Density Functional Theory Level Of Theory Research Articles

PREPARATION, CHARACTERISATION, EVALUATION AND DFT ANALYSIS OF CILNIDIPINE-L-PHENYLALANINE COCRYSTAL

Objective: The objective of this study was to prepare, characterise and evaluate pharmaceutical cocrystals of Cilnidipine using L-phenylalanine as the coformer to enhance the aqueous solubility of Cilnidipine. It was also proposed to study the mechanism of cocrystal formation based on Density Functional Theory (DFT) using Gaussian software. Methods: To overcome the limitation of poor aqueous solubility of Cilnidipine, a 1:1 pharmaceutical cocrystal of Cilnidipine was prepared using L-phenylalanine as the coformer by liquid assisted grinding (LAG) technique. The resultant cocrystals were characterised by Fourier transform-infrared spectroscopy (FTIR), powder X-ray diffraction (PXRD), differential scanning calorimetry (DSC) and field emission scanning electron microscopy (FE-SEM). They were evaluated for their saturation solubility in water. The mechanism of cocrystal formation was studied at the DFT level of theory. Results: The band broadening of the–NH and–NO peaks in FTIR spectra of Cilnidipine indicated the formation of hydrogen bonds in the prepared cocrystals. A single sharp melting endotherm at 218.40 °C in the DSC curve confirmed the formation of cocrystals. The appearance of new peaks in the PXRD pattern of the prepared cocrystals showed the formation of a new crystalline phase. FE-SEM analysis also confirmed the above findings. The prepared cocrystals exhibited 3.31 folds enhancement in saturation solubility. The DFT analysis showed the formation of intrmolecular hydrogen bonding between the–NO of Cilnidipine and–NH of L-phenylalanine. Conclusion: The present study demonstrated a successful approach for enhancing the solubility of poorly water-soluble drug Cilnidipine by cocrystallisation technique using L-phenylalanine as the coformer.

Exploring pyrrolizidine alkaloids in Crotalaria paulina: Isolation and identification of a promising compound

Studies involving the structural elucidation of organic compounds isolated from natural products, along with theoretical calculations based on density functional theory (DFT), have confirmed the structures of many complex molecules. This work demonstrates the use of Nuclear Magnetic Resonance (NMR) spectroscopy and theoretical calculations in the structural identification of a pyrrolizidine alkaloid (PA), a secondary metabolite isolated from the plant Crotalaria paulina. Secondary metabolites are found in a wide variety of plant species and have diverse biological applications. In this study, the structural elucidation of the alkaloid was performed using high resolution mass spectrometry and nuclear magnetic resonance spectroscopy. Eight candidate structures were subjected to theoretical calculations at DFT level of theory. The experimental and calculated results were compared using the probability distribution DP4+ and corrected mean absolute error (CMAE) methods. The DP4+ result was 99.9%, and the CMAE for 13C NMR chemical shifts was 2.1 ppm, indicating a strong agreement between the experimental and theoretical chemical shifts for the stereochemistry represented by structure CS3 ((3S,4R,5S,8aR,13aR)-3-ethyl-5‑hydroxy-3,4,5-trimethyl-4,5,8,8a,10,12,13,13a-octahydro-2H[1,6]dioxacycloundecino[2,3,4-gh]pyrrolizine-2,6(3H)‑dione). Ethylmethylcrotaline was coined as a nonsystematic nomenclature for structure CS3.

Molecular Docking and Quantum Chemical Computations of 4-Chloro-2-[(furan-2-ylmethyl)amino]-5-sulfamoylbenzoic Acid Based on Density Functional Theory

Quantum computational calculations of energies and geometries of 4-chloro-2-[(furan-2-ylmethyl)amino]-5-sulfamoylbenzoic acid have been performed by DFT level of theory using B3LYP/6-31G(d,p) basis set. The solid phase FT-Raman and FT-IR spectra of the Furosemide compound were recorded in the region 4000 cm−1 to 400 cm−1 and 4000 cm−1 to 400 cm−1 respectively. The molecular geometry, harmonic vibrational frequencies and bonding features of 4-chloro-2-[(furan-2-ylmethyl)amino]-5-sulfamoylbenzoic acid in the ground state have been calculated by using density functional theory (DFT) B3LYP method with standard 6–31 G(d,p) basis set. The scaled theoretical wavenumber showed very good agreement with the experimental values. The vibrational assignments were performed on the basis of the total energy distribution (TED) of the vibrational modes. Stability associated with molecule as a result of hyperconjugative interactions, charge delocalization has been analyzed utilizing Natural Bond Orbital (NBO) analysis through the use of B3LYP/6-31G(d,p) technique. The outcomes reveal that electron density (ED) within the σ* and π* orbitals which are antibonding second-order delocalization energies E (2) confirm the occurrence of intramolecular charge transfer (ICT) inside the molecule. Hirshfield surface analysis and Fukui functions calculation were also performed. From the calculations the first order hyperpolarisability was found to be 3.136 × 10−30esu. The molecule orbital contributions have been analyzed utilizing the total (TDOS), partial (PDOS), and overlap population (OPDOS) density of states. A molecular docking study has supported the anticonvulsant activity of the Furosemide molecule.

Regularized machine learning on molecular graph model explains systematic error in DFT enthalpies

A major goal of materials research is the discovery of novel and efficient heterogeneous catalysts for various chemical processes. In such studies, the candidate catalyst material is modeled using tens to thousands of chemical species and elementary reactions. Density Functional Theory (DFT) is widely used to calculate the thermochemistry of these species which might be surface species or gas-phase molecules. The use of an approximate exchange correlation functional in the DFT framework introduces an important source of error in such models. This is especially true in the calculation of gas phase molecules whose thermochemistry is calculated using the same planewave basis set as the rest of the surface mechanism. Unfortunately, the nature and magnitude of these errors is unknown for most practical molecules. Here, we investigate the error in the enthalpy of formation for 1676 gaseous species using two different DFT levels of theory and the ‘ground truth values’ obtained from the NIST database. We featurize molecules using graph theory. We use a regularized algorithm to discover a sparse model of the error and identify important molecular fragments that drive this error. The model is robust to rigorous statistical tests and is used to correct DFT thermochemistry, achieving more than an order of magnitude improvement.

Modeling microsolvation clusters with electronic-structure calculations guided by analytical potentials and predictive machine learning techniques.

We propose a new methodology to study, at the density functional theory (DFT) level, the clusters resulting from the microsolvation of alkali-metal ions with rare-gas atoms. The workflow begins with a global optimization search to generate a pool of low-energy minimum structures for different cluster sizes. This is achieved by employing an analytical potential energy surface (PES) and an evolutionary algorithm (EA). The next main stage of the methodology is devoted to establish an adequate DFT approach to treat the microsolvation system, through a systematic benchmark study involving several combinations of functionals and basis sets, in order to characterize the global minimum structures of the smaller clusters. In the next stage, we apply machine learning (ML) classification algorithms to predict how the low-energy minima of the analytical PES map to the DFT ones. An early and accurate detection of likely DFT local minima is extremely important to guide the choice of the most promising low-energy minima of large clusters to be re-optimized at the DFT level of theory. In this work, the methodology was applied to the Li+Krn (n = 2-14 and 16) microsolvation clusters for which the most competitive DFT approach was found to be the B3LYP-D3/aug-pcseg-1. Additionally, the ML classifier was able to accurately predict most of the solutions to be re-optimized at the DFT level of theory, thereby greatly enhancing the efficiency of the process and allowing its applicability to larger clusters.

Vibrational circular dichroism behavior of quinol cacalolides from Psacalium aff. sinuatum

In search to find levels of density functional theory (DFT) for the accurate prediction of vibrational circular dichroism (VCD) spectra of cacalolides, we undertook the evaluation of isomeric quinols. To gain compounds that provide experimental VCD spectra for comparative purposes to the calculated spectra, we prepared the hexanes extracts of the roots of Psacalium aff. sinuatum (Cerv.) H. Rob. & Brettell. They afforded the known furotetralin cacalol (1a), the isomeric quinols cacalone (2a) and epi‑cacalone (3a), and the furodehydrotetralin cacalohastine (4). In an earlier work we found that the absolute configuration (AC) determination of 1a by VCD required the study of its acetyl derivative 1b when comparing the experimental data with DFT spectra calculated at the commonly used B3LYP/DGDZVP level of theory. Herein the AC of acetylcacalone (2b) and of non-acetylated 3a were addressed using the same VCD methodology for which it is difficult to predict which DFT level of theory would provide satisfactory results for the uncommon quinol chromophores. It turned out that epi‑cacalone (3a) required the B3PW91/DGDZVP2 level of theory, while in the case of natural occurring 2a it was necessary, as in the case of 1a, to study the acetyl derivative 2b since in 2a the tertiary hydroxy group is prone to intermolecular associations in solution. In addition, the dihydronaphthofuran 4 required the PBEPBE/DGDZVP level of theory, mainly used for aromatic compounds, to be modeled satisfactorily.

Relativistic DFT Calculations of Hyperfine Coupling Constants in 5d Hexafluorido Complexes: [ReF6 ]2- and [IrF6 ]2.

The performance of relativistic density functional theory (DFT) methods has been investigated for the calculation of the recently measured hyperfine coupling constants of hexafluorido complexes [ReF6]2− and [IrF6]2−. Three relativistic methods were employed at the DFT level of theory: the 2‐component zeroth‐order regular approximation (ZORA) method, in which the spin–orbit coupling was treated either variationally (EV ZORA) or as a perturbation (LR ZORA), and the 4‐component Dirac–Kohn–Sham (DKS) method. The dependence of the results on the basis set and the choice of exchange‐correlation functional was studied. Furthermore, the effect of varying the amount of Hartree–Fock exchange in the hybrid functionals was investigated. The LR ZORA and DKS methods combined with DFT led to very similar deviations (about 20 %) from the experimental values for the coupling constant of complex [ReF6]2− by using hybrid functionals. However, none of the methods were able to reproduce the large anisotropy of the hyperfine coupling tensor of complex [ReF6]2−. For [IrF6]2−, the EV ZORA and DKS methods reproduced the experimental tensor components with deviations of ≈10 and ≈5 % for the hybrid functionals, whereas the LR ZORA method predicted the coupling constant to be around one order of magnitude too large owing to the combination of large spin–orbit coupling and very low excitation energies.

Redfield Treatment of Multipathway Electron Transfer in Artificial Photosynthetic Systems.

Coherence effects on electron transfer in a series of symmetric and asymmetric two-, three-, four-, and five-site molecular model systems for photosystem I in cyanobacteria and green plants were studied. The total site energies of the electronic Hamiltonian were calculated using the density functional theory (DFT) formalism and included the zero point vibrational energies of the electron donors and acceptors. Site energies and couplings were calculated using a polarizable continuum model to represent various solvent environments, and the site-to-site couplings were calculated using fragment charge difference methods at the DFT level of theory. The Redfield formalism was used to propagate the electron density from the donors to the acceptors, incorporating relaxation and dephasing effects to describe the electron transfer processes. Changing the relative energies of the donor, intermediate acceptor, and final acceptor molecules in these assemblies has profound effects on the electron transfer rates as well as on the amplitude of the quantum oscillations observed. Increasing the ratio of a particular energy gap to the electronic coupling for a given pair of states leads to weaker quantum oscillations between sites. Biasing the intermediate acceptor energies to slightly favor one pathway leads to a general decrease in electron transfer yield.

Shape, electronic structure and steric effects of organometallic nanocatalysts: relevant tools to improve the synergy between theory and experiment.

Working closely with experimentalists on the comprehension of the surface properties of catalytically active organometallic nanoparticles (NPs) requires the development of several computational strategies which significantly differ from the cluster domain where a precise knowledge of their optimal geometry is a mandatory prerequisite to computational modeling. Theoretical simulations can address several properties of organometallic nanoparticles: the morphology of the metal core, the surface composition under realistic thermodynamic conditions, the relationship between adsorption energies and predictive descriptors of reactivity. It is in such context that an integrated package has been developed or adapted in our group: (i) one tool aims at building a wide variety of the typical shapes exhibited by nanoparticles. Using Reverse Monte Carlo modeling, a given shape can be optimized in order to fit pair distribution function data obtained from X-ray diffraction measurements; (ii) trends in density functional theory (DFT) adsorption energies of surface species can be rationalized and predicted by making use of simple descriptors. This is why we have proposed an extension of the d-band center model, that leads to the formulation of a generalized ligand-field theory. A comparison between cobalt and ruthenium is proposed in the case of a 55-atoms nanocluster. The accuracy of the generalized coordination number [Angew. Chem., Int. Ed., 2014, 53, 8316], a very simple coordination-activity criterion, is also assessed; (iii) the builder package is completed by the steric-driven grafting of ligands on the surface of metal NPs. It easily generates structures with adjustable surface composition values and coordination modes; (iv) after a local optimization at the DFT level of theory, DFT energies and normal modes of vibration can feed a general tool based on the ab initio thermodynamics method. This method aims at easily calculating an optimal surface composition under realistic temperature and pressure conditions. In addition to that, we also show to what extent knowledge of the density of states (DOS) and of the crystal overlap Hamilton population (COHP), both projected from a plane-wave basis set to a local basis set, sheds light on metal core-ligand chemical bonding.

Electronic Coupling Calculations for Bridge-Mediated Charge Transfer Using Constrained Density Functional Theory (CDFT) and Effective Hamiltonian Approaches at the Density Functional Theory (DFT) and Fragment-Orbital Density Functional Tight Binding (FODFTB) Level.

In this article, four methods to calculate charge transfer integrals in the context of bridge-mediated electron transfer are tested. These methods are based on density functional theory (DFT). We consider two perturbative Green's function effective Hamiltonian methods (first, at the DFT level of theory, using localized molecular orbitals; second, applying a tight-binding DFT approach, using fragment orbitals) and two constrained DFT implementations with either plane-wave or local basis sets. To assess the performance of the methods for through-bond (TB)-dominated or through-space (TS)-dominated transfer, different sets of molecules are considered. For through-bond electron transfer (ET), several molecules that were originally synthesized by Paddon-Row and co-workers for the deduction of electronic coupling values from photoemission and electron transmission spectroscopies, are analyzed. The tested methodologies prove to be successful in reproducing experimental data, the exponential distance decay constant and the superbridge effects arising from interference among ET pathways. For through-space ET, dedicated π-stacked systems with heterocyclopentadiene molecules were created and analyzed on the basis of electronic coupling dependence on donor-acceptor distance, structure of the bridge, and ET barrier height. The inexpensive fragment-orbital density functional tight binding (FODFTB) method gives similar results to constrained density functional theory (CDFT) and both reproduce the expected exponential decay of the coupling with donor-acceptor distances and the number of bridging units. These four approaches appear to give reliable results for both TB and TS ET and present a good alternative to expensive ab initio methodologies for large systems involving long-range charge transfers.

Four-Component Relativistic Density-Functional Theory Calculations of Nuclear Spin-Rotation Constants: Relativistic Effects in p-Block Hydrides.

We present an implementation of the nuclear spin-rotation (SR) constants based on the relativistic four-component Dirac-Coulomb Hamiltonian. This formalism has been implemented in the framework of the Hartree-Fock and Kohn-Sham theory, allowing assessment of both pure and hybrid exchange-correlation functionals. In the density-functional theory (DFT) implementation of the response equations, a noncollinear generalized gradient approximation (GGA) has been used. The present approach enforces a restricted kinetic balance condition for the small-component basis at the integral level, leading to very efficient calculations of the property. We apply the methodology to study relativistic effects on the spin-rotation constants by performing calculations on XHn (n = 1-4) for all elements X in the p-block of the periodic table and comparing the effects of relativity on the nuclear SR tensors to that observed for the nuclear magnetic shielding tensors. Correlation effects as described by the density-functional theory are shown to be significant for the spin-rotation constants, whereas the differences between the use of GGA and hybrid density functionals are much smaller. Our calculated relativistic spin-rotation constants at the DFT level of theory are only in fair agreement with available experimental data. It is shown that the scaling of the relativistic effects for the spin-rotation constants (varying between Z(3.8) and Z(4.5)) is as strong as for the chemical shieldings but with a much smaller prefactor.

Geometries and Vertical Excitation Energies in Retinal Analogues Resolved at the CASPT2 Level of Theory: Critical Assessment of the Performance of CASSCF, CC2, and DFT Methods.

A systematic investigation of structural properties and vertical excitation energies of a series of structurally modified 11-cis-retinal chromophores in vacuo was performed by means of multiconfigurational second-order perturbation theory (CASPT2). CASPT2-based geometries agree reasonably well with Møller-Plesset second-order perturbation theory (MP2), local second-order approximate coupled cluster singles and doubles (LCC2), and density functional theory (DFT) geometries, while the complete active space self-consistent field (CASSCF) method exaggerates dramatically the bond length pattern in the polyene chain. The quality of the resulting vertical excitation energies obtained by employing CASSCF, second-order approximate coupled cluster singles and doubles (CC2), LCC2, and time-dependent density functional theory (TD-DFT) approaches is assessed with respect to the CASPT2 data. We show that the commonly used CASSCF/CASPT2 approach works reasonably well in the case of vertical excitation energies of planar structures, but lack of dynamic correlation leads to large errors in energetics for strongly strained structures. For example, the highly twisted conformers of 9,10-dimethyl and 9,10,13-trimethyl species are found as global minima at the CASSCF level, whereas they turn almost planar at the CASPT2, MP2, LCC2, and DFT levels of theory. The CC2 method has shown a remarkable performance, manifested by a maximum deviation of 0.05 eV from the reference CASPT2 results, whereas the local version of CC2 seems to fail to describe the charge-transfer character of the S0 → S1 transitions correctly. We believe that our CASPT2 benchmark set will provide a reference that can be utilized for validation and development studies on 11-cis-retinal protonated Schiff base chromophore analogues.

Potential Nonadiabatic Reactions: Ring-Opening 4,6-Dimethylidenebicyclo[3.1.0]hex-2-ene Derivatives to Aromatic Reactive Intermediates

Potential singlet-triplet surface crossings for the ring opening of 4,6-dimethylidenebicyclo[3.1.0]hex-2-ene derivatives were explored using density functional theory (DFT) and complete active space self-consistent field (CASSCF) methods. Since these ring openings involve relatively high energy species that lead to relatively stable aromatic species, a good scenario for potential nonadiabatic events, we posited that the reaction paths of these ring openings might come close to or cross excited state surfaces. At the DFT level of theory, all reaction paths exhibited characteristics suggestive of singlet-triplet intersections along their paths. 6-Methylidenebicyclo[3.1.0]hex-3-en-2-one and a closely related derivative (4-methylidenebicyclo[3.1.0]hex-2-en-6-one) were explored at the CASSCF level of theory; CASSCF results were qualitatively similar to DFT results and yielded spin-orbit couplings of 1.1-1.4 cm(-1) at the singlet-triplet crossing points.

Spin-Crossing in an Organometallic Pt-Benzene Complex.

The interaction between the Pt atom and the benzene (Bz) molecule was investigated theoretically, using a symmetric Pt-Bz half-sandwich complex. Various levels of wave function theory (HF, MP2, CCSD(T), CASPT2, multistate (MS) MS-CASPT2) together with several functionals (PBE, PBE+D3, PBE+vdW, PBE/EE+vdW) of the density functional theory (DFT) were complemented by quantum Monte Carlo (QMC) calculations. Spin-orbit coupling (SOC) effects were also taken into account at the CASPT2 and DFT levels of theory. The inclusion of dynamic correlation energy was found to be essential to maintaining the stability of the complex. The dative type of bonding was identified to be responsible for the Pt-Bz binding in the ground state. Single-reference CCSD(T) and MP2 as well as multireference CASPT2 and MS-CASPT2 methods reveal that the interaction curve has a single energy minimum (corresponding to the (1)S0 state) and a shoulder (arising from the crossing between the (1)S0 and (3)D3 states) at longer distances. The inclusion of SOC at the CASPT2 level leads to the appearance of another well-separated minimum, which corresponds to the triplet state (3)F4. The PBE/EE+vdW functional, which includes a fraction of exact-exchange (EE) and nonlocal electron correlation, shows the best qualitative agreement with respect to the CCSD(T) data among all DFT functionals used. Large-scale QMC calculations, based on DFT wave functions constructed using TPSSh and M11 functionals, were confronted with the CCSD(T) results. The QMC-TPSSh protocol favorably agrees with the CCSD(T) data, suggesting its possible use in other Pt-containing organometallic systems. All of the methods used (except for HF) show that the Pt-benzene binding leads to the quenching of the Pt high-spin triplet ground state, and the low-spin closed-shell singlet state is found to be preferred in the ground-state of the complex.

Optimization of a Genetic Algorithm for the Functionalization of Fullerenes.

We present the optimization of a genetic algorithm (GA) that is designed to predict the most stable structural isomers of hydrogenated and hydroxylated fullerene cages. Density functional theory (DFT) and density functional tight binding (DFTB) methods are both employed to compute isomer energies. We show that DFTB and DFT levels of theory are in good agreement with each other and that therefore both sets of optimized GA parameters are very similar. As a prototypical fullerene cage, we consider the functionalization of the C20 species, since for this smallest possible fullerene cage it is possible to compute all possible isomer energies for evaluation of the GA performance. An energy decomposition analysis for both C20Hn and C20(OH)n systems reveals that, for only few functional groups, the relative stabilities of different structural isomers may be rationalized simply with recourse to π-Hückel theory. However, upon a greater degree of functionalization, π-electronic effects alone are incapable of describing the interaction between the functional groups and the distorted cage, and both σ- and π-electronic structure must be taken into account in order to understand the relative isomer stabilities.

Quantitative prediction of gas-phase N15 and P31 nuclear magnetic shielding constants

High-level ab initio benchmark calculations of the (15)N and (31)P NMR chemical shielding constants for a representative set of molecules are presented. The computations have been carried out at the Hartree-Fock self-consistent field (HF-SCF), density functional theory (DFT) (B-P86 and B3-LYP), second-order Moller-Plesset perturbation theory (MP2), coupled cluster singles and doubles (CCSD), and CCSD augmented by a perturbative treatment of triple excitations [CCSD(T)] level of theory using basis sets of triple zeta quality or better. The influence of the geometry, the treatment of electron correlation, as well as basis set and zero-point vibrational effects on the shielding constants are discussed and the results are compared to gas-phase experimental shifts. As for the first time a study using high-level post-HF methods is carried out for a second-row element, we also propose a family of basis sets suitable for the computation of (31)P shielding constants. The mean deviations observed for (15)N and (31)P are 0.9 [CCSD(T)/13s9p4d3f] and -3.3 ppm [CCSD(T)/15s12p4d3f2g], respectively, when corrected for zero-point vibrational effects. Results obtained at the DFT level of theory are of comparable accuracy to MP2 for (15)N and of comparable accuracy to HF-SCF for (31)P. However, they are not improved by inclusion of zero-point vibrational effects. The PN molecule is an especially interesting case with exceptionally large electron correlation effects on shielding constants beyond MP2 which, therefore, represents an excellent example for further benchmark studies.

Analyzing ab initio infrared spectra and electronic properties of polyethylenimine water complexes in the solid state

We focused our study on the hydrated polyethylenimine (PEI) crystals which are characterized by the presence of 0.5, 1.5 or 2 water molecules per ethylenimine monomer unit. We propose a theoretical study in the framework of periodic linear combination of atomic orbitals (LCAO) using different Hamiltonians based on density functional theory (DFT) and hybrid Hartree–Fock (HF) – DFT level of theory. Once hydrogen atoms added when missing and redundant atoms withdrawn in the PEI structures, ab initio calculations yielded relaxed geometries at the ground state. The closest structural parameters to the experimental values are observed for hybrid Hamiltonians and the use of the 6-31++G∗ basis set reduces this difference. We provide the IR vibration modes at the Γ point, with assignments of the bands. The electronic study reveals that these PEI hydrates have an insulating character with a quasi constant band gap whatever the number of water molecules. From the projected density of states (PDOS), we have found that the nitrogen orbital has the major contribution to the valence band, while the conduction band is mainly constructed from hydrogen bondings.

Quantitative assessment of the effect of basis set superposition error on the electron density of molecular complexes by means of quantum molecular similarity measures

AbstractThe Chemical Hamiltonian Approach (CHA) method is applied to obtain Basis Set Superposition Error (BSSE)‐free molecular orbitals at the Hartree–Fock (HF) and Density Functional Theory (DFT) levels of theory. To assess qualitatively the effect of the BSSE on the first‐order electron density, we had previously applied Bader's analysis of the intermolecular critical points located on the electron density, as well as density difference maps for several hydrogen bonded complexes. In this work, Quantum Molecular Similarity Measures are probed as an alternative avenue to properly quantify the electronic relaxation due to the BSSE removal by means of distance indices between the uncorrected and corrected charge densities. It is shown that BSSE contamination is more important at the DFT level of theory, and in some cases, changes on the topology of the electron density are observed upon BSSE correction. Inclusion of diffuse functions have been found to dramatically decrease the BSSE effect in both geometry and electron density. The CHA method represents a good compromise to obtain accurate results with small basis sets. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009

Hybrid QM/MM simulation of the hydration phenomena of dipalmitoylphosphatidylcholine headgroup

The polar headgroup of dipalmitoylphosphatidylcholine (DPPC) molecule both in gas phase and aqueous solution is investigated by the hybrid quantum mechanical/molecular mechanical (QM/MM) method, in which the polar head of DPPC molecule and the bound water molecules are treated with density functional theory (DFT), while the apolar hydrocarbon chain of DPPC molecule is treated with MM method. It is demonstrated that the hybrid QM/MM method is both accurate and efficient to describe the conformations of DPPC headgroup. Folded structures of headgroup are found in gas phase calculations. In this work, both monohydration and polyhydration phenomena are investigated. In monohydration, different water association sites are studied. Both the hydration energy and the quantum properties of DPPC and water molecules are calculated at the DFT level of theory after geometry optimization. The binding force of monohydration is estimated by using the scan method. In polyhydration, more extended conformations are found and hydration energies in different polyhydration styles are estimated.

Spin−Orbit and Electron Correlation Effects on the Structure of EF3 (E = I, At, and Element 117)

Structures and vibrational frequencies of group 17 fluorides EF3 (E = I, At, and element 117) are calculated at the density functional theory (DFT) level of theory using relativistic effective core potentials (RECPs) with and without spin-orbit terms in order to investigate the effects of spin-orbit interactions and electron correlations on the structures and vibrational frequencies of EF3. Various tests imply that spin-orbit and electron correlation effects estimated presently from Hartree-Fock (HF) and DFT calculations with RECPs with and without spin-orbit terms are quite reasonable. Spin-orbit and electron correlation effects generally increase bond lengths and/or angles in both C2v and D3h structures. For IF3, the C2v structure is a global minimum, and the D3h structure is a second-order saddle point in both HF and DFT calculations with and without spin-orbit interactions. Spin-orbit effects for IF3 are negligible in comparison to electron correlation effects. The D3h global minimum is the only minimum structure for (117)F3 in all RECP calculations, and the C2v structure is neither a local minimum nor a saddle point. In the case of AtF3, the C2v structure is found to be a local minimum in all RECP calculations without spin-orbit terms, and the D3h structure becomes a local minimum at the DFT level of theory with and without spin-orbit interactions. In the HF calculation with spin-orbit terms, the D3h structure of AtF3 is a second-order saddle point. AtF3 is a borderline case between the valence-shell-electron-pair-repulsion (VSEPR) structure of IF3 and the non-VSEPR structure of (117)F3. Relativistic effects, including scalar relativistic and spin-orbit effects, and electron correlation effects together or separately stabilize the D3h structures more than the C2v structures. As a result, one may suggest that the VSEPR predictions agree very well with the structures optimized by the nonrelativistic HF level of theory even for heavy-atom molecules but not so well with those from more elaborate theoretical methods. Vibrational frequencies of AtF3 and (117)F3 are modified substantially and nonadditively by spin-orbit and electron correlation contributions. This is one of those rare cases for which vibrational frequencies of the closed-shell molecules are significantly affected by spin-orbit interactions. Spin-orbit interactions decrease all vibrational frequencies of EF3 molecules considered.