The Law of Attraction: Relating Computed Energetics of Physisorption with Performance of Graphene-Based Sensors for Nitroaromatic Contaminants

Law Of Attraction ◽

<div> <div> <div> <p>The ability to detect persistent nitroaromatic contaminants, e.g. DNT and TNT, with high sensitivity and selectivity is central to environmental science and medicinal diagnostics. Graphene-based materials rise to this challenge, offering supreme performance, biocompatibility, and low toxicity at a reasonable cost. In the first step of the electrochemical sensing process, these substrates establish non-covalent interactions with the analytes, which we show to be indicative of their respective detection limits. Employing a combination of semiempirical tight binding quantum chemistry, meta- dynamics, density functional theory, and symmetry-adapted perturbation theory in conjunction with curated data from experimental literature, we investigate the physisorption of DNT and TNT on a series of functionalised graphene derivatives. In agreement with experimental observations, systems with greater planarity and positively charged substrates afford stronger non-covalent interactions than their highly oxidised distorted counterparts. Despite the highly polar nature of the investigated species, their non-covalent interactions are largely driven by dispersion forces. To harness these design principles, we considered a series of boron and nitrogen (co)doped two-dimensional materials. One of these systems featuring a chain of B–N–C units was found to adsorb nitroaromatic molecules stronger than the pristine graphene itself. These findings form the basis for the design principles of sensing materials and illustrate the utility of relatively low cost in silico procedures for testing the viability of designed graphene-based sensors for a plethora of analytes. </p> </div> </div> </div>

The Law of Attraction: Relating Computed Energetics of Physisorption with Performance of Graphene-Based Sensors for Nitroaromatic Contaminants

10.26434/chemrxiv.14364800.v2 ◽

2021 ◽

Author(s):

Anna Piras ◽

Ganna Gryn'ova

Keyword(s):

Density Functional ◽

Environmental Science ◽

Tight Binding ◽

Design Principles ◽

Electrochemical Sensing ◽

Pristine Graphene ◽

Graphene Derivatives ◽

Law Of Attraction ◽

<div> <div> <div> <p>The ability to detect persistent nitroaromatic contaminants, e.g. DNT and TNT, with high sensitivity and selectivity is central to environmental science and medicinal diagnostics. Graphene-based materials rise to this challenge, offering supreme performance, biocompatibility, and low toxicity at a reasonable cost. In the first step of the electrochemical sensing process, these substrates establish non-covalent interactions with the analytes, which we show to be indicative of their respective detection limits. Employing a combination of semiempirical tight binding quantum chemistry, meta- dynamics, density functional theory, and symmetry-adapted perturbation theory in conjunction with curated data from experimental literature, we investigate the physisorption of DNT and TNT on a series of functionalised graphene derivatives. In agreement with experimental observations, systems with greater planarity and positively charged substrates afford stronger non-covalent interactions than their highly oxidised distorted counterparts. Despite the highly polar nature of the investigated species, their non-covalent interactions are largely driven by dispersion forces. To harness these design principles, we considered a series of boron and nitrogen (co)doped two-dimensional materials. One of these systems featuring a chain of B–N–C units was found to adsorb nitroaromatic molecules stronger than the pristine graphene itself. These findings form the basis for the design principles of sensing materials and illustrate the utility of relatively low cost in silico procedures for testing the viability of designed graphene-based sensors for a plethora of analytes. </p> </div> </div> </div>

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

10.26434/chemrxiv.12003186.v1 ◽

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 ◽

<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>

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

10.26434/chemrxiv.12003186 ◽

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 ◽

<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>

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

10.26434/chemrxiv.12003186.v2 ◽

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 ◽

<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>

Weak Interactions in Cocrystals of Isoniazid with Glycolic and Mandelic Acids

Crystals ◽

10.3390/cryst11040328 ◽

2021 ◽

Vol 11 (4) ◽

pp. 328

Author(s):

Raquel Álvarez-Vidaurre ◽

Alfonso Castiñeiras ◽

Antonio Frontera ◽

Isabel García-Santos ◽

Diego M. Gil ◽

...

Keyword(s):

Density Functional ◽

Glycolic Acid ◽

Weak Interactions ◽

Three Dimensional ◽

Functional Theory ◽

Molecular Systems ◽

X Ray Crystallography ◽

Hydroxycarboxylic Acids ◽

This work deals with the preparation of pyridine-3-carbohydrazide (isoniazid, inh) cocrystals with two α-hydroxycarboxylic acids. The interaction of glycolic acid (H2ga) or d,l-mandelic acid (H2ma) resulted in the formation of cocrystals or salts of composition (inh)·(H2ga) (1) and [Hinh]+[Hma]–·(H2ma) (2) when reacted with isoniazid. An N′-(propan-2-ylidene)isonicotinic hydrazide hemihydrate, (pinh)·1/2(H2O) (3), was also prepared by condensation of isoniazid with acetone in the presence of glycolic acid. These prepared compounds were well characterized by elemental analysis, and spectroscopic methods, and their three-dimensional molecular structure was determined by single crystal X-ray crystallography. Hydrogen bonds involving the carboxylic acid occur consistently with the pyridine ring N atom of the isoniazid and its derivatives. The remaining hydrogen-bonding sites on the isoniazid backbone vary based on the steric influences of the derivative group. These are contrasted in each of the molecular systems. Finally, Hirshfeld surface analysis and Density-functional theory (DFT) calculations (including NCIplot and QTAIM analyses) have been performed to further characterize and rationalize the non-covalent interactions.

1,3,5-Triaza-7-Phosphaadamantane (PTA) as a 31P NMR Probe for Organometallic Transition Metal Complexes in Solution

Molecules ◽

10.3390/molecules26051390 ◽

2021 ◽

Vol 26 (5) ◽

pp. 1390 ◽

Cited By ~ 1

Author(s):

Ilya G. Shenderovich

Keyword(s):

Chemical Shift ◽

Transition Metal ◽

Metal Complexes ◽

Transition Metal Complexes ◽

Density Functional ◽

Molecular Structures ◽

Basis Sets ◽

Functional Theory ◽

Due to the rigid structure of 1,3,5-triaza-7-phosphaadamantane (PTA), its 31P chemical shift solely depends on non-covalent interactions in which the molecule is involved. The maximum range of change caused by the most common of these, hydrogen bonding, is only 6 ppm, because the active site is one of the PTA nitrogen atoms. In contrast, when the PTA phosphorus atom is coordinated to a metal, the range of change exceeds 100 ppm. This feature can be used to support or reject specific structural models of organometallic transition metal complexes in solution by comparing the experimental and Density Functional Theory (DFT) calculated values of this 31P chemical shift. This approach has been tested on a variety of the metals of groups 8–12 and molecular structures. General recommendations for appropriate basis sets are reported.

Atoms in Highly Symmetric Environments: H in Rhodium and Cobalt Cages, H in an Octahedral Hole in MgO, and Metal Atoms Ca-Zn in C20 Fullerenes

Symmetry ◽

10.3390/sym13071281 ◽

2021 ◽

Vol 13 (7) ◽

pp. 1281

Author(s):

Zikri Altun ◽

Erdi Ata Bleda ◽

Carl Trindle

Keyword(s):

Density Functional Theory ◽

Quantum Theory ◽

Coordination Number ◽

Electronic Structures ◽

Density Functional ◽

Functional Theory ◽

Metal Atoms ◽

Tetragonal Pyramidal ◽

An atom trapped in a crystal vacancy, a metal cage, or a fullerene might have many immediate neighbors. Then, the familiar concept of valency or even coordination number seems inadequate to describe the environment of that atom. This difficulty in terminology is illustrated here by four systems: H atoms in tetragonal-pyramidal rhodium cages, H atom in an octahedral cobalt cage, H atom in a MgO octahedral hole, and metal atoms in C20 fullerenes. Density functional theory defines structure and energetics for the systems. Interactions of the atom with its container are characterized by the quantum theory of atoms in molecules (QTAIM) and the theory of non-covalent interactions (NCI). We establish that H atoms in H2Rh13(CO)243− trianion cannot be considered pentavalent, H atom in HCo6(CO)151− anion cannot be considered hexavalent, and H atom in MgO cannot be considered hexavalent. Instead, one should consider the H atom to be set in an environmental field defined by its 5, 6, and 6 neighbors; with interactions described by QTAIM. This point is further illustrated by the electronic structures and QTAIM parameters of M@C20, M=Ca to Zn. The analysis describes the systematic deformation and restoration of the symmetric fullerene in that series.

Performance of dispersion-corrected density functional theory for thermochemistry and non-covalent interactions

Journal of Cheminformatics ◽

10.1186/1758-2946-4-s1-p56 ◽

2012 ◽

Vol 4 (S1) ◽

Cited By ~ 2

Author(s):

Waldemar Hujo ◽

Stefan Grimme

Keyword(s):

Density Functional Theory ◽

Density Functional ◽

Functional Theory ◽

Armchair Boron Nitride nanotubes—heterocyclic molecules interactions: A computational description

Open Chemistry ◽

10.1515/chem-2015-0088 ◽

2015 ◽

Vol 13 (1) ◽

Cited By ~ 6

Author(s):

Ernesto Chigo Anota ◽

Gregorio Hernández Cocoletzi ◽

Andres Manuel Garay Tapia

Keyword(s):

Density Functional Theory ◽

Boron Nitride ◽

Ab Initio Calculations ◽

Ab Initio ◽

Density Functional ◽

Boron Nitride Nanotubes ◽

Functional Theory ◽

Heterocyclic Molecules ◽

AbstractAb-initio calculations using density functional theory (DFT) are used to investigate the non-covalent interactions between single wall armchair boron nitride nanotubes (BNNTs) with open ends and several heterocyclic molecules: thiophene (T; C