Alternative CNDOL Fockians for fast and accurate description of molecular exciton properties.

CNDOL is an a priori, approximate Fockian for molecular wave functions. In this study, we employ several modes of singly excited configuration interaction (CIS) to model molecular excitation properties by using four combinations of the one electron operator terms. Those options are compared to the experimental and theoretical data for a carefully selected set of molecules. The resulting excitons are represented by CIS wave functions that encompass all valence electrons in the system for each excited state energy. The Coulomb-exchange term associated to the calculated excitation energies is rationalized to evaluate theoretical exciton binding energies. This property is shown to be useful for discriminating the charge donation ability of molecular and supermolecular systems. Multielectronic 3D maps of exciton formal charges are showcased, demonstrating the applicability of these approximate wave functions for modeling properties of large molecules and clusters at nanoscales. This modeling proves useful in designing molecular photovoltaic devices. Our methodology holds potential applications in systematic evaluations of such systems and the development of fundamental artificial intelligence databases for predicting related properties.

The Challenge of ab Initio Calculations in Small Neon Clusters.

Weakly bound neon dimer, trimer and tetramers are studied at HF and CCSD(T) levels using Dunning, ANO and SIGMA-s basis sets. Their ground-state binding energies are studied along with some structural properties. SIGMA-s basis sets have been developed explicitly for this issue but in a manner that can be readily applied to other atoms for the study of larger weakly bound systems. The difficulties for attaining accurate results on these systems are assessed by the computation of total, atomization and correlation energies, as well as equilibrium distances, with several basis sets of increasing size, ranging from non-augmented to double-augmented versions. Extrapolations are proposed to predict stabilization energies and the results are compared with previously published data.

Evolutionary algorithm-based generation of optimum peptide sequences with dengue virus inhibitory activity.

Background: There is currently no effective dengue virus (DENV) therapeutic. We aim to develop a genetic algorithm-based framework for the design of peptides with possible DENV inhibitory activity. Methods & results: A Python-based tool (denominated AutoPepGEN) based on a DENV support vector machine classifier as the objective function was implemented. AutoPepGEN was applied to the design of three- to seven-amino acid sequences and ten peptides were selected. Peptide-protease (DENV) docking and Molecular Mechanics-Generalized Born Surface Area calculations were performed for the selected sequences and favorable binding energies were observed. Conclusion: It is hoped that AutoPepGEN will serve as an in silico alternative to the experimental design of positional scanning combinatorial libraries, known to be prone to a combinatorial explosion. AutoPepGEN is available at: https://github.com/sjbarigye/AutoPepGEN.

Generative Adversarial Networks (GANs) Based Synthetic Sampling for Predictive Modeling.

In the present report we evaluate the possible utility of the Generative Adversarial Networks (GANs) in mapping the chemical structural space for molecular property profiles, with the goal of subsequently yielding synthetic (artificial) samples for ligand-based molecular modeling. Two case studies are considered: BACE-1 (ß-Secretase 1) and DENV (Dengue Virus) inhibitory activities, with the former focused on data populating and the latter on data balancing tasks. We train GANs using subsamples extracted from datasets for each bioactivity endpoint, and apply the trained networks in generating synthetic examples from the respective bioactivity chemical spaces. Original and synthetic samples are pooled together and employed to build BACE-1 and DENV inhibitory activity classifiers and their performance evaluated over tenfold external validation sets. In both case studies, the obtained classifiers demonstrate satisfactory predictivity with the former yielding accuracy (ACC) and Mathew's correlation coefficient (MCC) values of 0.80 and 0.59, while the latter produces balanced accuracy(BACC) and MCC values of 0.81 and 0.70, respectively. Moreover, the statistics of these classifiers are compared with those of other models in the literature demonstrating comparable to better performance. These results suggest that GANs may be useful in mapping the chemical space for molecular property profiles of interest, and thus allow for the extraction of synthetic examples for computational modeling.

Role of Augmented Basis Sets and Quest for ab Initio Performance/Cost Alternative to Kohn-Sham Density Functional Theory.

Following a previous work, we have assessed the feasibility of MP2/CBS(d, t) as an alternative to state-of-the-art density functionals. The effect of using augmented basis sets is here tested on the 76 barrier heights and 10 isomerization reactions previously utilized. Moreover, calculations for 20 sets of the GMTKN24 database for thermochemistry, kinetics, and noncovalent interactions have been performed. For the density functional theory calculations, M06-2X and B3LYP-D3 functionals are utilized as two representative functionals, while MP2 and CCSD(T) methods are employed as the ab initio counterparts. The results show that MP2 calculations perform similarly to the ones obtained with M06-2X insofar as accuracy and computational cost are concerned. For all methods, the use of augmented basis sets yields enhanced results for anionic systems when compared with the ones from non-augmented bases. Otherwise, the basis-set change effect is found to be minimal. It is therefore concluded that the use of large basis sets is unjustified when facing the increase in computational cost.

Assessing How Correlated Molecular Orbital Calculations Can Perform versus Kohn-Sham DFT: Barrier Heights/Isomerizations.

To assess the title issue, 38 hydrogen transfer barrier heights and 38 non-hydrogen transfer barrier heights/isomerizations extracted from extensive databases have been considered, in addition to 4 2 p-isomerization reactions and 6 others for large organic molecules. All Kohn-Sham DFT calculations have employed the popular M06-2X functional, whereas the correlated molecular orbital (MO)-based ones are from single-reference MP2 and CCSD(T) methods. They have all utilized the same basis sets, with raw MO energies subsequently extrapolated to the complete basis set limit without additional cost. MP2 calculations are found to be as cost-effective as DFT ones and often slightly more, while showing a satisfactory accuracy when compared with the reference data. Although the focus is on barrier heights, the results may bear broader implications, in that one may see successes and difficulties of DFT when compared with traditional MO theories for the same data.

Theoretical Study on the Mechanism of the Thermal Retro-Cycloaddition of Isoxazolinofullerenes.

The retro-cycloaddition thermal reaction of isoxazolino[4,5:1,2][60]fullerenes to pristine fullerene seems to be guided by the electronic nature of the substituted nitrile oxide 1,3-dipole in the isoxazoline ring. Trapping experiments proved that the reaction mechanism occurs by thermal removal of the nitrile oxide 1,3-dipole in a process that is favored in the presence of a big excess of a highly efficient dipolarophile such as maleic anhydride. Theoretical gas phase calculations carried out at the B3LYP/6-31G(d) and M06-2X/6-31G(d) levels of theory underpin the experimental findings and predict that compound 1c, bearing the p-(CH3)2N-Ph substituent on the isoxazoline ring and with a remarkable experimental conversion efficiency in just 12 h, showed the lowest activation energy. Solvent calculations have predicted the same behavior in gas phase. Different approaches such as electrostatic natural population analysis and Houk's distortion/interaction model have been applied to understand how the electronic nature of these substituents affects the retro-cycloaddition reaction process. Analysis of the values of the condensed Fukui functions and dual descriptor shed light on the mechanism of the retro-cycloaddition reaction.

Understanding the Structure and Properties of Cholinium Amino Acid Based Ionic Liquids.

The molecular structure of novel ionic liquids based on cholinium amino acids (ChAA-ILs) has been analyzed. The polarization charge density for all ion pairs has been examined as a function of the hydrophobicity of the anion. The COnductor-like Screening MOdel σ-profiles and σ-potentials have been obtained and used to interpret the chemical behavior of ChAA-ILs. Some physicochemical properties such as density and viscosity have been estimated using the COnductor-like Screening MOdel for Realistic Solvation method. Furthermore, the effects of polarization on the molecular structure, physicochemical properties, and hydrophobicities have been evaluated. Finally, the results obtained have been compared with experimental data.

Self-interaction error in DFT-based modelling of ionic liquids.

The modern computer simulations of potential green solvents of the future, involving the room temperature ionic liquids, heavily rely on density functional theory (DFT). In order to verify the appropriateness of the common DFT methods, we have investigated the effect of the self-interaction error (SIE) on the results of DFT calculations for 24 ionic pairs and 48 ionic associates. The magnitude of the SIE is up to 40 kJ mol(-1) depending on the anion choice. Most strongly the SIE influences the calculation results of ionic associates that contain halide anions. For these associates, the range-separated density functionals suppress the SIE; for other cases, the revPBE density functional with dispersion correction and triple-ζ Slater-type basis is suitable for computationally inexpensive and reasonably accurate DFT calculations.

Alkyl substituent effect on density, viscosity and chemical behavior of 1-alkyl-3-methylimidazolium chloride.

Molecular structure of the conformers of 1-C n -3-methylimidazolium chloride (n = 1 to 4) ionic liquids has been explored and the relationships with density and viscosity have been studied using COSMO related methodologies. Effects of the number of conformers, ionic character, anion-cation relative positions and the alkyl chain length of the cation on predictions of properties have been analyzed. The quality of the predictions has been tested by comparing with experimental results. Moreover, COSMO polarization charge densities, σ-profiles and σ-potentials of the conformers have been analyzed. Predictions on the chemical behavior based on the values of these properties in the conformers have been used to elucidate the affinity for electrophilic and nucleophilic reagents of ionic liquids.

Electron density analysis of 1-butyl-3-methylimidazolium chloride ionic liquid.

An analysis of the electron density of different conformers of the 1-butyl-3-methylimidazolium chloride (bmimCl) ionic liquid by using DFT through the BVP86 density functional has been obtained within the framework of Bader's atom in molecules (AIM), localized orbital locator (LOL), natural bond orbital (NBO), and deformed atoms in molecules (DAM). We also present an analysis of the reduced density gradients that deliver the non-covalent interaction regions and allow to understand the nature of intermolecular interactions. The most polar conformer can be characterized as ionic by AIM, LOL, and DAM methods while the most stable and the least polar shows shared-type interactions. The NBO method allows to comprehend what causes the stabilization of the most stable conformer based on analysis of the second-order perturbative energy and the charge transferred among the natural orbitals involved in the interaction.

Natural bond orbital/natural J-coupling study of vicinal couplings.

NBO-NJC decomposition of vicinal (3)J HH spin-spin coupling constants into Lewis, delocalization, and repolarization contributions are presented. A deep study allows to assign the main contributions to specific orbitals or electron delocalizations between two orbitals. (3)J HH torsional dependence and the substituent effect are analyzed according to the main orbital contributions for ethane and fluoroethane molecules using different basis sets. The torsional dependence for the energies corresponding to electron delocalization is also studied.

Dumbbell-type fullerene-steroid hybrids: a join experimental and theoretical investigation for conformational, configurational, and circular dichroism assignments.

New [60]fullerene-steroid conjugates (4-6) have been synthesized by 1,3-dipolar cycloaddition and Bingel-Hirsch cyclopropanation reactions from suitably functionalized epiandrosterone and [60]fullerene. Since a new stereocenter is created in the formation of the Prato monoaduct, two different diastereomers were isolated by HPLC (4, 5) whose absolute configurations were assigned according to the highly reliable "sector rule" on fullerenes. A further reaction of the malonate-containing diastereomer 5 with a second C60 molecule has afforded dumbbell fullerene 6 in which the two fullerene units are covalently connected through an epiandrosterone moiety. The new compounds have been spectroscopically characterized and their redox potentials, determined by cyclic voltametry, reveal three reversible reduction waves for hybrids 4 and 5, whereas these signals are split in dumbbell 6. Theoretical calculations at semiempirical (AM1) and single point B3LYP/6-31G(d) levels have predicted the most stable conformations for the hybrid compounds (4-6), showing the importance of the chlorine atom on the D ring of the steroid. Furthermore, TDDFT calculations have allowed assignments of the experimentally determined circular dichroism (CD) of the [60]fullerene-steroid hybrids based on the sign and position of the Cotton effects, despite the exceptionally large systems under study.

Theoretical study of imidazole...NO complexes.

A set of weak complexes between imidazole (Imi) and nitric oxide (NO) were calculated with UMP2/6-31++G(d,p) and UMP2/6-311++G(2d,2p) levels of theory. Planar and nonplanar geometries were considered. Complexes of NO and protonated imidazole (ImiH(+)) were also studied due to the biological important effect of Imi protonation. It was found that ring protonation increases the stability of planar complexes and does not affect significantly nonplanar complexes. The Z-H...XY (Z = C, N and X, Y = N, O) interactions resulted as hydrogen bonds according to Koch and Popelier criteria based on AIM theory. Charge transfer was also found very important for complex stabilization within our theoretical framework. Planar NO...ImiH(+) complexes are more stable than those obtained with neutral Imi.

On the unusual 2J(C2-H(f)) coupling dependence on syn/anti CHO conformation in 5-X-furan-2-carboxaldehydes.

A remarkable difference for (2)J(C(2)-H(f)) coupling constant in syn and anti conformers of 5-X-furan-2-carboxaldehydes (X = CH(3), Ph, NO(2), Br) and a rationalization of this difference are reported. On the basis of the current knowledge of the Fermi-contact term transmission, a rather unusual dual-coupling pathway in the syn conformer is presented. The additional coupling pathway resembles somewhat that of the J(H-H) in homoallylic couplings, which are transmitted by hyperconjugative interactions involving the pi(C=C) electronic system. The homoallylic coupling pathway can be labeled as sigma*(C-H) <-- pi(C=C) --> sigma*(C-H). In the present case, this additional coupling pathway, using an analogous notation, can be labeled as sigma*(C(2)-C(C)) <-- LP(1)(O(1))...LP(2)(O(C)) --> sigma*(C(C)-H(f)) (sigma*(C(2)-C(C))) where O(1) and O(C) stand for the ring and carbonyl O atoms, respectively. This additional coupling pathway is not activated in the anti conformers since both oxygen lone pairs do not overlap.

Influence of Density Functionals and Basis Sets on One-Bond Carbon-Carbon NMR Spin-Spin Coupling Constants.

The basis set and the functional dependence of one-bond carbon-carbon NMR spin-spin coupling constants (SSCC) have been analyzed using density functional theory. Four basis sets (6-311G**, TZVP, EPR-III, and aug-cc-pVTZ-J) and four functionals (PBE, PW91, B3LYP, and B3P86) are tested by comparison with 70 experimental values corresponding to 49 molecules that represent multiple types of hybridization of the carbon atoms. The two hybrid functionals B3P86 and B3LYP combined either EPR-III or aug-cc-pVTZ-J basis sets lead to the best accuracy of calculated SSCC. However, a simple linear regression allows for the obtaining of scaled coupling constants that fit much better with the experimental data and where the differences between the different basis sets and/or functional results are significantly reduced. For large molecules the TZVP basis set can be an appropriate election presenting a good compromise between quality of results and computational cost.

CNDOL: A fast and reliable method for the calculation of electronic properties of very large systems. Applications to retinal binding pocket in rhodopsin and gas phase porphine.

Very large molecular systems can be calculated with the so called CNDOL approximate Hamiltonians that have been developed by avoiding oversimplifications and only using a priori parameters and formulas from the simpler NDO methods. A new diagonal monoelectronic term named CNDOL/21 shows great consistency and easier SCF convergence when used together with an appropriate function for charge repulsion energies that is derived from traditional formulas. It is possible to obtain a priori molecular orbitals and electron excitation properties after the configuration interaction of single excited determinants with reliability, maintaining interpretative possibilities even being a simplified Hamiltonian. Tests with some unequivocal gas phase maxima of simple molecules (benzene, furfural, acetaldehyde, hexyl alcohol, methyl amine, 2,5 dimethyl 2,4 hexadiene, and ethyl sulfide) ratify the general quality of this approach in comparison with other methods. The calculation of large systems as porphine in gas phase and a model of the complete retinal binding pocket in rhodopsin with 622 basis functions on 280 atoms at the quantum mechanical level show reliability leading to a resulting first allowed transition in 483 nm, very similar to the known experimental value of 500 nm of "dark state." In this very important case, our model gives a central role in this excitation to a charge transfer from the neighboring Glu(-) counterion to the retinaldehyde polyene chain. Tests with gas phase maxima of some important molecules corroborate the reliability of CNDOL/2 Hamiltonians.

Basis set superposition error in MP2 and density-functional theory: a case of methane-nitric oxide association.

A systematic study of basis set superposition error (BSSE) behavior in H(3)C-H[ellipsis (horizontal)][NO] complexes for both -H...N- and -H...O- orientations were carried out using MP2 and density-functional theory with Pople's [6-31G(d,p),6-311++G(nd,nd), where n=1,2,3, and 6-311++G(3df,3pd)] and Dunning's augmented correlation consistent basis sets [aug-cc-pVXZ (X=D and T)]. Corrected and uncorrected counterpoise potential-energy surfaces (PESs) were explored and differences obtained between them indicate that reliable optimizations of these molecular interactions must be carried out in a PES free of BSSE, even in the case of large basis sets and popularly used functionals such as B3LYP. Although all basis used could be always considered within a margin of approximation for representing molecular orbitals and show important values of BSSE, 6-311++G(2d,2p) basis set shows the best results in uncorrected PES with respect to the corrected ones. B3LYP functional produces erratic results: complexes appear repulsive and the intermolecular distances are always large, evidencing the lack of a correct dispersive forces treatment in the original parameterization. According to the MP2 results, the -H...N- interactions appear as slightly more stable than those of the -H...O- orientation.

Structural modulation of the dipolar-octupolar contributions to the NLO response in subphthalocyanines.

Second order nonlinear optical properties of a series of trinitrosubphthalocyanine (SubPc) isomers were studied experimentally by electric field induced second harmonic (EFISH) generation and hyper Rayleigh scattering (HRS). These experimental values were compared to the ones obtained theoretically employing both sum over states (SOS) and finite field (FF) methods. From these studies, it was shown that the dipolar contributions to the beta tensor are very much dependent on the substitution pattern at the periphery of the subphthalocyanine macrocycle, whereas the octupolar contributions remain mostly unchanged. Consequently, it was deduced that SubPc is extremely well suited for the decoupling of octupolar and dipolar contribution to the NLO response.