A Theoretical Exploration of the Photoinduced Breaking Mechanism of the Glycosidic Bond in Thymine Nucleotide.

DNA glycosidic bond cleavage may induce cancer under the ultraviolet (UV) effect. Yet, the mechanism of glycosidic bond cleavage remains unclear and requires more detailed clarification. Herein, quantum chemical studies on its photoinduced mechanism are performed using a 5'-thymidine monophosphate (5'-dTMPH) model. In this study, four possible paths were examined to study the glycosidic bond cleavage. The results showed that, upon excitation, the electronic transition from the π bonding to π antibonding orbitals of the thymine ring leads to the damage of the thymine ring. Afterwards, the glycosidic bond is cleaved. At first, the doublet ground state (GS) path of glycosidic bond cleavage widely studied by other groups is caused by free electron generated by photoirradiation, with a kinetically feasible energy barrier of ~23 kcal/mol. Additionally, then, the other three paths were proposed that also might cause the glycosidic bond cleavage. The first one is the doublet excited state (ES) path, triggered by free electron along with UV excitation, which can result in a very-high-energy barrier ~49 kcal/mol that is kinetically unfavorable. The second one is the singlet ES path, induced by direct UV excitation, which assumes DNA is directly excited by UV light, which features a very low-energy barrier ~16 kcal/mol that is favored in kinetics. The third one is the triplet ES path, from the singlet state via intersystem crossing (ISC), which refers to a feasible ~27 kcal/mol energy barrier. This study emphasizes the pivotal role of the DNA glycosidic bond cleavage by our proposed direct UV excitation (especially singlet ES path) in addition to the authorized indirect free-electron-induced path, which should provide essential insights to future mechanistic comprehension and novel anti-cancer drug design.

Theoretical design of durable and strong polycarbonates against photodegradation.

The photodegradation mechanism of polycarbonate (PC) was investigated by quantum chemistry, and a novel antidegradation molecular design using substituents was proposed. It was demonstrated that electron-withdrawing substituents in the phenyl moiety controlled bond alternation, leading to inhibition of the O-C bond cleavage in the carbonate moiety. These results provide a promising alternative for durable PC synthesis.

Fast and Accurate Calculation of the UV-Vis Spectrum with the Modified Local Excitation Approximation.

The local excitation approximation (LEA), a method for the calculation of electronic excitations localized in a specific region of a molecule, has been modified with new approaches to enhance the accuracy of the original method. The primary concept behind LEA involves isolating the region of interest as a submolecule from the full molecule using a localization method, followed by calculating electronic excitations solely within this submolecule. In this study, we examined approaches that improve the accuracy in describing the region of interest, particularly its molecular orbital energies. Additionally, the localization method was extended with a new projection technique to accelerate calculations. These approaches were studied in time-dependent density functional theory (TDDFT) calculations applied to four testing systems with a chromophore as the region of interest: two basic linear molecules, acrolein surrounded by 24 water molecules, and a model of a green fluorescent protein. For all studied systems, the results of TDDFT calculations combined with LEA exhibited near-zero error when groups of atoms adjacent to the chromophore were explicitly included in the submolecule. This was achieved with at least a quadratic speedup of the calculation time as a function of the submolecule size.

Why does 2-(2-aminoethylamino)ethanol have superior CO2 separation performance to monoethanolamine? A computational study.

Our computational reaction analysis shows that 2-(2-aminoethylamino)ethanol (AEEA) has superior performance to monoethanolamine for CO2 separation, in terms of its ability to sorb CO2 by its primary amine and desorb CO2 by its secondary amine.

Local electronic structure analysis by ab initio elongation method: A benchmark using DNA block polymers.

The ab initio elongation (ELG) method based on a polymerization concept is a feasible way to perform linear-scaling electronic structure calculations for huge aperiodic molecules while maintaining computational accuracy. In the method, the electronic structures are sequentially elongated by repeating (1) the conversion of canonical molecular orbitals (CMOs) to region-localized MOs (RLMOs), that is, active RLMOs localized onto a region close to an attacking monomer or frozen RLMOs localized onto the remaining region, and the subsequent (2) partial self-consistent-field calculations for an interaction space composed of the active RLMOs and the attacking monomer. For each ELG process, one can obtain local CMOs for the interaction space and the corresponding local orbital energies. Local site information, such as the local highest-occupied/lowest-unoccupied MOs, can be acquired with linear-scaling efficiency by correctly including electronic effects from the frozen region. In this study, we performed a local electronic structure analysis using the ELG method for various DNA block polymers with different sequential patterns. This benchmark aimed to confirm the effectiveness of the method toward the efficient detection of a singular local electronic structure in unknown systems as a future practical application. We discussed the high-throughput efficiency of our method and proposed a strategy to detect singular electronic structures by combining with a machine learning technique.

Ab initio multi-level layered elongation method and its application to local interaction analysis between DNA bulge and ligand molecules.

A multi-level layered elongation method was developed for efficiently analyzing the electronic states of local structures in large bio/nano-systems at the full ab initio level of theory. The original elongation method developed during the last three decades in our group has focused on the system in one direction from one terminal to the other terminal to sequentially construct the electronic states of a polymer, called a theoretical synthesis of polymers. In this study, an important region termed the central (C) part is targeted in a large polymer and the remainder are terminal (T) parts. The electronic structures along with polymer elongation are calculated repeatedly from both end T parts to the C central part at the same time. The important C part is treated with large basis sets (high level) and the other regions are treated with small basis sets (low level) in the ab initio theoretical framework. The electronic structures besides the C part can be reused for other systems with different structures at the C part, which renders the method computationally efficient. This multi-level layered elongation method was applied to the investigation on DNA single bulge recognition of small molecules (ligands). The reliability and validity of our approach were examined in comparison with the results obtained by direct calculations using a conventional quantum chemical method for the entire system. Furthermore, stabilization energies by the formation of the complex of bulge DNA and a ligand were estimated with basis set superposition error corrections incorporated into the elongation method.

Theoretical Analysis of Properties of Ground and Excited States for Photodissociation of the C-O Bond in Polycarbonates.

Quantum chemical calculations were carried out to investigate the properties of the ground state (GS) and the excited state (ES) of bisphenol-A polycarbonate (PC) with bisphenol-A hydrogen carbonate (BPAHC) as a model compound. Time-dependent density functional theory (TDDFT) was used to obtain the absorption spectrum and the corresponding transition natures of BPAHC. Furthermore, the ESs related to the transitions of the carbonate group and neighboring phenyl ring were optimized employing the TDDFT method for photodegradation. Our results showed that the carbonate group is broken at an ES with relatively high energy, which has a significant C-O bond cleavage within the carbonate group compared to that of GS geometry. The carbonate group C-O bond cleavage is caused by two reasons. One is the transition from the O lone pair to the carbonate π anti-bonding which is commonly known, and the other one is the transition from the O lone pair to the phenyl group (adjacent to the carbonate group) π anti-bonding that is newly proposed.

Quantum chemistry-machine learning approach for predicting and elucidating molecular hyperpolarizability: Application to [2.2]paracyclophane-containing push-pull polymers.

Nonlinear optical properties of organic chromophores are of great interest in diverse photonic and optoelectronic applications. To elucidate general trends in the behaviors of molecules, large amounts of data are required. Therefore, both an accurate and a rapid computational approach can significantly promote the theoretical design of molecules. In this work, we combined quantum chemistry and machine learning (ML) to study the first hyperpolarizability (ß) in [2.2]paracyclophane-containing push-pull compounds with various terminal donor/acceptor pairs and molecular lengths. To generate reference ß values for ML, the ab initio elongation finite-field method was used, allowing us to treat long polymer chains with linear scale efficiency and high computational accuracy. A neural network (NN) model was built for ß prediction, and the relevant molecular descriptors were selected using a genetic algorithm. The established NN model accurately reproduced the ß values (R2 > 0.99) of long molecules based on the input quantum chemical properties (dipole moment, frontier molecular orbitals, etc.) of only the shortest systems and additional information about the actual system length. To obtain general trends in molecular descriptor-target property relationships learned by the NN, three approaches for explaining the ML decisions (i.e., partial dependence, accumulated local effects, and permutation feature importance) were used. The effect of donor/acceptor alternation on ß in the studied systems was examined. The asymmetric extension of molecular regions end-capped with donors and acceptors produced unequal ß responses. The results revealed how the electronic properties originating from the nature of substituents on the microscale controlled the magnitude of ß according to the NN approximation. The applied approach facilitates the conceptual discoveries in chemistry by using ML to both (i) efficiently generate data and (ii) provide a source of information about causal correlations among system properties.

Elongation method with intermediate mechanical and electrostatic embedding for geometry optimizations of polymers.

The elongation method with intermediate mechanical and electrostatic embedding (ELG-IMEE) is proposed. The electrostatic embedding uses atomic charges generated by a charge sensitivity analysis (CSA) method and parameterized for three different population analyses, namely, the Merz-Singh-Kollman scheme, the charge model 5, and the atomic polar tensor. The obtained CSA models were tested on two model systems. Test calculations show that the electrostatic embedding provides several times of decrease in the difference of energies of testing and reference calculations in comparison with the conventional elongation approach (ELG). The mechanical embedding is implemented in a combination of the conventional elongation method and the ONIOM approach. Moreover, it was demonstrated that the geometry optimization with the ELG-IMEE reduces the errors in the optimized structures by about one order in root-mean-square deviation, when compared to ELG.

Monovalent sulfur oxoanions enable millimeter-long single-crystalline h-WO3 nanowire synthesis.

Here, we discuss a misunderstanding regarding chemical capping, which has intrinsically hindered the extension of the length of hexagonal (h)-WO3 nanowires in previous studies. Although divalent sulfate ions (SO42-) have been strongly believed to be efficient capping ions for directing anisotropic h-WO3 nanowire growth, we have found that the presence of SO42- is highly detrimental to the anisotropic crystal growth of the h-WO3 nanowires, and a monovalent sulfur oxoanion (HSO4-) rather than SO42- only substantially promotes the anisotropic h-WO3 nanowire growth. Ab initio electronic structure simulations revealed that the monovalent sulfur oxoanions were preferentially able to cap the sidewall plane (100) of the h-WO3 nanowires due to the lower hydration energy when compared with SO42-. Based on this capping strategy, using the monovalent sulfur oxoanion (CH3SO3-), which cannot generate divalent sulfur oxoanions, we have successfully fabricated ultra-long h-WO3 nanowires up to the millimeter range (1.2 mm) for a wider range of precursor concentrations. We have demonstrated the feasibility of these millimeter-long h-WO3 nanowires for the electrical sensing of molecules (lung cancer biomarker: nonanal) on flexible substrates, which can be operated at room temperature with mechanical flexibility with bending cycles up to 104 times due to the enhanced textile effect.

Synthesis of Monodispersedly Sized ZnO Nanowires from Randomly Sized Seeds.

We demonstrate the facile, rational synthesis of monodispersedly sized zinc oxide (ZnO) nanowires from randomly sized seeds by hydrothermal growth. Uniformly shaped nanowire tips constructed in ammonia-dominated alkaline conditions serve as a foundation for the subsequent formation of the monodisperse nanowires. By precisely controlling the sharp tip formation and the nucleation, our method substantially narrows the distribution of ZnO nanowire diameters from σ = 13.5 nm down to σ = 1.3 nm and controls their diameter by a completely bottom-up method, even initiating from randomly sized seeds. The proposed concept of sharp tip based monodisperse nanowires growth can be applied to the growth of diverse metal oxide nanowires and thus paves the way for bottom-up grown metal oxide nanowires-integrated nanodevices with a reliable performance.

Extent of structural change during the reaction and its relationship to isoselectivity in polypropylene polymerization with ansa-zirconocene/borate catalyst: A computational study.

The mechanism of isotactic polypropylene (iPP) polymerization with an (R,R)-ansa-zirconocene/borate catalyst system was analyzed using quantum chemistry (QC) calculations by focusing on the extent of structural change during monomer insertion. The activation energy for migratory insertion, Ea , was compared for four possible reaction paths with regard to monomer coordination, that is, 1,2-re, 1,2-si, 2,1-si, and 2,1-re, until the seventh monomer insertion step, explicitly including a borate anion cocatalyst. This indicated that the 1,2-re path was most favorable, except for the first step, which favored 1,2-si. As far as the first step, the product of 1,2-si is a conformational isomer to that of the 1,2-re path, and the exceptional favorability of 1,2-si does not affect the isoselectivity. These results support previous studies, except that our results address the unexplored seventh insertion step with a borate anion cocatalyst by QC calculations. The isoselectivity correlated with the extent of structural change in the whole system during the reaction. It was proved from our detail analysis that the advantage of 1,2-re with a small Ea is attributed to its smaller structural changes due to low steric repulsion in the system compared with other paths. Conversely, larger repulsion in the systems involved in other paths results in larger structural changes to minimize the structural strain. However, the relaxation appears insufficient due to structural restriction of the enforced four-membered ring transition state structure. A borate anion cocatalyst broke the C2 symmetry of the electronic structures of zirconocene, resulting in an odd-even Ea frequency for the monomer insertion. Molecular orbital analysis demonstrated that the d-π orbital overlaps can explain the approach direction of the olefin coordination and the bent structure of zirconocene, providing a different viewpoint from previous studies. The potential for catalyst control was discussed based on our results. © 2019 Wiley Periodicals, Inc.

Rational Method of Monitoring Molecular Transformations on Metal-Oxide Nanowire Surfaces.

Metal-oxide nanowires have demonstrated excellent capability in the electrical detection of various molecules based on their material robustness in liquid and air environments. Although the surface structure of the nanowires essentially determines their interaction with adsorbed molecules, understanding the correlation between an oxide nanowire surface and an adsorbed molecule is still a major challenge. Herein, we propose a rational methodology to obtain this information for low-density molecules adsorbed on metal oxide nanowire surfaces by employing infrared p-polarized multiple-angle incidence resolution spectroscopy and temperature-programmed desorption/gas chromatography-mass spectrometry. As a model system, we studied the surface chemical transformation of an aldehyde (nonanal, a cancer biomarker in breath) on single-crystalline ZnO nanowires. We found that a slight surface reconstruction, induced by the thermal pretreatment, determines the surface chemical reactivity of nonanal. The present results show that the observed surface reaction trend can be interpreted in terms of the density of Zn ions exposed on the nanowire surface and of their corresponding spatial arrangement on the surface, which promotes the reaction between neighboring adsorbed molecules. The proposed methodology will support a better understanding of complex molecular transformations on various nanostructured metal-oxide surfaces.

Automated property optimization via ab initio O(N) elongation method: Application to (hyper-)polarizability in DNA.

An automated property optimization method was developed based on the ab initio O(N) elongation (ELG) method and applied to the optimization of nonlinear optical (NLO) properties in DNA as a first test. The ELG method mimics a polymerization reaction on a computer, and the reaction terminal of a starting cluster is attacked by monomers sequentially to elongate the electronic structure of the system by solving in each step a limited space including the terminal (localized molecular orbitals at the terminal) and monomer. The ELG-finite field (ELG-FF) method for calculating (hyper-)polarizabilities was used as the engine program of the optimization method, and it was found to show linear scaling efficiency while maintaining high computational accuracy for a random sequenced DNA model. Furthermore, the self-consistent field convergence was significantly improved by using the ELG-FF method compared with a conventional method, and it can lead to more feasible NLO property values in the FF treatment. The automated optimization method successfully chose an appropriate base pair from four base pairs (A, T, G, and C) for each elongation step according to an evaluation function. From test optimizations for the first order hyper-polarizability (ß) in DNA, a substantial difference was observed depending on optimization conditions between "choose-maximum" (choose a base pair giving the maximum ß for each step) and "choose-minimum" (choose a base pair giving the minimum ß). In contrast, there was an ambiguous difference between these conditions for optimizing the second order hyper-polarizability (γ) because of the small absolute value of γ and the limitation of numerical differential calculations in the FF method. It can be concluded that the ab initio level property optimization method introduced here can be an effective step towards an advanced computer aided material design method as long as the numerical limitation of the FF method is taken into account.

Elongation method for electronic structure calculations of random DNA sequences.

We applied ab initio order-N elongation (ELG) method to calculate electronic structures of various deoxyribonucleic acid (DNA) models. We aim to test potential application of the method for building a database of DNA electronic structures. The ELG method mimics polymerization reactions on a computer and meets the requirements for linear scaling computational efficiency and high accuracy, even for huge systems. As a benchmark test, we applied the method for calculations of various types of random sequenced A- and B-type DNA models with and without counterions. In each case, the ELG method maintained high accuracy with small errors in energy on the order of 10(-8) hartree/atom compared with conventional calculations. We demonstrate that the ELG method can provide valuable information such as stabilization energies and local densities of states for each DNA sequence. In addition, we discuss the "restarting" feature of the ELG method for constructing a database that exhaustively covers DNA species.

Interaction of OH- with xylan and its hydrated complexes: structures and molecular dynamics study using elongation method.

The interaction of OH(-) group with (xylan)12 and its hydrated complexes were theoretically studied using elongation optimization (ELG-OPT) method and elongation ab initio molecular dynamics simulation (ELG-MD) method. OH(-) group could abstract a H-atom from the terminal xylan ring to form a complex (xylan)12(-)-H2O without any energy barrier. One and two extra water molecules were also added to the same terminal xylan ring. All the geometry optimization results obtained using elongation method were compared with conventional calculation results, and it suggested that ELG-OPT method worked well for (xylan)12, (xylan)12-OH(-), and its hydrated complexes. Moreover 10 ps ab initio molecular dynamics simulations were performed for complexes (xylan)12(-)-H2O, (xylan)12(-)-2H2O, and (xylan)12(-)-3H2O at 300 K, 500 K, and 700 K. (xylan)12(-)-H2O complex was stable at room temperature. However H2O molecule which was formed by OH(-) group could move at 500 K. At 700 K the H-abstract reaction reversed. Adding an extra water molecule only accelerated the water transfer reaction, but no more chemical reactions occurred, and the transfer time decreased when the temperature increased. The complex (xylan)12(-)-H2O became very stable when adding two extra water molecules even at high temperature, and it indicated that two extra water molecules stabilized the complex (xylan)12(-)-H2O.

Development of minimized mixing molecular orbital method for designing organic ferromagnets.

Predicting the high spin stability of organic radicals correctly for designing organic ferromagnets remains a significant challenge. We have developed a method with an index (L(min)) for predicting the high spin stability of conjugated organic radicals at the restricted open-shell Hartree-Fock level. Unitary transformations were performed for localizing the coefficients of nonbonding molecular orbitals, and subsequently the localized coefficients were used to calculate L(min) that indicates the high spin stability of conjugated organic radicals. This method can be combined with the elongation method to treat huge high spin open-shell systems. Thus, this method is useful for designing organic ferromagnets.

Intermediate electrostatic field for the generalized elongation method.

An intermediate electrostatic field is introduced to improve the accuracy of fragment-based quantum-chemical computational methods by including long-range polarizations of biomolecules. The point charge distribution of the intermediate field is generated by a charge sensitivity analysis that is parameterized for five different population analyses, namely, atoms-in-molecules, Hirshfeld, Mulliken, natural orbital, and Voronoi population analysis. Two model systems are chosen to demonstrate the performance of the generalized elongation method (ELG) combined with the intermediate electrostatic field. The calculations are performed for the STO-3G, 6-31G, and 6-31G(d) basis sets and compared with reference Hartree-Fock calculations. It is shown that the error in the total energy is reduced by one order of magnitude, independently of the population analyses used. This demonstrates the importance of long-range polarization in electronic-structure calculations by fragmentation techniques.

Ab initio O(N) elongation-counterpoise method for BSSE-corrected interaction energy analyses in biosystems.

An Elongation-counterpoise (ELG-CP) method was developed for performing accurate and efficient interaction energy analysis and correcting the basis set superposition error (BSSE) in biosystems. The method was achieved by combining our developed ab initio O(N) elongation method with the conventional counterpoise method proposed for solving the BSSE problem. As a test, the ELG-CP method was applied to the analysis of the DNAs' inter-strands interaction energies with respect to the alkylation-induced base pair mismatch phenomenon that causes a transition from G⋯C to A⋯T. It was found that the ELG-CP method showed high efficiency (nearly linear-scaling) and high accuracy with a negligibly small energy error in the total energy calculations (in the order of 10(-7)-10(-8) hartree/atom) as compared with the conventional method during the counterpoise treatment. Furthermore, the magnitude of the BSSE was found to be ca. -290 kcal/mol for the calculation of a DNA model with 21 base pairs. This emphasizes the importance of BSSE correction when a limited size basis set is used to study the DNA models and compare small energy differences between them. In this work, we quantitatively estimated the inter-strands interaction energy for each possible step in the transition process from G⋯C to A⋯T by the ELG-CP method. It was found that the base pair replacement in the process only affects the interaction energy for a limited area around the mismatch position with a few adjacent base pairs. From the interaction energy point of view, our results showed that a base pair sliding mechanism possibly occurs after the alkylation of guanine to gain the maximum possible number of hydrogen bonds between the bases. In addition, the steps leading to the A⋯T replacement accompanied with replications were found to be unfavorable processes corresponding to ca. 10 kcal/mol loss in stabilization energy. The present study indicated that the ELG-CP method is promising for performing effective interaction energy analyses in biosystems.