Solubility of amide functionalized single wall carbon nanotubes: A quantum mechanical study

Data-Driven and Multiscale Modeling of DNA-Templated Dye Aggregates

Dye aggregates are of interest for excitonic applications, including biomedical imaging, organic photovoltaics, and quantum information systems. Dyes with large transition dipole moments (μ) are necessary to optimize coupling within dye aggregates. Extinction coefficients (ε) can be used to determine the μ of dyes, and so dyes with a large ε (>150,000 M−1cm−1) should be engineered or identified. However, dye properties leading to a large ε are not fully understood, and low-throughput methods of dye screening, such as experimental measurements or density functional theory (DFT) calculations, can be time-consuming. In order to screen large datasets of molecules for desirable properties (i.e., large ε and μ), a computational workflow was established using machine learning (ML), DFT, time-dependent (TD-) DFT, and molecular dynamics (MD). ML models were developed through training and validation on a dataset of 8802 dyes using structural features. A Classifier was developed with an accuracy of 97% and a Regressor was constructed with an R2 of above 0.9, comparing between experiment and ML prediction. Using the Regressor, the ε values of over 18,000 dyes were predicted. The top 100 dyes were further screened using DFT and TD-DFT to identify 15 dyes with a μ relative to a reference dye, pentamethine indocyanine dye Cy5. Two benchmark MD simulations were performed on Cy5 and Cy5.5 dimers, and it was found that MD could accurately capture experimental results. The results of this study exhibit that our computational workflow for identifying dyes with a large μ for excitonic applications is effective and can be used as a tool to develop new dyes for excitonic applications.

Structural Stability and Electronic Properties of Boron Phosphide Nanotubes: A Density Functional Theory Perspective

Based on the Density Functional Theory (DFT) calculations, we analyze the structural and electronic properties of boron phosphide nanotubes (BPNTs) as functions of chirality. The DFT calculations are performed using the M06-2X method in conjunction with the 6-31G(d) divided valence basis set. All nanostructures, (n,0) BPNT (n = 5–8, 10, 12, 14) and (n,n) BPNT (n = 3–11), were optimized minimizing the total energy, assuming a non-magnetic nature and a total charge neutrality. Results show that the BPNT diameter size increases linearly with the chiral index “n” for both chiralities. According to the global molecular descriptors, the (3,3) BPNT is the most stable structure provided that it shows the largest global hardness value. The low chirality (5,0) BPNT has a strong electrophilic character, and it is the most conductive system due to the small |HOMO-LUMO| energy gap. The chemical potential and electrophilicity index in the zigzag-type BPNTs show remarkable chirality-dependent behavior. The increase in diameter/chirality causes a gradual decrease in the |HOMO-LUMO| energy gap for the zigzag BPNTs; however, in the armchair-type BPNTs, a phase transition is generated from a semiconductor to a conductor system. Therefore, the nanostructures investigated in this work may be suggested for both electrical and biophysical applications.

First-principles studies of substituent effects on squaraine dyes

Dye molecules that absorb light in the visible region are key components in many applications, including organic photovoltaics, biological fluorescent labeling, super-resolution microscopy, and energy transport. One family of dyes, known as squaraines, has received considerable attention recently due to their favorable electronic and photophysical properties. In addition, these dyes have a strong propensity for aggregation, which results in emergent materials properties, such as exciton delocalization. This will be of benefit in charge separation and energy transport along with fundamental studies in quantum information. Given the high structural tunability of squaraine dyes, it is possible that exciton delocalization could be tailored by modifying the substituents attached to the π-conjugated network. To date, limited theoretical studies have explored the role of substituent effects on the electronic and photophysical properties of squaraines in the context of DNA-templated dye aggregates and resultant excitonic behavior. We used ab initio theoretical methods to determine the effects of substituents on the electronic and photophysical properties for a series of nine different squaraine dyes. Solvation free energy was also investigated as an insight into changes in hydrophobic behavior from substituents. The role of molecular symmetry on these properties was also explored via conformation and substitution. We found that substituent effects are correlated with the empirical Hammett constant, which demonstrates their electron donating or electron withdrawing strength. Electron withdrawing groups were found to impact solvation free energy, transition dipole moment, static dipole difference, and absorbance more than electron donating groups. All substituents showed a redshift in absorption for the squaraine dye. In addition, solvation free energy increases with Hammett constant. This work represents a first step toward establishing design rules for dyes with desired properties for excitonic applications.

Squaraine dyes are candidates for DNA-templated excitonic interactions. This work presents substituent effects on the electronic and photophysicalproperties of squaraine dyes and a correlation between empirical Hammettconstant and those properties.

Substituent Effects on the Solubility and Electronic Properties of the Cyanine Dye Cy5: Density Functional and Time-Dependent Density Functional Theory Calculations

The aggregation ability and exciton dynamics of dyes are largely affected by properties of the dye monomers. To facilitate aggregation and improve excitonic function, dyes can be engineered with substituents to exhibit optimal key properties, such as hydrophobicity, static dipole moment differences, and transition dipole moments. To determine how electron donating (D) and electron withdrawing (W) substituents impact the solvation, static dipole moments, and transition dipole moments of the pentamethine indocyanine dye Cy5, density functional theory (DFT) and time-dependent (TD-) DFT calculations were performed. The inclusion of substituents had large effects on the solvation energy of Cy5, with pairs of withdrawing substituents (W-W pairs) exhibiting the most negative solvation energies, suggesting dyes with W-W pairs are more soluble than others. With respect to pristine Cy5, the transition dipole moment was relatively unaffected upon substitution while numerous W-W pairs and pairs of donating and withdrawing substituents (D-W pairs) enhanced the static dipole difference. The increase in static dipole difference was correlated with an increase in the magnitude of the sum of the Hammett constants of the substituents on the dye. The results of this study provide insight into how specific substituents affect Cy5 monomers and which pairs can be used to engineer dyes with desired properties.

Multiwalled carbon nanotubes bound beta-galactosidase: It's activity, stability and reusability

Carbon nanotubes (CNTs) based biosensors are recognized to be a next generation building block for ultrasensitive and fast biosensing systems. This article starting with a brief history on CNTs provides an overview on the recent expansion of research in the field of CNT-based biosensors. This is followed by the discussion on structure and properties related to CNTs. Furthermore, the basic and some newly developed synthetic methods of CNTs are summarized. In this chapter, we used polyaniline cobalt multiwalled CNTs to immobilize β-galactosidase, by adopting both noncovalent and covalent strategies. Herein, the methodologies of both techniques have been discussed in detail. The η (effectiveness factor) values for nanocomposite bound β-galactosidase by physical adsorption and covalent method were calculated to be 0.93 and 0.97, respectively. The covalently bound β-galactosidase retained 92% activity even after its 10th successive reuse as compared to the adsorbed enzyme which exhibited only 74% of its initial activity. CNT armored enzymes demonstrated remarkably high catalytic stability at both sides of temperature and pH-optima along with easy recovery from the reaction medium which can be utilized in various biotechnological applications. Lastly, the scientific and technological challenges in the field are discussed at the end of this chapter.

Hydrogen Adsorption on Nearly Zigzag-Edged Nanoribbons: A Density Functional Theory Study

The realistic shapes of N doped graphene nanoribbons (GNRs) can be realized by considering nearly zigzag-edged (NZE) imperfections and pyridine defects (3NV). The paper focuses on NZE-GNRs with 3NV that is populated by Scandium abbreviated as Sc/NZE-3NVGNRs. Systematic calculations have clarified roles of the nano-shapes of NZE-3NVGNRs in its formation, energetics, stability and electron states functionalized with Sc using density functional theory (DFT) formalisms. According to DFT calculations, the magnitude of the spin that is attributed to the rise of magnetic order is closely linked to the altered shape of the ribbon edges. Also, calculations show that the stability of Sc functionalization at the 3NV and NZE site is thermodynamically stable and is dictated by a strong binding energy (BE). The magnitude of the BE is enhanced when the zigzag edge is short or the ribbon width is narrow, suggesting a reduced clustering of Sc atoms over the Sc-doped NZE-3NVGNRs. Results also show that as the length of the zigzag edge in Sc/NZE-3NVGNRs increases it creates considerable distortion on the appearance of the structure. Finally, the Sc/NZE-3NVGNRs as a potential candidate for hydrogen storage was evaluated and it was found that it could adsorb multiple hydrogen molecules.