Substituent effects on 13C chemical shifts of ketenimines: a GIAO/HF and DFT study

GIAO/HF and DFT methods were utilized to predict the ¹³C chemical shifts of substituted ketenimines. GIAO HF/6–311+G(2d,p) and B3LYP/6–311+G(2d,p) methods were applied on the optimized B3LYP/6–31G(d) geometries and ¹³C chemical shifts of C_α and C_β of substituted ketenimines were correlated with group electronegativities. HF and DFT calculations indicated that increasing substituent group electronegativity leads to increasing chemical shift of C_β of substituted ketenimines, whereas the C_α values decrease. Copyright © 2003 John Wiley & Sons, Ltd.     

Substituent effect on intramolecular hydrogen bonding in 2‐hydroxybenzaldehyde

The effect of some substituents on intramolecular hydrogen bonding of 5‐X‐2‐hydroxybenzaldehyde (5‐X‐2‐HBA) has been studied by B3LYP and MP2 methods using 6‐311++G** and AUG‐cc‐PVTZ basis sets. The relationship between hydrogen bond energy E_HB and electron donation (or withdrawal) of substituents has been investigated. An approximately good linear relationship has been detected between Hammett coefficients and hydrogen bond formation energy (R² = 0.98). Herein, population analysis has been performed by atoms in molecules (AIM) and natural bond orbital (NBO) methods. The results of AIM and NBO analyses are in a good agreement with calculated energy values. Furthermore, correlation between ring aromaticity and hydrogen bonding has been investigated by nucleus‐independent chemical shift (NICS) at GIAO/B3LYP/6‐311++G** level of theory. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

1H, 13C and 15N NMR spectroscopic,x‐ray structural and ab initio/HF studies on nitramino and N‐alkylamino‐4‐nitro derivatives of pyridine N‐oxides and pyridines

The ¹H, ¹³C and ¹⁵N NMR spectra in DMSO‐d₆ were measured for eight nitraminopyridine N‐oxides, ten 4‐nitropyridine N‐oxides, four 2‐nitraminopyridines and five 4‐nitropyridines. Their chemical shift assignments are based on PFG ¹H,X (X = ¹³C and ¹⁵N) HMQC and HMBC experiments. The relative energies for the tautomers of two nitraminopyridine N‐oxides were determined by ab initio HF/6–311G** calculations. A single‐crystal x‐ray structural analysis was made for 4‐methyl‐2‐nitraminopyridine: C₆H₇O₂N₃, M = 153.15, triclinic, space group P‐1 (No. 2), a = 7.0275(4), b = 6.8034(3), c = 8.6086(5) Å, α = 103.620(2), β = 90.309(2), γ = 122.215(3)°, V = 334.11(3) ų, Z = 2. Copyright © 2003 John Wiley & Sons, Ltd.     

Computational studies on carbohydrates: I. Density functional ab initio geometry optimization on maltose conformations

Ab initio geometry optimization was carried out on 10 selected conformations of maltose and two 2‐methoxytetrahydropyran conformations using the density functional denoted B3LYP combined with two basis sets. The 6‐31G* and 6‐311++G** basis sets make up the B3LYP/6‐31G* and B3LYP/6‐311++G** procedures. Internal coordinates were fully relaxed, and structures were gradient optimized at both levels of theory. Ten conformations were studied at the B3LYP/6‐31G* level, and five of these were continued with full gradient optimization at the B3LYP/6‐311++G** level of theory. The details of the ab initio optimized geometries are presented here, with particular attention given to the positions of the atoms around the anomeric center and the effect of the particular anomer and hydrogen bonding pattern on the maltose ring structures and relative conformational energies. The size and complexity of the hydrogen‐bonding network prevented a rigorous search of conformational space by ab initio calculations. However, using empirical force fields, low‐energy conformers of maltose were found that were subsequently gradient optimized at the two ab initio levels of theory. Three classes of conformations were studied, as defined by the clockwise or counterclockwise direction of the hydroxyl groups, or a flipped conformer in which the ψ‐dihedral is rotated by ∼180°. Different combinations of ω side‐chain rotations gave energy differences of more than 6 kcal/mol above the lowest energy structure found. The lowest energy structures bear remarkably close resemblance to the neutron and X‐ray diffraction crystal structures. © 2000 John Wiley & Sons, Inc. * J Comput Chem 21: 1204–1219, 2000     

A molecular mechanics and ab initio prediction of the 1H chemical shifts of pinanes

Molecular mechanics calculations plus the application of a refined Karplus equation gave the conformations of 19 pinanes. These range from a Y‐shaped geometry in the apopinene and α‐pinene series to a pseudo chair conformation in β‐pinene, nopinone and verbanone, a flattened chair in pinocarvone and the pinocarveols and a distorted Y shape for iso‐verbanone. These structures were then used as input to predict the ¹H chemical shifts of these compounds by semi‐empirical (¹H‐NMR spectra (HSPEC)) and ab initio gauge‐invariant atomic orbital (GIAO) calculations, the latter at the B3LYP hybrid density functional theory level using 6‐31++G** basis set. The two methods gave generally good agreement with the 184 observed shifts with root mean square (RMS) errors 0.07 ppm (HSPEC) and 0.10 ppm (GIAO), but the GIAO calculations gave several significant (>0.25 ppm) errors. One was for the H₃ proton in apopinenone and other α,β unsaturated ketones; the others occurred for protons in close proximity to hydroxyl groups. To provide more information, smaller analogues of known geometry and chemical shifts were subject to the same analysis. In cyclopentenone, the Gaussian geometry gave good agreement with the observed shifts, but the MMFF94, MMX and MM3 geometries all gave errors for different protons. These results show clearly that the molecular geometries of the α,β unsaturated ketones are responsible for the errors. The errors for the alcohols were examined using ethanol as model and were shown to be due to the different possible conformations of the OH group. Similar GIAO calculations on substituted methanes gave good agreement for the methyl compounds but poor agreement for di and tri halosubstituted methanes. The aforementioned method of molecular mechanics plus GIAO calculations is shown to be a very useful tool for the investigation of molecular geometries and conformations. However, multihalogen compounds may require different basis sets for accurate calculations. Copyright © 2017 John Wiley & Sons, Ltd.     

1H, 13C, 17O NMR and quantum‐chemical study of the stereochemistry of the sulfoxide and sulfone derivatives of 3‐arylidene‐1‐thioflavan‐4‐one epoxides

The oxidation of the trans,cis‐( 2 ) and trans,trans‐epoxides ( 3 ) of differently substituted (Z)‐3‐arylidene‐1‐thioflavan‐4‐ones ( 1 ) with dimethyldioxirane (DMD) yielded the appropriate sulfoxides ( 4, 5 ) and sulfones ( 6, 7 ). The structures were elucidated by the extensive application of one‐ and two‐dimensional ¹H, ¹³C and ¹⁷O NMR spectroscopy. The conformational analysis was achieved by the application of ³J(C,H) coupling constants, NOESY responses and ab initio calculations. The preferred ground‐state conformers (twisted envelope‐A, twisted envelope‐B for 6 and twisted envelope‐A, envelope‐B for 7 ) were obtained as global minima of the theoretical ab initio MO study and also the examination of the ¹⁷O and ¹³C chemical shifts, calculated for the global minima structures of the sulfone isomers by the GIAO method. Analogous results, obtained for the sulfoxide isomers ( 4, 5 ), not only led to the preferred conformers but also gave evidence for the trans arrangement of the 2‐Ph group and the oxygen atom of the S?O group. Chemical shift differences between the isomers, sulfoxides and sulfones were corroborated by ab initio calculations of the anisotropic effects of the oxirane ring and the S?O and SO₂ groups. Copyright © 2003 John Wiley & Sons, Ltd.     

Quantum‐chemical,IR, NMR,and X‐ray diffraction studies on 2‐(4‐chlorophenyl)‐1‐methyl‐ 1H‐benzo[d]imidazole

The title molecule, 2‐(4‐chlorophenyl)‐1‐methyl‐1H‐benzo[d]imidazole (C₁₄H₁₁ClN₂), was prepared and characterized by ¹H NMR, ¹³C NMR, IR, and single‐crystal X‐ray diffraction. The molecular geometry, vibrational frequencies, and gauge including atomic orbital (GIAO) ¹H and ¹³C NMR chemical shift values of the title compound in the ground state have been calculated by using the Hartree‐Fock (HF) and density functional theory (DFT/B3LYP) method with 6‐31G(d) basis sets, and compared with the experimental data. The calculated results show that the optimized geometries can well reproduce the crystal structural parameters, and the theoretical vibrational frequencies and GIAO ¹H and ¹³C NMR chemical shifts show good agreement with experimental values. The energetic behavior of the title compound in solvent media has been examined using B3LYP method with the 6‐31G(d) basis set by applying the Onsager and the polarizable continuum model (PCM). Besides, molecular electrostatic potential (MEP), frontier molecular orbitals (FMO) analysis, and nonlinear optical (NLO) properties of the title compound were investigated by theoretical calculations. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Peptide models XXIII. Conformational model for polar side‐chain containing amino acid residues: A comprehensive analysis of RHF,DFT, and MP2 properties of HCO‐L‐SER‐NH2

Geometric and energetic properties of a diamide of serine, HCO‐NH‐L ‐CH(CH₂OH)CO‐NH₂, are investigated by standard methods of computational quantum chemistry. Similarly to other amino acid residues, conformational properties of HCO‐L ‐Ser‐NH₂ can be derived from the analysis of its E=E(ϕ,ψ;χ₁,χ₂) hypersurface. Reoptimization of 44 RHF/3‐21G conformers at the RHF/6‐311++G** level resulted in 36 minima. For all conformers, geometrical properties, including variation of H‐bond parameters and structural shifts in the torsional space, are thoroughly investigated. Results from further single‐point energy calculations at the RHF, DFT, and MP2 levels, performed on the entire conformational data set, form a database of 224 energy values, perhaps the largest set calculated so far for any single amino acid diamide. A comprehensive analysis of this database reveals significant correlation among energies obtained at six levels of ab initio theory. Regression parameters provide an opportunity for extrapolation in order to predict the energy of a conformer at a high level by doing explicit ab initio computations only for a few selected conformers. The computed conformational and relative energy data are compared with structural and occurrence results derived from a nonhomologous protein database incorporating 1135 proteins. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 626–655, 2000     

Peptide models XXXI. Conformational properties of hydrophobic residues shaping the core of proteins. An ab initio study of N‐formyl‐L‐valinamide and N‐formyl‐L‐phenylalaninamide

Employing introductory (3‐21G RHF) and medium‐size (6‐311++G** B3LYP) ab initio calculations, complete conformational libraries, containing as many as 27 conformers, have been determined for diamide model systems incorporating the amino acids valine (Val) and phenylalanine (Phe). Conformational and energetic properties of these libraries were analyzed. For example, significant correlation was found between relative energies from 6‐311++G** B3LYP and single‐point B3LYP/6‐311++G**//RHF/3‐21G calculations. Comparison of populations of molecular conformations of hydrophobic aromatic and nonaromatic residues, based on their ab initiorelative energies, with their natural abundance indicates that, at least for the hydrophobic core of proteins, the conformations of Val (Ile, Leu) and Phe (Tyr, Trp) are controlled by the local energetic preferences of the respective amino acids. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 732–751, 2001     

Synthesis and Chemical Shifts Calculation of a-Acyloxycarboxamides Derived from Indane-l,2,3-trione by DFT and HF Methods

α-Acyloxycarboxamides are synthesized from three-component Passerini reaction between indane-1,2,3-trione, isocyanides, and thiophenecarboxylic acids in quantitative yields. The structures of the final products were confirmed by IR, 1H and 13C NMR spectroscopy, mass spectrometry, and elemental analysis. The B3LYP/HF calculations for computation of 1H and 13C NMR chemical shifts have been carried out for the title compounds at the 6-311+G** and 6-311++G** basis set levels within GIAO and CSGT approaches. Predicted 1H and 13C NMR che-mical shifts have been assigned and compared with experimental 1H and 13C NMR spectra and they are supported each other.     

Ab initio, density functional theory and structural studies of 4-amino-2-methylquinoline

The Fourier transform infrared (FTIR) and FT-Raman spectra of 4-amino-2-methylquinoline (AMQ) have been recorded in the range 4000–400 and 4000–100 cm⁻¹, respectively. The experimental vibrational frequency was compared with the wavenumbers obtained theoretically by ab initio HF and DFT–B3LYP gradient calculations employing the standard 6-31G** and high level 6-311++G** basis sets for optimised geometry of the compound. The complete vibrational assignment and analysis of the fundamental modes of the compounds were carried out using the experimental FTIR and FT-Raman data, and quantum mechanical studies. The geometry and normal modes of vibration obtained from the HF and DFT methods are in good agreement with the experimental data. The potential energy distribution of the fundamental modes was calculated with ab initio force fields utilising Wilson's FG matrix method. The NH-π interactions and the influence of amino and methyl groups on the skeletal modes are investigated.     

The observed and calculated 1H and 13C chemical shifts of tertiary amines and their N-oxides

A series of model tertiary amines were oxidized in situ in an NMR tube to amine N-oxides and their (1)H and (13)C NMR spectra were recorded. Next, the chemical shifts induced by oxidation (Δδ) were calculated using different GIAO methods investigating the influence of the method [Hartree-Fock (HF), Moeller-Plesset perturbation, density functional theory (DFT)], the functional applied in the DFT (B3LYP, BPW, OPBE, OPW91) and the basis set used [6-31G*, 6-311G**, 6-311 + + G** and 6-311 + + G(3df,3pd)]. The best results were obtained with the HF/6-311 + + G** and OPBE/6-311 + + G** methods. The computation/experiment comparison approach was used for the configuration prediction of chiral amine N-oxides-(R) and (S)-agroclavine-6-N-oxide.     

Effects of different GIAO and CSGT models and basis sets on 2-aryl-1,3,4-oxadiazole derivatives

The direct molecular structure implementations of the gage-including atomic orbital (GIAO), individual gages for atoms in molecules (IGAIM) and continuous set of gage transformations (CSGT) methods for calculating nuclear magnetic shielding tensors at both the Hartree-Fock (HF) and density functional (B3LYP) levels of theory with 6-31G(d), 6-311G(d), 6-31++G(d,p), 6-311++G(d,p), and 6-311++G(df,pd) basis sets are presented. Dependence on the ¹H and ¹³C NMR chemical shifts on the choice of method and basis set have been investigated. Also, these chemical shifts of 2-aryl-1,3,4-oxadiazoles 5a–g have been performed related to dihedral angles (C4–C3–C2–O) of two conformers. The optimized molecular geometries and ¹H and ¹³C chemical shift values of 2-aryl-1,3,4-oxadiazoles 5a–g in the ground state have been obtained. The linear correlation coefficients of ¹³C NMR chemical shifts for these molecules were given. The new nuclear magnetic shielding tensors of tetramethylsilane (TMS) were calculated. The data of 2-aryl-1,3,4-oxadiazole derivatives display significant molecular structure and NMR analysis. Also, these provide the basis for future design of efficient materials having the 1,3,4-oxadiazole core.     

Theoretical Prediction of 31P NMR Chemical Shifts of Intermediates in Phosphoryl Ester Exchange and N → O Migration Reactions of Dialkyloxyphosphoryl Amino Acid

Based on a detailed ab initio study on the reaction mechanism of phosphoryl ester exchange and N → O migration reactions of dimethyloxyphosphoryl-threonine, ab initio GIAO magnetic shielding calculations have been carried out on the predicted stable intermediate and the corresponding reactant and product. The ³¹P NMR chemical shift of the most stable penta-coordinate phosphorus intermediate has been predicted as about –71 ppm. The theoretical results may lead to a possible way to experimentally examine our predictions and to monitor the most stable intermediate during the reaction process.     

Conformational study of the structure of free 12-thiacrown-4 and some of its cation metal complexes

Conformational search of 12-thiacrown-4, 12t4, was performed using the CONFLEX method and the MMFF94S force field whereby 156 conformations were predicted. Optimized geometries of the 156 predicted conformations were calculated at the HF, B3LYP, CAM-B3LYP, M06, M06L, M062x and M06HF levels using the 6-311G** basis set. The correlation energy was recovered at the MP2 level using the same 6-311G** basis set. Optimized geometries at the MP2/6-311G** level and G3MP2 energies were calculated for some of the low energy conformations. The D ₄ conformation was predicted to be the ground state conformation at all levels of theory considered in this work. Comparison between the dihedral angles of the predicted conformations indicated that for the stability of 12t4, a SCCS dihedral angle of 180° requirement is more important than a gauche CSCC dihedral angle requirement. Conformational search was performed also for the 12t4?CAg⁺, Bi³⁺, Cd²⁺, Cu⁺ and Sb³⁺ cation metal complexes using the CONFLEX method and the CAChe-augmented MM3 and MMFF94S force fields. Conformations with relative energies less than 10?kcal/mol at the MP2/6-31+G*//HF/6-31+G* level, with double zeta quality basis set on the metal cations, were considered for computations at the same levels as those used for free 12t4, using also the 6-311G** basis set. The cc-pVTZ-pp basis set was used for the metal cations. The predicted ground state conformations of the 12t4?CAg⁺, Bi³⁺, Cd²⁺, Cu⁺ and Sb³⁺ cation metal complexes are the C ₄, C ₄, C ₄, C _2v and C ₄ conformations, respectively. This is in agreement with the experimental X-ray data for the 12t4?CAg⁺ and Cd²⁺ cation metal complexes, but experimentally by X-ray, the 12t4?CBi³⁺ and Cu⁺ cation metal complexes have C _s and C ₄ structures, respectively.     

Ab initio and DFT studies on 1-(thionitrosomethylene) hydrazine: conformers, energies, and intramolecular hydrogen-bond strength

In the current study, we present an intramolecular HB, molecular structure, π-electrons delocalization and vibrational frequencies analysis of 25 possible conformers of 1-(thionitrosomethylene) hydrazine by means of DFT (B3LYP), MP2 methods in conjunction with the 6-311++G** and augmented correlation-consistent polarized-valence triple-zeta basis sets and G2MP2 theoretical level. The influence of the solvent on the stability order of conformers and the strength of intramolecular hydrogen-bonding was considered using the Tomasi’s polarized continuum model. Statistical analyses of quantitative definitions of aromaticity, nucleus independent chemical shift, harmonic oscillator model of aromaticity, aromatic fluctuation index, and the π-electron delocalization parameter (Q) as a geometrical indicator of a local aromaticity, evaluated for this conformers. Further verification of the obtained transition state structures were implemented via intrinsic reaction coordinate (IRC) analysis. Calculations of the ¹H NMR chemical shift at GIAO/B3LYP/6-311++G** levels of theory are also presented. The calculated highest occupied molecular orbital (MO) and lowest unoccupied MO energies show that charge transfer occur within the molecule. Hydrogen-bond energies for H-bonded conformers were obtained from Espinosa method and the natural bond orbital theory and the atoms in molecules theory were also applied to get a more precise insight into the nature of such H-bond interactions.     

OPLS all-atom force field for carbohydrates

The OPLS all-atom (AA) force field for organic and biomolecular systems has been expanded to include carbohydrates. Starting with reported nonbonded parameters of alcohols, ethers, and diols, torsional parameters were fit to reproduce results from ab initio calculations on the hexopyranoses, α,β-d -glucopyranose, α,β-d -mannopyranose, α,β-d -galactopyranose, methyl α,β-d -glucopyranoside, and methyl α,β-d -mannopyranoside. In all, geometry optimizations were carried out for 144 conformers at the restricted Hartree–Fock (RHF)/6–31G* level. For the conformers with a relative energy within 3 kcal/mol of the global minima, the effects of electron correlation and basis-set extension were considered by performing single-point calculations with density functional theory at the B3LYP/6–311+G** level. The torsional parameters for the OPLS-AA force field were parameterized to reproduce the energies and structures of these 44 conformers. The resultant force field reproduces the ab initio calculated energies with an average unsigned error of 0.41 kcal/mol. The α/β ratios as well as the relative energies between the isomeric hexopyranoses are in good accord with the ab initio results. The predictive abilities of the force field were also tested against RHF/6–31G* results for d -allopyranose with excellent success; a surprising discovery is that the lowest energy conformer of d -allopyranose is a β anomer. © 1997 John Wiley & Sons, Inc. J Comput Chem 18 : 1955–1970, 1997     

Torsion angle relationship of the 17O NMR chemical shift in α,β‐unsaturated carbonyl compounds

The torsion angle effect on the isotropic shielding of ¹⁷O nucleus in α,β‐unsaturated carbonyl groups is studied by means of density functional theory (DFT) calculations using a polarizable continuum model (PCM) for the solvent, employing the PBE0 functional together with the 6‐311G(d,p) basis set for geometry optimization, and the 6‐311+G(2d,p) basis set for calculating the NMR shielding with the gauge‐including atomic orbitals (GIAO) method. This study adds new information on the sensitivity of the ¹⁷O nucleus to conformational changes, revealing a strong dependence of the ¹⁷O NMR chemical shift on the dihedral angle between the carbonyl and the vinyl moiety in all studied compounds; remarkable differences are observed with the data reported for α‐diketones. Copyright © 2009 John Wiley & Sons, Ltd.     

Isomers of SiCl3Li

An ab initio study on the title compound was performed in this work. The structures at MP2(FULL)/6‐311G* level of theory and their energies at the CCSD(T)/6‐311G* level of theory were provided. Their vibrational frequencies and ²⁹Si nuclear magnetic resonance (NMR) chemical shift had been carried out too. The thermodynamic data were calculated in order to help judge the relative stability of the isomers of SiCl₃Li at experimental temperatures. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 79: 17–24, 2000