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Self-consistent molecular orbital methods 25. Supplementary functions for Gaussian basis sets
Abstract
Standard sets of supplementary diffuse s and p functions, multiple polarization functions (double and triple sets of d functions), and higher angular momentum polarization functions (f functions) are defined for use with the 6‐31G and 6‐311G basis sets. Preliminary applications of the modified basis sets to the calculation of the bond energy and hydrogenation energy of N2 illustrate that these functions can be very important in the accurate computation of reaction energies.
... IPs can exist as an equilibrium of E-and Z-isomers (Table 1) [9]. The assignment of IPs to Z-or E-isomers has recently been performed by means of 19 F and 31 P NMR spectroscopy [9,11,12]. The resonance signals of phosphorus and fluorine nuclei in Z-isomers of IPs (δР−0.1-3.3 ppm, δF−66.2-70.2 ...
... The isomeric ratio is determined by the nature of the substituents at the C = N double bond, and the decisive contribution to the stability of each of the isomers belongs to the substituent R 2 (Scheme 1). Thus, it is known that most derivatives with R 2 = aryl exist mainly in the E-form [Z/E ≈ 1: (12)(13)(14)(15)(16)(17)(18)(19)(20)], while IPs with fluoroalkyl R 2 groups are preferably Z-isomers [Z/E ≈ (6-10):1] ( Table 1). The variation of the alkyl substituent R 3 in the phosphoryl group has little effect, while the nature of the fluoroalkyl group R 2 can significantly influence the Z/E-isomeric ratio for IPs. ...
... All of the calculations were performed with the GAUSSIAN-09 set of programs [17]. The M062X [15,16] function in combination with 6-31+G** basis sets [18,19] were used for the geometry optimization and calculations of the vibrational frequencies. The equilibrium structures were utilized for the generation of the PROAIMS wave function files (wfn) at the RHF/6-31G* level of theory. ...
Esters of iminophosphonic acids (iminophosphonates, or IPs), including a fragment, >P(=O)-C=N, can be easily functionalized, for instance to aminophosphonic acids with a wide range of biological activity. Depending on the character of the substitution, the Z- or E-configuration is favorable for IPs, which in turn can influence the stereochemistry of the products of chemical transformations of IPs. While the Z,E-isomerism in IPs has been thoroughly studied by NMR spectroscopy, the factors stabilizing a definite isomer are still not clear. In the current work, density functional theory (DFT, using M06-2X functional) and ab initio spin-component–scaled second-order Møller–Plesset perturbation theory (SCS-MP2) calculations were carried out for a broad series of IPs. The calculations reproduce well a subtle balance between the preferred Z-configuration inherent for C-trifluoromethyl substituted IPs and the E-form, which is more stable for C-alkyl- or aryl-substituted IPs. The predicted trend of changing activation energy values agrees well with the recently determined experimental ΔG≠298 magnitudes. Depending on the substitution in the aromatic moiety, the Z/E-isomerization of N-aryl-substituted IPs proceeds via two types of close-in energy transition states. Not a single main factor but a combination of various contributions should be considered in order to explain the Z/E-isomerization equilibrium for different IPs.
... The neutral indolizine BODIPY dyes (2Ph and 1Ph) and the dimethylaniline literature benchmark dye (DMA) were evaluated computationally to predict absorption maxima, HOMO and LUMO orbital localization, and protonation position. These data were determined by density functional theory (DFT) at the B3LYP/6-311G (d,p) level of theory with dichloromethane implicit solvation via a polarizable continuum model [30][31][32][33][34][35]. All neutral targets exhibited NIR (DMA = 708 nm, 2Ph = 765 nm, and 1Ph = 761 nm) vertical transitions, with the indolizine-based dyes exhibiting lower energy vertical transitions compared to the aniline benchmark. ...
... These geometries were then optimized with the MMFF94 force field via Avogadro (1.2.0). Accurate geometry optimization was performed sequentially by DFT using Gaussian 16 [50] with the B3LYP functional [30,31] with the following basis sets: first 3-21G, second 6-31G (d,p) [51,52], and finally 6-311G (d,p) [32]. These were all in dichloromethane as a polarizable continuum model (PCM) [33][34][35]. ...
Fluorescent organic dyes that absorb and emit in the near-infrared (NIR, 700–1000 nm) and shortwave infrared (SWIR, 1000–1700 nm) regions have the potential to produce noninvasive high-contrast biological images and videos. BODIPY dyes are well known for their high quantum yields in the visible energy region. To tune these chromophores to the NIR region, fused nitrogen-based heterocyclic indolizine donors were added to a BODIPY scaffold. The indolizine BODIPY dyes were synthesized via microwave-assisted Knoevenagel condensation with indolizine aldehydes. The non-protonated dyes showed NIR absorption and emission at longer wavelengths than an aniline benchmark. Protonation of the dyes produced a dramatic 0.35 eV bathochromic shift (230 nm shift from 797 nm to 1027 nm) to give a SWIR absorption and emission (λmaxemis = 1061 nm). Deprotonation demonstrates that material emission is reversibly switchable between the NIR and SWIR.
... Introduction liquid phases, have been done using both DFT and TD-DFT formalisms [15,[22][23][24]. He, Fan, and Tang (2010) studied the energetic contributions and structural changes caused by intramolecular HB between the atoms of the functional groups of ASP and found 122 stable geometries. ...
Hydrogen bonds (HB) influence the conformational preferences of biomolecules and their optical and electronic properties. The objective of this work is to study some structures and the S 1 ← S 0 electronic transitions of aspartic acid (ASP) and complexes formed by HB between ASP-(H 2 O) 1,2 in the gas phase. To do this, the DFT and TD-DFT methods were used, using the B3LYP functional with six different basis sets. Interactions between the carboxylic groups of ASP with water molecules, forming cyclic structures with two HB, resulted in more stable and less polar complexes, than other conformers with formed HB between water and the NH 2 group. It was observed that there is a relationship between the deviation in the UV-Vis absorption band of the ASP and the stabilization/destabilization of the S 1 state to the S 0 of the complexes. The electrostatic destabilization of the S 1 state and interactions of water with the HOMO orbital caused a blueshift in the ASP absorption band, while the electrostatic stabilization of the S 1 state and interactions with the LUMO caused a redshift. But in some cases, as it was observed on 1:1 complex ASP-W2, this analysis may not be precise due to the small change in ΔE.
... Hartree-Fock method. 92 Four different basis sets have been used: 6-311G, 6-311++G(d,p), [93][94][95][96][97] aug-cc-pVDZ, and aug-cc-pVTZ. [98][99][100][101][102][103][104][105] All Δ-SCF results were obtained using the PIMOM method. ...
SCF methods have proven to be reliable computational tools for the assignment and interpretation of photoelectron spectra of isolated molecules. These results have increased the interest in △SCF techniques for electronic excited states based on improved algorithms that prevent convergence to ground states. In this work, one of these △SCF improved algorithms is studied to demonstrate its ability to explore the molecular properties for excited states. Results from △SCF calculations for a set of representative molecules are compared with results obtained using time-dependent density functional theory and single substitution configuration interaction method. For the △SCF calculations, the efficacy of a spin-purification technique is explored to remedy some of the spin-contamination presented in some of the SCF solutions. The obtained results suggest that the proposed projection-based SCF scheme, in many cases, alleviates the spin--contamination present in the SCF single determinants, and provides a computational alternative for the efficient exploration of the vibrational properties of excited states molecules.
... The geometry optimization, frequency test, and electronic analysis were performed using the Gaussian 09 program package (Kitao et al., 2009). In this study, we have chosen the method of hybrid density functional theory (H-DFT) with all electron basis sets, such as M06 (long-range exchange functional) and 6-31 + G (d), respectively after DFT calibration (Frisch et al., 1984;Zhao and Truhlar, 2008). ...
The first ultrasonic synthesis of [Cu(L)4(SCN)2] (L = 1-methylimidazole) nanocomplex was carried out under ultrasonic irradiation, and its photocatalytic performance for the degradation of remdesivir (RS) under sunlight irradiation was comprehensively investigated for the first time in this study. The physicochemical properties of the synthesized photocatalyst were examined by Fourier-transform infrared (FT-IR), field emission scanning electron microscopy (FE-SEM), X-ray diffraction (XRD), energy-dispersive X-ray (EDX), diffuse reflectance spectroscopy (DRS), and thermogravimetric analysis (TGA) techniques. The band gap of the synthesized [Cu(L)4(SCN)2] nanocomplex was determined to be 2.60 eV by the diffuse reflectance spectroscopy method using Kubelka-Munk formula. The photocatalytic performance of nanocomplex was examined for the removal of remdesivir under sunlight from water for which the results indicated that an amount of 0.5 gL-1 of the [Cu(L)4(SCN)2] nanocomplex was sufficient to remove more than 96% remdesivir from its 2 mg L-1 concentration within 20 min, at pH = 6. The kinetic data showed that the photodegradation onto the [Cu(L)4(SCN)2] nanocomplex has a high correlation (0.98) with the pseudo-second-order kinetic model. The decrease in chemical oxygen demand (COD) (from 70.5 mg L-1 to 36.4 mg L-1) under optimal conditions clearly confirmed the mineralization of the RS drug. The values of ΔS° (-0.131 kJ mol-1 K-1) and ΔH° (-49.750 kJ mol-1) were negative, indicating that the adsorption process was spontaneous and more favorable in lower temperatures. Moreover, the RS structure in the open shell state and the high HOMO and LUMO gaps based on the M06/6-31 + G (d) level of theory may be a confirmation of this fact. In addition, the Hirshfeld surface analysis (HSA) of the crystal packing of the prepared complex was discussed in detail to evaluate the interactions between the crystal packings. The results of this study confirm that the [Cu(L)4(SCN)2] nanocomplex can be successfully used for the photodegradation of pharmaceutical contaminants.
... All DFT/B3LYP [22,23] computations of HFPB and its five Ni(II) complexes were performed by using the G09W package [23,24] at LANL2DZ [25] for heavy atoms and 6-31 + + G** [26,27] for the remaining atoms. In theoretical chemistry, the Koopmans' Theorem [28] is the first important step in the prediction of the chemical reactivity behavior thereby using the FMO energies to calculate the ionization energy "I" and electron affinities "A" as follow I = − E HOMO and A = − E LUMO . ...
Five new nickel(II) complexes have been synthesised with an NNO donor tridentate aroylhydrazone (HFPB) employing the chloride, nitrate, acetate and perchlorate salts, and all the complexes are physiochemically characterized. Elemental analyses suggested stoichiometries as Ni(FPB)(NO3)]·2H2O (1), [Ni(HFPB)(FPB)]Cl (2), [Ni(FPB)(OAc)(DMF)] (3), [Ni(FPB)(ClO4)]·DMF (4), [Ni(FPB)2] (5). Aroylhydrazone is found coordinating in deprotonated iminolate form in four of the complexes (1, 3, 4, 5) however in one case (complex 2), two aroylhydrazone moieties are binding to the metal centre in the neutral and anionic forms. The structure of the bisligated complex 5, found using single crystal X ray diffraction studies confirmed that the metal has a distorted octahedral N4O2 coordination environment, with each of the two deprotonated ligands coordinating through the pyridine nitrogen, imino-hydrazone nitrogen and the enolate oxygen of the hydrazone moiety. To compare and study, the electronic interactions and stabilities of the metal complexes, various quantum chemical parameters were calculated. Moreover, Hirshfeld surface analysis was carried out for complex 5 to determine the intermolecular interactions. The biophysical attributes of the ligand and complex 5 have been investigated with CT-DNA and experimental outcomes show that the Ni(II) complex exhibited higher binding propensity towards DNA as compared to ligand. Furthermore, to specifically understand the type of interactions of the metal complexes with DNA, molecular docking studies were effectuated. In addition, the electronic and related reactivity behaviors of the ligand and five Ni(II) complexes were studied using B3LYP/6–31 + + G**/LANL2DZ level. As expected, the obtained results from Natural Bond Orbital (NBO) computations displayed that the resonance interactions (n → π* and π → π*) play a determinant role in evaluating the chemical attributes of the reported compounds.
Graphical abstract
... The optimized geometry of 1, highest occupied and lowest unoccupied molecular orbital (HOMO and LUMO, respectively) surfaces, and a molecular electrostatic potential (MEP) surface were calculated without symmetry restrictions in gas phase with the GaussView 6.0 molecular visualization program 45 and Gaussian 09, Revision D.01 program package 46 using the DFT/B3LYP hybrid functional 47,48 and cc-pVDZ 47,49 basis set. ...
Unlabelled:
Synthesis, characterization and theoretical studies of a novel coumarin-triazole-thiophene hybrid 4-(((4-ethyl-5-(thiophen-2-yl)-4H-1,2,4-triazol-3-yl)thio)methyl)-6,7-dimethyl-2H-chromen-2-one (1), which was fabricated from 4-ethyl-5-(thiophen-2-yl)-4H-1,2,4-triazole-3-thiol and 4-(chloromethyl)-6,7-dimethyl-2H-chromen-2-one, are reported. The resulting compound was characterized by microanalysis, IR, 1H, and 13C APT NMR spectroscopy. The DFT calculations examined the structure and electronic properties of 1 in gas phase. Its reactivity descriptors and molecular electrostatic potential revealed the reactivity and the reactive centers of 1. ADMET properties of 1 were evaluated using the respective online tools. It was established that 1 exhibit positive gastrointestinal absorption properties and negative human blood-brain barrier penetration. The Toxicity Model Report revealed that 1 belongs to toxicity class 4. Molecular docking was additionally applied to study the interaction of 1 with some SARS-CoV-2 proteins. It was established that the title compound is active against all the applied proteins with the most efficient interaction with Papain-like protease (PLpro). The interaction of 1 with the applied proteins was also studied using molecular dynamics simulations.
Graphical abstract:
A novel coumarin-triazole-thiophene hybrid 4-(((4-ethyl-5-(thiophen-2-yl)-4H-1,2,4-triazol-3-yl)thio)methyl)-6,7-dimethyl-2H-chromen-2-one (1) is reported. The structure and electronic properties of 1 were examined by the DFT calculations. ADMET properties of 1 were also evaluated. Molecular docking and molecular dynamics simulations were applied to study interactions of 1 with a series of the SARS-CoV-2 proteins.
Supplementary information:
The online version contains supplementary material available at 10.1007/s12039-022-02127-0.
... For this purpose, the calculations were performed at the theoretical Density Functional Theory (DFT) and Time-Dependent Density Functional Theory (TD-DFT) level using the Gaussian 09 package [34]. The compounds lowest energy structure was obtained through calculations using the B3LYP [35][36][37] hybrid functional and the conventional Pople's 6-311G(d,p) base set [38]. In addition, vibrational frequency calculations were performed to confirm that the structures minimum energy nature reached [3]. ...
... In total, 12 AcO-DHEA, eight DHEA, 10 MTTT and four Epoxy-P4 candidates were generated after the initial CREST searches. The final geometry optimizations were carried out at the B3LYP [49,50]-D3BJ/def2-TZVPD [51], B3LYP-D3BJ/6-31++G(2d,p) [52], and/or B3LYP-D3BJ/cc-pVTZ [53] levels of theory with the polarizable continuum model (PCM) [54] of DMSO. The D3 dispersion correction [55,56] with the Becke-Johnson (BJ) damping function [57] was used. ...
Steroid hormone molecules may exhibit very different functionalities based on the associated functional groups and their 3D arrangements in space, i.e., absolute configurations and conformations. Infrared (IR) and vibrational circular dichroism (VCD) spectra of four different steroid hormones, namely dehydroepiandrosterone (DHEA), 17α-methyltestosterone (MTTT), (16α,17)-epoxyprogesterone (Epoxy-P4), and dehydroepiandrosterone acetate (AcO-DHEA), were measured in deuterated dimethyl sulfoxide and some also in carbon tetrachloride. Extensive conformational searches were carried out using the recent developed conformer-rotamer ensemble sampling tool (CREST) which also accounts for solvent effects using an implicit solvation model. All the CREST conformational candidates were then reoptimized at the B3LYP-D3BJ/def2-TZVPD with the PCM of solvent. The good agreements between the experimental IR and VCD spectra and the theoretical simulations provide a conclusive information about their conformational distribution and absolute configurations. The experimental and theoretical IR and VCD spectra of AcO-DHEA in the carbonyl and alkene stretching region showed some discrepancies, and the possible causes related to solvent effects, large amplitude motions and levels of theory used in the modelling were explored in detail. As part of the investigation, additional calculations at the B3LYP-D3BJ/6-31++G (2d,p) and B3LYP-D3BJ/cc-pVTZ levels, as well as some 'mixed' calculations with the double-hybrid functional B2PLYP-D3 were also carried out. The results indicate that the double-hybrid functional is important for predicting the correct IR band pattern in the carbonyl and alkene stretching region.
... The calculations were performed using Gaussian 09 package [24]. The geometry of gossypol was fully optimized using a B3LYP [25][26][27][28] 6-311+G(2d,p) [29][30][31][32] level of theory together with Grimme's D3 empirical dispersion correction [33]. Vibrational analysis was carried out to confirm the correspondence of the optimized structure to a minimum on the potential energy surface. ...
A new metal–organic framework based on cadmium(II) cations, di(p-carboxyphenyl)sulphone and 4,7-di(imidazol-1-yl)-2,1,3-benzothiadiazole was prepared, and its crystal structure was determined using single-crystal XRD analysis. MOF demonstrated bright luminescence with a maximum near 500 nm and quantum yield reaching 20%. In addition, this MOF demonstrated sensing properties towards antibiotics and a toxic natural polyphenol gossypol through effective luminescence quenching in an ethanol suspension. The determined detection limit for gossypol was among the lowest reported so far (0.65 µM), and did not significantly change in the interference experiments with cottonseed oil as background, indicating the possibility of using this MOF as a sensor for the detection and determination of gossypol in real-life samples.
... The exchange-correlation potential is incorporated using the hybrid B3LYP [8] functional. We used Stuttgart energyconsistent relativistic pseudopotentials and the corresponding valence basis sets of polarized double-ζ [9,10] for Au and the 6-311 + g(d,p) basis set [11][12][13][14] for F. This basis set was also used in our joint theory-experiment paper in Ref. 5, and the agreement between theory and experiment was very good. The effect of the diffuse functions on the vertical detachment energy (VDE) was recently tested by Rachel et al. [15], on UAu 6 . ...
Due to relativistic effects, Au exhibits unusual properties among the coinage metals. In addition to being reactive at the nanoscale, Au behaves like a hydrogen atom in small clusters. It was recently shown that in Au2Fn (n = 1, 2) clusters, one of the Au atoms behaves like a normal metal atom while the other behaves like a halogen. To see whether this behavior persists in clusters containing a larger number of Au and F atoms, we have carried out a comprehensive study of the equilibrium geometries and electronic structure of neutral and anionic Au2Fn (n = 1–11), Au3Fn (n = 1–4), and Au4Fn (n = 1–5) clusters as well as their corresponding electron affinities using density functional theory. As the number of F atoms exceeds the number of Au atoms, the Au–Au bonds become weak and in most cases break, while those that exist are between the Au and F atoms. Analogous to Au2Fn (n = 1, 2) clusters, the Au atoms in the above neutral clusters carry a positive charge, but their amount depends upon the relative composition of AumFn clusters; the Au atoms bonded to F carry a larger charge than that bonded to an Au atom. In clusters where no Au–Au bonds exist, the Au atom bonded to more F atoms carries a larger positive charge than those bonded to a lesser number of F atoms. In anionic clusters, the situation is different; when the number of F atoms is less than or equal to the Au atoms, the Au atom bonded to F carries a positive charge while the other(s) carry a negative charge, mimicking the chemistry of halogens. This Janus behavior of Au in terms of the charge they carry depends upon the relative abundance of Au and F and is attributed to the relativistic effects. Equally interesting, contrary to the conventional rule, the electron affinities of Au3Fn (n = 2–4) and Au4Fn (n = 1, 3) clusters are larger than that of Cl, making them superhalogens.
... The Known Drug Indexes (KDI) were calculated from the molecular descriptors as described by Eurtivong and Reynisson [53] For application in Excel, columns for each property were created and the following equations used do derive the KDI numbers for each descriptor: The Gaussian 16 software suite [83] was used with unrestricted DFT. The B3LYP functional hybrid approach was employed [84][85][86] and standard 6-31+G(d,p) diffused basis set [87,88] was used for geometry optimization and frequency analysis (keywords: opt freq). The zero-point vibrational energies (ZPE) were scaled according to Wong (0.9804) [89]. ...
A series of latonduine derivatives, namely 11-nitro-indolo[2,3-d]benzazepine-7-(1-amino-hydantoin) (B), triazole-fused indolo[2,3-d]benzazepine-based Schiff bases HL1 and HL2 and metal complexes [M(p-cymene)(HL1)Cl]Cl, where M = Ru (1), Os (2), and [Cu(HL2)Cl2] (3) were synthesized and characterized by spectroscopic techniques (UV–vis, 1H, 13C, 15N–1H HSQC NMR) and ESI mass spectrometry. The molecular structures of B and HL1 were confirmed by single-crystal X-ray diffraction, while that of 3 by electron diffraction of nanometer size crystalline sample. Molecular docking calculations of species B in the binding pocket of PIM-1 enzyme revealed that the 1-amino-hydantoin moiety is not involved in any hydrogen-bonding interactions, even though a good accommodation of the host molecule in the ATP binding pocket of the enzyme was found. The antiproliferative activity of organic compounds B, HL1 and HL2, as well as complexes 1–3 was investigated in lung adenocarcinoma A549, colon adenocarcinoma LS-174 and triple-negative breast adenocarcinoma MDA-MB-231 cells and normal human lung fibroblast cells MRC-5 by MTT assays; then, the results are discussed.
... Optimization of geometries for MECP between the T 1 and S 0 states is carried out by the sobMECP program, 65 which is the modied version of the Harvey's MECP code. 66 In all the DFT calculations, the B3LYP/6-311++G(d,p) level of theory [67][68][69][70][71][72][73] is used for all the geometry optimization and energies computation, which is implemented using the Gaussian 09 program. 74 In addition, linear response time-dependent density functional theory (LR-TDDFT) 75 is employed to predict the spectroscopic properties of NPs, such as the vertical excitation energies (VEEs) and spin-orbit coupling (SOC) integrals. ...
We employ quantum chemical calculations to reveal the mechanisms of HONO generation from the photolysis of nitrophenols in both gas and aqueous phases, which show that there are considerable atmospheric HONO sources in the daytime.
... The conformational landscape of GA was explored using the DFT and MP2 methods. The B3LYP hybrid functional of Becke [67], Lee, Yang, and Parr [68] with 6-311++G(2d,p) [69] and def2-TZVP [70] basis sets and including GD3 [71] and GD3BJ [72] empirical dispersion corrections. Furthermore, ab initio MP2 [73] optimizations were done with 6-311++G(2d,p), aug-cc-pVDZ, and aug-cc-pVTZ [74] basis sets. ...
The rotational spectrum of laser-ablated gallic acid has been recorded using CP-FTMW spectroscopy. Two rotamers have been detected, and their rotational spectra have been assigned and analyzed to obtain the molecular spectroscopic parameters. The observed rotamers have been unambiguously identified in the light of theoretical computations, based on the comparison of the experimental line intensities and rotational parameters with the rotational constants and electric dipole moments predicted from theoretical calculations. The values of the planar inertial moments confirm that the observed conformers are planar, and their relative stability and population have been determined from relative intensity measurements. The B3LYP-D3/6-311++G(2d,p) level has been shown to be the best method among a series of levels normally used to predict the rotational parameters in rotational spectroscopy. In the observed conformers, the three adjacent OH groups are arranged in a sequential form, and the only difference between them lies in the orientation of the COOH group. Although weak attractive OH···O interactions seem to exist, the analysis of the electron density topology does not show the existence of any critical point corresponding to these interactions.
... To construct an initial classical free energy profile and to collect the necessary training data to build an MLP for each of the molecules, ab initio umbrella sampling simulations were performed with PSI4, 18 using a PBE0 functional 19 and a 6-311G(3df,3pd) Pople basis set. 20 From every ab initio umbrella simulation, the energies and forces of snapshots taken every 5 fs were used to train an equivariant MLP with our in-house developed code available at https://github.com/mcoolsce/ NNFFLIB and archived on 10.5281/zenodo.6606271. ...
Although many molecular dynamics simulations treat the atomic nuclei as classical particles, an adequate description of nuclear quantum effects (NQEs) is indispensable when studying proton transfer reactions. Herein, quantum free energy profiles are constructed for three typical proton transfers, which properly take NQEs into account using the path integral formalism. The computational cost of the simulations is kept tractable by deriving machine learning potentials. It is shown that the classical and quasi-classical centroid free energy profiles of the proton transfers deviate substantially from the exact quantum free energy profile.
... The functional was selected on the basis of previous studies [45,46]. The basis set used was 6-311++G(2df,2p) [47]. ...
Nanoscale control of chemical reactivity, manipulation of reaction pathways, and ultimately driving the outcome of chemical reactions are quickly becoming reality. A variety of tools are concurring to establish such capability. The confinement of guest molecules inside nanoreactors, such as the hollow nanostructures of carbon nanotubes (CNTs), is a straightforward and highly fascinating approach. It mechanically hinders some molecular movements but also decreases the free energy of translation of the system with respect to that of a macroscopic solution. Here, we examined, at the quantum mechanics/molecular mechanics (QM/MM) level, the effect of confinement inside CNTs on nucleophilic substitution (SN2) and elimination (syn-E2 and anti-E2) using as a model system the reaction between ethyl chloride and chloride. Our results show that the three reaction mechanisms are kinetically and thermodynamically affected by the CNT host. The size of the nanoreactor, i.e., the CNT diameter, represents the key factor to control the energy profiles of the reactions. A careful analysis of the interactions between the CNTs and the reactive system allowed us to identify the driving force of the catalytic process. The electrostatic term controls the reaction kinetics in the SN2 and syn/anti-E2 reactions. The van der Waals interactions play an important role in the stabilization of the product of the elimination process.
The anharmonicity of O-H stretching vibrations of water ice is characterized by use of a periodic implementation of the vibrational self-consistent field (VSCF) and vibrational configuration interaction (VCI) methods, which take phonon-phonon couplings explicitly into account through numerical evaluation of high-order terms of the nuclear potential. The low-temperature, proton-ordered phase of water ice (namely, ice-XI) is investigated. The net effect of a coupled anharmonic treatment of stretching modes is not just a rigid blue-shift of the respective harmonic spectral frequencies but rather a complex change of their relative spectral positions, which can not be captured by simple scaling strategies based on harmonic calculations. The adopted techniques allow for a hierarchical treatment of anharmonic terms of the nuclear potential, which is key to an effective identification of leading factors. We show that an anharmonic independent-mode approximation only describing the "intrinsic anharmonicity" of the O-H stretches is unable to capture the correct physics and that couplings among O-H stretches must be described. Inspection of harmonic normal coordinates allows to identify specific features of the O-H stretching motions which most likely enable strong mode-mode couplings. Finally, by coupling O-H stretches to all other possible modes of ice-XI (THz collective vibrations, molecular librations, bendings), we identify specific types of motion which significantly affect O-H stretching states: in particular, molecular librations are found to affect the stretching states more than molecular bendings.
The laws of the combined action of σ- and π-ligands on the electronic structure and thermodynamic parameters of Cu+ acidoaquachlorocomplexes were investigated using the method of quantum chemical modeling. It was found that anhydrous chloride complexes with molecules of unsaturated organic acids (acrylic, maleic, fumaric) have the best energy characteristics. They achieve the maximum binding energies of the central atom with the chloride ion (151 ± 2 kJ/mol) and the organic ligand (130 ± 1 kJ/mol), which are practically independent of the nature of the acid. The addition of water molecules to [Cu+(L)(Cl−)] is energetically beneficial in all cases. The value of ΔEr depends on the nature of the organic acid, its form of existence (molecules, anions), and the number of water molecules. Therefore, it varies in a wide range of values (10–60 kJ/mol). Hydration promotes the transition from σ-bonding by the central atom of anionic forms of organic ligands to π-bonding. Stable π-complexes [Cu+(L)(Cl−)(H2O)] exist with all forms of the studied acids. At the same time, the transition from the molecular form of organic acids to the anionic one totally worsens both the energetics of σ-bonds of Сu+ with chlorine anions and water molecules, as well as the energetics of π-bonds. The antagonism of the combined action of σ-ligands in [Cu+(L)(Cl−)(H2O)] was quantified by the change in the effective charge of the central atom. It was shown that in complexes with the molecular form of the studied unsaturated acids, chlorine anions reduce the electron donation of water molecules by 86 %, and water molecules reduce the electron donation of Cl− by 35 %.
New highly emissive copper( i ) complexes based on 3/4-pyridyltriazole have been synthesized and fully characterized. Photophysical properties and the mechanism of photo- and mechanochromic and excitation dependent luminescence are discussed.
Triacetone triperoxide (TATP) and hexamethylene triperoxide diamine (HMTD) are cyclic peroxides that exhibit atropisomerism resulting from restricted rotation around three peroxide bonds. As a result, one pair of enantiomers with D3 symmetry and another pair of enantiomers with C2 symmetry can be identified. Previous studies, based on mass spectrometry data and computational results, have shown that conformations of TATP with D3 and C2 symmetry can be isolated. Assuming that enantiomer samples of TATP and HMTD can be obtained with sufficient enantiopurity, we investigated their chiroptical properties, namely, optical rotatory dispersion (ORD), vibrational circular dichroism (VCD), and Raman optical activity (VROA). ORD curves and VCD spectra are seen to be very similar for D3- and C2-symmetric atropisomers with the same overall helicity. Predicted VROA results, however, show significant differences between D3- and C2-symmetric atropisomers with the same overall helicity. The D3-symmetric atropisomer is predicted to exhibit considerably larger magnitude vibrational optical activity signals than the C2-symmetric atropisomer.
A solvated proton in water is often characterized as a charge or structural defect, and it is important to track its evolution on-the-fly in certain dynamics simulations. Previously, we introduced the proton indicator, a pseudo-atom, whose position approximates the location of the excess proton modeled as a structural defect. The proton indicator generally yields a smooth trajectory of a hydrated proton diffusing in aqueous solutions, including in the events of stepwise proton transfer via the Grotthuss mechanism; however, the proton indicator did not perform well in the events of concerted proton transfer, for which it occasionally yielded large position displacements between two successive time steps. To overcome this hurdle, we develop a new algorithm of a proton indicator with greatly enhanced performance for concerted proton transfer in bulk water. A protocol is proposed to exhaustively explore the hydrogen-bonding network of the water wires over which the excess proton is delocalized and to properly account for the contributions of the water molecules in this network as the geometry evolves. The new proton indicator (called Indicator 2.0) is assessed in dynamics simulations of an excess proton in bulk water and in specially constructed model systems of more complex architectures. The results demonstrate that the new indicator yields a smooth trajectory in both stepwise and concerted proton transfers.
A peptide linkage −(C=O)NH− containing molecule, N-ethylformamide, was investigated by rotational spectroscopy in order to determine the molecular constants of its highest-energy conformer, cis-ac. Its rotational spectrum was observed in two different frequency ranges, in the 4−26 GHz frequency region using a Fourier transform microwave spectrometer and at millimeter wave frequencies between 75−116 GHz, employing a broadband high-resolution rotational spectrometer. The measurements at low frequencies allowed to resolve the hyperfine structure components due to nitrogen nuclear quadrupole coupling while the data at higher frequencies provided spectroscopic information about high order centrifugal effects. From a merged fit using all the observational data we have determined a total of thirteen molecular constants that provide a more accurate spectral modelling of the cis-ac conformer and serves a basis for their astronomical search. We have also observed spectra of five singly substituted isotopologues for the cis-ac conformer, three ¹³C and one for each of ¹⁵N and the deuterated species on the N–D position, from which we derived a partial r0 structure, in fair agreement with an ab initio result. In addition, the rotational transitions of the deuterated species of the most stable trans-sc conformer were observed and assigned and three rotational, five centrifugal distortion constants and nuclear quadrupole coupling constants of the nitrogen and deuterium nuclei were determined.
The choice of Gaussian basis functions for computing the ground-state properties of molecules, and clusters, employing wave-function-based electron-correlated approaches, is a well-studied subject. However, the same cannot be said when it comes to the excited-state properties of such systems, in general, and optical properties, in particular. The aim of the present study is to understand how the choice of basis functions affects the calculations of linear optical absorption in clusters, qualitatively, and quantitatively. For this purpose, we have calculated linear optical absorption spectra of several small charged and neutral clusters, namely, Li$_{2}$, Li$_{3}$, Li$_{4}$, B$_{2}^{+}$, B$_{3}^{+}$, Be$_{2}^{+}$, and Be$_{3}^{+}$, using a variety of Gaussian basis sets. The calculations were performed within the frozen-core approximation, and a rigorous account of electron correlation effects in the valence sector was taken by employing various levels of configuration interaction (CI) approach both for the ground and excited states. Our results on the peak locations in the absorption spectra of Li$_{3}$ and Li$_{4}$ are in very good agreement with the experiments. Our general recommendation is that for excited-state calculations, it is very important to utilize those basis sets which contain augmented functions. Relatively smaller aug-cc-pVDZ basis sets also yield high-quality results for photoabsorption spectra, and are recommended for such calculations if the computational resources are limited.
Piezocatalysis has attracted increasing attention in recent years for environment remediation. However, the efficiency of single piezocatalysis is not high enough because of the low piezo coefficient of most materials, thus limiting the practical application. Herein, we successfully constructed an advanced oxidation system for pollutants degradation by combining piezocatalysis with persulfate (PS) activation on Co doped ZnO nanorods. Theoretical calculations and experimental results revealed that the doped Co not only improves the piezoelectric property of ZnO, but also acts as the activation sites for PS. A non-radical oriented reaction was identified as the main process for pollutants degradation, and the Co-PS complex (Co-S2O8) was confirmed as the main reactive species in the present piezo assisted PS activation system. Moreover, a water flow stimulated reactor was constructed based on self-generated pressure, and the relations between flow field distribution and catalytic efficiency was revealed by computational fluid dynamics (CFD) simulation. This work opens new prospects for the development of piezo-based catalytic systems for efficient water purification by utilizing the kinetic energy of water flow.
Poly (ethylene terephthalate) has versatile commercial applications and after the use of PET products, a huge amount of waste is created all around. Chemical recycling is one of the emerging fields in PET waste minimization. Herein PET waste has been recycled using ammonolysis and aminolysis methods to obtain 1,4 benzene dicarboxamide, N,N′-dihydroxoethyl 1,4-benzene dicarboxamide and N,N′-diaminoethyl 1,4-benzene dicarboxamide. The molecules have been investigated through FTIR and UV–Visible spectroscopy techniques after recrystallization from DMSO solvent. The geometries of aromatic amide molecules were optimized and the molecules have been analyzed for vibrational frequencies and UV excitations. The calculations have been performed using general gradient approximation (GGA) with BLYP (Becke-Lee–Yang–Parr) D-3 exchange functional with double-ζ (DZ) basis set. Further HOMO and LUMO energy levels have also been reported to insight the excitation properties of the molecules. HOMO–LUMO energy gaps derived from Beer-Lambert’s law and Tauc equation. The molecules have been investigated as photoinitiating systems in acetic acid for UV curing of bisphenol-A glycerolate diacrylate using Differential Photocalorimeter. Maximum curing rates and degree of conversion have been estimated through DPC thermograms. The order of curing rates, enthalpy of polymerization and degree of conversion were found in agreement with the energy band gap values obtained through DFT simulations and Tauc equation. These molecules may find applications in UV cured composites, coatings, adhesives, paints, varnishes etc.
Bishomocubane, as a molecular scaffold, has been designed to functionalize the −Csp2−H bond of 1‐methyl pyrrole. The newly designed molecular scaffold showed noteworthy improvements in the reaction energetics than the phenylene scaffold. The DFT (ωB97XD/6‐31+G(d,p)) calculations revealed that the dimethyl amine (A) and piperidine (B) analogues of bishomocubane frustrated Lewis pairs (FLP) can catalyze the first −Csp2−H functionalization much more easily than that of the phenylene FLP. The previous results showed that the second −Csp2−H functionalization was found to be energetically difficult. The DFT calculations suggest that the piperidine analogue of bishomocubane, 1‐Pip‐2‐BH2‐C10H10 (B), can lead the second −Csp2−H functionalization facile than the reported FLPs. The rate‐determining step of the second −Csp2−H functionalization is significantly lower with the catalyst (B) by ∼9.0 kcal/mol compared to the phenylene catalyst (II). The improved reactivity of bishomocubane FLPs has been examined with molecular electrostatic potential (MESP) analysis and the conceptual density functional theory (CDFT) calculations. The hyperconjugative stabilization interaction (n→σ*) and the strain relief between the Lewis pairs play a crucial role in the stability of rate‐determining transition states. This study reveals that saturated hydrocarbon scaffolds are promising candidates as FLP catalysts in such reactions. A new amino‐borane frustrated Lewis pair (FLP) was designed using a saturated bishomocubane (BHC) molecular scaffold to study the 1‐methyl pyrrole's first and second −Csp2−H bond functionalization. The BHC – FLP can facilitate the second −Csp2−H bond functionalization more effectively compared to the Phenylene (Ph) – FLP catalyst.
Polymorph discrimination for a molecular crystal has long been a challenging task, which, nonetheless, is a major concern in the pharmaceutical industry. In this work, we have investigated polymorph discrimination on three different molecular crystals, tetrolic acid, oxalic acid, and oxalyl dihydrazide, covering both packing polymorphism and conformational polymorphism. To gain more understanding, we have performed energy decomposition analysis based on many‐body expansion, and have compared the results from the XO‐PBC method, that is, the eXtended ONIOM method (XO) with the periodic boundary condition (PBC), with those from some commonly used dispersion corrected density functional theory (DFT‐D) methods. It is shown here that, with the XYG3 doubly hybrid functional chosen as the target high level to capture the intra‐ and short‐range intermolecular interactions, and the periodic PBE as the basic low level to take long range interactions into account, the XO‐PBC(XYG3:PBE) method not only obtains the correct experimental stability orderings, but also predicts reasonable polymorph energy ranges for all three cases. Our results have demonstrated the usefulness of the present theoretical methods, in particular XO‐PBC, while highlighted the importance of a better treatment of different kinds of interactions to be beneficial to polymorph control. The eXtended ONIOM (XO) method with periodic boundary condition (PBC) is used for a reliable polymorph discrimination.
A dual‐level direct dynamics technique is used to explore the kinetic properties of the reaction of Cl atoms with methoxyflurane (CH3OCF2CHCl2). The energy profiles of two reaction channels of the two conformers are refined with the interpolated single‐point energies (ISPE) method at the CCSD(T)/M06‐2X level. The canonical variational transition state theory (CVT) with a small‐curvature tunneling (SCT) correction is used to assess the rate coefficients over a wide temperature range (250–500 K) in order to get accurate results. At a temperature of 296 K, the calculated CVT/SCT rate coefficient kCl = 2.71 × 10−13 cm3 molecule−1 s−1 is found to be in reasonably good agreement with the experimental result. Our calculations demonstrate that CH3OCF2CHCl2 + Cl → CH2OCF2CHCl2 + HCl (R1) reaction is the key pathway and a prominent conduit for CH3OCF2CHCl2 degradation in the troposphere. The atmospheric loss of C•H2OCF2CHCl2 and CH3OCF2C•Cl2 radicals are discussed. The rate coefficient value of the oxidation of the primary product HC(O)OCF2CHCl2 with the Cl atoms is 1.8 × 10−14 cm3 molecule−1 s−1, and for the first time, the rate coefficient of HC(O)OCF2CHCl2 + OH reaction has also been reported here.
Nuclear quadrupole resonances for 14N and 17O nuclei are exquisitely sensitive to interactions with surrounding atoms. As a result, nitrogen and oxygen solid‐state nuclear magnetic resonance (ssNMR) provides a powerful tool for investigating structure and dynamics in complex systems. First‐principles calculations are increasingly used to facilitate spectral assignment and to evaluate and adjust crystal structures. Recent work combining the strengths of planewave density functional theory (DFT) calculations with a single molecule correction obtained using a higher level of theory has proven successful in improving the accuracy of predicted chemical shielding tensors and 17O quadrupolar coupling constants (Cq). Here we extend this work by examining the accuracy of predicted 14N and 17O electric field gradient (EFG) tensor components obtained using alternative planewave‐corrections involving cluster and two‐body fragment‐based calculations. We benchmark the accuracy of chemical shielding (CS) and EFG tensor predictions for both nitrogen and oxygen using planewave, two‐body fragment, and enhanced planewave‐corrected techniques. Combining planewave and two‐body fragment calculations reduces the error in predicted 17O Cq values by 35% relative to traditional planewave calculations. These enhanced planewave correction methods improve the accuracy of 17O and 14N EFG tensor components by 15% relative to planewave DFT, but yield minimal improvement relative to a simple molecular correction. However, in structural environments involving either high symmetry or strong intermolecular interactions enhanced planewave‐corrected methods provide a distinct advantage.
The special properties of organic compounds are due to the polyvalence of the carbon atom. In this research, the organic single crystal of N-(4-acetyl −5-(4-(nitro) phenyl) −4,5-dihydro-1,3,4-thiadiazol-2-yl) -N-phenylacetamide (NTDZ) was successfully synthesized and crystallized in isopropanol by using slow evaporation solution growth method. FT-IR, ¹H and ¹³C NMR spectroscopic techniques were used to characterize the presence of various functional groups in the NTDZ molecular structure. Single crystal X-ray data have been collected and used for the structural determination of NTDZ. The title crystal crystallized in the monoclinic space group P21/c, according to X-ray analysis. Besides, quantum chemical studies were carried out using the density functional theory calculation method. The theoretical and experimental geometrical parameters were compared indicating a good accordance between them. Moreover, surface shapes were displayed using 3D-Hirshfeld surface analysis, and 2D-fingerprint graphs were used to quantify the contributions of C–H…O and C–H…N intermolecular interactions. Furthermore, the vibration spectrum of the NTDZ is calculated and compared with that obtained by FT-IR spectroscopy, and the predicted vibration assignments are made according to the potential energy distribution (PED). The chemical shifts of ¹H and ¹³C-NMR were calculated using the GIAO approximation and compared to experimental values. Using the TD-DFT method, the theoretical UV-Vis absorption spectrum was calculated in chloroform solvent to obtain the most important electronic transitions. Frontier molecular orbitals (HOMO and LUMO) indicate the charge transfer within the molecule. The global chemical reactivity descriptors (GCRD) were calculated. In addition, the MEP was also computed showing the functional groups responsible for building interactions with other molecules. Finally, the nonlinear optical behavior was investigated by the determination of the dipole moment (μ), the polarizability (α), and the first and second hyperpolarizabilities using the same level of theory. All of these findings suggest that the NTDZ crystal may be a viable candidate for NLO applications.
• Highlights
• New 1,3,4-thiadiazol derivative was synthesized.
• X-ray geometry was determined and confirmed by theoretical calculation.
• Electronic behavior was investigated by DFT and TD-DFT.
• NLO properties of the compound were also computed.
The 5‐(4‐aryl azo)‐8‐hydroxyquinolines (L1‐L3) and their metal complexes with Ni2+ and Zn2+ have been produced. Various spectroscopic techniques have been employed to analyze the ligand and complexes. The structures of the prepared compounds have been confirmed by Fourier transform infrared (FT‐IR), proton nuclear magnetic resonance (1H NMR), molar conductance, magnetic measurements, thermal gravimetric and differential thermal analyses (TG and DTA), and electronic transition. The FT‐IR spectra showed that the ligands are coordinated to the metal ions in a bidentate manner with donor sites of the azomethine‐N and phenolic‐OH. The FT‐IR and UV‐Visible spectra were compared with the calculated results and showed a good agreement. The mass spectra concluded that the ligands’ molecular weights and the calculated estimated m/z values match well. The complexes contain coordinated and hydrated water as confirmed by the TG results. The complexes are tetrahedral, trigonal bipyramid, and octahedral geometrical structures and act as non‐electrolytes in dimethylformamide (DMF) solvent. Using density functional theory (DFT) at the B3LYP level of theory and the 6‐311G** basis set for the C, H, N, Cl, and O‐atoms and the LANL2DZ basis set for the Ni and Zn‐atoms. Natural bond orbitals (NBO) analysis was used to compute and describe the natural charge population and precise electronic configuration. The small energy gap between HOMO and LUMO energies, suggests that charge transfer occurs within Ni2+ and Zn2+ complexes. The first‐order hyperpolarizability (β) of the complexes and the anisotropy of polarizability (α) values show promising optical properties. The electronic transitions of the prepared complexes were computed by time‐dependent density functional theory (TD‐DFT/PCM) with the B3LYP method using a 6‐31G** basis set. The ethanol polarizable continuum model (PCM) was used to simulate the solvent effect. Utilizing a computer virtual screening technique through molecular docking, the anticipation of binding of 8‐quinolinolazodye derivatives and their complexes with Human Coronavirus protein (PDB ID: 5epw) was done.
Radicals in advanced oxidation processes (AOPs) degrade micropollutants during water and wastewater treatment, but the transformation of dissolved organic matter (DOM) may be equally important. Ketone moieties in DOM are known disinfection byproduct precursors, but ketones themselves are intermediates produced during AOPs. We found that aromatic alcohols in DOM underwent transformation to ketones by one-electron oxidants (using SO4•- as a representative), and the formed ketones significantly increased trichloromethane (CHCl3) formation potential (FP) upon subsequent chlorination. CHCl3-FPs from aromatic ketones (Ar-CO-CH3, average of 22 mol/mol) were 6-24 times of CHCl3-FPs from aromatic alcohols (Ar-CH(OH)-CH3, average of 0.85 mol/mol). At a typical SO4•- exposure of 7.0 × 10-12 M·s, CHCl3-FPs from aromatic alcohol transformation increased by 24.8%-112% with an average increase of 53.4%. Notably, SO4•- oxidation of aliphatic alcohols resulted in minute changes in CHCl3-FPs due to their low reactivities with SO4•- (∼107 M-1 s-1). Other one-electron oxidants (Cl2•-, Br2•-,and CO3•-) are present in AOPs and also lead to aromatic alcohol-ketone transformations similar to SO4•-. This study highlights that subtle changes in DOM physicochemical properties due to one-electron oxidants can greatly affect the reactivity with free chlorine and the formation of chlorinated byproducts.
In this work, one geometrical aromaticity index and four electron sharing indexes are benchmarked for their application in excited state aromaticity calculations. Two computationally feasible and reliable procedures are identified, namely, CAM-B3LYP/cc-pVTZ and ωB97X-D/cc-pVTZ. Topological effects on the first excited singlet and triplet electronic manifold were investigated, and the latter was in general found to display more aromatic character compared to the S1 surface. Besides, geometrical relaxation on each of the manifolds was observed to hamper the aromaticity, thereby resulting in more antiaromatic character. The relative order of excited state aromaticity within the studied molecules was noted to resemble the reversed version of the relative order of ground state aromaticity. Thereby, the following generalization was postulated: The more aromatic a molecule is in its ground state, the more antiaromatic it will be in its electronic first excited manifolds.
Elucidating how the halogen‐bonding ability and strength are controlled by the substituent effect and how this control depends on halogen atom will be essential for finely‐tuned design of functionally important molecules. Here, this problem is tackled by analyzing the electron density differences/changes for variously substituted halobenzenes. It is shown that the anisotropy of the electron distribution around the halogen atom, which is an important factor for halogen‐bonding ability, is not much affected by the substituent effect and rather simply depends on the halogen atom, while the partial charge on the halogen atom, which is related to the bond dipole of the C–X bond, is significantly modulated by the substituent effect and gives rise to enhancement of the electrostatic potential on the line extended from the C–X bond. The properties related to the polarization effect are also discussed.
Sulfur-chlorine cycles play a role in the atmosphere of Venus. It is thought that many sulfur-chlorine bearing molecules could be present in Venus's atmosphere and play an important role in its chemical processes. The goal of this work is to provide new insight into the electronic structure and spectroscopy of the [Cl,S,S,O] molecular system. Eight isomers could be formed, but only three were found to be thermodynamically stable relative to the first dissociation limit. We spectroscopically characterized the two lowest energy stable isomers, C1-ClSSO and trans-ClSSO, using the accurate CCSD(T)-F12/aug-cc-pVTZ method. The dipole moments of the two lowest energy stable isomers are predicted to be 1.90 and 1.60 debye, respectively. The C1-ClSSO isomer is suitable for laser induced fluorescence detection since the lowest excited electronic states absorb in the visible, ~610 nm, and near UV region, 330 nm. We mapped the evolution of the low-lying excited electronic states along the ClS, SS, and SO bond lengths to find that the production of ClS, SO, or S 2 O is plausible, whereas the production of ClS 2 is not allowed.
Chemistry of coke formation has been subject to a wide array of experimental investigations since the advent of industrial coal carbonization process. Roles of different additives in inducing chemical modifications have been examined in this regard. However, similar computational quantum chemistry calculations attempting to obtain fundamental insights into the plausible molecular mechanism operating during the resolidification steps of semi‐coke and coke formation are elusive. Thus, a rational molecular level understanding pertaining to the evolution of chemical structure during coke formation has not developed likewise. In this context, density functional theory calculations have been employed in the present work to comprehend the plausible molecular mechanism of elementary steps driving the semi‐coke and coke formation. Influence of an additional organic H‐donor species on the mechanism has also been explored to ascertain its participation in coke making. Mechanistic steps involved in semi‐coke formation are found to be crucial in determining the final coke structure. Experimental observations relating to the liberation of H• and also molecular hydrogen (H2) during the generation of semi‐coke structure are well corroborated with our investigated mechanistic features. Overall, the work is believed to offer a molecular level interpretation of a much‐exploited chemical phenomenon. Insights into intrinsic reaction features and associated chemical structural transformation during coal to coke conversion in absence as well as in presence of additional organic additive system.
Metallophilic interactions between closed-shell metal centers are exemplified by d10 ions, with Au(I) aurophilic interactions as the archetype. Such an interaction extends to d8 species, and examples involving Au(III) are prevalent. Conversely, Ag(III) argentophilic interactions are uncommon. Here, we identify argentophilic interactions in silver corroles, which are authentic Ag(III) species. The crystal structure of a monomeric silver corrole is a dimer in the solid state, and the macrocycle exhibits an atypical domed conformation. In order to evaluate whether this represents an authentic metallophilic interaction or a crystal-packing artifact, the analogous cofacial or "pacman" corrole was prepared. The conformation of the monomer was recapitulated in the silver pacman corrole, exhibiting a short 3.67 Å distance between metal centers and a significant compression of the xanthene backbone. Theoretical calculations support the presence of a rare Ag(III)···Ag(III) argentophilic interaction in the pacman complex.
The choice of Gaussian basis functions for computing the ground-state properties of molecules and clusters, employing wave function-based electron-correlated approaches, is a well-studied subject. However, the same cannot be said when it comes to the excited-state properties of such systems, in general, and optical properties, in particular. The aim of the present study is to understand how the choice of basis functions affects the calculations of linear optical absorption in clusters, qualitatively and quantitatively. For this purpose, we have calculated linear optical absorption spectra of several small charged and neutral clusters, namely, Li2, Li3, Li4, B2⁺, B3⁺, Be2⁺, and Be3⁺, using a variety of Gaussian basis sets. The calculations were performed within the frozen-core approximation, and a rigorous account of electron correlation effects in the valence sector was taken by employing various levels of configuration interaction (CI) approach both for the ground and excited states. Our results on the peak locations in the absorption spectra of Li3 and Li4 are in very good agreement with the experiments. Our general recommendation is that for excited-state calculations, it is very important to utilize those basis sets which contain augmented functions. Relatively smaller aug-cc-pVDZ basis sets also yield high-quality results for photoabsorption spectra and are recommended for such calculations if the computational resources are limited.
Metal acetylacetonates of the general formula [M(acac)3] (MIII=Cr, Mn, Fe, Co) are among the best investigated coordination compounds. Many of these first‐row transition metal complexes are known to have unique electronic properties. Independently, photophysical research with different β‐diketonate ligands pointed towards the possibility of a special effect of the 2,4,6‐trimethylphenyl substituted acetylacetonate (mesacac) on the electron distribution between ligand and metal (MLCT). We therefore synthesized and fully characterized the previously unknown octahedral title complex. Its solid‐state structure shows a Jahn‐Teller elongation with two Mn−O bonds of 2.12/2.15 Å and four Mn−O bonds of 1.93 Å. Thermogravimetric data show a thermal stability up to 270 °C. High‐resolution mass spectroscopy helped to identify the decomposition pathways. The electronic state and spin configuration of manganese were characterized with a focus on its magnetic properties by measurement of the magnetic susceptibility and triple‐zeta density functional theory (DFT) calculations. The high‐spin state of manganese was confirmed by the determination of an effective magnetic moment of 4.85 μB for the manganese center. Synthesis and characterization of an octahedral manganese(III) complex with sterically demanding 1,3‐bis(2,4,6‐trimethylphenyl)propane‐1,3‐dionato (mesacac) ligands is reported. Density functional calculations and experimental results agree on t32ge1g high‐spin state (S=2) showing a strong Jahn–Teller elongation. The electronic structure is also confirmed by SQUID‐magnetometer measurements where a magnetic moment of 4.85 μB is associated with the metal centre.
Rotational spectroscopy relies on quantum chemical calculations to interpret observed spectra. Among the most challenging molecules to assign are those with additional angular momenta coupling to the rotation, contributing to the complexity of the spectrum. This benchmark study of computational methods commonly used by rotational spectroscopists targets the nuclear quadrupole coupling constants of chlorine containing molecules and the geometry of its complexes and clusters. For each method, the quality of both structural and electronic parameter predictions is compared with the experimental values. Ab initio methods are found to perform best overall in predicting both the geometry of the complexes and the coupling constants of chlorine with moderate computational cost. This cost can be reduced by combining these methods with density functional theory structure optimization, which still yields adequate predictions. This work constitutes a first step in expanding Bailey's quadrupole coupling data set to encompass molecular clusters. [W. C. Bailey, Calculation of Nuclear Quadrupole Coupling Constants in Gaseous State Molecule, 2019, https://nqcc.wcbailey.net/].
An extended basis set of atomic functions expressed as fixed linear combinations of Gaussian functions is presented for hydrogen and the first‐row atoms carbon to fluorine. In this set, described as 4–31 G, each inner shell is represented by a single basis function taken as a sum of four Gaussians and each valence orbital is split into inner and outer parts described by three and one Gaussian function, respectively. The expansion coefficients and Gaussian exponents are determined by minimizing the total calculated energy of the atomic ground state. This basis set is then used in single‐determinant molecular‐orbital studies of a group of small polyatomic molecules. Optimization of valence‐shell scaling factors shows that considerable rescaling of atomic functions occurs in molecules, the largest effects being observed for hydrogen and carbon. However, the range of optimum scale factors for each atom is small enough to allow the selection of a standard molecular set. The use of this standard basis gives theoretical equilibrium geometries in reasonable agreement with experiment.
A contracted Gaussian basis set (6‐311G∗∗) is developed by optimizing exponents and coefficients at the Møller–Plesset (MP) second‐order level for the ground states of first‐row atoms. This has a triple split in the valence s and p shells together with a single set of uncontracted polarization functions on each atom. The basis is tested by computing structures and energies for some simple molecules at various levels of MP theory and comparing with experiment.
The thermodynamic tabulations previously published in four collections are extended by 227 new and revised tables. The JANAF Thermochemical Tables cover the thermodynamic properties over a wide temperature range with single phase tables for the crystal, liquid, and ideal gas state. In addition some multiphase tables are given. The properties given are heat capacity, entropy, Gibbs energy function, enthalpy, enthalpy of formation, Gibbs energy of formation, and the logarithm of the equilibrium constant for formation of each compound from the elements in their standard reference states. Each tabulation lists all pertinent input data and contains a critical evaluation of the literature upon which these values are based. Literature references are given.
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The protonation energies of NH3 and H2O have been computed using a variety of basis sets. It is found that the effect of election correlation on these energies cannot reliably be determined without the use of large (triple-split and polarized) basis sets.
Least‐squares representations of Slater‐type atomic orbitals as a sum of Gaussian‐type orbitals are presented. These have the special feature that common Gaussian exponents are shared between Slater‐type 2s and 2p functions. Use of these atomic orbitals in self‐consistent molecular‐orbital calculations is shown to lead to values of atomization energies, atomic populations, and electric dipole moments which converge rapidly (with increasing size of Gaussian expansion) to the values appropriate for pure Slater‐type orbitals. The ζ exponents (or scale factors) for the atomic orbitals which are optimized for a number of molecules are also shown to be nearly independent of the number of Gaussian functions. A standard set of ζ values for use in molecular calculations is suggested on the basis of this study and is shown to be adequate for the calculation of total and atomization energies, but less appropriate for studies of charge distribution.
Generally contracted Gaussian basis functions are defined as those for which each contracted function may have a nonzero contribution from each primitive Gaussian. Alternatives for choice of such bases are tested and guidelines proposed. The basis is compared with standard methods in current use and is shown to be superior in terms of energy lowering obtained per additional basis function beyond a minimal number. A new program for computation of the required multicentered integrals is described.
Gas-phase reaction energies have been computed by means of ab initio SCF MO calculations with electron correlation computed by Møller-Plesset perturbation theory. Combined with computed vibrational, rotational, and translational energies, these give room temperature enthalpies in agreement with experimental data for the hydration reactions X + H2O → H2OX, where X = H+, Li+, and H2O. The effect of full deuteration on the enthalpies of these reactions is predicted.
Mø–Plesset theory, in which electron correlation energy is calculated by perturbation techniques, is used in second order to calculate energies of the ground states of atoms up to neon. The unrestricted Hartree–Fock (UHF) Hamiltonian is used as the unperturbed system and the technique is then described as unrestricted Mø–Plesset to second order (UMP2). Use of large Gaussian basis sets suggests that the limiting UMP2 energies with a complete basis of s, p, and d functions account for 75–84% of the correlation energy. Preliminary estimates of the contributions of basis functions with higher angular quantum numbers indicate that full UMP2 limits give even more accurate total energies.
Polarization functions are added in two steps to a split-valence extended gaussian basis set: d-type gaussians on the first row atoms C. N, O and F and p-type gaussians on hydrogen. The same d-exponent of 0.8 is found to be satisfactory for these four atoms and the hydrogen p-exponent of 1.1 is adequate in their hydrides. The energy lowering due to d functions is found to depend on the local symmetry around the heavy atom. For the particular basis used, the energy lowerings due to d functions for various environments around the heavy atom are tabulated. These bases are then applied to a set of molecules containing up to two heavy atoms to obtain their LCAO-MO-SCF energies. The mean absolute deviation between theory and experiment (where available) for heats of hydrogenation of closed shell species with two non-hydrogen atoms is 4 kcal/mole for the basis set with full polarization. Estimates of hydrogenation energy errors at the Hartree-Fock limit, based on available calculations, are given.
Two extended basis sets (termed 5–31G and 6–31G) consisting of atomic orbitals expressed as fixed linear combinations of Gaussian functions are presented for the first row atoms carbon to fluorine. These basis functions are similar to the 4–31G set [J. Chem. Phys. 54, 724 (1971)] in that each valence shell is split into inner and outer parts described by three and one Gaussian function, respectively. Inner shells are represented by a single basis function taken as a sum of five (5–31G) or six (6–31G) Gaussians. Studies with a number of polyatomic molecules indicate a substantial lowering of calculated total energies over the 4–31G set. Calculated relative energies and equilibrium geometries do not appear to be altered significantly.
Two new split-valence basis sets, termed 6-21G and 3-21G, are proposed for use in molecular orbital calculations on molecules containing first-row elements. The valence functions for the smaller representation (3-21G) have been taken directly from the larger (6-21G), preventing their collapse inwards to make up for deficiencies in the inner-shell region. This is necessary to ensure a good description of bonding interactions which necessarily involve overlap of valence functions. Equilibrium geometries, vibrational frequencies, relative energies, and electric dipole moments calculated using the 3-21G basis set are nearly identical with those obtained from the larger 6-21G representation. Compared to experiment they are consistently superior to properties derived from the STO-3G minimal basis set, and of comparable quality to those obtained from the larger 4-21G and 4-31G representations. One notable exception is that the 4-31G basis set yields hydrogenation energies in significantly better agreement with experiment than those obtained from 3-21G. The 3-21G basis set comprises the same number of primitive Gaussian functions as STO-3G (although nearly twice the number of basis functions) and should be nearly as efficient computationally as that representation for applications which require evaluation of energy derivatives as well as the energy itself (e.g., determination of equilibrium geometry and calculation of vibrational frequencies). It is less costly to apply than either the 4-21G or 4-31G split-valence basis sets, and in those areas where the performance of the two is comparable it would appear to be the method of choice.