DNA Antiadhesive Layer for Reusable Plasmonic Sensors: Nanostructure Pitch Effect

A long-term reusable sensor that provides the opportunity to easily regenerate the active surface and minimize the occurrence of undesired absorption events is an appealing solution that helps to cut down the costs and improve the device performances. Impressive advances have been made in the past years concerning the development of novel cutting-edge sensors, but the reusability can currently represent a challenge. Direct shielding of the sensor surface is not always applicable, because it can impact the device performance. This study reports an antiadhesive layer (AAL) made of 90 mg/mL DNA sodium salt from salmon testes (ssstDNA) for passivating gold plasmonic sensor surfaces. Our gold two-dimensional (2D) nanostructured plasmonic metasurfaces modified with AAL were used for DNA quantification. AAL is thin enough that the plasmonic sensor remains sensitive to subsequent deposition of DNA, which serves as an analyte. AAL protects the gold surface from unwanted nonspecific adsorption by enabling wash-off of the deposited analyte after analysis and thus recovery of the LSPR peak position (rLSPR). The calibration curve obtained on a single nanostructure (Achiral Octupolar, 100 nm pitch) gave an LOD = 105 ng/mL and an extraordinary dynamic range, performances comparable or superior to those of commercial UV-vis spectrometers for acid nucleic dosage. Two different analytes were tested: ssstDNA (∼2000 bp) in deionized water and double-strand DNA (dsDNA) of 546-1614 bp in 100 mM Tris buffer and 10 mM MgCl₂. The two nanostructures (Achiral Octupolar 25 and 100) were found to have the same sensitivity to DNA in deionized water but different sensitivity to DNA in a salt/buffer solution, opening a potential for solute discrimination. To the best of our knowledge, this is the first report on the use of AAL made of several kilobase-pairs-long dsDNA to produce a reusable plasmonic sensor. The working principle and limitations are drawn based on the LSPR and SERS study.

Visible light mediated synthesis of 6H-benzo[c]chromenes: transition-metal-free intramolecular direct C-H arylation

A synthetic approach towards the 6H-benzo[c]chromene ring under visible light and transition-metal-free conditions has been developed. Benzochromenes are synthesized from the corresponding (2-halobenzyl) phenyl ethers or (2-halophenyl) benzyl ethers using KO^tBu in dimethyl sulfoxide (DMSO) at room temperature (rt) and blue light-emitting diodes (LEDs) as the light source. This methodology replaces the use of ligands or additives, high temperatures and toxic solvents. The photostimulated reaction exhibits very good tolerance to different functional groups and 5H-dibenzo[c,f]chromenes are also effectively obtained. An electron donor-acceptor complex formed by the dimsyl anion and (2-halobenzyl) phenyl ethers was found and it induces the ET as the initial step in the photocyclization reaction. Furthermore, in order to explain the regiochemical outcome of this reaction, a theoretical analysis was performed using DFT methods.

Computation of Molecular Electron Affinities Using an Ensemble Density Functional Theory Method

The computation of electron attachment energies (electron affinities) was implemented in connection with an ensemble density functional theory method, the state-interaction state-averaged spin-restricted ensemble-referenced Kohn-Sham (SI-SA-REKS or SSR) method. With the use of the extended Koopmans' theorem, the electron affinities and the respective Dyson orbitals are obtained directly for the neutral molecule, thus avoiding the necessity to compute the ionized system. Together with the EKT-SSR (extended Koopmans' theorem-SSR) method for ionization potentials, which was developed earlier, EKT-SSR for electron affinities completes the implementation of the EKT-SSR formalism, which can now be used for obtaining electron detachment as well as the electron attachment energies of molecules in the ground and excited electronic states. The extended EKT-SSR method was tested in the calculation of several closed-shell molecules. For the molecules in the ground states, the EKT-SSR energies of Dyson's orbitals are virtually identical to the energies of the unoccupied orbitals in the usual single-reference spin-restricted Kohn-Sham calculations. For the molecules in the excited states, EKT-SSR predicts an increase of the most positive electron affinity by approximately the amount of the vertical excitation energy. The electron affinities of a number of diradicals were calculated with EKT-SSR and compared with the available experimental data. With the use of a standard density functional (BH&HLYP), the EKT-SSR electron affinities deviate on average by ca. 0.2 eV from the experimental data. It is expected that the agreement with the experiment can be improved by designing density functionals parametrized for ionization energies.

Approximate equation-of-motion coupled-cluster methods for electron affinities of closed-shell molecules

We investigate performance of the equation-of-motion coupled-cluster method at the single and doubles level (EOM-CCSD) and a series of approximate methods based on EOM-CCSD on electron affinities (EA) of closed-shell cations and neutral molecules with positive and negative EAs in this work. Our results confirm that P-EOM-MBPT2 can provide reasonable EAs when molecules with significant multireference character are not considered and its mean absolute error on EAs of these molecules is around or less than 0.2 eV. Its accuracy is comparable to that of the more expensive EOM-CCSD(2) method. Results of EOM-CCSD(2), P-EOM-MBPT2, and CIS(D_∞) indicate that the [[H, a_c ⁺], T₂] term in the 1h2p-1h block is more important on EAs than the term neglected in the 1h2p-1h2p block in P-EOM-MBPT2. We proposed an economical method where EAs from CIS(D_∞) are corrected by treating this [[H, a_c ⁺], T₂] term in the 1h2p-1h block perturbatively [corr-CIS(D_∞)]. EAs with corr-CIS(D_∞) agree very well with those of P-EOM-MBPT2 with a difference of less than 0.02 eV. Computational scaling of this method is N⁴ for the iterative part and N⁵ for some non-iterative steps. Its storage requirement is only of OV³. Corr-CIS(D_∞) is an economical and reliable method on EAs, and it can be applied to EAs of large molecules.

Simple DFT Scheme for Estimating Negative Electron Affinities

A simple density functional theory (DFT) scheme is proposed for estimating negative vertical electron affinities of neutral systems, based on a consideration of the integer discontinuity and density scaling homogeneity. The key feature is the derivation of two system-dependent exchange-correlation functionals, one appropriate for the electron deficient side of the integer and one appropriate for the electron abundant side. The electron affinity is evaluated as a linear combination of frontier orbital energies from self-consistent Kohn-Sham calculations on the neutral system using these functionals. For two assessments comprising a total of 43 molecules, the scheme provides electron affinities that are in good agreement with experimental values and which are an improvement over those from the DFT method of Tozer and De Proft [ J. Phys. Chem. A 2005 , 109 , 8923 ]. The scheme is trivial to implement in any Kohn-Sham program, and the computational cost is that of a series of generalized gradient approximation Kohn-Sham calculations. More generally, the study provides a prescription for performing low-cost, self-consistent Kohn-Sham calculations that yield frontier orbital energies that approximately satisfy the appropriate Koopmans conditions, without the need for exact exchange.

In search of the best DFT functional for dealing with organic anionic species

“And the winner is…” This work assesses the ability of different Density Functional Theory (DFT) functionals for a proper treatment of organic anionic species.

Understanding Solvent Effects on the Properties of Two-Dimensional Transition Metal Dichalcogenides

Two-dimensional (2D) transition metal dichalcogenides (TMDCs) have emerged as attractive direct bandgap semiconducting materials with remarkable properties. Recently, TMDC-based electronic and optoelectronic systems have been demonstrated with various chemical doping and functionalization approaches for modulating their physical properties and enhancing device performances. However, the dependence of intrinsic properties of TMDCs on diverse solvents, which are used necessarily in fabrication processes and chemical doping, remains largely unaddressed. Here we report a charge transfer mechanism in TMDCs by commonly used solvents such as chloroform, toluene, acetone, and 2-propanol, which significantly changes the physical properties of monolayer MoS2 and WSe2. We find that the relative difference in electronegativity between solvents and TMDCs drives the transfer of electrons from or to the TMDCs, which results in photoluminescence (PL) enhancement or quenching depending on the change of carrier density in TMDCs. The analysis of exciton and trion spectral weights in MoS2 as a function of solvent electronegativity provides evidence of charge transfer. Finally, conductive atomic force microscopy (C-AFM) on TMDCs before and after immersion in the solvents further supports the charge transfer mechanism and resulting changes in carrier density. Our results highlight the importance of selection of solvents for solution-processed 2D TMDC devices and systems.

Applicability of optimal functional tuning in density functional calculations of ionization potentials and electron affinities of adenine–thymine nucleobase pairs and clusters

Successful application of optimally tuned long-range corrected functionals for calculation of vertical ionization potentials and electron affinities of various adenine–thymine nucleobase pairs and clusters is demonstrated.

Experimental and DFT study on the indium-mediated synthesis of benzophenones via arylstannanes

A DFT analysis was performed with the aim to explaining the narrow scope of the indium-promoted reaction of aroyl chlorides with arylstannanes.

Excess electron localization in solvated DNA bases

We present a first-principles molecular dynamics study of an excess electron in condensed phase models of solvated DNA bases. Calculations on increasingly large microsolvated clusters taken from liquid phase simulations show that adiabatic electron affinities increase systematically upon solvation, as for optimized gas-phase geometries. Dynamical simulations after vertical attachment indicate that the excess electron, which is initially found delocalized, localizes around the nucleobases within a 15 fs time scale. This transition requires small rearrangements in the geometry of the bases.

Empirical correlation methods for temporary anions

A temporary anion is a short-lived radical anion that decays through electron autodetachment into a neutral molecule and a free electron. The energies of these metastable species are often predicted using empirical correlation methods because ab initio predictions are computationally very expensive. Empirical correlation methods can be justified in the framework of Weisskopf-Fano-Feshbach theory but tend to work well only within closely related families of molecules or within a restricted energy range. The reason for this behavior can be understood using an alternative theoretical justification in the framework of the Hazi-Taylor stabilization method, which suggests that the empirical parameters do not so much correct for the coupling of the computed state to the continuum but for electron correlation effects and that therefore empirical correlation methods can be improved by using more accurate electronic structure methods to compute the energy of the confined electron. This idea is tested by choosing a heterogeneous reference set of temporary states and comparing empirical correlation schemes based on Hartree-Fock orbital energies, Kohn-Sham orbital energies, and attachment energies computed with the equation-of-motion coupled-cluster method. The results show that using more reliable energies for the confined electron indeed enhances the predictive power of empirical correlation schemes and that useful correlations can be established beyond closely related families of molecules. Certain types of σ* states are still problematic, and the reasons for this behavior are analyzed. On the other hand, preliminary results suggest that the new scheme can even be useful for predicting energies of bound anions at a fraction of the computational cost of reliable ab initio calculations. It is then used to make predictions for bound and temporary states of the furantrione and croconic acid radical anions.

Should negative electron affinities be used for evaluating the chemical hardness?

Despite recent advances in computing negative electron affinities using density-functional theory, it is an open issue as to whether it is appropriate to use negative electron affinities, instead of zero electron affinity, to compute the chemical hardness of atoms and molecules with metastable anions. We seek to answer this question using the accepted empirical rules linking the chemical hardness to the atomic size and the polarizability; we also propose a new correlation with the C6 London dispersion coefficient. For chemical reactivity in the gas phase, it seems to make no difference whether negative, or zero, electron affinities are used for systems with metastable anions. For reactions in solution the evidence that is presently available is insufficient to establish a preference. In addressing this issue, we noted that electron affinity data from which atomic chemical hardness values are computed are out of date; an update to Pearson's classic 1988 table [Inorg. Chem., 1988, 27, 734-740] is thus provided.

Known drug space as a metric in exploring the boundaries of drug-like chemical space

In this work, marketed drug compounds (or known drug space) were used as a metric to test the principles of eliminating parent structures of the nitrenium ion (aryl-amine/nitro compounds) as well as sulphur and halogen containing molecules from screening compound collections. Molecules containing such moieties and/or atoms have biological and physiochemical properties, which possibly make them less attractive as leads in drug development. It was found that precursors to the nitrenium ion were relatively abundant in known drug space at 14%. Thus, their simple elimination from drug-like chemical space is not advisable. Interestingly, the mutagenic potential of the nitrenium ions is linked to their stability and quantum mechanical calculations can be used to estimate it. Furthermore, 24% of drugs investigated contained sulphur atoms and around 28% were halogenated. As some sulphur containing moieties were abundant whilst others were scarce, it was deduced that it would be more effective to eliminate specific molecular scaffolds rather than all sulphur containing molecules. In conclusion, it has been shown that by statistically analysing known drug space a better understanding of the boundaries of drug-like chemical space was established which can help medicinal chemists in finding rewarding regions of chemical space.

Guanine radical reaction processes: a computational description of proton transfer in X-irradiated 9-ethylguanine single crystals

Computational methods based on DFT procedures have been used to investigate proton-transfer processes in irradiated 9-ethylguanine crystals. Previous experimental results from X-irradiation and study of this system at 10 K found significant concentrations of two main products, R1, formed by N7-hydrogenation of the purine ring, and R2, the primary one-electron oxidation product (Jayatilaka, N.; Nelson, W. H. J. Phys. Chem. B 2007, 111, 7887). The objective of this work is to describe the processes leading to these products using computational methods that take into account molecular packing and bulk dielectric properties. The basic concept is that a proton will transfer following ionization if the net electronic energy of the system, consisting of the donor plus the acceptor plus any intervening molecules, becomes lower. Three approaches were used to investigate this concept, two based on energies computed for single molecules and one based on energies computed for two-molecule clusters arranged as in the crystals. The results are that the methods successfully predict the observed behavior, that it is energetically favorable on one-electron reduction for proton H1 to transfer from a neutral molecule to N7 of the neighbor, forming the N7-hydrogenated product, and that there is virtually no energy advantage for a proton to transfer upon one-electron oxidation. The results also support the proposal that the C8 H-addition radical, found only upon irradiation at 300 K, was the product of intramolecular transfer of the H7 proton to C8 in a process apparently requiring sufficient thermal energy for activation. Finally, the computations predict hyperfine couplings and tensors in very good agreement with those from experiment, thereby providing additional evidence for the success of the computations in describing the experimental observations.

Ab initio determination of the electron affinities of DNA and RNA nucleobases

High-level quantum-chemical ab initio coupled-cluster and multiconfigurational perturbation methods have been used to compute the vertical and adiabatic electron affinities of the five canonical DNA and RNA nucleobases: uracil, thymine, cytosine, adenine, and guanine. The present results aim for the accurate determination of the intrinsic electron acceptor properties of the isolated nucleic acid bases as described by their electron affinities, establishing an overall set of theoretical reference values at a level not reported before and helping to rule out less reliable theoretical and experimental data and to calibrate theoretical strategies.

Bisphosphonate inhibitors of ATP-mediated HIV-1 reverse transcriptase catalyzed excision of chain-terminating 3'-azido, 3'-deoxythymidine: a QSAR investigation

We report the results of an investigation of the inhibition of the ATP-mediated HIV-1 reverse transcriptase catalyzed phosphorolysis in vitro of AZT from AZT-terminated DNA primers by a series of 42 bisphosphonates. The four most active compounds possess neutral, halogen-substituted phenyl or biphenyl sidechains and have IC(50) values < 1 microM in excision inhibition assays. Use of two comparative molecular similarity analysis methods to analyze these inhibition results yielded a classification model with an overall accuracy of 94%, and a regression model having good accord with experiment (q(2)=0.63, r(2)=0.91), with the experimental activities being predicted within, on average, a factor of 2. The most active species had little or no toxicity against three human cell lines (IC(50)(avg) > 200 microM). These results are of general interest since they suggest that it may be possible to develop potent bisphosphonate-based AZT-excision inhibitors with little cellular toxicity, opening up a new route to restoring AZT sensitivity in otherwise resistant HIV-1 strains.

Microhydration of the guanine-cytosine (GC) base pair in the neutral and anionic radical states: a density functional study

A density functional study of the effects of microhydration on the guanine-cytosine (GC) base pair and its anion radical is presented. Geometries of the GC base pair in the presence of 6 and 11 water molecules were fully optimized in the neutral (GC-nH2O) and anion radical [(GC-nH2O)*-] (n = 6 and 11) states using the B3LYP method and the 6-31+G** basis set. Further, vibrational frequency analysis at the same level of theory (B3LYP/6-31+G**) was also performed to ensure the existence of local minima in these hydrated structures. It was found that water molecules surrounding the GC base pair have significant effects on the geometry of the GC base pair and promote nonplanarity in the GC base pair. The calculated structures were found to be in good agreement with those observed experimentally and obtained in molecular dynamics (MD) simulation studies. The water molecules in neutral GC-nH2O complexes lie near the ring plane of the GC base pair where they undergo hydrogen bonding with both GC and each other. However, in the GC anion radical complexes (GC-nH2O, n = 6, 11), the water molecules are displaced substantially from the GC ring plane. For GC-11H2O*-, a water molecule is hydrogen-bonded with the C6 atom of the cytosine base. We found that the hydration shell initially destabilizes the GC base pair toward electron capture as a transient anion. Energetically unstable diffuse states in the hydration shell are suggested to provide an intermediate state for the excess electron before molecular reorganization of the water molecules and the base pair results in a stable anion formation. The singly occupied molecular orbital (SOMO) in the anion radical complexes clearly shows that an excess electron localizes into a pi orbital of cytosine. The zero-point-energy (ZPE-) corrected adiabatic electron affinities (AEAs) of the GC-6H2O and GC-11H2O complexes, at the B3LYP/6-31+G** level of theory, were found to be 0.74 and 0.95 eV, respectively. However, the incorporation of bulk water as a solvent using the polarized continuum model (PCM) increases the EAs of these complexes to 1.77 eV.

Species with negative electron affinity and standard DFT methods. Finding the valence anions

Recently, we have shown that traditional bound-electron DFT models are reliable enough to reproduce negative electron affinities (EA) within a few meV, as long as the valence anion state is found, but they seem to fail in predicting the lowest EA when the ground anion state obtained is non-valence, which holds the extra electron in a diffuse orbital around the molecule; here we propose an alternative approach for finding the valence anion state, based on the stabilization exerted by a polar solvent; the methodology yields correct EA values (i.e. beyond the Koopman's theorem approximation) by gradually decreasing the dielectric constant of the medium.

Modeling temporary anions in density functional theory: calculation of the Fukui function

Two approaches are investigated for modeling electron densities of temporary anions in density functional theory (DFT). Both rely on an artificial binding of the excess electron, in one case by a compact basis set and in the other by a potential wall. The key feature of the calculations is that the degree of binding is controlled in both cases by knowledge of the negative electron affinity of the corresponding neutral, approximated in terms of DFT local functional frontier orbital eigenvalues and vertical ionization potential, A=-(epsilon(LUMO)+epsilon(HOMO))-I. To illustrate the two approaches, Fukui functions for nucleophilic attack are determined in four molecules with increasingly negative electron affinities. They yield very similar results, which are notably different to those determined without artificial electron binding. The use of a potential wall has the attractive feature that large, diffuse basis sets can be used, avoiding the need for a compact basis, tailored to a particular molecule.

On the position of the potential wall in DFT temporary anion calculations

A simple method was recently proposed [D. J. Tozer and F. De Proft, J. Chem. Phys., 2007, 127, 034108] for performing explicit density functional theory (DFT) calculations on temporary anions. The excess electron in the anion is bound by a potential wall, the position of which is determined by a single parameter lambda, chosen to reproduce an approximate, theoretical negative electron affinity in the corresponding neutral. In the present study, the system-dependence of lambda and the sensitivity of the negative affinities to this parameter are investigated for 34 organic molecules. The results demonstrate that the system-dependent lambda values can be replaced by a global, average value, with minimal effect on the affinities. It follows that the orbitals, electron density, and other properties of a temporary anion can be determined from a single DFT calculation on that anion, using a large, diffuse basis set. As an illustration, singly occupied molecular orbitals and spin densities are determined for the anions of guanine and adenine nucleobases. Despite the use of a diffuse basis set, the method yields quantities that are localised in the molecular framework, associated with vertical electron affinities of -1.2 eV and -0.8 eV, respectively.

Determination of Redox Potentials for the Watson−Crick Base Pairs, DNA Nucleosides, and Relevant Nucleoside Analogues

Redox potentials for the DNA nucleobases and nucleosides, various relevant nucleoside analogues, Watson-Crick base pairs, and seven organic dyes are presented based on DFT/B3LYP/6-31++G(d,p) and B3YLP/6-311+G(2df,p)//B3LYP/6-31+G* levels of calculations. The values are determined from an experimentally calibrated set of equations that correlate the vertical ionization (electron affinity) energy of 20 organic molecules with their experimental reversible oxidation (reduction) potential. Our results are in good agreement with those estimated experimentally for the DNA nucleosides in acetonitrile solutions (Seidel et al. J. Phys. Chem. 1996, 100, 5541). We have found that nucleosides with anti conformation exhibit lower oxidation potentials than the corresponding syn conformers. The lowering in the oxidation potential is due to the formation of an intramolecular hydrogen bonding interaction between the 5'-OH group of the sugar and the N3 of the purine bases or C2=O of the pyrimidine bases in the syn conformation. Pairing of adenine or guanine with its complementary pyrimidine base decreases its oxidation potential by 0.15 or 0.28 V, respectively. The calculated energy difference between the oxidation potential for the G.C base pair and that of the guanine base is in good agreement with the experimental value estimated recently (0.34 V: Caruso, T.; et al. J. Am. Chem. Soc. 2005, 127, 15040). The complete and consistent set of reversible redox values determined in this work for the DNA constituents is expected to be of considerable value to those studying charge and electronic energy transfer in DNA.