Changes In Bond Orders Research Articles

Strain‐induced tunable energy barrier of proton diffusion in Y‐doped BaCeO 3 and Y‐doped BaZrO 3

In this paper, the strain effects on the energy barrier of proton diffusion in Y-doped BaCeO3 (BCY) and Y-doped BaZrO3 (BZY) are investigated by detailed density functional theory calculations. The energy barrier of proton rotation decreases when the tensile strain is applied. For intra-octahedral proton transfer, the energy barrier decreases when the tensile strain is applied while for inter-octahedral proton transfer the energy barrier increases when the tensile strain is applied. However, we found that for intra-octahedral proton transfer the energy barrier of BZY shows the opposite strain effect. To understand the underlying mechanism behind this opposite trend we decomposed proton diffusion into three elementary steps and the opposite trend of the energy barrier of BCY and BZY during intra-octahedral proton transfer is pinpointed to the opposite bond order change of the hydrogen bond. In all, we explored the strain effects on the energy barrier of proton diffusion in BCY and BZY from a microscopic perspective, showing the potential to tune the energy barrier of proton transport in perovskite oxide with strain engineering and thus design novel proton conductors.

Tensile mechanical characteristics of ultra-thin carbon sulfur nanothreads in orientational order

Carbon sulfur nanothreads (CSNTs) mainly composed of two chiral long alkane chains have been recently fabricated from thiophene by a pressure-induced phase transition in low-temperature, but their mechanical properties remain unexplored. Here, the critical roles of morphology and temperature on the tensile characteristics of CSNTs are for the first time examined using molecular dynamic simulations with a first-principles-based ReaxFF forcefield. It is revealed that CSNTs exhibit high tensile Young's modulus, high tensile strength and excellent ductility, and their tensile properties are morphology and temperature dependent. Morphologically, atomic arrangement with various configurations makes every CSNTs possess unique mechanical properties. Thermally, as temperature varies from 1 to 1500 K, CSNTs become mechanically weakened. In comparison with conventional diamond nanothreads (DNTs) and carbon nitride nanothreads (CNNTs), CSNTs show distinct axial elongation mechanisms, with relatively insignificant changes in chemical bond orders and bond length in the skeleton prior to the final rupture. Instead, the stretching of bond angle and dihedral angle mainly contribute to the global axial elongation, while the torsional deformation is limited due to their perfect global symmetry in the configuration. This study provides fundamental insights into the mechanics of ultra-thin CSNT structures.

Elucidating the structure of the W and Mn sites on the Mn-Na2WO4/SiO2 catalyst for the oxidative coupling of methane (OCM) at real reaction temperatures

The performance of the Mn-Na2WO4/SiO2 catalyst for oxidative coupling of methane (OCM) has been ascribed to crystalline phases that are not present at reaction temperatures (>700 °C). The evolution of W and Mn sites structure was monitored via in situ TPO-XRD, -Raman, and -XANES spectroscopies. TPO-XRD shows that the crystalline phases identified on the Mn-Na2WO4/SiO2, Na2WO4/SiO2, and WO3/SiO2 catalysts at room temperature do not exist at relevant OCM temperatures. The γ → β → α-WO3, α → β-cristobalite, and cubic → orthorhombic → molten-Na2WO4 phase transitions occur upon heating. TPO-Raman spectra show that the bond order of W sites with octahedral (Oh) and tetrahedral (Td) symmetry changes during the δ → γ → β → α-WO3 and cubic → orthorhombic → molten-Na2WO4 transitions, respectively. TPO-XANES spectra show that bond order changes are due to distortion degree variations because all samples preserve essentially W6+ valence and Oh-Mn3+ sites are always present on Mn-Na2WO4/SiO2 catalyst. Steady-state OCM tests show that Oh-W6+ sites are inactive and Td-W6+ sites are less distorted and more active towards methane activation in the presence of Oh-Mn3+ sites.

Molecular deformation response of portlandite under compressive loading

Portlandite is an important naturally available mineral and also an important component of hydrated cement. The mineral is subjected to uniaxial, equi-biaxial, equi-triaxial compressive loading at molecular level. Changes in the stress-strain plots for different types of compressive loading have been presented in this manuscript along with explanations from deformations of the molecular structure. Changes in bond order and partial atomic charges have also been calculated and related to the stress-strain curves observed for different compressive loading situations. It should be noted that this change in partial atomic charges have not been highlighted for the reactive potentials in any previous publications.

The reaction of O(3P) with alkynes: a dynamic and computational study focusing on formyl radical production.

Production of formyl radical, HCO, from reactions of O(3P) with alkynes (acetylene, propyne, 1-butyne, and 1-pentyne) has been investigated using cavity ringdown laser absorption spectroscopy (CRDLAS) and computational methods. No HCO was detected from reaction with acetylene, while the amount of HCO increased for propyne and 1-butyne, dropping off somewhat for 1-pentyne. These results differ from trends previously observed for reactions of O(3P) with alkenes, which exhibit the largest HCO production for the smallest alkene and drop off as the alkene size increases. Computational studies employing density functional and coupled cluster methods have been employed to investigate the triplet and singlet state pathways for HCO production. Because intersystem crossing (ISC) has been shown to be important in these processes, the minimum energy crossing point (MECP) between the triplet and singlet surfaces has been studied. We find the MECP for propyne to possess C1 symmetry and to lie lower in energy than previous studies have found. Natural Bond Orbital and Natural Resonance Theory analyses have been performed to investigate the changes in spin density and bond order along the reaction pathways for formation of HCO. Explanations are suggested for the trend in HCO formation observed for the alkynes. The trend in alkyne HCO yield also is compared and contrasted with the trend previously observed for the alkenes.

Evaluation of Changes in Bond Parameters in Sulfolane Under the Influence of Electron Donating Substituents

Sulfolane is a promising solvent for electrolytes in lithium-ion batteries, because it possesses high thermal and oxidative stability, high flash point, well dissolves lithium salts. However, sulfolane has a high melting point (27.5 °C) and viscosity (0.01029 Pa • s at 30 °C). High melting point and viscosity due to the tendency of sulfolane to self-association. To reduce the degree of self-association is possible by introducing various substituents into the sulfolane molecule. The aim of the work was to investigate how the introduction of substituents into the sulfolane molecule affects its chemical stability. Chemical resistance was judged by changes in bond orders. Presented work summarizes the results of quantum-chemical calculations of the bond orders in the sulfolane molecule and its substituted analogs, including methyl-, ethyl-, propyl-, vinyl- and allylsulfolanes (Figure 2). Quantum chemical calculations were performed using the Gaussian09 software package. The optimization procedure was performed using the TPSS/cc-pVTZ method. Analysis of wave functions and calculation of bond orders by “fuzzy” method were performed in MultiWfn software package. The objects of study were sulfolane and analogs with electron donor substituents. A total of 21 structures. The nature of the change in bond orders shows the influence of the position of substituents on electron density distribution. It has been established that the substitution of hydrogen atoms for this groups has the greatest influence on the order of the C – S and C – C bonds, reducing it, and the smallest on the S = O bond. This is especially clearly observed when hydrogen atoms attached to carbons connected to sulfur are substituted. These data show the possible paths of reduction reactions. This work was performed as part of a Government Order to Ufa Institute of Chemistry of the Russian Academy of Sciences by the Ministry of Science and Higher Education of the Russian Federation (Theme No. AAAA-A17-117011910031-7) Russia and was also financially supported by the Russian Science Foundation (project No 17-73-20115). Figure 1

Influence of Nanotubes on the Relative Stability of Orthogonal Form of Dialane

Conformational transformations of the orthogonal and planar forms of dialane Al2H4 molecule in model single-walled carbon nanotubes have been studied by the PBE/3ζ DFT method. In most cases, the effect of the nanosystem force field on the encapsulated molecule has been reflected in shortening of the Al–Al and Al–H bonds, decrease in the bond angles, and change in partial charges and bond orders which have resulted in the inversion of the relative stability of the orthogonal and planar forms as well as generation of high negative charge on the molecule of Al2H4 in the nanotube cavity. The decisive effect of the molecular orbital energy of the dialane@nanotube cluster on the stabilization of the planar conformation has been concluded.

Evaluation of Changes in Bond Parameters in Sulfolane Under the Influence of Electron-Withdrawing Substituents

The results of quantum-chemical calculations of the bond orders in the sulfolane molecule during the substitution of hydrogen atoms for fluorine atoms are presented. The change in the bond parameters were estimated. Quantum chemical calculations were performed using the Gaussian09 software package. The optimization procedure and the calculation of the vibrational problem were performed using the TPSS/aug-cc-pVTZ method. Analysis of wave functions and calculation of bond orders by “fuzzy’ method were performed in MultiWFN software package. The objects of study were sulfolane, monosubstituted and disubstituted fluorosulfolanes. A total of 15 structures. The nature of the change in bond orders shows the influence of the position of substituents on bond strength. It has been established that the substitution of hydrogen atoms for fluorine atoms has the greatest influence on the order of the C–S bond, reducing it, and the smallest on the S=O bond. This work was performed as part of a Government Order to Ufa Institute of Chemistry of the Russian Academy of Sciences by the Ministry of Science and Higher Education of the Russian Federation (Theme No. AAAA-A17-117011910031-7). Figure 1

Navigating around Patented Routes by Preserving Specific Motifs along Computer-Planned Retrosynthetic Pathways

Summary By keeping track of lists of specific bonds one wishes to preserve, a computer program is able to identify the key disconnections used in the patented syntheses and design synthetic routes that circumvent these approaches. Here, we provide examples of computer-designed syntheses relevant to medicinal chemistry, in which the machine avoids “strategic” disconnections common to industrial patents and is forced to use different starting materials. The ability of modern retrosynthetic planners to navigate around patented solutions may have significant implications for the ways in which intellectual property related to multistep syntheses is protected and/or challenged.

Developing accurate intramolecular force fields for conjugated systems through explicit coupling terms

The accuracy of molecular mechanics force fields (FF) reveals critical for applications where precise molecular structures along a conformational sampling are required, as in the simulation of electronic spectroscopies. This implies abandoning generalized FFs in favor of specific FFs, with non-transferable parameters able to accurately describe the targeted species. A promising strategy in this direction consists in the so-called quantum mechanically derived FFs, in which the parameters are fitted onto reference data computed through quantum chemistry. However, in order to obtain a global set of parameters able to reliably describe the reference potential energy surface in different regions of the conformational space, the complexity of the analytical expressions of the FF becomes crucial. Regarding intramolecular interactions, the functional form of standard transferable FFs is restricted to terms that depend on only one internal coordinate. It will be shown that such models may reveal insufficient to describe systems as polyenic chains, where complex electronic effects, e.g., conjugation, intrinsically couple different internal coordinates (ICs). We propose a functional form for intramolecular FFs, which includes explicit couplings between flexible dihedrals and stiff ICs (bonds and angles), being able to properly describe the geometrical changes arising not only from steric interactions, but also from conjugation effects, i.e., the change of bond orders induced by conformational changes. The parameterization of the coupled FFs is carried out by means of automated and efficient computational protocols, purposely developed in the present work. All procedures are tested and validated by generating FFs for the two smallest compounds in the polyenic series (butadiene and hexatriene).

The role of Ga in the acetylene adsorption on PdGa intermetallic

We performed density functional calculation of the acetylene hydrogenation reaction on the PdGa(110) surface. The reaction C2H2+H2 → C2H4 is modeled and understood in terms of chemical bonding change. The evolution of electronic structure and electron density plot also shed more light on the role of Pd, Ga and C2H2 during the hydrogenation reactions. This new way of looking at a particular chemical reaction includes the changes in bond order in the different reaction steps. As mentioned before the role of Ga is revealed as a part of the active site and not a single spacer.

ETS-NOCV Decomposition of the Reaction Force: The HCN/CNH Isomerization Reaction Assisted by Water.

The partitioning of the reaction force based on the extended-transition-state natural orbital for chemical valence (ETS-NOCV) scheme has been proposed. This approach, together with the analysis of reaction electronic flux (REF), has been applied in a description of the changes in the electronic structure along the IRC pathway for the HCN/CNH isomerization reaction assisted by water. Two complementary ways of partitioning the system into molecular fragments have been considered ("reactant perspective" and "product perspective"). The results show that the ETS-NOCV picture is fully consistent with REF and bond-order changes. In addition, proposed ETS-NOCV decomposition of the reaction force allows for the quantitative assessment of the influence of the observed bond-breaking and bond-formation processes, providing detailed information about the reaction-driving and reaction-retarding force components within the assumed partitioning scheme. © 2017 Wiley Periodicals, Inc.

The chemical bond as an emergent phenomenon.

We first argue that the covalent bond and the various closed-shell interactions can be thought of as symmetry broken versions of one and the same interaction, viz., the multi-center bond. We use specially chosen molecular units to show that the symmetry breaking is controlled by density and electronegativity variation. We show that the bond order changes with bond deformation but in a step-like fashion, regions of near constancy separated by electronic localization transitions. These will often cause displacive transitions as well so that the bond strength, order, and length are established self-consistently. We further argue on the inherent relation of the covalent, closed-shell, and multi-center interactions with ionic and metallic bonding. All of these interactions can be viewed as distinct sectors on a phase diagram with density and electronegativity variation as control variables; the ionic and covalent/secondary sectors are associated with on-site and bond-order charge density wave, respectively, the metallic sector with an electronic fluid. While displaying a contiguity at low densities, the metallic and ionic interactions represent distinct phases separated by discontinuous transitions at sufficiently high densities. Multi-center interactions emerge as a hybrid of the metallic and ionic bond that results from spatial coexistence of delocalized and localized electrons. In the present description, the issue of the stability of a compound is that of the mutual miscibility of electronic fluids with distinct degrees of electron localization, supra-atomic ordering in complex inorganic compounds coming about naturally. The notions of electronic localization advanced hereby suggest a high throughput, automated procedure for screening candidate compounds and structures with regard to stability, without the need for computationally costly geometric optimization.

13C kinetic isotope effects on the reaction of a flavin amine oxidase determined from whole molecule isotope effects

A large number of flavoproteins catalyze the oxidation of amines. Because of the importance of these enzymes in metabolism, their mechanisms have previously been studied using deuterium, nitrogen, and solvent isotope effects. While these results have been valuable for computational studies to distinguish among proposed mechanisms, a measure of the change at the reacting carbon has been lacking. We describe here the measurement of a 13C kinetic isotope effect for a representative amine oxidase, polyamine oxidase. The isotope effect was determined by analysis of the isotopic composition of the unlabeled substrate, N, N’-dibenzyl-1,4-diaminopropane, to obtain a pH-independent value of 1.025. The availability of a 13C isotope effect for flavoprotein-catalyzed amine oxidation provides the first measure of the change in bond order at the carbon involved in this carbon-hydrogen bond cleavage and will be of value to understanding the transition state structure for this class of enzymes.

Protonation and Deprotonation Reaction of Aspartic Acid Side Chain Modulated by the Surrounding Dielectric Medium - AB Initio Quantum Chemical Studies on Aspartic Acid in Sixteen Different Solvents and Two Protein Structures

Side chain of aspartic acid constitutes of carboxylate group, pKa equals to 3.7, in aqueous solution. However, large pKa shifts are often observed in protein structures. Several aspartic acid side chains are found in protonated form in protein NMR structures, for example, Asp26 in human thioredoxin, Asp96 in bacteriorhodopsin etc. Local micro-environment plays a crucial role in pKa shift of this amino acid side chain. Question asked in this study - how variation in the local dielectric medium influence protonation of aspartic acid side chain? To answer this question, we have performed Density Functional Theory (DFT) and Möller-Plesset second order perturbation theory (MP2) calculations on aspartic acid side chain in 16 different implicit solvents with varying dielectric constants. These calculations show that bond order of carboxylic-OH group decreases steeply in low dielectric range (ε between 1 to 9). Change in bond order within high dielectric range (ε > 20) is small. This calculation suggests that carboxylic-OH bond order in aspartic acid side chain should be high in protein hydrophobic region (low dielectric medium) compared to protein hydrophilic region (high dielectric medium). This fact was verified from bond order, electron densities on aspartic acids in two different proteins, ASP96 for bacteriorhodopsin and ASP52 for hen-egg-white-lysozyme, using hybrid quantum mechanics/molecular mechanics (QM/MM) approaches. The aspartic acids and the surrounding hydrophobic region was treated quantum chemically and the remaining part of the proteins were treated with classical mechanics. The details of the QM/MM analyses will be discussed.

Effects of nanobuds and heat welded nanobuds chains on mechanical behavior of carbon nanotubes

This study reports an investigation on the effects of nanobuds and heat welded nanobuds chains (C60 chains attached or embedded on the surface of a SWCNT) on the mechanical properties of carbon nanotubes by molecular dynamics (MD) simulations. The bond order change and the stress concentration in the distorted connection area of nanobuds when C60 attaches to the surface of the SWCNT are first studied. Then the effect of multiple randomly scattered and attached C60 fullerenes on the ultimate tensile strength of SWCNT is discussed. It is found that both nanobuds and heat welded nanobuds chains lower the ultimate tensile strength of individual defect-free SWCNT. However, the mean post-peak strength of the CNT (after necking) is significantly enhanced by heat welded nanobuds chains. Moreover, the ultimate tensile strength of the SWCNT with vacancy defects does not decrease by heat welded nanobuds chains; interestingly, the maximum tensile strength of the SWCNTs bundles with intertube bridging and vacancy defects even can be enhanced by more than 20% by heat welded nanobuds chains.

The Dynamical Nature of Enzymatic Catalysis

ConspectusAs is well-known, enzymes are proteins designed to accelerate specific life essential chemical reactions by many orders of magnitude. A folded protein is a highly dynamical entity, best described as a hierarchy or ensemble of interconverting conformations on all time scales from femtoseconds to minutes. We are just beginning to learn what role these dynamics play in the mechanism of chemical catalysis by enzymes due to extraordinary difficulties in characterizing the conformational space, that is, the energy landscape, of a folded protein. It seems clear now that their role is crucially important. Here we discuss approaches, based on vibrational spectroscopies of various sorts, that can reveal the energy landscape of an enzyme–substrate (Michaelis) complex and decipher which part of the typically very complicated landscape is relevant to catalysis. Vibrational spectroscopy is quite sensitive to small changes in bond order and bond length, with a resolution of 0.01 Å or less. It is this sensitivity that is crucial to its ability to discern bond reactivity.Using isotope edited IR approaches, we have studied in detail the role of conformational heterogeneity and dynamics in the catalysis of hydride transfer by LDH (lactate dehydrogenase). Upon the binding of substrate, the LDH·substrate system undergoes a search through conformational space to find a range of reactive conformations over the microsecond to millisecond time scale. The ligand is shuttled to the active site via first forming a weakly bound enzyme·ligand complex, probably consisting of several heterogeneous structures. This complex undergoes numerous conformational changes spread throughout the protein that shuttle the enzyme·substrate complex to a range of conformations where the substrate is tightly bound. This ensemble of conformations all have a propensity toward chemistry, but some are much more facile for carrying out chemistry than others. The search for these tightly bound states is clearly directed by the forces that the protein can bring to bear, very much akin to the folding process to form native protein in the first place. In fact, the conformational subspace of reactive conformations of the Michaelis complex can be described as a “collapse” of reactive substates compared with that found in solution, toward a much smaller and much more reactive set.These studies reveal how dynamic disorder in the protein structure can modulate the on-enzyme reactivity. It is very difficult to account for how the dynamical nature of the ground state of the Michaelis complex modulates function by transition state concepts since dynamical disorder is not a starting feature of the theory. We find that dynamical disorder may well play a larger or similar sized role in the measured Gibbs free energy of a reaction compared with the actual energy barrier involved in the chemical event. Our findings are broadly compatible with qualitative concepts of evolutionary adaptation of function such as adaptation to varying thermal environments. Our work suggests a methodology to determine the important dynamics of the Michaelis complex.

Effect of methyl groups substitution on the strength of intramolecular hydrogen bonding of naphthazarin: DFT and NBO studies

A density functional theory (DFT) study-based method B3LYP/6-311++G** was carried out to investigate the methyl groups substitution effect on the structure and the strength of intramolecular hydrogen bonding in naphthazarin (NZ) (5,8-dihydroxy-1,4-naphthoquinone). The full geometry optimization of molecular structures, the difference between the energies of hydrogen-bonded and non-hydrogen-bonded rotamers, and the proton chemical shift of the hydroxyl groups in NZ and its methyl substituents obtained at the B3LYP/6-311++G** level. The vibrational frequencies of all samples and their deuterated analogues were calculated at the same theoretical level. The 1H chemical shifts for NZ and its methyl substituents were computed at the B3LYP/6-311++G** level using the gauge-including atomic orbital method. Furthermore, in order to investigate the changes in bond order, electron density, electron delocalization, and steric effects caused by methyl substituents, natural bond orbital analysis were carried out at the B3LYP/6-311++G** level. After comparing these effective parameters in methyl substituents with those of their parent, NZ, we concluded that, in general, intramolecular hydrogen bonding strength increases by substituting methyl groups in the different positions of NZ.

Structure and spectral-fluorescent properties of 6-pyrazolyl-4-methylumbelliferone

Spectral-fluorescent properties of 6-pyrazolyl-4-methylubbelliferone have been investigated in comparison with 4-methylumbelliferone and its methyl ester. Abnormally large Stokes shifts and the fluorescence ability of these compounds have been interpreted using quantum-chemical analysis by the DFT and TDDFT methods with the B3LYP/6-31G(d,p) basis set of the change of charge and bond orders in the ground and first excited states. It has been established that the significant difference in the absorption and fluorescence spectra of the studied 7-hydroxycoumarins in proton-donor solvents is caused by proton abstraction and transfer in their neutral form upon photoexcitation with probable formation of the anion and the tautomer depending the pH of the medium. It has been shown that the formation probability for these species is increased by introducing the pyrazolyl cycle in the 6-position of 4-methylumbelliferone.

A comprehensive analysis of hydrogen bond interactions based on local vibrational modes

AbstractLocal stretching modes for 69 different DH single bonds and 58 H···A H‐bonds are calculated at the ωB97X‐D/aug‐cc‐pVTZ level of theory to describe the changes in donor D and acceptor A upon forming the hydrogen‐bonded complex. The intrinsic strength of the DH and AH interactions is determined utilizing the properties of a well‐defined set of local, uncoupled vibrational modes. The local mode stretching force constant ka(HA) provides a unique measure of bond strength for both covalently and electrostatically bonded complexes. Generally applicable bond orders are derived, which can be related to the binding energies of the hydrogen bonded complexes. Although the red shifts in the DH stretching frequencies can be used to detect hydrogen bonding, they are not sufficient to assess the strength of hydrogen bonding. It is demonstrated that the calculated BSSE‐corrected binding energies of hydrogen bonded complexes are related to the sum of bond order changes caused by hydrogen bonding. The covalent character of charge assisted hydrogen bonds is explained. Because local mode frequencies can also be derived from experimental normal mode frequencies, a new dimension in the study of hydrogen bonding is gained. © 2012 Wiley Periodicals, Inc.