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Porphyrin complexes are of great importance due to their possible applications as sensors, solar cells and photocatalysts, as well as their ability to bind additional ligands. A valuable source of knowledge on their nature is their electric properties, which can be evaluated employing density functional theory (DFT) methods, supporting the experimental research. The present work aims at the application of small property-oriented basis sets in calculation of electric properties in transition metals, their oxides and test coordination complexes. Firstly, the existing polarized ZPol basis set for the first-row transition metals is modified in order to improve atomic polarizability results. For this purpose, optimization of the f-type polarization function exponent is carried out with respect to the value of average atomic polarizability of investigated metals. Next, both the original and the modified basis sets are employed in finite field CCSD(T) calculation of transition metal oxides' dipole moments, as well as DFT calculation of polarizabilities in porphyrin–zinc and porphyrin–zinc–thiazole complexes. The obtained results show that the ZPol and ZPol-A basis sets can be successfully employed in the calculation of linear electric properties in large systems. The optimization procedure used in the present work can be employed for other source basis sets and elements, leading to new efficient polarized basis sets. [ABSTRACT FROM AUTHOR]

This study compares results of four relativistic pseudopotential basis sets, which differ mainly by their size: double‐zeta introduced by Hay and Wadt from Los Alamos National Laboratory (LANL2DZ), triple‐zeta based on Stuttgart energy‐consistent scalar‐relativistic pseudopotential (SDD3), its extension with 2fg polarization functions, and combination of Stuttgart pseudopotentials with quintuple‐zeta cc‐pV5Z base (SDD5). Hydrides of transition metals from Cr to Zn group are chosen as reference molecules. The coupled cluster method (CCSD(T)) is used for evaluation of selected molecular characteristics. Interatomic distances, dissociation energies, vibration modes, and anharmonicity constants are determined and compared with available experimental data. As expected, the accuracy of basis depends mainly on its size. However, only moderate modification of SDD3 basis set significantly improves its accuracy, which becomes comparable to the largest basis set. Nevertheless, the time consumption is significantly lower. [ABSTRACT FROM AUTHOR]

The linear combination of atomic orbitals (LCAO) method is advantageous for calculating important bulk and surface properties of crystals and defects in/on them. Compared to plane wave calculations and contrary to common assumptions, hybrid density functional theory (DFT) functionals are actually less costly and easier to implement in LCAO codes. However, choosing the proper basis set (BS) for the LCAO calculations representing Guassian-type functions is crucial, as the results depend heavily on its quality. In this study, we introduce a new basis set (BS) visual representation, which helps us (1) analyze the collective behavior of individual atoms' shell exponents (s, p, and d), (2) better compare different BSs, (3) identify atom-type invariant relationships, and (4) suggest a robust method for building a local all-electron BS (denoted as BS1) from scratch for each atom type. To compare our BS1 with the others existing in the literature, we calculate the basic bulk properties of SrTiO 3 (STO) in cubic and tetragonal phases using several hybrid DFT functionals (B3LYP, PBE0, and HSE06). After adjusting the exact Hartree–Fock (HF) exchange of PBEx, HSEx, and the state-of-the-art meta-GGA hybrid r 2 SCANx functionals, we find the r 2 SCAN15 and HSE27 for BS1, with the amount of exact HF exchange of 0.15 and 0.27, respectively, perform equally well for reproducing several most relevant STO properties. The proposed robust BS construction scheme has the advantage that all parameters of the obtained BS can be reoptimized for each new material, thus increasing the quality of DFT calculation predictions. [ABSTRACT FROM AUTHOR]

The current study focusses on the use of quantum chemistry to elucidate the novel synthetic route for e mrlotinib from methyl 4,5-dihydroxy-2-isocyanobenzoate, which includes oxidative coupling, nucleophilic addition, cyclization and Williamson's ether synthesis. The overall reaction requires three intermediate and produces 13 transition states [TS]. Which are less than the earlier reported synthetic schemes. The energies of each reactant, intermediate and products were calculated using DFT (density functional theory) and B3LYP/6-311+G* as a basis set. The energies diagram obtained indicates the novel proposed scheme could follow the easy path to obtain the product, moreover, the energy barrier required to overcome the transition state is low indicating, very less activation energy is required for every reactant to take part in chemical reaction. [ABSTRACT FROM AUTHOR]

Chemical graph theory is an extension of mathematical chemistry that explores chemical phenomena and entities using the conceptual frameworks of graph theory. Chemical graph theory, in particular, uses chemical graphs to represent molecular structures. This chemical graph represents bonds and atoms, respectively, as edges and vertices. Cheminformatics predominantly uses chemical graphs as an essential data type for depicting chemical structures. The computable features of graphs lay the groundwork for (quantitative) structure-property and structure-activity predictions, which is an important component of cheminformatics. The physical and chemical characteristics of chemical compounds are thus reflected in these graphs, which can subsequently be reduced to graph-theoretical descriptors or indices. One of the most extensively researched distance-based graph descriptors is the resolving set W (metric dimension), which differentiates each pair of distinct vertices in every connected simple graph. The mixed metric dimension, which is the most significant variant of metric dimension, is determined for the complex molecular graph of a one-pentagonal carbon nanocone (PCN) in this manuscript. We show that only three distinct non-neighboring vertices (least possible requirement) from PCN can be adopted to uniquely identify all of the edges as well as vertices in PCN. [ABSTRACT FROM AUTHOR]

Chemical graph theory is an extension of mathematical chemistry that explores chemical phenomena and entities using the conceptual frameworks of graph theory. In particular, chemical graphs are used to represent molecular structures in chemical graph theory. Edges and vertices in this chemical graph substitute for bonds and atoms, respectively. The primary data types used throughout cheminformatics to depict chemical structures are chemical graphs. The basis for (quantitative) structure-property and structure-activity predictions, a central area of cheminformatics, is laid by the computable properties of graphs. The physical characteristics of molecules are thus reflected in these graphs, which can subsequently be reduced to graph-theoretical indices or descriptors. The resolving set Z , which distinguish every pair of distinct vertices in a connected simple graph, is one of the most well-studied distance-based graph descriptors. In this manuscript, we consider the most significant variation of a metric dimension known as partition dimension and determine it for the molecular complex graph of one-pentagonal carbon nanocone (PCN). We demonstrate that all of the vertices and edges in PCN can be uniquely identified only by considering three distinct non-neighboring partition sets (minimal requirement) from PCN. [ABSTRACT FROM AUTHOR]

γ‐Aminobutyric acid (GABA), as the primary inhibitory neurotransmitter, is extremely important for maintaining healthy brain function, and deviations from GABA homeostasis are related to various brain diseases. Short‐echo‐time (short‐TE) proton MR spectroscopy (1H‐MRS) has been employed to measure GABA concentration from various human brain regions at high magnetic fields. The aim of this study was to investigate the effect of spectral linewidth on GABA quantification and explore the application of an optimized basis‐set preparation approach using a spectral‐linewidth‐matched (LM) basis set in LCModel to improve the reproducibility of GABA quantification from short‐TE 1H‐MRS. In contrast to the fixed‐linewidth basis‐set approach, the LM basis‐set preparation approach, where all metabolite basis spectra were simulated with a linewidth 4 Hz narrower than that of water, showed a smaller standard deviation of estimated GABA concentration from synthetic spectra with varying linewidths and lineshapes. The test–retest reproducibility was assessed by the mean within‐subject coefficient of variation, which improved from 19.2% to 12.0% in the thalamus, from 27.9% to 14.9% in the motor cortex, and from 9.7% to 2.8% in the medial prefrontal cortex using LM basis sets at 7 T. We conclude that spectral linewidth has a large effect on GABA quantification from short‐TE 1H‐MRS data and that using LM basis sets in LCModel can improve the reproducibility of GABA quantification. [ABSTRACT FROM AUTHOR]

The linear combination of atomic orbitals (LCAO) method is advantageous for calculating important bulk and surface properties of crystals and defects in/on them. Compared to plane wave calculations and contrary to common assumptions, hybrid density functional theory (DFT) functionals are actually less costly and easier to implement in LCAO codes. However, choosing the proper basis set (BS) for the LCAO calculations representing Guassian-type functions is crucial, as the results depend heavily on its quality. In this study, we introduce a new basis set (BS) visual representation, which helps us (1) analyze the collective behavior of individual atoms’ shell exponents (s, p, and d), (2) better compare different BSs, (3) identify atom-type invariant relationships, and (4) suggest a robust method for building a local all-electron BS (denoted as BS1) from scratch for each atom type. To compare our BS1 with the others existing in the literature, we calculate the basic bulk properties of SrTiO3 (STO) in cubic and tetragonal phases using several hybrid DFT functionals (B3LYP, PBE0, and HSE06). After adjusting the exact Hartree–Fock (HF) exchange of PBEx, HSEx, and the state-of-the-art meta-GGA hybrid r2SCANx functionals, we find the r2SCAN15 and HSE27 for BS1, with the amount of exact HF exchange of 0.15 and 0.27, respectively, perform equally well for reproducing several most relevant STO properties. The proposed robust BS construction scheme has the advantage that all parameters of the obtained BS can be reoptimized for each new material, thus increasing the quality of DFT calculation predictions.

Adsorptions of small amide molecules, acetamide (AA) and N-methyl-acetamide (NMA) on the surface of kaolinite are investigated in this study. The focus is on the basis set effects towards the stabilities and the interaction energies of the molecules on the Al–O surface. With a fixed B3LYP functional, we increased the size of the basis sets for the single-point calculations, to find the converged interaction energies and obtain the relative stabilities. We found that, under the direct usage of Pople-type and Dunning’s correlation consistent basis sets, it is not possible to achieve the pattern of convergence for the interaction energies and the relative stabilities. Compared to the complete basis set (CBS) extrapolation scheme, the double zeta basis sets deviated the most, in the range of 21 to 27%, while it is from 1 to 7% for the triple zeta basis sets. Based on the results, we suggest using 6-311++G(2df,2pd) or cc-pVQZ for energy-related quantities. Compared to AA, NMA attached more strongly by 0.5 eV on the surface of Al–O.

In this article, a simple approach is proposed to reduce the basis set requirement for computing accurate interaction energies for bimolecular noncovalent complexes. A distributed multipole expansion is used to estimate the importance of basis functions in a given atom. Moderate truncation of basis sets results in reduced computational cost without compromising the accuracy. The approach was found fruitful for wavefunction‐based methods and density functional theory approximation using the Dunning, Karlsruhe, and Jensen basis sets. [ABSTRACT FROM AUTHOR]

The determination of the absolute configuration (AC) of an organic molecule is still a challenging task for which the combination of spectroscopic with quantum‐mechanical methods has become a promising approach. In this study, we investigated the accuracy of DFT methods (480 overall combinations of 15 functionals, 16 basis sets, and 2 solvation models) to calculate the VCD spectra of six chiral organic molecules in order to benchmark their capability to facilitate the determination of the AC. [ABSTRACT FROM AUTHOR]

The 13C NMR chemical shifts of fullerene C60 exo-derivatives were calculated using quantum chemical hybrid functionals combined with Pople, Dunning correlation-consistent, and def2-TZVP split valence basis sets taking into account the solvent effect (polarizable continuum model). A relationship between theoretical and experimental 13C NMR chemical shifts (CSs) is assessed quantitatively to select a functional/basis set combination. It is found that the CAM-B3LYP/6-31G and M06L/6-31G combinations have the best convergence with experimental data in modeling the 13С NMR CSs of sp3 fullerene carbon atoms in С60 derivatives, whereas X3LYP/6-31G and CAM-B3LYP/6-31G(d) in modeling the 13С NMR CSs of their sp2 fullerene carbon atoms. [ABSTRACT FROM AUTHOR]

In the present study, we benchmark computational protocols for predicting Co-59 NMR chemical shift. Quantum mechanical calculations based on density functional theory were used, in conjunction with our NMR-DKH basis sets for all atoms, including Co, which were developed in the present study. The best protocol included the geometry optimization at BLYP/def2-SVP/def2-SVP/IEF-PCM(UFF) and shielding constant calculation at GIAO-LC-ωPBE/NMR-DKH/IEF-PCM(UFF). This computational scheme was applied to a set of 34 Co(III) complexes, in which, Co-59 NMR chemical shift ranges from +1162 ppm to +15,100 ppm, and these were obtained in distinct solvents (water and organic solvents). The resulting mean absolute deviation (MAD), mean relative deviation (MRD), and coefficient of determination (R2) were 158 ppm, 3.0%, and 0.9966, respectively, suggesting an excellent alternative for studying Co-59 NMR. [ABSTRACT FROM AUTHOR]

Four ways are introduced for the comparative prediction on solid phase heat of formation ΔHof (s) of cubane through different level of theories (B3LYP/6‐31G(d,p), B3LYP/6‐311+G(2d,2p), B3PW91/6‐31G(d,p), MP2/6‐31G(d,p), and G2). It is based on the heats of sublimation ΔHsub derived from information obtained from the quantum‐mechanically calculated electrostatic potential of each isolated molecule. The ΔHsub are combined with the aforementioned gas phase heats of formation ΔHof (g) to produce condensed phase heats of formation ΔHof (s). Comparisons of the methods are given, along with the recommendations about the methods that could produce better agreement with experiment, wishing to offer some beneficial references. [ABSTRACT FROM AUTHOR]

The investigation of the sensitivity of the relativistic corrections to the NMR shielding constants (σ) to the configuration of angular spaces of the basis sets used on the atoms of interest was carried out within the four-component density functional theory (DFT). Both types of relativistic effects were considered, namely the so-called heavy atom on light atom and heavy atom on heavy atom effects, though the main attention was paid to the former. As a main result, it was found that the dependence of the relativistic corrections to σ of light nuclei (exemplified here by 1H and 13C) located in close vicinity to a heavy atom (exemplified here by In, Sn, Sb, Te, and I) on the basis set used on the light spectator atom was very much in common with that of the Fermi-contact contribution to the corresponding nonrelativistic spin-spin coupling constant (J). In general, it has been shown that the nonrelativistic J-oriented and σ-oriented basis sets, artificially saturated in the tight s-region, provided much better accuracy than the standard nonrelativistic σ-oriented basis sets when calculating the relativistic corrections to the NMR shielding constants of light nuclei at the relativistic four-component level of the DFT theory. [ABSTRACT FROM AUTHOR]

In vivo short echo time (TE) proton magnetic resonance spectroscopy (1H-MRS) is a useful method for the quantification of human brain metabolites. The purpose of this study was to evaluate the performance of an in-house, experimentally measured basis set and compare it with the performance of a vendor-provided basis set. A 3T clinical scanner with 32-channel receive-only phased array head coil was used to generate 16 brain metabolites for the metabolite basis set. For voxel localization, point-resolved spin-echo sequence (PRESS) was used with volume of interest (VOI) positioned at the center of the phantoms. Two different basis sets were subjected to linear combination of model spectra of metabolite solutions in vitro (LCModel) analysis to evaluate the in-house acquired in vivo 1H-MR spectra from the left prefrontal cortex of 22 healthy subjects. To evaluate the performance of the two basis sets, the Cramer-Rao lower bounds (CRLBs) of each basis set were compared. The LCModel quantified the following metabolites and macromolecules: alanine (Ala), aspartate (Asp), γ-amino butyric acid (GABA), glucose (Glc), glutamine (Gln), glutamate (Glu), glutathione (GHS), Ins (myo-Inositol), lactate (Lac), N-acetylaspartate (NAA), N-acetylaspartylglutamate (NAAG), taurine (Tau), phosphoryl-choline + glycerol-phosphoryl-choline (tCho), N-acetylaspartate + N-acetylaspartylglutamate (tNA), creatine + phosphocreatine (tCr), Glu + Gln (Glx) and Lip13a, Lip13b, Lip09, MM09, Lip20, MM20, MM12, MM14, MM17, Lip13a + Lip13b, MM14 + Lip13a + Lip13b + MM12, MM09 + Lip09, MM20 + Lip20. Statistical analysis showed significantly different CRLBs: Asp, GABA, Gln, GSH, Ins, Lac, NAA, NAAG, Tau, tCho, tNA, Glx, MM20, MM20 + Lip20 (p < 0.001), tCr, MM12, MM17 (p < 0.01), and Lip20 (p < 0.05). The estimated ratio of cerebrospinal fluid (CSF) in the region of interest was calculated to be about 5%. Fitting performances are better, for the most part, with the in-house basis set, which is more precise than the vendor-provided basis set. In particular, Asp is expected to have reliable CRLB (<30%) at high field (e.g., 3T) in the left prefrontal cortex of human brain. The quantification of Asp was difficult, due to the inaccuracy of Asp fitting with the vendor-provided basis set. [ABSTRACT FROM AUTHOR]

The cerebellum is considered a "learning machine" essential for time interval estimation underlying motor coordination and other behaviors. Theoretical work has proposed that the cerebellum's input recipient structure, the granule cell layer (GCL), performs pattern separation of inputs that facilitates learning in Purkinje cells (P-cells). However, the relationship between input reformatting and learning has remained debated, with roles emphasized for pattern separation features from sparsification to decorrelation. We took a novel approach by training a minimalist model of the cerebellar cortex to learn complex time-series data from time-varying inputs, typical during movements. The model robustly produced temporal basis sets from these inputs, and the resultant GCL output supported better learning of temporally complex target functions than mossy fibers alone. Learning was optimized at intermediate threshold levels, supporting relatively dense granule cell activity, yet the key statistical features in GCL population activity that drove learning differed from those seen previously for classification tasks. These findings advance testable hypotheses for mechanisms of temporal basis set formation and predict that moderately dense population activity optimizes learning. [ABSTRACT FROM AUTHOR]

Purpose: The purpose of this study is to present a cloud‐based spectral simulation tool "MRSCloud," which allows MRS users to simulate a vendor‐specific and sequence‐specific basis set online in a convenient and time‐efficient manner. This tool can simulate basis sets for GE, Philips, and Siemens MR scanners, including conventional acquisitions and spectral editing schemes with PRESS and semi‐LASER localization at 3 T. Methods: The MRSCloud tool was built on the spectral simulation functionality in the FID‐A software package. We added three extensions to accelerate computation (ie, one‐dimensional projection method, coherence pathways filters, and precalculation of propagators). The RF waveforms were generated based on vendors' generic pulse shapes and timings. Simulations were compared within MRSCloud using different numbers of spatial resolution (21 × 21, 41 × 41, and 101 × 101). Simulated metabolite basis functions from MRSCloud were compared with those generated by the generic FID‐A and MARSS, and a phantom‐acquired basis set from LCModel. Intraclass correlation coefficients were calculated to measure the agreement between individual metabolite basis functions. Statistical analysis was performed using R in RStudio. Results: Simulation time for a full PRESS basis set is approximately 11 min on the server. The interclass correlation coefficients ICCs were at least 0.98 between MRSCloud and FID‐A and were at least 0.96 between MRSCloud and MARSS. The interclass correlation coefficients between simulated MRSCloud basis spectra and acquired LCModel basis spectra were lowest for glutamine at 0.68 and highest for N‐acetylaspartate at 0.96. Conclusions: Substantial reductions in runtime have been achieved. High ICC values indicated that the accelerating features are running correctly and produce comparable and accurate basis sets. [ABSTRACT FROM AUTHOR]

Purpose: Metabolite amplitude estimates derived from linear combination modeling of MR spectra depend upon the precise list of constituent metabolite basis functions used (the "basis set"). The absence of clear consensus on the "ideal" composition or objective criteria to determine the suitability of a particular basis set contributes to the poor reproducibility of MRS. In this proof-of-concept study, we demonstrate a novel, data-driven approach for deciding the basis-set composition using Bayesian information criteria (BIC)., Methods: We have developed an algorithm that iteratively adds metabolites to the basis set using iterative modeling, informed by BIC scores. We investigated two quantitative "stopping conditions", referred to as max-BIC and zero-amplitude, and whether to optimize the selection of basis set on a per-spectrum basis or at the group level. The algorithm was tested using two groups of synthetic in-vivo-like spectra representing healthy brain and tumor spectra, respectively, and the derived basis sets (and metabolite amplitude estimates) were compared to the ground truth., Results: All derived basis sets correctly identified high-concentration metabolites and provided reasonable fits of the spectra. At the single-spectrum level, the two stopping conditions derived the underlying basis set with 77-87% accuracy. When optimizing across a group, basis set determination accuracy improved to 84-92%., Conclusion: Data-driven determination of the basis set composition is feasible. With refinement, this approach could provide a valuable data-driven way to derive or refine basis sets, reducing the operator bias of MRS analyses, enhancing the objectivity of quantitative analyses, and increasing the clinical viability of MRS.

Perkembangan teknologi informasi, komputasi dan ilmu fisika, khususnya fisika kuantum, diharapkan dapat melahirkan teknologi baru yang berguna untuk mewujudkan komputer kuantum sebagai komputer masa depan. Pada penelitian ini, algoritma kuantum telah diterapkan Variational Quantum Eigensolver (VQE) untuk menghitung energi keadaan dasar molekul dimer helium (He2). Komputasi menggunakan algoritma kuantum VQE dikerjakan dalam bahasa pemrograman Python dengan modul Qiskit. Untuk memastikan program algoritma kuantum VQE telah bekerja dengan baik pada sistem molekul, validasi program dilakukan terlebih dahulu untuk kasus molekul hidrogen ( ). Hasil validasi program pada molekul menunjukkan hasil yang sesuai dengan metode diagonalisasi dan literatur. Energi keadaan dasar molekul He2 yang diperoleh dengan metode algoritma VQE yaitu sebesar −5,74032590 pada jarak equilibrium 2,3 Å

In the present study, we benchmark computational protocols for predicting Co-59 NMR chemical shift. Quantum mechanical calculations based on density functional theory were used, in conjunction with our NMR-DKH basis sets for all atoms, including Co, which were developed in the present study. The best protocol included the geometry optimization at BLYP/def2-SVP/def2-SVP/IEF-PCM(UFF) and shielding constant calculation at GIAO-LC-ωPBE/NMR-DKH/IEF-PCM(UFF). This computational scheme was applied to a set of 34 Co(III) complexes, in which, Co-59 NMR chemical shift ranges from +1162 ppm to +15,100 ppm, and these were obtained in distinct solvents (water and organic solvents). The resulting mean absolute deviation (MAD), mean relative deviation (MRD), and coefficient of determination (R2) were 158 ppm, 3.0%, and 0.9966, respectively, suggesting an excellent alternative for studying Co-59 NMR.

In vivo short echo time (TE) proton magnetic resonance spectroscopy (1H-MRS) is a useful method for the quantification of human brain metabolites. The purpose of this study was to evaluate the performance of an in-house, experimentally measured basis set and compare it with the performance of a vendor-provided basis set. A 3T clinical scanner with 32-channel receive-only phased array head coil was used to generate 16 brain metabolites for the metabolite basis set. For voxel localization, point-resolved spin-echo sequence (PRESS) was used with volume of interest (VOI) positioned at the center of the phantoms. Two different basis sets were subjected to linear combination of model spectra of metabolite solutions in vitro (LCModel) analysis to evaluate the in-house acquired in vivo 1H-MR spectra from the left prefrontal cortex of 22 healthy subjects. To evaluate the performance of the two basis sets, the Cramer-Rao lower bounds (CRLBs) of each basis set were compared. The LCModel quantified the following metabolites and macromolecules: alanine (Ala), aspartate (Asp), γ-amino butyric acid (GABA), glucose (Glc), glutamine (Gln), glutamate (Glu), glutathione (GHS), Ins (myo-Inositol), lactate (Lac), N-acetylaspartate (NAA), N-acetylaspartylglutamate (NAAG), taurine (Tau), phosphoryl-choline + glycerol-phosphoryl-choline (tCho), N-acetylaspartate + N-acetylaspartylglutamate (tNA), creatine + phosphocreatine (tCr), Glu + Gln (Glx) and Lip13a, Lip13b, Lip09, MM09, Lip20, MM20, MM12, MM14, MM17, Lip13a + Lip13b, MM14 + Lip13a + Lip13b + MM12, MM09 + Lip09, MM20 + Lip20. Statistical analysis showed significantly different CRLBs: Asp, GABA, Gln, GSH, Ins, Lac, NAA, NAAG, Tau, tCho, tNA, Glx, MM20, MM20 + Lip20 (p < 0.001), tCr, MM12, MM17 (p < 0.01), and Lip20 (p < 0.05). The estimated ratio of cerebrospinal fluid (CSF) in the region of interest was calculated to be about 5%. Fitting performances are better, for the most part, with the in-house basis set, which is more precise than the vendor-provided basis set. In particular, Asp is expected to have reliable CRLB (

The quality of the positron wavefunction produced by applying the Schwinger variational principle (SVP) is scrutinized. An optical potential formalism is applied considering a semiempirical polarization potential. The positron wavefunction is expanded into a basis set formed by hydrogen-like atom eigenfunctions. Two different forms for the ansatz are tested out. The model is applied to positron scattering and annihilation by hydrogen, and by argon atoms as examples. The results are compared to the ones obtained through the direct integration of the Schrödinger equation. We found that the positron wavefunction generated by the SVP is of good quality only if the basis functions are mainly located inside the potential range. We also found that to provide the best scattering amplitude possible, the SVP may produce intentional deviations all along the positron wavefunction to compensate for local basis set deficiencies. We proposed a criterion based on the Lippmannâ€"Schwinger equation to evaluate the accuracy of the positron wavefunction. [ABSTRACT FROM AUTHOR]

ABSTRACT: The method of McCurdy, Baertschy, and Rescigno, J. Phys. B, 37, R137 (2004) [1] is generalised to obtain a straightforward, surprisingly accurate, and scalable numerical representation for calculating the electronic wave functions of molecules. It uses a basis set of product sinc functions arrayed on a Cartesian grid, and yields 1 kcal/mol precision for valence transition energies with a grid resolution of approximately 0.1 bohr. The Coulomb matrix elements are replaced with matrix elements obtained from the kinetic energy operator. A resolution-of-the-identity approximation renders the primitive one- and two-electron matrix elements diagonal; in other words, the Coulomb operator is local with respect to the grid indices. The calculation of contracted two-electron matrix elements among orbitals requires only O(Nlog (N)) multiplication operations, not O(N4), where N is the number of basis functions; N = n3 on cubic grids. The representation not only is numerically expedient, but also produces energies and properties superior to those calculated variationally. Absolute energies, absorption cross sections, transition energies, and ionisation potentials are reported for 1- (He+, H+2), 2- (H2, He), 10- (CH4), and 56-electron (C8H8) systems.

Recently, more attention have been paid on the construction of dipole moment functions (DMF) using theoretical methods. However, the computational methods to construct DMFs are not validated as much as those for potential energy surfaces do. In this letter, using Ar ⋯ He as an example, we tested how spectroscopy-accuracy DMFs can be constructed using ab initio methods. We especially focused on the basis set dependency in this scenario, i.e., the convergence of DMF with the sizes of basis sets, basis set superposition error, and mid-bond functions. We also tested the explicitly correlated method, which converges with smaller basis sets than the conventional methods do. This work can serve as a pictorial sample of all these computational technologies behaving in the context of constructing DMFs. [ABSTRACT FROM AUTHOR]

Most often, the substituent effects are described using rather troublesome Hammett constants. Quite recently, it has been proposed to use the so‐called substituent energy, which is based on total energies of the X‐substituted polycyclic aromatic hydrocarbon and phenyl. This article concerns the influence of the applied level of theory (i.e., both the basis set and the method) on the determined values of the substituent energies. For this purpose, the energies of the NH2 and NO2 groups in 16 unique positions of naphthalene, anthracene, tetracene, phenanthrene, and pyrene were calculated using 10 different basis sets and 23 various exchange‐correlation functionals representing the entire Jacob's Ladder, from local, through gradient‐ and meta‐gradient‐corrected, to hybrid and double‐hybrid ones. Additionally, using even larger 6‐311++G(2df,2p) basis set, the energies of NH2, NO2, CN, and Cl were also computed. Both the basis set and the method used have little effect on the substituent energy if the substituent is in the benzene‐like position. On the contrary, the effect of the level of theory is pronounced especially in the case of the most spatially crowded 4‐substituted phenanthrene. Substituent energies have been shown to be very useful theoretical parameters describing the proximity effect in the substituted derivatives of polycyclic aromatic hydrocarbons. [ABSTRACT FROM AUTHOR]

The aug‐cc‐pVTZ‐J basis set family is extended to include the fourth‐row p‐block elements Ga, Ge, As, Se, and Br. We use the established approach outlined by Sauer and coworkers (J. Chem. Phys. 115, 1324 [2001], J. Chem. Phys. 133, 054308 [2010], J. Chem. Theory Comput. 7, 4070 [2011], and J. Chem. Theory Comput. 7, 4077 [2011]) where the completely uncontracted aug‐cc‐pVTZ basis set is saturated with tight s‐, p‐, d‐, and f‐functions to form the aug‐cc‐pVTZ‐Juc basis set for the tested elements. The saturation is carried out on the simplest hydrides possible for the tested elements GaH, GeH4, AsH3, H2Se, and HBr until an improvement is less than 0.01% for all s‐, p‐, and d‐functions added. f‐Functions are added to an improvement less than or equal to 1.0% due to the computational expense these functions add. The saturated aug‐cc‐pVTZ‐Juc (26s16p12d5f) is then recontracted using the molecular orbital coefficients from self‐consistent field calculations on the simple hydrides to improve computational efficiency. During contraction of the basis set, we observe that the linear hydrogen bromide molecule has a slower convergence than the other tested molecules which sets a limit on the accuracy obtained. All calculations with the contracted aug‐cc‐pVTZ‐J [17s10p7d5f] gives results that are within 1.0% of the uncontracted results at considerable computational savings. [ABSTRACT FROM AUTHOR]

The role of platinum basis set (PTBS) and relativistic effects for predicting the vibrational frequencies and intramolecular force constants for cisplatin are discussed. Nonrelativistic and relativistic computational protocols were built at B3LYP/PTBS/jorge-DZP/C-PCM and B3LYP-DKH2/PTBS/jorge-DZP-DKH/C-PCM levels, respectively, where 19 distinct PTBS were tested. As expected, the structural parameters were not very sensitive to the PTBS, however, the inclusion of relativistic effects improves the description of the cisplatin structure. When it comes to the vibrational frequencies, the results show that the PTBS, and mainly the relativistic effects, are both important. Moreover, the PBE0 functional led to better results than B3LYP in the protocols PBE0/LANL2TZ(f)/jorge-DZP/C-PCM (P20) and PBE0-DKH2/Sapporo-DKH3-DZP-2012/jorge-DZP-DKH/C-PCM (P22), which provided a mean absolute deviation (MAD) of only 10.8 cm−1 and 9.5 cm−1, respectively, for vibrational frequencies, which are excellent choices to study Pt complexes. Finally, a discussion of the intramolecular force constants for cisplatin is carried out, with the calculated bond and angles force constants with P20 and P22 protocols being recommended for the parameterization of the force field of cisplatin. [ABSTRACT FROM AUTHOR]

Rare sugars are monosaccharides with tremendous potential for applications in pharmaceutical, cosmetics, nutraceutical, and flavors industries. The four rare sugars, including gulose, allose, altrose, and talose, are stereoisomers that are different in the hydroxyl group orientation (axial or equatorial) on the C2-4 atoms. The basis sets effect in evaluation of the possibility intramolecular hydrogen bonding (H-bonds) in the selected rare sugars was studied from 6-31G* to 6–311 ++ G(d,p) basis sets using DFT, AIM, and NBO methods. The results show that the selected rare sugars are more stable at 6–311 ++ G(d,p) basis sets compared to 6-31G* because their electronic energies were reduced between 158 and 164 (kcal.mol−1). The overall effect of basis set enhancement is to decrease H-bond energies in the range of 1.25 to 2.51 (kcal.mol−1) and stabilization energies between 2 and 5 (kcal.mol−1) in the selected rare sugars at the DFT level of theory. The intramolecular H-bond distances, H-bond energies obtained from the AIM analysis, and also the second-order stabilization energies obtained from the NBO analysis were fluctuated largely depending on the basis set. In summary, it was found that the use of 6–311 ++ G(d,p) basis set to be more efficient results in rare sugars geometry than the 6-31G* basis set. [ABSTRACT FROM AUTHOR]

Pt(0) complexes have been widely used as catalysts for important reactions, such as the hydrosilylation of olefins. In this context, nuclear magnetic resonance (NMR) spectroscopy plays an important role in characterising of new structures and elucidating reaction mechanisms. In particular, the Pt-195 NMR is fundamental, as it is very sensitive to the ligand type and the oxidation state of the metal. In the present study, quantum mechanics computational schemes are proposed for the theoretical prediction of the Pt-195 NMR chemical shift and ¹J(195Pt-31P) in Pt(0) complexes. The protocols were constructed using the B3LYP/LANL2DZ/def2-SVP/IEF-PCM(UFF) level for geometry optimization and the GIAO-PBE/NMR-DKH/IEF-PCM(UFF) level for NMR calculation. The NMR fundamental quantities were then scaled by empirical procedures using linear correlations. For a set of 30 Pt(0) complexes, the results showed a mean absolute deviation (MAD) and mean relative deviation (MRD) of only 107 ppm and 2.3%, respectively, for the Pt-195 NMR chemical shift. When the coupling constant is taken into account, the MAD and MRD for a set of 33 coupling constants in 26 Pt(0) complexes were of 127 Hz and 3.3%, respectively. In addition, the models were validated for a group of 17 Pt(0) complexes not included in the original group that had MAD/MRD of 92 ppm/1.7% for the Pt-195 NMR chemical shift and 146 Hz/3.6% for the ¹J(195Pt-31P). [ABSTRACT FROM AUTHOR]

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An extended benchmark study has been performed to find out a robust and accurate density functional for calculating the standard reduction potentials of vanadium compounds. Twenty eight density functionals of various types were chosen for testing. The effect of the functional nature, size of the basis set, and inclusion of dispersion interaction in the calculation on the accuracy of the results were studied. Among the tested functionals the smallest deviation from the experimental data was found for the meta-NGA functional MN12-L. Based on these results, the computational protocol was proposed for studies of the redox reactions of vanadium compounds. [ABSTRACT FROM AUTHOR]

In an effort to assist researchers in choosing basis sets for quantum mechanical modeling of molecules (i.e. balancing calculation cost versus desired accuracy), we present a systematic study on the accuracy of computed conformational relative energies and their geometries in comparison to MP2/CBS and MP2/AV5Z data, respectively. In order to do so, we introduce a new nomenclature to unambiguously indicate how a CBS extrapolation was computed. Nineteen minima and transition states of buta-1,3-diene, propan-2-ol and the water dimer were optimized using 45 different basis sets. Specifically, this includes one Pople (i.e. 6-31G(d)), 8 Dunning (i.e. VXZ and AVXZ, X = 2–5), 25 Jensen (i.e. pc-n, pcseg-n, aug-pcseg-n, pcSseg-n, and aug-pcSseg-n, n = 0–4), and 9 Karlsruhe (e.g. def2-SV(P), def2-QZVPPD) basis sets. The molecules were chosen to represent both common and electronically diverse molecular systems. In comparison to MP2/CBS relative energies computed using the largest Jensen basis sets (i.e. n = 2,3,4), the use of smaller sizes (n = 0,1,2 and n = 1,2,3) provides results that are within 0.11–0.24 and 0.09–0.16 kcal ⋅ mol − 1 . To practically guide researchers in their basis set choice, an equation is introduced that ranks basis sets based on a user-defined balance between their accuracy and calculation cost. Furthermore, we explain why the aug-pcseg-2, def2-TZVPPD and def2-TZVP basis sets are very suitable choices to balance speed and accuracy. [ABSTRACT FROM AUTHOR]

Pt(0) complexes have been widely used as catalysts for important reactions, such as the hydrosilylation of olefins. In this context, nuclear magnetic resonance (NMR) spectroscopy plays an important role in characterising of new structures and elucidating reaction mechanisms. In particular, the Pt-195 NMR is fundamental, as it is very sensitive to the ligand type and the oxidation state of the metal. In the present study, quantum mechanics computational schemes are proposed for the theoretical prediction of the Pt-195 NMR chemical shift and 1J(195Pt–31P) in Pt(0) complexes. The protocols were constructed using the B3LYP/LANL2DZ/def2-SVP/IEF-PCM(UFF) level for geometry optimization and the GIAO-PBE/NMR-DKH/IEF-PCM(UFF) level for NMR calculation. The NMR fundamental quantities were then scaled by empirical procedures using linear correlations. For a set of 30 Pt(0) complexes, the results showed a mean absolute deviation (MAD) and mean relative deviation (MRD) of only 107 ppm and 2.3%, respectively, for the Pt-195 NMR chemical shift. When the coupling constant is taken into account, the MAD and MRD for a set of 33 coupling constants in 26 Pt(0) complexes were of 127 Hz and 3.3%, respectively. In addition, the models were validated for a group of 17 Pt(0) complexes not included in the original group that had MAD/MRD of 92 ppm/1.7% for the Pt-195 NMR chemical shift and 146 Hz/3.6% for the 1J(195Pt–31P).

Nowadays cardiovascular diseases are the main cause of death among the population around the word. The development of new drugs, giving a possibility to normalize blood pressure, is a promising direction in the field of pharmacy and medicine. Now inhibitors of angiotensinconverting enzyme (ACE) are widely adopted for the treatment of hypertension and chronic heart failure. The principle of action of ACE inhibitors is based on blocking the conversion of angiotensin I into angiotensin II, which mediates vasodilation.The aim of the work is a selection of methods of lisinopril interaction with the active center of angiotensin-converting enzyme by molecular dynamics methods.Materials and methods. Lisinopril molecule was used as a ligand; the charges of that ligand were calculated with the density functional theory (DFT) and ub3lyp method with the basis sets 6-31G* and 6-311G**. Simulation of 75 ns of molecular dynamics of lisinopril interaction with the active center of ACE was carried out in the Bioevrica program. As a result of molecular dynamics simulation, the trajectory of the “lisinopril-ACE” system was obtained. After that a comparison of ligand conformations at different points in simulation time with the experimental conformation of the value of standard deviation of coordinates of atoms was made.Results and discussion.The results of simulation have showed that lisinopril with the charges corresponding to basis set 6-311G** behaves consistent with the x-ray data in the active center of the ACE, in contrast to lisinopril with the charges calculated by basis set 6-31G*.Conclusion. The methods of lisinopril interaction modeling with the active center of angiotensin-converting enzyme has been selected. The obtained technique can be used for studying the interaction of substances, similar in structure to lisinopril with the active center of the enzyme (ACE).

Abstract: The new approach for the determination of orbital exponents and contracted coefficients for STO-3G family basis sets has been proposed. Calculations of the necessary coefficients have been performed using Mathcad program package with Minerr solving block. This approach has been used to perform the approximation of the Slater-type orbital (STO) by three Gaussian-type orbitals (GTO). The performance of such modified basis sets has been tested for the calculations of atomic energies using STO(0)-3G basis set and for nuclear magnetic shielding tensors using STO(1M)-3G basis set. The obtained atomic energies are characterized by lower values than those calculated using old parameters. The results for 1H and 13C chemical shifts calculations demonstrate better agreement with the experimental data compared to the data obtained using standard basis sets, such as 6-311G (2d, p), cc-pVDZ and pcS-1. Required time of calculations using the basic set suggested by us is less than the time spent on the calculation using standard basic sets with a similar number of basis functions. Physically adapted and at the same time small by size basic set STO(1M)-3G is perspective for the calculation of magnetic properties of big molecular systems. Proton and 13C chemical shifts have been calculated for molecules of adenosine monophosphate (AMP) and flavinadenine dinucleotide (FAD), that play an important role in various biological processes. For both molecules the results of the calculation have shown values close to the experimental data. [ABSTRACT FROM AUTHOR]