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1.
J Chem Phys ; 155(4): 044110, 2021 Jul 28.
Artigo em Inglês | MEDLINE | ID: mdl-34340364

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
2.
J Phys Chem A ; 2021 Jul 28.
Artigo em Inglês | MEDLINE | ID: mdl-34319114

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.

3.
J Chem Phys ; 154(12): 124107, 2021 Mar 28.
Artigo em Inglês | MEDLINE | ID: mdl-33810676

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.

4.
J Comput Chem ; 41(25): 2203-2212, 2020 Sep 30.
Artigo em Inglês | MEDLINE | ID: mdl-32730684

RESUMO

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.

5.
Nanoscale ; 12(16): 9058-9066, 2020 Apr 28.
Artigo em Inglês | MEDLINE | ID: mdl-32285063

RESUMO

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.

6.
Nano Lett ; 20(1): 599-605, 2020 Jan 08.
Artigo em Inglês | MEDLINE | ID: mdl-31858802

RESUMO

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.

7.
J Comput Chem ; 40(30): 2622-2635, 2019 Nov 15.
Artigo em Inglês | MEDLINE | ID: mdl-31396976

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.

8.
Nano Lett ; 19(4): 2443-2449, 2019 04 10.
Artigo em Inglês | MEDLINE | ID: mdl-30888179

RESUMO

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.

9.
ACS Cent Sci ; 4(6): 664-665, 2018 Jun 27.
Artigo em Inglês | MEDLINE | ID: mdl-29974060
10.
J Chem Phys ; 145(2): 024107, 2016 Jul 14.
Artigo em Inglês | MEDLINE | ID: mdl-27421397

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 (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.


Assuntos
Modelos Químicos , Reconhecimento Automatizado de Padrão , DNA/química , Campos Eletromagnéticos , Modelos Lineares , Modelos Genéticos , Dinâmica não Linear , Fatores de Tempo
11.
J Comput Chem ; 36(28): 2103-13, 2015 Oct 30.
Artigo em Inglês | MEDLINE | ID: mdl-26337429

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
12.
J Comput Chem ; 36(16): 1232-9, 2015 Jun 15.
Artigo em Inglês | MEDLINE | ID: mdl-25903426

RESUMO

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.

13.
J Mol Model ; 21(5): 117, 2015 May.
Artigo em Inglês | MEDLINE | ID: mdl-25877528

RESUMO

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.

14.
Chemphyschem ; 16(7): 1551-6, 2015 May 18.
Artigo em Inglês | MEDLINE | ID: mdl-25765254

RESUMO

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.

15.
J Chem Phys ; 142(10): 104111, 2015 Mar 14.
Artigo em Inglês | MEDLINE | ID: mdl-25770530

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 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.


Assuntos
Técnicas de Química Analítica , Modelos Biológicos , Teoria Quântica
16.
J Mol Model ; 20(6): 2277, 2014 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-24878802

RESUMO

A simple way to improve the accuracy of the fragmentation methods is proposed. The formalism was applied to the elongation (ELG) method at restricted open-shell Hartree-Fock (ROHF) level of theory. The α-helix conformer of polyglycine was taken as a model system. The modified ELG method includes a simplified electrostatic field resulting from point-charge distribution of the system's environment. In this way the long-distance polarization is approximately taken into account. The field attenuates during the ELG process to eventually disappear when the final structure is reached. The point-charge distributions for each ELG step are obtained from charge sensitivity analysis (CSA) in force-field atoms resolution. The presence of the intermediate field improves the accuracy of ELG calculations. The errors in total energy and its kinetic and potential contributions are reduced by at least one-order of magnitude. In addition the SCF convergence of ROHF scheme is improved.

17.
Materials (Basel) ; 6(3): 870-885, 2013 Mar 06.
Artigo em Inglês | MEDLINE | ID: mdl-28809345

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.

18.
J Chem Theory Comput ; 9(9): 4035-45, 2013 Sep 10.
Artigo em Inglês | MEDLINE | ID: mdl-26592399

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.

19.
J Phys Chem A ; 116(51): 12492-502, 2012 Dec 27.
Artigo em Inglês | MEDLINE | ID: mdl-23214975

RESUMO

The conductivity and nonlinear optical properties of isonaphtothiophene (INT)(n) are investigated by quantum chemical techniques. The conducting properties of (INT)(n) are examined by density of states (DOS) and local DOS analyses. As the chain length n increases, the geometrical conformations of (INT)(n) changed, and the energy gap suddenly decreases. The energy potentials and rotation effect are explored to determine the most preferred stable structures. The geometrical and intrinsic charge character are analyzed by UV/vis/NIR spectra and confirmed by frontier orbital analysis. Interestingly, the (hyper)polarizabilities of (INT)(n) oligomers increase sharply as the chain length increased. Additionally, the importance of the side ß double bonds effect on the structural transformation is detected by a new quantum chemical technique resulting in a potential polymer conductor that can be controlled by modifying its side chains.

20.
Phys Chem Chem Phys ; 14(21): 7640-68, 2012 Jun 07.
Artigo em Inglês | MEDLINE | ID: mdl-22563579

RESUMO

The elongation method, proposed in the early 1990s, originally for theoretical synthesis of aperiodic polymers, has been reviewed. The details of derivation of the localization scheme adopted by the elongation method are described along with the elongation processes. The reliability and efficiency of the elongation method have been proven by applying it to various models of bio-systems, such as gramicidin A, collagen, DNA, etc. By means of orbital shift, the elongation method has been successfully applied to delocalized π-conjugated systems. The so-called orbital shift works in such a way that during the elongation process, some strongly delocalized frozen orbitals are assigned as active orbitals and joined with the interaction of the attacking monomer. By this treatment, it has been demonstrated that the total energies and non-linear optical properties determined by the elongation method are more accurate even for bio-systems and delocalized systems like fused porphyrin wires. The elongation method has been further developed for treating any three-dimensional (3D) systems and its applicability is confirmed by applying it to entangled insulin models whose terminal is capped by both neutral and zwitterionic sequences.


Assuntos
Modelos Teóricos , Colágeno/química , DNA/química , Gramicidina/química , Insulina/química , Insulina/metabolismo , Porfirinas/química , Teoria Quântica
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