Density functional computation of 55Mn NMR parameters

Gradient-corrected (GGA) and hybrid variants of density functional theory are used to compute geometries and ⁵⁵Mn chemical shifts of MnO₄ ⁻, Mn(CO)₆ ⁺, Mn₂(CO)₁₀, Mn(CO)₅ X [X=H, Cl, C(O)Me], Mn(CO)₅ ⁻, Mn(NO)₃(CO), and Mn(C₅H₅)L _x [L _x =(CO)₃, C₆H₆, C₇H₈]. For this set of compounds, substituent effects on δ(⁵⁵Mn) are significantly underestimated with the pure GGA functional BPW91 and are well described with hybrid functionals such as mPW1PW91 and, in particular, B3LYP. The computed data provide evidence for solvent and counterion effects on δ(⁵⁵Mn) of MnO₄ ⁻ and Mn(CO)₆ ⁺, respectively. The latter, in the presence of Cl⁻, may be described as highly fluxional Mn(CO)₅C(O)Cl. Electric field gradients computed with the B3LYP functional can be used for a qualitative rationalization of observed trends in ⁵⁵Mn NMR line widths. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s002140020338x Received: 17 January 2002 / Accepted: 13 March 2002 / Published online: 3 June 2002     

Four‐component relativistic DFT calculations of 77Se NMR chemical shifts: A gateway to a reliable computational scheme for the medium‐sized organoselenium molecules

A versatile high‐accuracy computational scheme for the ⁷⁷Se nuclear magnetic resonance (NMR) chemical shifts of the medium‐sized organoselenium compounds is suggested within a framework of a full four‐component relativistic density functional theory (DFT). The main accuracy factors (DFT functionals, relativistic geometry, vibrational corrections, and solvent effects) are addressed. The best result is achieved with NMR‐oriented KT2 functional of Keal–Tozer characterized by a fairly small error of only 30 ppm for the span of about 1700 ppm (<2%). © 2015 Wiley Periodicals, Inc.     

Comparative analysis of 13C shielding constants stereospecificity in the silicon and germanium derivatives of acetylenic aldehyde and ketone oximes based on the 13C NMR spectroscopy and GIAO calculations

In the acetylenic aldehyde oximes with substituents containing silicon and germanium, the ¹³C NMR signal of the C‐2 carbon of triple bond is shifted by 3.5 ppm to lower frequency and that of the C‐3 carbon is moved by 7 ppm to higher frequency on going from E to Z isomer. A greater low‐frequency effect of 5.5 ppm on the C‐2 carbon signal and a greater high‐frequency effect of 11 ppm on the C‐3 carbon signal are observed in the analogous acetylenic ketone oximes. The carbon chemical shift of the C?N bond is larger by 4 ppm in E isomer relative to Z isomer for the aldehyde and ketone oximes. The ²⁹Si chemical shifts in the silicon containing acetylenic aldehyde and ketone oximes are almost the same for the diverse isomers. The trends in changes of the measured chemical shifts are well reproduced by the gauge‐including atomic orbital (GIAO) calculations of the ¹³C and ²⁹Si shielding constants. Copyright © 2009 John Wiley & Sons, Ltd.     

A density functional theory study of a concerted mechanism for proton exchange between amino acid side chains and water

 A concerted mechanism for proton exchange between water and the amino acid side chains of cysteine, serine, arginine and glutamic acid has been investigated with hybrid density functional theory. The models used include, besides the amino acid side chain, a number of water molecules ranging from one to five in some cases. The modeling of the amino acids without their backbones is shown to be an excellent approximation. Long-range polarization effects were incorporated through a dielectric cavity method allowing a better comparison to existing measurements for free amino acids in water. The barriers converge rather fast with the number of water molecules for all the present amino acids and the converged values are in reasonable agreement with experiments with discrepancies in the range 2–6 kcal/mol. The dielectric effects were found to be small for all systems except cysteine, where there is a lowering of the barrier by 3–5 kcal/mol. The transition states for these concerted pathways form rings in which the separated charges can be stabilized. Received: 25 October 1999 / Accepted: 5 April 2000 / Published online: 21 June 2000     

Prediction of the Raman spectrum of the aqueous formate anion by a combined density functional theory and self-consistent-reaction-field study

Formate, HCOO⁻, is a small ion that can be used as a convenient model to represent general carboxylic acids as well as the terminal side chains of glutamic and aspartic amino acids in biological systems. Several ab initio techniques (Hartree–Fock and density functional theory methods) were used to study the formate anion in aqueous solution, where the solvent was treated as an electrostatic influence by means of a self-consistent-reaction-field (SCRF) method. The comparison of calculated frequencies with Raman experimental data constitutes a good test for the solvation model employed in this work. The results showed that the application of a SCRF method not only produced smaller errors but also improved the linear correlation between predicted and experimental values. This latter characteristic enables a more efficient application of a linear scaling factor, λ, which corrects the calculated frequencies. In fact, the application of λ to the values calculated for the continuum, when compared to those obtained for a vacuum, resulted in smaller root-mean-square errors of the deviations from the experimental data. Received: 15 May 2000 / Accepted: 19 June 2000 / Published online: 11 September 2000     

Pronounced stereospecificity of 1H, 13C, 15N and 77Se shielding constants in the selenophenyl oximes as shown by NMR spectroscopy and GIAO calculations

In the ¹H and ¹³C NMR spectra of 1‐(2‐selenophenyl)‐1‐alkanone oximes, the ¹H, the ¹³C‐3 and ¹³C‐5 signals of the selenophene ring are shifted by 0.1–0.4, 2.5–3.0 and 5.5–6.0 ppm, respectively, to higher frequencies, whereas those of the ¹³C‐1, ¹³C‐2 and ¹³C‐4 carbons are shifted by 4–5, ～11 and ～1.7 ppm to lower frequencies on going from the E to Z isomer. The ¹⁵N chemical shift of the oximic nitrogen is larger by 13–16 ppm in the E isomer relative to the Z isomer. An extraordinarily large difference (above 90 ppm) between the ⁷⁷Se resonance positions is revealed in the studied oxime isomers, the ⁷⁷Se peak being shifted to higher frequencies in the Z isomer. The trends in the changes of the measured chemical shifts are well reproduced by the GIAO calculations of the ¹H, ¹³C, ¹⁵N and ⁷⁷Se shielding constants in the energy‐favorable conformation with the syn orientation of the? C?N? O? H group relative to the selenophene ring. Copyright © 2009 John Wiley & Sons, Ltd.     

A density functional theory study of the conformational properties of 1,2-ethanediamine: protonation and solvent effects

 The structures and the conformational energies of nonprotonated, monoprotonated and diprotonated 1,2-ethanediamine have been investigated through density functional theory. The relative performance of local and gradient-corrected functionals is discussed. The existence of hydrogen-bond formation has been determined with electron localisation function calculations. Proton affinities for nonprotonated and monoprotonated 1,2-ethanediamine have been calculated and are in agreement with experimental data. The influence of solvation has been accounted for through the self-consistent isodensity polarisable continuum model. The results for the nonprotonated conformers show that solvation stabilises those conformers which have the lone pair in an antiperiplanar conformation. Solvation of the monoprotonated conformer stabilises significantly the “anti” conformation, which is unstable in the gas phase. For the di-protonated species, solvation stabilises slightly the gauche conformer, which is unstable in the gas phase. Received: 28 September 1999 / Accepted: 2 May 2000 / Published online: 27 September 2000     

On the importance of intramolecular hydrogen bond cooperativity in d‐glucose – an NMR and QTAIM approach

The idea that hydrogen bond cooperativity is responsible for the structure and reactivity of carbohydrates is examined. Density functional theory and gauge‐including atomic orbital calculations on the known conformers of the α and β anomers of d ‐glucopyranose in the gas phase are used to compute proton NMR chemical shifts and interatomic distances, which are taken as criteria for probing intramolecular interactions. Atom–atom interaction energies are calculated by the interacting quantum atoms approach in the framework of the quantum theory of atoms in molecules. Association of OH1 in the counterclockwise conformers with a strong acceptor, pyridine, is accompanied by cooperative participation from OH2, but there is no significant change in the bonding of the two following 1,2‐diol motifs. The OH6 ^... O5 (G?g+/cc/t and G+g?/cc/t conformers) or OH6 ^... O4 (Tg+/cc/t conformer) distance is reduced, and the OH6 proton is slightly deshielded. In the latter case, this shortening and the associated increase in the OH6–O4 interaction energy may be interpreted as a small cooperative effect, but intermolecular interaction energies are practically the same for all three conformers. In most of the pyridine complexes, one ortho proton interacts with the endocyclic oxygen O5. Analogous results are obtained when the clockwise conformer, G?g+/cl/g?, detected for the α anomer, and a hypothetical conformer, Tt/cl/g?, are complexed with pyridine through OH6. Generally, the cooperative effect does not go beyond the first two OH groups of a chain. Copyright © 2017 John Wiley & Sons, Ltd.     

The electron affinities of transition metal atoms at the CCSD(T) and density functional levels of theory

 The electron affinities of Ti, V, Cr, Fe, Co, Ni, and Cu are computed using the density function theory and CCSD(T) approaches. Overall the CCSD(T) approach yields the best results. For this property, the B3LYP, BLYP, and BP86 functionals perform better than the BPW91, PBEPBE, and PBE1PBE ones. The accuracy of all the methods is higher if the number of 3delectrons is the same in the neutral atom and the anion. This is especially true for the density functional theory methods. Received: 23 January 2002 / Accepted: 1 April 2002 / Published online: 24 June 2002     

The reduction of ribonucleotides catalyzed by the enzyme ribonucleotide reductase

This work is devoted to the study of the radical catalytic pathway for the ribonucleotide reduction process assisted by ribonucleotide reductase. The present study is directed toward the investigation of one of the most controversial steps in the reduction pathway – the elimination of the 2′ hydroxyl group from the ribonucleotide. Several groups have made different proposals for this step, which all fit available experimental data; however, so far, it has not been possible to demonstrate clearly which is the correct pathway for the elimination. Here, we resort to high-level quantum mechanical calculations to analyze the energetics of the proposed mechanisms, as well as to propose alternative pathways, and evaluate their feasibility, according to the observed kinetics of the enzyme and other existing experimental data. Our study shows that the elimination occurs via two different simultaneous acid-/base-catalyzed pathways, depending on the protonation state of one key active site amino acid, Glu441.     

Computational NMR spectroscopy: reversing the information flow

Work on computational NMR recently carried out at our Laboratory in Padova is reviewed. We summarize our results concerning the calculation of NMR properties (chemical shifts and spin–spin coupling constants) in a variety of contexts, from the structure elucidation of complex organic molecules or molecules containing heavy atoms to weakly interacting species, such as those involved in hydrogen bonding or van der Waals CH-π interactions. We also present some original results, viz. the calculated ¹H and ¹³C spectra of the putative natural substance nimbosodione, the first examples of calculated ¹⁸¹Ta chemical shifts, spin–spin couplings in and through-space coupling constants involving ²⁰⁵Tl.     

The calculation of electron localization and delocalization indices at the Hartree–Fock, density functional and post-Hartree–Fock levels of theory

 Localization, λ(A), and delocalization indices, δ(A,B), as defined in the atoms in molecules theory, are a convenient tool for the analysis of molecular electronic structure from an electron-pair perspective. These indices can be calculated at any level of theory, provided that first- and second-order electron densities are available. In particular, calculations at the Hartree–Fock (HF) and configuration interaction (CI) levels have been previously reported for many molecules. However, λ(A) and δ(A,B) cannot be calculated exactly in the framework of Kohn–Sham (KS) density functional theory (DFT), where the electron-pair density is not defined. As a practical workaround, one can derive a HF-like electron-pair density from the KS orbitals and calculate approximate localization and delocalization indices at the DFT level. Recently, several calculations using this approach have been reported. Here we present HF, CI and approximate DFT calculations of λ(A) and δ(A,B) values for a number of molecules. Furthermore, we also perform approximate CI calculations using the HF formalism to obtain the electron-pair density. In general, the approximate DFT and CI results are closer to the HF results than to the CI ones. Indeed, the approximate calculations take into account Coulomb electron correlation effects on the first-order electron density but not on the electron-pair density. In summary, approximate DFT and CI localization and delocalization indices are easy to calculate and can be useful in the analysis of molecular electronic structure; however, one should take into account that this approximation increases systematically the delocalization between covalently bonded atoms, with respect to the exact CI results. Received: 13 February 2002 / Accepted: 24 April 2002 / Published online: 18 June 2002     

Orbital-band interactions and the reactivity of molecules on oxide surfaces: from explanations to predictions

 The surface chemistry of oxides is relevant for many technological applications: catalysis, photoelectrolysis, electronic-device fabrication, prevention of corrosion, sensor development, etc. This article reviews recent theoretical works that deal with the surface chemistry of oxides. The account begins with a discussion of results for the adsorption of CO and NO on oxides, systems which have been extensively studied in the literature and constitute an ideal benchmark for testing the quality of different levels of theory. Then, systematic studies concerned with the behavior of adsorbied alkali metals and sulfur-containing molecules are presented. Finally, a correlation between the electronic and chemical properties of mixed-metal oxides is analyzed and basic principles for designing chemically active oxides are introduced. Advances in theoretical methods and computer capabilities have made possible a fundamental understanding of many phenomena associated with the chemistry of molecules on oxide surfaces. Still many problems in this area remain as a challenge, and the approximate nature of most theoretical methods makes necessary a close coupling between theory and experiment. Following this multidisciplinary approach, the importance of band-orbital interactions for the reactivity of oxide surfaces has become clear. Simple models based on band-orbital mixing can explain trends found for the interaction of many adsorbates with oxide surfaces. These simple models provide a conceptual framework for modifying or controlling the chemical activity of pure oxides and for engineering mixed-metal oxides. In this respect, theoretical calculations can be very useful for predicting the best ways for enhancing the reactivity of oxide systems and reducing the waste of time, energy and materials characteristic of an empirical design. Received: 21 June 2001 / Accepted: 8 October 2001 / Published online: 1 February 2002     

Heteroelectrocyclic reactions of 3-acyl-4-azido heterocycles: ab initio and density functional calculations on 3-azido-propenal as a model system

 Concerted as well as stepwise reaction pathways for cyclization of 3-azido-propenal to isoxazole have been investigated by density functional (B3LYP) and ab initio methods up to CCSD(T)/cc-pVQZ methods. These calculations clearly establish the pathway with concerted albeit asynchronous nitrogen extrusion and ring closure as the most feasible mechanism. Barriers for cyclization increase in the order Hartree–Fock<B3LYP<ACPF<CCSD(T). According to the geometrical parameters and the electronic structure of the TS as evidenced by natural bond order analysis this cyclization can be interpreted as a pseudopericyclic (heteroelectrocyclic) reaction. Received: 26 May 2002 / Accepted: 18 June 2002 / Published online: 14 February 2003     

Theoretical predictions of the structure, gas-phase acidity and aromaticity of 1,2-diseleno-3,4-dithiosquaric acid

Results of ab initio self-consistent-field (SCF) and density functional theory (DFT) calculations of the gas-phase structure, acidity (free energy of deprotonation, ΔG^o), and aromaticity of 1,2-diseleno-3,4-dithiosquaric acid (3,4-dithiohydroxy-3-cyclobutene-1,2-diselenone, H₂C₄Se₂S₂) are reported. The global minimum found on the potential energy surface of 1,2-diseleno-3,4-dithiosquaric acid presents a planar conformation. The ZZ isomer was found to have the lowest energy among the three planar conformers and the ZZ and ZE isomers are very close in energy. The optimized geometric parameters exhibit a bond length equalization relative to reference compounds, cyclobutanediselenone, and cyclobutenedithiol. The computed aromatic stabilization energy (ASE) by homodesmotic reaction (Eq 1) is −20.1 kcal/mol (MP2(fu)/6-311+G** //RHF/6-311+G**) and −14.9 kcal/mol (B3LYP//6-311+G**//B3LYP/6-311+G**). The aromaticity of 1,2-diseleno-3,4-dithiosquaric acid is indicated by the calculated diamagnetic susceptibility exaltation (Λ) −17.91 (CSGT(IGAIM)-RHF/6-311+G**//RHF/6-311+G**) and −31.01 (CSGT(IGAIM)-B3LYP/6-311+G**//B3LYP/6-311+G**). Thus, 1,2-diseleno-3,4-dithiosquaric acid fulfils the geometric, energetic and magnetic criteria of aromaticity. The calculated theoretical gas-phase acidity is ΔG^o _1(298K)=302.7 kcal/mol and ΔG^o _2(298K)=388.4 kcal/mol. Hence, 1,2-diseleno-3,4-dithiosquaric acid is a stronger acid than squaric acid(3,4-dihydroxy-3-cyclobutene-1,2-dione, H₂C₄O₄). Received: 11 April 2000 / Accepted: 7 July 2000 / Published online: 27 September 2000     

Recent applications of density functional theory calculations to biomolecules

The purpose of this overview is to highlight the broad scope and utility of current applications of density functional theory (DFT) methods for the study of the properties and reactions of biomolecules. This is illustrated using examples selected from research carried out within our research group and in collaboration with others. The examples include the hyperfine coupling constants of amino acid radicals, the use of an amino acid as a chiral catalyst for the formation of carbon–carbon bonds in the aldol reaction, hydrogen-bond mediated catalysis of an aminolysis reaction, radiation-induced protein–DNA cross-links, and the mechanism by which an antitumor drug cleaves DNA. We demonstrate that DFT-based methods can be applied successfully to a broad range of problems that remain beyond the scope of conventional electron-correlation methods. Furthermore, we show that contemporary computational quantum chemistry complements experiment in the study of biological systems. Received: 19 December 2001 / Accepted: 8 April 2002 / Published online: 4 July 2002     

Structures and stability of N7+ and N7− clusters

Ab initio molecular orbital theory and density functional theory have been used to study nine isomers of N₇ ionic clusters with low spin at the HF/6-31G*, MP2/6-31G*, B3LYP/6-31G*, and B3LYP/6-311(+)G* levels of theory. All stationary points are examined with harmonic vibrational frequency analyses. Four N₇ ⁺ isomers and five N₇ ⁻ isomers are determined to be local minima or very close to the minima on their potential-energy hypersurfaces, respectively. For N₇ ⁺ and N₇ ⁻, the energetically low lying isomers are open-chain structures (C _{2 v} and C _{2 v} or C₂). The results are very similar to those of other known odd-number nitrogen ions, such as N₅ ⁺, N₉ ⁺, and N₉ ⁻, for which the open-chain structures are also the global minima. This research suggests that the N₇ ionic clusters are likely to be stable and to be potential high-energy-density materials if they could be synthesized. Received: 16 July 2001 / Accepted: 8 October 2001 / Published online: 21 January 2002