Relative Potential Energies Research Articles

Computational study of the dimerization of glyphosate: mechanism and effect of solvent.

A computational study on the structure and stability of different series of glyphosate (Glyph) dimers comprising nonionized (N) and zwitterionic structures (Z) for neutral monomers, followed by an analysis of energetics of Glyph dimerization process have been performed by means of quantum chemical calculations in different media. Optimized geometries for energy minima, as well as relative potential and free energies of the possible various conformers of each series of Glyph dimer were computed as a function of the medium at B3LYP-D3/6-311++G(2d,2p) level. The solvation model based on density (SMD) is employed for all solution phase computations. Non-ionized dimers (DN), anion-cation (AC) and either zwitterion-zwitterion (DZP and DZC) or non-ionized-phosphonate zwitterion (NZP) ionized neutral forms of Glyph dimer are predicted to exist in the gas phase and in solution in large contrast to Glyph monomers. The DZC dimer form exhibiting a centrosymmetric arrangement of two carboxylate zwitterion units was found to be the most stable dimer structure in all media. In aqueous solution, the DZP and AC dimer type structures are significantly stabilized by hydration. The tautomerisms between DZC, DZP and AC dimer type structures have been investigated in the gas phase and in solution. The DZC type structures are more prone to experience proton transfer in water than in the gas phase and in cyclohexane. The mechanism for the tautomerization process in neutral ionized Glyph dimers proceeds via two direct proton transfer paths: DZP ⇋ AC ⇋ DZC. Results show that solvents play a key role in modulating the energetics of the dimerization process of Glyph. Solvation in cyclohexane, favors the dimerization process however, hydration opposed it. In aqueous solution, the mechanism of the dimerization of Glyph from its phosphonate zwitterionic monomer form (ZP) could be described by a set of equilibria including direct proton transfer paths as follows: 2ZP ⇋ DZP ⇋ AC ⇋ DZC. According to our results, in aqueous solution, DZC Glyph dimers and their corresponding DZP and AC tautomers should be present in higher concentration than phosphonate zwitterionic Glyph monomers for high Glyph concentration, a fact that seems controversial in the literature.

Toward a general neural network force field for protein simulations: Refining the intramolecular interaction in protein.

Molecular dynamics (MD) is an extremely powerful, highly effective, and widely used approach to understanding the nature of chemical processes in atomic details for proteins. The accuracy of results from MD simulations is highly dependent on force fields. Currently, molecular mechanical (MM) force fields are mainly utilized in MD simulations because of their low computational cost. Quantum mechanical (QM) calculation has high accuracy, but it is exceedingly time consuming for protein simulations. Machine learning (ML) provides the capability for generating accurate potential at the QM level without increasing much computational effort for specific systems that can be studied at the QM level. However, the construction of general machine learned force fields, needed for broad applications and large and complex systems, is still challenging. Here, general and transferable neural network (NN) force fields based on CHARMM force fields, named CHARMM-NN, are constructed for proteins by training NN models on 27 fragments partitioned from the residue-based systematic molecular fragmentation (rSMF) method. The NN for each fragment is based on atom types and uses new input features that are similar to MM inputs, including bonds, angles, dihedrals, and non-bonded terms, which enhance the compatibility of CHARMM-NN to MM MD and enable the implementation of CHARMM-NN force fields in different MD programs. While the main part of the energy of the protein is based on rSMF and NN, the nonbonded interactions between the fragments and with water are taken from the CHARMM force field through mechanical embedding. The validations of the method for dipeptides on geometric data, relative potential energies, and structural reorganization energies demonstrate that the CHARMM-NN local minima on the potential energy surface are very accurate approximations to QM, showing the success of CHARMM-NN for bonded interactions. However, the MD simulations on peptides and proteins indicate that more accurate methods to represent protein-water interactions in fragments and non-bonded interactions between fragments should be considered in the future improvement of CHARMM-NN, which can increase the accuracy of approximation beyond the current mechanical embedding QM/MM level.

Highly Distorted Multiple Helicenes: Syntheses, Structural Analyses, and Properties

A series of hexapole helicenes (HHs) and nonuple helicenes (NHs) were prepared from 1,3,5-tris[2-(arylethynyl)phenyl]benzene through two steps, namely, iodocyclization and subsequent palladium-catalyzed annulation with ortho-bromoaryl carboxylic acids. The crucial advantages of this synthetic method are the facile introduction of substituents, high regioselectivity, and efficient backbone extension. Three-dimensional structures of three C1-symmetric HHs and one C3-symmetric NH were elucidated using X-ray crystallography. Unlike most conventional multiple helicenes, the HHs and NHs investigated herein possess a unique structural feature where some double helical moieties share a terminal naphthalene unit. Chiral resolution of a HH and an NH was successfully achieved, and the enantiomerization barrier (ΔH‡) of the HH was experimentally determined to be 31.2 kcal/mol. A straightforward method for predicting the most stable diastereomer was developed based on density functional theory calculations and structural considerations. It was found that the relative potential energies (ΔHrs) of all diastereomers for two HHs and one NH can be obtained using minimal computational effort to analyze the types, helical configurations, numbers, and ΔH(MP-MM)s [= H(M,P/P,M) - H(M,M/P,P)] of the double helicenyl fragments.

Constituent Isomerism-Induced Quasicrystal and Frank–Kasper σ Superlattices Based on Nanosized Shape Amphiphiles

Naturally, subtle variations in the chemical structures of constituent molecules may significantly affect their multiscale spatial arrangements, properties, and functions. Deceptively simple spheri...

A density functional theory study on the shape of the primary cellulose microfibril in plants: effects of C6 exocyclic group conformation and H-bonding

Periodic planewave and molecular cluster density functional theory (DFT) calculations were performed on three potential arrangements of 18 chain chain cellulose microfibrils (CMFs). To determine the most probable arrangement in plant cell walls, the molecular structure, 13C NMR chemical shifts and WAXS diffractograms resulting from the DFT model calculations were compared to experimental data. In addition, the relative potential energies of the 18-chain model CMFs were considered as evidence for the most likely arrangement. The preponderance of evidence for the CMF arrangement that is most probable in plant cell walls is a 6-layer CMF in an arrangement of 234432 glucan chains where each integer represents the number of chains in a given layer. An accurate model for the habit of the CMF in plant cell walls is necessary for further modeling of CMF interactions with other plant cell wall components and studies of cellulose degradation.

Density functional theory modeling of chromate adsorption onto ferrihydrite nanoparticles

Density functional theory (DFT) calculations were performed on a model of a ferrihydrite nanoparticle interacting with chromate ( {text{CrO}}_{4}^{2 - } ) in water. Two configurations each of monodentate and bidentate adsorbed chromate as well as an outer-sphere and a dissolved bichromate ( {text{HCrO}}_{4}^{ - } ) were simulated. In addition to the 3-D periodic planewave DFT models, molecular clusters were extracted from the energy-minimized structures. Calculated interatomic distances from the periodic and cluster models compare favorably with Extended X-ray Absorption Fine Structure spectroscopy values, with larger discrepancies seen for the clusters due to over-relaxation of the model substrate. Relative potential energies were derived from the periodic models and Gibbs free energies from the cluster models. A key result is that the bidentate binuclear configuration is the lowest in potential energy in the periodic models followed by the outer-sphere complex. This result is consistent with observations of the predominance of bidentate chromate adsorption on ferrihydrite under conditions of high surface coverage (Johnston Environ Sci Technol 46:5851–5858, 2012). Cluster models were also used to perform frequency analyses for comparison with observed ATR FTIR spectra. Calculated frequencies on monodentate, bidentate binuclear, and outer-sphere complexes each have infrared (IR)-active modes consistent with experiment. Inconsistencies between the thermodynamic predictions and the IR-frequency analysis suggest that the 3-D periodic models are not capturing key components of the system that influence the adsorption equilibria under varying conditions of pH, ionic strength and electrolyte composition. Model equilibration via molecular dynamics (MD) simulations is necessary to escape metastable states created during DFT energy minimizations based on the initial classical force field MD-derived starting configurations.

Small Alcohols Revisited: CCSD(T) Relative Potential Energies for the Minima, First- and Second-Order Saddle Points, and Torsion-Coupled Surfaces.

The elucidation of conformations and relative potential energies (rPEs) of small molecules has a long history across a diverse range of fields. Periodically, it is helpful to revisit what conformations have been investigated and to provide a consistent theoretical framework for which clear comparisons can be made. In this paper, we compute the minima, first- and second-order saddle points, and torsion-coupled surfaces for methanol, ethanol, propan-2-ol, and propanol using consistent high-level MP2 and CCSD(T) methods. While for certain molecules more rigorous methods were employed, the CCSD(T)/aug-cc-pVTZ//MP2/aug-cc-pV5Z theory level was used throughout to provide relative energies of all minima and first-order saddle points. The rPE surfaces were uniformly computed at the CCSD(T)/aug-cc-pVTZ//MP2/aug-cc-pVTZ level. To the best of our knowledge, this represents the most extensive study for alcohols of this kind, revealing some new aspects. Especially for propanol, we report several new conformations that were previously not investigated. Moreover, two metrics are included in our analysis that quantify how the selected surfaces are similar to one another and hence improve our understanding of the relationship between these alcohols.

Atom Types Independent Molecular Mechanics Method for Predicting the Conformational Energy of Small Molecules.

We previously implemented a well-known qualitative chemical principle into an accurate quantitative model computing relative potential energies of conformers. According to this principle, hyperconjugation strength correlates with electronegativity of donors and acceptors. While this earlier version of our model applies to σ bonds, lone pairs, disregarded in this earlier version, also have a major impact on the conformational preferences of molecules. Among the well-established principles used by organic chemists to rationalize some organic chemical behaviors are the anomeric effect, the alpha effect, basicity, and nucleophilicity. These effects are directly related to the presence of lone pairs. We report herein our effort to incorporate lone pairs into our model to extend its applicability domain to any saturated small molecules. The developed model H-TEQ 2 has been validated on a wide variety of molecules from polyaromatic molecules to carbohydrates and molecules with high heteroatoms/carbon ratios. Interestingly, this method, in contrast to common force field-based methods, does not rely on atom types and is virtually applicable to any organic molecules.

Ammonia Catalyzed Formation of Sulfuric Acid in Troposphere: The Curious Case of a Base Promoting Acid Rain.

Electronic structure calculations have been performed to investigate the role of ammonia in catalyzing the formation of sulfuric acid through hydrolysis of SO3 in Earth's atmosphere. The uncatalyzed process involves a high activation barrier and, until date, is mainly known to occur in Earth's atmosphere only when catalyzed by water and acids. Here we show that hydrolysis of SO3 can be very efficiently catalyzed by ammonia, the most abundant basic component in Earth's atmosphere. It was found, based on magnitude of relative potential energies as well as rate coefficients, that ammonia is the best among all the catalysts studied until now (water and acids) and could be a considerable factor in formation of sulfuric acid in troposphere. The calculated rate coefficient (at 298 K) of ammonia catalyzed reaction has been found to be ∼105-107 times greater than that for water catalyzed ones. It was found, based on relative rates of ammonia and water catalyzed processes, that in troposphere ammonia, together with water, could be the key factor in determining the rate of formation of sulfuric acid. In fact, ammonia could surpass water in catalyzing sulfuric acid formation via hydrolysis of SO3 at various altitudes in troposphere depending upon their relative concentrations.

Retraction Note to: All-Atom Molecular-Level Analysis of the Ballistic-Impact-Induced Densification and Devitrification of Fused Silica

All-atom molecular-level computations are carried out to infer the dynamic response and material microstructure/topology changes of fused silica subjected to ballistic impact by a hard projectile. The analysis was focused on the investigation of specific aspects of the dynamic response and of the microstructural changes such as the deformation of highly sheared and densified regions and the conversion of amorphous fused silica to SiO2 crystalline allotropic modifications (in particular, α-quartz and stishovite). The microstructural changes in question were determined by carrying out a post-processing atom-coordination procedure. This procedure suggested the formation of stishovite (and perhaps α-quartz) within fused silica during ballistic impact. To rationalize the findings obtained, the all-atom molecular-level computational analysis is complemented by a series of quantum-mechanics density functional theory (DFT) computations. The latter computations enable determination of the relative potential energies of the fused silica, α-quartz, and stishovite under ambient pressure (i.e., under their natural densities) as well as under imposed (as high as 50 GPa) pressures (i.e., under higher densities) and shear strains. In addition, the transition states associated with various fused-silica devitrification processes were identified. The results obtained are found to be in good agreement with their respective experimental counterparts.

Apparent contradiction between calculated kinetic and potential energy fractions of phonons in molecular solids with implications on condensed-phase chemistry

ABSTRACTMany computational and experimental analyses of molecular excitation rely on relative atomic velocities to identify the excitation of chemical bonds. These are often interpreted through the aid of normal mode calculations. We address two potential gaps in this approach: 1. Relative velocities may not reflect the total potential energy absorbed by the bond. 2. Normal mode calculations omit interactions between neighboring molecules, effectively assuming a similarity between condensed- and gas-phase chemistry. Phonon calculations implicitly include interactions between neighboring molecules and allow analyses of both relative velocities and potential energies in solids.In the present work, we compare kinetic and potential energy fractions of the phonon modes of the molecular solids nitromethane and β-HMX. We show that velocity-based methods are likely sufficient to analyze nitromethane. However, they cannot detect the majority of excitation ofthe N-N bonds in β-HMX, the scission of which appears to begin major decomposition pathways in the molecules.In the broader context of condensed-phase chemistry, this implies that important interactions may not all be identifiable through analyses that rely solely on relative atomic velocities.

RETRACTED ARTICLE: All-Atom Molecular-Level Analysis of the Ballistic-Impact-Induced Densification and Devitrification of Fused Silica

All-atom molecular-level computations are carried out to infer the dynamic response and material microstructure/topology changes of fused silica subjected to ballistic impact by a hard projectile. The analysis was focused on the investigation of specific aspects of the dynamic response and of the microstructural changes such as the deformation of highly sheared and densified regions and the conversion of amorphous fused silica to SiO2 crystalline allotropic modifications (in particular, α-quartz and stishovite). The microstructural changes in question were determined by carrying out a post-processing atom-coordination procedure. This procedure suggested the formation of stishovite (and perhaps α-quartz) within fused silica during ballistic impact. To rationalize the findings obtained, the all-atom molecular-level computational analysis is complemented by a series of quantum-mechanics density functional theory (DFT) computations. The latter computations enable determination of the relative potential energies of the fused silica, α-quartz, and stishovite under ambient pressure (i.e., under their natural densities) as well as under imposed (as high as 50 GPa) pressures (i.e., under higher densities) and shear strains. In addition, the transition states associated with various fused-silica devitrification processes were identified. The results obtained are found to be in good agreement with their respective experimental counterparts.

Densification and Devitrification of Fused Silica Induced by Ballistic Impact: A Computational Investigation

A molecular‐level computational investigation is carried out to determine the dynamic response and material topology changes of fused silica subjected to ballistic impact by a hard projectile. The analysis was focused on the investigation of specific aspects of the dynamic response and of the topological changes such as the deformation of highly sheared and densified regions, and the conversion of amorphous fused silica to SiO2 crystalline polymorphs (in particular, α‐quartz and stishovite). The topological changes in question were determined by carrying out a postprocessing atom‐coordination procedure. This procedure suggested the formation of stishovite (and perhaps α‐quartz) within fused silica during ballistic impact. To rationalize the findings obtained, the all‐atom molecular‐level computational analysis is complemented by a series of quantum‐mechanics density functional theory (DFT) computations. The latter computations enable determination of the relative potential energies of the fused silica, α‐quartz and stishovite, under ambient pressure (i.e., under their natural densities) as well as under imposed (as high as 50 GPa) pressures (i.e., under higher densities) and shear strains. In addition, the transition states associated with various fused‐silica devitrification processes were identified. The results obtained are found to be in good agreement with their respective experimental counterparts.

On the Choice of the Ab Initio Level of Theory for Potential Energy Surface Developments

We test the accuracy of various standard, explicitly correlated F12, and composite ab initio methods with different correlation consistent basis sets for high-dimensional potential energy surface (PES) developments, thereby providing a practical guidance for reaction dynamics studies. Relative potential energies are computed at 15 geometries covering the energy range and configuration space of chemical importance for each of the six prototypical polyatomic reactions, X + CH4 → HX + CH3 [X = F, O, Cl] and X(-) + CH3Y → Y(-) + CH3X [X/Y = F/F, OH/F, F/Cl]. The average accuracies of the Hartree-Fock and MP2 methods are 1500-8000 and 400-1000 cm(-1), respectively. The standard CCSD(T) method provides errors of 900-1400 and 250-450 cm(-1) with aug-cc-pVDZ and aug-cc-pVTZ basis sets, respectively. The explicitly correlated CCSD(T)-F12 method reduces the corresponding errors to about 200 and 100 cm(-1); thus, we recommend using the F12 methods for PES developments. For F12 computations, the cc-pVnZ-F12 [n = D and T] basis sets usually, but not always, perform better than the corresponding aug-cc-pVnZ bases. We do not find clear preference between the F12a and F12b methods for PES developments. Composite methods are advocated instead of standard CCSD(T) because for example, one can obtain CCSD(T)/aug-cc-pVnZ quality results on the expense of MP2/aug-cc-pVnZ [n = T and Q] computations. The post-CCSD(T), the core correlation, and the scalar relativistic effects are found to be ∼100, 80-130, and 10-50 cm(-1), respectively. The all-electron CCSD(T)/aug-cc-pCVnZ relative energies differ from the complete-basis-set limit by about 1000, 300, 100, and 50 cm(-1) for n = D, T, Q, and 5, respectively.

Does Morphology of a Metal Nanoparticle Play a Role in Ostwald Ripening Processes?

The Ostwald ripening theory is commonly adopted to rationalize the growth of large metal nanoparticles that are formed at the expense of small-sized nanoparticles of higher chemical potential energies. This classical theory did not describe whether the morphology of a metal nanoparticle plays a role in controlling the shape evolution in the ripening processes. Here we show the direct observation of shape evolution among Ag nanoparticles of different morphologies in solutions, and experimental measurements of the relative chemical potential energies (or the electrochemical oxidation potentials) of Ag NPs of different morphologies, including, nanocubes, nanospheres, triangular plates, and decahedral nanoparticles. Theoretical calculation shows that when the diameter of a metal NP is beyond 35 nm, the influence of particle sizes on the oxidation potentials becomes very small. Chemical etching of Ag NPs by Fe(NO3)3 results in preferential removal of atoms at sharp edges/corners, and negative shift in the oxid...

Density Functional Study of the High-Temperature Oxidation of o-, m- and p-Xylyl Radicals

Theoretical calculations at the CBS-QB3 level of theory have been performed to investigate the potential energy surface for the reaction of o-, m- and p-xylyl with molecular oxygen. The differences of the relative potential energies for the products and the transition states of o-, m- and p-xylyl with molecular oxygen were found to be within 8.5 kJ/mol at the CBS-QB3 level of theory. Although the reaction of m- and p-xylyl radicals with molecular oxygen have the same reaction pathways and also the same reaction thermochemistry as that of benzyl radicals, the o-xylylperoxy radicals formed by the reaction of o-xylyl + O(2) had an additional intramolecular isomerization pathway to form the o-xylyl hydroperoxy radicals. The rate constants and the product branching ratios for the o-xylyl + O(2) and its subsequent reactions were evaluated by the RRKM and master equation analysis. Possible roles for these reaction pathways on the combustion of o-xylenes are discussed.

Ammonia synthesis and decomposition on a Ru-based catalyst modeled by first-principles

A recently published first-principles model for the ammonia synthesis on an unpromoted Ru-based catalyst is extended to also describe ammonia decomposition. In addition, further analysis concerning trends in ammonia productivity, surface conditions during the reaction, and macro-properties, such as apparent activation energies and reaction orders are provided. All observed trends in activity are captured by the model and the absolute value of ammonia synthesis/decomposition productivity is predicted to within a factor of 1–100 depending on the experimental conditions. Moreover it is shown: (i) that small changes in the relative adsorption potential energies are sufficient to get a quantitative agreement between theory and experiment ( Appendix A) and (ii) that it is possible to reproduce results from the first-principles model by a simple micro-kinetic model ( Appendix B).

Origin of a Large Temperature Dependence of Regioselectivity Observed for [2 + 2] Photocycloaddition (Paternò-Büchi Reaction) of 1,3-Dimethylthymine with Benzophenone and Its Derivatives: Conformational Property of the Intermediary Triplet 1,4-Diradicals

[reaction: see text] The [2 + 2] photochemical additions of 1,3-dimethylthymine (DMT) with benzophenone and its 4,4'-substituted derivatives (BPs), difluoro, di-tert-butyl, and dimethoxy benzophenones, have been investigated at a temperature range from -40 to 70 degrees C. The photochemical reactions, which are cycloaddition of the 5-6 double bond of DMT with the carbonyl group of BPs, the so-called the Paternò-Büchi (PB) reaction, reveal largely temperature-dependent regioselectivity. The chemical yields of one series of regioisomers, 2, decrease with the increase of the reaction temperature, but those of another regioisomer series, 3, increase, and thus the ratio of 2/3 is strongly dependent on the temperature (2/3 = ca. 70:30 to 30:70). The temperature dependence of the regioselectivity yields two linear functions in the corresponding Eyring diagrams. The Eyring plot with changed slopes is clearly indicative of the change for the selectivity-determining step in the PB reaction, in which the triplet 1,4-diradicals play a crucial role. Computational studies reveal the conformational equilibrium structures of the triplet 1,4-diradicals, energy barriers between the conformers, and the conjectural equilibrium constants from relative potential energies of the stable conformers. A proposed mechanism can reasonably explain the temperature-dependent regioselectivity and chemical yields of two regioisomers varying with the reaction temperature.

Conformers of n-Si6Me14: Ab Initio, Molecular Mechanics, and Additive Increment Methods

The stable backbone conformers of n-Si6Me14 have been identified through geometry optimizations with the HF/3-21G(d), MM2, and MM3 methods. With the exception of the MM2 method, their relative potential energies, and also single-point energies calculated by the HF/6-31G(d) and MP2/6-31G(d) methods at HF/3-21G(d) optimized geometries (Ecalc), agree with energies , obtained using additive increment sets previously derived from results for n-Si4Me10 and n-Si5Me12, with mean deviations of 0.11−0.15 kcal/mol. The energy is a simple function of the number of gauche, ortho, and transoid Si backbone bond conformations and of SiSi adjacent bond interactions. With the MM2 method the deviations from additivity are larger; and Ecalc agree only with a mean deviation of 0.52 kcal/mol. Improved increment sets were obtained by a simultaneous least-squares treatment of data for n-Si4Me10, n-Si5Me12 and n-Si6Me14, including a few increments for interaction between next-nearest bond conformations. This yields energies that ...

Spectroscopy of Neurotransmitters and Their Clusters. 1. Evidence for Five Molecular Conformers of Phenethylamine in a Supersonic Jet Expansion

The neurotransmitter molecule phenethylamine (PEA) is studied by fluorescence excitation, mass-resolved excitation, hole burning, and dispersed emission spectroscopies. The excitation spectrum of PEA exhibits a group of five transition bands in the S1 ← region. This group of transitions appears repetitively with the same spectral separations and intensity pattern in the higher energy regions up to 1000 cm-1 above the origin. The hole burning spectra of these five bands show different independent spectral hole depletion features. With the observation of no blue shifted emission bands higher than the excitation energy in the dispersed emission spectra, these five transition bands can be assigned to five different molecular conformers of PEA. These molecular conformers are distinguished from each other in their alkylamine side chain conformations and the amino group spatial orientations. With the assistance of ab initio calculations, we are able to identify the conformations of these five isomers. The effects of the alkylamino chain conformation, as well as the amino group orientation, on the relative potential energies of these conformers are discussed. The significance of this work for future studies of PEA/solvent molecule clusters and the other neurotransmitters is demonstrated by the amphetamine (AMP) excitation spectrum. The conformation of the alkylamine side chain is found to have little impact on in-plane vibrational modes of the phenyl ring such as ν6b and ν12.