydrogenation at the N9 site in the adenine and guanine transient anions is the lowest‐cost channel of hydrogen loss, and the N9? H bond scission has Gibbs free energies of dissociation ΔG° of 8.8 kcal mol^?1 for the anionic adenine and 13.9 kcal mol^?1 for the anionic guanine. The relatively high feasibility of low‐energy electron (LEE)‐induced N9? H bond cleavage in the purine nucleobases arises from high electron affinities of their H‐deleted counterparts. Unlike adenine, other N? H bond dissociations are competitive with the N9? H bond fission in the anionic guanine. The replacement of hydrogen in the ring of purine has a significant effect on the N9? H bond fragmentation. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Electron attachment to DNA and RNA nucleobases: An EOMCC investigation

We report a benchmark theoretical investigation of both vertical and adiabatic electron affinities of DNA and RNA nucleobases: adenine, guanine, cytosine, thymine, and uracil using equation of motion coupled cluster method. The vertical electron affinity (VEA) values of the first five states of the DNA and RNA nucleobases are computed. It is observed that the first electron attached state is energetically accessible in gas phase. Furthermore, an analysis of the natural orbitals exhibits that the first electron attached states of uracil and thymine are valence‐bound in nature and undergo significant structural changes on attachment of an extra electron, which reflects in the deviation of the adiabatic electron affinity (AEA) than that of the vertical ones. Conversely, the first electron attached states of cytosine, adenine, and guanine are in the category of dipole‐bound anions. Their structure, by and large, remain unaffected on attachment of an extra electron, which is evident from the observed small difference between the AEA and VEA values. VEA and AEA values of all the DNA and RNA nucleobases are found to be negative, which implies that the first electron attached states are not stable rather quasi bound. The results of all previous theoretical calculations are out of track and shows large deviation with respect to the experimentally measured values, whereas, our results are found to be in good agreement. Therefore, our computed values can be used as a reliable standard to calibrate new theoretical methods. © 2015 Wiley Periodicals, Inc.     

Electron Attachment to Solvated dGpdG: Effects of Stacking on Base‐Centered and Phosphate‐Centered Valence‐Bound Radical Anions

To explore the nature of electron attachment to guanine‐centered DNA single strands in the presence of a polarizable medium, a theoretical investigation of the DNA oligomer dinucleoside phosphate deoxyguanylyl‐3′,5′‐deoxyguanosine (dGpdG) was performed by using density functional theory. Four different electron‐distribution patterns for the radical anions of dGpdG in aqueous solution have been located as local minima on the potential energy surface. The excess electron is found to reside on the proton of the phosphate group (dGp^H?dG), or on the phosphate group (dGp^.?dG), or on the nucleobase at the 5′ position (dG^.?pdG), or on the nucleobase at the 3′ position (dGpdG^.?), respectively. These four radical anions are all expected to be electronically viable species under the influence of the polarizable medium. The predicted energetics of the radical anions follows the order dGp^.?dG>dG^.?pdG>dGpdG^.?>dGp^H?dG. The base–base stacking pattern in DNA single strands seems unaffected by electron attachment. On the contrary, intrastrand H‐bonding is greatly influenced by electron attachment, especially in the formation of base‐centered radical anions. The intrastrand H‐bonding patterns revealed in this study also suggest that intrastrand proton transfer might be possible between successive guanines due to electron attachment to DNA single strands.     

Reference Values for the B‐X Bond Lengths of BI3 and BBr3

High‐resolution X‐ray analysis of BI₃ and BBr₃ single crystals as well as high‐level theoretical calculations agree on accurate but long B‐X bond distances that should be used as future reference to account for their structure, bonding and reactivity.     

New transition metal complexes of 9,10‐phenanthrenequinone p‐toluyl hydrazone Schiff base: Synthesis,spectroscopy, DNA and HSA interactions,antimicrobial, DFT and docking studies

The new complexes of Cu (II) and Ni (II) of a tridentate Schiff base ligand derived from 9,10‐phenanthrenequinone and p‐toluic hydrazide have been synthesized and characterized by elemental analysis, electrical conductometry, FT‐IR, Mass, NMR and UV–Vis. The DFT calculations were carried out at B3LYP/6‐31G*(d) level for the determination of the optimized structure of the ligand and its complexes. The as‐synthesized compounds were screened for their antimicrobial activity. Also, their binding behavior with fish salmon‐DNA (FS‐DNA) and human serum albumin (HSA) were studied by different kinds of spectroscopic and molecular modeling techniques. The fluorescence data at different temperatures were applied in order to estimate the thermodynamics parameters of interactions of ligand and its complexes with DNA and HSA. The results showed that the as‐made compounds could bind to FS‐DNA and HSA via the groove binding as the major binding mode. According to molecular docking calculation and competitive binding experiments, these compounds bind to the minor groove of DNA and hydrophobic residues located in the subdomain IB of HSA. In addition, the molecular docking results kept in good consistence with experimental data.     

Gas‐phase intramolecular hydroxyl‐amino exchange of protonated arginine and verified by the synthetic intermediate compound

A new fragmentation process was proposed to interpret the characteristic product ion at m/z 130 of protonated arginine. The α‐amino group was dissociated from protonated arginine and then combined with the (M + H‐NH₃) fragment to form an ion‐neutral complex which further generated a hydroxyl‐amino exchange intermediate compound through an ion‐molecule reaction. This intermediate compound was synthesized from argininamide through a diazo reaction, and then the reaction mixture was analyzed using liquid chromatography combined with mass spectrometry (LC‐MS). The collision‐induced dissociation experiments under the same conditions revealed that this intermediate compound produced the characteristic product ion at m/z 130 as well as protonated arginine, and in addition, density functional theory calculations were performed to confirm simultaneous loss of NH₃ and CO from this intermediate to give the m/z 130 ion.     

Rational design of outer‐expanded purine analogues as building blocks of DNA‐based nanowires with enhanced electronic properties

Due to the fact that natural DNA may lack sufficient conductance for direct application in molecular electronics, a novel design of outer‐expanded purine analogues was proposed by incorporating an aromatic ring at the N7‐C8 site into natural G and A bases from the outside. The effect of the outer‐expansion modification on electronic properties of DNA was investigated by density functional theory and molecular dynamics. The analyses revealed that these purine analogues not only preserve the same sizes of natural purine bases, thus avoiding distortions of DNA skeleton induced by the normal ring‐inner‐expansion modification, but also keep the selectivity of pairing with their natural counterpart C and T bases. More importantly, their electronic properties are enhanced, indicated by the narrowed HOMO–LUMO gaps, the lowered ionization potentials and the improved ultraviolet absorption spectra. This work may provide helpful information for designing of artificial bases as promising building blocks of biomolecular nanowires. © 2014 Wiley Periodicals, Inc.     

Role of the electronic properties of azurin active site in the electron‐transfer process

Electron transfer proteins, such as azurin (a blue copper protein), are promising candidates for the implementation of biomolecular nanoelectronic devices. To understand the details of electron transfer in redox active azurin molecules, we performed plane‐wave pseudo‐potential density functional theory (DFT) calculations of the protein active site in the two possible oxidation states Cu(I) and Cu(II). The ab initio results are used to discuss how the electronic spectrum and wavefunctions may mediate the shuttling of electrons through the copper ion. We find that the Cu‐ligand hybridization is very similar in the two charge states of the metal center, but the energy spectrum changes substantially. This result might indicate important effects of electronic correlations in the redox activity and consequent electron transfer through the Cu site. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Second‐order nonlinear optical responses switching of N∧N∧N ruthenium carboxylate complexes with proton‐electron transfer

In this article, the nonlinear optical (NLO) switching action of Ru(III/II) carboxylate complexes was investigated by density functional theory (DFT). Among the studied complexed, Ru(III)PhCOO^? has the largest β value of 4972 × 10^?30 esu. Through the proton transfer (PT) process, the ? COOH group of Ru(III)PhCOOH and Ru(III)COOH complexes can form the ? COO^? group. Then, ? COO^? group acts as a strong donor and Ru(III) acts as an acceptor, which may be the most favorably used in the development of metal complexes NLO material. The redox NLO switching and PT NLO switching of Ru(III)PhCOO^?, Ru(III)PhCOOH, Ru(II)PhCOO^?, and Ru(II)PhCOOH complexes have been studied. The β value of Ru(III)PhCOO^? complex is ～36 and ～48 times larger than those of reduced Ru(II)PhCOO^? and Ru(II)PhCOOH, respectively. Note that the β value of deprotonated Ru(III)PhCOO^? is ～215 times larger than that of Ru(III)PhCOOH. The molecular electrostatic potential analysis also confirms that Ru(III)PhCOOH may have poor performance in the second‐order NLO response. In addition, the TDDFT calculations show that the ligand to metal charge transfer transition lead to the largest β value of the Ru(III)PhCOO^? complex. This investigation provides important insight into the remarkably large NLO properties and NLO switching of Ru(III/II) carboxylate complexes. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem 000: 000–000, 2011     

Electron Attachment to Hydrated Oligonucleotide Dimers: Guanylyl‐3′,5′‐Cytidine and Cytidylyl‐3′,5′‐Guanosine

The dinucleoside phosphate deoxycytidylyl‐3′,5′‐deoxyguanosine (dCpdG) and deoxyguanylyl‐3′,5′‐deoxycytidine (dGpdC) systems are among the largest to be studied by reliable theoretical methods. Exploring electron attachment to these subunits of DNA single strands provides significant progress toward definitive predictions of the electron affinities of DNA single strands. The adiabatic electron affinities of the oligonucleotides are found to be sequence dependent. Deoxycytidine (dC) on the 5′ end, dCpdG, has larger adiabatic electron affinity (AEA, 0.90 eV) than dC on the 3′ end of the oligomer (dGpdC, 0.66 eV). The geometric features, molecular orbital analyses, and charge distribution studies for the radical anions of the cytidine‐containing oligonucleotides demonstrate that the excess electron in these anionic systems is dominantly located on the cytosine nucleobase moiety. The π‐stacking interaction between nucleobases G and C seems unlikely to improve the electron‐capturing ability of the oligonucleotide dimers. The influence of the neighboring base on the electron‐capturing ability of cytosine should be attributed to the intensified proton accepting–donating interaction between the bases. The present investigation demonstrates that the vertical detachment energies (VDEs) of the radical anions of the oligonucleotides dGpdC and dCpdG are significantly larger than those of the corresponding nucleotides. Consequently, reactions with low activation barriers, such as those for O? C σ bond and N‐glycosidic bond breakage, might be expected for the radical anions of the guanosine–cytosine mixed oligonucleotides.     

A Case Study of the Likes and Dislikes of DNA and RNA in Self‐Assembly

Programmed self‐assembly of nucleic acids (DNA and RNA) is an active research area as it promises a general approach for nanoconstruction. Whereas DNA self‐assembly has been extensively studied, RNA self‐assembly lags much behind. One strategy to boost RNA self‐assembly is to adapt the methods of DNA self‐assembly for RNA self‐assembly because of the chemical and structural similarities of DNA and RNA. However, these two types of molecules are still significantly different. To enable the rational design of RNA self‐assembly, a thorough examination of their likes and dislikes in programmed self‐assembly is needed. The current work begins to address this task. It was found that similar, two‐stranded motifs of RNA and DNA lead to similar, but clearly different nanostructures.     

DFT approach to calculate electronic transfer through a segment of DNA double helix

The electronic structures of an entire segment of a DNA molecule were calculated in its single‐strand and double‐helix cases using the DFT method with an overlapping dimer approximation and negative factor counting method. The hopping conductivity of the segment was calculated by the random walk theory from the results of energy levels and wave functions obtained. The results of the single‐strand case show that the DFT method is quantitatively in agreement with that of the HF MP2 method. The results for the double helix are in good agreement with that of the experimental data. Therefore, the long‐range electron transfer through the DNA molecule should be caused by hopping of electronic charge carriers among different energy levels whose corresponding wave functions are localized at different bases of the DNA molecule. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 1109–1117, 2000     

Multiple Pentafluorophenylation of 2,2,3,3,5,6,6‐Heptafluoro‐3,6‐dihydro‐2H‐1,4‐oxazine with an Organosilicon Reagent: NMR and DFT Structural Analysis of Oligo(perfluoroaryl) Compounds

The reagent Me₃Si(C₆F₅) was used for the preparation of a series of perfluorinated, pentafluorophenyl‐substituted 3,6‐dihydro‐2H‐1,4‐oxazines ( 2 – 8 ), which, otherwise, would be very difficult to synthesize. Multiple pentafluorophenylation occurred not only on the heterocyclic ring of the starting compound 1 (Scheme), but also in para position of the introduced C₆F₅ substituent(s) leading to compounds with one to three nonafluorobiphenyl (C₁₂F₉) substituents. While the tris(pentafluorophenyl)‐substituted compound 3 could be isolated as the sole product by stoichiometric control of the reagent, the higher‐substituted compounds 5 – 8 could only be obtained as mixtures. The structures of the oligo(perfluoroaryl) compounds were confirmed by ¹⁹F‐ and ¹³C‐NMR, MS, and/or X‐ray crystallography. DFT simulations of the ¹⁹F‐ and ¹³C‐NMR chemical shifts were performed at the B3LYP‐GIAO/6‐31++G(d,p) level for geometries optimized by the B3LYP/6‐31G(d) level, a technique that proved to be very useful to accomplish full NMR assignment of these complex products.