Basis Set Combinations Research Articles

Spatial Bayesian latent factor regression modeling of coordinate-based meta-analysis data.

Now over 20 years old, functional MRI (fMRI) has a large and growing literature that is best synthesised with meta-analytic tools. As most authors do not share image data, only the peak activation coordinates (foci) reported in the article are available for Coordinate-Based Meta-Analysis (CBMA). Neuroimaging meta-analysis is used to (i) identify areas of consistent activation; and (ii) build a predictive model of task type or cognitive process for new studies (reverse inference). To simultaneously address these aims, we propose a Bayesian point process hierarchical model for CBMA. We model the foci from each study as a doubly stochastic Poisson process, where the study-specific log intensity function is characterized as a linear combination of a high-dimensional basis set. A sparse representation of the intensities is guaranteed through latent factor modeling of the basis coefficients. Within our framework, it is also possible to account for the effect of study-level covariates (meta-regression), significantly expanding the capabilities of the current neuroimaging meta-analysis methods available. We apply our methodology to synthetic data and neuroimaging meta-analysis datasets.

Synthesis, crystal structures, spectroscopic and nonlinear optical properties of chalcone derivatives: A combined experimental and theoretical study

A set of chalcone compounds were prepared by reacting p-bromoacetophenone with various substituted aromatic aldehyde in ethanol using sodium ethoxide as base. The synthesized molecules were well characterized using spectroscopic techniques like UV–Vis, fourier transform infrared (FT-IR) and nuclear magnetic resonance (1H &13C) spectroscopy. The compounds were crystalized and their final structures were confirmed after diffracting these on single crystal X-ray diffractometer. The spectroscopic and molecular information were compared with simulated properties calculated via density functional theory (DFT). Geometries of all chalcone compounds have been optimized by density functional theory (DFT) at B3LYP level with 6-311 + G(d,p) basis set combination. Theoretical investigations about UV–Vis and FT-IR spectra of chalcone derivatives were reported using time dependent TD/DFT/B3LYP/6-311 + G(d,p) and B3LYP/6-311 + G(d,p) level respectively. The current study revealed that the theoretical findings complement the experimental results. Nonlinear optical properties of chalcone systems were calculated to gain insights the possibility of designing these compounds as NLO materials. The findings suggested that the first order hyperpolarizability of all the molecules except 1-(4-bromophenyl)-3-(1-methyl-1H-pyrrol-3-yl)prop-2-en-1-oneis also greater than the value of urea (β = 0.372 × 10−30 esu). These high values might be produced because of the dipole, molecular alignment and also from the non-covalent interactions. The domination of a particular component indicates a substantial delocalization of charges in that direction.

Mapping Interaction Energies in Chorismate Mutase with the Fragment Molecular Orbital Method.

The Claisen rearrangement of chorismate to prephenate is mapped across the entire reaction pathway using the fragment molecular orbital (FMO) method. Three basis sets (6-31G(d), cc-pVDZ, and pcseg-1) are studied to provide guidance toward obtaining high accuracy with the FMO method on such systems. Using a fragmentation scheme of one residue per fragment, the FMO method using the 6-31G(d) basis set and second-order Møller-Plesset perturbation theory (MP2) with the hybrid orbital projection fragmentation scheme provides the most reliable results across the entire reaction pathway. Calculations using the multilayer FMO method are performed and shown to be in agreement with single-layer calculations in all cases with differences of less than one kilocalorie per mole for all tested basis set combinations along the entire reaction path. The use of restricted Hartree-Fock for the lower-level layer and MP2 for the higher-level layer gives the most consistent results when using the same basis set for both layers. Pair interaction energy decomposition analysis calculations confirm that electrostatic interactions are the predominant force between three key arginine residues and chorismate and that dispersion and charge transfer interactions in the binding pocket also play a role in the local chemistry of the reaction.

Theoretical evaluation of NMR shifts in polycyclic aromatic hydrocarbons

ABSTRACTUsing computational chemistry methodology, we evaluate the proton magnetic shieldings and the corresponding chemical shifts of 12 polycyclic aromatic hydrocarbons that derive from chrysene, perylene and picene. Due to the large size of the studied compounds, we resort to density functional theory (DFT) and use it together with the B3LYP and the KT1 functionals. After a systematic method and basis set selection study carried out on methane, benzene and anthracene, the DFT(B3LYP) method and the 6-31G*, 6-31G** and 6-311++G** bases are selected to carry out the calculations, because of the efficiency in providing shifts close to the experimental data available. Additionally, we select the DFT(KT1) method together with the aug-pcS-1 basis set, and HF/6-31G* shifts are also calculated. In order to estimate the error in the theoretical results, we take as reference accurate experimental chemical shifts obtained for the molecules under investigation. Extra measurements are needed for this purpose and are included in the present work. The best combination of method and basis set is DFT(B3LYP)/6-31G**, proving to be very efficient in getting shifts close to experiment at a relatively low computational cost, and therefore we recommend it for the evaluation of proton shifts in larger polycyclic aromatic hydrocarbons.

Calibrating Reaction Enthalpies: Use of Density Functional Theory and the Correlation Consistent Composite Approach in the Design of Photochromic Materials.

Acquisition of highly accurate energetic data for chromium-containing molecules and various chromium carbonyl complexes is a major step toward calibrating bond energies and thermal isomerization energies from mechanisms for Cr-centered photochromic materials being developed in our laboratories. The performance of six density functionals in conjunction with seven basis sets, utilizing Gaussian-type orbitals, has been evaluated for the calculation of gas-phase enthalpies of formation and enthalpies of reaction at 298.15 K on various chromium-containing systems. Nineteen molecules were examined: Cr(CO)6, Cr(CO)5, Cr(CO)5(C2H4), Cr(CO)5(C2ClH3), Cr(CO)5(cis-(C2Cl2H2)), Cr(CO)5(gem-(C2Cl2H2)), Cr(CO)5(trans-(C2Cl2H2)), Cr(CO)5(C2Cl3H), Cr(CO)5(C2Cl4), CrO2, CrF2, CrCl2, CrCl4, CrBr2, CrBr4, CrOCl2, CrO2Cl2, CrOF2, and CrO2F2. The performance of 69 density functionals in conjunction with a single basis set utilizing Slater-type orbitals (STO) and a zeroth-order relativistic approximation was also evaluated for the same test set. Values derived from density functional theory were compared to experimental values where available, or values derived from the correlation consistent composite approach (ccCA). When all reactions were considered, the functionals that exhibited the smallest mean absolute deviations (MADs, in kcal mol-1) from ccCA-derived values were B97-1 (6.9), VS98 (9.0), and KCIS (9.4) in conjunction with quadruple-ζ STO basis sets and B97-1 (9.3) in conjunction with cc-pVTZ basis sets. When considering only the set of gas-phase reaction enthalpies (ΔrH°gas), the functional that exhibited the smallest MADs from ccCA-derived values were B97-1 in conjunction with cc-pVTZ basis sets (9.1) and PBEPBE in conjunction with polarized valence triple-ζ basis set/effective core potential combination for Cr and augmented and multiple polarized triple-ζ Pople style basis sets (9.5). Also of interest, certainly because of known cancellation of errors, PBEPBE with the least-computationally expensive basis set combination considered in the present study (valence double-ζ basis set/effective core potential combination for Cr and singly-polarized double-ζ Pople style basis sets) also provided reasonable accuracy (11.1). An increase in basis set size was found to have an improvement in accuracy for the best performing functional (B97-1).

Benchmarking of density functionals for a soft but accurate prediction and assignment of 1H and 13C NMR chemical shifts in organic and biological molecules

A number of programs and tools that simulate 1 H and 13 C nuclear magnetic resonance (NMR) chemical shifts using empirical approaches are available. These tools are user-friendly, but they provide a very rough (and sometimes misleading) estimation of the NMR properties, especially for complex systems. Rigorous and reliable ways to predict and interpret NMR properties of simple and complex systems are available in many popular computational program packages. Nevertheless, experimentalists keep relying on these "unreliable" tools in their daily work because, to have a sufficiently high accuracy, these rigorous quantum mechanical methods need high levels of theory. An alternative, efficient, semi-empirical approach has been proposed by Bally, Rablen, Tantillo, and coworkers. This idea consists of creating linear calibrations models, on the basis of the application of different combinations of functionals and basis sets. Following this approach, the predictive capability of a wider range of popular functionals was systematically investigated and tested. The NMR chemical shifts were computed in solvated phase at density functional theory level, using 30 different functionals coupled with three different triple-ζ basis sets. © 2016 Wiley Periodicals, Inc.

Solvents effect on the stability and reactivity of Tamoxifen and its nano metabolites as the breast anticancer drug

The effect of protic and aprotic solvents polarity on optimized geometry and some chemical reactivity indices for Tamoxifen (TAM) and three of its important metabolites, i.e. 3-hydroxy Tamoxifen (3-HTAM), Droloxifen, 4-hydroxy Tamoxifen (4-HTAM), Afimoxifen, and Z-N-desmethyl-4-hydroxy Tamoxifen, Endoxifen (ENDX), antitumor are studied theoretically by density functional theory calculations (B3LYP) with 6-311++G(d, p) basis set in combination with polarizable continuum model (PCM) in selected non polar (CCl4), polar protic (H2O, Ethanol) and polar aprotic (DMSO, Acetone) solvents. The solvent-induced stretching vibrational frequency shifts (SFS) and the solvation influence on the DFT based chemical reactivity indices such as atomic charges, HOMO-LUMO energies, stabilization energies, variation of dipole moment of the conformers, ionization potential, electron affinity, chemical potential, hardness and softness have been investigated. The present results show the high kinetic stability and low chemical reactivity of Tam and its important active metabolite, Endoxifen, in water medium. So a drug carrier with good aqueous solubility should be applied to improve the bioavailability of these antitumor drugs.

Rate coefficients for fuel + NO2: Predictive kinetics for HONO and HNO2 formation

High-accuracy electronic structure calculations and transition state theory are used to predict the rate coefficients for the H-abstraction reactions H2+NO2 and CH4+NO2. In each case, three different HNO2 isomers are formed: cis-HONO, trans-HONO, and HNO2. These results are used as benchmarks to test different combinations of density functionals and basis sets. The performance of these DFT methods are evaluated both with and without the use of subsequent CCSD(T)-F12a single-point energy corrections. The compound method CCSD(T)-F12a/cc-pVTZ-f12//B2PLYPD3/cc-pVTZ is used to predict the rate coefficients for C2–C4 alkanes and alkenes+NO2, and the resulting activation energies are generalized into rate rules. These new rules will enable accurate rate coefficients for RH+NO2 reactions for larger hydrocarbons. In all cases, the dominant product for RH+NO2 is R+cis-HONO, followed by R+HNO2. Although trans-HONO is the most stable HNO2 isomer, the rate constants leading to its formation are roughly an order of magnitude smaller.

A study on the conformational space of the all-trans retinal deprotonated Schiff base

The conformational space of the all-trans retinal deprotonated Schiff base (DSBT) molecule around its four internal backbone torsional angles was studied. A total of eight different conformers were detected from potential energy surface exploration corresponding to the four internal backbone torsional angles. The standard split-valence 6-311++G(d,p) basis set in combination with MP2 andB3LYP levels were carried out to analyze the structural characteristics (relative energies, dipole moments and bond length alternation) and spectral properties (electronic absorption spectrum and Raman spectrum) of the conformers. Results presented in this paper showed that the relative stability order of the conformers might be independent of the level of theory used. It was also reconfirmed that the TD-DFT method would systematically underestimate the excitation energy by 38.60–67.54kJmol−1; a trend had been reported in several previous studies. The characteristic peak nearby 1600cm−1 corresponding to the ECC mode could be notably observed from the predicted Raman spectrum calculated at both the MP2andthe B3LYP level of theories. Moreover, the spectral profile acquired based on the B3LYP level was more apparent and distinguishable than that from the MP2 method. It is suggested that B3LYP level may be a proper choice for theoretically study of Raman spectrum, especially concerning the polyene conjugated systems.

A Computational and Experimental Study of the Conformers of Pyrrolidinium Ionic Liquid Cations Containing an Ethoxy Group in the Alkyl Side Chain

We investigate the conformers of the N-methoxyethyl-N-methylpyrrolidinium (PYR1(2O1)) and N-ethoxyethyl-N-methylpyrrolidinium (PYR1(2O2)) ionic liquid cations by means of DFT calculations at the B3LYP/6-31G⁎⁎ level and we calculate their infrared vibration frequencies. The comparison with the absorbance spectra of two ionic liquids containing these ions indicates good performance of such a combination of theory and basis set. The lowest energy conformer of each pyrrolidinium cation displays equatorial-envelope geometry; however, in contrast with the prototypical PYR14, the main alkyl side chain is not in an all-trans configuration, but it tends to be bent. Moreover, calculations indicate that the LUMO orbital extends more along the alkyl side chain in PYR1(2O1) and PYR1(2O2) than in the parent ion 1-butyl-1-methylpyrrolidinium (PYR14).

The conformational and vibrational behavior of the inhibitory neuropeptide derived from beta-endorphin

In this study, conformational behavior, structural, and vibrational characterization of the carboxy terminal dipeptide of β-endorphin (glycy-l-glutamine, glycyl-glutamine, beta-endorphin30-31), which is an inhibitory neuropeptide synthesized from beta-endorphin1-31 in brain stem regions, has been investigated. The theoretically possible stable conformers were searched by means of molecular mechanics method to determine their energetically preferred conformations. The 360 different conformations were calculated with the φ, Ψ, χ dihedral angles using the Ramachandran maps. The most stable conformation of the title molecule is characterized by the extended backbone shape (e) in the BR conformational range with −.78 kcal/mol energy. The cis- and trans-dimeric forms of the dipeptide were also formed and energetically preferred conformations of dimers were investigated. The experimental methods (FT-IR, micro-Raman spectroscopies) coupled with quantum chemical calculations based on density functional theory (DFT) have been used to identify the geometrical, energetic, and vibrational characteristics of the dipeptide. The assignment of the vibrational spectra was performed based on the potential energy distribution of the vibrational modes. To investigate the electronic properties, such as nonlinear optical properties, the electric dipole moment, the mean polarizability, the mean first hyperpolarizability, and HOMO–LUMO energy gaps were computed using the DFT with the B3LYP/6-31++G(d,p) basis set combination. The second-order interaction energies were derived from natural bonding orbital analysis. The focus of this study is to determine possible stable conformation on inhibitory neuropeptide and to investigate molecular geometry, molecular vibrations of monomeric and dimeric forms, and hydrogen bonding interactions of glycy-l-glutamine dipeptide.

The molecular structure of phenetole studied by microwave spectroscopy and quantum chemical calculations

ABSTRACTA pulsed molecular beam Fourier transform microwave spectrometer operating in the frequency range 2–26.5 GHz was used to measure the spectrum of phenetole (ethyl phenyl ether or ethoxybenzene, C6H5OC2H5). The conformational landscape is completely determined by the orientations of the phenyl ring and the ethyl group. A two-dimensional potential energy surface was calculated at the MP2/6-311++G(d,p) level of theory. Two conformers were found: the trans conformer has a Cs symmetry, and the gauche conformer has the ethyl group tilted out of the phenyl plane by about 70°. Totally, 186 rotational transitions were assigned to the more stable planar trans conformer, and fitted using a semi-rigid rotor model to measure accuracy. Highly accurate rotational and centrifugal distortion constants were determined. Several method and basis set combinations were applied to check for convergence and to compare with the experimentally deduced molecular parameters.

Molecular structures, charge distributions, and vibrational analyses of the tetracoordinate Cu(II), Zn(II), Cd(II), and Hg(II) bromide complexes of p-toluidine investigated by density functional theory in comparison with experiments

The Cu(II), Zn(II), Cd(II), and Hg(II) bromide complexes of p-toluidine have been studied with B3LYP calculations by using def2-TZVP basis set at the metal atoms and using def2-TZVP and 6-311G+(d,p) basis sets at the remaining atoms. Both basis set combinations give analogous results, which validate the use of quickly converging 6-311G+(d,p) basis set in future studies. The molecular structures, atomic charge and spin distributions, and harmonic vibrational frequencies of the complexes have been calculated. The Zn, Cd and Hg complexes have been found to have distorted tetrahedral environments around the metal atoms whereas Cu complex has a square planar geometry. The NBO charge analysis have been found more accurate and less misleading compared with the Mulliken scheme. The present vibrational spectra calculations allow accurate assignment of the vibrational bands, which otherwise assigned tentatively in previous experimental-only studies.

The infrared spectrum of bis(fluorosulfonyl)imide revisited: Attractive performances of the PBE0/6-31G** model

We report a systematic investigation of the far- and mid-infrared spectra of ionic liquids (ILs) containing the bis(fluorosulfonyl)imide (FSI) anion, both in the liquid state at room temperature and in solid phases at low temperatures. We extended to lower frequencies a previous study, and we observed four additional vibration bands below 500cm−1, attributable to FSI. Moreover, DFT calculations of vibration frequencies were performed using three combinations of theory and basis set: (1) B3LYP/6-31G**, (2) B3LYP/6-311+G(3df) and (3) PBE0/6-31G**. Model 1, largely used in the previous literature concerning ILs, shows the poorest performances; model 2, which generally gives a good agreement with the experiments, misses the vibration frequencies by ∼40cm−1 in the range 650–900cm−1 where one finds the largest spectral differences between cis- and trans-FSI; model 3 gives the best agreement with the experiments and, moreover, is much less time consuming than model 2. The comparison with calculations suggests that the band centered around 1217cm−1 is a good marker of the occurrence of the cis-FSI conformer. Finally, the bands located around 730 and 750cm−1 are attributable to cis- and trans- conformer of FSI, respectively.

High‐Level Ab Initio Calculations of Molecular Properties of Chromium Monocarbonyl, CrCO

Chromium monocarbonyl (CrCO) is the simplest unsaturated transition metal carbonyl, and ab initio methods that include a dynamic electron correlation effect are necessary to calculate the molecular properties of CrCO. We employed post Hartree–Fock ab initio methods with various all‐electron basis sets to calculate the molecular properties of CrCO including the molecular structures, vibrational frequencies, and bond dissociation energy. The methods including triple excitation and a quadruple‐ζ level basis set are required to reasonably describe the molecular properties of CrCO. We found that the most efficient combination of theoretical method and basis set for this weakly interacting system is the unrestricted coupled‐cluster singles and doubles with perturbative triples (UCCSD(T)) with the Sapporo‐DKH3‐QZP basis set.

Structural and spectral properties of tartrato complexes of vanadium(V) from quantum chemical calculations

Structural and spectral properties of three complex anions of vanadium(V) with tartrato ligands were theoretically studied by all-electron DFT calculations employing various functionals, such as BP86, BLYP, B3LYP, BHHLYP, and the M06-family. Results were statistically evaluated, with the aim to find a reliable, fairly accurate, and yet computationally efficient combination of methods and basis sets to be used in computational chemistry of vanadium(V) complex anions at even larger scale. Subsequent vibrational analysis based upon BP86 and B3LYP data provided a fair agreement with the experimental vibrational spectra. Additionally, the absorption UV–Vis and the electronic circular dichroism spectra of studied compounds were simulated via time-dependent density functional theory calculations with the long-range corrected functionals (CAM-B3LYP, LC-ωPBE, and ωB97XD). Finally, the 51V NMR chemical shifts were calculated using the GIAO approach at the B3PW91 level. The solvent effect was simulated within the PCM model. Where available, the calculated spectral properties were compared with experimental data.

Density functional theory (DFT) prediction of structural and spectroscopic parameters of cytosine using harmonic and anharmonic approximations

The applicability of popular and efficient B3LYP hybrid density functional and medium-size Pople-type basis set in combination with computationally expensive anharmonic model to obtain more accurate theoretical structure, vibrational frequencies and GIAO NMR parameters of cytosine was tested. We report on prediction of cytosine equilibrium (R e ) and rovibrationally averaged (R v ) structures and vibrational frequencies in the gas phase and DMSO solution using density functional theory combined with 6-311++G** basis set. The harmonic and anharmonic vibrational frequencies (using second-order vibrational perturbation theory, VPT2) were critically discussed. In comparison with initial harmonic data, a significantly better agreement between scaled and anharmonic frequencies and experiment was observed. Proton and carbon nuclear magnetic shieldings were calculated at R e and R v structures of cytosine in the gas phase and DMSO solution using BHandH and B3LYP density functionals combined with 6-311++G**, aug-cc-pVTZ-J and STO-3Gmag basis sets. The obtained NMR results were compared with available experimental data and discussed at length.

Conformation stability, halogen and solvent effects on C[dbnd]O stretching of 4-chloro-3-halogenobenzaldehydes

The effects of halogen and solvent on the conformation and carbonyl stretching of 4-chloro-3-halogenobenzaldehydes [C7H4ClXO; X=F (CFB), Cl (CCB) or Br (CBB)] were investigated using the density functional theory (DFT) method. The B3LYP functional was used by the 6-311+G(3df,p) basis set in combination with the polarizable continuum model (PCM). Computations were focused on the cis and trans isomers of the compounds in 18 different polar or non-polar organic solvents. The theoretical frequencies of the solvent-induced CO stretching vibrations were correlated with the empirical solvent parameters such as the Kirkwood–Bauer–Magat (KBM) equation, the solvent acceptor number (AN), Swain parameters and the linear solvation energy relationships (LSER). The present work explores the effect of both the halogen and medium on the conformational preference and CO vibrational frequency. The findings of this work can be useful to those systems involving changes in the conformations analogous to the compounds studied.

Prediction of molecular crystal structures by a crystallographic QM/MM model with full space-group symmetry.

A crystallographic quantum-mechanical/molecular-mechanical model (c-QM/MM model) with full space-group symmetry has been developed for molecular crystals. The lattice energy was calculated by quantum-mechanical methods for short-range interactions and force-field methods for long-range interactions. The quantum-mechanical calculations covered the interactions within the molecule and the interactions of a reference molecule with each of the surrounding 12-15 molecules. The interactions with all other molecules were treated by force-field methods. In each optimization step the energies in the QM and MM shells were calculated separately as single-point energies; after adding both energy contributions, the crystal structure (including the lattice parameters) was optimized accordingly. The space-group symmetry was maintained throughout. Crystal structures with more than one molecule per asymmetric unit, e.g. structures with Z' = 2, hydrates and solvates, have been optimized as well. Test calculations with different quantum-mechanical methods on nine small organic molecules revealed that the density functional theory methods with dispersion correction using the B97-D functional with 6-31G* basis set in combination with the DREIDING force field reproduced the experimental crystal structures with good accuracy. Subsequently the c-QM/MM method was applied to nine compounds from the CCDC blind tests resulting in good energy rankings and excellent geometric accuracies.

Electronic Structure, Nonlinear Optical Properties, and Vibrational Analysis of Ethyl benzoate by Density Functional Theory

This work deals with the vibrational spectroscopy of Ethyl benzoate (C9H10O2). The fundamental vibrational frequencies and intensity of vibrational bands were evaluated using density functional theory (DFT) using standard HF/6-31G(d,p) and B3LYP/6-31G(d,p) methods and basis set combinations. The vibrational spectra were interpreted, with the aid of normal coordinate analysis based on a scaled quantum mechanical force field. The infrared and Raman spectra were also predicted from the calculated intensities. Comparison of simulated spectra with the experimental spectra provides important information about the ability of the computational method to describe the vibrational modes.