Extended Basis Sets Research Articles

Novel complex compounds of nickel with 3-(1-phenyl-2,3-dimethyl-pyrazolone-5)azopentadione-2,4: synthesis, NBO analysis, reactivity descriptors and in silico and in vitro anti-cancer and bioactivity studies

A synthesized azo compound based on 4-amino antipyrine and its complexes with Ni(II) in solution and solid phase is reported. The structures of these compounds have been testified by IR and NMR spectroscopy. The combined experimental and theoretical approach was used. To study the structure and properties of the synthesized compound, as well as its possible complex formation with the Ni(II), ab initio quantum-chemical calculations were carried out using the Hartree-Fock (HF) method with the 6-31 G basis set and the electron density functional theory (DFT) method with hybrid three-parameter potential B3LYP and extended basis set 6-311++G(d,p) taking into account polarization and diffuse functions for all atoms. The geometric, energy, and electronic parameters were calculated and analyzed. The HOMO-LUMO energy gap has been calculated to determine chemical activity. Both complexes had effective inhibition against butyrylcholinesterase and acetylcholinesterase. IC50 values were found as 19.43 and 27.08 µM for AChE, 2.37 and 7.40 µM for BChE, respectively. For the anticancer outcome, high doses of compound E1 inhibited viability by about 40–45%, while this rate was around 65–70% for compound E2 at the same doses. Anticholinesterase and anticancer potential of compounds E1 and E2 also evaluated by in silico techniques. Both compounds show strong binding to VEGFR1, with E2 exhibiting superior inhibitory activity in hAChE and hBChE through shorter and stronger interactions. MD simulations suggest that E2 forms more stable complexes with hAChE and hBChE compared to E1, making it a promising candidate for further exploration in anticancer and anticholinesterase therapies. Communicated by Ramaswamy H. Sarma

Effect of Benzothiadiazole-Based π-Spacers on Fine-Tuning of Optoelectronic Properties of Oligothiophene-Core Donor Materials for Efficient Organic Solar Cells: A DFT Study.

In this work, five novel A-π-D-π-A type molecules D1-D5 were designed by adding unusual benzothiadiazole derivatives as π-spacer blocks to the efficient reference molecule DRCN5T for application as donor materials in organic solar cells (OSCs). Based on a density functional theory approach, a comprehensive theoretical study was performed with different functionals (B3LYP, B3LYP-GD3, B3LYP-GD3BJ, CAM-B3LYP, M06, M062X, and wB97XD) and with different solvent types (PCM and SMD) at the extended basis set 6-311+g(d,p) to evaluate the structural, optoelectronic, and intramolecular charge transfer properties of these molecules. The B3LYP-GD3BJ hybrid functional was used to optimize the studied molecules in CHCl3 solution with the SMD model solvent as it provided the best results compared to experimental data. Transition density matrix maps were simulated to examine the hole-electron localization and the electronic excitation processes in the excited state, and photovoltaic parameters including open-circuit photovoltage and fill factor were investigated to predict the efficiency of these materials. All the designed materials showed promising optoelectronic and photovoltaic characteristics, and for most of them, a red shift. Out of the proposed molecules, [1,2,5]thiadiazolo[3,4-d]pyridazine was selected as a promising π-spacer block to evaluate its interaction with PC61BM in a composite to understand the charge transfer between the donor and acceptor subparts. Overall, this study showed that adding π-spacer building blocks to the molecular structure is undoubtedly a potential strategy to further enhance the performance of donor materials for OSC applications.

MP2-Based Correction Scheme to Approach the Limit of a Complete Pair Natural Orbitals Space in DLPNO-CCSD(T) Calculations.

The domain-based local pair natural orbital (PNO) coupled-cluster DLPNO-CCSD(T) method has been proven to provide accurate single-point energies at a fraction of the cost of canonical CCSD(T) calculations. However, the desired "chemical accuracy" can only be obtained with a large PNO space and extended basis set. We present a simple yet accurate and efficient correction scheme based on a perturbative approach. Here, in addition to DLPNO-CCSD(T) energy, one calculates DLPNO-MP2 correlation energy with the same settings as in the preceding coupled-cluster calculation. In the next step, the canonical MP2 correlation energy is obtained in the same orbital basis. This can be efficiently performed for essentially all molecule sizes accessible with the DLPNO-CCSD(T) method. By taking the difference between the canonical MP2 and DLPNO-MP2 energies, we obtain a correction term that can be added to the DLPNO-CCSD(T) correlation energy. This way, one can obtain the total correlation energy close to the limit of the complete PNO space (cPNO). The presented approach allows us to significantly increase the accuracy of the DLPNO-CCSD(T) method for both closed- and open-shell systems. The latter are known to be especially challenging for locally correlated methods. Unlike the previously developed PNO extrapolation procedure by Altun, Neese, and Bistoni ( J. Chem. Theory Comput. 2020, 16, 6142-6149), this strategy allows us to get the DLPNO-CCSD(T) correlation energy at the cPNO limit in a cost-efficient way, resulting in a minimal overall increase in calculation time as compared to the uncorrected method.

RETRACTED:Exploring the intermolecular interactions in carbon disulfide dimer: An ab initio study using an improved Lennard–Jones potential energy surface for physical insights

AbstractCarbon disulfide dimer (CS2)2 is a model system that has been widely studied in the field of computational chemistry because of its relevance to a variety of chemical and biological processes. The (CS2)2 dimer is a relatively simple molecular system composed of two carbon disulfide (CS2) molecules interacting with each other through intermolecular forces. Despite its apparent simplicity, the (CS2)2 dimer exhibits a rich array of structural and dynamical properties that are of great interest to researchers. In this research, we present an ab initio study of the intermolecular interactions in the carbon disulfide dimer (CS2)2 using an improved Lennard–Jones (ILJ) potential with CCSD(T)/QZVPP calculations. The potential energy surface of (CS2)2 is calculated using high‐level quantum mechanical calculations based on the CCSD(T)/def2‐qzvpp method, which accurately accounts for electron correlation effects. The resulting potential energy surface is then fitted to an ILJ potential energy function, which includes both long‐range dipole–dipole interactions and short‐range repulsive interactions. The calculated potential energy surface reveals a rich variety of structural and dynamical properties of (CS2)2, including multiple minima and saddle points, which are sensitive to the relative orientation of the two CS2 molecules. It is essential to use extended basis sets to accurately incorporate the significant quadrupole moment of CS2, which we have calculated to be 2.44 a.u. The results of this study demonstrate the importance of using high‐level ab initio methods for the accurate calculation of potential energy surfaces in complex molecular systems such as (CS2)2. The use of an ILJ potential, which takes into account both dipole–dipole interactions and short‐range repulsive interactions, provides a more accurate and efficient approach for modeling intermolecular interactions in (CS2)2 and other similar systems. The results of this study will be useful for understanding the behavior of carbon disulfide dimers in different environments and for the development of new materials and chemical processes.

Effects of non-ideality of classical plasmas on the 1Se resonance states in H−

The effects of the non-ideality (NI) of the classical plasmas on the 1Se resonance states of the negative ion of hydrogen (H−) have been investigated theoretically by using the stabilization method. The organized effect of the plasma charged particles is represented by a pseudopotential, which depends on the Debye length D and the non-ideality parameter γ. Densities of the resonance states as a function of D and γ are calculated by employing a highly correlated and extensive basis set. Convergence of the resonance parameters (energy and width) is ensured by increasing the number of terms in the basis. Three 1Se resonance states are found to emerge below the H(4S) excitation threshold. Our present results for lowest lying resonance for plasma-free cases as well as in weakly coupled plasmas are in excellent agreement with the established results in the literature. An extensive study is carried out to explore the changes in the resonance parameters of the three states due to the effects of plasma NI. It is found that, for a given Debye length, the resonance energy increases, and the resonance width decreases with increasing plasma non-ideality.

Electron Attachment to DNA: The Protective Role of Amino Acids.

We have studied the effect of amino acids on the electron attachment properties of a DNA nucleobase, with cytosine as a model system. The equation of motion coupled cluster theory with an extended basis set has been used to simulate the electron-attached state of the DNA model system. Arginine, alanine, lysine, and glycine are the four amino acids considered to investigate their role in electron attachment to a DNA nucleobase. The electron attachment to cytosine in all the four cytosine-amino acid gas-phase dimer complexes follows a doorway mechanism, where the electron gets transferred from the initial dipole-bound doorway state to the final nucleobase-bound state through the mixing of electronic and nuclear degrees of freedom. When cytosine is bulk-solvated with glycine, the glycine-bound state acts as the doorway state, where the initial electron density is localized on the bulk amino acid and away from the nucleobase, thus leading to the physical shielding of the nucleobase from the incoming electron. At the same time, the presence of amino acids can increase the stability of the nucleobase-bound anionic state, which can suppress the sugar-phosphate bond rupture caused by dissociative electron attachment to DNA.

Electron Attachment to Wobble Base Pairs

We have analyzed the low-energy electron attachment to wobble base pairs using the equation of motion coupled cluster method and extended basis sets. A doorway mechanism exists for the attachment of the additional electron to the base pairs, where the initially formed dipole-bound anion captures the incoming electron. The doorway dipole-bound anionic state subsequently leads to the formation of a valence-bound state, and the transfer of extra electron occurs by mixing of electronic and nuclear degrees of freedom. The formation of the valence-bound anion is associated with proton transfer in hypoxanthine-cytosine and hypoxanthine-adenine base pairs, which happens through a concerted electron-proton transfer process. The calculated rate constant for the dipole-bound to valence-bound transition in wobble base pairs is slower than that observed in the Watson-Crick guanine-cytosine base pair.

Теоретическое квантово-химическое моделирование структуры и свойств дипептида карнозина методом DFT

The spatial and electronic structure of the natural carnosine dipeptide in the N3H tautomeric form of its imidazole ring in gas and water environment was studied by the quantum-chemical method in the framework of the electron density functional theory (DFT) with the three-parameter B3LYP hybrid functional. The sufficiently reliable and time-saving extended basis set, taking into account the polarization and diffuse functions 6-31+G (d, p) was used for calculations. All calculations were carried our using the Gaussian 09 software package. GaussView 6.0.16 was used to visualize the obtained results. Geometrical parameters, values of electronic energy, energies of HOMO and LUMO orbitals and the energy gap between them, reactivity descriptors, values of dipole moments, partial charges on atoms, and theoretical IR spectra for gaseous and aqueous media are obtained. Calculations show that the proposed model of the molecule forms a stable structure. The resulting structure is stabilized due to non-covalent interactions in the dipeptide. Molecular electrostatic potential maps (MEP) are constructed to identify potential binding sites. To study the charge transfer and intramolecular interactions that determine the stability of the molecule, an analysis of natural bond orbitals (NBOs) was carried out. Structural rearrangements and changes in various parameters depending on the dielectric constant of the medium are analyzed.

Microsolvation of electrons by a handful of ammonia molecules.

Microsolvation of electrons in ammonia is studied here via anionic NH3 n - clusters with n = 2-6. Intensive samplings of the corresponding configurational spaces using second-order perturbation theory with extended basis sets uncover rich and complex energy landscapes, heavily populated by many local minima in tight energy windows as calculated from highly correlated coupled cluster methods. There is a marked energetical preference for structures that place the excess electron external to the molecular frame, effectively coordinating it with the three protons from a single ammonia molecule. Overall, as the clusters grow in size, the lowest energy dimer serves as the basic motif over which additional ammonia molecules are attached via unusually strong charge-assisted hydrogen bonds. This is apriori quite unexpected because, on electrostatic grounds, the excess electron would be expected to be in contact with as many protons as possible. Accordingly, a full quantum mechanical treatment of the bonding interactions under the tools provided by the quantum theory of atoms in molecules is carried out in order to dissect and understand the nature of intermolecular contacts. Vertical detachment energies reveal bound electrons even for n = 2.

X-ray photoelectron spectroscopy of Thymine and 5-Bromouracil studied by Symmetry-Adapted-Cluster Configuration-Interaction (SAC-CI) theory

The X-ray Photoelectron Spectra (XPS) of thymine (T) and 5-Bromouracil (BrU) were studied and assigned using Symmetry-Adapted-Cluster Configuration-Interaction (SAC-CI) theory. The differences between theory and experiment were within 1.0 eV when compared with the spectra measured in vacuum conditions. It was clarified that inner-core ionization processes involve many electronic processes like ionizations, accompanying excitations, reorganizations, and electron correlations. Therefore, accurate calculations require both good theory and good basis set. The present SAC-CI calculations with extended basis sets including even Rydberg basis functions may satisfy these requirements.

2,15-dibutoxy-6,11-dicyano[6]Helicene: Synthesis, electrochemical, photophysical properties and computational studies

2,15-Dibutoxy-6,11-dicyano[6]Helicene (CN-HEL) has been prepared through a two-step sequence under mild conditions, in an overall 78% yield, starting from 2,7-bis(cyanomethyl)naphthalene as a suitable material. The Helicene has been experimentally characterized and its absorption and photoluminescence (PL) properties have been evaluated showing a blue emission in the visible spectrum. A strong absorption is entirely in the UV region (λmax = 290 nm), yet fluorescence occurs at 400 nm. This equates to a Stokes shift of 1.17 eV (9482 cm−1) which is among the largest Stokes shifts reported for small molecules, making it a promising candidate for optoelectronic applications. Furthermore, the 1H NMR, FT-IR, UV-vis and PL spectra were computed by means of the very efficient time-dependent density functional theory (TD-DFT) approach. The computed spectra with two recommended density functional (PBEPBE and cam/B3LYP) and extended basis sets compare very well with the corresponding experimental data. HOMO and LUMO energy levels were also investigated experimentally, showing an electrochemical band gap of 2.54 eV. Results obtained throughout this work are of great importance and prove the relevance of the target Helicene to be used in a wide range of both existing and new applications such as fluorescence probes and molecular sensors.

A Comparative study of the characteristic vibrations of methyl acrylate, methyl methacrylate, methyl trans crotonate and methyl -3-methoxy-2-propenoate

A relative quantum chemical study of the vibrational spectra of of methyl acrylate (MA), methyl methacrylate (MMA), methyl trans crotonate (MTC) and methyl -3-methoxy-2-propenoate(MMP) in their electronic ground state has been reported. Based on the Hartree-Fock and Density Functional Theory with extended basis sets and polarization functions calculations the results of the possible conformers are compared in terms of frequency, form and intensity of vibrations and potential energy distribution across the symmetry coordinates in ground state. A relationship between the bond length and bond order is also studied.

Analysis of Conformational Preferences in Caffeine.

High level DLPNO–CCSD(T) electronic structure calculations with extended basis sets over B3LYP–D3 optimized geometries indicate that the three methyl groups in caffeine overcome steric hindrance to adopt uncommon conformations, each one placing a C–H bond on the same plane of the aromatic system, leading to the C–H bonds eclipsing one carbonyl group, one heavily delocalized C–N bond constituent of the fused double ring aromatic system, and one C–H bond from the imidazole ring. Deletion of indiscriminate and selective non-Lewis orbitals unequivocally show that hyperconjugation in the form of a bidirectional –CH aromatic system charge transfer is responsible for these puzzling conformations. The structural preferences in caffeine are exclusively determined by orbital interactions, ruling out electrostatics, induction, bond critical points, and density redistribution because the steric effect, the allylic effect, the Quantum Theory of Atoms in Molecules (QTAIM), and the non-covalent interactions (NCI), all predict wrong energetic orderings. Tiny rotational barriers, not exceeding 1.3 kcal/mol suggest that at room conditions, each methyl group either acts as a free rotor or adopts fluxional behavior, thus preventing accurate determination of their conformations. In this context, our results supersede current experimental ambiguity in the assignation of methyl conformation in caffeine and, more generally, in methylated xanthines and their derivatives.

Photodetachment of H− in non-ideal classical plasmas

The effects of non-ideality of classical plasmas on the cross sections of the photodetachment of the negative ion of hydrogen (H−) have been investigated within the framework of the dipole approximation. An effective potential, deduced from a solution of Bogolyubov's hierarchy equations, has been used to model the interactions among the charged particles in the non-ideal classical plasmas. Wave functions and energies of H−(1S) and H(1s) are calculated accurately by employing extensive basis sets within the framework of Ritz's variational principle. A detailed study is made on the changes of photodetachment cross section due to the varying non-ideality of plasma in a wide range. It is found that the wavelength corresponding to the maximum value of the photodetachment cross section moves forward due to the increasing non-ideality of plasma.

A black-box, general purpose quadratic self-consistent field code with and without Cholesky decomposition of the two-electron integrals

We present the implementation of a quadratically convergent self-consistent field (QCSCF) algorithm based on an adaptive trust-radius optimisation scheme for restricted open-shell Hartree–Fock (ROHF), restricted Hartree–Fock (RHF), and unrestricted Hartree–Fock (UHF) references. The algorithm can exploit Cholesky decomposition (CD) of the two-electron integrals to allow calculations on larger systems. The most important feature of the QCSCF code lies in its black-box nature – probably the most important quality desired by a generic user. As shown for pilot applications, it does not require one to tune the self-consistent field (SCF) parameters (damping, Pulay's DIIS, and other similar techniques) in difficult-to-converge molecules. Also, it can be used to obtain a very tight convergence with extended basis sets – a situation often needed when computing high-order molecular properties – where the standard SCF algorithm starts to oscillate. Nevertheless, trouble may appear even with a QCSCF solver. In this respect, we discuss what can go wrong, focusing on the multiple UHF solutions of ortho-benzyne.

Modeling of photoabsorption spectra of small helium cluster cations through ab initio and semi-empirical approaches. A comparative study

A comparative study has been performed to assess the reliability of a diatomics-in-molecules (DIM) representation of the potential energy surfaces in calculations of the photoabsorption spectra of selected charged helium clusters, He N + ( N = 3 , 4 , 10 ). Results of the computationally cheap DIM approach have been compared to data resulting from accurate ab initio methods (MRCI, EOM-CCSD) and extended basis sets (up to d-aug-cc-pVQZ). Both single-point calculations and averaged photoabsorption spectra calculations have been performed to observe the effect of approximations employed within the DIM approach. DIM predictions of photoabsorption spectra are in a fairly good agreement with the ab initio ones, which seems to indicate that the semi-empirical DIM approach is suitable for simulating larger ionic helium clusters for which more elaborate ab initio models are not practicable.

57Fe Mössbauer isomer shift of pure iron and iron oxides at high pressure-An experimental and theoretical study.

The 57Fe isomer shift (IS) of pure iron has been measured up to 100GPa using synchrotron Mössbauer spectroscopy in the time domain. Apart from the expected discontinuity due to the α → ε structural and spin transitions, the IS decreases monotonically with increasing pressure. The absolute shifts were reproduced without semi-empirical calibrations by periodic density functional calculations employing extensive localized basis sets with several common density functionals. However, the best numerical agreement is obtained with the B1WC hybrid functional. Extension of the calculations to 350GPa, a pressure corresponding to the Earth's inner core, predicted the IS range of 0.00 to -0.85 mm/s, covering the span from Fe(0) to Fe(VI) compounds measured at ambient pressure. The calculations also reproduced the pressure trend from polymorphs of prototypical iron oxide minerals, FeO and Fe2O3. Analysis of the electronic structure shows a strong donation of electrons from oxygen to iron at high pressure. The assignment of formal oxidation to the Fe atom becomes ambiguous under this condition.

Compound-tunable embedding potential method and its application to calcium niobate crystal CaNb2O6 with point defects containing tantalum and uranium

The compound-tunable embedding potential (CTEP) method developed for simulating the influence of environment on a fragment in the ionic-covalent crystal is presented in the form of a linear combination of particular short-range semilocal pseudopotentials for the atoms of nearest environment and the long-range Coulomb potentials from optimized fractional point charges centered on both nearest and more distant atoms of the environment. A pilot application of the CTEP method to calcium niobate crystal, ${\mathrm{CaNb}}_{2}{\mathrm{O}}_{6}$, is performed. A very good agreement of the electronic density and interatomic distances within the relaxed fragment with those of the original periodic crystal calculation is attained. Calcium niobate crystal can be considered as an idealized fersmite $({\mathrm{CaNb}}_{2\ensuremath{-}x}{\mathrm{Ta}}_{x}{\mathrm{O}}_{6},x\ensuremath{\approx}0.3)$ mineral when neglecting the contributions of the impurities with smaller molar fractions, and substitution $\mathrm{Nb}\ensuremath{\rightarrow}\mathrm{Ta}$ is considered here as a point Ta defect in ${\mathrm{CaNb}}_{2}{\mathrm{O}}_{6}$. Besides, uranium-containing point defects are also studied since the euxenite group minerals, to which fersmite belongs, are considered as prospective matrices for long-term immobilization of high-level waste. The chemical shifts of ${K}_{{\ensuremath{\alpha}}_{1,2}}$ and ${K}_{{\ensuremath{\beta}}_{1,2}}$ lines of x-ray emission (fluorescence) spectra in niobium are evaluated to analyze its chemical state in the crystal. Potential of CTEP for studying properties of point defects containing $f$ and heavy $d$ elements with relativistic effects, extended basis set, and broken crystal symmetry taken into account is discussed.

A trust-region augmented Hessian implementation for restricted and unrestricted Hartree-Fock and Kohn-Sham methods.

We present a new implementation of a trust-region augmented Hessian approach (TRAH-SCF) for restricted and unrestricted Hartree-Fock and Kohn-Sham methods. With TRAH-SCF, convergence can always be achieved even with tight convergence thresholds, which requires just a modest number of iterations. Our convergence benchmark study and our illustrative applications focus on open-shell molecules, also antiferromagnetically coupled systems, for which it is notoriously complicated to converge the Roothaan-Hall self-consistent field (SCF) equations. We compare the number of TRAH iterations to reach convergence with those of Pulay's original and Kollmar's (K) variants of the direct inversion of the iterative subspace (DIIS) method and also analyze the obtained SCF solutions. Often, TRAH-SCF finds a symmetry-broken solution with a lower energy than DIIS and KDIIS. For unrestricted calculations, this is accompanied by a larger spin contamination, i.e., larger deviation from the desired spin-restricted ⟨S2⟩ expectation value. However, there are also rare cases in which DIIS finds a solution with a lower energy than KDIIS and TRAH. In rare cases, both TRAH-SCF and KDIIS may also converge to a non-aufbau solution. For those calculations, standard DIIS always diverges. For cases that converge smoothly with either method, TRAH usually needs more iterations to converge than DIIS and KDIIS because for every new set of orbitals, the level-shifted Newton-Raphson equations are solved approximately and iteratively. In such cases, the total runtime of TRAH-SCF is still competitive with the DIIS-based approaches even if extended basis sets are employed, which is illustrated for a large hemocyanin model complex.

The Vibronic Absorption Spectrum and Electronic States of Nile Red in Aqueous Solution

AbstractThe TD‐DFT was applied to calculate the vibronic absorption spectrum of Nile red (NR) in an aqueous solution. Various hybrid functionals have been used. The O3LYP/6‐31G(d,p) theory level gave an excellent agreement with the experimental absorption spectrum both in the position of the maximum and in the shape. Extended basis sets with diffuse functions and showed the worst results compared to the compact 6‐31G(d,p) basis. The dipole moments and atomic charges of the ground and excited states of the NR molecule have been calculated. According to our calculations, the dipole moment of a molecule increases upon photoexcitation, which is consistent with the positive solvatochromism of NR. An insignificant photoinduced electron transfer from the aminodiethyl group to the center of the chromophore and carbonyl group was found. According to our calculations, vibronic coupling plays a significant role in the absorption spectrum of the NR.