4‐Amino‐3‐methyl‐6‐phenyl‐1,2,4‐triazin‐5(4H)‐one (metamitron) and 4‐amino‐6‐methyl‐3‐phenyl‐1,2,4‐triazin‐5(4H)‐one (isometamitron)

The title structures, both C₁₀H₁₀N₄O, are substitutional isomers. The N—N bond lengths are longer and the C=N bond lengths are shorter by ca 0.025 Å than the respective average values in the C=N—N=C group of asymmetric triazines; the assessed respective bond orders are 1.3 and 1.7. There are N—H⋯O and N—H⋯N hydrogen bonds in both structures, with 4‐­amino‐3‐methyl‐6‐phenyl‐1,2,4‐triazin‐5(4H)‐one containing a rare bifurcated N—H⋯N,N hydrogen bond. The structures differ in their mol­ecular stacking and the hydrogen‐bonding patterns.     

Glycosidic linkage,N‐acetyl side‐chain,and other structural properties of methyl 2‐acetamido‐2‐deoxy‐β‐d‐glucopyranosyl‐(1→4)‐β‐d‐mannopyranoside monohydrate and related compounds

The crystal structure of methyl 2‐acetamido‐2‐deoxy‐β‐d ‐glycopyranosyl‐(1→4)‐β‐d ‐mannopyranoside monohydrate, C₁₅H₂₇NO₁₁·H₂O, was determined and its structural properties compared to those in a set of mono‐ and disaccharides bearing N‐acetyl side‐chains in βGlcNAc aldohexopyranosyl rings. Valence bond angles and torsion angles in these side chains are relatively uniform, but C—N (amide) and C—O (carbonyl) bond lengths depend on the state of hydrogen bonding to the carbonyl O atom and N—H hydrogen. Relative to N‐acetyl side chains devoid of hydrogen bonding, those in which the carbonyl O atom serves as a hydrogen‐bond acceptor display elongated C—O and shortened C—N bonds. This behavior is reproduced by density functional theory (DFT) calculations, indicating that the relative contributions of amide resonance forms to experimental C—N and C—O bond lengths depend on the solvation state, leading to expectations that activation barriers to amide cis–trans isomerization will depend on the polarity of the environment. DFT calculations also revealed useful predictive information on the dependencies of inter‐residue hydrogen bonding and some bond angles in or proximal to β‐(1→4) O‐glycosidic linkages on linkage torsion angles ? and ψ. Hypersurfaces correlating ? and ψ with the linkage C—O—C bond angle and total energy are sufficiently similar to render the former a proxy of the latter.     

A DFT-based study of the hydrogen-bonding interactions between epicatechin and methanol/water

Tea polyphenols are essential components that give tea its medicinal properties. Methanol and water are frequently used as solvents in the extraction of polyphenols. Hydrogen-bonding interactions are significant in the extraction reaction. Density functional theory (DFT) techniques were used to conduct a theoretical investigation on the hydrogen-bonding interactions between methanol or water and epicatechin, an abundant polyphenol found in tea. After first analyzing the epicatechin monomer's molecular geometry and charge characteristics, nine stable epicatechin (EC) H₂O/CH₂OH complex geometries were discovered. The presence of hydrogen bonding in these improved structures has been proven. The calculated hydrogen bond structures are very stable, among which the hydrogen bond bonded with a hydroxyl group has higher stability. The nine complex structures’ hydrogen bonds were thought to represent closed-shell-type interactions. The interaction energy with 30O-31H on the epicatechin benzene ring is the strongest in the hydrogen bond structure. While the other hydrogen bonds were weak in strength and mostly had an electrostatic nature, the hydrogen bonds between the oxygen atoms in H₂O or CH₂OH and the hydrogen atoms of the hydroxyl groups in epicatechin were of moderate strength and had a covalent character. Comparing the changes in the hydrogen bond structure vibration peak, the main change in concentration peak is the hydrogen bond vibration peak in the complex. Improved the study on the hydrogen bond properties of CH₂OH and H₂O of EC.     

Classifying Structural Characteristics to Enhance Computation of Enthalpy of Formation of Halohydrocarbons

Density functional theory (DFT) calculations are made and least squares calibration performed for various halohydrocabons, which were 27 straight‐chain alkyl halides, 20 branch‐chain alkyl halides and 19 aromatic halides, to determine their enthalpies of formation (ΔH_f). The mean absolute error (M. |A.E.|) in ΔH_f across 66 molecular computations was only 7.8 kJ/mol (1.9 kcal/mol). Grouping the molecules by their structural characteristics improved M. |A.E.| of ΔH_f by 0.2–2.2 kJ/mol over that obtained using corresponding modified data for the same 66 unclassified molecules.     

Density functional complete study of hydrogen bonding between the water molecule and the hydroxyl radical (H2O · HO)

The hydrogen bonding complexes formed between the H₂O and OH radical have been completely investigated for the first time in this study using density functional theory (DFT). A larger basis set 6‐311++G(2d,2p) has been employed in conjunction with a hybrid density functional method, namely, UB3LYP/6‐311++G(2d,2p). The two degenerate components of the OH radical ²Π ground electronic state give rise to independent states upon interaction with the water molecule, with hydrogen bonding occurring between the oxygen atom of H₂O and the hydrogen atom of the OH radical. Another hydrogen bond occurs between one of the H atoms of H₂O and the O atom of the OH radical. The extensive calculation reveals that there is still more hydrogen bonding form found first in this investigation, in which two or three hydrogen bonds occur at the same time. The optimized geometry parameter and interaction energy for various isomers at the present level of theory was estimated. The infrared (IR) spectrum frequencies, IR intensities, and vibrational frequency shifts are reported. The estimates of the H₂O · OH complex's vibrational modes and predicted IR spectra for these structures are also made. It should be noted that a total of 10 stationary points have been confirmed to be genuine minima and transition states on the potential energy hypersurface of the H₂O · HO system. Among them, four genuine minima were located. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002     

TD-DFT Study on the Excited-State Hydrogen Bonding of the p-Cresol–NH3–H2O Complex

In this work, the time-dependent density functional theory (TD-DFT) method was used to study the electronic excited-state dynamics of the hydrogen-bonded p-Cresol–NH₃–H₂O complex. The intermolecular hydrogen bonds O₁–H₁···N and C–O₁···H₂ were demonstrated by the optimized geometric structure of the hydrogen-bonded p-Cresol–NH₃–H₂O complex. The infrared spectra (IR spectra) of the hydrogen-bonded p-Cresol–NH₃–H₂O complex in the ground and excited states were also calculated by using the density functional theory (DFT) and TD-DFT methods. It is demonstrated that hydrogen bond O₁–H₁···N can be strengthened while hydrogen bond C–O₁···H₂ is weakened upon photoexcitation to the S₁ state. The significant changes of the hydrogen bond from the calculated bond lengths in different electronic states can be observed. In addition, the spectral shifts of the stretching vibrational mode of the hydrogen-bonded O–H group in different electronic states are accounted for the hydrogen bond changes in the S₁ state too.     

A density functional study of chemical reactions

Density functional theory (DFT ) was used to study reactions involving small molecules. Relative energies of isomers and transition structures of diazene, formaldehyde, and methylenimine were determined using various DFT functionals and results were compared with MP 2 and MP 4 calculations. DFT reaction barriers were found to be consistently lower. For some reactions, such as OH + H₂→ H₂O + H, gradient-corrected functionals predict very low or nonexistent barriers. The hybrid Hartree–Fock–DFT adiabatic connection method (ACM ) often provides much better results in such cases. The performance of several density functionals, including ACM , was tested in calculations on over 100 atomization, hydrogenation, bond dissociation, and isodesmic reactions. The ACM functional provides consistently better geometries and reaction energetics than does any other functional studied. In cases where both HF and gradient-corrected DFT methods underestimate bond distances, the ACM geometries may be inferior to those predicted by gradient-corrected DFT methods. © 1995 John Wiley & Sons, Inc.     

New insight into the substituent effects on the hydrolytic deamination of saturated and unsaturated cytosine

Ab initio calculations were carried out to understand the effect of electron donating groups (EDG) and electron withdrawing groups (EWG) at the C5 position of cytosine (Cyt) and saturated cytosine (H₂Cyt) of the deamination reaction. Geometries of the reactants, transition states, intermediates, and products were fully optimized at the B3LYP/6-31G(d,p) level in the gas phase as this level of theory has been found to agree very well with G3 theories. Activation energies, enthalpies, and Gibbs energies of activation along with the thermodynamic properties (ΔE, ΔH, and ΔG) of each reaction were calculated. A plot of the Gibbs energies of activation (ΔG^‡) for C5 substituted Cyt and H₂Cyt against the Hammett σ-constants reveal a good linear relationship. In general, both EDG and EWG substituents at the C5 position in Cyt results in higher ΔG^‡ and lower σ values compared to those of H₂Cyt deamination reactions. C5 alkyl substituents ( H,  CH₃,  CH₂CH₃,  CH₂CH₂CH₃) increase ΔG^‡ values for Cyt, while the same substituents decrease ΔG^‡ values for H₂Cyt which is likely due to steric effects. However, the Hammett σ-constants were found to decrease at the C5 position of cytosine (Cyt) and saturated cytosine (H2Cyt) on the deamination reaction. Both ΔG^‡ and σ values decrease for the substituents Cl and Br in the Cyt reaction, while ΔG^‡ values increase and σ decrease in the H₂Cyt reaction. This may be due to high polarizability of bromine which results in a greater stabilization of the transition state in the case of bromine compared to chlorine. Regardless of the substituent at C5, the positive charge on C4 is greater in the TS compared to the reactant complex for both the Cyt and H₂Cyt. Moreover, as the charges on C4 in the TS increase compared to reactant, ΔG^‡ also increase for the C5 alkyl substituents ( H,  CH₃,  CH₂CH₃,  CH₂CH₂CH₃) in Cyt, while ΔG^‡ decrease in H₂Cyt. In addition, analysis of the frontier MO energies for the transition state structures shows that there is a correlation between the energy of the HOMO–LUMO gap and activation energies.     

Optimized structures and vibration frequencies of the ether–water complex: a DFT and FTIR study

The infrared spectrum of ether was studied using Fourier transform infrared spectroscopy in conjunction with the density functional theory (DFT). The optimized structures and vibrational frequencies of the ether·(H₂O) _n (n = 1–3) complexes were obtained at B3LYP/6-31G(d) theory levels. Compared to those of free-form ether, the C–O stretching vibrational frequencies of the ether–water complexes are found to shift to red by up to 39 cm^?1 with an increase in the C–O length of 0.016 Å. Meanwhile, the frequency of the O–H stretching modes of water in the complexes appears significantly redshifted to a varying degree. The DFT calculations suggest that these shifts are caused by the hydrogen bonding between ether and water.     

β-Position Electronic Effects on the Singlet–Triplet Gaps of Divalent Five-Membered Rings XC4H3M (M˭C,Si, and Ge)

Abstract

Full geometry optimizations were carried out on the singlet and triplet states of β-substituted divalent five-membered rings XC₄H₃M (X? ?NH₂, ?OH, ?CH₃ ?H, ?CH₃, ?Br, ?Cl, ?F, ?CF₃, and ?NO₂; M?C, Si, and Ge) by the B3LYP method by using 6-311++G** basis set. The thermal energy gaps, ΔE_t–s; enthalpy gaps, ΔH_t–s; and Gibbs free energy gaps, ΔG_t–s, between the singlet (s) and triplet (t) states of the above structures were calculated by using the GAUSSIAN 03 program. The ΔG_t–s of XC₄H₃C was changed in the order: X? ?Cl > ?Br > ?CH₃ > ?H > ?CF₃ > ?F > ?NO₂ > ?OH > ?NH₂. The changes of ΔG_t–s for XC₄H₃Si and XC₄H₃Ge were in the order: X? ?NH₂ > OH > F > Cl > Br > CH₃ > H > CF₃ > NO₂. The geometrical parameters, including bond lengths (R), bond angles (A), dihedral angles (D), natural bonding orbital (NBO) charge at atoms, HOMO and LUMO, and dipole moments, were presented and discussed.

Supplemental materials are available for this article. Go to the publisher's online edition of Phosphorus, Sulfur, and Silicon and the Related Elements to view the free supplemental file.

GRAPHICAL ABSTRACT      

A detailed theoretical study on the excited‐state hydrogen‐bonding dynamics and the proton transfer mechanism for a novel white‐light fluorophore

In this work, density functional theory (DFT) and time‐dependent DFT (TDDFT) methods were used to investigate the excited‐state dynamics of the excited‐state hydrogen‐bonding variations and proton transfer mechanism for a novel white‐light fluorophore 2‐(4‐[dimethylamino]phenyl)‐7‐hyroxy‐6‐(3‐phenylpropanoyl)‐4H‐chromen‐4‐one ( 1 ). The methods we adopted could successfully reproduce the experimental electronic spectra, which shows the appropriateness of the theoretical level in this work. Using molecular electrostatic potential (MEP) as well as the reduced density gradient (RDG) versus the product of the sign of the second largest eigenvalue of the electron density Hessian matrix and electron density (sign[λ₂]ρ), we demonstrate that an intramolecular hydrogen bond O1–H2···O3 should be formed spontaneously in the S₀ state. By analyzing the chemical structures, infrared vibrational spectra, and hydrogen‐bonding energies, we confirm that O1–H2·O3 should be strengthened in the S₁ state, which reveals the possibility of an excited‐state intramolecular proton transfer (ESIPT) process. On investigating the excitation process, we find the S₀ → S₁ transition corresponding to the charge transfer, which provides the driving force for ESIPT. By constructing the potential energy curves, we show that the ESIPT reaction results in a dynamic equilibrium in the S₁ state between the forward and backward processes, which facilitates the emission of white light.     

Importance of aliphatic C–H hydrogen bonding on anion recognition

We have designed and synthesised new anion receptors 1 and 2, both of their C–H groups were at the α positions to carbonyl groups and further polarised by the attached polarising substituents. This enabled us to study hydrogen bonding donor ability of C–H bonds. The polarising substituents are electron withdrawing cyano group for host 1, while charged pyridinium group for host 2. As expected from charge effects, host 2 shows roughly an order of magnitude higher binding constants against various anion guests than those of receptor 1. Since the magnitude of polarisation change should be greatest for C–H group among various hydrogen bonding groups, this indicates the importance of C–H hydrogen bonding. In contrast, the relative order of binding constants was the same for both host 1 and 2. The order of association constants was found to be (CH₃)₂POO^? > CH₃COO^? > C₆H₅COO^? > Cl^? > Br^?. DFT calculation results were in good agreement with experimental binding constants and confirmed the importance of charged group substitution. In addition, receptor 1 showed the highest association constant for dimethyl phosphinate, which is implicated in many metabolic diseases.     

Temperature-dependent polymorphism of N-(4-fluorophenyl)-1,5-dimethyl-1H-imidazole-4-carboxamide 3-oxide: experimental and theoretical studies on intermolecular interactions in the crystal state

X-ray analysis of N-(4-fluorophenyl)-1,5-dimethyl-1H-imidazole-4-carboxamide 3-oxide reveals the temperature-dependent polymorphism associated with the crystallographic symmetry conversion. The observed crystal structure transformation corresponds to a symmetry reduction from I4₁ /a (I) to P4₃ (II) space groups. The phase transition mainly concerns the subtle but clearly noticeable reorganization of molecules in the crystal space, with the structure of individual molecules left almost unchanged. The Hirshfeld surface analysis shows that various intermolecular contacts play an important role in the crystal packing, revealing graphically the differences in spatial arrangements of the molecules in both polymorphs. The N-oxide oxygen atom acts as a formally negatively charged hydrogen bonding acceptor in intramolecular hydrogen bond of N–H…O^? type. The combined crystallographic and theoretical DFT methods demonstrate that the observed intramolecular N-oxide N–H…O hydrogen bond should be classified as a very strong charge-assisted and closed-shell non-covalent interaction.     

Synthesis,XRD, spectral (IR,UV–Vis,NMR) characterization and quantum chemical exploration of benzoimidazole‐based hydrazones: A synergistic experimental‐computational analysis

Present study advocates the joint experimental and computational studies of two potent benzoimidazole‐based hydrazones with chemical formula C₂₃H₁₈F₂N₄O ( 5a ) and C₂₅H₂₂FN₅O₃ ( 5b ). Both 5a and 5b were synthesized and resolved into their crystal structures using SC‐XRD for the assessment of bond lengths, bond angles, unit cells and space groups. The structures of 5a and 5b were chemically characterized using infrared (FT‐IR), UV–Visible, nuclear magnetic resonance (¹H‐NMR and ¹³C‐NMR), EIMS and elemental analysis. DFT at M06‐2X/6‐31G(d,p) level of theory was performed to get optimized structures and countercheck the experimental findings. Overall, DFT findings show excellent concurrence with the experimental data which confirms the purity of both compounds. FMO, NBO analysis, MEP surfaces and nonlinear optical (NLO) properties were explored at same level of theory. UV–Vis analysis at TDDFT/M06‐2X/6‐31G(d,p) level of theory showed that 5b is red shifted with λ_max 331.69 nm as compared to 5a with λ_max 240.25 nm. Global reactivity parameters were estimated using energy of FMOs indicated the greater harness value than the softness values of 5a and 5b . NBO analysis confirmed that the presence of non‐covalent interactions, hydrogen bonding and hyper conjugative interactions are pivotal cause for the existence of 5a and 5b in the solid‐state. NLO results of 5a and 5b were observed better than standard molecule recommended the NLO activity of said molecules for optoelectronic applications.     

Cooperative Effect of Noncovalent Interactions on Tetrel Bonding in Halogenated Silanes

Tetrel bond, a weak noncovalent interaction between the σ-hole of a Group IV element (silicon in our case) and the cloud of an electronegative element (oxygen in our case) is the focus of this work. The percentage strengthening of tetrel bond has been investigated by optimizing 16 binary complexes of halogenated silane and water of general formula SiX_nH_4−n−H₂O and 16 ternary complexes, of general formula NaX−SiX_nH_4−n−H₂O, where X=F, Cl, Br and I and n=1, 2, 3 and 4 at various levels of theory defined within the formalism of density functional theory (DFT). With the addition of NaX, tetrel bond between Si and O in SiX_nH_4−n−H₂O gets strengthened up to 49 %, owing to cooperativity effect exerted by hydrogen bonding between X and H in the ternary complex NaX−SiX_nH_4−n−H₂O. In the series of complexes studied here, overall stabilization due to cooperativity lies between 10 kJ/mol to 170 kJ/mol. This large extent of reinforcement due to cooperativity has never been showcased before. The exceptional stabilization and reinforcement owe its genesis to the transformation of the ternary complex into a cluster orchestrated by the H-bonding in most of the cases and covalent bonding in few of the cases.     

Density functional theory and topological analysis on the hydrogen bonding interactions in cysteine‐thymine complexes

Hydrogen bonding interactions between amino acids and nucleic acid bases constitute the most important interactions responsible for the specificity of protein binding. In this study, complexes formed by hydrogen bonding interactions between cysteine and thymine have been studied by density functional theory. The relevant geometries, energies, and IR characteristics of hydrogen bonds (H‐bonds) have been systematically investigated. The quantum theory of atoms in molecule and natural bond orbital analysis have also been applied to understand the nature of the hydrogen bonding interactions in complexes. More than 10 kinds of H‐bonds including intra‐ and intermolecular H‐bonds have been found in complexes. Most of intermolecular H‐bonds involve O (or N) atom as H‐acceptor, whereas the H‐bonds involving C or S atom usually are weaker than other ones. Both the strength of H‐bonds and the structural deformation are responsible for the stability of complexes. Because of the serious deformation, the complex involving the strongest H‐bond is not the most stable structures. Relationships between H‐bond length (ΔR_X‐H), frequency shifts (Δv), and the electron density (ρ_b) and its Laplace (?²ρ_b) at bond critical points have also been investigated. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Density Functional Theory Study on Hydrogen Bonding Interaction of Catechin-(H2O)n

Density functional theory B3LYP method with 6‐31G* basis set has been used to optimize the geometries of the catechin, water and catechin‐(H₂O)_n complexes. The vibrational frequencies have been studied at the same level to analyze these complexes. Six and eleven stable structures for the catechin‐H₂O and catechin‐(H₂O)₂ have been found, respectively. Theories of atoms in molecules (AIM) and natural bond orbital (NBO) have been utilized to investigate the hydrogen bonds involved in all the systems. The interaction energies of all the complexes corrected by basis set superposition error, are from ?13.27 to ?83.56 kJ/mol. All calculations also indicate that there are strong hydrogen‐bonding interactions in catechin‐water complexes. The strong hydrogen‐bonding contributes to the interaction energies dominantly. The O–H stretching motions in all the complexes are red‐shifted relative to that of the monomer.     

An X‐ray crystallographic and density functional theory study of (3Z)‐4‐(5‐ethylsulfonyl‐2‐hydroxyanilino)pent‐3‐en‐2‐one and (3Z)‐4‐(5‐tert‐butyl‐2‐hydroxyanilino)pent‐3‐en‐2‐one

The Schiff base enaminones (3Z)‐4‐(5‐ethylsulfonyl‐2‐hydroxyanilino)pent‐3‐en‐2‐one, C₁₃H₁₇NO₄S, (I), and (3Z)‐4‐(5‐tert‐butyl‐2‐hydroxyanilino)pent‐3‐en‐2‐one, C₁₅H₂₁NO₂, (II), were studied by X‐ray crystallography and density functional theory (DFT). Although the keto tautomer of these compounds is dominant, the O=C—C=C—N bond lengths are consistent with some electron delocalization and partial enol character. Both (I) and (II) are nonplanar, with the amino–phenol group canted relative to the rest of the molecule; the twist about the N(enamine)—C(aryl) bond leads to dihedral angles of 40.5 (2) and −116.7 (1)° for (I) and (II), respectively. Compound (I) has a bifurcated intramolecular hydrogen bond between the N—H group and the flanking carbonyl and hydroxy O atoms, as well as an intermolecular hydrogen bond, leading to an infinite one‐dimensional hydrogen‐bonded chain. Compound (II) has one intramolecular hydrogen bond and one intermolecular C=O...H—O hydrogen bond, and consequently also forms a one‐dimensional hydrogen‐bonded chain. The DFT‐calculated structures [in vacuo, B3LYP/6‐311G(d,p) level] for the keto tautomers compare favourably with the X‐ray crystal structures of (I) and (II), confirming the dominance of the keto tautomer. The simulations indicate that the keto tautomers are 20.55 and 18.86 kJ mol⁻¹ lower in energy than the enol tautomers for (I) and (II), respectively.     

A Combined Experimental and Theoretical Electron Density Study of Intra‐ and Intermolecular Interactions in Thiourea S,S‐Dioxide

The thiourea S,S‐dioxide molecule is recognized as a zwitterion with a high dipole moment and an unusually long C? S bond. The molecule has a most interesting set of intermolecular interactions in the crystalline state—a relatively strong O???H? N hydrogen bond and very weak intermolecular C???S and N???O interactions. The molecule has C_s symmetry, and each oxygen atom is hydrogen‐bonded to two hydrogen atoms with O???H? N distances of 2.837 and 2.826 Å and angles of 176.61 and 158.38°. The electron density distribution is obtained both from Xray diffraction data at 110 K and from a periodic density functional theory (DFT) calculation. Bond characterization is made in terms of the analysis of topological properties. The covalent characters of the C? N, N? H, C? S, and S? O bonds are apparent, and the agreement on the topological properties between experiment and theory is adequate. The features of the Laplacian distributions, bond paths, and atomic domains are comparable. In a systematic approach, DFT calculations are performed based on a monomer, a dimer, a heptamer, and a crystal to see the effect on the electron density distribution due to the intermolecular interactions. The dipole moment of the molecule is enhanced in the solid state. The typical values of ρ_b and H_b of the hydrogen bonds and weak intermolecular C???S and N???O interactions are given. All the interactions are verified by the location of the bond critical point and its associated topological properties. The isovalue surface of Laplacian charge density and the detailed atomic graph around each atomic site reveal the shape of the valence‐shell charge concentration and provide a reasonable interpretation of the bonding of each atom.