Design and computational characterization of non-fullerene acceptors for use in solution-processable solar cells.

In an effort to seek high-performance small molecule electron acceptor materials for use in heterojunction solar cells, computational chemistry was used to examine a variety of terminal acceptor-conjugated bridge-core acceptor-conjugated bridge-terminal acceptor small molecules. In particular, we have systematically predicted the geometric, electronic, and optical properties of 16 potential small-molecule acceptors based upon a series of electron deficient π-conjugated building blocks that have been incorporated into materials exhibiting good electron transport properties. Results show that the band gap, HOMO/LUMO energy levels, orbital spatial distribution, and intrinsic dipole moments can be systematically altered by varying the electron properties of the terminal or core acceptor units.

A computational proposal for the experimentally observed discriminatory behavior of hypoxanthine, a weak universal nucleobase.

A computational model composed of six nucleobases was used to investigate why hypoxanthine does not yield duplexes of equal stability when paired opposite each of the natural DNA nucleobases. The magnitudes of all nearest-neighbor interactions in a DNA helix were calculated, including hydrogen-bonding, intra- and interstrand stacking interactions, as well as 1-3 intrastrand stacking interactions. Although the stacking interactions in DNA relevant arrangements are significant and account for at least one third of the total stabilization energy in our nucleobase complexes, the trends in the magnitude of the stacking interactions cannot explain the relative experimental melting temperatures previously reported in the literature.

Modeling the chemical step utilized by human alkyladenine DNA glycosylase: a concerted mechanism AIDS in selectively excising damaged purines.

Human alkyladenine DNA glycosylase (AAG) initiates the repair of a wide variety of (neutral or cationic) alkylated and deaminated purines by flipping damaged nucleotides out of the DNA helix and catalyzing the hydrolytic N-glycosidic bond cleavage. Unfortunately, the limited number of studies on the catalytic pathway has left many unanswered questions about the hydrolysis mechanism. Therefore, detailed ONIOM(M06-2X/6-31G(d):AMBER) reaction potential energy surface scans are used to gain the first atomistic perspective of the repair pathway used by AAG.

Effects of extending the computational model on DNA-protein T-shaped interactions: the case of adenine-histidine dimers.

The MP2/6-31G*(0.25) π-π or π(+)-π T-shaped (edge-to-face) interactions between neutral or protonated histidine and adenine were considered using computational models of varying size to determine the effects of the protein and DNA backbones on the preferred dimer structure and binding strength. The overall consequences of the backbones are reasonably subtle for the neutral adenine-histidine T-shaped dimers.

Effects of the biological backbone on stacking interactions at DNA-protein interfaces: the interplay between the backbone···π and π···π components.

The (gas-phase) MP2/6-31G*(0.25) π···π stacking interactions between the five natural bases and the aromatic amino acids calculated using (truncated) monomers composed of conjugated rings and/or (extended) monomers containing the biological backbone (either the protein backbone or deoxyribose sugar) were previously compared. Although preliminary energetic results indicated that the protein backbone strengthens, while the deoxyribose sugar either strengthens or weakens, the interaction calculated using truncated models, the reasons for these effects were unknown.

A preliminary investigation of the additivity of pi-pi or pi+-pi stacking and T-shaped interactions between natural or damaged DNA nucleobases and histidine.

Previous computational studies have examined pi-pi and pi(+)-pi stacking and T-shaped interactions in nucleobase-amino acid dimers, yet it is important to investigate how additional amino acids affect these interactions since simultaneous contacts often appear in nature. Therefore, this paper investigates the geometries and binding strengths of amino acid-nucleobase-amino acid trimers, which are compared to the corresponding nucleobase-amino acid dimer interactions. We concentrate on systems containing the natural nucleobase adenine or its (cationic) damaged counterpart, 3-methyladenine, and the aromatic amino acid histidine, in both the neutral and protonated forms.

Effects of the biological backbone on DNA-protein stacking interactions.

The pi-pi stacking (face-to-face) interactions between the five natural DNA or RNA nucleobases and the four aromatic amino acids were compared using three different types of dimers: (1) a truncated nucleoside (nucleobase) stacked with a truncated amino acid; (2) a truncated nucleoside (nucleobase) stacked with an extended amino acid; and (3) a nucleoside (extended nucleobase) stacked with a truncated amino acid. Systematic (MP2/6-31G*(0.25)) potential energy surface scans reveal important information about the effects of the deoxyribose sugar and protein backbone on the structure and binding energy between truncated nucleobase and amino acid models that are typically implemented in the literature.

Evidence for Stabilization of DNA/RNA-Protein Complexes Arising from Nucleobase-Amino Acid Stacking and T-Shaped Interactions.

The stacking and T-shaped interactions between the natural DNA or RNA nucleobases (adenine, cytosine, guanine, thymine, uracil) and all aromatic amino acids (histidine, phenylalanine, tyrosine, tryptophan) were investigated using ab initio quantum mechanical calculations. We characterized the potential energy surface of nucleobase-amino acid dimers using the MP2/6-31G*(0.25) method.

Remarkably Strong T-Shaped Interactions between Aromatic Amino Acids and Adenine: Their Increase upon Nucleobase Methylation and a Comparison to Stacking.

T-shaped geometries and interaction energies between select DNA nucleobases (adenine or 3-methyladenine) and all aromatic amino acids (histidine, phenylalanine, tyrosine, or tryptophan) were examined using BSSE-corrected MP2/6-31G*(0.25) potential energy surface scans, which determined the preferred nucleobase (face)-amino acid (edge) and nucleobase (edge)-amino acid (face) interactions. The energies of dimers with the strongest interactions were further studied at the CCSD(T)/CBS level of theory, which suggests that the T-shaped interactions in adenine dimers are very strong (up to -35 kJ mol(-1)).

yDNA versus xDNA pyrimidine nucleobases: computational evidence for dependence of duplex stability on spacer location.

The structural and binding properties of the natural and x- and y-pyrimidines were compared using computational methods. Our calculations show that although the x-pyrimidines favor different orientations about the glycosidic bond compared to the natural pyrimidines, which could have implications for the formation and resulting stability of xDNA duplexes and jeopardize the selectivity of expanded nucleobases, y-pyrimidines have rotational profiles more similar to the natural bases. Increasing the pyrimidine size using a benzene spacer leads to relatively minor changes in the hydrogen-bond strength of isolated Watson-Crick base pairs.

Computational comparison of the stacking interactions between the aromatic amino acids and the natural or (cationic) methylated nucleobases.

The strongest gas-phase MP2/6-31G*(0.25) stacking energies between the aromatic amino acids and the natural or methylated nucleobases were considered. The potential energy surfaces of dimers were searched as a function of the vertical separation, angle of rotation and horizontal displacement between monomers stacked according to their centers of mass.

A computational characterization of the hydrogen-bonding and stacking interactions of hypoxanthine.

The hydrogen-bonding and stacking interactions of hypoxanthine, a potential universal nucleobase, were calculated using a variety of methodologies (CCSD(T), MP2, B3LYP, PWB6K, AMBER). All methods predict that the hydrogen-bonding interaction in the hypoxanthine-cytosine pair is approximately 25 kJ mol(-1) stronger than that in the other dimers. Although the calculations support suggestions from experiments that hypoxanthine preferentially binds with cytosine, the trend in the calculated hydrogen-bond strengths for the remaining natural nucleobases do not show a strong correlation with the experimentally predicted binding preferences.

Characterization of nucleobase-amino acid stacking interactions utilized by a DNA repair enzyme.

The present work characterizes the gas-phase stacking interactions between four aromatic amino acid residues (histidine, phenylalanine, tyrosine, and tryptophan) and adenine or 3-methyladenine due to the proposed utilization of these interactions by enzymes that repair DNA alkylation damage. The MP2 potential energy surfaces of the stacked dimers are considered as a function of four variables (vertical displacement, angle of rotation, horizontal displacement, and tilt angle) using a variety of basis sets. It is found that the maximum stacking interaction energy decreases with the amino acid according to TRP > TYR approximately HIS > PHE for both nucleobases.

The hydrogen bonding properties of cytosine: a computational study of cytosine complexed with hydrogen fluoride, water, and ammonia.

Density functional theory is used to study the hydrogen bonding pattern in cytosine, which does not contain alternating proton donor and acceptor sites and therefore is unique compared with the other pyrimidines. Complexes between various small molecules (HF, H(2)O, and NH(3)) and four main binding sites in (neutral and (N1) anionic) cytosine are considered. Two complexes (O2(N1) and N3(N4)) involve neighboring cytosine proton acceptor and donor sites, which leads to cooperative interactions and bidendate hydrogen bonds.