Pople-style Basis Sets Research Articles

Toward Post-Hartree-Fock Accuracy for Protein-Ligand Affinities Using the Molecules-in-Molecules Fragmentation-Based Method.

The complexity and size of large molecular systems, such as protein-ligand complexes, pose computational challenges for accurate post-Hartree-Fock calculations. This study delivers a thorough benchmarking of the Molecules-in-Molecules (MIM) method, presenting a clear and accessible strategy for layer/theory selections in post-Hartree-Fock computations on substantial molecular systems, notably protein-ligand complexes. An approach is articulated, enabling augmented computational efficiency by strategically canceling out common subsystem energy terms between complexes and proteins within the supermolecular equation. Employing DLPNO-based post-Hartree-Fock methods in conjunction with the three-layer MIM method (MIM3), this study demonstrates the achievement of protein-ligand binding energies with remarkable accuracy (errors <1 kcal mol-1), while significantly reducing computational costs. Furthermore, noteworthy correlations between theoretically computed interaction energies and their experimental equivalents were observed, with R2 values of approximately 0.90 and 0.78 for CDK2 and BZT-ITK sets, respectively, thus validating the efficacy of the MIM method in calculating binding energies. By highlighting the crucial role of diffuse or small Pople-style basis sets in the middle layer for reducing energy errors, this work provides valuable insights and practical methodologies for interaction energy computations in large molecular complexes and opens avenues for their application across a diverse range of molecular systems.

Comprehensive Basis-Set Testing of Extended Symmetry-Adapted Perturbation Theory and Assessment of Mixed-Basis Combinations to Reduce Cost.

Hybrid or "extended" symmetry-adapted perturbation theory (XSAPT) replaces traditional SAPT's treatment of dispersion with better performing alternatives while at the same time extending two-body (dimer) SAPT to a many-body treatment of polarization using a self-consistent charge embedding procedure. The present work presents a systematic study of how XSAPT interaction energies and energy components converge with respect to the choice of Gaussian basis set. Errors can be reduced in a systematic way using correlation-consistent basis sets, with aug-cc-pVTZ results converged within <0.1 kcal/mol. Similar (if slightly less systematic) behavior is obtained using Karlsruhe basis sets at much lower cost, and we introduce new versions with limited augmentation that are even more efficient. Pople-style basis sets, which are more efficient still, often afford good results if a large number of polarization functions are included. The dispersion models used in XSAPT afford much faster basis-set convergence as compared to the perturbative description of dispersion in conventional SAPT, meaning that "compromise" basis sets (such as jun-cc-pVDZ) are no longer required and benchmark-quality results can be obtained using triple-ζ basis sets. The use of diffuse functions proves to be essential, especially for the description of hydrogen bonds. The "δ(Hartree-Fock)" correction for high-order induction can be performed in double-ζ basis sets without significant loss of accuracy, leading to a mixed-basis approach that offers 4× speedup over the existing (cubic scaling) XSAPT approach.

QTAIM, NBO, and NMR studies of hydrogen bonds in capecitabine

Intramolecular and Intermolecular hydrogen bonds of capecitabine, a pharmaceutically active substance in the group of fluorinated cytosines, have been investigated by density functional calculations at B3LYP level of theory using some Pople-style basis sets augmented with polarized and diffuse functions. To perform the calculations, one molecule (CAP-M) and three molecules (CAP-T) of capecitabine are modeled by available X-ray crystal analysis in the literature. The topological parameters of the electron density distributions have been analyzed in terms of the quantum theory of atoms in molecules (QTAIM). The calculated hydrogen bond energies, together with the structural parameters, confirm two intramolecular hydrogen bonds, and only one intermolecular hydrogen bond in the trimer or cluster. Calculated ring critical points approve the resonance-assisted hydrogen bonds in the intramolecular hydrogen bonds. Moreover, the natural bond orbital analysis (NBO) has been used to evaluate the nature of hydrogen bonding interactions and charge analysis. The calculated 1H NMR and 17O NMR chemical shifts (CS) are significantly influenced by forming the hydrogen bond bridges. CS values are in excellent agreement with the structural parameters, QTAIM, and NBO results. Molecular electrostatic potential maps confirm the regions of hydrogen bonds donor and hydrogen bonds acceptor of the title molecule.

Structural and Antioxidant Properties of Compounds Obtained from Fe2+Chelation by Juglone and Two of Its Derivatives: DFT, QTAIM, and NBO Studies

The chelating ability of juglone and two of its derivatives towards Fe2+ion and the antioxidant activity (AOA) of the resulting chelates and complexes (in the presence of H2O and CH3OH as ligands) in gas phase is reported via bond dissociation enthalpy, ionization potential, proton dissociation enthalpy, proton affinity, and electron transfer enthalpy. The DFT/B3LYP level of theory associated with the 6-31+G(d,p) and 6-31G(d) Pople-style basis sets on the atoms of the ligands and the central Fe(II), respectively, was used. Negative chelation free energies obtained revealed that juglone derivatives possessing the O-H substituent (L2) have the greatest ability to chelate Fe2+ ion. Apart from 1B, thermodynamic descriptors of the AOA showed that the direct hydrogen atom transfer is the preferred mechanism of the studied molecules. NBO analysis showed that the Fe-ligand bonds are all formed through metal to ligand charge transfer. QTAIM studies revealed that among all the Fe-ligand bonds, the O1-Fe bond of 1A is purely covalent. The aforementioned results show that the ligands can be used to fight against Fe(II) toxicity, thus preserving human health, and fight against the deterioration of industrial products. In addition, most of the complexes studied have shown a better AOA than their corresponding ligands.

Computational methodology study of the optical and thermochemical properties of a molecular photoswitch.

We assess how the utilization of different DFT functionals for obtaining the equilibrium geometries and vibrational frequencies affect the description of the thermochemistry and subsequent calculation of the optical properties of a dihydroazulene-vinylheptafulvene photoswitch. The assessment covers nine popular DFT functionals (BLYP, B3LYP, CAM-B3LYP, M06-L, M06, M06-2X, PBE, PBE0, and ωB97X-D) in conjugation with five different Pople style basis sets (6-31+G(d), 6-31++G(d,p), 6-311+G(d), 6-311++G(d,p), and 6-311++G(3df,3pd)). It is identified that only CAM-B3LYP, M06-2X, and PBE0 are able to quantitatively describe the correct trends in the thermochemical properties. The subsequent calculation of the optical properties using the CAM-B3LYP functional shows that there is little difference in whether the CAM-B3LYP, M06-2X, or PBE0 functionals have been used to calculate the equilibrium geometries. Utilizing the identified functionals, we investigate how the number of electron withdrawing cyano substituents influence the thermochemistry and optical properties of the molecular photoswitch.

Very strong intramolecular hydrogen bonding of 1,2-dithenoylcyclopentadiene; DFT and spectroscopic studies

Structure and intramolecular hydrogen bond (IHB) of 1,2-dithenoylcyclopentadiene (DTCP) have been investigated with quantum mechanical calculations using density functional theory at B3LYP level using some Pople-style basis sets augmented with polarized and diffuse functions. The full isomeric and conformational analyses have been done, and the relative stabilities for different chelated and non-chelated enol and different keto forms have been reported. The estimated IHB energy and the barrier height for proton transfer (19.34 and 0.31kcal/mol, respectively), together with the value of 0.082Å for the Q Gilli’s symmetry coordinate and the σ-skeleton of the molecule (O⋯O distance of 1.463Å), confirm a very strong, nearly symmetric, linear and short distance resonance assisted IHB (RAHB) in DTCP. The values of 18.29ppm for the enolated proton chemical shift and 1128cm−1 for out-of-plain bending of the OH bond, besides investigations on other IR and Raman bands associated with the IHB strength and electron delocalization in different segments of the molecule, confirm the results of the theoretical studies and a very strong RAHB in DTCP.

The effects of conformation and intermolecular hydrogen bonding on the structural and vibrational spectral data of naproxen molecule

The structural and vibrational properties of naproxen, an inhibitor of cyclooxygenase (COX) enzyme, were investigated by molecular modeling and experimental IR and Raman spectroscopic techniques. Possible conformers of the molecule were searched via a molecular dynamics simulation carried out with MM2 force field. The total energies, equilibrium geometries, force fields, IR and Raman spectral data of the found stable conformers were determined by means of geometry optimization and harmonic frequency calculations carried out using the B3LYP method and Pople-style basis sets of different size. The stability order obtained for the lowest-energy conformers was confirmed by high-accuracy thermochemistry calculations performed with G3MP2B3 composite method. Some electronic structure parameters of naproxen and the anharmonicity characters of its vibrational modes were determined by means of natural population analysis (NPA) and anharmonic frequency calculations at B3LYP/6-31++G(d,p) and B3LYP/6-311++G(d,p) levels of theory. A part of these calculations carried out for free naproxen molecule were repeated also for its energetically most favored dimer forms. Two different scaling procedures ((1) “SQM-FF methodology” and (2) “Dual scale factors”) were independently applied to the obtained harmonic vibrational spectral data to fit them to the corresponding experimental data. In the light of the obtained calculation results, which confirm the remarkable effects of conformation and intermolecular hydrogen bonding on the structural and vibrational spectral data, in particular, on those associated with the functional groups in the propanoic acid chain, a reliable assignment of the fundamental bands observed in the experimental IR and Raman spectra of the molecule was achieved.

A conformational analysis and vibrational spectroscopic investigation on 1,2- bis( o- carboxyphenoxy) ethane molecule

The minima on the potential energy surface of 1,2- bis( o- carboxyphenoxy) ethane ( CPE) molecule in its electronic ground state were searched by a molecular dynamics simulation performed with MM2 force field. For each of the found minimum-energy conformers, the corresponding equilibrium geometry, charge distribution, HOMO–LUMO energy gap, force field, vibrational normal modes and associated IR and Raman spectral data were determined by means of the density functional theory (DFT) based electronic structure calculations carried out by using B3LYP method and various Pople-style basis sets. The obtained theoretical data confirmed the significant effects of the intra- and inter-molecular hydrogen bonding interactions on the conformational structure, force field, and group vibrations of the molecule. The same data have also revealed that two of the determined stable conformers, both of which exhibit pseudo-crown structure, are considerably more favorable in energy to the others and accordingly provide the major contribution to the experimental spectra of CPE. In the light of the improved vibrational spectral data obtained within the “SQM FF” methodology and “Dual Scale Factors” approach for the monomer and dimer forms of these two conformers, a reliable assignment of the fundamental bands observed in the experimental room-temperature IR and Raman spectra of the molecule was given, and the sensitivities of its group vibrations to conformation, substitution and dimerization were discussed.

Comparison of Experimental and Computationally Predicted Sulfoxide Bond Dissociation Enthalpies

The accurate estimation of S-O bond dissociation enthalpies (BDE) of sulfoxides by computational chemistry methods has been a significant challenge. One of the primary causes for this challenge is the well-established requirement of including high-exponent d functions in the sulfur basis set for accurate energies. Unfortunately, even when high-exponent d functions were included in Pople-style basis sets, the relative strength of experimentally determined S-O BDE was incorrectly predicted. The aug-cc-pV(n+d)Z basis sets developed by Dunning include an additional high-exponent d function on sulfur. Thus, it was expected that the aug-cc-pV(n+d)Z basis sets would improve the prediction of sulfoxide S-O BDE. This study presents the S-O BDE predicted by B3LYP, CCSD, CCSD(T), M05-2X, M06-2X, and MP2 combined with aug-cc-pV(n+d)Z, aug-cc-pVnZ, and Pople-style basis sets. The accuracy of these predictions was determined by comparing the computationally predicted values to the experimentally determined S-O BDE. Values within experimental error were obtained for dialkyl sulfoxides when the S-O BDEs were estimated using an isodesmic oxygen transfer reaction at the M06-2X/aug-cc-pV(T+d)Z level of theory. However, the S-O BDE of divinyl sulfoxide was overestimated by this method.

An experimental and theoretical vibrational spectroscopic study on niflumic acid, a non-steroidal anti-inflammatory drug

The theoretically possible stable conformers of niflumic acid (NFA) molecule in electronic ground state were investigated by means of potential energy surface scan and thermochemistry calculations carried out at room temperature using DFT-B3LYP method and different Pople-style basis sets. The data obtained from these calculations confirmed that the two planar conformers in which the carboxyl and fluoromethyl functional groups are located either in “trans” or in “cis” position to each other are the most favorable ones in energy among all the stable conformers of the free molecule. This conclusion was also confirmed by the energy values obtained from the higher-accuracy thermochemistry calculations carried out using G3MP2B3 composite method. For both conformers and also for their most favorable dimer forms in energy, the equilibrium geometry, force field and vibrational spectral data were calculated first at B3LYP/6-31G(d) and then at B3LYP/6-311++G(d,p) levels of theory. On the basis of these theoretical data, the effects of the conformation and dimerization on the corresponding experimental data of NFA molecule were discussed in detail. The overestimations of the calculated harmonic wavenumbers were corrected by the aid of two different empirical scaling procedures referred to as “scaled quantum mechanical force field (SQM FF) methodology” and “dual scale factors”. In the light of the improved theoretical data obtained in these two approaches applied independently from each other, a successful assignment of the fundamental bands observed in the room-temperature IR and Raman spectra of the molecule was given.

Density Functional Theory Calculations of the Lowest Energy Quintet and Triplet States of Model Hemes: Role of Functional, Basis Set, and Zero-Point Energy Corrections

We investigated the effect of several computational variables, including the choice of the basis set, application of symmetry constraints, and zero-point energy (ZPE) corrections, on the structural parameters and predicted ground electronic state of model 5-coordinate hemes (iron(II) porphines axially coordinated by a single imidazole or 2-methylimidazole). We studied the performance of B3LYP and B3PW91 with eight Pople-style basis sets (up to 6-311+G*) and B97-1, OLYP, and TPSS functionals with 6-31G and 6-31G* basis sets. Only hybrid functionals B3LYP, B3PW91, and B97-1 reproduced the quintet ground state of the model hemes. With a given functional, the choice of the basis set caused up to 2.7 kcal/mol variation of the quintet-triplet electronic energy gap (DeltaEel), in several cases, resulting in the inversion of the sign of DeltaEel. Single-point energy calculations with triple-zeta basis sets of the Pople (up to 6-311G++(2d,2p)), Ahlrichs (TZVP and TZVPP), and Dunning (cc-pVTZ) families showed the same trend. The zero-point energy of the quintet state was approximately 1 kcal/mol lower than that of the triplet, and accounting for ZPE corrections was crucial for establishing the ground state if the electronic energy of the triplet state was approximately 1 kcal/mol less than that of the quintet. Within a given model chemistry, effects of symmetry constraints and of a "tense" structure of the iron porphine fragment coordinated to 2-methylimidazole on DeltaEel were limited to 0.3 kcal/mol. For both model hemes the best agreement with crystallographic structural data was achieved with small 6-31G and 6-31G* basis sets. Deviation of the computed frequency of the Fe-Im stretching mode from the experimental value with the basis set decreased in the order: nonaugmented basis sets, basis sets with polarization functions, and basis sets with polarization and diffuse functions. Contraction of Pople-style basis sets (double-zeta or triple-zeta) affected the results insignificantly for iron(II) porphyrin coordinated with imidazole. Poor performance of a "locally dense" basis set with a large number of basis functions on the Fe center was observed in calculation of quintet-triplet gaps. Our results lead to a series of suggestions for density functional theory calculations of quintet-triplet energy gaps in ferrohemes with a single axial imidazole; these suggestions are potentially applicable for other transition-metal complexes.

π−H···O Hydrogen Bonds: Multicenter Covalent π−H Interaction Acts as the Proton-Donating System

The MP2 method and the Pople-style basis sets 6-311++G(d,p), 6-311++G(2df,2pd), and 6-311++G(3df,3pd) were used to perform calculations on H3O+...C2H2 and C2H3+...C2H2 complexes and related species. Hydrogen bonds existing for the analyzed complexes were investigated as well as related pi-H...O --> pi...H-O and pi-H...pi --> pi...H-pi proton-transfer processes. For some of the complexes analyzed the multicenter pi-H interaction possessing the properties of a covalent bond acts as a proton donor; more generally it is classified as the Lewis acid. The quantum theory of "atoms in molecules" (QTAIM) was also applied to deepen the nature of these interactions in terms of characteristics of bond critical points. The pi-H...O, O-H...pi, and pi-H...pi interactions analyzed here may be classified as hydrogen bonds since their characteristics are the same as or at least similar to those of typical hydrogen bonds. H...pi interactions are common in crystal structures of organic and organometallic compounds. The analyses performed here show a continuum of such interactions since there are H...pi contacts possessing the characteristics of weak intermolecular interactions on the one hand and pi-H multicenter covalent bonds on the other. Ab initio and QTAIM results support the latter statements.

Determination of the Stereochemistry of 3-Hydroxymethyl-2,3-dihydro-[1,4]dioxino[2,3-b]- pyridine by Vibrational Circular Dichroism and the Effect of DFT Integration Grids

Vibrational circular dichroism (VCD) spectra are presented for 3-hydroxymethyl-2,3-dihydro-[1,4]dioxino[2,3-b]pyridine. The assignment of the stereochemistry has been done by comparison between the experimental spectra and theoretically calculated spectra for both enantiomers. The DFT calculations were found capable to correctly assign absolute configurations. The influence of the basis set used in the DFT calculations on the extent of the agreement between the theoretical and experimental findings was investigated by use of different Pople-style basis sets and correlation consistent basis sets, showing that 6-31G* is an acceptable basis set, and that cc-pVTZ yields the best agreement. Similarly, the effect of DFT integration grids was examined. A quantitative measure for the similarity between experimental and theoretical spectra is used.