Inclusion Scenarios and Conformational Flexibility of the SSRI Paroxetine as Perceived from Polymorphism of β-Cyclodextrin–Paroxetine Complex

Depression, a global mental health problem, is prevalent during the coronavirus disease 2019 (COVID-19) pandemic and can be efficiently treated by selective serotonin reuptake inhibitors (SSRIs). Our study series aims at forwarding insights on the β-cyclodextrin (β-CD)–SSRI inclusion complexes by X-ray crystallography combined with density functional theory (DFT) calculation. Here, we report a new crystal form (II) of the 1:1 β-CD–paroxetine (PXT) complex, which is inspired by the reported 2:1 β-CD–PXT complex (crystal form I), reflecting an elusive phenomenon of the polymorphism in CD inclusion complexes. The β-CD–PXT polymorphism stems from the PXT conformational flexibility, which is defined by torsion angles κ, ε around the -CH2–O- group bridging the A- and C–D-rings, of which those of PXT in I and II are totally different. While PXT (II) in an open V-shaped conformation that has the B-ring shallowly inserted in the β-CD cavity, PXT (I) in a closed U-shaped structure is mostly entirely embedded in the β-CD dimeric cavity, of which the A-ring is deeply inserted in the main β-CD cavity. However, PXT molecules in both crystal forms are similarly maintained in the CD cavity via host–guest N–H···O5/O6 H-bonds and C/O–H···π(B/C) interactions and β-CDs have similar 3D arrangements, channel (II) vs. screw-channel (I). Further theoretical explorations on the β-CD–PXT thermodynamic stabilities and the PXT conformational stabilities based on their potential energy surfaces (PESs) have been completed by DFT calculations. The 2:1 β-CD–PXT complex with the greater presence of dispersion interactions is more energetically favorable than the unimolar complex. Conversely, whereas free PXT, PXT (II) and PXT in complex with serotonin transporter are more energetically stable, PXT (I) is least stable and stabilized in the β-CD cavity. As SSRIs could lessen the COVID-19 severity, the CD inclusion complexation not only helps to improve the drug bioavailability, but also promotes the use of antidepressants and COVID-19 medicines concurrently.

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Supramolecular Complexes of β-Cyclodextrin with Clomipramine and Doxepin: Effect of the Ring Substituent and Component of Drugs on Their Inclusion Topologies and Structural Flexibilities

Pharmaceuticals ◽

10.3390/ph13100278 ◽

2020 ◽

Vol 13 (10) ◽

pp. 278

Author(s):

Thammarat Aree

Keyword(s):

Side Effects ◽

Density Functional ◽

Dft Calculation ◽

Drug Stability ◽

Inclusion Complexation ◽

Drug Carriers ◽

Supramolecular Complexes ◽

Drug Bioavailability ◽

X Ray ◽

Global Threat

Depression is a global threat. Tricyclic antidepressants (TCAs) are still efficacious in treating depression, albeit with more side effects. Cyclodextrins (CDs) with a suitable nanocavity are potential drug carriers and can enhance the drug bioavailability. Aiming for an atomistic understanding of the CD encapsulation facilitating the improvement of drug stability and the reduction of side effects, a comprehensive study series of the β-CD–TCA inclusion complexes through single crystal X-ray diffraction and density functional theory (DFT) calculation was undertaken. This work reports the supramolecular complexes of β-CD with two pivotal TCAs, clomipramine (CPM; 1) and doxepin (DXP; 2). The different inclusion topologies of the β-CD–TCA complexes were notable. X-ray analysis revealed that, in 1, the CPM B-ring (without chloro group) was entrapped in the β-CD cavity, whereas, in 2, the E-DXP A-ring and the Z-DXP B-ring were disordered in the cavity, yielding energetically favorable complexes primarily maintained by intermolecular C–H⋯π interactions, as indicated by DFT calculation. Because both wings of TCAs were similar, an alternative inclusion scenario of the A-ring was evidenced crystallographically in four other TCA complexes. The enhanced TCA thermodynamic stabilities via CD inclusion complexation helped to reduce the side effects and to increase the bioavailability. Moreover, the scrutinization of six TCAs in different lattice circumstances revealed the greater TCA structural flexibilities for their optimum pharmacological activity while binding with proteins.

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

Molecules ◽

10.3390/molecules26123574 ◽

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.

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Single-crystalline epitaxial TiO film: A metal and superconductor, similar to Ti metal

Science Advances ◽

10.1126/sciadv.abd4248 ◽

2021 ◽

Vol 7 (2) ◽

pp. eabd4248

Author(s):

Fengmiao Li ◽

Yuting Zou ◽

Myung-Geun Han ◽

Kateryna Foyevtsova ◽

Hyungki Shin ◽

...

Keyword(s):

Transition Metal ◽

Density Functional ◽

Tight Binding ◽

Crystal Form ◽

Titanium Monoxide ◽

Binding Model ◽

Functional Theory ◽

Single Crystalline ◽

First Time ◽

Lattice Matched

Titanium monoxide (TiO), an important member of the rock salt 3d transition-metal monoxides, has not been studied in the stoichiometric single-crystal form. It has been challenging to prepare stoichiometric TiO due to the highly reactive Ti2+. We adapt a closely lattice-matched MgO(001) substrate and report the successful growth of single-crystalline TiO(001) film using molecular beam epitaxy. This enables a first-time study of stoichiometric TiO thin films, showing that TiO is metal but in proximity to Mott insulating state. We observe a transition to the superconducting phase below 0.5 K close to that of Ti metal. Density functional theory (DFT) and a DFT-based tight-binding model demonstrate the extreme importance of direct Ti–Ti bonding in TiO, suggesting that similar superconductivity exists in TiO and Ti metal. Our work introduces the new concept that TiO behaves more similar to its metal counterpart, distinguishing it from other 3d transition-metal monoxides.

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Effect of dispersion on surface interactions of cobalt(ii) octaethylporphyrin monolayer on Au(111) and HOPG(0001) substrates: a comparative first principles study

Physical Chemistry Chemical Physics ◽

10.1039/c4cp01762e ◽

2014 ◽

Vol 16 (27) ◽

pp. 14096-14107 ◽

Cited By ~ 38

Author(s):

Bhaskar Chilukuri ◽

Ursula Mazur ◽

K. W. Hipps

Keyword(s):

Density Functional Theory ◽

Electronic Properties ◽

First Principles ◽

Density Functional ◽

Surface Interactions ◽

Dispersion Interactions ◽

Functional Theory ◽

First Principles Study ◽

Conductive Surfaces

Implication of dispersion interactions on geometric, adsorption and electronic properties of porphyrin monolayer on conductive surfaces using density functional theory.

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ChemInform Abstract: Dispersion Interactions in Density-Functional Theory

ChemInform ◽

10.1002/chin.201014273 ◽

2010 ◽

Vol 41 (14) ◽

Author(s):

Erin R. Johnson ◽

Iain D. Mackie ◽

Gino A. Di Labio

Keyword(s):

Density Functional Theory ◽

Density Functional ◽

Dispersion Interactions ◽

Functional Theory

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

10.26434/chemrxiv.10050737 ◽

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>

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

Pharmaceuticals ◽

10.3390/ph14080812 ◽

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.

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Migration of Zeolite-Encapsulated Pt and Au Under Reducing Atmospheres

10.26434/chemrxiv.14456316.v1 ◽

2021 ◽

Author(s):

Dianwei Hou ◽

Christopher Heard

Keyword(s):

Monte Carlo ◽

Potential Energy Surfaces ◽

Density Functional ◽

Noble Metals ◽

Kinetic Monte Carlo ◽

Pore System ◽

Kinetic Monte Carlo Simulations ◽

Zeolite Lta ◽

Metal Migration ◽

Energy Surfaces

Unbiased density functional global optimisation calculations, followed by kinetic Monte Carlo simulations are used to enumerate the potential energy surfaces for migration of noble metals Pt and Au inside the pore system of siliceous zeolite LTA. The effects of reducing adsorbates CO and H2 are determined. It is found that the two metals differ significantly in the strength and type of interaction with the framework, with strong, framework breaking interactions between Pt and and the zeolite, but only weak dispersive interactions between Au and the zeolite. Adsorbates are found to dramatically interfere with Pt-framework binding, leading to poorer atom-trapping, enhanced metal migration and faster equilibration.

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Impact of Van der Waals interactions on structural and nonlinear optical properties of azobenzene switches

10.26434/chemrxiv.14731428.v1 ◽

2021 ◽

Author(s):

carmelo Naim ◽

Frédéric Castet ◽

Eduard Matito

Keyword(s):

Density Functional ◽

Nonlinear Optical ◽

Van Der Waals Interactions ◽

Dispersion Interactions ◽

Geometrical Structures ◽

Hartree Fock ◽

Meta Position ◽

Good Account ◽

London Dispersion ◽

Azobenzene Derivatives

<div> <div> <div> <p>The geometrical structures, relative Z-E energies, and second-order nonlinear responses of a collection of azobenzene molecules symmetrically substituted in meta- position with functional groups of different bulkiness are investigated using various ab initio and DFT levels of approximation. We show that RI-MP2 and RI-CC2 approximations provide very similar geometries and relative energies and evidence that London dispersion interactions existing between bulky meta-substituents stabilize the Z con- former. The !B97-X-D exchange-correlation functional provides an accurate description of these effects and gives a good account of the nonlinear optical response of the molecules. We show that density functional approximations should include no less than 50% of Hartree-Fock exchange to provide accurate hyperpolarizabilities. A property-structure analysis of the azobenzene derivatives reveals that the main contribution to the first hyperpolarizability comes from the azo bond, but phenyl meso-substituents can enhance it.</p> </div> </div> </div>

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Optical Properties and van der Waals-London Dispersion Interactions in Inorganic and Biomolecular Assemblies

MRS Proceedings ◽

10.1557/opl.2014.301 ◽

2014 ◽

Vol 1619 ◽

Author(s):

Daniel M. Dryden ◽

Yingfang Ma ◽

Jacob Schimelman ◽

Diana Acosta ◽

Lijia Liu ◽

...

Keyword(s):

Optical Properties ◽

Spectroscopic Ellipsometry ◽

Density Functional ◽

Type I Collagen ◽

Strong Dependence ◽

Van Der Waals ◽

Fundamental Absorption Edge ◽

Type I ◽

Dispersion Interactions ◽

London Dispersion

ABSTRACTThe optical properties and electronic structure of AlPO4, SiO2, Type I collagen, and DNA were examined to gain insight into the van der Waals-London dispersion behavior of these materials. Interband optical properties of AlPO4 and SiO2 were derived from vacuum ultraviolet spectroscopy and spectroscopic ellipsometry, and showed a strong dependence on the crystals’ constituent tetrahedral units, with strong implications for the role of phosphate groups in biological materials. The UV-Vis decadic molar absorption of four DNA oligonucleotides was measured, and showed a strong dependence on composition and stacking sequence. A film of Type I collagen was studied using spectroscopic ellipsometry, and showed a characteristic shoulder in the fundamental absorption edge at 6.05 eV. Ab initio calculations based on density functional theory corroborated the experimental results and provided further insights into the electronic structures, interband transitions and vdW-Ld interaction potentials for these materials.

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