Your browser doesn't support javascript.
loading
Show: 20 | 50 | 100
Results 1 - 20 de 40
Filter
Add more filters










Publication year range
1.
Heliyon ; 10(12): e33159, 2024 Jun 30.
Article in English | MEDLINE | ID: mdl-39021983

ABSTRACT

The conformational properties of Alanine (Ala) residue have been investigated to understand protein folding and develop force fields. In this work, we examined the neighbor effect on the conformational spaces of Ala residue using model azapeptides, Ac-Ala-azaGly-NHMe (3, AaG), and Ac-azaGly-Ala-NHMe (4, aGA1). Ramachandran energy maps were generated by scanning (φ, ψ) dihedral angles of the Ala residues in models with the fixed dihedral angles (φ = ±90°, ψ = ±0° or ±180°) of azaGly residue using LCgau-BOP and LCgau-BOP + LRD functionals in the gas and water phases. The integral-equation-formalism polarizable continuum model (IEF-PCM) and a solvation model density (SMD) were employed to mimic the solvation effect. The most favorable conformation of Ala residue in azapeptide models is found as the polyproline II (ßP), inverse γ-turn (γ'), ß-sheet (ßS), right-handed helix (αR), or left-handed helix (αL) depending on the conformation of neighbor azaGly residue in isolated form. Solvation methods exhibit that the Ala residue favors the ßP, δR, and αR conformations regardless of its position in azapeptides 3 and 4 in water. Azapeptide 5, Ac-azaGly-Ala-NH2 (aGA2), was synthesized to evaluate the theoretical results. The X-ray structure showed that azaGly residue adopts the polyproline II (ßP) and Ala residue adopts the right-handed helical (αR) structure in aGA2. The conformational preferences of aGA2 and the dimer structure of aGA2 based on the X-ray structure were examined to assess the performance of DFT functionals. In addition, the local minima of azapeptide 6, Ac-Phe-azaGly-NH2 (FaG), were compared with the previous experimental results. SMD/LCgau-BOP + LRD methods agreed well with the reported experimental results. The results suggest the importance of weak dispersion interactions, neighbor effect, and solvent influence in the conformational preferences of Ala residue in model azapeptides.

2.
J Hazard Mater ; 465: 133036, 2024 03 05.
Article in English | MEDLINE | ID: mdl-38000286

ABSTRACT

A highly efficient system incorporates the real-time visualization of the two toxic molecules (H2S and N2H4) and the recognition of corresponding transforms using a fluorescent sensor. In this paper, a dual-responsive probe (QS-DNP) based on methylquinolinium-salicyaldehyde-2,4-dinitrophenyl was developed that can simultaneously detect H2S and N2H4 at two independent fluorescent channels without signal crosstalk. QS-DNP showed excellent anti-interference, high selectivity, outstanding water solubility, low LOD values (H2S: 51 nM; N2H4: 40 nM), low cytotoxicity, and mitochondrial localization properties. The 2,4-dinitrophenyl site was sensitive to H2S, and the CC bridge was reactive to N2H4, with strong fluorescence at 680 and 488 nm, respectively. The wavelength gap between these two channels is 192 nm; verify that there is no signal crosstalk throughout detection. By this means, the probe was used to simultaneously detect H2S and N2H4 in real soil samples, food samples, and living cells. The endogenous H2S and N2H4 were monitored in HeLa cells and investigated the mitochondria organelle of living cells with a positive charge on QS-DNP. Overall, all results emphasize that the QS-DNP probe is a powerful tool for the simultaneous detection of H2S and N2H4 and presents a potential new sensing approach.


Subject(s)
Fluorescent Dyes , Hydrazines , Hydrogen Sulfide , Humans , HeLa Cells , Mitochondria , Spectrometry, Fluorescence
3.
Molecules ; 28(14)2023 Jul 17.
Article in English | MEDLINE | ID: mdl-37513326

ABSTRACT

Azapeptides have gained much attention due to their ability to enhance the stability and bioavailability of peptide drugs. Their structural preferences, essential to understanding their function and potential application in the peptide drug design, remain largely unknown. In this work, we systematically investigated the conformational preferences of three azaamino acid residues in tripeptide models, Ac-azaXaa-Pro-NHMe [Xaa = Asn (4), Asp (5), Ala (6)], using the popular DFT functionals, B3LYP and B3LYP-D3. A solvation model density (SMD) was used to mimic the solvation effect on the conformational behaviors of azapeptides in water. During the calculation, we considered the impact of the amide bond in the azapeptide models on the conformational preferences of models 4-6. We analyzed the effect of the HB between the side-chain main chain and main-chain main-chain on the conformational behaviors of azapeptides 4-6. We found that the predicted lowest energy conformation for the three models differs depending on the calculation methods. In the gas phase, B3LYP functional indicates that the conformers tttANP-1 and tttADP-1 of azapeptides 4 and 5 correspond to the type I of ß-turn, the lowest energy conformation with all-trans amide bonds. Considering the dispersion correction, B3LYP-D3 functional predicts the conformers tctANP-2 and tctADP-3 of azapeptide 4 and 5, which contain the cis amide bond preceding the Pro residue, as the lowest energy conformation in the gas phase. The results imply that azaAsx and Pro residues may involve cis-trans isomerization in the gas phase. In water, the predicted lowest energy conformer of azapeptides 4 and 5 differs from the gas phase results and depends on the calculational method. For azapeptide 6, regardless of calculation methods and phases, tttAAP-1 (ß-I turn) is predicted as the lowest energy conformer. The results imply that the effect of the side chain that can form HBs on the conformational preferences of azapeptides 4 and 5 may not be negligible. We compared the theoretical results of azaXaa-Pro models with those of Pro-azaXaa models, showing that incorporating azaamino acid residue in peptides at different positions can significantly impact the folding patterns and stability of azapeptides.


Subject(s)
Amides , Peptides , Protein Conformation , Peptides/chemistry , Water/chemistry
4.
Food Chem ; 418: 135854, 2023 Aug 30.
Article in English | MEDLINE | ID: mdl-37023668

ABSTRACT

Understanding the structural properties of keratin is of great importance to managing their potential application in keratin-inspired biomaterials and its management of wastes. In this work, the molecular structure of chicken feather keratin 1 was characterized by AlphaFold2 and quantum chemistry calculation. The predicted IR spectrum of the N-terminal region of feather keratin 1, consisting of 28 amino acid residues, was used to assign the Raman frequencies of the extracted keratin. The MW of experimental samples were 6 & 1 kDa while the predicted MW (∼10 kDa) of ß-keratin. Experimental analysis shows the magnetic field treatment could affect the functional and surface structural properties of keratin. The particle size distribution curve illustrates the dispersion of particle size concentration, while TEM analysis demonstrates the reduction of particle diameter to 23.71 ± 1.1 nm following treatment. High-resolution XPS analysis confirmed the displacement of molecular elements from their orbital.


Subject(s)
Keratins , beta-Keratins , Animals , beta-Keratins/metabolism , Chickens/metabolism , Industrial Waste , Keratin-1 , Keratins/chemistry
5.
J Phys Condens Matter ; 34(19)2022 Mar 07.
Article in English | MEDLINE | ID: mdl-35158348

ABSTRACT

The Kohn-Sham density functional theory (KS-DFT) with the long-range corrected (LC) functional is applied to the benchmark dataset of 401 valence ionization potentials (IPs) of 63 small molecules of Chong, Gritsenko and Baerends (the CGB set). The vertical IP of the CGB set are estimated as negative orbital energies within the context of the Koopmans' prediction using the LCgau-core range-separation scheme in combination with PW86-PW91 exchange-correlation functional. The range separation parameterµof the functional is tuned to minimize the error of the negative HOMO orbital energy from experimental IP. The results are compared with literature data, includingab initioIP variant of the equation-of-motion coupled cluster theory with singles and doubles (IP-EOM-CCSD), the negative orbital energies calculated by KS-DFT with the statistical averaging of orbital potential, and those with the QTP family of functionals. The optimally tuned LC functional performs better than other functionals for the estimation of valence level IP. The mean absolute deviations (MAD) from experiment and from IP-EOM-CCSD are 0.31 eV (1.77%) and 0.25 eV (1.46%), respectively. LCgau-core performs quite well even with fixedµ(not system-dependent). Aµvalue around 0.36 bohr-1gives MAD of 0.40 eV (2.42%) and 0.33 eV (1.96%) relative to experiment and IP-EOM-CCSD, respectively. The LCgau-core-PW86-PW91 functional is an efficient alternative to IP-EOM-CCSD and it is reasonably accurate for outer valence orbitals. We have also examined its application to core ionization energies of C(1s), N(1s), O(1s) and F(1s). The C(1s) core ionization energies are reproduced reasonably [MAD of 46 cases is 0.76 eV (0.26%)] but N(1s), O(1s) and F(1s) core ionization energies are predicted less accurately.

6.
J Phys Chem A ; 125(16): 3489-3502, 2021 Apr 29.
Article in English | MEDLINE | ID: mdl-33874719

ABSTRACT

In the present study, we have investigated the applicability of long-range-corrected (LC) functionals to a Kohn-Sham (KS) Koopmans'-type theorem. Specifically, we have examined the performance of optimally tuned LCgau-core functionals (in combination with BOP and PW86-PW91 exchange-correlation functionals) by calculating the ionization potential (IP) within the context of Koopmans' prediction. In the LC scheme, the electron repulsion operator, 1/r12, is divided into short-range and long-range components using a standard error function, with a range separation parameter µ determining the weight of the two ranges. For each system that we have examined (H2O, CO, benzene, N2, HF, H2CO, C2H4, and five-membered ring compounds cyclo-C4H4X, with X = CH2, NH, O, and S, and pyridine), the value of µ is optimized to minimize the deviation of the negative HOMO energy from the experimental IP. Our results demonstrate the utility of optimally tuned LC functionals in predicting the IP of outer valence levels. The accuracy is comparable to that of highly accurate ab initio theory. However, our Koopmans' method is less accurate for the inner valence and core levels. Overall, our results support the notion that orbitals in KS-DFT, when obtained with the LC functional, provide an accurate one-electron energy spectrum. This method represents a one-electron orbital theory that is attractive in its simple formulation and effective in its practical application.

7.
Anal Chim Acta ; 1148: 238178, 2021 Mar 01.
Article in English | MEDLINE | ID: mdl-33516382

ABSTRACT

A tetraphenylethene (TPE) derivative was designed and synthesized upon conjugation with bis(thiophen-2-ylmethyl) amine (BTA) containing a mercury-binding moiety and further characterized by using Nuclear magnetic resonance (NMR), LC-MS, UV-Vis, and fluorescence spectroscopic methods. The resulting TPE-BTA exhibited comprehensive aggregation-induced emission while expressing a high quantum yield and emission intensity at 70% water fraction. The probe exhibited a good photochromic effect with a Stokes shift of 178 nm, and the emission intensity at 550 nm increased considerably with the color turning from dark green to bright green under a UV lamp upon the addition of 5 µM Hg2+. The lowest-energy conformation of the probe showed that two thiophene rings were perpendicular to the phenyl ring, while two BTA molecules were situated in a staggered form to each other. The sulfur and nitrogen atoms present in TPE-BTA were coordinated to the Hg2+ ion, and these binding sites were confirmed by the NMR parameters, X-ray photoelectron spectroscopy signals, and structural calculations. The binding of Hg2+ to TPE-BTA was believed to restrict the intramolecular motion of TPE-BTA, thus inducing it to shine brighter according to the unique aggregation-induced emission effect. The concentration of Hg2+ was determined based on the enhancement of the emission intensity, and the present probe showed an extremely high sensitivity with a limit of detection of 10.5 nM. Furthermore, TPE-BTA enabled selective detection of Hg2+ even in the presence of a 1000-fold excess of other interfering metal ions. The proposed method was successfully employed to determine Hg2+ in living HeLa cells and real water samples.


Subject(s)
Fluorescent Dyes , Mercury , HeLa Cells , Humans , Spectrometry, Fluorescence , Water
8.
J Comput Chem ; 42(7): 505-515, 2021 Mar 15.
Article in English | MEDLINE | ID: mdl-33349942

ABSTRACT

Time-dependent (TD) density functional theory (DFT) and Franck-Condon Hertzberg-Teller (FCHT) calculations of various DFT functionals [B3LYP, CAM-B3LYP, ωB97XD, and optimally tuned (OT) long-range corrected (LC)-BLYP] were performed to examine how well DFT functionals can predict the experimental absorption and fluorescence spectra of a 12-carbon nanobelt (CNB). OT-LC-BLYP reproduced the experimental absorption spectrum well in terms of the peak position and intensity in the case of using a basis set with a diffuse function, such as 6-31+G(d,p) and 6-311+G(d,p), whereas B3LYP showed a red-shift in the peak positions and CAM-B3LYP and ωB97XD, which have a long-range HF exchange, showed blue shifts. Regarding the fluorescence spectrum calculations with FCHT using 6-311+G(d,p), the OT-LC-BLYP reproduced both the peak intensities and positions closest to the experimental spectrum. B3LYP, however, showed red-shifted peaks, and ωB97XD showed blue-shifted peaks. CAM-B3LYP provided less blue-shifted peaks, but the relative peak intensities mismatched the experimental ones. Furthermore, calculations of the absorption and vibrationally resolved fluorescence spectra of 16-CNB and 24-CNB using OT-LC-BLYP/6-311+G(d,p) showed absorption and fluorescence spectra close to the experimental spectra with high accuracy. Moreover, the application of a polarizable continuum model (dichloromethane) produced a red shift in the peak positions of the absorption spectrum with increasing intensity but an increase in the peak intensities of the fluorescence calculations without shifting the peak position.

9.
J Phys Chem A ; 124(50): 10482-10494, 2020 Dec 17.
Article in English | MEDLINE | ID: mdl-33275438

ABSTRACT

The core electron binding energies (CEBEs) and core-level excitation energies of thymine, adenine, cytosine, and uracil are studied by the Kohn-Sham (KS) method with long-range corrected (LC) functionals. The CEBEs are estimated according to the Koopmans-type theorem for density functional theory. The excitation energies from the core to the valence π* and Rydberg states are calculated as the orbital energy differences between core-level orbitals of a neutral parent/cation and unoccupied π* or Rydberg orbitals of its cation. The model is intuitive, and the spectra can easily be assigned. Core excitation energies from oxygen 1s, nitrogen 1s, and carbon 1s to π* and Rydberg states, and the chemical shifts, agree well with previously reported theoretical and experimental data. The straightforward use of KS orbitals in this scheme carries the advantage that it can be applied efficiently to large systems such as biomolecules and nanomaterials.


Subject(s)
Nucleic Acids/chemistry , Density Functional Theory , Nucleic Acid Conformation , Quantum Theory , Thermodynamics
10.
J Phys Chem A ; 124(39): 8079-8087, 2020 Oct 01.
Article in English | MEDLINE | ID: mdl-32901484

ABSTRACT

Previously proposed theoretical schemes for estimating one-electron excitation energies using Kohn-Sham (KS) solutions with long-range corrected (LC) functionals are applied to the charge-transfer (CT) excitations of the ethylene···tetrafluoroethylene (C2H4-C2F4) system, and the CT complex between an aromatic donor (Ar = benzene, toluene, o-xylene, naphthalene, anthracene, and various meso-substituted anthracenes) and the tetracyanoethylene (TCNE) acceptor. The CT excited state is described well as a single-electron excitation between specific orbitals of donor and acceptor. Thus, CT excitation energies are well approximated by the orbital energies because of the satisfaction of the Koopmans-type theorem and the asymptotic behavior of the LC functional. We have examined three computational schemes: scheme 1 employs the orbital energies for the neutral and cationic systems, scheme 2 utilizes orbital energies of just the cation, and in scheme 3, because the electron affinity of a molecule is the ionization energy of its anion, a scale factor is applied to enforce this identity. The present schemes reproduce the correct asymptotic behavior of CT excitation energy of C2H4···C2F4 for the long intermolecular distances and give good agreement with accurate ab initio results. Calculated CT excitation energies for Ar-TCNE are compared with those of TD-DFT and ΔSCF methods. Scheme 1 with the optimal range-separation parameter µ accurately reproduces CT excitation energies for all Ar-TCNE systems and gives good agreement with the best TD-DFT calculations and experiment. Scheme 1, scheme 3, and TD-DFT show similar tendencies with respect to the variation in µ. Scheme 2 and ΔSCF approaches are rather insensitive to changes in µ, but both considerably underestimate the CT excitation energies for these systems. KS orbital energies are physically meaningful and they are practically useful; if the range-separation parameter is tuned, then good results can be obtained.

11.
J Phys Chem Lett ; 11(12): 4668-4677, 2020 Jun 18.
Article in English | MEDLINE | ID: mdl-32441939

ABSTRACT

The magnetic field effect (MFE) in exciplex emission (ExE) has been studied for decades, but it has been observed to occur only in solvents with a limited range of polarity. This limitation is mainly due to the reversible interconversion collapse between two quenching products of the photoinduced electron transfer, the exciplex and magnetic field-sensitive radical ion pair (RIP) beyond that polarity range. In a nonpolar solvent, the formation of RIPs is suppressed, whereas in a polar solvent, the probability of their re-encounter forming the exciplexes decreases. In this study, we developed new exciplex-forming (phenyl-phenanthrene)-(phenyl-N,N-dimethylaniline)-peptoid conjugates (PhD-PCs) to overcome this limitation. The well-defined peptoid structure allows precise control of the distance and the relative orientation between two conjugated moieties. Steady-state and time-resolved spectroscopic data indicate that the PhD-PCs can maintain the reversibility, which allows MFEs in ExE regardless of the solvent polarity. Subtle differences between the ExEs of the PhD-PCs were observed and explained by their exciplex geometries obtained through time-dependent density functional theory (TD-DFT) calculations.

12.
J Chem Phys ; 152(10): 104105, 2020 Mar 14.
Article in English | MEDLINE | ID: mdl-32171211

ABSTRACT

Several different types of density functional theory (DFT) exchange correlation functionals were applied to a periodic boundary condition (PBC) system [carbon monoxide (CO) adsorbed on Cu(111): CO/Cu(111)] and the differences in the results calculated using these functionals were compared. The exchange correlation functionals compared were those of Perdew-Burke-Ernzerhof (PBE) and those of long-range corrected density functional theory (LC-DFT), such as LC-ωPBE(2Gau) and LC-BLYP(2Gau). Solid state properties such as the partial density of states were calculated in order to elucidate the detailed adsorption mechanisms and back-bonding peculiar to the CO/Cu(111) system. In addition, our benchmark analysis of the correlations among the orbitals of CO and Cu metal using LC-DFT reasonably was in line with the experimentally observed adsorption site. The computation time was reasonable, and other numerical results were found to agree well with the experimental results and also with the theoretical results of other researchers. This suggests that the long-range Hartree-Fock exchange integral should be included to correctly predict the electronic nature of PBC systems.

13.
J Comput Chem ; 41(14): 1368-1383, 2020 May 30.
Article in English | MEDLINE | ID: mdl-32108955

ABSTRACT

A new simple and conceptual theoretical scheme is proposed for estimating one-electron excitation energies using Kohn-Sham (KS) solutions. One-electron transitions that are dominated by the promotion from one initially occupied orbital to one unoccupied orbital of a molecular system can be expressed in a two-step process, ionization, and electron attachment. KS with long-range corrected (LC) functionals satisfies Janak's theorem and LC total energy varies almost linearly as a function of its fractional occupation number between the integer electron points. Thus, LC reproduces ionization energies (IPs) and electron affinities (EAs) with high accuracy and one-electron excitation energies are expressed as the difference between the occupied orbital energy of a neutral molecule and the corresponding unoccupied orbital energy of its cation. Two such expressions can be used, with one employing the orbital energies for the neutral and cationic systems, while the other utilizes orbital energies of just the cation. Because the EA of a molecule is the IP of its anion, if we utilize this identity, the two expressions coincide and give the same excitation energies. Reasonable results are obtained for valence and core excitations using only orbital energies.

14.
J Comput Chem ; 41(13): 1261-1270, 2020 May 15.
Article in English | MEDLINE | ID: mdl-32058612

ABSTRACT

The interaction of a carbon nanotube (CNT) with various aromatic molecules, such as aniline, benzophenone, and diphenylamine, was studied using density functional theory able to compute intermolecular weak interactions (B3LYP-D3). CNTs of varying lengths were used, such as 4-CNT, 6-CNT, and 8-CNT (the numbers denoting relative lengths), with the lengths being chosen appropriately to save computation times. All aromatic molecules were found to exhibit strong intermolecular binding energies with the inner surface of the CNT, rather than the outer surface. Hydrogen bonding between two aromatic molecules that include N and O atoms is shown to further stabilize the intermolecular adsorption process. Therefore, when benzophenone and diphenylamine were simultaneously allowed to interact with a CNT, the aromatic molecules were expected to preferably enter the CNT. Furthermore, additional calculations of the intermolecular adsorption energy for aniline adsorbed on a graphene surface showed that the concavity of graphene-like carbon sheet is in proportion to the intermolecular binding energy between the graphene-like carbon sheet and the aromatic molecule.

15.
J Phys Chem A ; 123(32): 7034-7041, 2019 Aug 15.
Article in English | MEDLINE | ID: mdl-31322358

ABSTRACT

We have previously reported that, whereas conventional density functional theory (DFT) functionals have provided poor calculations on the alkane isodesmic reaction energy and isomerization reaction energy of organic molecules that include C, N, and O atoms, our developed long-range corrected (LC)- and LC including Gaussian attenuation (LCgau)-DFT + local response dispersion (LRD) functionals, which can accurately calculate inter- and intramolecular weak interactions, give accurate isomerization energies on these reactions. In this work, we found that B3LYP-D3, LC-ωPBE-D3, and ωB97XD, known for their good descriptions of weak interaction calculations, fail to reproduce the isomerization reaction energies of the molecules that include the S atom, such as methyl-thiourea, ethyl-thiourea, and propyl-thiourea. In contrast, LC- and LCgau-BOP+LRD functionals provide isomerization reaction energies that are very close to those produced by highly accurate wave function methods. These results show that an accurate description of the intramolecular weak interaction between the alkyl group and the S atom, unlike in the case of urea, is significant to reproduce the correct energy of the molecules with an alkyl group and S atom.

16.
Anal Chim Acta ; 1066: 112-120, 2019 Aug 20.
Article in English | MEDLINE | ID: mdl-31027525

ABSTRACT

A new boronic acid derivative functionalized with a 4-(3-(4-(4,5-diphenyl-1H-imidazole-2-yl)phenyl)-1,2,4-oxadiazol-5-yl)phenyl (IOP) moiety was synthesized for use as a sequential "on-off-on"-type relay fluorescence probe for Fe3+ ions and F- ions with high selectivity and sensitivity under physiological conditions. The introduction of Fe3+ to IOP boronic acid (IOPBA) formed an Fe3+IOPBA complex, which led to quenching of the blue fluorescence intensity at 458 nm. The lowest-energy conformation of IOPBA was theoretically predicted to adopt an extended structure, and the Fe3+ ion in the Fe3+IOPBA complex was coordinated to two phenyl groups to form a π-complex. Upon addition of F- to the Fe3+IOPBA complex, the original fluorescence was recovered due to formation of [FeF6]3‒, resulting in "on-off-on"-type sensor behavior. IOPBA showed high selectivity towards Fe3+ among other cations. Moreover, the Fe3+IOPBA complex showed specific selectivity towards F-, with other cations and anions not interfering with detection. Both sensing processes showed 1:1 stoichiometry with binding constants of 6.87 × 106 and 4.49 × 106 mol-1 L for Fe3+ with IOPBA and F- with Fe3+IOPBA, respectively. The limits of detection for Fe3+ and F- were 10 and 1 nM, respectively. The proposed method was successfully applied in real water samples. Furthermore, the probe had low cytotoxicity and was successfully used as a bioimaging reagent to detect intracellular Fe3+ and F- in living HeLa cells.


Subject(s)
Ferric Compounds/analysis , Fluorescence , Fluorides/analysis , Cell Survival , HeLa Cells , Humans , Ions/analysis , Molecular Structure , Optical Imaging
17.
Molecules ; 24(4)2019 Feb 25.
Article in English | MEDLINE | ID: mdl-30823577

ABSTRACT

We estimated the redox potential of a model heme compound by using the combination of our density functionals with a computational scheme, which corrects the solvation energy to the normal solvent model. Among many density functionals, the LC-BOP12 functional gave the smallest mean absolute error of 0.16 V in the test molecular sets. The application of these methods revealed that the redox potential of a model heme can be controlled within 200 mV by changing the protonation state and even within 20 mV by the flipping of the ligand histidine. In addition, the redox potential depends on the inverse of the dielectric constant, which controls the surroundings. The computational results also imply that a system with a low dielectric constant avoids the charged molecule by controlling either the redox potential or the protonation system.


Subject(s)
Coordination Complexes/chemistry , Density Functional Theory , Heme/chemistry , Models, Molecular , Transition Elements/chemistry , Electrochemical Techniques , Histidine/chemistry , Ligands , Oxidation-Reduction , Protein Conformation
18.
J Comput Chem ; 40(1): 105-112, 2019 Jan 05.
Article in English | MEDLINE | ID: mdl-30451312

ABSTRACT

Recently, we proposed a simple yet efficient method for the computation of a long-range corrected (LC) hybrid scheme [LC-DFT(2Gau)], which uses a modified two-Gaussian attenuating operator instead of the error function for the long-range HF exchange integral. This method dramatically reduced the computational time while maintaining the improved features of the LC density functional theory (DFT). Here, we combined an LC hybrid scheme using a two-Gaussian attenuating operator with one-parameter progressive correlation functional and Becke88 exchange functional with varying range-separation parameter values [LC-BOP(2Gau) with various µ values of 0.16, 0.2, 0.25, 0.3, 0.35, 0.4, and 0.42] and demonstrated that LC-BOP(2Gau) reproduces well the thermochemical and frontier orbital energies of LC-BOP. Additionally, we revised the scaling factors of the Gaussian multipole screening scheme for LC-DFT(2Gau) to correspond to the angular momentum of orbitals, which decreased the energy deviations from the energy with the no-screening scheme. © 2018 Wiley Periodicals, Inc.

19.
Angew Chem Int Ed Engl ; 56(51): 16180-16185, 2017 12 18.
Article in English | MEDLINE | ID: mdl-29024369

ABSTRACT

We herein report a facile, cost-competitive, and scalable method for producing viscoelastic conductors via one-pot melt-blending using polymers and supramolecular gels composed of carbon nanotubes (CNTs), diphenylamine (DP), and benzophenone (BP). When mixed, a non-volatile eutectic liquid (EL) produced by simply blending DP with BP (1:1 molar ratio) enabled not only the gelation of CNTs (EL-CNTs) but also the dissolution of a number of commodity polymers. To make use of these advantages, viscoelastic conductors were produced via one-pot melt-blending the EL and CNTs with a model thermoplastic elastomer, poly(styrene-b-butadiene-b-styrene) (SBS, styrene 30 wt %). The resulting composites displayed an excellent electromechanical sensory along with re-mendable properties. This simple method using cost-competitive EL components is expected to provide an alternative to the use of expensive ionic liquids as well as to facilitate the fabrication of novel composites for various purposes.

20.
J Chem Phys ; 145(12): 124105, 2016 Sep 28.
Article in English | MEDLINE | ID: mdl-27782652

ABSTRACT

In the past decade, a number of approaches have been developed to fix the failure of (semi)local density-functional theory (DFT) in describing intermolecular interactions. The performance of several such approaches with respect to highly accurate benchmarks is compared here on a set of separation-dependent interaction energies for ten dimers. Since the benchmarks were unknown before the DFT-based results were collected, this comparison constitutes a blind test of these methods.

SELECTION OF CITATIONS
SEARCH DETAIL
...