scholarly journals Towards an Atomistic Understanding of Polymorphism in Molecular Solids

2021 ◽  
Author(s):  
Arturo Sauza-de la Vega ◽  
Leonardo J. Duarte ◽  
arnaldo silva ◽  
Jonathan Skelton ◽  
Tomás Rocha-Rinza ◽  
...  
Keyword(s):  
Decomposition Analysis ◽  
Relative Energy ◽  
Energy Partitioning ◽  
Energy Decomposition Analysis ◽  
Molecular Solids ◽  
Total System ◽  
Energy Gradient ◽  
A New Technique ◽  
The Many ◽  
Energy Balances

Many chemical phenomena are ultimately due to energy balances between atoms. In order to reach firm and clear conclusions one needs a reliable energy decomposition analysis (EDA). The Interacting Quantum Atoms (IQA) energy partitioning method is one of the most recent EDA methods. IQA is a topological energy partitioning that generates well-defined intra- and interatomic contributions, of steric, electrostatic or covalent (exchange) character. IQA has a minimal and powerful architecture and does not suffer from a number of conceptual and practical problems that plague the more traditional non-topological EDAs (<i>Chem. Soc. Rev.</i>, <b>44</b> (2015) 3177).<div><br></div><div>For the first time, our manuscript reports on a protocol for using the IQA to understand polymorphism, which we apply to the three polymorphs of succinic acid (SA), including the unusual polymorph that was recently discovered serendipitously (<i>CrystEngComm</i>, <b>20</b> (2018) 3971). The many intra- and interatomic energy terms from the EDA scheme are processed using a new technique that we developed called the Relative Energy Gradient (REG) method, which clearly identifies the atoms and corresponding energetic terms that govern the behaviour of the total system, in a minimal and unbiased way. <br></div>

scholarly journals Towards an Atomistic Understanding of Polymorphism in Molecular Solids

2021 ◽  
Author(s):  
Arturo Sauza-de la Vega ◽  
Leonardo J. Duarte ◽  
arnaldo silva ◽  
Jonathan Skelton ◽  
Tomás Rocha-Rinza ◽  
...  
Keyword(s):  
Decomposition Analysis ◽  
Relative Energy ◽  
Energy Partitioning ◽  
Energy Decomposition Analysis ◽  
Molecular Solids ◽  
Total System ◽  
Energy Gradient ◽  
A New Technique ◽  
The Many ◽  
Energy Balances

Many chemical phenomena are ultimately due to energy balances between atoms. In order to reach firm and clear conclusions one needs a reliable energy decomposition analysis (EDA). The Interacting Quantum Atoms (IQA) energy partitioning method is one of the most recent EDA methods. IQA is a topological energy partitioning that generates well-defined intra- and interatomic contributions, of steric, electrostatic or covalent (exchange) character. IQA has a minimal and powerful architecture and does not suffer from a number of conceptual and practical problems that plague the more traditional non-topological EDAs (<i>Chem. Soc. Rev.</i>, <b>44</b> (2015) 3177).<div><br></div><div>For the first time, our manuscript reports on a protocol for using the IQA to understand polymorphism, which we apply to the three polymorphs of succinic acid (SA), including the unusual polymorph that was recently discovered serendipitously (<i>CrystEngComm</i>, <b>20</b> (2018) 3971). The many intra- and interatomic energy terms from the EDA scheme are processed using a new technique that we developed called the Relative Energy Gradient (REG) method, which clearly identifies the atoms and corresponding energetic terms that govern the behaviour of the total system, in a minimal and unbiased way. <br></div>

Vapour Pressure Isotope Effect on Evaporation from Pure Organic Phases - a PIMD Approach

2020 ◽  
Author(s):  
Luis Vasquez ◽  
Agnieszka Dybala-Defratyka
Keyword(s):  
Path Integral ◽  
Vapour Pressure ◽  
Density Functional ◽  
Isotope Effects ◽  
Tight Binding ◽  
Decomposition Analysis ◽  
Energy Decomposition Analysis ◽  
Special Importance ◽  
Non Covalent Interactions ◽  
Covalent Interactions

<p></p><p>Very often in order to understand physical and chemical processes taking place among several phases fractionation of naturally abundant isotopes is monitored. Its measurement can be accompanied by theoretical determination to provide a more insightful interpretation of observed phenomena. Predictions are challenging due to the complexity of the effects involved in fractionation such as solvent effects and non-covalent interactions governing the behavior of the system which results in the necessity of using large models of those systems. This is sometimes a bottleneck and limits the theoretical description to only a few methods.<br> In this work vapour pressure isotope effects on evaporation from various organic solvents (ethanol, bromobenzene, dibromomethane, and trichloromethane) in the pure phase are estimated by combining force field or self-consistent charge density-functional tight-binding (SCC-DFTB) atomistic simulations with path integral principle. Furthermore, the recently developed Suzuki-Chin path integral is tested. In general, isotope effects are predicted qualitatively for most of the cases, however, the distinction between position-specific isotope effects observed for ethanol was only reproduced by SCC-DFTB, which indicates the importance of using non-harmonic bond approximations.<br> Energy decomposition analysis performed using the symmetry-adapted perturbation theory (SAPT) revealed sometimes quite substantial differences in interaction energy depending on whether the studied system was treated classically or quantum mechanically. Those observed differences might be the source of different magnitudes of isotope effects predicted using these two different levels of theory which is of special importance for the systems governed by non-covalent interactions.</p><br><p></p>

On the Nature of Halide-Water Interactions: Insights from Many-Body Representations and Density Functional Theory

2019 ◽  
Author(s):  
Brandon B. Bizzarro ◽  
Colin K. Egan ◽  
Francesco Paesani
Keyword(s):  
Density Functional Theory ◽  
Charge Transfer ◽  
Molecular Orbital ◽  
Density Functional ◽  
Decomposition Analysis ◽  
Orbital Energy ◽  
Energy Decomposition Analysis ◽  
Interaction Energies ◽  
Many Body ◽  
Functional Theory

<div> <div> <div> <p>Interaction energies of halide-water dimers, X<sup>-</sup>(H<sub>2</sub>O), and trimers, X<sup>-</sup>(H<sub>2</sub>O)<sub>2</sub>, with X = F, Cl, Br, and I, are investigated using various many-body models and exchange-correlation functionals selected across the hierarchy of density functional theory (DFT) approximations. Analysis of the results obtained with the many-body models demonstrates the need to capture important short-range interactions in the regime of large inter-molecular orbital overlap, such as charge transfer and charge penetration. Failure to reproduce these effects can lead to large deviations relative to reference data calculated at the coupled cluster level of theory. Decompositions of interaction energies carried out with the absolutely localized molecular orbital energy decomposition analysis (ALMO-EDA) method demonstrate that permanent and inductive electrostatic energies are accurately reproduced by all classes of XC functionals (from generalized gradient corrected (GGA) to hybrid and range-separated functionals), while significant variance is found for charge transfer energies predicted by different XC functionals. Since GGA and hybrid XC functionals predict the most and least attractive charge transfer energies, respectively, the large variance is likely due to the delocalization error. In this scenario, the hybrid XC functionals are then expected to provide the most accurate charge transfer energies. The sum of Pauli repulsion and dispersion energies are the most varied among the XC functionals, but it is found that a correspondence between the interaction energy and the ALMO EDA total frozen energy may be used to determine accurate estimates for these contributions. </p> </div> </div> </div>

scholarly journals Nanotechnology-based approaches for targeting and delivery of drugs via Hexakis (m-PE) macrocycles

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Samaneh Pasban ◽  
Heidar Raissi
Keyword(s):  
Drug Delivery ◽  
Density Functional ◽  
Water Solution ◽  
Decomposition Analysis ◽  
Binding Energies ◽  
Energy Decomposition Analysis ◽  
Partial Density ◽  
High Propensity ◽  
The Stability ◽  
Novel Applications

AbstractHexakis (m-phenylene ethynylene) (m-PE) macrocycles, with aromatic backbones and multiple hydrogen-bonding side chains, had a very high propensity to self-assemble via H-bond and π–π stacking interactions to form nanotubular structures with defined inner pores. Such stacking of rigid macrocycles is leading to novel applications that enable the researchers to explored mass transport in the sub-nanometer scale. Herein, we performed density functional theory (DFT) calculations to examine the drug delivery performance of the hexakis dimer as a novel carrier for doxorubicin (DOX) agent in the chloroform and water solvents. Based on the DFT results, it is found that the adsorption of DOX on the carrier surface is typically physisorption with the adsorption strength values of − 115.14 and − 83.37 kJ/mol in outside and inside complexes, respectively, and so that the essence of the drug remains intact. The negative values of the binding energies for all complexes indicate the stability of the drug molecule inside and outside the carrier's cavities. The energy decomposition analysis (EDA) has also been performed and shown that the dispersion interaction has an essential role in stabilizing the drug-hexakis dimer complexes. To further explore the electronic properties of dox, the partial density of states (PDOS and TDOS) are calculated. The atom in molecules (AIM) and Becke surface (BS) methods are also analyzed to provide an inside view of the nature and strength of the H-bonding interactions in complexes. The obtained results indicate that in all studied complexes, H-bond formation is the driving force in the stabilization of these structures, and also chloroform solvent is more favorable than the water solution. Overall, our findings offer insightful information on the efficient utilization of hexakis dimer as drug delivery systems to deliver anti-cancer drugs.

scholarly journals Direct estimate of the internal π-donation to the carbene centre within N-heterocyclic carbenes and related molecules

2015 ◽  
Vol 11 ◽  
pp. 2727-2736 ◽  
Author(s):  
Diego M Andrada ◽  
Nicole Holzmann ◽  
Thomas Hamadi ◽  
Gernot Frenking
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Decomposition Analysis ◽  
Heterocyclic Carbenes ◽  
Energy Decomposition Analysis ◽  
Energy Decomposition ◽  
Direct Estimate ◽  
Functional Theory ◽  
Bonding Analysis

Fifteen cyclic and acylic carbenes have been calculated with density functional theory at the BP86/def2-TZVPP level. The strength of the internal X→p(π) π-donation of heteroatoms and carbon which are bonded to the C(II) atom is estimated with the help of NBO calculations and with an energy decomposition analysis. The investigated molecules include N-heterocyclic carbenes (NHCs), the cyclic alkyl(amino)carbene (cAAC), mesoionic carbenes and ylide-stabilized carbenes. The bonding analysis suggests that the carbene centre in cAAC and in diamidocarbene have the weakest X→p(π) π-donation while mesoionic carbenes possess the strongest π-donation.

Characterization of cisplatin/membrane interactions by QM/MM energy decomposition analysis

2021 ◽  
Vol 23 (36) ◽  
pp. 20533-20540
Author(s):  
Gustavo Cárdenas ◽  
Álvaro Pérez-Barcia ◽  
Marcos Mandado ◽  
Juan J. Nogueira
Keyword(s):  
Decomposition Analysis ◽  
Energy Decomposition Analysis ◽  
Energy Decomposition ◽  
Membrane Interactions

The interactions that control the permeation of cisplatin through a DOPC bilayer are unveiled by a QM/MM EDA scheme.

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