Hydrogen bond and internal rotations barrier: DFT study on heavier group‐14 analogues of formamide

A theoretical study on heavier group‐14 substituting effect on the essential property of formamide, strong hydrogen bond with water and internal rotational barrier was performed within the framework of natural bond orbital (NBO) analysis and based on the density functional theory calculation. For heavier group‐14 analogues of formamide (YHONH₂, Y = Si, Ge and Sn), the n_N–π_Y=O conjugation strength does not always reduce as Y becomes heavier, for example, silaformamide and germaformamide have similar strength of delocalization. Heavier formamides prefer being H‐bond donors to form FYO–H₂O complexes to being H‐bond acceptors to form FYH–H₂O complexes. The NEDA analysis indicates that H‐bond energies of FYO–H₂O complexes increase as moving down group 14 due to concurrently stronger charge transfer (CT) and electrostatic attraction and for the FYH–H₂O complexes H‐bond strengths are similar. The model of CTs from FYO to H₂O differs from that at FYH–H₂O complexes, which are contributed not only by aligning lone‐pair orbital of O but also by another lone‐pair orbital. At two lowest lying excited states (the triplet and S₁ excited states), formamide and its heavier analogues form double H‐bonds with H₂O molecule at the same time. The barrier heights of internal rotation become gradually low from C to Sn, formamide (15.73 kcal/mol) > silaformamide (11.73 kcal/mol) > germaformamide (9.45 kcal/mol) > stannaformamide (7.50 kcal/mol) at the CCSD(T)/aug‐cc‐pVTZ//B3LYP/cc‐pVTZ level. NBO analysis indicates that the barrier does not only come from the n_N→π*_YO conjugation, and for heavier analogues of formamide, the n_N→σ*_YO hyperconjugation effect and steric effect considerably contribute to the overall rotational barrier. Copyright © 2013 John Wiley & Sons, Ltd.     

Raman spectroscopic study of the uranyl mineral,compreignacite, K2[(UO2)3O2(OH)3]2·7H2O

Raman spectra of the uranyl oxyhydroxy‐hydrated mineral compreignacite, K₂[(UO₂)₃O₂(OH)₃]₂·7H₂O, were measured and interpreted. Observed bands were attributed to the stretching and bending vibrations of uranyl units, molecular water and hydroxyl ions. U O bond lengths in uranyl and O HO hydrogen bond lengths were inferred from the spectra and compared with those from the X‐ray single crystal structure data. The importance of this spectroscopic study rests with the ability to analyze very small amounts of the mineral. Copyright © 2008 John Wiley & Sons, Ltd.     

Raman spectroscopic study of the uranyl mineral metauranospinite Ca[(UO2)(AsO4)]2·8H2O

Raman spectra of metauranospinite Ca[(UO₂)(AsO₄)]₂·8H₂O complemented with infrared spectra were studied. Observed bands were assigned to the stretching and bending vibrations of (UO₂)²⁺ and (AsO₄)³⁻ units and of water molecules. U O bond lengths in uranyl and O H···O hydrogen bond lengths were calculated from the Raman and infrared spectra. Copyright © 2009 John Wiley & Sons, Ltd.     

Raman spectroscopic study of the hydrogen and arsenate bonding environment in isostructural synthetic arsenates of the variscite group—M3+ AsO4·2H2O (M3+ = Fe,Al, In and Ga): implications for arsenic release in water

The Raman spectra of synthetic compounds equivalent to the variscite group: FeAsO₄·2H₂O AlAsO₄·2H₂O, GaAsO₄·2H₂O, and InAsO₄·2H₂O are reported. In particular, upon comparison of FeAsO₄·2H₂O to AlAsO₄·2H₂O, it is observed that the Type II (weak) H‐bond lengths in the latter are slightly longer, which is postulated to affect the stability (As release) in water at pH 5 and 7. Arsenate stretching and bending vibrations were found to be distinct in terms of spectral structure and therefore well suited for fingerprinting. The calculated As O bond strengths from existing crystallographic data showed no significant variations. The strongest ν₁ (AsO₄³⁻) stretch was used to monitor the As O bonding interactions in the four As O M units, where a shift of 114 cm⁻¹ was observed in the order FeAsO₄·2H₂O (lowest) < InAsO₄·2H₂O < GaAsO₄·2H₂O < AlAsO₄·2H₂O (highest); this order also followed exactly the measured arsenic release of these phases. This shift in ν₁ (AsO₄³⁻) position was rationalized to stem from the differences in the electronegativities of the M³⁺ cations. The trends mentioned above were verified and found to also hold for the isostructural phosphate analogues strengite (FePO₄·2H₂O) and variscite (AlPO₄·2H₂O) using published data. Therefore, it is postulated that, as observed with the stability of solution complexes, there may be a correlation between the electronegativity of the M³⁺ cation in these isostructural phases and their stability (As or P release) in water. Copyright © 2010 John Wiley & Sons, Ltd.     

Vibrational analysis of the H4I2O102− ion in CuH4I2O10·6H2O

Vibrational wavenumbers (IR and Raman) have been calculated for the diperiodate ion H₄I₂O₁₀²⁻ on the basis of a DFT method and assigned to experimental wavenumbers obtained from CuH₄I₂O₁₀·6H₂O. To obtain vibrational wavenumbers in the range comparable to the experiment it was necessary to use the complex [(H₄I₂O₁₀)₇(Cu(H₂O)₆)₆]²⁻. Smaller complexes lead to much too high wavenumbers for the O‐H stretching vibrations and to too small wavenumbers in the range of the internal vibrations of the anion. On the basis of the results of the calculations an assignment of the Raman lines observed for CuH₄I₂O₁₀· 6H₂O to the vibrational modes is given. Copyright © 2008 John Wiley & Sons, Ltd.     

Raman spectroscopic study of the uranyl sulphate mineral jáchymovite (UO2)8(SO4)(OH)14· 13H2O

Raman spectra of jáchymovite, (UO₂)₈(SO₄)(OH)₁₄·13H₂O, were studied, complemented with infrared spectra, and compared with published Raman and infrared spectra of uranopilite, [(UO₂)₆(SO₄)O₂(OH)₆(H₂O)₆]·6H₂O. Bands related to the stretching and bending vibrations of (UO₂)²⁺, (SO₄)²⁻, (OH)⁻ and water molecules were assigned. U O bond lengths in uranyl and O H· · ·O hydrogen bond lengths were calculated from the Raman and infrared spectra. Copyright © 2009 John Wiley & Sons, Ltd.     

Raman microscopy of haidingerite Ca(AsO3OH)·H2O and brassite Mg(AsO3OH)·4H2O

Raman spectroscopy has been used to study the arsenate minerals haidingerite Ca(AsO₃OH)·H₂O and brassite Mg(AsO₃OH)·4H₂O. Intense Raman bands in the haidingerite spectrum observed at 745 and 855 cm⁻¹ are assigned to the (AsO₃OH)²⁻ν₃ antisymmetric stretching and ν₁ symmetric stretching vibrational modes. For brassite, two similarly assigned intense bands are found at 809 and 862 cm⁻¹. The observation of multiple Raman bands in the (AsO₃OH)²⁻ stretching and bending regions suggests that the arsenate tetrahedrons in the crystal structures of both minerals studied are strongly distorted. Broad Raman bands observed at 2842 cm⁻¹ for haidingerite and 3035 cm⁻¹ for brassite indicate strong hydrogen bonding of water molecules in the structure of these minerals. OH···O hydrogen‐bond lengths were calculated from the Raman spectra based on empirical relations. Copyright © 2009 John Wiley & Sons, Ltd.     

Hydrogen bonding and excited state properties of the photoexcited hydrogen‐bonded (E)‐S‐(2‐aminopropyl) 3‐(4‐hydroxyphenyl)prop‐2‐enethioate complexes

The time‐dependent density functional theory (TDDFT) method has been performed to investigate the excited state and hydrogen bonding dynamics of a series of photoinduced hydrogen‐bonded complexes formed by (E)‐S‐(2‐aminopropyl) 3‐(4‐hydroxyphenyl)prop‐2‐enethioate with water molecules in vacuum. The ground state geometric optimizations and electronic transition energies as well as corresponding oscillator strengths of the low‐lying electronic excited states of the (E)‐S‐(2‐aminopropyl) 3‐(4‐hydroxyphenyl)prop‐2‐enethioate monomer and its hydrogen‐bonded complexes O₁‐H₂O, O₂‐H₂O, and O₁O₂‐(H₂O)₂ were calculated by the density functional theory and TDDFT methods, respectively. It is found that in the excited states S₁ and S₂, the intermolecular hydrogen bond formed with carbonyl oxygen is strengthened and induces an excitation energy redshift, whereas the hydrogen bond formed with phenolate oxygen is weakened and results in an excitation energy blueshift. This can be confirmed based on the excited state geometric optimizations by the TDDFT method. Furthermore, the frontier molecular orbital analysis reveals that the states with the maximum oscillator strength are mainly contributed by the orbital transition from the highest occupied molecular orbital to the lowest unoccupied molecular orbital. These states are of locally excited character, and they correspond to single‐bond isomerization while the double bond remains unchanged in vacuum.     

Effect of proton donors on the intramolecular coordination C=O→Si–F in (acyloxymethyl)trifluorosilanes. Ab initio,DFT and FTIR study,QTAIM analysis

The intramolecular С=O→Si coordination in H‐complexes of (acetoxymethyl)trifluorosilane and (benzoyloxymethyl)trifluorosilane with proton donors HCl, PhOH, MeOH, and CHCl₃ was investigated by density functional theory and second‐order Møller‐Plesset perturbation theory (MP2) methods. Interrelation and mutual influence of the intramolecular coordination bond С=O→Si and intermolecular hydrogen bonds C=O···H and Si–F···H in H‐complexes was established using the AIM and NBO analyses. The С=O→Si coordination is weakened by the C=O···H hydrogen bonding but enhanced by the Si–F_ax···H hydrogen bonding. The structure of H‐complexes of (acetoxymethyl)trifluorosilane with proton donors in solution was determined by comparing the ν(C=O) and ν(Si–F) frequencies calculated using the conductor‐like polarizable continuum model and their experimental Fourier transform infrared values. Copyright © 2014 John Wiley & Sons, Ltd.     

Raman spectroscopy of hydrogen‐arsenate group (AsO3OH) in solid‐state compounds: cobalt mineral phase burgessite Co2(H2O)4[AsO3OH]2·H2O

Raman spectrum of burgessite, Co₂(H₂O)₄[AsO₃OH]₂· H₂O, was studied, interpreted and compared with its infrared spectrum. The stretching and bending vibrations of (AsO₃) and As‐OH units, as well as the stretching, bending and libration modes of water molecules and hydroxyl ions were assigned. The range of O H···O hydrogen bond lengths was inferred from the Raman and infrared spectra of burgessite. The presence of (AsO₃OH)²⁻ units in the crystal structure of burgessite was proved, which is in agreement with its recently solved crystal structure. Raman and infrared spectra of erythrite inferred from the RRUFF database are used for comparison. Copyright © 2010 John Wiley & Sons, Ltd.     

A Raman spectroscopic study of bukovskýite Fe2(AsO4)(SO4)(OH)· 7H2O,a mineral phase with a significant role in arsenic migration

The Raman spectrum of bukovskýite [Fe³⁺₂(OH)(SO₄)(AsO₄)· 7H₂O] has been studied and compared with that of an amorphous gel containing specifically Fe, As and S, which is understood to be an intermediate product in the formation of bukovskýite. The observed bands are assigned to the stretching and bending vibrations of (SO₄)²⁻ and (AsO₄)³⁻ units, stretching and bending vibrations and vibrational modes of hydrogen‐bonded water molecules, stretching and bending vibrations of hydrogen‐bonded (OH)⁻ ions and Fe³⁺ (O,OH) units. The approximate range of O H···O hydrogen bond lengths was inferred from the Raman spectra. Raman spectra of crystalline bukovskýite and of the amorphous gel differ in that the bukovskýite spectrum is more complex, the observed bands are sharp and the degenerate bands of (SO₄)²⁻ and (AsO₄)³⁻ are split and more intense. Lower wavenumbers of δ H₂O bending vibrations in the spectrum of the amorphous gel may indicate the presence of weaker hydrogen bonds compared to those in bukovskýite. Copyright © 2011 John Wiley & Sons, Ltd.     

Elaborating the excited state behavior of 2‐(4′‐N,N‐dimethylaminophenyl)‐imidazo[4,5‐c]pyridine coupling with methanol solvent

We present a theoretical investigation about the excited state dynamical mechanism of 2‐(4′‐N,N‐dimethylaminophenyl)‐imidazo[4,5‐c]pyridine (DMAPIP‐c). Within the framework of density functional theory and time‐dependent density functional theory methods, we reasonably repeat the experimental electronic spectra, which further confirm the theoretical level used in this work is feasible. Given the best complex model, 3 methanol (MeOH) solvent molecules should be connected with DMAPIP‐c forming DMAPIP‐c‐MeOH complex in both ground state and excited state. Exploring the changes about bond lengths and bond angles involved in hydrogen bond wires, we find the O7‐H8···N9 one should be largely strengthened in the S₁ state, which plays an important role in facilitating the excited state intermolecular proton transfer (ESIPT) process. In addition, the analyses about infrared vibrational spectra also confirm this conclusion. The redistribution about charges distinguished via frontier molecular orbitals based on the photoexcitation, we do find tendency of ESIPT reaction due to the most charges located around N9 atom in the lowest unoccupied molecular orbital. Based on constructing the potential energy curves of both S₀ and S₁ states, we not only confirm that the ESIPT process should firstly occur along with hydrogen bond wire O7‐H8···N9, but also find a low potential energy barrier 8.898 kcal/mol supports the ESIPT reaction in the S₁ state forming DMAPIP‐c‐MeOH‐PT configuration. Subsequently, DMAPIP‐c‐MeOH‐PT could twist its dimethylamino moiety with a lower barrier 3.475 kcal/mol forming DMAPIP‐c‐MeOH‐PT‐TICT structure. Our work not only successfully explains previous experimental work but also paves the way for the further applications about DMAPIP‐c sensor in future.     

The structure and vibrational spectral parameters of a complex of HF with the planar (H<Subscript>2</Subscript>CO)<Subscript>2</Subscript> dimer

Equilibrium nuclear configurations of the planar formaldehyde homodimer (H₂CO)₂ and the (H₂CO)₂···HF complex are determined in the MP2/6-311++G(3df, 3pd) approximation taking into account the superposition error of basis sets of monomers. Harmonic values of the frequencies and intensities of fundamental transitions between vibrational states of these hydrogen-bonded complexes were calculated using the Gaussian 09 package of programs. Anharmonic values of the frequencies and intensities of the ν(H–F) stretching vibration and several intermolecular vibrations in the (H₂CO)₂···HF trimer were obtained from variational solutions of one-, two-, and three-dimensional vibrational Schrödinger equations. The anharmonic influence of the C=O and hydrogen bond O···H–F stretching vibrations, as well as of librational vibrations of monomers, on the spectral parameters of the strongest ν(H–F) absorption band of trimer was studied.     

Raman spectroscopic study of the uranyl selenite mineral marthozite Cu[(UO2)3(SeO3)2O2]·8H2O

The mineral marthozite, a uranyl selenite, has been characterised by Raman spectroscopy at 298 K. The bands at 812 and 797 cm⁻¹ were assigned to the symmetric stretching modes of the (UO₂)²⁺ and (SeO₃)²⁻ units, respectively. These values gave the calculated U O bond lengths in uranyl of 1.799 and/or 1.814 Å. Average U O bond length in uranyl is 1.795 Å, inferred from the X‐ray single crystal structure analysis of marthozite by Cooper and Hawthorne. The broad band at 869 cm⁻¹ was assigned to the ν₃ antisymmetric stretching mode of the (UO₂)²⁺ (calculated U O bond length 1.808 Å). The band at 739 cm⁻¹ was attributed to the ν₃ antisymmetric stretching vibration of the (SeO₃)²⁻ units. The ν₄ and the ν₂ vibrational modes of the (SeO₃)²⁻ units were observed at 424 and 473 cm⁻¹. Bands observed at 257, and 199 and 139 cm⁻¹ were assigned to OUO bending vibrations and lattice vibrations, respectively. O H···O hydrogen bond lengths were inferred using Libowiztky's empirical relation. The infrared spectrum of marthozite was studied for complementation. Copyright © 2008 John Wiley & Sons, Ltd.     

Hydrogen-bonding studies of amino acid side-chains with DNA base pairs

The interactions of the amino acid side-chains arginine (ARG), aspartic acid (ASP), asparagine (ASN), lysine (LYS) and serine (SER) with nucleic acid base pairs have been investigated using theoretical methods. The interaction energy of the short intermolecular N–H?···?N, N–H?···?O, O–H?···?O, O–H?···?N, C–H?···?O and C–H?···?N hydrogen bonds present in both isolated base pairs and complexes and its role in providing stability to the complexes have been explored. The homonuclear interactions are found to be stronger than the heteronuclear interactions. An improper hydrogen bond has been observed for some of the N–H?···?O and N–H?···?N hydrogen-bond interactions with the contraction of the N–H bond varying from 0.001 to 0.0260?Å and the corresponding blue shift of the stretching frequency by 4–291?cm^?1. Localized molecular orbital energy decomposition analysis (LMOEDA) reveals that the major contributions to the energetics are from the long-range polarization (PL) interaction, and the short-range attractive (ES, EX) and repulsive (REP) interactions. The Bader's atoms in molecules (AIM) theory shows good correlation for the electron density and its Laplacian at the bond critical points (BCP) with the N–H?···?N and N–H?···?O hydrogen-bond lengths in the complexes, and gives a proper explanation for the stability of the structure. The charge-transfer from the proton acceptor to the antibonding orbital of the X–H bond in the complexes was studied using natural bond orbital (NBO) analysis.     

Theoretical studies on the nature and strength of an intermolecular non-covalent Te•••π interaction

ABSTRACT

DFT and MP2 calculations were used to determine the nature of non-covalent tellurium–π interactions in R₂Te???C₆H₆ (R = H, F, Cl, CH₃) and C₄H₄Te???C₆H₆ systems. The results showed that the strength of Te···π interaction follows the order F₂Te > Cl₂Te > tellurophene > H₂Te > Me₂Te. Also, the F₂X···π system complexes (X = Te or Se, π system = C₆F₆, C₆(CH₃)₆, Cr(C₆H₆)₂ and coronene) were studied for investigating the direction of charge flow in Te···π interaction. The obtained data expressed that the existence of electron withdrawing group on Te atom increases the strength of Te???π interaction while the fluorine atoms on benzene ring decrease it. The breakdown of ΔE_int in the R₂Te···C₆H₆ (R = H, F, Cl, CH₃) and C₄H₄Te···C₆H₆ systems using two dispersion corrected DFT methods showed that when the R group on divalent tellurium atom is an electron withdrawing substituent, the contribution of ΔE_elstat and ΔE_orb in total interaction energy increases and the value of ΔE_int is relatively large. The present data also showed that the intermolecular Te···π interactions are slightly stronger than corresponding Se···π interactions.     

Density functional theory study of substituent effects on gas‐phase heterolytic Fe–O and Fe–S bond energies of m‐G‐C6H4OFe(CO)2(η5‐C5H5) and m‐G‐C6H4SFe(CO)2(η5‐C5H5)

The knowledge of accurate bond strengths is a fundamental basis for a proper analysis of chemical reaction mechanisms. Quantum chemical calculations at different levels of theory have been used to investigate heterolytic Fe–O and Fe–S bond energies of (meta‐substituted phenoxy)dicarbonyl(η⁵‐cyclopentadienyl) iron [m‐G‐C₆H₄OFp ( 1 )] and (meta‐substituted benzenethiolato)dicarbonyl(η⁵‐cyclopentadienyl) iron [m‐G‐C₆H₄SFp ( 2 )] complexes. In this study, Fp is (η⁵‐C₅H₅)Fe(CO)₂, and G is NO₂, CN, COMe, CO₂Me, CF₃, Br, Cl, F, H, Me, MeO, and NMe₂. The results show that Tao–Perdew–Staroverov–Scuseria and Becke's power‐series ansatz from 1997 with dispersion corrections functionals can provide the best price/performance ratio and accurate predictions of ΔH_het(Fe–O)'s and ΔH_het(Fe–S)'s. The excellent linear free energy relations [r = 1.00 (g, 1e), 1.00 (g, 2b)] among the ΔΔH_het (Fe–O)'s and δΔG⁰ of O?H bonds of m‐G‐C₆H₄OH or ΔΔH_het(Fe–S)'s and ΔpK_a's of S?H bonds of m‐G‐C₆H₄SH imply that the governing structural factors for these bond scissions are similar. And, the linear correlations [r = ?0.97 (g, 1 g), ?0.97 (g, 2 h)] among the ΔΔH_het (Fe–O)'s or ΔΔH_het(Fe–S)'s and the substituent σ_m constants show that these correlations are in accordance with Hammett linear free energy relationships. The inductive effects of these substituents and the basis set effects influence the accuracy of ΔH_het(Fe–O)'s or ΔH_het(Fe–S)'s. The ΔΔH_het(Fe–O)'s(g) (1) and ΔΔH_het(Fe–S)'s(g)(2) follow the capto‐dative Principle. The substituent effects on the Fe–O bonds are much stronger than those on the less polar Fe–S bonds. Insight from this work may help the design of more effective catalytic processes. Copyright © 2016 John Wiley & Sons, Ltd.     

Raman spectroscopic study of the arsenite mineral vajdakite [(Mo6+O2)2(H2O)2As3+2O5]·H2O

Raman spectra of vajdakite, [(Mo⁶⁺O₂)₂(H₂O)₂As O₅]·H₂O, were studied and interpreted in terms of the structure of the mineral. The Raman spectra were compared with the published infrared spectrum of vajdakite. The presence of dimolybdenyl and diarsenite units and of hydrogen bonded water molecules was inferred from the Raman spectra which supported the known and published crystal structure of vajdakite. Mo O and O H···O bond lengths were calculated from the Raman spectra. Copyright © 2009 John Wiley & Sons, Ltd.     

An ab initio study on substituent and cooperative effects in bifurcated fluorine bonds

Bifurcated fluorine bond (BFB) interactions are studied in model binary complexes pairing N-formyl formamide derivatives and FX molecules (X = F, CN, NC, CF₃ and CCH) by means of ab initio calculations. The calculated F···O binding distances in these complexes are in the range of 2.813–3.048 Å. The corresponding interaction energies lie in a narrow range, from?2.25 to ?16.49 kJ/mol. The nature of BFBs is analysed by a vast number of methods including molecular electrostatic potential, quantum theory of atoms in molecules, non-covalent interaction index and natural bond orbital methods. According to the energy decomposition analysis, the electrostatic and dispersion effects have a dominant role in the formation of these complexes. The formation of a hydrogen- and lithium-bonding interaction tends to increase the strength of BFBs in the ternary XF:NFF-H:NH₃ and XF:NFF-Li:NH₃ complexes, respectively.     

Halogen bond between hypervalent halogens YF3/YF5 (Y=Cl,Br, I) and H2X (X= O,S, Se)

ABSTRACT

The complexes of H₂X (X?=?O, S, Se) with hypervalent halogens YF₃ and YF₅ (Y?=?Cl, Br, I) have been studied. The σ-hole on the Y atom participates in a halogen bond with the lone pair on the chalcogen atom. In addition, some secondary interactions coexist with the halogen bond in most complexes. The interaction energy correlates with the nature of both X and Y atoms. In most cases, the complex is more stable for the heavier Y atom and the lighter X atom. Of course, there are some exceptions in H₂X···YF₃. YF₃ forms a more stable complex with H₂X than does YF₅. These complexes are dominated by electrostatic interaction and the halogen bond involving H₂S and H₂Se exhibits some covalent character.

Halogen bond plays an important role in chemical reactions and multivalent halogens can regulate chemical reactions by participating in a halogen bond. Thus we compare the effect of the chalcogen electron donor on the strength and nature of halogen bonding involving multivalent halogens.