An incremental empirical approach to non-covalent interactions in and with DNA

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. 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. 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.

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Non-Covalent Interactions with Aromatic Rings: Current Understanding and Implications for Rational Drug Design

Current Pharmaceutical Design ◽

10.2174/13816128113199990440 ◽

2013 ◽

Vol 19 (36) ◽

pp. 6522-6533 ◽

Cited By ~ 15

Author(s):

Shanshan Li ◽

Yuan Xu ◽

Qiancheng Shen ◽

Xian Liu ◽

Jing Lu ◽

...

Keyword(s):

Drug Design ◽

Rational Drug Design ◽

Current Understanding ◽

Aromatic Rings ◽

Rational Drug ◽

Non Covalent Interactions ◽

Covalent Interactions

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Heterogenisation of polyoxometalates and other metal-based complexes in metal–organic frameworks: from synthesis to characterisation and applications in catalysis

Chemical Society Reviews ◽

10.1039/d0cs00323a ◽

2021 ◽

Author(s):

P. Mialane ◽

C. Mellot-Draznieks ◽

P. Gairola ◽

M. Duguet ◽

Y. Benseghir ◽

...

Keyword(s):

Metal Organic Frameworks ◽

Coordination Complexes ◽

Metal Organic ◽

Non Covalent Interactions ◽

Molecular Catalysts ◽

Covalent Interactions

This review provides a thorough overview of composites with molecular catalysts (polyoxometalates, or organometallic or coordination complexes) immobilised into MOFs via non-covalent interactions.

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Revealing new non-covalent interactions in polymorphs and hydrates of Acyclovir: Hirshfeld surface analysis, NCI plots and energetic calculations

Computational and Theoretical Chemistry ◽

10.1016/j.comptc.2020.113133 ◽

2020 ◽

pp. 113133

Author(s):

Juan J. Piña ◽

Diego M. Gil ◽

Hiram Pérez

Keyword(s):

Surface Analysis ◽

Hirshfeld Surface ◽

Hirshfeld Surface Analysis ◽

Non Covalent Interactions ◽

Covalent Interactions

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Magnetic imprinted nanoparticles with synergistic tailoring of covalent and non-covalent interactions for purification and detection of procyanidin B2

Microchimica Acta ◽

10.1007/s00604-020-04693-x ◽

2021 ◽

Vol 188 (1) ◽

Author(s):

Haipin Zhang ◽

Huijia Song ◽

Xuemeng Tian ◽

Yue Wang ◽

Yi Hao ◽

...

Keyword(s):

Non Covalent Interactions ◽

Covalent Interactions

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Interactions between large molecules pose a puzzle for reference quantum mechanical methods

Nature Communications ◽

10.1038/s41467-021-24119-3 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Yasmine S. Al-Hamdani ◽

Péter R. Nagy ◽

Andrea Zen ◽

Dennis Barton ◽

Mihály Kállay ◽

...

Keyword(s):

Experimental Information ◽

Quantum Mechanical ◽

Interaction Energies ◽

Small Organic Molecules ◽

Large Molecules ◽

Reference Information ◽

Mechanical Methods ◽

Non Covalent Interactions ◽

Semi Empirical ◽

Covalent Interactions

AbstractQuantum-mechanical methods are used for understanding molecular interactions throughout the natural sciences. Quantum diffusion Monte Carlo (DMC) and coupled cluster with single, double, and perturbative triple excitations [CCSD(T)] are state-of-the-art trusted wavefunction methods that have been shown to yield accurate interaction energies for small organic molecules. These methods provide valuable reference information for widely-used semi-empirical and machine learning potentials, especially where experimental information is scarce. However, agreement for systems beyond small molecules is a crucial remaining milestone for cementing the benchmark accuracy of these methods. We show that CCSD(T) and DMC interaction energies are not consistent for a set of polarizable supramolecules. Whilst there is agreement for some of the complexes, in a few key systems disagreements of up to 8 kcal mol−1 remain. These findings thus indicate that more caution is required when aiming at reproducible non-covalent interactions between extended molecules.

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Amino Acids as the Potential Co-Former for Co-Crystal Development: A Review

Molecules ◽

10.3390/molecules26113279 ◽

2021 ◽

Vol 26 (11) ◽

pp. 3279

Author(s):

Ilma Nugrahani ◽

Maria Anabella Jessica

Keyword(s):

Amino Acids ◽

Physicochemical Properties ◽

Deep Eutectic Solvent ◽

Strong Interactions ◽

Green Method ◽

Pharmaceutical Ingredients ◽

Gastrointestinal Fluid ◽

Non Covalent Interactions ◽

Natural Deep Eutectic Solvent ◽

Covalent Interactions

Co-crystals are one of the most popular ways to modify the physicochemical properties of active pharmaceutical ingredients (API) without changing pharmacological activity through non-covalent interactions with one or more co-formers. A “green method” has recently prompted many researchers to develop solvent-free techniques or minimize solvents for arranging the eco-friendlier process of co-crystallization. Researchers have also been looking for less-risk co-formers that produce the desired API’s physicochemical properties. This review purposed to collect the report studies of amino acids as the safe co-former and explored their advantages. Structurally, amino acids are promising co-former candidates as they have functional groups that can form hydrogen bonds and increase stability through zwitterionic moieties, which support strong interactions. The co-crystals and deep eutectic solvent yielded from this natural compound have been proven to improve pharmaceutical performance. For example, l-glutamine could reduce the side effects of mesalamine through an acid-base stabilizing effect in the gastrointestinal fluid. In addition, some amino acids, especially l-proline, enhances API’s solubility and absorption in its natural deep eutectic solvent and co-crystals systems. Moreover, some ionic co-crystals of amino acids have also been designed to increase chiral resolution. Therefore, amino acids are safe potential co-formers, which are suitable for improving the physicochemical properties of API and prospective to be developed further in the dosage formula and solid-state syntheses.

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