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1.
J Comput Chem ; 45(22): 1936-1944, 2024 Aug 15.
Artigo em Inglês | MEDLINE | ID: mdl-38703182

RESUMO

In symmetry-adapted perturbation theory (SAPT), accurate calculations on non-covalent interaction (NCI) for large complexes with more than 50 atoms are time-consuming using large basis sets. More efficient ones with smaller basis sets usually result in poor prediction in terms of dispersion and overall energies. In this study, we propose two composite methods with baseline calculated at SAPT2/aug-cc-pVDZ and SAPT2/aug-cc-pVTZ with dispersion term corrected at SAPT2+ level using bond functions and smaller basis set with δ MP2 corrections respectively. Benchmark results on representative NCI data sets, such as S22, S66, and so forth, show significant improvements on the accuracy compared to the original SAPT Silver standard and comparable to SAPT Gold standard in some cases with much less computational cost.

2.
J Comput Chem ; 2024 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-38946399

RESUMO

Intermolecular interactions with polycyclic aromatic hydrocarbons (PAHs) represent an important area of physisorption studies. These investigations are often hampered by a size of interacting PAHs, which makes the calculation prohibitively expensive. Therefore, methods designed to deal with large molecules could be helpful to reduce the computational costs of such studies. Recently we have introduced a new systematic approach for the molecular fragmentation of PAHs, denoted as AROFRAG, which decomposes a large PAH molecule into a set of predefined small PAHs with a benzene ring being the smallest unbreakable unit, and which in conjunction with the Molecules-in-Molecules (MIM) approach provides an accurate description of total molecular energies. In this contribution we propose an extension of the AROFRAG, which provides a description of intermolecular interactions for complexes composed of PAH molecules. The examination of interaction energy partitioning for various test cases shows that the AROFRAG3 model connected with the MIM approach accurately reproduces all important components of the interaction energy. An additional important finding in our study is that the computationally expensive long-range electron-correlation part of the interaction energy, that is, the dispersion component, is well described at lower AROFRAG levels even without MIM, which makes the latter models interesting alternatives to existing methods for an accurate description of the electron-correlated part of the interaction energy.

3.
Chemphyschem ; 25(3): e202300552, 2024 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-37983746

RESUMO

Remdesivir (RDV) emerged as an effective drug against the SARS-CoV-2 virus pandemic. One of the crucial steps in the mechanism of action of RDV is its incorporation into the growing RNA strand. RDV, an adenosine analogue, forms Watson-Crick (WC) type hydrogen bonds with uridine in the complementary strand and the strength of this interaction will control efficacy of RDV. While there is a plethora of structural and energetic information available about WC H-bonds in natural base pairs, the interaction of RDV with uridine has not been studied yet at the atomic level. In this article, we aim to bridge this gap, to understand RDV and its hydrogen bonding interactions, by employing density functional theory (DFT) at the M06-2X/cc-pVDZ level. The interaction energy, QTAIM analysis, NBO and SAPT2 are performed for RDV, adenosine, and their complex with uridine to gain insights into the nature of hydrogen bonding. The computations show that RDV has similar geometry, energetic, molecular orbitals, and aromaticity as adenosine, suggesting that RDV is an effective adenosine analogue. The important geometrical parameters, such as bond distances and red-shift in the stretching vibrational modes of adenosine, RDV and uridine identify two WC-type H-bonds. The relative strength of these two H-bonds is computed using QTAIM parameters and the computed hydrogen bond energy. Finally, the SAPT2 study is performed at the minima and at non-equilibrium base pair distances to understand the dominant intermolecular physical force. This study, based on a thorough analysis of a variety of computations, suggests that both adenosine and RDV have similar structure, energetic, and hydrogen bonding behaviour.


Assuntos
Adenosina , Alanina/análogos & derivados , Teoria Quântica , Ligação de Hidrogênio , Uridina , Monofosfato de Adenosina/farmacologia
4.
Chemphyschem ; : e202400403, 2024 May 21.
Artigo em Inglês | MEDLINE | ID: mdl-38771647

RESUMO

Ab initio calculations were employed to investigate the interactions between selected electron-donating groups, characterized by M-H bonds (where M represents a transition metal and H denotes a hydridic hydrogen), and electron-accepting groups featuring both σ- and π-holes. The study utilized the ωB97X-D3BJ/def2-TZVPPD level of theory. Hydridic hydrogen complexes were found in all complexes with σ- and π-holes. A comparative analysis was conducted on the properties hydridic H-bond complexes, presented here and those studied previously, alongside an extended set of protonic H-bonds complexes. While the stabilization energies changes in M-H bond lengths, vibrational frequencies, intensities of the spectral bands, and charge transfer for these complexes are comparable, the nature of hydridic and protonic H-bonds fundamentally differ. In protonic H-bond complexes, the main stabilization forces arise from electrostatic contributions, while in hydridic H-bond complexes, dispersion energy, is the primary stabilization factor due to the excess of electrons and thus larger polarizability at hydridic H. The finding represents an important characteristic that distinguishes hydridic H-bonding from protonic H-bonds.

5.
Chem Rec ; : e202400055, 2024 Jul 12.
Artigo em Inglês | MEDLINE | ID: mdl-38994665

RESUMO

Carbon-based allotropes are propelling a technological revolution in communication, sensing, and computing, concurrently challenging fundamental theories of the previous century. Nevertheless, the demand for advanced carbon-based materials remains substantial. The crux lies in the efficient and reliable engineering of novel carbon allotrope. Although C18 has undergone theoretical and experimental investigation for an extended period, its preparation and direct observation in the condensed phase occurred only recently through STM/AFM techniques. The distinctive cyclic ring structure and the dual 18-center π delocalization character introduce various uncommon properties to C18, rendering it a subject worthy of in-depth exploration. In this context, this review delves into past developments contributing to the state-of-the-art understanding of C18 and provides insights into how future endeavours can expedite practical applications. Encompassing a broad spectrum, this review comprehensively investigates almost all facets of C18, including geometric characteristics, electron delocalization, bonding nature, aromaticity, reactivity, electronic excitation, UV/Vis spectrum, intermolecular interaction, response to external fields, electron affinity, ionization, and other molecular properties. Moreover, the review also outlines representative strategies for the direct synthesis and characterization of C18 using atom manipulation techniques. Following this, C18-based complexes are summarized, and potential applications in catalysis, electrochemical devices, optoelectronics, and sensing are discussed.

6.
Int J Mol Sci ; 25(15)2024 Jul 29.
Artigo em Inglês | MEDLINE | ID: mdl-39125845

RESUMO

The benzene dimer (BD) is an archetypal model of π∙∙∙π and C-H∙∙∙π noncovalent interactions as they occur in its cofacial and perpendicular arrangements, respectively. The enthalpic stabilization of the related BD structures has been debated for a long time and is revisited here. The revisit is based on results of computations that apply the coupled-cluster theory with singles, doubles and perturbative triples [CCSD(T)] together with large basis sets and extrapolate results to the complete basis set (CBS) limit in order to accurately characterize the three most important stationary points of the intermolecular interaction energy (ΔE) surface of the BD, which correspond to the tilted T-shaped (TT), fully symmetric T-shaped (FT) and slipped-parallel (SP) structures. In the optimal geometries obtained by searching extensive sets of the CCSD(T)/CBS ΔE data of the TT, FT and SP arrangements, the resulting ΔE values were -11.84, -11.34 and -11.21 kJ/mol, respectively. The intrinsic strength of the intermolecular bonding in these configurations was evaluated by analyzing the distance dependence of the CCSD(T)/CBS ΔE data over wide ranges of intermonomer separations. In this way, regions of the relative distances that favor BD structures with either π∙∙∙π or C-H∙∙∙π interactions were found and discussed in a broader context.


Assuntos
Benzeno , Dimerização , Benzeno/química , Termodinâmica , Modelos Moleculares , Teoria Quântica , Ligação de Hidrogênio
7.
Int J Mol Sci ; 25(9)2024 Apr 23.
Artigo em Inglês | MEDLINE | ID: mdl-38731806

RESUMO

This study reveals a new non-covalent interaction called a π-hole halogen bond, which is directional and potentially non-linear compared to its sister analog (σ-hole halogen bond). A π-hole is shown here to be observed on the surface of halogen in halogenated molecules, which can be tempered to display the aptness to form a π-hole halogen bond with a series of electron density-rich sites (Lewis bases) hosted individually by 32 other partner molecules. The [MP2/aug-cc-pVTZ] level characteristics of the π-hole halogen bonds in 33 binary complexes obtained from the charge density approaches (quantum theory of intramolecular atoms, molecular electrostatic surface potential, independent gradient model (IGM-δginter)), intermolecular geometries and energies, and second-order hyperconjugative charge transfer analyses are discussed, which are similar to other non-covalent interactions. That a π-hole can be observed on halogen in halogenated molecules is substantiated by experimentally reported crystals documented in the Cambridge Crystal Structure Database. The importance of the π-hole halogen bond in the design and growth of chemical systems in synthetic chemistry, crystallography, and crystal engineering is yet to be fully explicated.


Assuntos
Halogênios , Eletricidade Estática , Halogênios/química , Modelos Moleculares , Teoria Quântica , Elétrons , Termodinâmica , Bases de Lewis/química , Halogenação
8.
Molecules ; 29(14)2024 Jul 10.
Artigo em Inglês | MEDLINE | ID: mdl-39064837

RESUMO

Accurate calculation of non-covalent interaction energies in nucleotides is crucial for understanding the driving forces governing nucleic acid structure and function, as well as developing advanced molecular mechanics forcefields or machine learning potentials tailored to nucleic acids. Here, we dissect the nucleotides' structure into three main constituents: nucleobases (A, G, C, T, and U), sugar moieties (ribose and deoxyribose), and phosphate group. The interactions among these fragments and between fragments and water were analyzed. Different quantum mechanical methods were compared for their accuracy in capturing the interaction energy. The non-covalent interaction energy was decomposed into electrostatics, exchange-repulsion, dispersion, and induction using two ab initio methods: Symmetry-Adapted Perturbation Theory (SAPT) and Absolutely Localized Molecular Orbitals (ALMO). These calculations provide a benchmark for different QM methods, in addition to providing a valuable understanding of the roles of various intermolecular forces in hydrogen bonding and aromatic stacking. With SAPT, a higher theory level and/or larger basis set did not necessarily give more accuracy. It is hard to know which combination would be best for a given system. In contrast, ALMO EDA2 did not show dependence on theory level or basis set; additionally, it is faster.


Assuntos
Ligação de Hidrogênio , Nucleotídeos , Teoria Quântica , Nucleotídeos/química , Eletricidade Estática , Modelos Moleculares , Água/química , Termodinâmica
9.
J Comput Chem ; 44(10): 1073-1087, 2023 Apr 15.
Artigo em Inglês | MEDLINE | ID: mdl-36578228

RESUMO

Modern Density Functional Theory models are now suitable for many molecular and condensed phase studies. The study of noncovalent interactions, a well-known drawback, is no longer an insurmountable obstacle through design and empirical corrections. However, using empirical corrections as in the DFT-D methods might not be an all-in-one solution. This work uses a simple system, X2 -H2 O with X = Cl or Br, with two different interactions, halogen-bonded (XB) and hydrogen-halogen (HX), to investigate the capability of current density functional approximations (DFA) in predicting interaction energies with eight different exchange-correlation functionals. SAPT(DFT) provides, for all the studied cases, better predictions than the widely used supermolecular approach. In addition, the components of the interaction energy suggest where some of the shortcomings originate in each DFA. The analysis of the functionals used confirms that PBE0 and ω-B97X-D have a physically correct behavior. Using SAPT(DFT) and PBE0, and ω-B97X-D, we obtained the interaction energy of Cl2 and Br2 inside different clathrate cages and satisfactorily compared with wavefunction results; hence, the lower and upper limits of this value are defined: Cl2 @512 , -5.3 ± 0.3 kcal/mol; Cl2 @512 62 , -5.5 ± 0.1 kcal/mol; Br2 @512 62 , -7.6 ± 1.0 kcal/mol; Br2 @512 63 , -10.6 ± 1.0 kcal/mol; Br2 @512 64 , -10.9 ± 0.8 kcal/mol.

10.
Chemphyschem ; 24(23): e202300413, 2023 Dec 01.
Artigo em Inglês | MEDLINE | ID: mdl-37712533

RESUMO

The importance of noncovalent interaction has gained attention in various domains covering drug and novel catalyst design. The present study mainly characterizes the role of hydrogen bond (H-bond) and other intermolecular interactions in different (1 : 1) complex analogues formed between the N-aryl-thiazol-2-ylidene (YR) and five proton donor (HX) molecules. The analysis of the singlet-triplet energy gap ( Δ E S - T ${{\rm{\Delta }}E_{\left( {S - T} \right)} }$ ) confirmed the stability of the singlet state for this class of N-aryl-thiazol-2-ylidenes than the triplet state. The interaction energy values of the YR-HX complexes follow the order: YR-NH3

11.
Int J Mol Sci ; 24(17)2023 Aug 28.
Artigo em Inglês | MEDLINE | ID: mdl-37686131

RESUMO

2,3,5,6-Tetramethyl-1,4-diisocyanobenzene (1), 1,4-diisocyanobenzene (2), and 1,4-dicyanobenzene (3) were co-crystallized with 1,3,5-triiodotrifluorobenzene (1,3,5-FIB) to give three cocrystals, 1·1,3,5-FIB, 2·2(1,3,5-FIB), and 3·2(1,3,5-FIB), which were studied by X-ray diffraction. A common feature of the three structures is the presence of I···Cisocyanide or I···Nnitrile halogen bonds (HaBs), which occurs between an iodine σ-hole and the isocyanide C-(or the nitrile N-) atom. The diisocyanide and dinitrile cocrystals 2·2(1,3,5-FIB) and 3·2(1,3,5-FIB) are isostructural, thus providing a basis for accurate comparison of the two types of noncovalent linkages of C≡N/N≡C groups in the composition of structurally similar entities and in one crystal environment. The bonding situation was studied by a set of theoretical methods. Diisocyanides are more nucleophilic than the dinitrile and they exhibit stronger binding to 1,3,5-FIB. In all structures, the HaBs are mostly determined by the electrostatic interactions, but the dispersion and induction components also provide a noticeable contribution and make the HaBs attractive. Charge transfer has a small contribution (<5%) to the HaB and it is higher for the diisocyanide than for the dinitrile systems. At the same time, diisocyanide and dinitrile structures exhibit typical electron-donor and π-acceptor properties in relation to the HaB donor.


Assuntos
Cianetos , Iodo , Halogênios , Nitrilas
12.
Int J Mol Sci ; 24(9)2023 Apr 26.
Artigo em Inglês | MEDLINE | ID: mdl-37175586

RESUMO

The set of TX3-TrX2 (T = C, Si, Ge; Tr = B, Al, Ga; X = F, Cl, Br) molecules offers a rather unique opportunity to study both σ-hole and π-hole dimerization on the tetrel and triel ends, respectively. According to the molecular electrostatic potential (MEP) distribution, the π-hole extrema (acidic sites) were more intense than their σ-hole counterparts. The molecules owning the most (CX3-AlX2) and least (SiX3-BX2) intense π-holes were chosen to evaluate their capacities to attract one and two HCN molecules (Lewis bases). We discovered that the energetic characteristics of π-hole dimers severely conflict with the monomers MEP pattern since the weakest π-hole monomer forms a dimer characterized by interaction energy compared to those created by the monomers with noticeably greater power in the π-hole region. This outcome is due to the deformation of the weakest π-hole donor. Furthermore, the MEP analysis for monomers in the geometry of respective dimers revealed a "residual π-hole" site that was able to drive second ligand attachment, giving rise to the two "unusual trimers" examined further by the NCI and QTAIM analyses. Apart from them, the π-hole/π-hole and σ-hole/π-hole trimers have also been obtained throughout this study and described using energetic and geometric parameters. The SAPT approach revealed details of the bonding in one of the "unusual trimers". Finally, Born-Oppenheimer Molecular Dynamics (BOMD) simulations were carried out to investigate the time evolution of the interatomic distances of the studied complexes as well as their stability.


Assuntos
Cianeto de Hidrogênio , Simulação de Dinâmica Molecular , Eletricidade Estática
13.
Molecules ; 28(11)2023 May 31.
Artigo em Inglês | MEDLINE | ID: mdl-37298953

RESUMO

It has been recognized that the C-H⋯O structural motif can be present in destabilizing as well as highly stabilizing intermolecular environments. Thus, it should be of interest to describe the strength of the C-H⋯O hydrogen bond for constant structural factors so that this intrinsic strength can be quantified and compared to other types of interactions. This description is provided here for C2h-symmetric dimers of acrylic acid by means of the calculations that employ the coupled-cluster theory with singles, doubles, and perturbative triples [CCSD(T)] together with an extrapolation to the complete basis set (CBS) limit. Dimers featuring the C-H⋯O and O-H⋯O hydrogens bonds are carefully investigated in a wide range of intermolecular separations by the CCSD(T)/CBS approach, and also by the symmetry-adapted perturbation theory (SAPT) method, which is based on the density-functional theory (DFT) treatment of monomers. While the nature of these two types of hydrogen bonding is very similar according to the SAPT-DFT/CBS calculations and on the basis of a comparison of the intermolecular potential curves, the intrinsic strength of the C-H⋯O interaction is found to be about a quarter of its O-H⋯O counterpart that is less than one might anticipate.


Assuntos
Polímeros , Teoria da Densidade Funcional , Ligação de Hidrogênio
14.
Molecules ; 29(1)2023 Dec 22.
Artigo em Inglês | MEDLINE | ID: mdl-38202661

RESUMO

The Osme bond is defined as pairing a Group 8 metal atom as an electron acceptor in a noncovalent interaction with a nucleophile. DFT calculations with the ωB97XD functional consider MO4 (M = Ru, Os) as the Lewis acid, paired with a series of π electron donors C2H2, C2H4, C6H6, C4H5N, C4H4O, and C4H4S. The calculations establish interaction energies in the range between 9.5 and 26.4 kJ/mol. Os engages in stronger interactions than does Ru, and those involving more extensive π-systems within the aromatic rings form stronger bonds than do the smaller ethylene and acetylene. Extensive analysis questions the existence of a true Osme bond, as the bonding chiefly involves interactions with the three O atoms of MO4 that lie closest to the π-system, via π(C-C)→σ*(M-O) transfers. These interactions are supplemented by back donation from M-O bonds to the π*(CC) antibonding orbitals of the π-systems. Dispersion makes a large contribution to these interactions, higher than electrostatics and much greater than induction.

15.
Molecules ; 28(13)2023 Jun 30.
Artigo em Inglês | MEDLINE | ID: mdl-37446809

RESUMO

A comprehensive analysis of the intermolecular interaction energy and anharmonic vibrations of 41 structures of the HXeY⋯HX (X, Y = F, Cl, Br, I) family of noble-gas-compound complexes for all possible combinations of Y and X was conducted. New structures were identified, and their interaction energies were studied by means of symmetry-adapted perturbation theory, up to second-order corrections: this provided insight into the physical nature of the interaction in the complexes. The energy components were discussed, in connection to anharmonic frequency analysis. The results show that the induction and dispersion corrections were the main driving forces of the interaction, and that their relative contributions correlated with the complexation effects seen in the vibrational stretching modes of Xe-H and H-X. Reasonably clear patterns of interaction were found for different structures. Our findings corroborate previous findings with better methods, and provide new data. These results suggest that the entire group of the studied complexes can be labelled as "naturally blueshifting", except for the complexes with HI.

16.
Int J Mol Sci ; 23(24)2022 Dec 12.
Artigo em Inglês | MEDLINE | ID: mdl-36555413

RESUMO

There has been a growing interest in quantitative predictions of the intermolecular binding energy of large complexes. One of the most important quantum chemical techniques capable of such predictions is the domain-based local pair natural orbital (DLPNO) scheme for the coupled cluster theory with singles, doubles, and iterative triples [CCSD(T)], whose results are extrapolated to the complete basis set (CBS) limit. Here, the DLPNO-based focal-point method is devised with the aim of obtaining CBS-extrapolated values that are very close to their canonical CCSD(T)/CBS counterparts, and thus may serve for routinely checking a performance of less expensive computational methods, for example, those based on the density-functional theory (DFT). The efficacy of this method is demonstrated for several sets of noncovalent complexes with varying amounts of the electrostatics, induction, and dispersion contributions to binding (as revealed by accurate DFT-based symmetry-adapted perturbation theory (SAPT) calculations). It is shown that when applied to dimeric models of poly(3-hydroxybutyrate) chains in its two polymorphic forms, the DLPNO-CCSD(T) and DFT-SAPT computational schemes agree to within about 2 kJ/mol of an absolute value of the interaction energy. These computational schemes thus should be useful for a reliable description of factors leading to the enthalpic stabilization of extended systems.


Assuntos
Teoria Quântica , Análise Custo-Benefício , Termodinâmica , Teoria da Densidade Funcional , Eletricidade Estática
17.
Int J Mol Sci ; 23(6)2022 Mar 14.
Artigo em Inglês | MEDLINE | ID: mdl-35328534

RESUMO

In the current study, unexplored type IV halogen⋯halogen interaction was thoroughly elucidated, for the first time, and compared to the well-established types I−III interactions by means of the second-order Møller−Plesset (MP2) method. For this aim, the halobenzene⋯halobenzene homodimers (where halogen = Cl, Br, and I) were designed into four different types, parodying the considered interactions. From the energetic perspective, the preference of scouted homodimers was ascribed to type II interactions (i.e., highest binding energy), whereas the lowest binding energies were discerned in type III interactions. Generally, binding energies of the studied interactions were observed to decline with the decrease in the σ-hole size in the order, C6H5I⋯IC6H5 > C6H5Br⋯BrC6H5 > C6H5Cl⋯ClC6H5 homodimers and the reverse was noticed in the case of type IV interactions. Such peculiar observations were relevant to the ample contributions of negative-belt⋯negative-belt interactions within the C6H5Cl⋯ClC6H5 homodimer. Further, type IV torsional trans → cis interconversion of C6H5X⋯XC6H5 homodimers was investigated to quantify the π⋯π contributions into the total binding energies. Evidently, the energetic features illustrated the amelioration of the considered homodimers (i.e., more negative binding energy) along the prolonged scope of torsional trans → cis interconversion. In turn, these findings outlined the efficiency of the cis configuration over the trans analog. Generally, symmetry-adapted perturbation theory-based energy decomposition analysis (SAPT-EDA) demonstrated the predominance of all the scouted homodimers by the dispersion forces. The obtained results would be beneficial for the omnipresent studies relevant to the applications of halogen bonds in the fields of materials science and crystal engineering.


Assuntos
Halogênios , Hidrocarbonetos Halogenados , Benzeno , Halogênios/química , Modelos Teóricos
18.
Int J Mol Sci ; 23(22)2022 Nov 08.
Artigo em Inglês | MEDLINE | ID: mdl-36430173

RESUMO

It is postulated that the overexpression of Carbonic Anhydrase isozyme IX in some cancers contributes to the acidification of the extracellular matrix. It was proved that this promotes the growth and metastasis of the tumor. These observations have made Carbonic Anhydrase IX an attractive drug target. In the light of the findings and importance of the glycoprotein in the cancer treatment, we have employed quantum-chemical approaches to study non-covalent interactions in the binding pocket. As a ligand, the acetazolamide (AZM) molecule was chosen, being known as a potential inhibitor exhibiting anticancer properties. First-Principles Molecular Dynamics was performed to study the chalcogen and other non-covalent interactions in the AZM ligand and its complexes with amino acids forming the binding site. Based on Density Functional Theory (DFT) and post-Hartree-Fock methods, the metric and electronic structure parameters were described. The Non-Covalent Interaction (NCI) index and Atoms in Molecules (AIM) methods were applied for qualitative/quantitative analyses of the non-covalent interactions. Finally, the AZM-binding pocket interaction energy decomposition was carried out. Chalcogen bonding in the AZM molecule is an important factor stabilizing the preferred conformation. Free energy mapping via metadynamics and Path Integral molecular dynamics confirmed the significance of the chalcogen bond in structuring the conformational flexibility of the systems. The developed models are useful in the design of new inhibitors with desired pharmacological properties.


Assuntos
Calcogênios , Neoplasias , Humanos , Anidrase Carbônica IX/química , Ligantes , Inibidores da Anidrase Carbônica/farmacologia , Inibidores da Anidrase Carbônica/química , Acetazolamida/farmacologia , Acetazolamida/química , Calcogênios/química
19.
Molecules ; 27(7)2022 Apr 01.
Artigo em Inglês | MEDLINE | ID: mdl-35408698

RESUMO

The intra- and intermolecular interactions of selected quinolone carboxylic acid derivatives were studied in monomers, dimers and crystals. The investigated compounds are well-recognized as medicines or as bases for further studies in drug design. We employed density functional theory (DFT) in its classical formulation to develop gas-phase and solvent reaction field (PCM) models describing geometric, energetic and electronic structure parameters for monomers and dimers. The electronic structure was investigated based on the atoms in molecules (AIM) and natural bond orbital (NBO) theories. Special attention was devoted to the intramolecular hydrogen bonds (HB) present in the investigated compounds. The characterization of energy components was performed using symmetry-adapted perturbation theory (SAPT). Finally, the time-evolution methods of Car-Parrinello molecular dynamics (CPMD) and path integral molecular dynamics (PIMD) were employed to describe the hydrogen bond dynamics as well as the spectroscopic signatures. The vibrational features of the O-H stretching were studied using Fourier transformation of the autocorrelation function of atomic velocity. The inclusion of quantum nuclear effects provided an accurate depiction of the bridged proton delocalization. The CPMD and PIMD simulations were carried out in the gas and crystalline phases. It was found that the polar environment enhances the strength of the intramolecular hydrogen bonds. The SAPT analysis revealed that the dispersive forces are decisive factors in the intermolecular interactions. In the electronic ground state, the proton-transfer phenomena are not favourable. The CPMD results showed generally that the bridged proton is localized at the donor side, with possible proton-sharing events in the solid-phase simulation of stronger hydrogen bridges. However, the PIMD enabled the quantitative estimation of the quantum effects inclusion-the proton position was moved towards the bridge midpoint, but no qualitative changes were detected. It was found that the interatomic distance between the donor and acceptor atoms was shortened and that the bridged proton was strongly delocalized.


Assuntos
Teoria Quântica , Quinolonas , Ácidos Carboxílicos , Ligação de Hidrogênio , Simulação de Dinâmica Molecular , Compostos Orgânicos , Prótons
20.
Molecules ; 27(22)2022 Nov 16.
Artigo em Inglês | MEDLINE | ID: mdl-36432040

RESUMO

Intermolecular complexes with calixarenes are intriguing because of multiple possibilities of noncovalent binding for both polar and nonpolar molecules, including docking in the calixarene cavity. In this contribution calix[6]arenes interacting with amino acids are studied with an additional aim to show that tools such as symmetry-adapted perturbation theory (SAPT), functional-group SAPT (F-SAPT), and systematic molecular fragmentation (SMF) methods may provide explanations for different numbers of noncovalent bonds and of their varying strength for various calixarene conformers and guest molecules. The partitioning of the interaction energy provides an easy way to identify hydrogen bonds, including those with unconventional hydrogen acceptors, as well as other noncovalent bonds, and to find repulsive destabilizing interactions between functional groups. Various other features can be explained by energy partitioning, such as the red shift of an IR stretching frequency for some hydroxy groups, which arises from their attraction to the phenyl ring of calixarene. Pairs of hydrogen bonds and other noncovalent bonds of similar magnitude found by F-SAPT explain an increase in the stability of both inclusion and outer complexes.


Assuntos
Aminoácidos , Calixarenos , Ligação de Hidrogênio , Fenômenos Físicos , Hidrogênio
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