sp3-C Atoms Research Articles

Molecular Dynamics Investigation of Metastable Structure and Hybridization Bond Evolution in High-Entropy CoCrFeNi Heterostructured Amorphous Carbon Films.

Heterogeneous element doping in amorphous carbon films can reduce residual stresses and improve plastic deformation. Nevertheless, the effects of dopant content and size on the metastable transition mechanism between sp2-C and sp3-C atoms during the deformation process are unclear and difficult to be in situ observed and researched, experimentally. In this work, the mechanical properties and the structural evolution during the nanoindentation of amorphous CoCrFeNi sphere-doped carbon heterostructured films with different radii were simulated. The results indicate that the hardness H and elastic modulus E of the films decreased with the increase of the dopant addition. H decreases from 50.69 to 28.94 GPa, and E decreases from 664.39 to 448.62 GPa. The decrease in the elastic recovery and the enlargement of the shear transition zones indicate that the presence of the amorphous CoCrFeNi dopant can significantly improve the plastic deformation capacity of the films. During the nanoindentation process, the spherical dopants reduce the stress and shear strain of the regions under the indenter in a-C films. The reduction of compressive and shear stresses in the film can inhibit the C atom metastable transition from sp2-C to sp3-C. This can provide a theoretical basis for the development and design of heavy-load and high-deformation-rate a-C films.

Hydrothermal carbonization and pyrolysis in wetland engineering: Carbon sequestration, phosphorus recovery, and structural characterization of willow-based chars with X-ray μ-computed tomography

Willows from engineered wetland systems (EWS) offer a sustainable approach to wastewater treatment and biomass production. Our study assesses their potential for nutrient recovery and carbon sequestration using slow pyrolysis (600 °C) and hydrothermal carbonization (250 °C). Here, we propose EWS-pyrochars as a ready-to integrate opportunity for soil amendment, as they exhibit a predominant CO2 release and the absence of harmful compounds in pyrolysis-chromatograms, indicating higher stability than hydrochars. Using sequential P-extractions, we observed a high bioavailability in the willow-woodchips and a significant P-retention in EWS-chars—up to 92 % in pyrochars and near-complete retention in hydrochars, along with a higher labile-P fraction of 21 % in hydrochars than 5 % in pyrochars. Utilizing X-ray-based techniques, Raman spectroscopy, scanning electron microscopy, and gas physisorption, we characterized the EWS-chars' structures. We revealed innovative 3D-visualizations, which transcend previous literature by providing insights into the chars' internal porosity and quantifying, for the first time, their carbonaceous structural thickness via a meshing algorithm and the mean Feret diameter. EWS-pyrochars exhibit remarkable aromaticity with a higher concentration of overall sp2 C-atoms at 63 % vs. 43 % in hydrochars. Moreover, unlike hydrochars, which depict occluded porosity, EWS-pyrochars exhibited 92 % water storage-like pores. Although hydrochars indicated lower carbonization and thermal stability than pyrochars, their higher carbon retention (55 vs. 41 % in pyrochar) suggest superior annual benefits—on a 10 ha EWS scale—of 80-tons of carbon sequestration and 334 kg of phosphorus recovery versus 60-tons of carbon and 298 kg of phosphorus with pyrochars. Our findings suggest innovative materials for resource recovery, advancing the engineered wetland systems field, shifting their traditional use, and opening the opportunity for future integration into biorefineries.

Correction for the calculated XANES spectra of 1,4,7,10-alkyltetracenes considering the total electron yield (TEY) efficiency of sp2- and sp3-carbon atoms.

The calculated X-ray-absorption-near-edge-structure (XANES) spectra in the CK region of 1,4,7,10-alkyltetracenes, which are composed of both sp2-C atoms in the tetracene ring and sp3-C atoms in the alkyl-chains, can be corrected by considering the total electron yield (TEY) efficiency of sp3-C relative to sp2-C. In the correction, the previously measured TEY efficiency of k = 0.51 is applied to the calculated transition probabilities for sp3-C atoms. Then the calculated CK-XANES obtained from density functional theory (DFT) calculations can well reproduce the measured TEY-CK-XANES. Especially, the calculated π*/σ* peak intensity ratios are in good agreement with the measured ones. This suggests that a similar correction for the calculated XANES is necessary for compounds composed of multi-components with different TEY efficiencies.

Total electron yield (TEY) efficiency of sp2 and sp3 carbon atoms in the TEY-X-ray absorption near-edge structure (XANES) of 1,4,7,10-alkyltetracenes.

X-ray absorption near-edge structure (XANES) in the CK region of 1,4,7,10-alkyltetracenes, which are composed of sp2-C atoms in the tetracene ring and sp3-C atoms in the alkyl-chains, are measured using the total electron yield (TEY) and theoretically analyzed by DFT calculations to quantitatively investigate the π* and σ* peak intensities in the TEY-CK-XANES. The calculated π*/σ* peak intensity ratios are well approximated by the linear functions passing through the origin as a function of the sp2-C fraction, which is expressed as sp2-C/(sp2-C + sp3-C). In contrast, the measured π*/σ* peak intensity ratios are well approximated by curve functions passing through the origin, considering the TEY efficiency between sp2-C and sp3-C. The approximated curve functions indicate that the TEY efficiency of sp3-C is lower than that of sp2-C even in molecules. This confirms that the TEY efficiency of sp2-C and sp3-C should be considered in quantitative discussions on the sp2-C and sp3-C fractions from TEY-CK-XANES of carbon materials.

Quantifying Amide-Aromatic Interactions at Molecular and Atomic Levels: Experimentally Determined Enthalpic and Entropic Contributions to Interactions of Amide sp2O, N, C and sp3C Unified Atoms with Naphthalene sp2C Atoms in Water.

In addition to amide hydrogen bonds and the hydrophobic effect, interactions involving π-bonded sp2 atoms of amides, aromatics, and other groups occur in protein self-assembly processes including folding, oligomerization, and condensate formation. These interactions also occur in aqueous solutions of amide and aromatic compounds, where they can be quantified. Previous analysis of thermodynamic coefficients quantifying net-favorable interactions of amide compounds with other amides and aromatics revealed that interactions of amide sp2O with amide sp2N unified atoms (presumably C═O···H-N hydrogen bonds) and amide/aromatic sp2C (lone pair π, n-π*) are particularly favorable. Sp3C-sp3C (hydrophobic), sp3C-sp2C (hydrophobic, CH-π), sp2C-sp2C (hydrophobic, π-π), and sp3C-sp2N interactions are favorable, sp2C-sp2N interactions are neutral, while sp2O-sp2O and sp2N-sp2N self-interactions and sp2O-sp3C interactions are unfavorable. Here, from determinations of favorable effects of 14 amides on naphthalene solubility at 10, 25, and 45 °C, we dissect amide-aromatic interaction free energies into enthalpic and entropic contributions and find these vary systematically with amide composition. Analysis of these results yields enthalpic and entropic contributions to intrinsic strengths of interactions of amide sp2O, sp2N, sp2C, and sp3C unified atoms with aromatic sp2C atoms. For each interaction, enthalpic and entropic contributions have the same sign and are much larger in magnitude than the interaction free energy itself. The amide sp2O-aromatic sp2C interaction is enthalpy-driven and entropically unfavorable, consistent with direct chemical interaction (e.g., lone pair-π), while amide sp3C- and sp2C-aromatic sp2C interactions are entropy-driven and enthalpically unfavorable, consistent with hydrophobic effects. These findings are relevant for interactions involving π-bonded sp2 atoms in protein processes.

Probing the role of sp2-C in high-temperature tribology of a-C films by a comparative study of ta-C film and a-C film

The high-temperature tribological properties of ta-C and a-C films are comparatively studied. The ta-C film shows friction coefficients of around 0.10 at 450 °C and 500 °C, but the a-C film shows high friction coefficients above 0.5 at 450 °C. Surprisingly, the lubrication failure of the a-C film at 450 °C is not due to the failure (wear-out) of the film. Furthermore, the graphitization degree of the wear track of a-C film at 450 °C is higher than those of ta-C films at 450 °C and 500 °C. The underlying frictional mechanism is clarified, and the role of sp2-C atoms at the rubbing surfaces is highlighted. The higher sp2-C content is, the more water needs to achieve sufficient passivation.

Friction-induced metastable transformation of amorphous carbon film: Exploration by experimental and molecular dynamics simulations

The previous experimental research showed that the structure of the amorphous carbon film transformed from sp3-C atom to sp2-C atom after the frictional process. However, due to its metastable characteristics of the amorphous carbon film, whether the transformation can occur from the sp2-C atom to the sp3-C atom during friction is unclear. This study is conducted to get an insight into the effect of frictional load and velocity on the structural transformation of the amorphous carbon film. The relevant results have shown that due to the effect of pressure and shear force, the amorphous carbon film generates sp3-C atoms during the friction process, and this metastable structural transformation recovers with the disappearance of the force. Furthermore, there are differences in the effects of frictional load and velocity on structural transformation. The increased frictional load and velocity inhibit the increase in the proportion of sp2-C atoms, and the structural order of the frictional contact interface is significantly enhanced under a larger frictional load, while the frictional velocity has no obvious effect in this regard. The proportion of sp2-C atoms and the degree of structural order of the friction contact interface in combination affect the tribological performance of the amorphous carbon film.

Metastable hybridized structure transformation in amorphous carbon films during friction—A study combining experiments and MD simulation

Amorphous carbon films have attracted substantial interest due to their exceptional mechanical and tribological properties. Previous studies revealed that the amorphous carbon films exhibited lower coefficient of friction (COF) because of the transformation in bond structure from sp3-C to sp2-C during friction processes. However, the mechanism for such a transformation during friction is not well understood. This study is conducted to get an insight into the metastable transformation in amorphous carbon film during friction by means of experiments and molecular dynamics (MD) simulation. Relevant wear tests showed that wear of the film changed from an abrasive wear mode to a mixture of abrasion and adhesive wear, resulting in a decrease in growth rate of the wear rate after the running-in stage. It is worth noting that the sp3-C atoms were increased during the running-in stage when the films contained lower sp3/sp2 ratios. However, the formed sp3-C atoms could only be short-lived and gradually transformed to sp2-C atoms with the graphitization generated on the wearing surface of the films. The radial distribution function and translational order parameter indicated that the films’ high sp3/sp2 ratio led to an increased sp2-C proportion on the wear scar after friction, which caused an increased structural ordering.

Brief insight into the in silico properties, structure–activity relationships and biotransformation of fruquintinib, an anticancer drug of a new generation containing a privileged benzofuran scaffold

Current trends in drug design notably consider so-called privileged scaffolds as the core structural fragments with decisive impact on affinity to properly chosen biological targets, potency, selectivity and toxicological characteristics of drugs and prospective drug candidates. Fruquintinib (1) is a novel synthetic selective inhibitor of vascular endothelial growth factor receptor (VEGFR) isoforms, i.e., VEGFR-1, VEGFR-2 and VEGFR-3. The therapeutic agent (1) consists of a flat bicyclic heteroaromatic ring, in which two nitrogens are suitablyincorporated, a core bicyclic heteroaromatic ring – privileged (substituted) benzofuran scaffold, and a pair of hydrogen bond (H-bond) donor and acceptor group, i.e., amide functional moiety. Fruquintinib (1) was first approved in China for the treatment of metastatic colorectal cancer, a severe malignant disease with a high mortality rate. The review article offered a brief insight into the topic of privileged structures, their drug- -like ranges of several parameters, pharmacodynamic characteristics of fruquintinib (1) and various in silico descriptors characterizing drug’s structural and physicochemical properties (molecular weight, number of heavy atoms, number of aromatic heavy atoms, fraction of sp3 C-atoms, number of H-bond acceptors, number of H-bond donors, total polar surface area, molar refractivity, molecular volume as well as parameters of lipophilicity and solubility). Some of these descriptors were related to pharmacokinetics and distribution of fruquintinib (1), and, in addition, might help predict its ability to cross passively the blood–brain barrier (BBB). Moreover, a possible connection between the induction potential on cytochrome P450 isoenzymes (CYP1A2 and CYP3A4) and passive transport of a given drug into the central nervous system via BBB was investigated. Current clinical experience and future directions regarding of fruquintinib (1) were also briefly outlined.

Diastereoselective synthesis and structure-affinity relationships of σ1 receptor ligands with spirocyclic scaffold.

Spirocyclic scaffolds play an increasing role in drug discovery as they define a rigid three-dimensional space to increase specific interactions with protein binding sites. Herein, a spirocyclic center was introduced into the lead compound 1 to rigidify its flexible benzylaminoethyl side chain. The key step of the synthesis was the reaction of different α,β-unsaturated amides 6 and 13-16 with methyl acrylate in the presence of TBDMSOTf. DFT calculations explain the mechanism of this transformation as concerted Diels-Alder reaction (functionals B3LYP and TPSS) or double (aza)-Michael addition (functionals PBE and wB97X-D). After separation of the diastereomeric spirocyclic products 8 and 17-20, LiAlH4 reduction provided the spirocyclic hydroxymethyl piperidines 21a,b-25a,b showing low nanomolar σ1 affinity (Ki < 100 nM). trans-Configured ligands (a-series) showed higher or equal σ1 affinity and higher selectivity over σ2 receptors and GluN2B-NMDA receptors than their cis-configured analogs (b-series). The additional hydroxymethyl moiety brings the log D7.4 value in a promising range. The high σ1 affinity (Ki = 3.6 nM) and the low lipophilicity result in the highest lipophilic ligand efficiency for the dispiro compound 23a (LLE = 6.0). The spirocyclic compounds reported herein and in particular the dispiro compound 23a demonstrate that ligands containing a large number of sp3 C-atoms possess favorable pharmacological (σ1 receptor affinity, receptor selectivity) and physicochemical properties (log D7.4 value) resulting in promising LLE.

Fatigue behaviors of diamond-like carbon films

This work investigates the fatigue behaviors of diamond-like carbon (DLC) films by conducting cyclic tensile tests and interfacial fatigue tests via molecular dynamics. It is found that the strength of DLC films is reduced with the increasing cycle number due to the irreversible sp3-sp2 transition of carbon atoms induced by tensile deformation. Regions with high sp2C fraction are easy to deform owing to their weak strength, thus the atomic strains are almost localized in such regions. The weakest region is regarded as the defect of the films and suffers from the most severe strain localization. As a result, many sp3C atoms are transformed into sp2 hybridization in the defect, destroying the integrity of sp3C network. Hence, the film failure occurs in the defect because of its badly degraded strength. Furthermore, interfacial fatigue of DLC films is induced by the sp3-sp2 transition during the cyclic tensile tests.

C6N3: A novel 2D carbon nitride with sp-N as support for efficient hydrogen production

Two-dimensional (2D) carbon nitrides (CxNy) have great potential in advanced fields such as energy harvest and storage. We report a novel 2D CxNy, C6N3, comprising sp-N and sp2-C atoms. Density functional theory calculations indicate that electronically, thermally, and dynamically stable C6N3 is metallic even when cut into very narrow nanoribbons. C6N3 adsorbed single atoms of 3d, 4d, and 5d transition metals to fabricate single-atom catalysts (SACs) for an electrocatalytic hydrogen evolution reaction (HER). Among all SACs studied, Ti-, Cr-, Zr-, and Hf-embedded C6N3 had excellent overall performance including promising stability, moderate binding strength of H and H2, and good electrical conductivity. Our results suggest a novel C6N3 with an sp-N skeleton that has great potential for HER. More investigations are needed to further understand the properties and applications of C6N3 in other fields.

The sp2-sp3 transition and shear slipping dominating the compressive deformation of diamond-like carbon

The uniaxial compression tests of diamond-like carbon (DLC) films are conducted via molecular dynamics to investigate their mechanical properties and deformation mechanisms by considering different factors including strain rates, temperatures, void defects and compliance. It is found that during the compression, large sp3C clusters expand themselves by annexing neighboring sp2C atoms which experience sp2-sp3 transition. Moreover, the sp3C-sp3C bonds along the direction perpendicular to the compressive direction are elongated and the rupture of such bonds leads to the compressive failure of DLC films. Furthermore, the stress relief of DLC films is the result of competition between internal relative slip and diffusion relaxation. The relative slip is dominant with low temperature and high compression strain rate, which makes the DLC films own high strength and exhibit brittleness. However, with high temperature and low strain rate, these films become ductile and their strength are degraded due to the activation of diffusion relaxation.

Nanofriction behaviors between silicon-doped diamond-like carbon films under different testing conditions

Influence of Si contents on nanofriction behaviors between two Si-doped diamond-like carbon (Si-DLC) films is investigated via molecular dynamics simulation. The Si doping induces the friction of these films based on two reasons. The first reason is that the Si doping causes the formation of C-Si bonds in the films and decreases their internal friction, resulting in weak resistances for the relative sliding between them. The other is that the increase in Si content leads to an increase in the proportion of sp3-C atoms but makes them easier to transit to sp2 bonding states, raising the graphitization degree of the films. With high velocities and loads, the friction reductions of these films are also attributed to friction temperatures. A high friction temperature degrades the mechanical strength of the films and enhances their thermal expansions and their graphitization degree, leading to the easy-shear properties of friction interfaces.

Effects of substrate bias voltage on structure and internal stress of amorphous carbon films on γ-Fe substrate: Molecular dynamics simulation

In this paper, the deposition process of amorphous carbon (a-C) films on γ-Fe substrate was simulated by molecular dynamics (MD). The effects of substrate bias voltage (abbreviated as bias) on structure and internal stress of a-C films was investigated. The results showed that the growth process of a-C films on γ-Fe substrate can be divided into five stages, namely, the diffusion stage of C atoms, island-like nucleation stage of a-C films, formation stage of the pseudo diffusion zone, diffusion stage of Fe atoms and stable growth stage of a-C films. The structure of a-C films after deposition can be divided into four zones, namely, the substrate zone, pseudo diffusion zone, intrinsic zone and surface zone. The intrinsic zone is the main part of a-C films, and its structure is mainly composed of sp3-C and sp2-C atoms. The percentage of sp3-C atoms is fluctuated with the increase of bias. When bias is 25 V, the percentage of sp3-C atoms is the largest, which is 26.19%. When bias is 75 V, the percentage of sp3-C atoms is the smallest, which is 23.92%. The percentage of sp2-C atoms is increased with the increase of bias. When bias is 75 V, the percentage of sp2-C atoms is the largest, which is 73.69%. With the increase of bias, the internal stress of the intrinsic zone is firstly increased. When bias is 25 V, the internal stress is the highest, which is 6.94GPa and then is decreased gradually. The pseudo diffusion zone is a transition zone between a-C films and γ-Fe substrate, and is a mixed zone composed of C and Fe atoms. With the increase of bias, the internal stress in the pseudo diffusion zone is decreased gradually. When bias is 75 V, the internal stress is the lowest, which is 0.40GPa.

Relationship between bonding characteristic and thermal property of amorphous carbon structure: Ab initio molecular dynamics study

In this study, the bonding characteristic and thermal property of amorphous carbon (a-C) structures with different densities (2.0, 2.3, 2.6, 2.9 and 3.2 g/cm3) were investigated using ab initio molecular dynamics (AIMD). The results show that all structural models with different densities constructed are amorphous structures with short-range order, long-range disorder and a weak anisotropy. With the increase of density of a-C structure, the content of sp3-C atoms and degree of amorphization increase. The residual stress of a-C structure also changes from tensile stress to compressive stress with the increase of density. For electronic property and bonding characteristic of a-C structure, with the increase of density of a-C structure, electronic density of states near Ef of a-C structure decreased gradually and the density of states near Ef is mainly contributed by electrons in 2p orbital of sp2-C atoms. With the increase of the density of a-C structure, number of bonds and 3D-nodes increase while the polarity of covalent bond in a-C structure decreases, which is due to the increase of sp3-C atoms. For the thermal stability of a-C structure, the increase of 3-D nodes and the decrease of polarity of covalent bond can improve the thermal stability of a-C structures carbon and the thermal stability of a-C structure with high density is higher than that with low density.

Correlation between surface topological defects and fracture mechanism of γ-graphyne-like boron nitride nanosheets

The fracture mechanism of γ-graphyne-like boron nitride (GYBNN) and its analogous nanosheets, sp-GYBNNS (sp-C atoms situated at acetylenic linkages) and sp2-GYBNNS (sp2-C atoms situated in hexagonal rings) was patterned as a function of temperature in both the zigzag and armchair directions via Molecular Dynamic Simulation. Next, the effect of acetylenic chain length on the Young’s modulus and failure stress was studied. The applied stress was distributed on both hexagonal rings and acetylenic chains in the zigzag direction. However, in the direction of armchair the stress was mainly concentrated on the acetylenic chains. The failure stress varied less considerably by increasing the acetylenic chains’ length in zigzag direction than in armchair. The sp2-GYBNNS and GYBNNS had the highest and lowest tensile strength in both zigzag and armchair directions, respectively. The crack length increase from L/12 (25 Å) to L/2 (150 Å) led to a significant reduction in the Young’s modulus of sp2-GYBNNS from 270.05 to 177.25 GPa. The stress intensity factor for crack-contained sp2-GYBNNS (length = L/12) was declined from the value of 2.622 to 2.212 by increasing the temperature from 200 to 900 K.

Deformation mechanisms of Si-doped diamond-like carbon films under uniaxial tension conditions

Element-doped diamond-like carbon (DLC) films have been fabricated to achieve excellent mechanical properties but their elastic/plastic deformation mechanisms are unclear due to experimental limitations in characterizing the deformation process. This study investigates the deformation mechanisms of Si-doped DLC films by simulating their uniaxial tensile tests. It is found that these films show many strain-localized regions under tensile deformations. The coordination number (CN) of Si atoms in such regions decreases even with a small tensile strain. The sp3-sp2 bonding transition of C atoms also happen in these regions with a large tensile strain. As a result, these regions show highly-degraded structures with weak mechanical strength and can be regarded as the defects in the Si-DLC films. In this case, the tensile forces are mainly undertaken by the networks formed of both sp3C atoms and Si atoms with large CN, and hence such networks can be regarded as backbones of Si-DLC films. Their fracture finally initiates in the strain-localized regions. Furthermore, Si-DLC films with an increased Si content show large fraction of sp3C atoms but still exhibit a decreased strength due to the rapid presence of strain-localized regions.

Argon atoms insertion in diamond: New insights in the identification of carbon C 1s peak in X-ray photoelectron spectroscopy analysis

The C 1s peak's electron binding energy position in X-ray photoelectron spectroscopy (XPS) analysis of single crystal diamond (SCD) and crystalline and polycrystalline diamond and graphite films has been extensively investigated. A key issue is the experimental identification of C 1s peaks position from graphite sp2 and diamond sp3 C-atoms bonding in the diamond lattice, based on expected energy shifts of C 1s peaks from theory. Because of material charging upon electron photoemission, the absolute binding energy of the C 1s/sp3 related peak cannot be determined. The systematic study of C 1s peaks from XPS analysis of crystalline diamond, polycrystalline diamond films and graphite show key findings: 1) Ar+ ion bombardment is a reliable technique to characterize Diamond vs graphite materials during XPS analysis; 2) A low energy peak reported as C 1s/sp2 bonding, is attributed to the C 1s/sp3 in the presence of Ar atoms inserted in the lattice. 3) The data show direct correlation between the energy of the Ar+ ion beam used for surface sputter-cleaning and binding energy shifts of XPS C 1s peaks.

Quantifying Interactions of Nucleobase Atoms with Model Compounds for the Peptide Backbone and Glutamine and Asparagine Side Chains in Water.

Alkylureas display hydrocarbon and amide groups, the primary functional groups of proteins. To obtain the thermodynamic information that is needed to analyze interactions of amides and proteins with nucleobases and nucleic acids, we quantify preferential interactions of alkylureas with nucleobases differing in the amount and composition of water-accessible surface area (ASA) by solubility assays. Using an established additive ASA-based analysis, we interpret these thermodynamic results to determine interactions of each alkylurea with five types of nucleobase unified atoms (carbonyl sp2O, amino sp3N, ring sp2N, methyl sp3C, and ring sp2C). All alkylureas interact favorably with nucleobase sp2C and sp3C atoms; these interactions become more favorable with an increasing level of alkylation of urea. Interactions with nucleobase sp2O are most favorable for urea, less favorable for methylurea and ethylurea, and unfavorable for dialkylated ureas. Contributions to overall alkylurea-nucleobase interactions from interactions with each nucleobase atom type are proportional to the ASA of that atom type with proportionality constant (interaction strength) α, as observed previously for urea. Trends in α-values for interactions of alkylureas with nucleobase atom types parallel those for corresponding amide compound atom types, offset because nucleobase α-values are more favorable. Comparisons between ethylated and methylated ureas show interactions of amide compound sp3C with nucleobase sp2C, sp3C, sp2N, and sp3N atoms are favorable while amide sp3C-nucleobase sp2O interactions are unfavorable. Strongly favorable interactions of urea with nucleobase sp2O but weakly favorable interactions with nucleobase sp3N indicate that amide sp2N-nucleobase sp2O and nucleobase sp3N-amide sp2O hydrogen bonding (NH···O═C) interactions are favorable while amide sp2N-nucleobase sp3N interactions are unfavorable. These favorable amide-nucleobase hydrogen bonding interactions are prevalent in specific protein-nucleotide complexes.