Alanine is a transfer standard dosimeter using in gamma-ray and electron beam calibration. One of the important factor affecting its dosimetric response is amount of humidity which can deviate the dosimetry expert from the exact value of absorbed doses. Ab initio molecular dynamics calculations were performed to determine the environmental effects on the EPR parameters of L-α-Alanine radicals in acidic and alkaline solutions. Similar to the closed-shell amino acid molecule alanine, the zwitterionic form of alanine radical is the stable form in the gas phase while the non-zwitterionic neutral alanine radical is not a stable structure. Geometric and EPR parameters of radicals in both gas and solution phases are found to be dependent on hydrogen bonding of water molecules with the polar groups and by dynamic solvation. Calculations on the optimized free radicals in the gas phase revealed that for neutral radical, hydrogen bonding to water molecules drives a decrease in the magnitudes of g-tensor components gxx and gyy without affecting neither gzz component nor the HFCCs. For the transfer from the gas to solution phase of the alanine radical anion is accompanied with an increase in the spin density on the carboxylic group’s oxygen atoms. However, for the neutral radical, this transfer from gas to solution phase is accompanied with the decrease in the spin density on oxygen atoms. Calculated isotropic HFCCs and g-tensor of all radicals were in good agreement with their experimental counterparts in both acidic and alkaline solutions, which enhances the confidence in our calculated results.
The existence and stability of MNg42+(Sb2F11−1)2 (Ng=Ar,Ne,He,M=Au, Ag, Cu) salt compounds are theoretically investigated in this study. This undertaking is carried out to address the following challenges: (1) synthesizing a bulk salt compound containing a noble gas lighter than krypton and (2) synthesizing the congeners of AuXe42+(Sb2F11−1)2 containing noble gases other than Xe. The reliability of our calculations on the MNg42+(Sb2F11−1)2 (Ng=Ar,Ne,He,M=Au, Ag, Cu) systems is assessed by benchmark calculations of the well-known AuXe42+(Sb2F11−1)2 salt. In the benchmark calculations, a two-pronged evaluation strategy, including direct and indirect evaluation methods, is used to theoretically investigate the spectroscopic constants of AuXe42+and the existence and stability of the AuXe42+(Sb2F11−1)2 salt. The validity of the theoretical calculation methods in the benchmark calculations of AuXe42+(Sb2F11−1)2 allows us to adopt a similar methodology to effectively predict the existence and stability of MNg42+(Sb2F11−1)2 (Ng=Ar,Ne,He,M=Au, Ag, Cu) salt compounds. Calculations based on the Born–Haber cycle using estimated lattice energies and some necessary ancillary thermochemical data show that MAr42+(Sb2F11−1)2 (M=Au, Ag, Cu) salt compounds can be synthesized. The upper-limit stable temperatures are estimated to be −224.43, −146.21, and −80.39 °C. The CuAr42+(Sb2F11−1)2salt compound is a promising candidate. Our calculations also show that the MNg42+(Sb2F11−1)2 (Ng=Ne,He,M=Au, Ag, Cu) salt compounds cannot be stabilized.
Carbazole (Cz) dimers in various cofacial conformations, including staggered (Stg), anti, and syn, were explored by means of ab initio calculations at SOS-MP2, SOS-CIS(D0), and additional coupled cluster calculation levels. As in other π-conjugated molecules, strong Cz excimers form in the syn conformation in both the S1 and T1 states, leading to significantly reduced optical excitation energies, whereas the dimers in the Stg and anti conformations, upon excitation, remain as simple excited dimers, showing similar optical energy gaps to that of the monomer. Being far more stable in the ground state, however, the Stg dimer turned out to be nearly isoenergetic to the syn dimer in the S1 state, and even more stable in the T1 state. In addition, a considerable potential energy barrier between the syn and Stg dimers was found in the calculated S1-state potential energy surface. Given that the ground-state intermolecular interactions are expected to govern the dimer conformations of Cz-based materials in the solid-state films of organic electronics, these results strongly demonstrate that the electronic excitation of Cz dimers do not necessarily lead to the strong excimer formation, unless Cz molecules were forced to be arranged in the syn conformation.
Pyrazolidines are very important compounds that widely exist in many natural products. Herein, we have employed high-level DFT calculations to systematically investigate the underlying mechanism of Cu(OTf)2 catalyzed [3+2] cycloaddition reactions that synthesis CF3substituted pyrazolidines. About eight possible initial configurations of the [3+2] reaction is considered and all relevant reactants, transition states and products are optimized. Based on these structures, IRC paths and the wavefunction analysis, we concluded that the Cu(OTf)2 catalyzed [3+2] cycloaddition follow a concerted asynchronous mechanism. The CN bond forms immediately after the formation of the CC bond. Among all eight reaction paths, the energy barrier for the [3+2] reaction that lead to the CF3substituted synpyrazolidine is the lowest one, ca. 3.2 kcal/mol, which might result in the diastereoselectivity that observed in experiment. We have also investigated the reaction processes that without Cu(OTf)2 molecule. The computational results indicate that the energy barriers that form the diastereoisomers are much closer and also larger than the Cu(OTf)2 catalyzed one. Therefore, Cu(OTf)2 catalyst plays an important role for the diastereoselectivity of the [3+2] cycloaddition reaction. Our present work not only gives the detail mechanism of the Cu(OTf)2 catalyzed [3+2] cycloaddition, but can also be helpful for the future designation of Cu(OTf)2 based cycloaddition processes.
Calcium carbonate (CaCO3) is an inorganic compound which is widely used in industry, chemistry, construction, ocean acidification and biomineralization due to its rich constituent on earth and excellent performance, in which calcium carbonate hydrates are important systems. In Z.Y. Zou et al’s work (Science, 2019, 363, 396–400), they found a novel calcium carbonate hemihydrate phase, but the structure stability, optical and mechanical properties has not been studied. In this work, the stability, electronic, optical, and mechanical properties of novel calcium carbonate hydrates were investigated by using the first-principles calculations within density functional theory (DFT). CaCO3·xH2O (x=1/2, 1 and 6) are determined dynamically stable phases by phonon spectrum, but the Gibbs energy of reaction of CaCO3·1/2H2O is higher than other calcium carbonate hydrates. That’s why the CaCO3·1/2H2O is hard to synthesize in the experiments. In addition, the optical and mechanical properties of CaCO3·xH2O (x=1/2, 1 and 6) are expounded in detail. It shows that the CaCO3·1/2H2O has the largest bulk modulus, shear modulus, Young’s modulus with the values 60.51, 36.56 and 91.28 GPa with respect to other two calcium carbonate hydrates investigated in this paper. This work will provide guidance for experiments and its applications, such as biomineralization, geology, and industrial processes.
On the example of forty ion pairs, the study demonstrates how the core-level binding energy values can be calculated and used to plot theoretical spectra at a low computational cost using density functional theory methods. Three approaches for obtaining the binding energy values are based on delta Kohn–Sham (ΔKS) calculations, 1s Kohn–Sham orbital energies, and atomic charges. The ΔKS results show a good agreement between the available experimental X-ray photoelectron data. 1s Kohn–Sham orbital energies and atomic charges also correlate with the ΔKS results.
We investigate the ability of mechanical and electronic density functional theory (DFT)-based embedding approaches to describe the solvent effects on nuclear magnetic resonance (NMR) shielding constants of the ⁹⁵Mo nucleus in the molybdate ion in aqueous solution. From the description obtained from calculations with two- and four-component relativistic Hamiltonians, we find that for such systems spin-orbit coupling effects are clearly important for absolute shielding values, but for relative quantities a scalar relativistic treatment provides a sufficient estimation of the solvent effects. We find that the electronic contributions to the solvent effects are relatively modest yet decisive to provide a more accurate magnetic response of the system, when compared to reference supermolecular calculations. We analyze the errors in the embedding calculations by statistical methods as well as through a real-space representation of NMR shielding densities, which are shown to provide a clear picture of the physical processes at play.
Local correlation methods rely on the assumption that electronic correlation is nearsighted. In this work, we develop a method to alleviate this assumption. The first step is to approximately decompose the electron correlation to the nearsighted and farsighted components based on the wavelength decomposition of electron correlation by Langreth and Perdew. The nearsighted component is then calculated using the recently developed embedded cluster density approximation (ECDA) which is a local correlation method formulated in the context of density functional theory. The farsighted component is calculated based on the system’s Kohn-Sham orbitals. The accuracy of this new method depends on the quality of the decomposition. We examined the method’s accuracy by patching the random phase approximation (RPA) correlation energy in a H₂₄ chain in which the electron correlation is highly nonlocal. This new method predicts bond stretching energies, RPA correlation potential, and Kohn-Sham eigenvalues in good agreement with the benchmarks. Our results demonstrate the importance of including the farsighted part of electron correlation for studying systems having nonlocal correlations.
In this work, geometries, stabilities and electronic properties of carbon monoxide (CO) molecule as an adsorbent on simple carbon nanotube (CNT) and N, B, S-doped carbon nanotubes (NCNT, BCNT and SCNT) with parallel and perpendicular configurations are fully considered using ONIOM, natural bond orbital (NBO), and quantum theory of atom in molecule (QTAIM) calculations. The adsorption energies (Ead) demonstrate that CO molecule could be adsorbed on the surface of the simple carbon nanotube with parallel configuration (CNT-p) and N-doped carbon nanotube with perpendicular configuration (NCNT-d) in exothermic process. QTAIM calculations are showed the close-shell (non-covalent) interactions between CO molecule and CNT or N, B, S-doped CNTs. Also, the energy gap (Eg) values between the highest occupied molecular orbital and the lowest unoccupied molecular orbital are calculated. In accordance to the results of energy gap, simple and N-doped carbon nanotubes could be used as CO-sensors.
The presence of long abandoned, hexagonal omega (ω) phase in steel samples is recently gaining momentum on account of accurate transmission electron microscopy (TEM) measurements. The formation and stabilization of this metastable phase down to room temperature is attributed to the combined effect of factors such as accelerated cooling, special atomic constraints at twin boundaries, and the enrichment of solute elements such as Al, Mn, Si, C, and Cr in the nanometer sized regimes. Here, we present a density functional theory (DFT) study of the effect of the above alloying elements in ω-Fe and confirm the predictions using high resolution TEM observations of the structure of an experimental steel at high magnifications. It is found that the FM and ++- spin states are the most stable for a primitive cell of ω-Fe. The density of states calculations show that the d band occupancy of ω-Fe is changing in presence of the alloying elements, and this in turn will affect the cohesive energy. Further, the dynamical stability analysis from phonon band structure reveals that only ω-Fe with substitutional C exhibits thermodynamic stability. This is in line with experimental indications that the stabilization of ω-phase in ferritic/martensitic steels occurs due to the presence of special symmetry constraints at grain boundaries
Motivated by the particularly short metal-metal distance that has been predicted for the D3h [BeH3Be]+ cation, comparable to those anticipated for triple bonds, we investigate the nature of the bonding interactions in the D3h [MH3M]+ cations (M = Be, Mg). CCSD(T)/cc pVQZ calculations are used to determine optimized geometries for all of the various species, including those ‘capped’ by He or Ne atoms (as proxies for an inert gas matrix). The primary tools that are then used to investigate the nature of the chemical bonding are spin-coupled generalized valence bond calculations and the analysis of localized natural orbitals and of domain-averaged Fermi holes. The various results for all of the systems considered indicate the presence of highly polar three-centre two-electron M−H−M bonding character instead of any significant direct metal-metal bonding.
Building on a previous work, pseudopotential sets are developed and tested for a variety of \(sp^2\) and \(sp^3\) carbon fragments. These fragments contain only one or two explicit protons and electrons, and make use of non-atom-centred potentials. They are tested with Density Functional Theory calculations in a selection of chemical environments in which several physical characteristics, including orbital and first ionisation energies, are found to be well-reproduced. They are then employed in the reproduction of molecular absorption spectra for large organic molecules and carbon allotropes, and are found to recreate both absorption and ECD spectra to a high accuracy. They are also found significantly to increase the computational efficiency of TDDFT calculations in which they are used.
We have developed a new database of structures and bond energies of 45 noble-gas containing molecules. The structures were calculated by CCSD(T)/aug-cc-pVTZ methods and the bond energies were obtained using CCSD(T)/CBS (complete basis set) method. Many wavefunction-based and density functional theory methods have been benchmarked against the 45 accurate bond energies. Our result showed that the MPW1B95, B2GP-PLYP, and DSD-BLYP functionals with the aug-cc-pVTZ basis set excel on predicting the bond energies of the noble-gas molecules with MUEs (mean unsigned errors) of 1.5-1.9 kcal/mol. When combinations of Dunning’s basis sets are used, the MPW1B95, MPW1PW91, and B2GP-PLYP functional give significantly lower MUEs of 1.1-1.3 kcal/mol. Doubly hybrid methods using B2GP-PLYP and DSD-BLYP functionals and MP2 calculation also provide satisfactory accuracy with MUEs of 1.3-1.4 kcal/mol. If the noble-gas bond energies and the total atomization energies of a group of 109 main-group molecules are considered at the same time, the MPW1B95/aug-cc-pVTZ single-level method (MUE = 2.7 kcal/mol) and the B2GP-PLYP functional with combinations of basis sets (MUEs = 1.8 kcal/mol) give the overall best result.
Skin sensitization occurs when an exogenous chemical substance forms a covalent adduct with a dermal protein electrophile or nucleophile. This instigates an immune response which leads to inflammation. The local lymph node assay (LLNA) is an in-vivo model used in the assessment of relative skin sensitizing potency of chemicals. The method is time consuming and expensive, as well as poses ethical questions given that a number of mice must be sacrificed for each compound assessed. In this work we investigate the use of an inexpensive, rapid and ethical method to predict the skin sensitization potential of Schiff base chemicals. We employ quantum chemical methods to rationalize the sensitization potential of 22 compounds with a diverse range of activities. To this end we have evaluated the mechanistic profile associated with this type of reaction using gas-phase models. We subsequently use the predicted rate determining barriers and key physico-chemical parameters (such as logP) to establish SAR guidelines to predict the skin sensitization potential for new chemicals. We find that the predicted rate determining barriers for aldehydes, ketone and 1,2 and 1,3 diones generally decrease in the given order, which concurs with the overall trends in sensitization. We find that lipophilicity also plays a role, with those chemicals displaying both low barriers to reaction, and lower lipophilicity (i.e. diones), being more likely to display undesirable skin sensitization effects. These findings are in line with experimental based observations in the literature and point to the value 3D quantum chemical simulations can play in the combination of approaches used to estimate skin sensitization potential of chemicals.