Computational study on the structural and optoelectronic properties of a carbazole-benzothiadiazole based conjugated oligomer with various alkyl side-chain lengths

The effect of the alkyl side-chain length on the structural and optoelectronic properties of poly[N-9′-heptadecanyl-27-carbazole-alt-55-(4′,7′-di-2-thienyl-2′,1′,3′-benzothiadiazole)] (PCDTBT) conjugated oligomers have been studied by density functional theory (DFT) and time-dependent density functional theory (TD-DFT). The study was carried out by varying the length of alkyl side-chain attached to the nitrogen atom of the carbazole unit of the PCDTBT oligomers. The structural properties of the optimised oligomers were then studied by determining the bond-length alternation and dihedral angles (Φ) for various side-chain lengths. Total energy calculations for the determination of HOMO energy (E_HOMO), LUMO energy (E_LUMO), and fundamental energy gap (E_Gap) were performed using DFT at the B3LYP/6-31G(d), while the first singlet excitation energies (E_Opt) were calculated by TD-DFT also at the same level of theory. It was observed that there are no significant structural changes occurring as the alkyl chain lengths are varied. For the electronic properties, very small differences (i.e. ~0.01 eV) were observed for E_Gap and E_Opt while the exciton binding energies (E_B) were virtually the same. The results suggest that using shorter alkyl side-chains do not significantly affect the structural and optoelectronic properties of the carbazole-benzothiadiazole based polymer. The observations can aid future computational design studies of analogous systems by reducing large structures thus decreasing computational costs.     

DFT study of conductive properties of three polymers formed by bicyclic furans

Density functional theory methods were employed to study the electronic, structural and conductive properties of classical bicyclic furans. In this paper, studies of monomers, oligomers and polymers of furo[3,4-b]furan, furo[2,3-b]furan and furo[3,2-b]furan are presented. To gain detailed information on conjugational degree, we selected the nucleus-independent chemical shift as a method for examining the changes in conjugational degree. Furthermore, three parameters of density of state, effective mass (m*) and kinetic model of mobility (μ) were also investigated. The variable trends of all parameters from monomers to tetramers indicate that poly(4,4′-bifuro[3,4-b]furan), poly(trans-2,2′-bifuro[3,2-b]furan) and poly(cis-2,2′-bifuro[3,2-b]furan) are good candidates for conductive materials, which are consistent with band structure analyses showing that the three polymers had narrower band gaps (1.21, 1.93 and 1.89 eV, respectively) than other polymers.     

Optical activity of single-stranded polydeoxyadenylic and polyriboadenylic acids; dependence of adenine chromophore cotton effects on polymer conformation

Circular dichroism (CD) curves are reported for poly dA, (pdA)₆, (pdA)₂, poly A, ApAp, ApA, AMP, dApA, pdApA, A-2′-O-methyl pA, and A-2′-O-methyl pAp. Analysis of these curves indicated the presence of single CD bands at 228–230 mμ and at 278–280 mμ in oligomers longer than dinucleotides. In the case of dinucleotides and mononucleotides (from the literature, in addition to those studied here), the 230 mμ CD of band appears but the 280 mμ CD band does not. We assign the 230 mμ band to a very weak π–π* transition at this wavelength. From theoretical considerations, we show that the 280 mμ band is not an exciton component of the strong π–π* transition at 260 mμ in adenine. We conclude that the 280 mμ CD band must be assigned to a distinct absorption, not previously reported, which we suggest arises from an n–π* transition. The fact that the n–π* CD band at 280 mμ is not seen in mononucleotides or dinucleotides is ascribed to solvation of the adenine ring by water, which shifts the band to shorter wavelengths. Therefore, only interior residues of oligomers have the 280 mμ band, and the optical activity of a polymer cannot be computed from that of a dinucleotide, by using a nearest-neighbor approximation. The existence of this end effect hag been tested, by taking it into account in computing the rotational strengths of the 278 mμ n–π* transition for several oligomers; it is pointed out that a more sensitive test of this end effect would require CD data for the oligo dA series of 3 to 5 residues. We speculate about the structural and optical differences between poly dA and poly A, and point out the need for a theoretical treatment of n–π* Cotton effects in polynucleotides.     

Molecular states in single-stranded adenylate chains by relaxation analysis

The single-strand helix-coil transition in various oligo- and polyadenylates is characterized by means of an improved cable temperature-jump technique. In all the polymers studied {poly(rA), poly(dA), poly[A(m^2′)] and poly[A(e^2′)]} helix-coil relaxation is observed in the time range from 30 to 1000 nsec. Relaxation-time constants observed at wavelengths λ<280 nm (τ_α) are different from those found at λ >280 nm (τβ), indicating the presence of more than two conformational states. The time constants τ_α increase in the series poly(dA), poly[A(m^2′)], constants τ_β/τ_α is approximately 2.5, except in poly(dA) where τ_β/τ_α ≈ 9. Relaxation measurements with r(A)_n- oligomers show a decrease in conformational mobility with increasing chain length. The relaxation curves also demonstrate that “internal” residues have lower reaction rates than residues at the ends of the oligomer chain. Measurement in D₂O reveal a solvent isotope effect for τ_α of +87% for poly(rA), and of +53% for poly(dA), whereas no isotope effect is found in τ_β. The absence of “slow” relaxation processes in the model compound 9,9′ -trimethylenebisadenine shows that the relatively low rate of the single-strand helix-coil transitions is due to the coupling of base stacking with the folding of the sugar–phosphate chain. The absence of a seprate relaxation process (corresponding to τ_β) in 9,9′-trimethylenebisadenine, as well as in the dinucleotides ApC and CpA, suggests that this relaxation process is dependent upon the presence of both the sugar–phosphate chain and of adjacent adenine bases. The experimental data provide evidence that there is more than one ordered conformation in various single-stranded oligo- and polyadenylates and that the transition between these conformations is influenced by the sugar conformation.     

The electronic properties of poly(p-phenylenevinylene) derivatives and their monomers and oligomers

The electronic structures of monomers, oligomers and polymers of poly(p-phenylenevinylene) (PPV) derivatives are calculated and analysed based on density functional theory (DFT) methods. The influences of different substituent groups on the band gaps are discussed. Strong relationships are found between band-gap and bond length alternation (BLA) of polymers, and between band-gap and Wiberg bond index (WBI). Analysis of nuclear independent chemical shift (NICS) reveals that oligomers with similar energy gaps have close values of NICS.     

Balancing High Open Circuit Voltage over 1.0 V and High Short Circuit Current in Benzodithiophene‐Based Polymer Solar Cells with Low Energy Loss: A Synergistic Effect of Fluorination and Alkylthiolation

Based on the most recently significant progress within the last one year in organic photovoltaic research from either alkylthiolation or fluorination on benzo[1,2‐b:4,5‐b′]dithiophene moiety for high efficiency polymer solar cells (PSCs), two novel simultaneously fluorinated and alkylthiolated benzo[1,2‐b:4,5‐b′] dithiophene (BDT)‐based donor–acceptor (D–A) polymers, poly(4,8‐bis(5′‐((2″‐ethylhexyl)thio)‐4′‐fluorothiophen‐2′‐yl)benzo[1,2‐b:4,5‐b′]dithiophene‐2,6‐diyl)‐alt‐2′‐ethylhexyl‐3‐fluorothieno[3,4‐b]thiophene‐2‐carboxylate (PBDTT‐SF‐TT) and poly(4,8‐bis(5′‐((2″‐ethylhexyl)thio)‐4′‐fluorothiophen‐2′‐yl)benzo[1,2‐b:4,5‐b′]dithiophene‐2,6‐diyl)‐alt‐1,3‐bis(thiophen‐2‐yl)‐5,7‐bis(2‐ethylhexyl)benzo[1,2‐c:4,5‐c′]dithiophene‐4,8‐dione (PBDTT‐SF‐BDD), namely, via an advantageous and synthetically economic route for the key monomer are reported herein. Synergistic effects of fluorination and alkylthiolation on BDT moieties are discussed in detail, which is based on the superior balance between high V_oc and large J_sc when PBDTT‐SF‐TT/PC₇₁BM and PBDTT‐SF‐BDD/PC₇₁BM solar cells present their high V_oc as 1.00 and 0.97 V (associated with their deep highest occupied molecular orbital level of ?5.54 and ?5.61 eV), a moderately high J_sc of 14.79 and 14.70 mA cm^?2, and thus result a high power conversion efficiency of 9.07% and 9.72%, respectively. Meanwhile, for PBDTT‐SF‐TT, a very low energy loss of 0.59 eV is pronounced, leading to the promisingly high voltage, and furthermore performance study and morphological results declare an additive‐free PSC from PBDTT‐SF‐TT, which is beneficial to practical applications.     

The Effect of PCBM Dimerization on the Performance of Bulk Heterojunction Solar Cells

Increasing the lifetime of polymer based organic solar cells is still a major challenge. Here, the photostability of bulk heterojunction solar cells based on the polymer poly[4,4′‐bis(2‐ethylhexyl)dithieno[3,2‐b:2′,3′‐d]silole)‐2,6‐diyl‐alt‐[2,5‐bis(3‐tetradecylthiophen‐2‐yl)thiazole[5,4‐d]thiazole)‐1,8‐diyl] (PDTSTzTz) and the fullerene [6,6]‐phenyl‐C₆₁‐butyric acid methyl ester (PC₆₀BM) under inert atmosphere is investigated. Correlation of electrical measurements on complete devices and UV‐vis absorption measurements as well as high‐performance liquid chromatography (HPLC) analysis on the active materials reveals that photodimerization of PC₆₀BM is responsible for the observed degradation. Simulation of the electrical device parameters shows that this dimerization results in a significant reduction of the charge carrier mobility. Both the dimerization and the associated device performance loss turn out to be reversible upon annealing. BisPC₆₀BM, the bis‐substituted analog of PC₆₀BM, is shown to be resistant towards light exposure, which in turn enables the manufacture of photostable PDTSTzTz:bisPC₆₀BM solar cells.     

The impact of Cu atoms on the reactivity of ZrO2 oligomers

A theoretical study on (ZrO₂) _n (n = 1–5) and Cu/ZrO₂ oligomers is presented, DFT/B3LYP/6-31G** calculations along with Lanl2DZ pseudopotentials on metallic centers have been used to predict ionization potentials and electron affinities, chemical potentials and bandgaps indicating that the reactivity reaches reasonably constant values at n = 5. The effect of copper atoms adsorbed on (ZrO₂) _n is discussed and the reactivity of oligomers of ZrO₂ and Cu/ZrO₂ are compared, results indicate that Cu activates the systems by localizing the specific nucleophilic and electrophilic reactivity.     

Germanium‐ and Silicon‐Substituted Donor–Acceptor Type Copolymers: Effect of the Bridging Heteroatom on Molecular Packing and Photovoltaic Device Performance

The effects of heteroatom substitution from a silicon atom to a germanium atom in donor‐acceptor type low band gap copolymers, poly[(4,4′‐bis(2‐ethylhexyl)dithieno[3,2‐b:2′,3′‐d]silole)‐2,6‐diyl‐alt‐(2,1,3‐benzothiadiazole)‐4,7‐diyl] (PSiBTBT) and poly[(4,4′‐bis(2‐ethylhexyl)dithieno[3,2‐b:2′,3′‐d]germole)‐2,6‐diyl‐alt‐(2,1,3‐benzothiadiazole)‐4,7‐diyl] (PGeBTBT), are studied. The optoelectronic and charge transport properties of these polymers are investigated with a particular focus on their use for organic photovoltaic (OPV) devices in blends with phenyl‐C₇₀‐butyric acid methyl ester (PC₇₀BM). It is found that the longer C‐Ge bond length, in comparison to C‐Si, modifies the molecular conformation and leads to a more planar chain conformation in PGeBTBT than PSiBTBT. This increase in molecular planarity leads to enhanced crystallinity and an increased preference for a face‐on backbone orientation, thus leading to higher charge carrier mobility in the diode configuration. These results provide important insight into the impact of the heavy atom substitution on the molecular packing and device performance of polymers based on the poly[2,6‐(4,4‐bis‐(2‐ethylhexyl)‐4H‐cyclopenta[2,1‐b;3,4‐b]‐dithiophene)‐alt‐4,7‐(2,1,3‐benzothiadiazole) (PCPDTBT) backbone.     

A Thieno[3,2‐c]Isoquinolin‐5(4H)‐One Building Block for Efficient Thick‐Film Solar Cells

An aromatic lactam acceptor unit, thieno[3,2‐c]isoquinolin‐5(4H)‐one (TIQ), is developed. Compared with its analogues, dithieno[3,2‐b:2′,3′‐d]pyridin‐5(4H)‐one (DTP) and phenanthridin‐6(5H)‐one (PN), TIQ shows its advantage in constructing donor–acceptor (D–A) copolymers for efficient solar cells. TIQ‐based D–A copolymer PTIQ4TFBT delivers a power conversion efficiency (PCE) of 10.16% in polymer:fullerene solar cells, while those based on DTP and PN copolymers, PDTP4TFBT and PPN4TFBT, afford PCEs around 8.5%. The higher performance of PTIQ4TFBT:PC₇₁BM solar cells originates from enhanced short‐circuit current density (J_sc) and fill factor (FF), because of favorable morphology, less bimolecular recombination, and balanced charge transport in the active layer. Moreover, the performance for PTIQ4TFBT:PC₇₁BM solar cells is less sensitive to active layer thickness than PDTP4TFBT:PC₇₁BM and PPN4TFBT:PC₇₁BM solar cells. Over 8% PCEs can be obtained from PTIQ4TFBT:PC₇₁BM solar cells when the active layer thickness is over 500 nm.     

Fluorescent 2-aza-epsilon-adenosine derivatives of polyadenylic acid, polyuridylic acid, and polyinosinic acid.

A new fluorescent analog of adenosine, 1,N⁶-etheno-2-aza-adenosine, has been incorporated into polynucleotides by polynucleotide phosphorylase polymerization of 1,N⁶-etheno-2-aza-adenosine-5′-diphosphate and adenosine-5′-diphosphate, uridine-5′-diphosphate, or inosine-5′-diphosphate. These new oligonucletides possess high fluorescence when excited at 358 nm and emit at 495 nm. The ratio of the fluorescent and nonfluorescent portions of the copolymer can be controlled by the initial composition of the 2-aza-ε-adenosine-diphosphate and the corresponding nucleoside diphosphate. Fluorescent copolymers with a ratio varying from 1.6 to 35 have thus been synthesized. The physicochemical study of copolymers containing less than 10% of the 1,N⁶-etheno-2-aza-adenosine moiety showed that they are similar to poly(A), poly(U), or poly(I). Therefore, fluorescence and polarization study of the 1,N⁶-etheno-2-aza-adenosine residues that have been incorporated into the copolymer provides a sensitive indicator for the structure of the copolymer. Potentially these new copolymers may provide unique roles in probing the structure of poly(C) and poly(A) in cellular mRNA.     

Chiroptical properties of 2,2’‐bioxirane

The two enantiomers of 2,2′‐bioxirane were synthesized, and their chiroptical properties were thoroughly investigated in various solvents by polarimetry, vibrational circular dichroism (VCD), and Raman optical activity (ROA). Density functional theory (DFT) calculations at the B3LYP/aug‐cc‐pVTZ level revealed the presence of three conformers (G₊, G_?, and cis) with Gibbs populations of 51, 44, and 5% for the isolated molecule, respectively. The population ratios of the two main conformers were modified for solvents exhibiting higher dielectric constants (G_? form decreases whereas G₊ form increases). The behavior of the specific optical rotation values with the different solvents was correctly reproduced by time‐dependent DFT calculations using the polarizable continuum model (PCM), except for the benzene for which explicit solvent model should be necessary. Finally, VCD and ROA spectra were perfectly reproduced by the DFT/PCM calculations for the Boltzmann‐averaged G₊ and G_? conformers.     

Crosslinkable Amino‐Functionalized Conjugated Polymer as Cathode Interlayer for Efficient Inverted Polymer Solar Cells

A novel crosslinkable aminoalkyl‐functionalized polymer, poly[9,9‐bis(6‐(N,N‐diethylamino)propyl)fluorene‐alt‐9,9‐bis(hex‐5‐en‐1‐yl)‐fluorene] (PFN‐V), is designed and synthesized. The resulting polymer can be rapidly crosslinked by UV‐curing within 5 s in a nearly quantitative yield based on the “click” chemistry of alkyene end‐groups of the PFN‐V side chains and the addition of 1,8‐octanedithiol. The crosslinked PFN‐V film exhibits excellent solvent resistance property and can act as effective cathode interlayer to modify the indium tin oxide (ITO) electrode, which can thus facilitate the formation of Ohmic contact between cathode and active layer. The surface energy of PFN‐V is quite comparable to that of PC₇₁BM, which is favorable for the formation of vertical phase separation in the bulk heterojunction film that can facilitate extraction of charges as verified by transient photocurrent measurements. Based on the resulting PFN‐V as the cathode interlayer, the fabricated polymer solar cells with inverted device structure show a remarkable enhancement of power conversion efficiency from 3.11% for the control device to 9.18% for PFN‐V based device. These observations indicate that the synthesized PFN‐V can be a promising crosslinked copolymer as the cathode interlayer for high performance polymer solar cells.     

Density functional theory study of the potassium complexation of an unsymmetrical 1,3-alternate calix[4]-crown-5-N-azacrown-5 bearing two different crown rings

Theoretical studies of an unsymmetrical calix[4]-crown-5-N-azacrown-5 (1) in a fixed 1,3-alternate conformation and the complexes 1·K⁺(a), 1·K⁺(b), 1·K⁺(c) and 1·K⁺K⁺ were performed using density functional theory (DFT) at the B3LYP/6-31G* level. The fully optimized geometric structures of the free macroligand and its 1:1 and 1:2 complexes, as obtained from DFT calculations, were used to perform natural bond orbital (NBO) analysis. The two main types of driving force metal–ligand and cation–π interactions were investigated. NBO analysis indicated that the stabilization interaction energies (E ₂) for O…K⁺ and N…K⁺ are larger than the other intermolecular interactions in each complex. The significant increase in electron density in the RY* or LP* orbitals of K⁺ results in strong host–guest interactions. In addition, the intermolecular interaction thermal energies (ΔE, ΔH, ΔG) were calculated by frequency analysis at the B3LYP/6-31G* level. For all structures, the most pronounced changes in the geometric parameters upon interaction are observed in the calix[4]arene molecule. The results indicate that both the intermolecular electrostatic interactions and the cation–π interactions between the metal ion and π orbitals of the two pairs that face the inverted benzene rings play a significant role.     

Estimation of the circular dichroism exhibited by statistical coils of poly(L-alanine) and unionized poly(L-lysine) in water

The circular dichroism of Ac-(Ala)_x-OMe and H-Lys-(Lys)_x-OH with x = 1, 2, 3, and 4 has been measured in aqueous solutions. The oligomers with x = 4 show similar circular dichroism spectra in water when the lysyl amino groups are protonated, and they respond in similar fashion to heating and to sodium perchlorate. Both oligomers at 15°C exhibit a positive circular dichroism band at 217–218 nm, which is eliminated by the isothermal addition of 4 M sodium perchlorate or by heating. The positive circular dichroism of the lysine oligomer is also eliminated when the pH is elevated to deprotonate the amino groups. Positive circular dichroism is still observed for Ac-(Ala)₄-OMe at elevated pH. Circular dichroism spectra have been estimated for poly(L -alanine) and poly(L -lysine) as statistical coils under the above conditions, based on the trends established with the oligomers. Poly(L -lysine) and poly(L -alanine) are predicted to exhibit similar circular dichroism behavior in aqueous solution so long as the lysyl amino groups are protonated. The circular dichroism of the statistical coil of poly(L -lysine), but not poly(L -alanine), is predicted to change when the pH is elevated sufficiently to deprotonate the lysyl amino groups. These results suggest that the unionized lysyl side chains participate in interactions that are not available to poly(L -alanine). Hydrophobic interactions may occur between the unionized lysyl side chains. Protonation of the lysyl amino groups is proposed to disrupt these interactions, causing poly(L -alanine) and protonated poly(L -lysine) to have similar circular dichroism properties.     

8.0% Efficient All‐Polymer Solar Cells with High Photovoltage of 1.1 V and Internal Quantum Efficiency near Unity

In very recent years, growing efforts have been devoted to the development of all‐polymer solar cells (all‐PSCs). One of the advantages of all‐PSCs over the fullerene‐based PSCs is the versatile design of both donor and acceptor polymers which allows the optimization of energy levels to maximize the open‐circuit voltage (V_oc). However, there is no successful example of all‐PSCs with both high V_oc over 1 V and high power conversion efficiency (PCE) up to 8% reported so far. In this work, a combination of a donor polymer poly[4,8‐bis(5‐(2‐octylthio)thiophen‐2‐yl)benzo[1,2‐b:4,5‐b′]dithiophene‐2,6‐diyl‐alt‐(5‐(2‐ethylhexyl)‐4H‐thieno[3,4‐c]pyrrole‐4,6(5H)‐dione)‐1,3‐diyl] (PBDTS‐TPD) with a low‐lying highest occupied molecular orbital level and an acceptor polymer poly[[N,N′‐bis(2‐octyldodecyl)‐naphthalene‐1,4,5,8‐bis(dicarboximide)‐2,6‐diyl]‐alt‐thiophene‐2,5‐diyl] (PNDI‐T) with a high‐lying lowest unoccupied molecular orbital level is used, realizing high‐performance all‐PSCs with simultaneously high V_oc of 1.1 V and high PCE of 8.0%, and surpassing the performance of the corresponding PC₇₁BM‐based PSCs. The PBDTS‐TPD:PNDI‐T all‐PSCs achieve a maximum internal quantum efficiency of 95% at 450 nm, which reveals that almost all the absorbed photons can be converted into free charges and collected by electrodes. This work demonstrates the advantages of all‐PSCs by incorporating proper donor and acceptor polymers to boost both V_oc and PCEs.     

A Comparative Semiempirical, Ab initio and DFT Study of Decarbonylation of Cyclic Ketones Part 1: Thermal Fragmentation of Cyclopropanone

Calculations using different quantum mechanical methods including semiempirical (MNDO,AM1 and PM3), ab initio (RHF and MP2 calculations using the 6-311G and 6-311++G^** basis sets), and density functional theory (LSDA, BP, MIXBP and B3LYP, i.e., B3LYP/6-311+G**//B3LYP/6-31G*) have been performed on the thermal fragmentation of cyclopropanone to ethylene and carbon monoxide. All RHF calculations predict a concerted single step mechanism for this conversion. The estimated activation energies vary from 34.4 to 54.6 kcal·mol^-1, mainly localized around 37±2 kcal·mol^-1, depending on the method. Whereas the calculated RHF reaction energies also varied from 14.5 to -33.3 kcal·mol^-1, the B3LYP/6-311+G**//B3LYP/6-31G* method predicts the experimental value (-17.7 kcal·mol^-1) within experimental uncertainties. Remarkably, semiempirical AM1 and PM3 methods and simple DFT calculations, LSDA, predict comparable results to the more advanced methods. UHF ab initio calculations predict the same single step mechanism, whereas a multistep biradical mechanism with an unrealistically low activation energy is favored by the semiempirical methods. Structures of the activated complex of the single step mechanism, estimated by different methods, are very similar and consistent with a nonlinear cheletropic [_2s + _2a] reaction, as predicted by the orbital symmetry rules and earlier EHT calculations.Electronic Supplementary Material available.     

Effect of Benzylic Oxygen on the Cytotoxic Activity for Colon 26 Cell Line of Phenolic Lignans

The cytotoxic activity for colon 26 cell line of matairesinol, oxidized matairesinol, 9,9′-epoxylignan and oxidized 9,9′-epoxylignan were examined. (?)-Matairesinol (Mat 1) showed greatest cytotoxic activity (LC₅₀=9 μg/ml) of the lactone-type lignans. 7,7′-Oxomatairesinol having same steric configuration as that of (?)-matairesinol showed greater activity (LC₅₀=25 μg/ml) than hydroxy or mono-oxomatairesinol. The activities of 9,9′-epoxylignan and 7,7′-oxo-9,9′-epoxylignan having same steric configurations as (?)-matairesinol were weaker than that of corresponding matairesinols. Different activity levels were observed between enantiomers.     

Structure?Activity Relationship of Polypyridyl Ruthenium(II) Complexes as DNA Intercalators,DNA Photocleavage Reagents,and DNA Topoisomerase and RNA Polymerase Inhibitors

To investigate the relationship between the molecular structure and biological activity of polypyridyl Ru^II complexes, such as DNA binding, photocleavage ability, and DNA topoisomerase and RNA polymerase inhibition, six new [Ru(bpy)₂(dppz)]²⁺ (bpy=2,2′‐bipyridine; dppz=dipyrido[3,2‐a:2,′,3′‐c]phenazine) analogs have been synthesized and characterized by means of ¹H‐NMR spectroscopy, mass spectrometry, and elemental analysis. Interestingly, the biological properties of these complexes have been identified to be quite different via a series of experimental methods, such as spectral titration, DNA thermal denaturation, viscosity, and gel electrophoresis. To explain the experimental regularity and reveal the underlying mechanism of biological activity, the properties of energy levels and population of frontier molecular orbitals and excited‐state transitions of these complexes have been studied by density‐functional theory (DFT) and time‐depended DFT (TDDFT) calculations. The results suggest that DNA intercalative ligands with better planarity, greater hydrophobicity, and less steric hindrance are beneficial to the DNA intercalation and enzymatic inhibition of their complexes.     

Proton magnetic resonance study of nucleosides,nucleotides, and dideoxynucleoside monophosphates containing a syn pyrimidine base

Proton magnetic resonance data have been obtained for 6-methyl-2′-deoxyuridine (dT*), its 3′- and 5′-monophosphates, and its 3′,5′-diphosphate, as well as for the corresponding thymine derivatives. The synthesis of the dideoxynucleoside monophosphates—d(TpT), d(T*pT), d(TpT*), and d(T*pT*)—was accomplished, and spectral data were obtained for these four dimers. The data show that the 6-methyluracil base prefers the syn conformation about the N-glycosyl bond at the monomer and dimer levels. The presence of the syn base leads to increases in the cis couplings of the sugar ring, J_1′2″ and J_2′3′, which indicate a trend towards eclipsing of the substituents on the C1′-C2′ and C2′-C3′ fragments. This trend is discussed in terms of changes in the pseudorotational parameters which describe the pucker of the ring. The syn base destabilizes the g⁺ conformer about the C4′-C5′ bond, leading to a preference for the t conformer in all dT* residues at the monomer and dimer levels. Preliminary work on the formation of cyclobutane-type photodimers in d(T*pT) and d(T*pT*) is discussed and presented as evidence for the capability of the syn 6-methyluracil base to form base-stacked complexes.