Abinitio interpretation of conformer stabilization through bonding in the acetyl derivatives of two representative heterocyclic methine bases

1995 ◽  
Vol 73 (8) ◽  
pp. 1287-1293 ◽  
Author(s):  
Kathleen M. Gough ◽  
Janice Millington
Keyword(s):  
Internal Rotation ◽  
Closed Shell ◽  
Theoretical Explanation ◽  
Atoms In Molecules ◽  
Basis Set ◽  
Basis Sets ◽  
Side Chain ◽  
Derivatives Of ◽  
Favorable Structure ◽  
Oxygen Interaction

Abinitio calculations (STO-3G and 3-21G* basis sets) have been performed on 2 and 3 to determine the most favorable structure and to provide an estimate of the barrier to internal rotation of the acyl group. The Z configuration is preferred in 2, the E configuration in 3, with calculated barriers to internal rotation of 79.9 and 68.7 kJ/mol, respectively, at the 3-21G* level. The wave functions from the 3-21G* calculations are analyzed with the theory of atoms in molecules. The identification of bond critical points characteristic of a closed shell interaction establishes the existence of a weak bond between [Formula: see text] in 2 and between [Formula: see text] in 3, for the preferred configurations. The energy required to break this bond as well as the loss of extended conjugation throughout the hetero ring and its side chain are responsible for the asymmetry in the barrier. These findings provide a theoretical explanation for experimental observations on this class of molecules in which one conformer is preferred to any other and only one crystal structure is identified. Keywords: nonbonded sulfur–oxygen interaction, closed shell interaction, hydrogen bonding, 3-21G* basis set, theory of atoms in molecules.

scholarly journals Quasi-Relativistic Calculation of EPR g-Tensors with Derivatives of the Decoupling Transformation, Gauge-Including Atomic Orbitals, and Magnetic Balance

2021 ◽  
Author(s):  
Yannick J. Franzke ◽  
Jason M. Yu
Keyword(s):  
Density Functional ◽  
Hyperfine Coupling Constant ◽  
Basis Set ◽  
Basis Sets ◽  
Generalized Gradient ◽  
Atomic Orbitals ◽  
Experimental Findings ◽  
The Impact ◽  
Derivatives Of ◽  
Magnetic Balance

We present an exact two-component (X2C) ansatz for the EPR g-tensor using gauge-including atomic orbitals (GIAOs) and a magnetically balanced basis set expansion. In contrast to previous X2C and "fully" relativistic ansätze for the g-tensor, this implementation results in a gauge-origin invariant formalism. Furthermore, the derivatives of the relativistic decoupling matrix are considered to form the complete analytical derivative of the X2C Hamiltonian. To reduce the associated computational costs, we apply the diagonal local approximation to the unitary decoupling transformation (DLU) and the (multipole-accelerated) resolution of the identity approximation. The X2C ansatz is compared to Douglas-Kroll-Hess theory and the zeroth-order regular approximation for 11 diatomic molecules. The impact of the relativistic Hamiltonian, the basis set, and the density functional approximation is subsequently assessed for a set of 17 transition-metal complexes to complement our previous work on the hyperfine coupling constant [DOI: 10.33774/chemrxiv-2021-wnz1v-v2]. In total, 24 basis sets and 22 density functional approximations are considered. The quasi-relativistic X2C and DLU-X2C Hamiltonians accurately reproduce the results of the parent "fully" relativistic four-component theory when accounting for two-electron picture-change effects with the modified screened nuclear spin-orbit approximation in the respective one-electron integrals and integral derivatives. Generally, the uncontracted Dyall and segmented-contracted Karlsruhe x2c-type basis sets perform well when compared to large even-tempered basis sets. Moreover, (range-separated) hybrid density functional approximations are needed to match the experimental findings. Here, hybrids based on the meta -generalized gradient approximation are not an a priori improvement. Compared to the other computational parameters, the impact of the GIAOs and the magnetic balance on the actual results in standard calculations is less pronounced. Routine calculations of large molecules are possible with widely available and comparably low- cost hardware as demonstrated for [Pt(C6Cl5)4]− with 3360 basis functions and three spin-(1/2) La(II) and Lu(II) compounds. Both approaches based on a common gauge origin and GIAOs using triple- ζ basis sets lead to a good agreement with the experimental findings. The best agreement is found with hybrid functionals such as PBE0 and ωB97X-D.

Ab initio Studies of Hydrazines: Equilibrium Structures of 1,1-Dimethylhydrazine and Transition Structures Connecting Them

1987 ◽  
Vol 40 (11) ◽  
pp. 1783 ◽  
Author(s):  
NV Riggs ◽  
L Radom
Keyword(s):  
Internal Rotation ◽  
Vibrational Energy ◽  
Zero Point ◽  
Basis Set ◽  
Basis Sets ◽  
Primary Amines ◽  
Rotational Angle ◽  
Small Rise ◽  
Equilibrium Structures ◽  
Anti Form

Optimization of the geometries of various stationary structures of 1,1-dimethylhydrazine has been carried out with the 3-21G and 3-21G(N*) basis sets, and the energies of each of the latter optimized structures have been evaluated with the 6.31G* basis set. The gauche form with a (mean) internal rotational angle near 80� (hydrazine, approx. 90�) is the lowest-energy form. After zero-point vibrational -energy corrections, the anti form lies in a shallow well 14kJ mol-1 higher on the potential-energy surface for internal rotation, and the transition structure connecting them lies approx. 1 kJ mol-1 higher still. The anti form is thus a true equilibrium species, unlike the case for hydrazine, but constitutes less than 0.5% of the molecules present at room temperature. It is estimated to have a half-life of less than 10 ps , so its observation by present physical methods may prove to be difficult. The barrier to internal rotation via the syn form (41kJ mol-1) coincides with that for hydrazine. gem-Dimethyl substitution in hydrazine leads to a small rise (1-2 kJ mol-1) in the barrier to inversion at the unsubstituted nitrogen atom, but to an unexpectedly high (by 8-9 kJ mol-1) calculated barrier to inversion at the substituted centre, whether the result be referred to the barrier in hydrazine or to that in dimethylamine. Calculated NH stretching frequencies for the gauche form show a spacing much larger than that for 'simple' primary amines, as is found experimentally.

An ab initio Study of the Equilibrium Structures of Prop-2-ynamine (Propargylamine) and the Transition Structures Connecting Them

1987 ◽  
Vol 40 (3) ◽  
pp. 435 ◽  
Author(s):  
NV Riggs
Keyword(s):  
Ab Initio ◽  
Internal Rotation ◽  
Vibrational Energy ◽  
Vibrational Analysis ◽  
Zero Point ◽  
Basis Set ◽  
Basis Sets ◽  
Experimental Result ◽  
Transition Structure ◽  
Equilibrium Structures

Optimization with the 3-21G and 3-21G(N*) basis sets finds, in agreement with previous ab initio studies and the experimental result, the anti conformation of prop-2-ynamine to be of lowest energy and, after zero-point vibrational -energy ( Ezpv ) corrections, the gauche form to lie 11 kJ mol-l higher; by vibrational analysis, both are confirmed as equilibrium structures. The synform was not able to be optimized with the 3.21G basis set but, with the 3-21G(N*) basis set, is found to lie 8.6 kJ mol-1 (after Ezpv corrections) above the gauche form, and is shown by vibrational analysis to be a transition structure connecting enantiomeric gauche forms by internal rotation about the N-C bond. The transition structure connecting gauche and anti forms by internal rotation lies 6.3 kJ mol-1 (after Ezpv corrections) above the gauche form, and the transition structure for inversion at the nitrogen atom lies 31.1 kJ mol- l (after Ezpvcorrections) above the anti form.

Study on the cooperativity of hydrogen bonds between H2Y and HX (X = F, Cl, Br; Y = O, S, Se)

2014 ◽  
Vol 13 (05) ◽  
pp. 1450037 ◽  
Author(s):  
Hexiu Liu ◽  
Ruilin Man ◽  
Zhaoxu Wang ◽  
Jianping Liao ◽  
Xiaofang Li ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Electrostatic Interactions ◽  
Closed Shell ◽  
Atoms In Molecules ◽  
Basis Set ◽  
Strong Interactions ◽  
Interaction Energies ◽  
Structure Characteristics ◽  
Title System ◽  
The Stability

The structure characteristics, interaction energies, cooperative energies of the complexes between chalcogen hydrides ( H 2 Y ) and halogen hydrides (HX) have been studied theoretically at the MP2 level with aug-cc-pVTZ basis set in this paper. The conclusions show that there are strong interactions between H 2 Y and HX. The stability of the complex is decided by the electronegativity of the negatively charged atom. The cooperativity is observed in the two or three hydrogen bonds of each trimer structures in title system. The values of the cooperative energies and the cooperative contributions all illustrate that the cooperativity is of great importance in these complexes. The "atoms in molecules" (AIM) analyses show that the complexes in title system are mainly electrostatic interactions (closed-shell interactions) in character. For H ⋯ O bonds in H 2 O ⋯ HF ⋯ H 2 O , H 2 O ⋯ HBr ⋯ H 2 O and HF ⋯ H 2 O ⋯ HF , the 1 < |Vc|/Gc < 2 and -Gc < Hc < 0 indicate the interactions in these compounds are between closed-shell interaction and opened-shell interaction.

A Systematic DFT Study of Two Elementary Steps Involving Hydrogen Peroxide and the Hydroxyl Radical in the Fenton Reaction

2018 ◽  
Author(s):  
Danilo Carmona ◽  
David Contreras ◽  
Oscar A. Douglas-Gallardo ◽  
Stefan Vogt-Geisse ◽  
Pablo Jaque ◽  
...  
Keyword(s):  
Hydrogen Peroxide ◽  
Hydroxyl Radical ◽  
Ab Initio ◽  
Fenton Reaction ◽  
Basis Set ◽  
Basis Sets ◽  
Dft Methods ◽  
Elementary Steps ◽  
Oxygen Oxygen ◽  
Complete Basis Set

The Fenton reaction plays a central role in many chemical and biological processes and has various applications as e.g. water remediation. The reaction consists of the iron-catalyzed homolytic cleavage of the oxygen-oxygen bond in the hydrogen peroxide molecule and the reduction of the hydroxyl radical. Here, we study these two elementary steps with high-level ab-initio calculations at the complete basis set limit and address the performance of different DFT methods following a specific classification based on the Jacob´s ladder in combination with various Pople's basis sets. Ab-initio calculations at the complete basis set limit are in agreement to experimental reference data and identified a significant contribution of the electron correlation energy to the bond dissociation energy (BDE) of the oxygen-oxygen bond in hydrogen peroxide and the electron affinity (EA) of the hydroxyl radical. The studied DFT methods were able to reproduce the ab-initio reference values, although no functional was particularly better for both reactions. The inclusion of HF exchange in the DFT functionals lead in most cases to larger deviations, which might be related to the poor description of the two reactions by the HF method. Considering the computational cost, DFT methods provide better BDE and EA values than HF and post--HF methods with an almost MP2 or CCSD level of accuracy. However, no systematic general prediction of the error based on the employed functional could be established and no systematic improvement with increasing the size in the Pople's basis set was found, although for BDE values certain systematic basis set dependence was observed. Moreover, the quality of the hydrogen peroxide, hydroxyl radical and hydroxyl anion structures obtained from these functionals was compared to experimental reference data. In general, bond lengths were well reproduced and the error in the angles were between one and two degrees with some systematic trend with the basis sets. From our results we conclude that DFT methods present a computationally less expensive alternative to describe the two elementary steps of the Fenton reaction. However, choice of approximated functionals and basis sets must be carefully done and the provided benchmark allows a systematic validation of the electronic structure method to be employed

DFT Benchmark Study of the O--O Bond Dissociation Energy in Peroxides Validated with High-Level Ab-Initio Calculations

2019 ◽  
Author(s):  
Danilo Carmona ◽  
Pablo Jaque ◽  
Esteban Vöhringer-Martinez
Keyword(s):  
Reference Value ◽  
Basis Set ◽  
Basis Sets ◽  
Mean Deviation ◽  
Bond Dissociation ◽  
Dissociation Energies ◽  
The Mean ◽  
Experimental Values ◽  
High Level ◽  
Almost All

<div><div><div><p>Peroxides play a central role in many chemical and biological pro- cesses such as the Fenton reaction. The relevance of these compounds lies in the low stability of the O–O bond which upon dissociation results in radical species able to initiate various chemical or biological processes. In this work, a set of 64 DFT functional-basis set combinations has been validated in terms of their capability to describe bond dissociation energies (BDE) for the O–O bond in a database of 14 ROOH peroxides for which experimental values ofBDE are available. Moreover, the electronic contributions to the BDE were obtained for four of the peroxides and the anion H2O2− at the CBS limit at CCSD(T) level with Dunning’s basis sets up to triple–ζ quality provid- ing a reference value for the hydrogen peroxide anion as a model. Almost all the functionals considered here yielded mean absolute deviations around 5.0 kcal mol−1. The smallest values were observed for the ωB97 family and the Minnesota M11 functional with a marked basis set dependence. Despite the mean deviation, order relations among BDE experimental values of peroxides were also considered. The ωB97 family was able to reproduce the relations correctly whereas other functionals presented a marked dependence on the chemical nature of the R group. Interestingly, M11 functional did not show a very good agreement with the established order despite its good performance in the mean error. The obtained results support the use of similar validation strategies for proper prediction of BDE or other molecular properties by DF Tmethods in subsequent related studies.</p></div></div></div>

Benchmark of Simplified Time-Dependent Density Functional Theory for UV-Vis Spectral Properties of Porphyrinoids

2019 ◽  
Author(s):  
Kamal Batra ◽  
Stefan Zahn ◽  
Thomas Heine
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Large Scale ◽  
Absolute Error ◽  
Time Dependent ◽  
Basis Set ◽  
Basis Sets ◽  
Functional Theory ◽  
Framework Materials ◽  
Dependent Density

<p>We thoroughly benchmark time-dependent density- functional theory for the predictive calculation of UV/Vis spectra of porphyrin derivatives. With the aim to provide an approach that is computationally feasible for large-scale applications such as biological systems or molecular framework materials, albeit performing with high accuracy for the Q-bands, we compare the results given by various computational protocols, including basis sets, density-functionals (including gradient corrected local functionals, hybrids, double hybrids and range-separated functionals), and various variants of time-dependent density-functional theory, including the simplified Tamm-Dancoff approximation. An excellent choice for these calculations is the range-separated functional CAM-B3LYP in combination with the simplified Tamm-Dancoff approximation and a basis set of double-ζ quality def2-SVP (mean absolute error [MAE] of ~0.05 eV). This is not surpassed by more expensive approaches, not even by double hybrid functionals, and solely systematic excitation energy scaling slightly improves the results (MAE ~0.04 eV). </p>

Absolute configuration at C(20) of the derivatives of 21-nor-5α-cholane-20,24-diol

1980 ◽  
Vol 45 (9) ◽  
pp. 2443-2451
Author(s):  
Vladimír Pouzar ◽  
Miroslav Havel
Keyword(s):  
Absolute Configuration ◽  
Side Chain ◽  
Chemical Correlation ◽  
The Absolute ◽  
Derivatives Of

Derivatives of 21-nor-5α-cholane-20,24-diol XI and XIX were prepared by stepwise construction of the side-chain in the position 17β. Their absolute configuration at C(20) was determined on the basis of chemical correlation with the derivatives of 21-nor-5α-cholan-20-ol, XVI and XXIV. The absolute configuration of alcohols XVI and XXIV was determined from the ratio of the yields in which they are formed during the reduction of ketone X and using the benzoate rule. To compounds XI-XVIII the configuration 20R and to compounds XIX-XXVI the configuration 20S has been assigned.

scholarly journals Synthesis of New Derivatives of BEDT-TTF: Installation of Alkyl, Ethynyl, and Metal-Binding Side Chains and Formation of Tris(BEDT-TTF) Systems

2021 ◽  
Vol 7 (8) ◽  
pp. 110
Author(s):  
Songjie Yang ◽  
Matteo Zecchini ◽  
Andrew Brooks ◽  
Sara Krivickas ◽  
Desiree Dalligos ◽  
...  
Keyword(s):  
Metal Binding ◽  
Tricarboxylic Acid ◽  
Metal Salts ◽  
Side Chain ◽  
Side Chains ◽  
Ethynyl Group ◽  
X Ray ◽  
Transition Metal Salts ◽  
Alkyl Side Chains ◽  
Derivatives Of

The syntheses of new BEDT-TTF derivatives are described. These comprise BEDT-TTF with one ethynyl group (HC≡C-), with two (n-heptyl) or four (n-butyl) alkyl side chains, with two trans acetal (-CH(OMe)2) groups, with two trans aminomethyl (-CH2NH2) groups, and with an iminodiacetate (-CH2N(CH2CO2−)2 side chain. Three transition metal salts have been prepared from the latter donor, and their magnetic properties are reported. Three tris-donor systems are reported bearing three BEDT-TTF derivatives with ester links to a core derived from benzene-1,3,5-tricarboxylic acid. The stereochemistry and molecular structure of the donors are discussed. X-ray crystal structures of two BEDT-TTF donors are reported: one with two CH(OMe)2 groups and with one a -CH2N(CH2CO2Me)2 side chain.

AlN Nanotubes: A DFT Study of Al-27 and N-14 Electric Field Gradient Tensors

2007 ◽  
Vol 62 (12) ◽  
pp. 711-715 ◽  
Author(s):  
Ahmad Seif ◽  
Mahmoud Mirzaei ◽  
Mehran Aghaie ◽  
Asadollah Boshra
Keyword(s):  
Electric Field ◽  
Electric Field Gradient ◽  
Field Gradient ◽  
Density Functional ◽  
Quadrupole Coupling Constant ◽  
Basis Set ◽  
Basis Sets ◽  
B3lyp Method ◽  
Package Program ◽  
Nqr Parameters

Density functional theory (DFT) calculations were performed to calculate the electric field gradient (EFG) tensors at the sites of aliminium (27Al) and nitrogen (14N) nuclei in an 1 nm of length (6,0) single-walled aliminium nitride nanotube (AlNNT) in three forms of the tubes, i. e. hydrogencapped, aliminium-terminated and nitrogen-terminated as representatives of zigzag AlNNTs. At first, each form was optimized at the level of the Becke3,Lee-Yang-Parr (B3LYP) method, 6-311G∗∗ basis set. After, the EFG tensors were calculated at the level of the B3LYP method, 6-311++G∗∗ and individual gauge for localized orbitals (IGLO-II and IGLO-III) types of basis sets in each of the three optimized forms and were converted to experimentally measurable nuclear quadrupole resonance (NQR) parameters, i. e. quadrupole coupling constant (qcc) and asymmetry parameter (ηQ). The evaluated NQR parameters revealed that the considered model of AlNNT can be divided into four equivalent layers with similar electrostatic properties.With the exception of Al-1, all of the three other Al layers have almost the same properties, however, N layers show significant differences in the magnitudes of the NQR parameters in the length of the nanotube. Furthermore, the evaluated NQR parameters of Al-1 in the Al-terminated form and N-1 in the N-terminated form revealed the different roles of Al (base agent) and of N (acid agent) in AlNNT. All the calculations were carried out using the GAUSSIAN 98 package program.

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