Performance of wave function and density functional methods for water hydrogen bond spin–spin coupling constants

Spin–spin coupling constants in water monomer and dimer have been calculated using several wave function and density functional-based methods. CCSD, MCSCF, and SOPPA wave functions methods yield similar results, specially when an additive approach is used with the MCSCF. Several functionals have been used to analyze their performance with the Jacob’s ladder and a set of functionals with different HF exchange were tested. Functionals with large HF exchange appropriately predict ¹ J _{O H} , ² J _{H H} and ^2h J _{O O} couplings, while ^1h J _{O H} is better calculated with functionals that include a reduced fraction of HF exchange. Accurate functionals for ¹ J _{O H} and ² J _{H H} have been tested in a tetramer water model. The hydrogen bond effects on these intramolecular couplings are additive when they are calculated by SOPPA(CCSD) wave function and DFT methods.

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Graphical Abstract Evaluation of the additive effect of the hydrogen bond on spin-spin coupling constants of water using WF and DFT methods.

     

A hybrid model of intercellular tension and cell–matrix mechanical interactions in a multicellular geometry

Biomechanics and Modeling in Mechanobiology - Epithelial cells form continuous sheets of cells that exist in tensional homeostasis. Homeostasis is maintained through cell-to-cell junctions that...     

Transformation of the θ-phase in Mg-Li-Al alloys: a density functional theory study

In Mg-Li-Al alloys, θ-phase MgAlLi₂ is a strengthening and metastable phase which is liable to be transformed to the equilibrium phase AlLi on overaging. While the structural details of the θ-phase MgAlLi₂ and the microscopic transformation are still unknown. In this paper, the structure of MgAlLi₂ unit cell was determined through X-ray powder diffraction simulation. Microscopic transformation process of θ-phase MgAlLi₂ was discussed in detail using first principles method.     

Cation-π interactions induce kinking of a molecular hinge in the RNA polymerase bridge-helix domain

RNAPs (RNA polymerases) are complex molecular machines that contain a highly conserved catalytic site surrounded by conformationally flexible domains. High-throughput mutagenesis in the archaeal model system Methanocaldococcus jannaschii has demonstrated that the nanomechanical properties of one of these domains, the bridge-helix, exert a key regulatory role on the rate of the NAC (nucleotide-addition cycle). Mutations that increase the probability and/or half-life of kink formation in the BH-HC (bridge-helix C-terminal hinge) cause a substantial increase in specific activity ('superactivity'). Fully atomistic molecular dynamics simulations show that kinking of the BH-HC appears to be driven by cation-π interactions and involve amino acid side chains that are exceptionally highly conserved in all prokaryotic and eukaryotic species.     

Antioxidant activity of phenolic and related compounds: a density functional theory study on the O–H bond dissociation enthalpy

Abstract

We report here on calculations at the hybrid DFT/HF (B3-LYP/6-31G(d, p)) level of the O–H bond dissociation enthalpy (O–H BDE) of phenylpropenoic acids (caffeic, ferulic, p-coumaric and cinnamic) and phenolic acids and related compounds (gallic, methylgallate, vanillic and gentisic) in order to gain insight into the understanding of structure–antioxidant activity relationships. The results were correlated and discussed mainly on the basis of experimental data in a companion work (Galato D, Giacomelli C, Ckless K, Susin MF, Vale RMR, Spinelli A. Antioxidant capacity of phenolic and related compounds: correlation among electrochemical, visible spectroscopy methods and structure-antioxidant activity. Redox Report 2001; 6: 243–250). The O–H BDE values showed remarkable dependence on the hydroxyl position in the benzene ring and the existence of additional interaction due to hydrogen bonding. For parent molecules, the experimental antioxidant activity (AA) order was properly obeyed only when intramolecular hydrogen bonding was present in the radicalized structures of o-dihydroxyl moieties. In structurally related compounds, excellent correlation with experimental data was in general observed (0.64 < ρ < 0.99). However, it is shown that excellent correlation can also be obtained for this series of compounds considering p-radicalized structures which were not stabilized by intramolecular hydrogen bonding, but this had no physical meaning. These findings suggested that the antioxidant activity evaluation of phenolic and related compounds must take into consideration the characteristics of each particular compound.     

Molecular structure,vibrational spectra and HOMO,LUMO analysis of 4-piperidone by density functional theory and ab initio Hartree–Fock calculations

Vibrational frequencies and geometrical parameters of 4-piperidone (4-PID) in the ground state have been calculated by using the Hartree–Fock (HF) and density functional methods (B3LYP) with 6-311++G(d,p) and 6-311+G(3df,2p) basis sets. These methods are proposed as a tool to be applied in the structural characterisation of 4-PID (C₅H₉NO). The title molecule has C _s point group symmetry, thus providing useful support in the interpretation of experimental IR and Raman data. The DFT-B3LYP/6-311+G(3df,2p) calculations have been found more reliable than the ab initio HF/6-311++G(d,p) calculations for the vibrational study of 4-PID. The calculated highest occupied molecular orbital and lowest unoccupied molecular orbital energies show that charge transfer occurs within the molecule. The theoretical spectrograms for FT-IR and FT-Raman spectra of the title molecule have been constructed.     

Br?nsted-Evans-Polanyi relationships for C–C bond forming and C–C bond breaking reactions in thiamine-catalyzed decarboxylation of 2-keto acids using density functional theory

The concept of generalized enzyme reactions suggests that a wide variety of substrates can undergo enzymatic transformations, including those whose biotransformation has not yet been realized. The use of quantum chemistry to evaluate kinetic feasibility is an attractive approach to identify enzymes for the proposed transformation. However, the sheer number of novel transformations that can be generated makes this impractical as a screening approach. Therefore, it is essential to develop structure/activity relationships based on quantities that are more efficient to calculate. In this work, we propose a structure/activity relationship based on the free energy of binding or reaction of non-native substrates to evaluate the catalysis relative to that of native substrates. While Br?nsted-Evans-Polanyi (BEP) relationships such as that proposed here have found broad application in heterogeneous catalysis, their extension to enzymatic catalysis is limited. We report here on density functional theory (DFT) studies for C–C bond formation and C–C bond cleavage associated with the decarboxylation of six 2-keto acids by a thiamine-containing enzyme (EC 1.2.7.1) and demonstrate a linear relationship between the free energy of reaction and the activation barrier. We then applied this relationship to predict the activation barriers of 17 chemically similar novel reactions. These calculations reveal that there is a clear correlation between the free energy of formation of the transition state and the free energy of the reaction, suggesting that this method can be further extended to predict the kinetics of novel reactions through our computational framework for discovery of novel biochemical transformations.     

Copper(II) complexes based on a new chelating 4-(3,5-diphenyl-1H-pyrazol-1-yl)-6-(piperidin-1-yl)pyrimidine ligand: Synthesis and crystal structures. Lone pair-π, C-H···π, π-π and C-H···A (A = N, Cl) non-covalent interactions

A new bidentate chelating pyrazolylpyrimidine ligand bearing a strong electron-donating substituent, i.e. 4-(3,5-diphenyl-1H-pyrazol-1-yl)-6-(piperidin-1-yl)pyrimidine (L) (Scheme 1), has been synthesized and used to obtain the copper(II) complexes by reaction with CuCl₂. The molar ratio Cu:L = 1:2 leads to isolation of a complex having CuL₂Cl₂ empirical formula, while the molar ratio Cu:L = 1:1 gives a complex with CuLCl₂ empirical formula. The crystal structure of L as well as the structures of both complexes were studied by single crystal X-ray diffraction. The crystal structure of CuL₂Cl₂ compound is formed by trans-[CuL₂Cl₂] mononuclear molecules. Surprisingly, in contrast to the previous compound having molecular structure, the crystal structure of CuLCl₂ consists of mononuclear [CuL₂Cl]⁺ complex cations and dinuclear [Cu₂Cl₆]²⁻ anions. Thus, formula of CuLCl₂ complex can be represented as [CuL₂Cl]₂[Cu₂Cl₆]. In both complexes molecules of L adopt bidentate chelating coordination mode through N² atom of pyrazole and N³ atom of pyrimidine rings forming five-membered CuN₃C metallocycles. Owing to C-H···N interactions and π-π-stacking L molecules form 2D network. In the structure of trans-[CuL₂Cl₂] there exist double lone pair(N(piperidine))-π(pyrimidine) interactions and C-H···Cl contacts resulting in the formation of 1D chains. Layered 2D structure of [CuL₂Cl]₂[Cu₂Cl₆] results from C-H···Cl, C-H···π and double lone pair(Cl([CuL₂Cl]⁺ complex cation)-π(pyrimidine) interactions.     

Structures, spectroscopic and thermodynamic properties of U2On (n = 0 ∼ 2, 4) molecules: a density functional theory study

The equilibrium structures, spectroscopic and thermodynamic parameters [entropy (S), internal energy (E), heat capacity (C _p)] of U₂, U₂O, U₂O₂ and U₂O₄ uranium oxide molecules were investigated systematically using density functional theory (DFT). Our computations indicated that the ground electronic state of U₂ is the septet state and the equilibrium bond length is 2.194 Å; the ground electronic state of U₂O and U₂O₂ were found to be $ {\tilde{X}}^3\varPhi $ and $ {\tilde{X}}^3{\sum}_{\mathrm{g}} $ with stable C _∞v and D _∞h linear structures, respectively. The bridge-bonded structure with D _2h symmetry and $ {\tilde{X}}^3{\mathrm{B}}_{1\mathrm{g}} $ state is the most stable configuration for the U₂O₄ molecule. Mulliken population analyses show that U atoms always lose electrons to become the donor and O atoms always obtain electrons as the acceptor. Molecular orbital analyses demonstrated that the frontier orbitals of the title molecules were contributed mostly by 5f atomic orbitals of U atoms. Vibrational frequencies analyses indicate that the maximum absorption peaks stem from the stretching mode of U–O bonds in U₂O, U₂O₂ and U₂O₄. In addition, thermodynamic data of U₂O_n (n?=?0?～?4) molecules at elevated temperatures of 293.0 K to 393.0 K was predicted.     

Intramolecular hydrogen bonding, π-π stacking interactions,and substituent effects of 8-hydroxyquinoline derivative supermolecular structures: a theoretical study

Journal of Molecular Modeling - Syn and anti dihydropyrene (DHP) are excellent thermochromes, and therefore extensively studied for their thermochromic and photochromic properties, respectively....     

The effects of tautomerization and protonation on the adenine–cytosine mismatches: a density functional theory study

In the present work, we demonstrate the results of a theoretical study concerned with the question how tautomerization and protonation of adenine affect the various properties of adenine–cytosine mismatches. The calculations, in gas phase and in water, are performed at B3LYP/6-311++G(d,p) level. In gas phase, it is observed that any tautomeric form of investigated mismatches is more stabilized when adenine is protonated. As for the neutral mismatches, the mismatches containing amino form of cytosine and imino form of protonated adenine are more stable. The role of aromaticity on the stability of tautomeric forms of mismatches is investigated by NICS(1)_ZZ index. The stability of mispairs decreases by going from gas phase to water. It can be explained using dipole moment parameter. The influence of hydrogen bonds on the stability of mismatches is examined by atoms in molecules and natural bond orbital analyses. In addition to geometrical parameters and binding energies, the study of the topological properties of electron charge density aids in better understanding of these mispairs.     

Comparison of the activation energy barrier for succinimide formation from α- and β-aspartic acid residues obtained from density functional theory calculations

The l-α-Asp residues in peptides or proteins are prone to undergo nonenzymatic reactions to form l-β-Asp, d-α-Asp, and d-β-Asp residues via a succinimide five-membered ring intermediate. From these three types of isomerized aspartic acid residues, particularly d-β-Asp has been widely detected in aging tissue. In this study, we computationally investigated the cyclization of α- and β-Asp residues to form succinimide with dihydrogen phosphate ion as a catalyst (H₂PO₄⁻). We performed the study using B3LYP/6-31 + G(d,p) density functional theory calculations. The comparison of the activation barriers of both residues is discussed. All the calculations were performed using model compounds in which an α/β-Asp-Gly sequence is capped with acetyl and methylamino groups on the N- and C-termini, respectively. Moreover, H₂PO₄⁻ catalyzes all the steps of the succinimide formation (cyclization-dehydration) acting as a proton-relay mediator. The calculated activation energy barriers for succinimide formation of α- and β-Asp residues are 26.9 and 26.0 kcal mol^− 1, respectively. Although it was experimentally confirmed that β-Asp has higher stability than α-Asp, there was no clear difference between the activation barriers. Therefore, the higher stability of β-Asp residue than α-Asp residue may be caused by an entropic effect associated with the succinimide formation.     

Natural bond orbital, nuclear magnetic resonance analysis and hybrid-density functional theory study of σ-aromaticity in Al2F6, Al2Cl6, Al2Br6 and Al2I6

Natural bond orbital (NBO), nuclear magnetic resonance (NMR) analysis and hybrid-density functional theory based method (B3LYP/Def2-TZVPP) were used to investigate the correlation between the nucleus-independent chemical shifts [NICS, as an aromaticity criterion], σ _Al(1)-X2(b) → σ*_Al(3)-X4(b) electron delocalizations and the dissociation energies of Al₂F₆, Al₂Cl₆, Al₂Br₆ and Al₂I₆ to 2AlX₃ (X?=?F, Cl, Br, I). The results obtained showed that the dissociation energies of Al₂F₆, Al₂Cl₆, Al₂Br₆ and Al₂I₆ decrease from Al₂F₆ to Al₂I₆. Like aromatic molecules, these compounds have relatively significant negative NICS_iso(0) values. Clearly, based on magnetic criteria, they exhibit aromatic character and make it possible to consider them as σ-delocalized aromatic species, such as Möbius σ-aromatic species. The σ-aromatic character which is demonstrated by their NICS_iso(0) values decreases from Al₂F₆ to Al₂I₆. The NICS_iso values are dominated by the in-plane σ₂₂ (i.e., σ_yy, the plane containing halogen atoms bridged) chemical shift components. The increase of the NICS_iso values explains significantly the decrease of the corresponding dissociation energies of Al₂F₆, Al₂Cl₆, Al₂Br₆ and Al₂I₆. Importantly, the NBO results suggest that in these compounds the dissociation energies are controlled by the stabilization energies associated with σ _Al(1)-X2(b) →σ*_Al(3)-X4(b) electron delocalizations. The decrease of the stabilization energies associated with σ _Al(1)-X2(b) →σ*_Al(3)-X4(b) electron delocalizations is in accordance with the variation of the calculated NICS_iso values. The correlations between the dissociation energies of Al₂F₆, Al₂Cl₆, Al₂Br₆ and Al₂I₆, σ _Al(1)-X2(b) →σ*_Al(3)-X4(b) electron delocalizations, natural atomic orbitals (NAOs) and NICS_iso values have been investigated.     

Mössbauer identification of a protonated ferryl species in catalase from Proteus mirabilis: density functional calculations on related models

The Proteus mirabilis catalase is one of the most efficient heme-containing catalase and forms a relatively stable compound II. Samples of compound II were prepared from PMC enriched in (57)Fe. For the first time, two different forms of compound II, namely low pH compound II (LpH II) (43%) and high pH compound II (HpH II) (25%), have been characterized by M?ssbauer spectroscopy at pH 8.3. The ratio LpH II/HpH II increases irreversibly with decreasing pH. The large quadrupole splitting value of LpH II (DeltaE(Q)=2.29 (2) mm/s, with delta(/Fe)=0.03 (2) mm/s), compared to that of HpH II (DeltaE(Q)=1.47 (2) mm/s, with delta(/Fe)=0.07 (2) mm/s), reflects the protonation of the ferryl group. Quadrupole splitting values of 1.46 and 2.15mm/s have been computed by DFT for optimized models of the ferryl compound II (model 1) and the protonated ferryl compound II (model 2), respectively, starting from the Fe(IV)O model initially published by Rovira and Fita [C. Rovira, I. Fita, J. Phys. Chem. B 107 (2003) 5300-5305]. Therefore, we attribute the LpH II compound to a protonated ferryl Fe(IV)-OH complex, whereas the HpH II compound corresponds to the classical ferryl Fe(IV)O complex.     

External shocks,agent interactions,and endogenous feedbacks — Investigating system resilience with a stylized land use model

Dynamics of coupled Social-Ecological Systems (SES) result from the interplay of society and ecology. To assess SES resilience, we constructed an Agent-Based Model (ABM) of a land use system as a stereotypical example of SES and investigated how resilience of the represented system is affected by both external disturbances and internal dynamics. The model explicitly considered different aspects of resilience in a framework derived from literature, which includes “resilience to”, “resilience of”, “resilience at”, “resilience due to”, and “indicators of resilience”. External disturbances were implemented as shocks in crop yields. Internal dynamics comprised of two types of social interaction between agents (learning and cooperation), an ecological feedback of soil depletion and an economic feedback of agglomeration benefits. We systematically varied these mechanisms and measured indicators that reflected spatial, social, and economic resilience. Results showed that (1) internal mechanisms increased the ability of the system to recover from external shocks, (2) feedbacks resulted in different regimes of crop cultivation, each with a distinctive set of functions, and (3) resilience is not a generic system property, but strongly depends on what system function is considered. We recommend future studies to include internal dynamics, especially feedbacks, and to systematically assess them across different aspects of resilience.     

Relationship between β4 hydrogen bond and β6 hydrophobic interactions during aggregate, fiber or crystal formation in oversaturated solutions of hemoglobin A and S

Oversaturated deoxy-α₂β₂^T4V aggregated instantly without a delay time, which is in contrast to the delay time before the generation of fibers of deoxy-HbS and deoxy-α₂β₂^E6V,D73H. Solubility of deoxy-α₂β₂^T4V was ∼10-fold lower than that of deoxy-HbS and was similar to oxy- and deoxy-α₂β₂^E6V,T4V. These results indicate that β4Val in HbA in the oxy and deoxy forms with or without β6Val facilitates hydrophobic interaction of the A-helix with the EF helix of adjacent molecules without forming a β4/β73 hydrogen bond. Deoxy-HbA generated crystals following aggregation as does HbC-Harlem(α₂β₂^E6V,D73N), while α₂β₂^T4V and α₂β₂^D73H as well as HbS, α₂β₂^E6V,D73H and α₂β₂^E6V,T4V in the oxy and deoxy forms did not form crystals, indicating in addition to the strength of β6 amino acid hydrophobicity that the synergism between the β4Thr hydrogen bond and β6 hydrophobic interaction free energies on the A-helix play a critical role in formation of fibers versus crystalline nuclei during phase transition.     

The role of CS<Subscript>2</Subscript> in CS<Subscript>2</Subscript>/NMP mixed solvent in weakening the hydrogen bond of OH–N in coal: a DFT investigation

The interaction processes of trace amounts of N-methyl-2-pyrrolidinone (NMP), CS₂/NMP (1:1 by volume) and pure NMP solvent with the hydrogen bond of OH?N in coal were constructed and simulated by density functional theory methods. The distances and bond orders between the main related atoms, and the hydrogen bond energy of OH?N were calculated. The calculated results show that pure NMP solvent does not weaken the hydrogen bond of OH?N in coal. However, trace amounts of NMP and CS₂/NMP (1:1 by volume) have a strong capacity to weaken the hydrogen bond of OH?N in coal. The H2–N3 distances are elongated from 1.87 Å to 3.80 Å and 3.44 Å, the bond orders of H2–N3 all disappear, and the corresponding hydrogen bond energies of OH?N in coal decrease from 45.72 kJ mol^?1 to 7.06 and 11.24 kJ mol^?1, respectively. These results show that CS₂ added to pure NMP solvent plays an important role in releasing the original capacity of NMP to weaken the hydrogen bond of OH?N in coal, in agreement with experimental observations.     

Structural analysis and the effect of cyclo(His–Pro) dipeptide on neurotoxins—a dynamics and density functional theory study

The switching propensity and maximum probability of occurrence of the side chain imidazole group in the dipeptide cyclo(His–Pro) (CHP) were studied by applying molecular dynamics simulations and density functional theory. The atomistic behaviour of CHP with the neurotoxins glutamate (E) and paraquat (Pq) were also explored; E and Pq engage in hydrogen bond formation with the diketopiperazine (DKP) ring of the dipeptide, with which E shows a profound interaction, as confirmed further by NH and CO stretching vibrational frequencies. The effect of CHP was found to be greater on E than on Pq neurotoxin. A ring puckering study indicated a twist boat conformation for the six-membered DKP ring. Molecular electrostatic potential (MESP) mapping was also used to explore the hydrogen bond interactions prevailing between the neurotoxins and the DKP ring. The results of this study reveal that the DKP ring of the dipeptide CHP can be expected to play a significant role in reducing effects such as oxidative stress and cell death caused by neurotoxins.