Hydrogen Bond Lengths Research Articles

Hydrogen Bond Length as a Key To Understanding Sweetness.

Neutron diffraction experiments have been performed to investigate and compare the structure of the hydration shell of three monosaccharides, namely, fructose, glucose, and mannose. It is found that despite their differences with respect to many thermodynamical quantities, bioprotective properties against environmental stresses, and taste, the influence of these monosaccharides on the bulk water solvent structure is virtually identical. Conversely, these sugars interact with the neighboring water molecules by forming H bonds of different length and strength. Interestingly, the sweetness of these monosaccharides, along with that of the disaccharide trehalose, is correlated with the length of these H bonds. This suggests that the small differences in stereochemistry between the different sugars determine a relevant change in polarity, which has a fundamental impact on the behavior of these molecules in vivo.

Vibrational and electronic absorption spectroscopic profiling, natural hybrid orbital, charge transfer, electron localization function and molecular docking analysis on 3-amino-3-(2-nitrophenyl) propionic acid

The organic amine 3-Amino-3-(2-nitrophenyl) propionic acid (3-ANPPA) was characterized by spectroscopic profiling employing FT-IR, FT-Raman and UV–Visible spectra both experimentally and theoretically. In addition, the bonding and anti-bonding nature, nonlinear optical, electronic and thermodynamic nature of the molecule was analyzed by using density functional theory (DFT) B3LYP method with the 6–311++G (d,p) basis set. The electronic absorption spectrum of organic molecules that shows alteration due to the solvation processes was evaluated by TD-DFT in the gas and solvent phase in addition to the recorded UV–Visible spectrum. The low toxicity levels of 3-ANPPA calculated in terms of the softness value and the electrophilicity index calculated that acts as a biological descriptor led to molecular docking investigations. The hydrogen bond lengths and binding energy of the title molecule with different proteins were identified. A minimum binding energy of −5.42 kcal/mol is seen in the interaction of protein 5T30 with the bonded residues LYS′1, GLU′43 and MET′0.

Exploring Effective Factors on Energy Data of Some Benzofuran Derivatives

Benzofuran derivatives have many useful applications. Computational quantum chemistry method was used to study the relationship between energy data and molecular properties of the 5,6-dihydroxy-2-methyl-1-benzofuran-3-carboxylate derivatives (molecules 3a–3f). Results indicate that there is a good relationship between intramolecular hydrogen bond lengths and energy data of these molecules. Also, X-ray of molecule 3e was used to compare experimental and computational geometrical parameters. Chemical hardness, chemical potential and electronegativity values were calculated to recognize relation between energy data and reactivity of these molecules. Atomic net charges and molecular electrostatic potential values were employed for better insight regarding energy data of the molecules. Electronic charge densities were calculated using atoms in molecules method. The correlation coefficients between experimental and computational 13 C NMR chemical shifts were examined. Total spin– spin coupling constant and its components were evaluated to understand the contribution of these properties in energy data of the molecules. The relation between energy data of the molecules and aromaticity of the rings was also determined.

Raman spectra of terephthalic acid crystals in the temperature range 5 K–300 K

Raman spectra of terephthalic acid crystals were taken in the temperature range 5K–300K. The temperature dependence of the vibrational frequency of the O⋯O hydrogen bond is found to contain information on the mechanism of the proton motion along the bond (hopping and/or tunneling). Onset temperatures of both tunneling and ordering (termination of the hopping) process are determined. Triplet exciton bands observed in the high-wavenumber spectral range also exhibit the relation with proton motions between oxygen atoms. The energy spectra of molecular chains of terephthalic acid, the proton potential energy along the bond, and the probabilities of tunneling as a function of the hydrogen bond lengths are calculated.

Stimuli-responsive luminescent coumarin thiazole hybrid dye: Mechanism of excited-state intramolecular double proton transfer

Recently, a novel coumarin thiazole hybrid dye with azomethine linkage is synthesized. It is revealed that the symmetrical structures 3,3'-(5,5'-((1E,1'E)-hydrazine-1,2-diylidenebis(methanylylidene))bis(2-morpholinothiazole-5,4-diyl))bis(4-hydroxy-2H-chromen-2-one) (abbreviated as CS) takes shape two intramolecular hydrogen bonds and that excited-state intramolecular proton transfer (ESIPT) takes place with thiazole nitrogen atoms [Dyes Pigments. 142, 2017, 121]. However the corresponding reaction mechanisms are lacking. This study uses density functional and time-dependent density functional theory to calculate hydrogen-bond lengths, hydrogen-bond angles, infrared vibrational spectra and Mulliken charges of relevant groups, which confirm the excited-state hydrogen-bond strengthening mechanism. Enhanced hydrogen-bond strength facilitates the ESIPT process of the CS molecule. The absorption and fluorescence emission spectra of CS in dimethyl formamide (DMF) are calculated, which are consistent with the observed results in experiment. To further illustrate mechanism of excited-state double proton transfer (ESDPT) reactions, the potential energy surfaces of CS are constructed and analyzed, which demonstrate ESDPT more likely occur stepwise rather than concertedly. The frontier molecular orbitals of CS system are also calculated and display the nature of the charge redistribution, which demonstrate that CS system exhibits light fastness because ESIPT process inhibits intramolecular charge transfer.

Hydrogen Bonds: Simple after All?

Hydrogen bonds play integral roles in biological structure, function, and conformational dynamics and are fundamental to life as it has evolved on Earth. However, our understanding of these fundamental and ubiquitous interactions has seemed fractured and incomplete, and it has been difficult to extract generalities and principles about hydrogen bonds despite thousands of papers published on this topic, perhaps in part because of the expanse of this subject and the density of studies. Fortunately, recent hydrogen bond proposals, discussions, and debates have stimulated new tests and models and have led to a remarkably simple picture of the structure of hydrogen bonds. This knowledge also provides clarity concerning hydrogen bond energetics, limiting and simplifying the factors that need be considered. Herein we recount the advances that have led to this simpler view of hydrogen bond structure, dynamics, and energetics. A quantitative predictive model for hydrogen bond length can now be broadly and deeply applied to evaluate current proposals and to uncover structural features of proteins, their conformational restraints, and their correlated motions. In contrast, a quantitative energetic description of molecular recognition and catalysis by proteins remains an important ongoing challenge, although our improved understanding of hydrogen bonds may aid in testing predictions from current and future models. We close by codifying our current state of understanding into five "Rules for Hydrogen Bonding" that may provide a foundation for understanding and teaching about these vital interactions and for building toward a deeper understanding of hydrogen bond energetics.

TDDFT investigation of excitation of water tetramer under femtosecond laser pulse irradiation

We study the static properties of water tetramer in ground state, the optical absorption spectra and ultrafast nonadiabatic dynamical response of water tetramer to short and intense laser pulses with different intensities by a real-space, real-time implementation of time-dependent density functional theory coupled to molecular dynamics (TDDFT–MD) nonadiabatically. The calculated results are in good agreement with available values in literature. Four typical irradiated scenarios of water tetramer in laser field, which are “normal vibration,” “break and reorganization,” “fragmentation and new formation” and “pure fragmentation”, are explored by discussing the ionization, the bond lengths of OH bonds and hydrogen bonds and the kinetic energy of ions. The dynamic simulation shows that the reaction channel of water tetramer can really be controlled by choosing appropriate laser parameters referring to the optical absorption spectra and hydrogen ions play an important role in the reaction channel. Furthermore, it is found that the laser intensity affects the kinetic energy of ejected protons more than that of the remaining fragments and all dynamic processes are somehow directly related to the velocity of departing protons.

Spectra, Electronic Properties, Biological Activities and Molecular Docking Investigation on Sulfonamide Derivative Compound: An Experimental and Computational Approach

The title compound methyl (2E)-2-{[N-(2-formylphenyl)-4-methylbenzene sulfonamido] methyl}-3- phenylprop-2-enoate (MFMSPE) is a derivative of sulfonamide. FT-IR spectra of MFMSPE in the solid phase were recorded and analyzed. The optimized geometry and vibrational wave numbers were computed using DFT/B3LYP method with aid of 6-311++G (d,p) basis set. Stability of the molecule arising from hyper conjugative interactions, charge delocalization has been analyzed using natural bond orbital (NBO) analysis. The calculated HOMO and LUMO energies confirm that charge transfer occurs within the molecule. Molecular electrostatic potentials (MEP) was carried out at and interpreted. To recognize the biological activity of MFMSPE, molecular docking was done to recognize the hydrogen bond lengths and binding energy with antibacterial protein (1KE4).

Vibrational tug-of-war: The pKA dependence of the broad vibrational features of strongly hydrogen-bonded carboxylic acids.

Medium and strong hydrogen bonds give rise to broad vibrational features frequently spanning several hundred wavenumbers and oftentimes exhibiting unusual substructures. These broad vibrational features can be modeled from first principles, in a reduced dimensional calculation, that adiabatically separates low-frequency modes, which modulate the hydrogen bond length, from high-frequency OH stretch and bend modes that contribute to the vibrational structure. Previously this method was used to investigate the origin of an unusual vibrational feature frequently found in the spectra of dimers between carboxylic acids and nitrogen-containing aromatic bases that spans over 900 cm-1 and contains two broad peaks. It was found that the width of this feature largely originates from low-frequency modes modulating the hydrogen bond length and that the structure results from Fermi resonance interactions. In this report, we examine how these features change with the relative acid and base strength of the components as reflected by their aqueous pKA values. Dimers with large pKA differences are found to have features that can extend to frequencies below 1000 cm-1. The relationships between mean OH/NH frequency, aqueous pKA, and O-N distance are examined in order to obtain a more rigorous understanding of the origin and shape of the vibrational features. The mean OH/NH frequencies are found to correlate well with O-N distances. The lowest OH stretch frequencies are found in dimer geometries with O-N distances between 2.5 and 2.6 Å. At larger O-N distances, the hydrogen bonding interaction is not as strong, resulting in higher OH stretch frequencies. When the O-N distance is smaller than 2.5 Å, the limited space between the O and N determines the OH stretch frequency, which gives rise to frequencies that decrease with O-N distances. These two effects place a lower limit on the OH stretch frequency which is calculated to be near 700 cm-1. Understanding how the vibrational features of strongly hydrogen-bonded structures depend on the relative pKA and other structural parameters will guide studies of biological structures and analysis of proton transfer studies using photoacids.

Teobromin ve Teobromin-Su Bileşikleri Üzerine Deneysel ve Teorik Çalışmalar

In this study, the solvent effects on structural, spectroscopic, electronic and thermochemical properties of Theobromine (tbH) were theoretically investigated. The dichloromethane (DCM), dimethylsulfoxide (DMSO) and water (H2O) solvents have been chosen for investigations. Optimized molecular structures of tbH were obtained by using the DFT/B3LYP method with 6-311++G(d,p) basis set in vacuum and in solvent media. Calculated geometric structure parameters were compared with experimental data. In the experimental section, the mid-IR spectrum of tbH was recorded using ATR equipment and compared with calculated vibrational frequencies. tbH-H2O complexes were studied for various binding ratios. The total energies and hydrogen bond lengths of these complexes were discussed in detail. It is seen as the result of this study that N⋯H-O and O⋯H-O non-covalent bonded structures are more stable for all binding versions and hydrogen bond lengths for all tbH-H2O complexes range from 1.8-2.5 A.

Maximally resolved anharmonic OH vibrational spectrum of the water/ZnO(101¯0) interface from a high-dimensional neural network potential.

Unraveling the atomistic details of solid/liquid interfaces, e.g., by means of vibrational spectroscopy, is of vital importance in numerous applications, from electrochemistry to heterogeneous catalysis. Water-oxide interfaces represent a formidable challenge because a large variety of molecular and dissociated water species are present at the surface. Here, we present a comprehensive theoretical analysis of the anharmonic OH stretching vibrations at the water/ZnO(101¯0) interface as a prototypical case. Molecular dynamics simulations employing a reactive high-dimensional neural network potential based on density functional theory calculations have been used to sample the interfacial structures. In the second step, one-dimensional potential energy curves have been generated for a large number of configurations to solve the nuclear Schrödinger equation. We find that (i) the ZnO surface gives rise to OH frequency shifts up to a distance of about 4 Å from the surface; (ii) the spectrum contains a number of overlapping signals arising from different chemical species, with the frequencies decreasing in the order ν(adsorbed hydroxide) > ν(non-adsorbed water) > ν(surface hydroxide) > ν(adsorbed water); (iii) stretching frequencies are strongly influenced by the hydrogen bond pattern of these interfacial species. Finally, we have been able to identify substantial correlations between the stretching frequencies and hydrogen bond lengths for all species.

Vibrational and electronic spectral analysis of thymol an isomer of carvacrol isolated from Trachyspermum ammi seed: A combined experimental and theoretical study

Abstract Phytochemical study of a natural product, Thymol an antiseptic drug was isolated from the seeds of Trachyspermum Ammi. The structure of thymol was established using spectroscopic techniques such as FT-IR, UV and GC–MS method. Density functional theory calculations were carried out for thymol and compared with its isomer carvacrol. DFT calculations have been performed at B3LYP/6–31 + G (d,p) level of theory for obtaining geometric and spectroscopic properties of thymol and carvacrol. The simulated vibrational spectrum of thymol at B3LYP/6–31 + G (d,p) shows a nice correlation with the experimental IR spectrum there by to confirm the structure of the isolated compound. The biological activity of thymol was carried out using molecular docking to identify the hydrogen bond lengths and binding energy with different antimicrobial protein. Further, electronic properties such as band gap, Ionization potential and electron affinities, inter-molecular interaction and thermodynamic properties were also simulated and reported for the first time.

Elaborating a new excited state intramolecular proton transfer (ESPT) mechanism for a new π-conjugated dye 2, 2′-((5-(2-(4-methoxyphenyl)ethenyl)-benzene-1,1-diyl)-bis-(nitrilomethylylidene)-diphenol)

In this work, the excited state dynamical behavior of a novel π-conjugated dye 2,2′-((5-(2-(4-methoxyphenyl)ethenyl)-benzene-1,1-diyl)-bis-(nitrilomethylylidene)-diphenol) (C1) has been investigated. Two intramolecular hydrogen bonds of C1 are tested to pre-existing in the ground state via AIM and reduced density gradient. Using a time-dependent density functional theory (TDDFT) method, it has been substantiated that the intramolecular hydrogen bonds of C1 should be strengthened in the S1 state via analyzing fundamental bond length, bond angles, and corresponding infrared vibrational modes. The most obvious variation of these two hydrogen bonds is the O4–H5···N6 bond, which might play important roles in excited state behavior for the C1 system. Furthermore, based on electronic excitation, charge transfer could occur. Just due to this kind of charge re-distribution, two hydrogen bonds should be tighter in the first excited state, which is consistent with the variation of hydrogen bond lengths. Thus, the phenomenon of charge transfer is reasonable evidence for confirming the occurrence of the excited state proton transfer (ESPT) process in the S1 state. Our theoretically constructed potential energy surfaces of C1 show that excited state single proton transfer should occur along with the O4–H5···N6 hydrogen bond rather than the O1–H2···N3 bond. We not only clarify the ESIPT mechanism for C1 but put forward new affiliation and explain a previous experiment successfully.

Physicochemical properties, NMR, Ab initio calculations and the molecular interactions in a binary mixture of N-methylimidazole and water

For a binary mixture of xN-methylimidazole (hereafter abbreviated to N-mim)+(1-x) water, over a full molar fraction range, the mass density, sound velocity, refractive index, viscosity, mixing enthalpy, conductivity, and pH at (298.15, 308.15, 318.15) K and 0.1MPa, and 1H NMR and 13C NMR at room temperature combined with Ab initio calculations, were measured and carried out. The excess molar volume (VmE), sound deviation (∆u), refractive index deviation (∆nD), viscosity deviation (∆η), excess Gibbs energy of activation of viscous flow (∆G⁎E), molar mixing enthalpy (∆mixHm), 1H NMR chemical shift changes of N-mim and water protons (∆δH), 13C NMR chemical shift change of N-mim (∆δC), sum of the chemical shift changes (∑∆δH(N-mim), ∑∆δC), and the interaction energy, hydrogen bond length, second-order perturbation stabilization energy, electron density, and the electronic energy density of the trimer hydrogen-bonded complexes were calculated. The values of VmE, ∆u, ∆nD, ∆η, ∆G⁎E, and ∆mixHm were fitted to a Redlich-Kister equation. The extreme positions of these quantities and the chemical shift changes were compared and discussed with regard to the intermolecular interaction between N-mim and water, and a possible molecular interaction scheme was suggested for N-mim added to water. There occurs an ionization process and hydrogen-bonded interactions between N-mim and water. The ionization process may not be neglected at an infinite dilution of water, and hydrogen bonds predominate the primary interaction in the mixture. The predominant hydrogen-bonded complex in the mixture transforms with increasing x, which is consistent with the calculation results.

Spectroscopic investigation on structure (monomer and dimer), molecular characteristics and comparative study on vibrational analysis of picolinic and isonicotinic acids using experimental and theoretical (DFT & IVP) methods

In this investigation, the monomeric structure is determined for picolinic and isonicotinic acids based on geometry optimization for one of the four possible conformers and intramolecular hydrogen bond of OH⋯O using density functional theory (DFT) employing B3LYP functional supplemented with 6–311++G(d,p) basis set. Using this optimized monomeric form, the dimer structure is determined based on minimum energy and length of hydrogen bonds obtained for two possible dimeric forms yielded due to head-to-tail intermolecular OH⋯N hydrogen bond (dimer 1) linkage and tail-to -tail intermolecular OH⋯O hydrogen bond (dimer 2) linkage between pyridine ring and carboxyl group. The structure parameters obtained for monomer and dimer forms are in good agreement with the experimental literature values. The vibrational assignments have been made unambiguously for all the vibrations from FTIR and FT-Raman spectra based on the potential energy distribution (PED) and eigen vectors obtained in DFT and inverse vibrational problem (IVP) computations. The rms error between the observed and scaled frequencies is 7.7 and 9.4 cm−1 for PIA and INA, respectively. A 74-element modified valence force field is derived by Wilson's GF matrix method using 58 experimental frequencies of the two molecules in overlay least-squares technique. The average error between observed and computed frequencies by this method is calculated to be 10.39 cm−1. The results of both DFT and IVP computations yielded good agreement between observed and calculated frequencies. The NLO behaviour using hyperpolarizability values; and HOMO and LUMO energies; of the two molecules are investigated by DFT. Charge density distribution and site of chemical reactivity of the molecules are studied by molecular electrostatic surface potential (MESP). Stability of the molecules arising from hyper conjugative interactions and charge delocalization has been analyzed using natural bond orbital (NBO) analysis. The 13C and 1H NMR chemical shifts of the molecules are calculated by the gauge independent atomic orbital (GIAO) method and compared with experimental results. UV–visible (UV–Vis) spectra of the compounds are also recorded in the region 200–400 nm. Thermodynamic parameters and rotational constants are also determined and found that they are comparable with experimental literature values for these molecules.

An in-depth study on noncovalent stacking interactions between DNA bases and aromatic drug fragments using DFT method and AIM analysis: conformers, binding energies, and charge transfer

This work is aimed at providing physical insights about the π–π stacking interactions of some popular drug fragments (DF) including indole (I), benzothiophene (Bt), benzofuran (Bf) and guanine (G), adenine (A), A-thymine (AT), G-cytosine (GC) base pairs using density functional theory (DFT), the atoms in molecule (AIM) theory, and natural bond orbital (NBO) analysis. Several stable conformers of present molecules and complexes were optimized at the M062X/6-311++G(d,p) level of theory. The result shows that the IG1 (see the notation below) and IA6 have maximum interaction energy in all of the two G-based and A-based conformers; and order of the adsorption strength is IG1 > BtG6 > BfG1 for G-based complexes and IA6 > BtA6 > BfG6 for A-based complexes. For the base pair–drug fragment complexes, the order of interaction energy was found according to IAT4 > BtAT3 > BfAT4 and IGC3 > BtGC2 > BfGC2, for AT and GC base pairs, respectively. Furthermore, our results show that stacking interaction leads to an increase and decrease in hydrogen bond length that involved in the nucleic base–drug fragment interactions. DFT-calculated interaction energies for all present conformers were found to be in a good agreement with the bond critical points data from AIM analysis. In contrast, no reasonable linear correlation was observed between NBO analysis and stability of the all studied conformers. Finally, in order to verify the DFT and AIM results, docking calculations were performed using AutoDock software. According to the binding energy of drug–DNA from AutoDock calculations, the D2-Bt and D1-Bf are the most and the least stable structures, respectively.

Структура и колебательные свойства гидратов оксианионных кристаллов из первых принципов

AbstractStructural parameters and IR spectra of hydrates of lithium and sodium perchlorates, calcium sulfate hydrate (gypsum), and lithium nitrate hydrate are calculated ab initio using the density functional theory. The bond lengths in the water molecules are established as functions of length and energy of hydrogen bonds. The relationship between lengths of intra-anionic and hydrogen bonds is considered. The splitting of intramolecular vibrations of water is highlighted. The stretching vibration frequency of water is determined as a function of length and energy of hydrogen bonds. The combined (mixed) vibrations of anions and molecules of water with frequencies below 1400 cm^–1 are feasible as well.

Intermolecular charge fluxes and far-infrared spectral intensities of liquid formamide.

The intensity generation mechanisms of the far-infrared (far-IR) [or terahertz (THz)] spectrum of liquid formamide, particularly with regard to the behavior of electrons induced by modulations of the hydrogen-bonding conditions of the molecules, are examined theoretically. The theoretical analysis is done in the following two steps. First, density functional theory (DFT) calculations are carried out for the dimers and larger clusters of formamide to analyze the change in the dipole derivative (the square of which is proportional to the IR intensity) induced by hydrogen-bond formation. Then, by using the information derived in the first step, molecular dynamics-based spectral simulations are carried out. It is shown that, upon formation of a hydrogen bond, a change in the dipole derivative is induced along the direction of the hydrogen bond, and is reasonably modeled by the intermolecular charge flux mechanism, where a certain amount of electron density is transferred between molecules according to the modulation of the hydrogen-bond length, similarly to the case of liquid water. This model is in a form that is suitable for use in molecular dynamics-based spectral simulations. From these spectral simulations, it is found that the observed spectral features of the far-IR spectrum of liquid formamide are reasonably reproduced, and that the inclusion of the effect of intermolecular charge flux is essential for it. Contrary to the case of liquid water, the molecular libration band (rather than the molecular translation band) is significantly enhanced by the intermolecular charge flux. It is discussed that this difference is related to the geometrical relation between the hydrogen bonds and the atomic displacements in the molecular translations and librations (rotations). It is considered that, in general, in hydrogen-bonding liquids, modulations of hydrogen-bond lengths occurring upon dynamics of molecules give rise to intermolecular charge fluxes, significantly affecting the dipole derivatives, and hence, the IR intensity distributions in the spectra.

Counter anion effect on structural, opto-electronic and charge transport properties of fused π-conjugated imidazolium compound

ABSTRACTThe structure–activity relationship of fused π-conjugated imidazolium cation with three counter anion molecules, BF4−, CF3SO3− and (CF3SO2)2N−, was studied using electronic structure calculations. The structural, opto-electronic and charge transport properties of these complexes were studied. The charge transfer from π-conjugated imidazolium(I) to counter anion was confirmed in all the studied complexes. Interaction energy varies significantly depending on the counter anion and the stability was found higher for I-BF4 complex than both I–CF3SO3 and I–(CF3SO2)2N complexes. The strong (C–H)+···F− hydrogen bond of length 1.95 Å between fused π-conjugated imidazolium and BF−4 anion is the driving force for the strongest interaction energy in I–BF4 complex. The energy decomposition analysis confirms that the interaction between imidazolium and counter anion is mainly driven by electrostatic and orbital interaction. It has been observed that the absorption spectra of the complex are independent of anion nature but the influence of anion character is observed on frontier molecular orbital pattern. The charge transport property of I–BF4 complex was studied by using tight-binding Hamiltonian approach and found that the hole mobility in I–BF4 is 1.13 × 10−4 cm2 V−1 s−1.

Designing a polytope for use in a broad-spectrum dengue virus vaccine.

ObjectivesDengue virus surface proteins are often used in the development of vaccines that protect against dengue virus infection. However, the surface proteins on the four serotypes of dengue virus display high variation, which increases the difficulty of developing a vaccine that can protect against all viral strains. In this study, a polytope that is recognized by broadly neutralizing antibodies (bnAbs) was designed using conserved epitopes from the four serotypes.MethodsWe constructed a polytope using four conserved dengue virus epitopes such that two aligned epitopes were separated from the other two epitopes by a histidyl-tRNA synthetase spacer. The epitopes were selected based on our previous docking studies. We then performed molecular docking of the polytope with the four bnAbs.ResultsThe polytope bound precisely to the four bnAbs—B7, C8, A11, and C10. Moreover, the polytope had a higher affinity for the bnAbs compared to the DENV2 antigen. The polytope and A11 antibody complex had the lowest binding energy relative to complexes between the polytope and the other three antibodies assessed. The highest total number of hydrogen bonds was found in the polytope and B7 antibody complex. The hydrogen bond length in all the complexes ranged from 2.07 to 3.03 Å, implying that hydrogen bonds stabilized the complexes.ConclusionThe developed polytope interacted with four different bnAbs that recognize the four serotypes of dengue virus. The results of this study suggest that this polytope warrants further development for use in a broad-spectrum vaccine against dengue virus.