Journal of Theoretical and Computational Chemistry

The normalized electron affinity of the hydrogen atom, is the fundamental measure of anionic electron correlation. The three-body H(−) and AB(−) systems analogous to Efimov three-body bosons support multiple excited states. The first complete set of ground state electron affinities of the main group atoms and homonuclear diatomic molecules are reported using the Hylleraas variational binding energy of the hydride anion. Thermal electron affinities and activation energies for the formation of the 27 bonding states of O₂(−) are reported from electron capture detector and atmospheric pressure negative ion mass spectrometry. These are iterated through magnetron, flame, swarm, electron impact, photodetachment, and negative ion photoelectron spectra to obtain more precise self-consistent values. Electron affinities for NO are similarly reported. These data are used to calculate Herschbach ionic Morse Person electron curves for the 54 O₂(−) and 87 NO(−) states predicted by adiabatic correlation rules. A new ground state adiabatic electron affinity of SF₆ 3.00(10) eV is determined from negative ion mass spectra.

The decarboxylation of pyrrole-2-carboxylic acid comprises the addition of water to the carboxyl group and the C–C bond cleavage leading to the protonated carbonic acid. Herein possible concerted and stepwise mechanisms for the C-protonated and O-protonated pathways were extensively investigated by using the cluster-continuum model. The calculated results indicate that the initial hydration or the nucleophilic attack of water at the carbonyl group of both C- and O-protonated derivatives is the rate-determining step for the overall reaction, and the O-protonated pathway will dominate the whole reaction. The predicted activation Gibbs energies for the overall reaction initialized by the O-protonated species fall in the range of 83.3 ∼ 123.0 kJ/mol, showing good agreement with experimental values of 91.6 ∼ 101.3 kJ/mol. On the basis of extensive calculations, the remarkable dependence of the predicted mechanisms and thermodynamic values on the number of explicit water molecules in the cluster-continuum model was discussed.

, framework-isoelectronic to , have been investigated at the B3LYP/6-311+G** level of theory. The most stable positional isomers of individual are similar to those of and in framework configuration. The energy analysis reveals that the cage with the icosahedron framework, with the octahedron framework and with the bicapped square antiprism framework are, in order, the most stable in the system. Furthermore, three-dimensional aromaticity of all is characterized. The most stable cages, , and , also have relatively large aromaticity. All the predicted N–N stretching frequencies (2127–2303 cm⁻¹) of the most stable positional isomers in the system are lower than the computational N–N stretching frequency (2445 cm⁻¹) of free N₂ at the same level, which results from the σ donation of N₂ to B frameworks. The stretching frequencies of N–N in the cages increase with the decrease of N–N distances or the increase of B–N distance. In addition, B_n−1H_n−1 fragment has larger affinity for group CH than that for group BNN, namely, it favors to form the rather than the .

A zwitterionic glycine (zGLY) is adopted as an example to study the impact of water environment (310 H₂O molecules) on the molecular structure and energetics using a self-consistent-charge density-functional tight-binding theory based molecular dynamics (SCC-DFTB/MD) method. It is found that maximal eight hydrogen bonds could be formed simultaneously between eight water molecules and the zGLY. The ability of the COO^- terminal to adsorb water molecules is stronger than the terminal with respect to hydrogen bonding with more water molecules and exhibits lower adiabatic adsorption energies. The zGLY's intramolecular hydrogen bond appeared unpredictably, without involving any proton transfer and generally helpful for enhancing the system stability. Water molecules play an important role to stabilize the zwitterionic amino acids and restrain the proton migration from the to the COO⁻ group. Our results show that the SCC-DFTB/MD method could successfully describe geometry dynamical evolutions and energetics of biomolecules in a nanoscale simulation with the presence of a large number of water molecules. Our study not only verified the feasibility of a QM level methodology for describing the aqueous states of biochemical molecules, but also gave a clear evidence for the impact of water environment on amino acids.

The monofunctional (the first substitution reactions) and bifunctional (the second substitution reactions) binding of the title antitumor drugs to purine bases were studied computationally by using density functional theory and IEF-PCM solvation models. For the first substitutions with guanine and adenine, our calculations demonstrate that the trans monoaqua and diaqua reactant complexes (RCs) can generate trans- or cis-monoadducts via identical or very similar trigonal-bipyramidal transition-state structures, predicting that the cis-monoadducts generated by trans RCs can subsequently close by coordination to the adjacent purine bases to form 1,2-intrastrand Pt–DNA adducts and eventually distort DNA in the same way as cisplatin. Thus it is likely that the transplatin analogues have the same mechanism of anticancer activity of cisplatin. In general, the monoaqua and diaqua monofunctional substitutions prefer guanine over adenine. The calculated lowest activation free energy in aqueous solution is 15.2 kcal/mol in the monoaqua substitutions (substituted by guanine from trans-[Pt{HN = C(CH₃)₂}₂Cl(H₂O)]⁺ to trans/cis-monoadduct), and 11.4 kcal/mol in the diaqua substitutions (substituted by guanine from cis-[Pt{HN = C(CH₃)₂}₂(H₂O)₂]²⁺ to cis-monoadduct). For the second substitutions, all the reactants are started from the diaqua product complexes of the first substitutions substituted by guanine. The data obtained for the complexation energy difference between guanine and adenine RCs suggest that a thermodynamic favors the formation of GG over GA adducts by ∼ 5 - 12 kcal/mol in aqueous solution. Moreover, there is a kinetic preference for the formation of GG over GA adduct for the cis-monoadduct to cis-diadduct paths, while for the trans-monoadduct to trans-diadduct paths there is no certain trend biased toward GG adduct. In addition, the second substitutions of the trans-monoadduct to trans-diadduct paths have lower activation barriers than the corresponding cis-monoadduct to cis-diadduct paths. The lowest activation energy in the bifunctional substitutions from cis-monoadduct to cis-diadduct is 20.5 kcal/mol in the Pt(acetonimine)₂GG²⁺ head-to-head (HH) path, while it is 17.7 kcal/mol from trans-monoadduct to trans-diadduct in the Pt(NH₃)(acetonimine)GA²⁺ head-to-tail (HT) path. For the first and second substitutions, hydrogen-bonds play an important role in stabilizing these species.

A systematic theoretical study on various maleic acid (MA) clusters has been carried out employing density functional theory (DFT) methods. The performance of two different functionals namely B3LYP and M06 in the prediction of geometries, ¹⁷O and ²H nuclei quadrupole coupling constant (C_Q) values of the MA clusters has been assessed comparing the results to those experimental data. For DFT calculations, several basis sets have been used, including the recently developed Jensen's polarization-consistent basis set families, pcJ-n and pcS-n (n = 0,1,2,3). Calculations at the basis set limit indicate that the value of C_Q(²H) in monomer MA, changes by 0.01–0.04 kHz for each of the final two basis set increments, and seems reasonable to conclusion that the pcJ-3 result is within a few kHz of the basis set limit. Convergence with respect to basis set size was found to be very good, and the pcJ-1 and pcS-1 basis sets provided a good compromise between the basis set limit and computational expense. In most cases, the differences between B3LYP and M06 results for a given basis set are in a range of 1–2%. On the other hand, no systematic changes in the C_Q(¹⁷O) or C_Q(²H) were found for basis sets larger than double-ζ. Thus, the usual assumption that double-ζ basis set (pcJ-1 and pcS-1) results in the acceptable C_Q values, seems to be valid in the case of ¹⁷O and ²H nuclei.

Quantum chemistry calculations together with modeling of ligand–water exchange reactions are used to investigate, for the first time, the interaction mechanisms between emodin of anthraquinones and the catalytic zinc ion in matrix metalloproteinases (MMPs), and the coordinating mode between them is determined. The calculations indicate that the electron transfer from the emodin molecule to the catalytic zinc ion in MMPs occurs when the catalytic zinc ion coordinates with the O atoms of substituent groups at various positions of emodin molecule, and the more the number of the electron transfer from the coordinating O atom of substituent group of emodin molecule to the catalytic zinc ion, the stronger the coordinating ability between them. It is found that comparing with the O atoms of hydroxy groups at 1-position, 8-position and 3-position and the O atom of carbonyl group at 9-position of emodin molecule, the coordinating ability for the O atom of carbonyl group at 10-position of emodin molecule with the catalytic zinc ion in MMPs is the strongest. Therefore, when emodin inhibits MMPs activity, the catalytic zinc ion in MMPs should coordinate with the carbonyl group at 10-position of emodin molecule, rather than the hydroxy groups and carbonyl group at its other positions. Our calculated results are in agreement with previous relevant experimental results. This paper may be helpful for designing the new MMPs inhibitors having higher biological activities by carrying out the structural modifications of emodin molecule.

Aurantio-obtusin (2,6,8-trihydroxy-1,7-dimethoxy-3-methyl anthraquinone), an anthraquinone derivative isolated from the seeds of Cassia tora L., has been studied by DFT calculations at the B3LYP/6-311+g(2df,p)//B3LYP/6–31G(d,p) level in vacuum and in methanol polarized continuum model (PCM). Eight conformers have been located by conformational search and optimization. Our results indicate that the titled compound has planar structures, and five intramolecular hydrogen bonds are found in the lowest-energy structure, including three OH⋯O and two CH⋯O hydrogen bonds. The electronic spectra in methanol have been determined by the time-dependent density functional theory (TD-DFT) approach, showing that the first singlet exited state of the title compound arises from π → π* electron transition. The antioxidant activity of aurantio-obtusin is evaluated by means of calculating O−H bond dissociated enthalpy (BDE) and the adiabatic ionization energy (IE). The calculated BDE and IE values of aurantio-obtusin are 341.8 and 732.3 kJ mol^-1, respectively, lower than the corresponding values of phenol (348.4 and 801.7 kJ mol^-1) and purpurin (360.4 and 747.8 kJ mol^-1), suggesting that aurantio-obtusin is a better antioxidant.

In the present work a conformational analysis of 3-amino-propeneselenal (APS) was performed using several computational methods, including DFT (B3LYP), MP2 and G2MP2. Harmonic vibrational frequencies were estimated at the same levels to confirm the nature of the stationary points found and also to account for the zero point vibrational energy (ZPVE) correction. Two intramolecular hydrogen bonds (HBs) established between the polar groups were identified by the structural geometric parameters. The excited-state properties of intramolecular hydrogen bonding in hydrogen bonded systems have been investigated theoretically using the time dependent density functional theory (TDDFT) method. The influence of the solvent on the stability order of conformers and the strength of intramolecular hydrogen bonding was considered using the polarized continuum model (PCM), the self-consistent isodensity polarized continuum model (SCI-PCM) and the integral equation formalism-polarizable continuum model (IEF-PCM) methods. The "atoms in molecules" theory of Bader was used to analyze critical points and to study the nature of HB in these systems. Natural bond orbital (NBO) analysis was also performed for better understanding the nature of intramolecular interactions. The calculated the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) energies show that charge transfer occur within the molecule. Further verification of the obtained transition state structures were implemented via intrinsic reaction coordinate (IRC) analysis. Calculations of the ¹H NMR chemical shift at GIAO/B3LYP/6–311++G** level of theory are also presented.

The thermodynamic integration/path integral Monte Carlo (TI/PIMC) method of calculating the temperature dependence of the equilibrium constant quantum mechanically is applied to O + HCl ⇌ OH + Cl reaction. The method is based upon PIMC simulations for energies of the reactants and the products and subsequently on thermodynamic integration for the ratios of partition functions. PIMC calculations are performed with the primitive approximation (PA) and the Takahashi–Imada approximation (TIA).

Hydroxyl-radical-induced damage to cytosine leads to a multitude of base modifications, which contribute to the natural processes of aging, mutagenesis and carcinogenesis. The stable products resulting from the main hydroxyl-radical-induced cytosine hydroperoxide, 5-hydroxy-6-hydroperoxyl-5,6-dihydrocytosine (5-OH-6-OOH-DHC), have been mapped out in the present work for the first time using ab initio calculations. Optimized geometries of all stationary structures in the gas phase were determined at the MP2 and B3LYP using the 6-31G(d) basis set and at the B3LYP/6-311++G(d,p) levels of theory. Energies were also determined at the G3MP2 level of theory. Meanwhile, full optimization of all stationary points were also performed in aqueous solution at the B3LYP/CPCM/6-31G(d) level of theory to evaluate the solvent effect. Three distinct possible pathways, pathways A–C, were evaluated. For pathway C, four channels, channels D–G, were characterized in turn. In each pathway, both the direct and the water-mediated processes were considered. The calculated results clearly manifest that (i) pathway C is kinetically favored over pathways A and B and is the most energetically feasible decomposition process of 5-OH-6-OOH-DHC; (ii) for pathway C, channels D, E and G are energetically feasible mechanisms and 6,7-dihydroxy-[1,3,5]triazepane-2,4-dione, 1-carbamoyl-2-oxo-4,5-dihydroxyimidazolidine, and biuret therefore are predicted to be the kinetically favored decomposition products of 5-OH-6-OOH-DHC; (iii) channel G may be kinetically favored over channels D and E and have the highest possibility to occur; (iv) the thermal decomposition of 5-OH-6-OOH-DHC can be significantly promoted by the presence of one explicit water molecule. Apart from characterizing the experimental products well, the main striking result of the present DFT computational study is the identification of a new theoretical optimum decomposition product, i.e. 6,7-dihydroxy-[1,3,5]triazepane-2,4-dione. The data and insights presented here have elucidated the chemical properties of 5-OH-6-OOH-DHC in free radical reactions and should facilitate to assess their mutagenic features.

An ab initio study has been carried out to investigate the structures, binding energies and atomic charge of the binary complexes HBr⋯BrX and ternary complexes HBr⋯BrX⋯HBr (X = F, Cl, Br) at the MP2/aug-cc-pvdz theoretical level. Four types of interactions are observed among these systems: hydrogen bond, halogen bond, unusual hydrogen bond and unusual halogen bond. Two types of stable structures existed in the trimers: acyclic and monocyclic. The stabilities of the complexes may be decided by three factors: the strength of the halogen bond, the nature of halogen or hydrogen bond of intermolecular interaction and the type of the trimer's structure. The absolute value of the cooperativity contribution in these triads is in range of 0.77 ∼ 21.59%, which shows that the cooperative energy is of importance in them. The nature of the intermolecular interactions has been also investigated through the electrostatic potential and the theory of atoms in molecules (AIM). The values of ∇²ρ at BCPs are positive in all complexes, indicating that the interactions are closed-shell. The ratio |Vc|∕G_c of all complexes ranges from 0.782 to 0.935 (satisfy the condition |V_c|∕G_c < 1) along with H_c > 0, revealing that these complexes are predominantly electrostatic in character.

The nonlinear optical (NLO) properties of Λ-shaped diarylethene (DAE) derivatives 1a(b)–4a(b) and their NLO switching effects were studied by using the density functional theory (DFT) methods. The results demonstrate that all of the open-ring molecules and their own closed-ring forms meet the model of NLO switching tuned by photoisomerization. The β_tot values of 1b–3b are 16 times as small as that of their open-ring forms, and β_tot value of 4b is 4 times as large as that of 4a. The spin interactions of open-shell closed-ring molecules are larger than that of their open-ring forms, and it could increase the NLO responses to some degree. Nature bond orbital (NBO) calculations indicate that large charge differences between electron-deficient and electron-rich centers are beneficial to charge transfer (CT), and the overlap between frontier molecular orbital (FMO) is also advantageous to the CT and NLO responses. Time-dependent density functional theory (TD-DFT) calculations show β_tot values of all molecules meet the two-level model very well, and the smaller the ΔE_ge, the larger the β_tot value.

The quantum time dependent wave packet (TDWP) and quasiclassical trajectory (QCT) calculations were carried out to study the exchange reaction H(²S) + H^′S(²Π) → HS(²Π) + H^′(²S) on the ¹A^′ potential energy surface (PES). The integral cross sections of the H + H^′S(v = j = 0) → HS + H^′ reaction calculated by the two methods were presented. The results reveal that the integral cross sections (ICS) decrease with the collision energy increasing. The result of the QCT calculations is reasonably consistent with the time-dependent wave packet. Moreover, the differential cross sections (DCS) were calculated by the QCT method at the four different collision energies, which display a forward–backward symmetry. A long-lifetime H₂S intermediate complex of the exchange reaction was found according to the trajectories. In the stereodynamics investigation, the polar and dihedral angle distribution functions were calculated, which have the distinct oscillations. The oscillations could be attributed to the deep well on the ¹A^′ PES. However, based on the polar-angle and dihedral angle distribution functions, it could be predicted that the main product rotational angular momentum preferentially point to the positive or negative direction of y-axes.