MO Calculations Research Articles

Ab Initio Chemical Kinetics for Oxidation of CH3OH by N2O4: Elucidation of the Mechanism for Major Product Formation and Its Relevancy to Tropospheric Chemistry.

Next to CH4, CH3OH is the most abundant C1 organics in the troposphere. The redox reaction of CH3OH with N2O4 had been shown experimentally to produce CH3ONO, instead of CH3ONO2. The mechanism for the reaction remains unknown to date. We have investigated the reaction by ab initio MO calculations at the UCCSD(T)/6-311+G(3df,2p)//UB3LYP/6-311+G(3df,2p) level. The result indicates that the reaction takes place primarily by the isomerization of N2O4 to ONONO2 through a very loose transition state within the N2O4-CH3OH collision complex with a 14.3 kcal/mol barrier, followed by the rapid attack of ONONO2 at CH3OH producing CH3ONO and HNO3. The predicted mechanism for the redox reaction compares closely with the hydrolysis of N2O4. The computed rate constant, k1 = 1.43 × 10-8 T1.96 exp (-9092/T) (200-2000 K) cm3molecule-1s-1, for the formation of CH3ONO and HNO3 agrees reasonably with available low-temperature kinetic data and is found to be similar to that of the isoelectronic N2O4 + CH3NH2 reaction. We have also estimated the kinetics for the termolecular reaction, 2 NO2 + CH3OH, and compared it with the direct bimolecular process; the latter was found to be 4.4 × 105 times faster under the troposphere condition. On the basis of the known pollution levels of NO2, N2O4, and CH3OH, both processes were estimated to be of negligible importance to tropospheric chemistry, however.

DFT study, and natural bond orbital (NBO) population analysis of 2-(2-Hydroxyphenyl)-1-azaazulene tautomers and their mercapto analouges

Theoretical research on the keto-enol tautomerization of 2-(2-Hydroxyphenyl)-1-aza azulene (2HPhAZ) and its thiol-thione (2MPhAZ) analouge has been performed using the density functional B3LYP method with the 6–311 + + G(2d,2p) basis set in gas and ethanol phases. The findings of the MO computation on the energy scale and the prediction of the frontier molecular orbital (FMO) energies demonstrate that the tautomeric structures exist in a static mixture in the ground state, with the enol and thiol structure being more stable than the keto and thione structures in gas phase. The ethanol solvent causes some reordering of the relative stability of 2HPhAZ and 2MPhAZ conformers. The geometries created at the B3LYP/6–311 + + G(2d,2p) level of theory were used for NBO analysis. In the tautomerization of 2HPhAZ and its mercapto analogue 2-(2-Mercaptophenyl)-1-azaazulene (2MPhAZ), it has been found that the O(S)-C sigma bond is weak due to nO(S)—> σ*C25-O26(S26) and nO(S)—> σ*C15-N16 delocalization. It is also noted that the resulting p character of the corresponding oxygen (sulfur) natural hybrid orbital (NHO) of σO(S)-C bond orbital is related to the decreased occupancy of the localized σO(S)-C orbital in the idealized Lewis structure or the increased occupancy of σ*O(S)-C of the non-Lewis orbital and their subsequent impact on molecular stability and geometry (bond lengths) in gas phase and ethanol. Additionally, the energy of charge transfer decreases as the potential rotamers' Hammett constants (R1–R3 for O(S) atoms) increase. The partial charge distribution on the skeleton atoms demonstrates that the intra- and intermolecular interactions can be significantly influenced by the electrostatic attraction or repulsion between atoms. Lastly, the currently applied NBO-based HB strength indicator enables a fair prediction of the frequency of the proton donor NH stretching mode, but this simple picture is hidden by abundant hype conjugative effects.

Dissipative particle dynamics simulation for peptoid nanosheet with non-empirical parameter set

Peptoids are biomimetic materials in which the substituent groups are located on the nitrogen atom of the peptide bond, facilitating the formation of nanosheet structures as reported by Mannige et al. [Nature, 526, 415 (2015)]. Dissipative particle dynamics (DPD) simulations were performed to investigate the aggregation stability of peptoids with different unit lengths. The crucial effective interaction parameters were determined by fragment MO (FMO) calculations, which allowed to evaluate different molecular interactions (electrostatic and dispersion) in a balanced way. The experimental observation of the unit length dependence was finally reproduced by this FMO-DPD method.

5‐Amino‐2‐isopropenyltetrazole and its Cupric Chloride Complex: Synthesis, Structure and Magnetism

AbstractA new tetrazole ligand, 5‐amino‐2‐isopropenyltetrazole, was prepared by regioselective alkylation of 5‐aminotetrazole with allyl bromide in sulfuric acid followed by dehydrobromination of intermediate 5‐amino‐2‐(1‐bromopropan‐2‐yl)tetrazole. 5‐Amino‐2‐isopropenyltetrazole (L) was found to react with copper(II) chloride to generate complex [CuL2Cl2]n. The ligand and its complex were characterized by single crystal X‐ray and thermal analyses. Complex [CuL2Cl2]n presents 1D coordination polymer, formed at the expense of double chlorido bridges between neighbouring octahedral coordinated CuII cations. Tetrazole ligand acts as monodentate ligand coordinated by CuII cations via the heteroring N4 atoms only. Magnetic studies revealed that the copper(II) ions were weakly antiferromagnetically coupled. Natural bond orbital analysis was performed to explain the structural peculiarities of the ligand. Its basicity and the relative stability of the protonated forms were investigated using MO calculations.

Access to Pyridinyl or Pyridinium Aza-BODIPYs with Tunable Near-Infrared Fluorescence through ICT from 4-Pyridinyl Pyrroles.

Aza-dipyrromethene boron difluoride (Aza-BODIPY) dyes have attracted much interest in recent decades. In this manuscript, we provide a facile way to access pyridine-substituted pyrroles. A series of 1/7-pyridinyl and pyridinium near-infrared (NIR) Aza-BODIPYs with/without rigidity were constructed and their spectroscopic properties were extensively investigated. These pyridinyl Aza-BOIDIPYs displayed slight bathochromic shifts and maintained bright NIR emission. Pyridinium Aza-BODIPYs showed increased bathochromic shift, however, the molar extinction coefficients and fluorescence quantum yields were decreased owing to ICT effect. The impacts followed the order of pyridin-4-ium>pyridin-2-ium>pyridin-3-ium, which was in consistence with their ICT strength. MO calculation was performed to provide possible explanation to the red-shifted absorption/emission, and apparent charge separation in pyridin-4-ium Aza-BODIPYs. The pyridinium Aza-BODIPY localized in lysosome and potentially avoided harmful ''alkalinizing effects'' of traditional lysosome-targeting fluorescent dyes containing amine moiety. We are working on construction of pyridinyl and pyridinium Aza-BODIPY photosensitizers against microbials or tumors.

Interactions b/w Collagen and Polylactic-Acid Molecular Models Due to DFT Calculations

Collagen and Polylactic Acid (PLA) as biomaterials in the tissue engineering have been investigated for the structure and function in considerably large progress. From a viewpoint of its electronic structures in the subnano-meter range, we investigate the bonding nature for five models of the type I collagen, PLA models and the bimolecular interaction between the models by using Density Functional Theory (DFT) calculations with Frontier MO theory. In order to confirm the accuracy of the models, we compare the simulated IR and C1s X-ray photoelectron spectra with experimental results. Especially, the interaction between PLA and (AspHypGly)-collagen models was obtained as the chemical bond energy (1540 kJ/mol), and the results of PLA-other four collagen bimolecular models were given as intermolecular bond energies of 30 ∼ 81 kJ/mol. The intermolecular interaction is due to inter-H-bond of –OH---O=, -NH---O=, and –CH---O= functional groups, respectively, using MO calculations.

First-Principles calculations of the interconfigurational transition energies of 4f - 4f-15d of Ln3+ ions in LiYF4 and CaF2

In studying the design of novel phosphors and solid-state laser materials, luminescence with a characteristically long lifetime originates from f - f emissions (infrared, visible and ultraviolet). However, due to high demand for novel luminescence materials which excite in the ultraviolet (UV) and vacuum ultraviolet (VUV) ranges, the interconfigurational f - d transition has been of great interest. In this work, we investigated the 4 f n - 4 f n -1 5 d transition energy of trivalent lanthanide ions in LiYF 4 and CaF 2 host crystals (LiYF 4 : Ln 3+ and CaF 2 : Ln 3+ ) without referring to any empirical parameters. These crystals are considered to be promising fluoride hosts for solid-state laser crystals. LnF 8 5− atomic clusters were built based on the crystal structures of LiYF 4 and CaF 2 . The relativistic MO calculations were done using the relativistic Discrete Variational Xα (DV-Xα) algorithm. The relativistic version of discrete variational multi-electron method (DVME) algorithm was used to calculate the multiplet energies. We considered the effect of lattice relaxation by a simple estimation using Shannon's crystal radii. Given that the theoretical transition energies are typically underestimated due to the underestimation of the corresponding effects, the absolute transitional energies have received corrections based on one-electron calculations utilizing the Slater's transition-state technique. The in-depth study indicates that the lattice-relaxation effect does not substantially impact LiYF 4 : Ln 3+ , but greatly affects the transitional energy of heavy lanthanides doped in CaF 2 from 4 f n - 4 f n -1 5 d . The energy corrections based on Slater's transition-state method are necessary to improve the accuracy of our calculations. By a combination of these two methods, the transition energies of 4 f n - 4 f n -1 5 d of LiYF 4 : Ln 3+ and CaF 2 : Ln 3+ agree very well with the experimental data. This research is important to providing guidance in the search for new lanthanide-based phosphors in UV or VUV regions. • The 4 f n - 4 f n -1 5 d transition energies of LiYF 4 :Ln 3+ and CaF 2 :Ln 3+ have been studied. • Effect of lattice relaxation was simply estimated based on Shannon's crystal radii. • Energy corrections utilizing Slater's transition-state method were considered. • The lattice relaxation greatly affects the transitional energy of heavy CaF 2 :Ln 3+ . • The energy corrections are necessary to improve the accuracy.

Enantioselective Vinylogous Mannich Reaction of Acyclic Vinylketene Silyl Acetals with Acyclic Ketimines

AbstractThe first enantioselective vinylogous Mannich reaction of acyclic vinylketene silyl acetals with acyclic ketimines derived from alkynyl ketoesters was developed. Excellent yields and enantioselectivities were obtained from the reaction using bis(imidazoline)‐Zn(II) catalyst. Based on experiments and MO calculation, a plausible transition state was proposed to explain the stereoselectivity of the reaction. The obtained products were converted into various amines and a lactam. This process provides an efficient route for the synthesis of acyclic δ‐amino‐α,β‐unsaturated carbonyl compounds and their derivatives.magnified image

Intrinsic Dynamic and Static Nature of Halogen Bonding in Neutral Polybromine Clusters, with the Structural Feature Elucidated by QTAIM Dual-Functional Analysis and MO Calculations.

The intrinsic dynamic and static nature of noncovalent Br-∗-Br interactions in neutral polybromine clusters is elucidated for Br4–Br12, applying QTAIM dual-functional analysis (QTAIM-DFA). The asterisk (∗) emphasizes the existence of the bond critical point (BCP) on the interaction in question. Data from the fully optimized structures correspond to the static nature of the interactions. The intrinsic dynamic nature originates from those of the perturbed structures generated using the coordinates derived from the compliance constants for the interactions and the fully optimized structures. The noncovalent Br-∗-Br interactions in the L-shaped clusters of the Cs symmetry are predicted to have the typical hydrogen bond nature without covalency, although the first ones in the sequences have the vdW nature. The L-shaped clusters are stabilized by the n(Br)→σ*(Br–Br) interactions. The compliance constants for the corresponding noncovalent interactions are strongly correlated to the E(2) values based on NBO. Indeed, the MO energies seem not to contribute to stabilizing Br4 (C2h) and Br4 (D2d), but the core potentials stabilize them, relative to the case of 2Br2; this is possibly due to the reduced nuclear–electron distances, on average, for the dimers.

The structure and stability of faecal pigment-Zinc(II) complexes

This work presents an in-depth study on the nature of the faecal pigment-zinc(II) complexes using spectroscopic, thermodynamic and computational studies towards a molecular level understanding regarding its structure, complexation and stability. The analysis of faecal pigments (FPs), specifically urobilin (UB) and stercobilin (SB), is often carried out using Schlesinger's test, that uses the zinc complexation induced enhancement of FPs fluorescence. It was observed that in addition to the expected 1:1 stoichiometry, FP-Zn(II) complex with 1:2 stoichiometry also form. This was confirmed by the ESI-MS mass spectral fragmentation patterns. A rigorous benchmarking process towards using optimized basis set and functionals for molecular orbital TD-DFT calculations on UB-Zn(II) complex suggested the use of B3LYP hybrid functional and LANL2DZ basis set as the optimized combination. Molecular geometries and transition energies predicted from MO calculations corroborated well with FTIR and mass spectrometric results. FP-Zn(II) complexation equilibria in aqueous media involve disaggregation of higher FPs followed by metal-ligand complexation. The binding constant values of FP-Zn(II) complexes were estimated to be 101 M−1 & 22 M−1 for 1:1 and 1:2 stoichiometries of SB-Zn(II) complexes and 105 M−1 & 11 M−1 for 1:1 and 1:2 stoichiometries of UB-Zn(II) complexes in aqueous media. For the 1:1 complexes, the enthalpy (∆H0) and entropy (∆S0) values for SB-Zn(II) are 65 k J mol−1 and 269 J K−1 mol−1, respectively. Similarly, enthalpy (∆H0) and entropy (∆S0) for UB-Zn(II) complexes are 69 kJ mol−1 and 256 J K−1 mol−1, respectively. This understanding of the structure and thermodynamics of FP-Zn(II) complex is expected to aid in developing aqueous phase analytical strategies towards the fluorescence-based analysis of FPs, an important component of water quality analysis.

A study on the synthesis, characterization, structural optimization, and conformational behaviors of bromo-substituted pyromelliticdiimide-based [2+2] macrocycle as structural units of covalently linked molecular tubes

Synthesis and structural, photo physical, and conformational behaviors at variable temperature and structural optimization of the pyromelliticdiimide-based bromo-substituted [2 + 2] macrocycles are described. Cyclization of the diamine (3) with dianhydride (4) in THF, followed by dehydration of the resultant amic acids resulted in the isolation of the bromo-substituted [2 + 2] macrocycle 1 (4.5%). The dynamic temperature-dependent 1H NMR spectra and MO calculations revealed the presence of two possible conformers for the [2 + 2] macrocycle 1. The UV/Vis spectrum of 1 reveals the presence of a weak intramolecular CT interaction of electron-withdrawing pyromelliticdiimide moiety with the electron-donating hexyloxy-substituted xylyl moiety. The cyclic voltammetric measurement shows two two-electron reversible reduction processes.

S=12 ferromagnetic Heisenberg chain in a verdazyl-based complex

We present a model compound for the $S$=1/2 ferromagnetic Heisenberg chain composed of the verdazyl-based complex $[$Zn(hfac)$_2]$$[$4-Cl-$o$-Py-V-(4-F)$_2]$. $Ab$ $initio$ MO calculations indicate a predominant ferromagnetic interaction forming an $S$=1/2 ferromagnetic chain. The magnetic susceptibility and specific heat indicate a phase transition to an AF order owing to the finite interchain couplings. We explain the magnetic susceptibility and magnetization curve above the phase transition temperature based on the $S$=1/2 ferromagnetic Heisenberg chain. The magnetization curve in the ordered phase is described by a conventional AF two-sublattice model. Furthermore, the obtained magnetic specific heat reproduces the almost temperature-independent behavior of the $S$=1/2 ferromagnetic Heisenberg chain. In the low-temperature region, the magnetic specific heat exhibits $\sqrt{T}$ dependence, which is attributed to the energy dispersion in the ferromagnetic chain.

Synthesis and structure of bis(ethylenedioxy)‐1,4,5,8‐tetraselenanaphthalene

AbstractBis (ethylenedioxy)‐1,4,5,8‐tetraselenanaphthalene (BEDO‐TSeN) has been synthesized by the reaction of diselenolate with tetraiodoethylene or tetrabromoethylene. The structure of BEDO‐TSeN was determined by X‐ray analysis, and its π‐donor property was estimated by MO calculations and determined by CV analysis.

Atomic Charges.

The problem of deriving atomic charges from the results of ab Initio MO calculations has been studied by the use of several reported methods: Mulliken population analysis, the minimal basis set (MBS) procedure, the natural population analysis (NPA), two electrostatic potential fitting methods, M-K and ChelpG, the Hirshfeld population analysis, and CM5 (charge model 5), which is related to the Hirshfeld method. The first set of studies were concerned with hydrogen charges. It was found that the MBS charges were linearly related to the Hirshfeld charges. The Hirshfeld, CM5, and MBS methods, but not the others, provided an excellent correlation for H atomic charge with the H-C-H bond angle, and with calculated gas-phase acidity. The two methods that were linearly related and gave hydrogen charges in agreement with an experimental study of partially deuterated methanes are MBS and Hirshfeld. In order to see which of the two methods is the more satisfactory, the methanol dimer was examined. The calculated H bond energy was 6.2 kcal/mol, which was in good agreement with studies of hydrogen bonds. The Coulombic interaction for the O···H bond was estimated using the MBS and Hirshfeld charges. The latter gave a calculated energy of 3-6 kcal/mol, whereas MBS gave an energy of ∼35 kcal/mol. Clearly, the Hirshfeld method is more satisfactory and should be the method of choice.

Mechanistic Studies on the Base-Promoted Conversion of Alkoxy-Substituted, Ring-Fused gem-Dihalocyclopropanes into Furans: Evidence for a Process Involving Electrocyclic Ring Closure of a Carbonyl Ylide Intermediate.

The mechanism associated with the base-promoted conversion of alkoxy-substituted and ring-fused gem-dihalocyclopropanes such as 40 into annulated furans has been explored. Treatment of compound 40 with potassium tert-butoxide affords a mixture of furans 23/27 and 41, an outcome that suggests the intermediacy of the slowly interconverting carbonyl ylides 42 and 43 that undergo rapid [1,5]-electrocyclizations and subsequent dehydrohalogenation to afford the observed products. This proposal is supported by ab initio MO and DFT calculations that also suggest a vinylcarbene insertion pathway is less likely to be operative.

Deltaarenes; novel macrocyclic molecules that are readily available from 1,4-benzoquinone and benzene dithiols

New types of macrocyclic compounds, deltaarenes, are prepared. The compounds were readily synthesized in three steps from an arenedithiol and benzoquinone, and the yields of the macrocyclization reaction reached up to 40% under high dilution conditions. X-ray crystallographic analysis revealed that the macrocycle has a relatively rigid trimeric structure with a unique triangular hole, the size of which was approximately 11 Å along each side. NMR data suggests that the ring has a C3-symmetric structure. The X-ray analysis showed that the hole is large enough to capture one molecule of chlorobenzene. Use of a variety of dithiols allowed the synthesis of different types of deltaarene derivatives. MO calculations showed that the hole size depends on the dithiol unit. Deprotection of the twelve methoxyl groups was easily achieved by treatment with BBr3 and yielded the free-OH deltaarene derivative.

Synthesis and photophysical properties of long wavelength absorbing BODIPY/aza-BODIPY bearing a five-membered ring

Five-membered-ring fused BODIPYs and aza-BODIPY were herein prepared. X-ray crystallographic analysis revealed that the core skeleton of six-membered-ring fused BODIPY is nonplanar but twisted. Such five-membered-ring fused BODIPY/aza-BODIPY dyes have long wavelength absorptions/emissions, high extinction coefficients, peak fluorescence and narrow excitations/emissions. MO calculations well supported and explained the same absorption maxima between BODIPY bearing the five-membered ring and BODIPY bearing the six-membered ring.

Does Metal Ion Complexation Make Radical Clocks Run Fast? An Experimental Perspective.

The rate constant for the β-scission of the cumyloxyl radical (kβ) was measured in the presence of various added electrolytes in acetonitrile and DMSO solvent. The results show that in CH3CN, kβ increases in the presence of added electrolyte, roughly paralleling the size of the cation: Li+ > Mg2+ ≈ Na+ > nBu4N+ > no added electrolyte. As suggested by Bietti et al. earlier, this effect is attributable to stabilizing ion-dipole interactions in the transition state of the developing carbonyl group, a conclusion further amplified by MO calculations (gas phase) reported herein. Compared to the gas phase predictions, however, this effect is seriously attenuated in solution because complexation of the cation to the electrophilic alkoxyl radical (relative to the solvent, CH3CN) is very weak. Because the interaction of Li+ and Na+ is much stronger with DMSO than with CH3CN, addition of these ions has no effect on the rate of β-scission.

Modulating the Structural Properties of α,γ-Hybrid Peptides by α-Amino Acid Residues: Uniform 12-Helix Versus "Mixed" 12/10-Helix.

The most important natural α- and 310 -helices are stabilized by unidirectional intramolecular hydrogen bonds along the helical cylinder. In contrast, we report here on 12/10-helical conformations with alternately changing hydrogen-bond directionality in sequences of α,γ-hybrid peptides P1-P5 [P1: Boc-Ala-Aic-Ala-Aic-COOH; P2: Boc-Leu-Aic-Leu-Aic-OEt; P3: Boc-Leu-Aic-Leu-Aic-Leu-Aic-Aib-OMe; P4: Boc-Ala-Aic-Ala-Aic-Ala-Aic-Ala-OMe; P5: Boc-Leu-Aic-Leu-Aic-Leu-Aic-Leu-Aic-Aib-OMe; Aic=4-aminoisocaproic acid, Aib=2-aminoisobutyric acid] composed of natural α-amino acids and the achiral γ4,4 -dimethyl substituted γ-amino acid Aic in solution and in single crystals. The helical conformations are stabilized by alternating i→i+3 and i→i-1 intramolecular hydrogen bonds. The experimental data are supported by ab initio MO calculations. Surprisingly, replacing the natural α-amino acids of the sequence by the achiral dialkyl amino acid Ac6 c [P6: Boc-Ac6 c-Aic-Ac6 c-Aic-Ac6 c-Aic-Ac6 c-Aic-Ac6 c-CONHMe; Ac6 c = 1-aminocyclohexane-1-carboxylic acid] led to a 12-helix with unidirectional hydrogen bonds showing an entirely different backbone conformation. The results presented here emphasize the influence of the structure of the α-amino acid residues in dictating the helix types in α,γ-hybrid peptide foldamers and demonstrate the consequences for folding of small structural variations in the monomers.

Computer-Aided Insight into the Relative Stability of Enamines

Venerable aldol, Michael, and Mannich reactions have undergone a renaissance in the past fifteen years, as a consequence of the development of direct organocatalytic versions, mediated by chiral amines. Chiral enamines are key intermediates in these reactions. This review focuses on the formation of enamines from secondary amines and their relative thermodynamic stability, as well as on the reverse reactions (hydrolysis). Experimental results and predictions based on MO calculations are reviewed to show which enamine forms may predominate in the reaction medium and to compare several secondary amines as organocatalysts.1 Introduction2 Relative Stability of Enamines as Determined Experimentally3 Pyrrolidine Enamines4 Enamines of the Jørgensen–Hayashi Catalyst5 Proline Enamines6 Free Enthalpies and Polar Solvent Effects7 Comparison of Organocatalysts8 Summary and Outlook9 Appendix