scholarly journals Unusual Complexes of P(CH)3 with FH, ClH, and ClF

Molecules ◽  
2020 ◽  
Vol 25 (12) ◽  
pp. 2846
Author(s):  
Janet E. Del Bene ◽  
Ibon Alkorta ◽  
José Elguero
Keyword(s):  
Potential Energy Surfaces ◽  
Symmetry Axis ◽  
Dipole Moments ◽  
Binding Energies ◽  
Coupling Constants ◽  
Coupled Cluster ◽  
Halogen Bonds ◽  
Energy Component ◽  
P Values ◽  
Energy Surfaces

Ab initio MP2/aug’-cc-pVTZ calculations have been performed to determine the structures and binding energies of complexes formed by phosphatetrahedrane, P(CH)3, and HF, HCl, and ClF. Four types of complexes exist on the potential energy surfaces. Isomers A form at the P atom near the end of a P-C bond, B at a C-C bond, C at the centroid of the C-C-C ring along the C3 symmetry axis, and D at the P atom along the C3 symmetry axis. Complexes A and B are stabilized by hydrogen bonds when FH and ClH are the acids, and by halogen bonds when ClF is the acid. In isomers C, the dipole moments of the two monomers are favorably aligned but in D the alignment is unfavorable. For each of the monomers, the binding energies of the complexes decrease in the order A > B > C > D. The most stabilizing Symmetry Adapted Perturbation Theory (SAPT) binding energy component for the A and B isomers is the electrostatic interaction, while the dispersion interaction is the most stabilizing term for C and D. The barriers to converting one isomer to another are significantly higher for the A isomers compared to B. Equation of motion coupled cluster singles and doubles (EOM-CCSD) intermolecular coupling constants J(X-C) are small for both B and C isomers. J(X-P) values are larger and positive in the A isomers, negative in the B isomers, and have their largest positive values in the D isomers. Intramolecular coupling constants 1J(P-C) experience little change upon complex formation, except in the halogen-bonded complex FCl:P(CH3) A.

scholarly journals N…C and S…S Interactions in Complexes, Molecules, and Transition Structures HN(CH)SX:SCO, for X = F, Cl, NC, CCH, H, and CN

Molecules ◽  
2019 ◽  
Vol 24 (18) ◽  
pp. 3232
Author(s):  
Janet E. Del Bene ◽  
Ibon Alkorta ◽  
José Elguero
Keyword(s):  
Potential Energy ◽  
Potential Energy Surfaces ◽  
Second Order ◽  
Binding Energies ◽  
Coupling Constants ◽  
Spin Coupling ◽  
Order Dependence ◽  
Transition Structures ◽  
Bond Charge ◽  
Energy Surfaces

Ab initio Møller–Plesset perturbation theory (MP2)/aug’-cc-pVTZ calculations have been carried out in search of complexes, molecules, and transition structures on HN(CH)SX:SCO potential energy surfaces for X = F, Cl, NC, CCH, H, and CN. Equilibrium complexes on these surfaces have C1 symmetry, but these have binding energies that are no more than 0.5 kJ·mol–1 greater than the corresponding Cs complexes which are vibrationally averaged equilibrium complexes. The binding energies of these span a narrow range and are independent of the N–C distance across the tetrel bond, but they exhibit a second-order dependence on the S–S distance across the chalcogen bond. Charge-transfer interactions stabilize all of these complexes. Only the potential energy surfaces HN(CH)SF:SCO and HN(CH)SCl:SCO have bound molecules that have short covalent N–C bonds and significantly shorter S…S chalcogen bonds compared to the complexes. Equation-of-motion coupled cluster singles and doubles (EOM-CCSD) spin-spin coupling constants 1tJ(N–C) for the HN(CH)SX:SCO complexes are small and exhibit no dependence on the N–C distance, while 1cJ(S–S) exhibit a second-order dependence on the S–S distance, increasing as the S–S distance decreases. Coupling constants 1tJ(N–C) and 1cJ(S–S) as a function of the N–C and S–S distances, respectively, in HN(CH)SF:SCO and HN(CH)SCl:SCO increase in the transition structures and then decrease in the molecules. These changes reflect the changing nature of the N…C and S…S bonds in these two systems.

scholarly journals van der Waals potential energy surfaces from the exchange-hole dipole moment dispersion model

2016 ◽  
Vol 94 (12) ◽  
pp. 1049-1056 ◽  
Author(s):  
Joseph B. Dizon ◽  
Erin R. Johnson
Keyword(s):  
Dipole Moment ◽  
Potential Energy ◽  
Potential Energy Surfaces ◽  
Reference Data ◽  
Dispersion Model ◽  
Binding Energies ◽  
Coupled Cluster ◽  
Global Minima ◽  
Hybrid Functional ◽  
Energy Surfaces

The potential energy surfaces (PESs) of 28 simple van der Waals complexes, each consisting of a rare-gas (Rg) atom interacting with a linear molecule, are calculated using the exchange-hole dipole moment (XDM) dispersion model in conjunction with three base density functionals (HFPBE, PW86PBE, and a commensurate hybrid functional). Results are compared with literature coupled-cluster reference data. The quality of the computed PESs is assessed based on the positions of the global minima and the corresponding binding energies. Only the hybrid functional is found to provide generally reliable PESs. Dispersion-corrected HFPBE strongly underestimates the equilibrium intermolecular separations and predicts different global minima than the reference PESs for Rg–HCl, Rg–HBr, and two of the Rg–HCN complexes. Analysis of the binding-energy errors reveals that the performance of HFPBE degrades as the size of the Rg atoms increase down the group, while the performance of PW86PBE is significantly worse for strongly-polar molecules. PW86PBE, and to a lesser extent the hybrid, strongly overbind Kr–HF due to charge-transfer error. Despite this, the XDM-corrected hybrid functional displays the best overall error statistics and provides binding energies to within ca. 10 cm–1 of the coupled-cluster reference data at a greatly reduced computational cost.

scholarly journals Perturbing the O–H…O Hydrogen Bond in 1-oxo-3-hydroxy-2-propene

Molecules ◽  
2021 ◽  
Vol 26 (11) ◽  
pp. 3086
Author(s):  
Ibon Alkorta ◽  
José Elguero ◽  
Janet E. Del Bene
Keyword(s):  
Potential Energy Surfaces ◽  
Correlation Coefficients ◽  
Binding Energies ◽  
Coupling Constants ◽  
Spin Coupling ◽  
Transition Structures ◽  
Equilibrium Structures ◽  
Acid Potential ◽  
Energy Surfaces ◽  
Spin Spin Coupling

Ab initio MP2/aug’-cc-pVTZ calculations have been carried out to identify and characterize equilibrium structures and transition structures on the 1-oxo-3-hydroxy-2-propene: Lewis acid potential energy surfaces, with the acids LiH, LiF, BeH2, and BeF2. Two equilibrium structures, one with the acid interacting with the C=O group and the other with the interaction occurring at the O–H group, exist on all surfaces. These structures are separated by transition structures that present the barriers to the interconversion of the two equilibrium structures. The structures with the acid interacting at the C=O group have the greater binding energies. Since the barriers to convert the structures with interaction occurring at the O–H group are small, only the isomers with interaction occurring at the C=O group could be experimentally observed, even at low temperatures. Charge-transfer energies were computed for equilibrium structures, and EOM-CCSD spin–spin coupling constants 2hJ(O–O), 1hJ(H–O), and 1J(O–H) were computed for equilibrium and transition structures. These coupling constants exhibit a second-order dependence on the corresponding distances, with very high correlation coefficients.

Serine–Ca2+ versus serine–Cu2+ complexes — A theoretical perspective

2010 ◽  
Vol 88 (8) ◽  
pp. 759-768 ◽  
Author(s):  
Al Mokhtar Lamsabhi ◽  
Otilia Mó ◽  
Manuel Yáñez
Keyword(s):  
Gas Phase ◽  
Electron Density ◽  
Potential Energy Surfaces ◽  
Metal Ion ◽  
Theoretical Perspective ◽  
Binding Energies ◽  
Interacting Systems ◽  
Intramolecular Hydrogen ◽  
Energy Surfaces ◽  
Doubly Charged

The association of Ca2+ and Cu2+ to serine was investigated by means of B3LYP DFT calculations. The [serine–M]2+ (M = Ca, Cu) potential energy surfaces include, as does the neutral serine, a large number of conformers, in which a drastic reorganization of the electron density of the serine moiety is observed. This leads to significant changes in the number and strength of the intramolecular hydrogen bonds existing in the neutral serine tautomers. In some cases, a proton is transferred from the carboxylic OH group to the amino group and accordingly, some of the more stable [serine–M]2+ complexes can be viewed as the result of the interaction of the zwiterionic form of serine with the doubly charged metal ion. Whereas the interaction between Ca2+ and serine is essentially electrostatic, that between Cu2+ and serine has a non-negligible covalent character, reflected in larger electron densities at the bond critical points between the metal and the base, in the negative values of the electron density between the two interacting systems, and in much larger Cu2+ than Ca2+ binding energies. More importantly, the interaction with Cu2+ is followed by a partial oxidation of the base, which is not observed when the metal ion is Ca2+. The main consequence is that in Cu2+ complexes a significant acidity enhancement of the serine moiety takes place, which strongly favors the deprotonation of the [serine–Cu]2+ complexes. This is not the case for Ca2+ complexes. Thus, [serine–Ca]2+ complexes, like those formed by urea, thiourea, selenourea, or glycine, should be detected in the gas phase. Conversely, the complexes with Cu2+ should deprotonate spontaneously and therefore only [(serine–H)–Cu]+ monocations should be experimentally accessible.

scholarly journals The ANI-1ccx and ANI-1x Data Sets, Coupled-Cluster and Density Functional Theory Properties for Molecules

2020 ◽  
Author(s):  
Justin S. Smith ◽  
Roman Zubatyuk ◽  
Benjamin T. Nebgen ◽  
Nicholas Lubbers ◽  
Kipton Barros ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Potential Energy Surfaces ◽  
Density Functional ◽  
Atomic Charge ◽  
Density Functional Theory Calculations ◽  
Coupled Cluster ◽  
Data Sets ◽  
Data Set ◽  
Functional Theory ◽  
Energy Surfaces

<p>Maximum diversification of data is a central theme in building generalized and accurate machine learning (ML) models. In chemistry, ML has been used to develop models for predicting molecular properties, for example quantum mechanics (QM) calculated potential energy surfaces and atomic charge models. The ANI-1x and ANI-1ccx ML-based eneral-purpose potentials for organic molecules were developed through active learning; an automated data diversification process. Here, we describe the ANI-1x and ANI-1ccx data sets. To demonstrate data set diversity, we visualize them with a dimensionality reduction scheme, and contrast against existing data sets. The ANI-1x data set contains multiple QM properties from 5M density functional theory calculations, while the ANI-1ccx data set contains 500k data points obtained with an accurate CCSD(T)/CBS extrapolation. Approximately 14 million CPU core-hours were expended to generate this data. Multiple QM properties from density functional theory and coupled cluster are provided: energies, atomic forces, multipole moments, atomic charges, and more. We provide this data to the community to aid research and development of ML models for chemistry.</p>

Accuracy of Coupled Cluster Excited State Potential Energy Surfaces

2018 ◽  
Vol 14 (11) ◽  
pp. 5859-5869 ◽  
Author(s):  
Attila Tajti ◽  
John F. Stanton ◽  
Devin A. Matthews ◽  
Péter G. Szalay
Keyword(s):  
Excited State ◽  
Potential Energy ◽  
Potential Energy Surfaces ◽  
Coupled Cluster ◽  
State Potential ◽  
Energy Surfaces

Using one halogen bond to change the nature of a second bond in ternary complexes with P⋯Cl and F⋯Cl halogen bonds

2017 ◽  
Vol 203 ◽  
pp. 29-45 ◽  
Author(s):  
Janet E. Del Bene ◽  
Ibon Alkorta ◽  
José Elguero
Keyword(s):  
Halogen Bond ◽  
Synergistic Effects ◽  
Ternary Complexes ◽  
Binding Energies ◽  
Coupling Constants ◽  
Spin Coupling ◽  
Halogen Bonds ◽  
Binary Complexes ◽  
Spin Coupling Constants ◽  
Spin Spin Coupling

Ab initio MP2/aug’-cc-pVTZ calculations have been carried out to determine the effect of the presence of one halogen bond on the nature of the other in ternary complexes H2XP:ClF:ClH and H2XP:ClF:ClF, for X = F, Cl, H, NC, and CN. The P⋯Cl bonds remain chlorine-shared halogen bonds in the ternary complexes H2XP:ClF:ClH, although the degree of chlorine sharing increases relative to the corresponding binary complexes. The F⋯Cl bonds in the ternary complexes remain traditional halogen bonds. The binding energies of the complexes H2XP:ClF:ClH increase relative to the corresponding binary complexes, and nonadditivities of binding energies are synergistic. In contrast, the presence of two halogen bonds in the ternary complexes H2XP:ClF:ClF has a dramatic effect on the nature of these bonds in the four most strongly bound complexes. In these, chlorine transfer occurs across the P⋯Cl halogen bond to produce complexes represented as (H2XP–Cl)+:−(F:ClF). In the ion-pair, the cation is also halogen bonded to the anion by a Cl⋯F− halogen bond, while the anion is stabilized by an −F⋯Cl halogen bond. The central ClF molecule no longer exists as a molecule. The binding energies of the ternary H2XP:ClF:ClF complexes are significantly greater than the binding energies of the H2XP:ClF:ClH complexes, and nonadditivities exhibit large synergistic effects. The Wiberg bond indexes for the complexes H2XP:ClF, H2XP:ClF:ClH, and H2XP:ClF:ClF, and the cations (H2XP–Cl)+ reflect the changes in the P–Cl and Cl–F bonds. Similarly, EOM-CCSD spin–spin coupling constants are also consistent with the changes in these same bonds. In particular, 1xJ(P–Cl) in H2XP:ClF complexes becomes 1J(P–Cl) in the ternary complexes with chlorine-transferred halogen bonds. A plot of these coupling constants shows a change in the curvature of the trendline as chlorine-shared halogen bonds in H2XP:ClF:ClH become chlorine-transferred halogen bonds in H2XP:ClF:ClF. 1xJ(F–Cl) coupling constants also reflect changes in the nature of F⋯Cl halogen bonds.

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