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1.
Chemphyschem ; 2020 Jul 09.
Artigo em Inglês | MEDLINE | ID: mdl-32643813

RESUMO

For many years non-covalently bonded complexes of nucleobases have attracted considerable interest. However, there is a lack of information about the nature of hydrogen bonding between nucleobases when the bonding is affected by metal coordination to one of the nucleobases and how the individual hydrogen bonds and aromaticity of nucleobases respond to the presence of the metal cation. Here we report a DFT computational study of nucleobase pairs interacting with alkali metal cations. The metal cations contribute to the stabilization of the base pairs to varying degrees depending on their position. The energy decomposition analysis revealed that the nature of bonding between nucleobases does not change much upon metal coordination. The effect of the cations on individual hydrogen bonds were described by changes in VDD charges on frontier atoms, H-bond length, bond energy from NBO analysis, and delocalization index from QTAIM calculations. The aromaticity changes were determined by HOMA index.

2.
J Chem Inf Model ; 60(3): 1317-1328, 2020 Mar 23.
Artigo em Inglês | MEDLINE | ID: mdl-32003997

RESUMO

Halogen bonds are highly important in medicinal chemistry as halogenation of drugs, generally, improves both selectivity and efficacy toward protein active sites. However, accurate modeling of halogen bond interactions remains a challenge, since a thorough theoretical investigation of the bonding mechanism, focusing on the realistic complexity of drug-receptor systems, is lacking. Our systematic quantum-chemical study on ligand/peptide-like systems reveals that halogen bonding is driven by the same bonding interactions as hydrogen bonding. Besides the electrostatic and the dispersion interactions, our bonding analyses, based on quantitative Kohn-Sham molecular orbital theory together with energy decomposition analysis, reveal that donor-acceptor interactions and steric repulsion between the occupied orbitals of the halogenated ligand and the protein need to be considered more carefully within the drug design process.

3.
Nat Protoc ; 15(2): 649-667, 2020 02.
Artigo em Inglês | MEDLINE | ID: mdl-31925400

RESUMO

Understanding chemical reactivity through the use of state-of-the-art computational techniques enables chemists to both predict reactivity and rationally design novel reactions. This protocol aims to provide chemists with the tools to implement a powerful and robust method for analyzing and understanding any chemical reaction using PyFrag 2019. The approach is based on the so-called activation strain model (ASM) of reactivity, which relates the relative energy of a molecular system to the sum of the energies required to distort the reactants into the geometries required to react plus the strength of their mutual interactions. Other available methods analyze only a stationary point on the potential energy surface, but our methodology analyzes the change in energy along a reaction coordinate. The use of this methodology has been proven to be critical to the understanding of reactions, spanning the realms of the inorganic and organic, as well as the supramolecular and biochemical, fields. This protocol provides step-by-step instructions-starting from the optimization of the stationary points and extending through calculation of the potential energy surface and analysis of the trend-decisive energy terms-that can serve as a guide for carrying out the analysis of any given reaction of interest within hours to days, depending on the size of the molecular system.


Assuntos
Modelos Químicos , Cicloparafinas/química , Modelos Moleculares , Conformação Molecular , Termodinâmica
4.
Chemistry ; 26(9): 2080-2093, 2020 Feb 11.
Artigo em Inglês | MEDLINE | ID: mdl-31815315

RESUMO

It is shown, quantum chemically, how structural distortion of an aromatic dye molecule can be leveraged to rationally tune its optoelectronic properties. By using a quantitative Kohn-Sham molecular orbital (KS-MO) approach, in combination with time-dependent DFT (TD-DFT), the influence of various structural and electronic tuning parameters on the HOMO-LUMO gap of a benzenoid model dye have been investigated. These parameters include 1) out-of-plane bending of the aromatic core, 2) bending of the bridge with respect to the core, 3) the nature of the bridge itself, and 4) π-π stacking. The study reveals the coupling of multiple structural distortions as a function of bridge length and number of bridges in benzene to be chiefly responsible for a decreased HOMO-LUMO gap, and consequently, red-shifting of the absorption wavelength associated with the lowest singlet excitation (λ≈560 nm) in the model cyclophane systems. These physical insights together with a rational approach for tuning the oscillator strength were leveraged for the proof-of-concept design of an intense near-infrared (NIR) absorbing cyclophane dye at λ=785 nm. This design may contribute to a new class of distortion-controlled NIR absorbing organic dye molecules.

5.
Dalton Trans ; 49(1): 171-178, 2020 Jan 07.
Artigo em Inglês | MEDLINE | ID: mdl-31793589

RESUMO

A new organometallic alkynyl-gold(i) complex capable of exhibiting aggregation induced emission was designed and synthesized. The linear complex structure possesses a central Au(i) atom, bearing two axial ligands: (1) 1,3,5-triaza-7-phosphaadamantane and (2) 2-acetamido-7-ethynyl-1,8-naphthyridine. While the former accounts for its partial solubility in an aqueous environment, the latter acts as a receptor unit for binding guanosine nucleotides and derivatives via multiple hydrogen bonding interactions. At high concentrations, aggregation of the complex was observed by the formation of new absorption (λmax∼ 400 nm) and emission bands (550-700 nm). Formation of aggregates of ca. 60 nm diameter was confirmed by Small Angle X-ray Scattering (SAXS). Disruption of the aggregates in the presence of guanosine derivatives resulted in a ratiometric signal with apparent association constants in the order of 105 M-1 and high sensitivity (around 63% signal change) which are, to the best of our knowledge, in line with the highest values recorded for nucleotide sensors based on hydrogen bonding and capable of working in water. Computational studies indicate the presence of additional hydrogen bonding interactions that account for the strong binding of the Au(i) complex to phosphorylated guanosine nucleotides.

6.
Dalton Trans ; 48(34): 12974-12985, 2019 Sep 14.
Artigo em Inglês | MEDLINE | ID: mdl-31397469

RESUMO

For a series of organonitrile [RCN (R = Me, CF3, Ph, CH3Ph, CF3Ph)] ligands, the nature of the N-Pt bond in the related cis-/trans-(RCN)2PtCl2 complexes has been computationally investigated by Density Functional Theory. A fragment based bond analysis has been performed in the canonical Kohn-Sham molecular orbitals framework, and it has been ultimately assessed that this bond is characterized both by N→Pt σ and by N←Pt π contributions. Voronoi Deformation Density charges further confirms the occurrence of N←Pt π interactions. Moreover, the Energy Decomposition Analysis-Natural Orbital for Chemical Valence (EDA-NOCV) method shows that the strength of the N←Pt π interaction is not negligible by contributing to about 30-40% of the total orbital interaction. Finally, the well-known νC[triple bond, length as m-dash]N blue-shift occurring upon coordination to PtII, has been thoroughly investigated by exploiting the EDA-NOCV and by evaluating νC[triple bond, length as m-dash]N and force constants. The origin of the νC[triple bond, length as m-dash]N blue-shift in these systems has been discussed on the basis of the CN bond polarization. N←Pt π backbonding causes only a systematic decrease of the observed νC[triple bond, length as m-dash]N blue-shift when compared to the one calculated for RCN-X (X = H+, alkaline, Lewis acids) herein reported (X = purely σ acceptors).

7.
J Phys Chem A ; 123(42): 9137-9148, 2019 Oct 24.
Artigo em Inglês | MEDLINE | ID: mdl-31294982

RESUMO

We have carried out an extensive quantum chemical exploration of gas-phase alkali metal cation affinities (AMCAs) of archetypal neutral bases across the periodic system using relativistic density functional theory. One objective of this work is to provide an intrinsically consistent set of values of the 298 K AMCAs of all neutral maingroup-element hydrides XHn of groups 15-18 along the periods 1-6. Our main purpose is to understand these trends in terms of the underlying bonding mechanism using Kohn-Sham molecular orbital theory together with a canonical energy decomposition analysis (EDA). We compare the trends in XHn AMCAs with the trends in XHn proton affinities (PAs). We also examine the differences between the trends in AMCAs of the neutral XHn bases with those in the corresponding anionic XHn-1- bases. Furthermore, we analyze how the cation affinity of our neutral Lewis bases changes along the group-1 cations H+, Li+, Na+, K+, Rb+, and Cs+.

8.
Chem Asian J ; 14(16): 2760-2769, 2019 Aug 16.
Artigo em Inglês | MEDLINE | ID: mdl-31241855

RESUMO

Hydrogen bonds are a complex interplay between different energy components, and their nature is still subject of an ongoing debate. In this minireview, we therefore provide an overview of the different perspectives on hydrogen bonding. This will be done by discussing the following individual energy components: 1) electrostatic interactions, 2) charge-transfer interactions, 3) π-resonance assistance, 4) steric repulsion, 5) cooperative effects, 6) dispersion interactions and 7) secondary electrostatic interactions. We demonstrate how these energetic factors are essential in a correct description of the hydrogen bond, and discuss several examples of systems whose energetic and geometrical features are not captured by easy-to-use predictive models.

9.
ChemistryOpen ; 8(2): 134, 2019 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-30740287

RESUMO

Invited for this month's cover picture are Professor Célia Fonseca Guerra from Vrije Universiteit Amsterdam and Leiden University (The Netherlands) and André Nicolai Petelski from UTN-FRRe University of Argentine (Argentina). The cover picture shows a colored pallet of melamine and ammeline tautomers that form hydrogen-bonded hexameric rosettes. When it comes to self-assembling capabilities, one of the ammeline structures (red) is shown to be distinctly superior to melamine, both in the gas phase and in water. Quantum chemical computations explain that this is due to the presence of stronger pair interactions and the manifestation of a large cooperativity effect. Read the full text of their Full Paper at 10.1002/open.201800210.

10.
ChemistryOpen ; 8(2): 135-142, 2019 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-30740288

RESUMO

In supramolecular chemistry, the rational design of self-assembled systems remains a challenge. Herein, hydrogen-bonded rosettes of melamine and ammeline have been theoretically examined by using dispersion-corrected density functional theory (DFT-D). Our bonding analyses, based on quantitative Kohn-Sham molecular orbital theory and corresponding energy decomposition analyses (EDA), show that ammeline is a much better building block than melamine for the fabrication of cyclic complexes based on hydrogen bonds. This superior capacity is explained by both stronger hydrogen bonding and the occurrence of a strong synergy.

11.
Chemistry ; 25(3): 785-795, 2019 Jan 14.
Artigo em Inglês | MEDLINE | ID: mdl-30379364

RESUMO

A current objective in supramolecular chemistry is to mimic the transitions between complex self-sorted systems that represent a hallmark of regulatory function in nature. In this work, a self-sorting network, comprising linear hydrogen motifs, was created. Selecting six hydrogen-bonding motifs capable of both high-fidelity and promiscuous molecular recognition gave rise to a complex self-sorting system, which included motifs capable of both narcissistic and social self-sorting. Examination of the interactions between individual components, experimentally and computationally, provided a rationale for the product distribution during each phase of a cascade. This reasoning holds through up to five sequential additions of six building blocks, resulting in the construction of a biomimetic network in which the presence or absence of different components provides multiple unique pathways to distinct self-sorted configurations.

12.
J Comput Chem ; 39(32): 2690-2696, 2018 12 15.
Artigo em Inglês | MEDLINE | ID: mdl-30515900

RESUMO

Principles are presented for the design of functional near-infrared (NIR) organic dye molecules composed of simple donor (D), spacer (π), and acceptor (A) building blocks in a D-π-A fashion. Quantitative Kohn-Sham molecular orbital analysis enables accurate fine-tuning of the electronic properties of the π-conjugated aromatic cores by effecting their size, including silaaromatics, adding donor and acceptor substituents, and manipulating the D-π-A torsional angle. The trends in HOMO-LUMO gaps of the model dyes correlate with the excitation energies computed with time-dependent density functional theory at CAMY-B3LYP. Design principles could be developed from these analyses, which led to a proof-of-concept linear D-π-A with a strong excited-state intramolecular charge transfer and a NIR absorption at 879 nm. © 2018 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.

13.
Chemistry ; 24(61): 16315-16322, 2018 Nov 02.
Artigo em Inglês | MEDLINE | ID: mdl-30215872

RESUMO

DNA quadruplexes have been the subject of investigation because of their biological relevance and because of their potential application in supramolecular chemistry. Similarly, RNA quadruplexes are now gaining increasing attention. Although DNA and RNA quadruplexes are structurally very similar, the latter show higher stability. In this study we report dispersion-corrected density functional theory (DFT-D) quantum chemical calculations that were undertaken to understand the difference in stabilities of RNA and DNA quadruplexes. The smallest meaningful model of a stack of quartets, interacting with alkali metal cations, was simulated in an aqueous environment. The energy decomposition analysis allows for in-depth examination of the interaction energies, emphasising the role of noncovalent interactions and better electrostatics in determining RNA-GQs higher stabilities, particularly pinpointing the role of the extra 2'-OH groups. Furthermore, our computations present new insights on why the cation is required for self-assembly: unexpectedly the cation is not necessary to relieve the repulsion between the oxygen atoms in the central cavity, but it is needed to overcome the entropic penalty.


Assuntos
DNA/química , Quadruplex G , RNA/química , Cátions/química , Ligação de Hidrogênio , Metais Alcalinos/química , Modelos Moleculares , Conformação de Ácido Nucleico , Eletricidade Estática , Termodinâmica
14.
Phys Chem Chem Phys ; 20(32): 20874-20885, 2018 Aug 15.
Artigo em Inglês | MEDLINE | ID: mdl-30066704

RESUMO

The reactivity of diselenides and ditellurides of general formula (RX)2 (X = Se, Te; R = H, CH3, Ph) toward hydrogen peroxide was studied through a computational approach based on accurate Density Functional Theory (DFT) calculations. The aliphatic and aromatic dichalcogenides have been chosen in light of their activity in glutathione peroxidase (GPx)-like catalytic cycles and their promising features as efficient antioxidant compounds. The reaction products, the energetics and the mechanistic details of these oxidations are discussed. Analogous disulfides are included in our analysis for completeness. We find that the barrier for oxidation of dichalcogenides decreases from disulfides to diselenides to ditellurides. On the other hand, variation of the substituents at the chalcogen nucleus has relatively little effect on the reactivity.


Assuntos
Antioxidantes/química , Peróxido de Hidrogênio/química , Compostos Organometálicos/química , Selênio/química , Telúrio/química , Catálise , Dissulfetos/química , Glutationa Peroxidase/química , Modelos Moleculares , Estrutura Molecular , Compostos Organosselênicos/química , Oxirredução , Termodinâmica
15.
Inorg Chem ; 57(15): 8796-8805, 2018 Aug 06.
Artigo em Inglês | MEDLINE | ID: mdl-30024150

RESUMO

The redox interconversion between Co(III) thiolate and Co(II) disulfide compounds has been investigated experimentally and computationally. Reactions of cobalt(II) salts with disulfide ligand L1SSL1 (L1SSL1 = di-2-(bis(2-pyridylmethyl)amino)-ethyl disulfide) result in the formation of either the high-spin cobalt(II) disulfide compound [CoII2(L1SSL1)Cl4] or a low-spin, octahedral cobalt(III) thiolate compound, such as [CoIII(L1S)(MeCN)2](BF4)2. Addition of thiocyanate anions to a solution containing the latter compound yielded crystals of [CoIII(L1S)(NCS)2]. The addition of chloride ions to a solution of [CoIII(L1S)(MeCN)2](BF4)2 in acetonitrile results in conversion of the cobalt(III) thiolate compound to the cobalt(II) disulfide compound [CoII2(L1SSL1)Cl4], as monitored with UV-vis spectroscopy; subsequent addition of AgBF4 regenerates the Co(III) compound. Computational studies show that exchange by a chloride anion of the coordinated acetonitrile molecule or thiocyanate anion in compounds [CoIII(L1S)(MeCN)2]2+ and [CoIII(L1S)(NCS)2] induces a change in the character of the highest occupied molecular orbitals, showing a decrease of the contribution of the p orbital on sulfur and an increase of the d orbital on cobalt. As a comparison, the synthesis of iron compounds was undertaken. X-ray crystallography revealed that structure of the dinuclear iron(II) disulfide compound [FeII2(L1SSL1)Cl4] is different from that of cobalt(II) compound [CoII2(L1SSL1)Cl4]. In contrast to cobalt, reaction of ligand L1SSL1 with [Fe(MeCN)6](BF4)2 did not yield the expected Fe(III) thiolate compound. This work is an unprecedented example of redox interconversion between a high-spin Co(II) disulfide compound and a low-spin Co(III) thiolate compound triggered by the nature of the anion.

16.
J Phys Chem Lett ; 9(13): 3720-3724, 2018 Jul 05.
Artigo em Inglês | MEDLINE | ID: mdl-29927254

RESUMO

NMR spectroscopy is one of the most useful methods for detection and characterization of hydrogen bond (H-bond) interactions in biological systems. For H bonds X-H···Y, where X and Y are O or N, it is generally believed that a decrease in 1H-shielding constants relates to a shortening of H-bond donor-acceptor distance. Here we investigated computationally the trend of 1H-shielding constants for hydrogen-bonded protons in a series of guanine C8-substituted GC pair model compounds as a function of the molecular structure. Furthermore, the electron density distribution around the hydrogen atom was analyzed with the Voronoi deformation density (VDD) method. Our findings demonstrate that 1H-shielding values of the hydrogen bond are determined by the depletion of charge around the hydrogen atom, which stems from the fact that electrons obey the Pauli exclusion principle.

17.
Chem Sci ; 9(14): 3544-3554, 2018 Apr 14.
Artigo em Inglês | MEDLINE | ID: mdl-29780486

RESUMO

Recently, we studied glucose-nucleobase pairs, a binding motif found in aminoglycoside-RNA recognition. DNA duplexes with glucose as a nucleobase were able to hybridize and were selective for purines. They were less stable than natural DNA but still fit well on regular B-DNA. These results opened up the possible use of glucose as a non-aromatic DNA base mimic. Here, we have studied the incorporation and thermal stability of glucose with different types of anchoring units and alternative apolar sugar-nucleobase pairs. When we explored butanetriol instead of glycerol as a wider anchoring unit, we did not gain duplex thermal stability. This result confirmed the necessity of a more conformationally restricted linker to increase the overall duplex stability. Permethylated glucose-nucleobase pairs showed similar stability to glucoside-nucleobase pairs but no selectivity for a specific nucleobase, possibly due to the absence of hydrogen bonds between them. The three-dimensional structure of the duplex solved by NMR located both, the hydrophobic permethylated glucose and the nucleobase, inside the DNA helix as in the case of glucose-nucleobase pairs. Quantum chemical calculations on glucose-nucleobase pairs indicate that the attachment of the sugar to the DNA skeleton through the OH1 or OH4 positions yields the highest binding energies. Moreover, glucose was very selective for guanine when attached through OH1 or OH4 to the DNA. Finally, we examined DNA polymerase insertion of nucleotides in front of the saccharide unit. KF- polymerase from E. coli inserted A and G opposite glc and 6dglc with low efficiency but notable selectivity. It is even capable of extending the new pair although its efficiency depended on the DNA sequence. In contrast, Bst 2.0, SIII and BIOTAQ™ DNA polymerases seem to display a loop-out mechanism possibly due to the flexible glycerol linker used instead of deoxyribose.

18.
Chemistry ; 24(46): 11983-11991, 2018 Aug 14.
Artigo em Inglês | MEDLINE | ID: mdl-29742299

RESUMO

Supramolecular ring-versus-chain equilibria are ubiquitous in biological and synthetic systems. Understanding the factors that decide whether a system will fall on one side or the other is crucial to the control of molecular self-assembly. This work reports results with two kinds of dinucleoside monomers, in which the balance between closed cycles and open polymers is found to depend on subtle factors that rule conformational equilibria, such as steric hindrance, intramolecular interactions, or π-conjugation pathways.

19.
Chem Commun (Camb) ; 54(28): 3448-3451, 2018 Apr 03.
Artigo em Inglês | MEDLINE | ID: mdl-29537051

RESUMO

Our quantum chemical activation strain analyses demonstrate how Mg2+ lowers the barrier of the enzymatic triphosphate hydrolysis through two distinct mechanisms: (a) weakening of the leaving-group bond, thereby decreasing activation strain; and (b) transition state (TS) stabilization through enhanced electrophilicity of the triphosphate PPP substrate, thereby strengthening the interaction with the nucleophile.


Assuntos
DNA Polimerase Dirigida por DNA/metabolismo , Magnésio/metabolismo , Polifosfatos/metabolismo , DNA Polimerase Dirigida por DNA/química , Hidrólise , Íons/química , Íons/metabolismo , Magnésio/química , Polifosfatos/química , Teoria Quântica
20.
J Phys Chem A ; 122(6): 1813-1820, 2018 Feb 15.
Artigo em Inglês | MEDLINE | ID: mdl-29357252

RESUMO

The nature of resonance-assisted hydrogen bonds (RAHB) is still subject of an ongoing debate. We therefore analyzed the σ and π charge redistributions associated with the formation of intramolecular hydrogen bonds in malonaldehyde (MA) and its saturated analogue 3-hydroxypropanal (3-OH) and addressed the question whether there is a resonance assistance phenomenon in the sense of a synergistic interplay between the σ and π electron systems. Our quantum chemical calculations at the BP86/TZ2P level of theory show that the π charge flow is indeed in line with the Lewis structure as proposed by the RAHB model. This typical rearrangement of charge is only present in the unsaturated system, and not in its saturated analogue. Resonance in the π electron system assists the intramolecular hydrogen bond by reducing the hydrogen bond distance, and by providing an additional stabilizing component to the net bonding energy. The σ orbital interaction plays an important role in the enhanced hydrogen bond strength in MA as well. However, there is no resonance assistance in the sense of an interplay between σ charge transfer and π polarization; σ and π contribute independently from each other.

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