scholarly journals Distinctive Supramolecular Features of β-Cyclodextrin Inclusion Complexes with Antidepressants Protriptyline and Maprotiline: A Comprehensive Structural Investigation

2021 ◽  
Vol 14 (8) ◽  
pp. 812
Author(s):  
Thammarat Aree
Keyword(s):  
Inclusion Complexes ◽  
Density Functional ◽  
Water Solubility ◽  
Geometry Optimization ◽  
Binding Constants ◽  
Basis Set ◽  
Full Geometry Optimization ◽  
Basis Set Superposition Error ◽  
X Ray ◽  
Molecular Stability

Depression, a global mental illness, is worsened due to the coronavirus disease 2019 (COVID-2019) pandemic. Tricyclic antidepressants (TCAs) are efficacious for the treatment of depression, even though they have more side effects. Cyclodextrins (CDs) are powerful encapsulating agents for improving molecular stability, water solubility, and lessening the undesired effects of drugs. Because the atomic-level understanding of the β-CD–TCA inclusion complexes remains elusive, we carried out a comprehensive structural study via single-crystal X-ray diffraction and density functional theory (DFT) full-geometry optimization. Here, we focus on two complexes lining on the opposite side of the β-CD–TCA stability spectrum based on binding constants (Kas) in solution, β-CD–protriptyline (PRT) 1—most stable and β-CD–maprotiline (MPL) and 2—least stable. X-ray crystallography unveiled that in the β-CD cavity, the PRT B-ring and MPL A-ring are aligned at a nearly perfect right angle against the O4 plane and primarily maintained in position by intermolecular C–H···π interactions. The increased rigidity of the tricyclic cores is arising from the PRT -CH=CH- bridge widens, and the MPL -CH2–CH2- flexure narrows the butterfly angles, facilitating the deepest and shallower insertions of PRT B-ring (1) and MPL A-ring (2) in the distorted round β-CD cavity for better complexation. This is indicated by the DFT-derived complex stabilization energies (ΔEstbs), although the complex stability orders based on Kas and ΔEstbs are different. The dispersion and the basis set superposition error (BSSE) corrections were considered to improve the DFT results. Plus, the distinctive 3D arrangements of 1 and 2 are discussed. This work provides the first crystallographic evidence of PRT and MPL stabilized in the β-CD cavity, suggesting the potential application of CDs for efficient drug delivery.

scholarly journals ß-Cyclodextrin Inclusion Complexes with Catechol-Containing Antioxidants Protocatechuic Aldehyde and Protocatechuic Acid—An Atomistic Perspective on Structural and Thermodynamic Stabilities

Molecules ◽  
2021 ◽  
Vol 26 (12) ◽  
pp. 3574
Author(s):  
Thammarat Aree
Keyword(s):  
Inclusion Complexes ◽  
Protocatechuic Acid ◽  
Inclusion Complexation ◽  
Geometry Optimization ◽  
Therapeutic Effects ◽  
Full Geometry Optimization ◽  
Oh Groups ◽  
X Ray ◽  
Protocatechuic Aldehyde ◽  
Crystal Contacts

Protocatechuic aldehyde (PCAL) and protocatechuic acid (PCAC) are catechol derivatives and have broad therapeutic effects associated with their antiradical activity. Their pharmacological and physicochemical properties have been improved via the cyclodextrin (CD) encapsulation. Because the characteristics of b-CD inclusion complexes with PCAL (1) and PCAC (2) are still equivocal, we get to the bottom of the inclusion complexation by an integrated study of single-crystal X-ray diffraction and DFT full-geometry optimization. X-ray analysis unveiled that PCAL and PCAC are nearly totally shielded in the b-CD wall. Their aromatic rings are vertically aligned in the b-CD cavity such that the functional groups on the opposite side of the ring (3,4-di(OH) and 1-CHO/1-COOH groups) are placed nearby the O6–H and O2–H/O3–H rims, respectively. The preferred inclusion modes in 1 and 2 help to establish crystal contacts of OH×××O H-bonds with the adjacent b-CD OH groups and water molecules. By contrast, the DFT-optimized structures of both complexes in the gas phase are thermodynamically stable via the four newly formed host–guest OH⋯O H-bonds. The intermolecular OH×××O H-bonds between PCAL/PCAC 3,4-di(OH) and b-CD O6–H groups, and the shielding of OH groups in the b-CD wall help to stabilize these antioxidants in the b-CD cavity, as observed in our earlier studies. Moreover, PCAL and PCAC in distinct lattice environments are compared for insights into their structural flexibility.

A density functional approach toward structural features and properties of C20…N2X2 (X = H, F, Cl, Br, Me) molecules

2014 ◽  
Vol 13 (04) ◽  
pp. 1450023 ◽  
Author(s):  
Reza Ghiasi ◽  
Morteza Zaman Fashami ◽  
Amir Hossein Hakimioun
Keyword(s):  
Density Functional ◽  
Chemical Shifts ◽  
Geometry Optimization ◽  
Structural Features ◽  
Nbo Analysis ◽  
Basis Set ◽  
Basis Sets ◽  
Basis Set Superposition Error ◽  
Homo And Lumo ◽  
Lowest Unoccupied Molecular Orbitals

In this work, the interaction of C 20 with N 2 X 2 ( X = H , F , Cl , Br , Me ) molecules has been explored using the B3LYP, M062x methods and 6-311G(d,p) and 6-311+G(d,p) basis sets. The interaction energies (IEs) obtained with standard method were corrected by basis set superposition error (BSSE) during the geometry optimization for all molecules at the same levels of theory. It was found C 20… N 2 H 2 interaction is stronger than the interaction of other N 2 X 2 ( X = F , Cl , Br , Me ) with C 20. Highest occupied and lowest unoccupied molecular orbitals (HOMO and LUMO, respectively) levels are illustrated by density of states spectra (DOS). The nucleus-independent chemical shifts (NICSs) confirm that C 20… N 2 X 2 molecules exhibit aromatic characteristics. Geometries obtained from DFT calculations were used to perform NBO analysis. Also, 14 N NQR parameters of the C 20… N 2 X 2 molecules are predicted.

scholarly journals Synthesis, Crystal Structure, and Theoretical Studies of N-(4-((4-chlorobenzyl)oxy)phenyl)-4- (trifluoromethyl)pyrimidin-2-amine

2013 ◽  
Vol 2013 ◽  
pp. 1-5 ◽  
Author(s):  
Jian-Chang Jin ◽  
Zhao-Hui Sun ◽  
Ming-Yan Yang ◽  
Jing Wu ◽  
Xing-Hai Liu
Keyword(s):  
Title Compound ◽  
Geometry Optimization ◽  
Basis Set ◽  
Orbital Energy ◽  
Monoclinic Space Group ◽  
X Ray Diffraction ◽  
Full Geometry Optimization ◽  
X Ray ◽  
Compound C ◽  
Frontier Orbital Energy

The title compound (C18H13ClF3N3O) were synthesized and recrystallized from CH3OH. The compound was characterized byH1NMR, MS, HRMS, and X-ray diffraction. The compound crystallized in the monoclinic space groupP2(1)/nwitha=8.2354(14),b=12.686(2),c=16.633(3) Å,α=90,β=97.951(3),γ=90∘,V=1721.0(5)  Å3,Z=4,andR=0.0376for 1933 observed reflections withI>2σ(I).X-ray analysis reveals that intermolecular N–H⋯N interactions exist in the adjacent molecules. Theoretical calculation of the title compound was carried out with HF/6-31G(d,p), B3LYP/6-31G(d,p). The full geometry optimization was carried out using 6-31G(d,p)basis set and the frontier orbital energy. The optimized geometric bond lengths and bond angles obtained by using HF and DFT (B3LYP) showed the best agreement with the experimental data.

scholarly journals r2SCAN-3c: An Efficient “Swiss Army Knife” Composite Electronic-Structure Method

2020 ◽  
Author(s):  
Stefan Grimme ◽  
Andreas Hansen ◽  
Sebastian Ehlert ◽  
Jan-Michael Mewes
Keyword(s):  
Electronic Structure ◽  
Density Functional ◽  
Chemical Space ◽  
Noncovalent Interactions ◽  
New Method ◽  
Basis Set ◽  
Basis Set Superposition Error ◽  
Benchmark Database ◽  
The Cost ◽  
Conformational Energies

The recently proposed second revision of the SCAN meta-GGA density-functional approximation (DFA) {Furness et al., J. Phys. Chem. Lett. 2020, 11, 8208-8215, termed r<sup>2</sup>SCAN} is used to construct an efficient composite electronic-structure method termed r<sup>2</sup>SCAN-3c, expanding the "3c'' series (hybrid: HSE/PBEh-3c, GGA: B97-3c, HF: HF-3c) to themGGA level. To this end, the unaltered r<sup>2</sup>SCAN functional is combined with a tailor-made <br>triple-zeta Gaussian AO-basis as well as with refitted D4 and gCP corrections for London-dispersion and basis-set superposition error. The performance of the new method is evaluated for the GMTKN55 thermochemical database covering large parts of chemical space with about 1500 <br>data points, as well as additional benchmarks for noncovalent interactions, organometallic reactions, lattice energies of organic molecules and ices, as well as for the adsorption on polar salt and non-polar coinage-metal surfaces. These comprehensive tests reveal a spectacular performance and robustness of r<sup>2</sup>SCAN-3c for reaction energies and noncovalent interactions in molecular and periodic systems, as well as outstanding conformational energies, and consistent structures. At just one tenth of the cost, r<sup>2</sup>SCAN-3c provides one of the best results of all semi-local DFT/QZ methods ever tested for the GMTKN55 benchmark database. Specifically for reaction and conformational energies as well as for noncovalent interactions, the new method outperforms hybrid-DFT/QZ approaches, compared to which the computational savings are even larger (factor 100-1000).<br>In relation to other "3c'' methods, r<sup>2</sup>SCAN-3c by far surpasses the accuracy of its predecessor B97-3c at only about twice the cost. The perhaps most relevant remaining systematic deviation of r<sup>2</sup>SCAN-3c is due to self-interaction-error, owing to its mGGA nature. However, SIE is notably reduced compared to other (m)GGAs, as is demonstrated for several examples. After all, this remarkably efficient and robust method is chosen as our new group default, replacing previous low-level DFT and partially even expensive high-level methods in most standard applications for systems with up to several hundreds of atoms.<br><br>

scholarly journals r2SCAN-3c: An Efficient “Swiss Army Knife” Composite Electronic-Structure Method

2020 ◽  
Author(s):  
Stefan Grimme ◽  
Andreas Hansen ◽  
Sebastian Ehlert ◽  
Jan-Michael Mewes
Keyword(s):  
Electronic Structure ◽  
Density Functional ◽  
Chemical Space ◽  
Noncovalent Interactions ◽  
New Method ◽  
Basis Set ◽  
Basis Set Superposition Error ◽  
Benchmark Database ◽  
The Cost ◽  
Conformational Energies

The recently proposed second revision of the SCAN meta-GGA density-functional approximation (DFA) {Furness et al., J. Phys. Chem. Lett. 2020, 11, 8208-8215, termed r<sup>2</sup>SCAN} is used to construct an efficient composite electronic-structure method termed r<sup>2</sup>SCAN-3c, expanding the "3c'' series (hybrid: HSE/PBEh-3c, GGA: B97-3c, HF: HF-3c) to themGGA level. To this end, the unaltered r<sup>2</sup>SCAN functional is combined with a tailor-made <br>triple-zeta Gaussian AO-basis as well as with refitted D4 and gCP corrections for London-dispersion and basis-set superposition error. The performance of the new method is evaluated for the GMTKN55 thermochemical database covering large parts of chemical space with about 1500 <br>data points, as well as additional benchmarks for noncovalent interactions, organometallic reactions, lattice energies of organic molecules and ices, as well as for the adsorption on polar salt and non-polar coinage-metal surfaces. These comprehensive tests reveal a spectacular performance and robustness of r<sup>2</sup>SCAN-3c for reaction energies and noncovalent interactions in molecular and periodic systems, as well as outstanding conformational energies, and consistent structures. At just one tenth of the cost, r<sup>2</sup>SCAN-3c provides one of the best results of all semi-local DFT/QZ methods ever tested for the GMTKN55 benchmark database. Specifically for reaction and conformational energies as well as for noncovalent interactions, the new method outperforms hybrid-DFT/QZ approaches, compared to which the computational savings are even larger (factor 100-1000).<br>In relation to other "3c'' methods, r<sup>2</sup>SCAN-3c by far surpasses the accuracy of its predecessor B97-3c at only about twice the cost. The perhaps most relevant remaining systematic deviation of r<sup>2</sup>SCAN-3c is due to self-interaction-error, owing to its mGGA nature. However, SIE is notably reduced compared to other (m)GGAs, as is demonstrated for several examples. After all, this remarkably efficient and robust method is chosen as our new group default, replacing previous low-level DFT and partially even expensive high-level methods in most standard applications for systems with up to several hundreds of atoms.<br><br>

scholarly journals Double-Hybrid DFT Functionals for the Condensed Phase: Gaussian and Plane Waves Implementation and Evaluation

Molecules ◽  
2020 ◽  
Vol 25 (21) ◽  
pp. 5174
Author(s):  
Frederick Stein ◽  
Jürg Hutter ◽  
Vladimir V. Rybkin
Keyword(s):  
Condensed Phase ◽  
Density Functional ◽  
Plane Waves ◽  
Basis Set ◽  
Basis Sets ◽  
Density Functionals ◽  
Basis Set Superposition Error ◽  
Super Cell ◽  
Long Range Interactions ◽  
Function Correlation

Intermolecular interactions play an important role for the understanding of catalysis, biochemistry and pharmacy. Double-hybrid density functionals (DHDFs) combine the proper treatment of short-range interactions of common density functionals with the correct description of long-range interactions of wave-function correlation methods. Up to now, there are only a few benchmark studies available examining the performance of DHDFs in condensed phase. We studied the performance of a small but diverse selection of DHDFs implemented within Gaussian and plane waves formalism on cohesive energies of four representative dispersion interaction dominated crystal structures. We found that the PWRB95 and ωB97X-2 functionals provide an excellent description of long-ranged interactions in solids. In addition, we identified numerical issues due to the extreme grid dependence of the underlying density functional for PWRB95. The basis set superposition error (BSSE) and convergence with respect to the super cell size are discussed for two different large basis sets.

A DENSITY FUNCTIONAL THEORY INVESTIGATION ON THE TAUTOMERS AND CRYSTAL OF 2-DIAZO-4,6-DINITROPHENOL

2004 ◽  
Vol 03 (04) ◽  
pp. 599-607 ◽  
Author(s):  
XUE-HAI JU ◽  
HE-MING XIAO
Keyword(s):  
Density Functional ◽  
Density Functional Method ◽  
Lattice Energy ◽  
Functional Method ◽  
Basis Set ◽  
Functional Theory ◽  
Basis Set Superposition Error ◽  
Conduction Bands ◽  
Valence Bands ◽  
Good Agreement

Density functional method was applied to the study of the highly efficient primary explosive 2-diazo-4,6-dinitrophenol (DDNP) in both gaseous tautomers and its bulk state. Two stable tautomers were located. It was found that the structure (I) with open diazo, i.e. with linear CNN, is more stable than that with diazo ring tautomer (II) of DDNP. The structure I is in good agreement with the structure in the bulk. The lattice energy is -89.01 kJ/mol, and this value drops to -83.29 kJ/mol when a 50% correction of the basis set superposition error was adopted. The frontier bands are quite flat. The carbon atoms in DDNP make up the upper valence bands. While the lower conduction bands mainly consist of carbon and diazo N atoms. The bond populations of C–N bonds (both C–Nitro and C–Diazo) are much less than those of the other bonds and the detonation may be initiated through the breakdown of C–N bonds.

Ab initio studies on amides: conformational preferences of formimide and barriers to interconversion of the conformers

1980 ◽  
Vol 33 (8) ◽  
pp. 1635 ◽  
Author(s):  
L Radom ◽  
NV Riggs
Keyword(s):  
Ground State ◽  
Room Temperature ◽  
Geometry Optimization ◽  
Basis Set ◽  
Partial Geometry ◽  
Electrostatic Repulsion ◽  
Full Geometry Optimization ◽  
Vapour State ◽  
Conformational Preferences ◽  
Model Transition

Formimide (diformamide), the parent of the diacylamines, is capable of existing in three basic ground-state conformations about the N-C bonds. Full geometry optimization with the STO-3G basis set predicts that all three conformers are fully coplanar, that the E,E (1) and E,Z(3) conformers are of similar energy, and that the Z,Z (2) conformer is of somewhat higher energy (by 11 kJ mol-1); 4-31G evaluation of the energies suggests that (2) is by far the least stable and that (1) is of higher energy than (3) by 6.5 kJ mol-1. Analysis of the calculated charge distribution suggests that (2) is destabilized by electrostatic repulsion. These results are consistent with experimental conclusions that planar (3) is strongly preferred in the vapour state at room temperature and that (2) has not been observed in the vapour state or in solution. Partial geometry optimization with the STO-3G basis set of model transition states for internal rotation suggests a barrier height of 52 kJ mol-1 (72 kJ mol-1 when evaluated with the 4-31G basis set) for the conversion (3) → (1).

Binding Energies of Organic Charge-Transfer Complexes Calculated by First-Principles Methods

1998 ◽  
Vol 63 (8) ◽  
pp. 1223-1244 ◽  
Author(s):  
Cordula Rauwolf ◽  
Achim Mehlhorn ◽  
Jürgen Fabian
Keyword(s):  
Density Functional Theory ◽  
Charge Transfer ◽  
Ground State ◽  
Density Functional ◽  
Binding Energies ◽  
Basis Set ◽  
Dispersion Energy ◽  
Functional Theory ◽  
Basis Set Superposition Error ◽  
Donor And Acceptor

Weak interactions between organic donor and acceptor molecules resulting in cofacially-stacked aggregates ("CT complexes") were studied by second-order many-body perturbation theory (MP2) and by gradient-corrected hybrid Hartree-Fock/density functional theory (B3LYP exchange-correlation functional). The complexes consist of tetrathiafulvalene (TTF) and related compounds and tetracyanoethylene (TCNE). Density functional theory (DFT) and MP2 molecular equilibrium geometries of the component structures are calculated by means of 6-31G*, 6-31G*(0.25), 6-31++G**, 6-31++G(3df,2p) and 6-311G** basis sets. Reliable molecular geometries are obtained for the donor and acceptor compounds considered. The geometries of the compounds were kept frozen in optimizing aggregate structures with respect to the intermolecular distance. The basis set superposition error (BSSE) was considered (counterpoise correction). According to the DFT and MP2 calculations laterally-displaced stacks are more stable than vertical stacks. The charge transfer from the donor to the acceptor is small in the ground state of the isolated complexes. The cp-corrected binding energies of TTF/TCNE amount to -1.7 and -6.3 kcal/mol at the DFT(B3LYP) and MP2(frozen) level of theory, respectively (6-31G* basis set). Larger binding energies were obtained by Hobza's 6-31G*(0.25) basis set. The larger MP2 binding energies suggest that the dispersion energy is underestimated or not considered by the B3LYP functional. The energy increases when S in TTF/TCNE is replaced by O or NH but decreases with substitution by Se. The charge-transferred complexes in the triplet state are favored in the vertical arrangement. Self-consistent-reaction-field (SCRF) calculations predicted a gain in binding energy with solvation for the ground-state complex. The ground-state charge transfer between the components is increased up to 0.8 e in polar solvents.

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