Theoretical Study on Electron Transfer Matrix Element in Oxidation of α—Amino Carbon—Centered Radical by O2

As a successive work of our previous paper,^1the electron transfer matrix element(Vrp)in the oxidation of the simplified model molecule of α-amino carbon-centered radical by O2 has been investigated with ab initio calculation at the level of UHF/6-31 G**.Based on the optimized geometries of the reactgant and the ion-pair complex obtained previously,the reaction heat and the iuner reorganization energy have been obtained by constructing the potential energy curves of reactant and product states considering the solvent effect with the conductor-like screening model(COSMO).The solvent reorganization energy has been estimated using Lippert-Mataga relationship.The calculated results show that the value of Vrp is several times larger than that of RT,which means that the model reaction is an adiabatic one.Theoretical investigation indicates that the solvent effect on the direct electron transfer (ET) process of oxidation of α-amino carbon-centered radical by oxygen is remarkable.     

A novel potent non‐nucleoside reverse transcriptase inhibitor acyl­thio­carbamate derivative with extensive intra­molecular π–π inter­actions

In the crystal structure of the novel acyl­thio­carbamate derivative O‐[2‐(1,3‐dioxo‐2,3‐dihydro‐1H‐isoindol‐2‐yl)­ethyl] N‐(4‐methyl­phenyl)‐N‐(3‐nitro­benzoyl)thio­carbamate, C₂₅H₁₉N₃O₆S, intra‐ and inter­molecular π–π inter­actions occur between the phthalimide and N‐benzoyl moieties. The partial atomic charges, calculated by ab initio methods, are consistent with the observed structure.     

Quantum chemical and physicochemical influences on structure–activity relations and drug design

Quantum chemical results will be presented on drugs, carcinogens, teratogens, and endogenous biomolecules using our new nonempirical ab initio MODPOT /VRDDO method, which incorporates as options to our ab initio LCAO -MO -SCF /CI programs ab initio effective core model potentials (MODPOT ) permitting one to calculate only the valence electrons explicitly yet accurately and an integral prescreening technique (VRDDO , variable retention of diatomic differential overlap) especially effective for spatially extended molecules. For molecules of the size of those of interest the MODPOT /VRDDO calculations run an order-of-magnitude faster than with our own fast ab initio programs and still retain accuracy to the third decimal place for the valence electron properties. We have also just implemented a new efficient MERGE technique which allows us to reuse integrals from a common skeletal fragment and only to have to recalculate those for a new atom or group or a change in its position. Examples will be presented of the use of this technique on a carcinogenic polycyclic aromatic hydrocarbon and its metabolites. The pK_a's, oil-water partition, and drug distribution coefficients as a sensitive function of pH have been measured for a number of drugs as well as for relevant endogenous biomolecules. The pH dependence of the lipophilicities of such molecules has profound implication on appropriate use of such data in QSAR studies.     

Molecular orbital theory of the hydrogen bond. 25. Water–uracil complexes in excited n → π states

Hydrogen bonding of uracil with water in excited n → π* states has been investigated by means of ab initio SCF -CI calculations on uracil and water–uracil complexes. Two low-energy excited states arise from n → π* transitions in uracil. The first is due to excitation of the C₄? O group, while the second is associated with excitation of the C₂? O group. In the first n → π* state, hydrogen bonds at O₄ are broken, so that the open water–uracil dimer at O₄ dissociates. The “wobble” dimer, in which a water molecule is essentially free to move between its position in an open structure at N₃? H and a cyclic structure at N₃? H and O₄ in the ground state, collapses to a different “wobble” dimer at N₃? H and O₂ in the excited state. The third dimer, a “wobble” dimer at N₁? H and O₂, remains intact, but is destabilized relative to the ground state. Although hydrogen bonds at O₂ are broken in the second n → π* state, the three water–uracil dimers remain bound. The “wobble” dimer at N₁? H and O₂ changes to an excited open dimer at N₁? H. The “wobble” dimer at N₃? H and O₄ remains intact, and the open dimer at O₄ is further stabilized upon excitation. Dimer blue shifts of n → π* bands are nearly additive in 2:1 and 3:1 water:uracil structures. The fates of the three 2:1 water:uracil trimers and the 3:1 water:uracil tetramer in the first and second n → π* states are determined by the fates of the corresponding excited dimers in these states.     

Tosyl esters of cinchonidine and cinchonine alkaloids: the structure–reactivity relationship in the hydrolysis to 9‐epibases

In the crystal structures of the diastereoisomers of O‐tosylcinchonidine [(9R)‐cinchon‐9‐yl 4‐methylbenzenesulfonate], (I), and O‐tosylcinchonine [(9S)‐cinchon‐9‐yl 4‐methylbenzenesulfonate], (II), both C₂₆H₂₈N₂O₃S, both molecules are in an anti‐closed conformation and, in each case, the position of the aryl ring of the tosylate system is influenced by an intramolecular C—H...O hydrogen bond. The molecular packing in (I) is influenced by weak intermolecular C—H...O and C—H...π interactions. The crystal structure of (II) features C—H...π interactions and van der Waals forces only. The computational investigations using RHF/6–31G** ab initio and AM1 semi‐empirical methods performed for (I) and (II) and their protonated species show that the conformational and energetic parameters of the molecules are correlated with differences in their reactivity in hydrolysis to the corresponding 9‐epibases.     

Theoretical studies on quinones I. The structure of p-benzoquinone and two of its excited triplet states

Ab initio calculations on the ground and two excited triplet states (³B_1g and ³B_1u) of p-benzoquinone are described. The geometries of the three states were fully optimised at the SCF level using the 3-21G basis set. For the excited states, both D_2h and C_2v geometries were investigated. Comparison was made between UHF and ROHF levels of theory.     

A barrier‐free atomic radical‐molecule reaction: N (2D) NO2 (2A1) mechanistic study

The reaction of N (²D) radical with NO₂ molecule has been studied theoretically using density functional theory and ab initio quantum chemistry method. Singlet electronic state [N₂O₂] potential energy surfaces (PES) are calculated at the CCSD(T)/aug‐cc‐pVDZ//B3LYP/6‐311+G(d) + ZPE and G3B3 levels of theory. All the involved transition states for generation of (2NO) and (O₂ + N₂) lie much lower than the reactants. Thus, the novel reaction N + NO₂ can proceed effectively even at low temperatures and it is expected to play a role in both combustion and interstellar processes. On the basis of the analysis of the kinetics of all pathways through which the reactions proceed, we expect that the competitive power of reaction pathways may vary with experimental conditions for the title reaction. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Theoretical study of the intermolecular hydrogen bond interaction for furan-HCl and furan-CHCl<Subscript>3</Subscript> complexes

The nature of the intermolecular hydrogen bond for the furan-HCl and furan-CHCI₃ complexes has been studied using ab initio calculations with MP2 level of theory. The new hydrogen bond type of C(CI)-H...O and π interactions are studied also. It is shown that, for the optimized geometries of furan-CHCI₃, C-H bond lengths contract and vibrational frequencies are blue-shifted, while for the furan-HCl complex, H-CI bond lengths elongate and vibrational frequencies are red-shifted. In addition, the NBO analysis indicates that, for the furan-CHCI₃ complex, the charge transfers from the lone pair of the proton acceptor to both σ *(CH) antibonding MO and lone pairs of CI atom.     

Front Cover: High-level ab initio evidence of bipyramidal Cu5 clusters as fluxional Jahn-Teller molecules (ChemPhysChem 19/2023)

Novel highly selective synthesis techniques have enable the production of atomically precise monodisperse metal clusters (AMCs) of subnanometer size. These AMCs exhibit ‘molecule-like’ structures that have distinct physical and chemical properties, significantly different from those of nanoparticles and bulk material. In this work, we study copper pentamer Cu₅ clusters as model AMCs by applying both density functional theory (DFT) and high-level (wave-function-based) ab initio methods, including those which are capable of accounting for the multi-state multi-reference character of the wavefunction at the conical intersection (CI) between different electronic states and augmenting the electronic basis set till achieving well-converged energy values and structures. After assessing the accuracy of a high-level multi-multireference ab initio protocol for the well-known Cu₃ case, we apply it to demonstrate that bypiramidal Cu₅ clusters are distorted Jahn-Teller (JT) molecules. The method is further used to evaluate the accuracy of single-reference approaches, finding that the coupled cluster singles and doubles and perturbative triples CCSD(T) method delivers the results closer to our ab initio predictions and that dispersion-corrected DFT can outperform the CCSD method. Finally, we discuss how JT effects and, more generally, conical intersections, are intimately connected to the fluxionality of AMCs, giving them a ‘floppy’ character that ultimately facilitates their interaction with environmental molecules and thus enhances their functioning as catalysts.     

Theoretical studies of uracil–(H2O)n (n = 1–7) clusters by ab initio and ABEEMσπ/MM fluctuating charge model

Uracil–(H₂O)_n (n = 1–7) clusters were systemically investigated by ab initio methods and the newly constructed ABEEMσπ/MM fluctuating charge model. Water molecules have been gradually placed in an average plane containing uracil. The geometries of 38 uracil–water complexes were obtained using B3LYP/6-311++G** level optimizations, and the energies were determined at the MP2/6-311++G** level with BSSE corrections. The ABEEMσπ/MM potential model gives reasonable properties of these clusters when comparing with the present ab initio data. For interaction energies, the root mean square deviation is 0.96 kcal/mol, and the linear coefficient reaches 0.997. Furthermore, the ABEEMσπ charges changed when H₂O interacted with the uracil molecule, especially at the sites where the hydrogen bond form. These results show that the ABEEMσπ/MM model is fine giving the overall characteristic hydration properties of uracil–water systems in good agreement with the high-level ab initio calculations.     

5β,6β‐Epoxy‐17‐oxoandrostan‐3β‐yl acetate and 5β,6β‐epoxy‐20‐oxopregnan‐3β‐yl acetate

In the title compounds, C₂₁H₃₀O₄, (I), and C₂₃H₃₄O₄, (II), respectively, which are valuable intermediates in the synthesis of important steroid derivatives, rings A and B are cis‐(5β,10β)‐fused. The two molecules have similar conformations of rings A, B and C. The presence of the 5β,6β‐epoxide group induces a significant twist of the steroid nucleus and a strong flattening of the B ring. The different C17 substituents result in different conformations for ring D. Cohesion of the molecular packing is achieved in both compounds only by weak intermolecular interactions. The geometries of the molecules in the crystalline environment are compared with those of the free molecules as given by ab initio Roothan Hartree–Fock calculations. We show in this work that quantum mechanical ab initio methods reproduce well the details of the conformation of these molecules, including a large twist of the steroid nucleus. The calculated twist values are comparable, but are larger than the observed values, indicating a possible small effect of the crystal packing on the twist angles.     

Ab initio Hartree–Fock and multiple-scattering Xα calculation of the g factors for CuF2

Ab initio Hartree–Fock and multiple-scattering wave functions are calculated for linear CuF₂. These wave functions are used to calculate the spin–orbit coupling in a new way where the neglect of two- and many-center terms is avoided and where experimental or calculated spin–orbit coupling constants for the atomic ions are used. The calculated value of g is too small by the MS Xα method and too large by the ab initio method, indicating too much 3d–L interaction in the MS Xα case and too little in the ab initio case.     

Molecular symmetry. IV. The coupled perturbed Hartree–Fock method

Symmetry methods employed in the ab initio polyatomic program HONDO are extended to the coupled perturbed Hartree–Fock (CPHF) formalism, a key step in the analytical computation of energy first derivatives for configuration interaction (CI) wavefunctions, and energy second derivatives for Hartree–Fock (HF) wavefunctions. One possible computational strategy is to construct Fock-like matrices for each nuclear coordinate in which the one- and two-electron integrals of the usual Fock matrix are replaced by the integral first derivatives. “Skeleton” matrices are constructed from the unique blocks of electron-repulsion integral derivatives. The correct matrices are generated by applying a symmetrization operator. The analysis is valid for many wavefunctions, including closed- or open-shell spin-restricted and spin-unrestricted HF wavefunctions. To illustrate the method, we compare the computer time required for setting up the coupled perturbed HF equations for eclipsed ethane using D_3h symmetry point group and various subgroups of D_3h. Computational times are roughly inversely proportional to the order of the point group.     

Ab initio copper–water interaction potential for the simulation of aqueous solutions

A new ab initio effective two-body potential that aims at mimicking the average copper–water interaction energy of the first solvation shell was developed. This new potential, together with the MCY water–water potential and a three-body ion–water–water induction potential, is tested in simulations of gas-phase clusters [Cu²⁺? (H₂O)₂₀] and diluted solutions [Cu²⁺? (H₂O)₂₀₀] at T = 298 K. The results of simulations with conventional ab initio pair potentials, with and without three-body induction corrections, are also presented. The different types of copper–water interaction potentials are evaluated comparatively and the efficiency of the newly proposed effective pair potential is discussed. © 1993 John Wiley & Sons, Inc.     

Theoretical Study on Reactivity of Electron Transfer in Model—System of Oxidation of α—Amino Carbon—centered Radical by O2

Electron transfer reaction between a simplified model model molecule of α－amino carbon-centered radical and O2 has studied with ab initio calculations at the MP2/6-31 G^**//UHF/6-31 G^** level,The reactant complex and the ion pair complex have been optimized and employed to perform calculation of the reaction heat and the reorganization energy,Solvent effects have been considered by applyning the conductor-like screening model,Theoretical results show that the highly endothermic charge separation process ,in which one electron transfers from the α－amino carbon-centered radical to O2,so as to form an ion pair complex,is difficult to occur in gas-phase,By apply-ing an external electronic field to prepare the charge-locallized molecular orbitals,the charge-separated state has been obtained using the initial-guess-induced self-consistent field technique,The theoretical investigations indicate that the solvent effect in the process of the oxidation of α-animo carbon-centered radical by O2 is remarkable.From the rate constant estima-tion ,it can be predicted that the oxidation of the model donor molecule by O2 can proceed,but not very fast.A peroxyl radi-cal compound has been found to be a competitive intermediate in the oxidation process.     

Ab initio computations of spin-orbit interactions in polyatomic molecules. Splitting of sulfur LII,III states and singlet–triplet transitions in SO2

Spin-orbit interactions among the ground and the first few excited electronic states of SO₂, are computed with ab initio molecular wave functions and Gaussian atomic orbitals. All spin-other orbits contributions to the matrix elements are included. The computed intensity of the first singlet–triplet transition is found to be in broad agreement with experiment and sensitive to an extension of the configuration interaction expansion of molecular wave functions. Also, the splitting of sulfur L_{II ,III} states in SO₂ is derived as an example of large spin-orbit interactions among electronic states.     

3‐Hydro­xy­benz­aldehyde

The title compound, C₇H₆O₂, forms infinite chains where the mol­ecules are hydrogen bonded via the hydroxyl and aldehyde groups, with an O?O distance of 2.719 (3) Å. Interchain interactions are weak. The geometry of the ring differs from the ideal form due to the effect of the substituents. Abinitio (Hartree–Fock self‐consistent field–molecular orbital and density functional theory) calculations for the free mol­ecule reproduce well the observed small distortions of the ring. In the crystal, the geometry deviates from the ideal C_s symmetry of the free mol­ecule, as given by the ab initio calculations. The aldehyde and hydroxyl groups are twisted around the single bonds which join them to the ring as a result of the intermolecular hydrogen‐bond interactions. These are also responsible for an elongation of the hydroxy C—OH bond compared with that calculated for the free mol­ecule.     

A study of the structure of high-energy states of nitrogen trioxide and the (NO)<Subscript>2</Subscript> dimer: DFT calculations within the symmetrized Kohn-Sham formalism

The electronic structure, geometry, and thermodynamic parameters of the high-energy states of NO₃ and the (NO)₂ dimer are calculated at the DFT B3LYP/6–311++G(3df) level within the symmetrized Kohn-Sham formalism. The results of the DFT calculation of the excited states of NO₃ well agree with the experimental data and precise ab initio calculations. The reactivity of high-energy nitrogen trioxide in the activation of molecular nitrogen and nitrogen protoxide is analyzed. The assumption is substantiated that the Karavaev effect (gain of nitrogen oxides in an air mixture with nitric acid vapors) is due to the photochemical activation of molecular nitrogen in the presence of an NO₃ high-energy state as a decomposition product of nitric acid.     

Theoretical investigation of the structures and spectroscopic properties of (H2O4)n (n = 1–4) clusters

Density functional theory and ab initio calculations were performed to elucidate the hydrogen interactions in (H₂O₄)_n (n = 1–4) clusters. The optimized geometries, binding energies, and harmonic vibrational frequencies were predicted at various levels of theory. The trans conformer of the H₂O₄ monomer was predicted to be the most stable structure at the CCSD(T)/aug‐cc‐pVTZ level of theory. The binding energies per H₂O₄ monomer increased in absolute value by 9.0, 10.1, and 11.8 kcal/mol from n = 2 to n = 4 at the MP2/cc‐pVTZ level of theory (after the zero‐point vibrational energy and basis set superposition error corrections). This result implies that the intermolecular hydrogen bonds were stronger in the long‐chain clusters, that is, the formation of the longer chain in the (H₂O₄)_n clusters was more energetically favorable.     

Investigation on the potential barrier to internal rotation in molecules——Ab initio calculation and energy partition of the internal rotation barrier in complex molecule H_3N-BH_3

Based on the ab initio/6-31G~* calculation, the potential barrier to internal rotation in mol-ecule H_3N--BH_3 has been studed by means of PD/LSF atomic charge model and Buckingham(exp--6-1)energy partition method. The results indicate that the order of the contributions of the componentsto the total energy barrier △E is |△V_(es)|(electrostatic) >|△V_(et)| (charge transfer)>|△V_(ex)| (exchangerepulsion)>|△V_(di)| (dispersion). For △V_(es) there are maxima at θ= 30°and 90°, and a saddle atθ= 60°. There are good linear relationships for the total barrier △E, △V_(ex) and △V_(di) with cos3θrespectively, and the same for the dipole moment from PD/LSF model (μ_(PD)) and that from abinitio calculation (μ_(QM)) vs. cos3θ respectively.