*J Chem Phys ; 155(4): 044110, 2021 Jul 28.*

##### RESUMO

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.

##### Assuntos

DNA/química , Conformação de Ácido Nucleico , Química Computacional , Descoberta de Drogas , Ligantes , Teoria Quântica*J Phys Chem A ; 2021 Jul 28.*

##### RESUMO

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.

*J Chem Phys ; 154(12): 124107, 2021 Mar 28.*

##### RESUMO

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.

*J Comput Chem ; 40(30): 2622-2635, 2019 Nov 15.*

##### RESUMO

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.

*J Chem Phys ; 145(2): 024107, 2016 Jul 14.*

##### RESUMO

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 (Î³) because of the small absolute value of Î³ 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.

##### Assuntos

Modelos Químicos , Reconhecimento Automatizado de Padrão , DNA/química , Campos Eletromagnéticos , Modelos Lineares , Modelos Genéticos , Dinâmica não Linear , Fatores de Tempo*J Comput Chem ; 36(28): 2103-13, 2015 Oct 30.*

##### RESUMO

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.

##### Assuntos

DNA/química , Teoria Quântica , Sequência de Bases , Elétrons , Conformação de Ácido Nucleico*J Chem Phys ; 142(10): 104111, 2015 Mar 14.*

##### RESUMO

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 Gâ¯C to Aâ¯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 Gâ¯C to Aâ¯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 Aâ¯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.

##### Assuntos

Técnicas de Química Analítica , Modelos Biológicos , Teoria Quântica*Sci Rep ; 4: 7199, 2014 Nov 26.*

##### RESUMO

Wet chemical reduction of metal ions, a common strategy for synthesizing metal nanoparticles, strongly depends on the electric potential of the metal, and its applications to late transition metal clusters have been limited to special cases. Here, we describe copper nanoclusters grown by synchrotron radiolysis in concert with wet chemistry. The local structure of copper aggregates grown by reducing Cu(II) pentanedionate using synchrotron x-ray beam was studied in situ by x-ray absorption spectroscopy. A detailed analysis of the XANES and EXAFS spectra, compared with DFT calculations and full-potential non-muffin-tin multiple scattering calculations, identified the nanocluster as Cu13 with icosahedral symmetry. The novel "charged" nanoclusters tightly bound to electron-donating amido molecules, which formed as a result of photo-induced deprotonation of ligand amines, were stabilized by irradiation. Monodispersive deposition of nanoclusters was enabled by controlling the type and density of "monomers", in remarkable contrast to the conventional growth of metallic nanoparticles.

*Materials (Basel) ; 6(3): 870-885, 2013 Mar 06.*

##### RESUMO

A new local ab initio molecular dynamics method, namely elongation molecular dynamics (ELG-MD) is proposed for highly efficient simulations of aperiodic polymer systems. ELG-MD combines the elongation method (ELG) with the Gear predictor corrector (GPC) algorithm of molecular dynamics simulation. In this method, the local gradients acting on the atom's nucleus in the active region are calculated by the ELG method while the equations of the nucleus's motion are solved by the GPC algorithm. In this work, the first application of this ELG-MD method is described to investigate the stable conformation of polyglycine with surrounding water molecules. The water effects on the structure of polyglycine are examined. The ELG-MD simulations show that the formation of the polyglycine helix is strongly induced by the hydrogen bonds observed in two types of H-bond rings.

*J Chem Theory Comput ; 9(9): 4035-45, 2013 Sep 10.*

##### RESUMO

In this study, we developed a method to interpret the mechanism of acceleration for Menshutkin-type reactions in solutions theoretically, from the orbital interaction view, utilizing the through-space/bond (TS/TB) interaction analysis in the polarizable continuum model (PCM). Different method levels were tested to determine the substituent effects on the reactions of NH3 attacking para-substituted benzyl bromide. The geometrical structures and Mulliken charge distributions were analyzed to elucidate the substituent effects on the SN2 reaction center. The results of Mulliken charge analysis showed that the para-substituted benzyl group (-C6H4Y) received negative charge through the reaction process, and both electron-donating and electron-withdrawing substituents Y made -C6H4Y groups receive greater charges. Solvent effects on the structures of transition states (T-S(s)) were significant. The structures of T-S(s) were found to be exhibiting longer bond lengths in solutions, especially in polar solvents such as water. Our TS/TB-PCM analysis method can predict the substituent effects in solutions by evaluating contributions from orbital interactions in question. The orbital interaction analysis results revealed that the key orbital interactions for stabilizing the T-S(s) of the systems with substituents Y = NH2 and NO2 in water were n(NH2)-π*(ph) (ph = phenyl) and π(ph)-π*(NO2) interactions, respectively. Stronger interactions between π*(ph) and σ*(Cα-Br) occurred because of the n(NH2)-π*(ph) and π(ph)-π*(NO2) interactions that resulted when para-substituents -NH2 and -NO2, respectively, were added to the system. These stronger π*(ph)-σ*(Cα-Br) interactions stabilized the transition state and enabled the Br leaving group to leave more easily.

*J Chem Phys ; 127(8): 084702, 2007 Aug 28.*

##### RESUMO

The elongation finite-field (elongation-FF) method is applied to donor/acceptor substituted polydiacetylenes (PDAs) for the estimation of substituent effects on nonlinear optical (NLO) properties. The first hyperpolarizability (beta) and the second hyperpolarizability (gamma) of PDA with separated donor and acceptor substitution blocks have much larger values than those of the other substituted PDAs. For the PDAs with donor and acceptor substitution blocks, the relationship between the NLO properties and the block period is examined. It is shown, from the local density of states, that gamma of a system with a quantum well structure has a maximum value at a certain block size. This indicates that by tuning the size of proper block it is possible to achieve the largest gamma value in block polymers. Furthermore, the through-space/bond interaction analysis is performed to examine the pi-conjugation effects on the NLO properties for particular substituted PDA. It is demonstrated by our quantitative analysis that beta is affected by electron transfers in the molecule, and the quantum well structure is critical for gamma improvement.

*J Phys Chem A ; 111(33): 8241-9, 2007 Aug 23.*

##### RESUMO

Nonlinear optical properties of zwitterionic sigma-conjugated systems were theoretically investigated with relation to the electron correlation effects at the ab initio molecular orbital level. We examined the strong electron correlation effects on the first- and second-order hyperpolarizabilities in the specific systems with effective "pi-sigma-pi" and (or) "pi-sigma-n" interactions. The electron correlation effects on the hyperpolarizabilities strongly depend on the type of substituents, conformations, spacer size, and basis sets. It was found that the Hartree-Fock level calculations qualitatively predict the behavior of the hyperpolarizabilities after considering the correlation effects. Through-space/-bond interaction analysis quantitatively revealed that the electron correlation effects on the hyperpolarizabilities were induced mainly by the sigma-conjugations on the spacer unit in the zwitterionic sigma-systems.

*J Chem Phys ; 126(21): 215104, 2007 Jun 07.*

##### RESUMO

Elongation method was applied to determine the electronic structures of B-type poly(dG).poly(dC) DNA at the ab initio molecular orbital level as a first step toward the calculation of aperiodic DNA. The discrepancy in total energy between the elongation method and a conventional calculation was negligibly small in the order of 10(-8) hartreeat. for 14 G-C base pair model. The local density of states for 10 G-C base pair model estimated by the elongation method well reproduced the results by the conventional calculation. It was found that the band gap of the whole system is mainly due to the energy difference between the valence band of guanine and the conduction band of cytosine. Moreover, the electron transfer path through stacking G-C base pairs rather than sugar-phosphate backbones has been confirmed by the authors' calculations.

##### Assuntos

DNA/química , Polidesoxirribonucleotídeos/química , Simulação por Computador , Eletroquímica , Modelos Moleculares , Conformação de Ácido Nucleico*J Phys Chem A ; 110(17): 5803-8, 2006 May 04.*

##### RESUMO

Interaction path analyses for pi-conjugated organic systems were performed at the ab initio molecular orbital level to examine the relationship between inter-radical interactions and the high-spin stability of the system. It was found that the high-spin stability results from through-bond interactions between radicals, not from through-space interactions, in relation to the stabilization of a low-spin state due to the effects of electron correlation. L(ij)(min) value for estimating the mixing of nonbonding molecular orbitals well predicted the relationship between the through-bond interactions and the high-spin stability. Furthermore, molecular orbital calculations revealed that the all-trans type interaction path between radicals produces long-range exchange interactions, and the additivity of high-spin stability is observed by keeping short-range through-bond interaction paths.

*J Chem Theory Comput ; 2(3): 786-96, 2006 May.*

##### RESUMO

It has been demonstrated that the high-spin stability of benzyl radical oligomers can be predicted without any quantum chemical calculations. This method is composed of three steps: (1) predicting the shapes of nonbonding molecular orbitals (NBMOs), (2) counting up the mixings of NBMOs, and (3) formulating the mixings for the number of radical centers (N). This treatment enables us to predict the high-spin stability evaluated by ab initio MO calculations involving the post-Hartree-Fock method or the density functional theory (DFT) method.

*Org Biomol Chem ; 3(12): 2244-9, 2005 Jun 21.*

##### RESUMO

Ab initio through-space/bond interaction analysis was applied to [3 + 2] annulation based on Brook rearrangement using beta-phenylthio-acryloylsilanes with alkyl methyl ketone enolates. An uncertain reaction mechanism, wherein a bulky cyclopentenol with large substituents on the same side of the five-membered ring was obtained as a major product, can be explained by the low activation energy of its reaction pathway. Intramolecular orbital interactions related to the carbanion generated by Brook rearrangement preferentially provide the stabilization of the reaction pathway to the bulky cyclopentenol (major product) compared with that provided to the non-bulky cyclopentenol (minor product). In addition, ab initio molecular orbital calculations suggest the existence of an E/Z conformational inversion after Brook rearrangement. This result accurately explains the loss of the E/Z stereochemical integrity in the starting materials of the experiment.