The effect of hydrogen bonding on structural parameters : IV. An ab initio study of formamide—ammonia complexes

Four hydrogen-bonded formamide—ammonia complexes have been studied by ab initio calculations, two where the amino group acts as a donor and two where the carbonyl oxygen is acceptor. In all cases the formation of a hydrogen bond leads to increased conjugation, expressed as a shortening of the CN bond and a corresponding lengthening of the CO bond. In two of the complexes the effect of varying the hydrogen bond length has been studied in some detail. It is found that the effect on the conjugated system depends on the length of the hydrogen bond. Potential functions for the N—HN and N—HO hydrogen bonds have been derived.     

The effect of hydrogen bonding on structural parameters I: An ab initio study of the keto and enol tautomers of formamide and their hydrogen bonded dimers

In order to study the variation of CO and CN bond lengths as functions of the hydrogen bond length, a series of ab initio calculations have been performed on the keto and enol tautomers of formamide. The formation of hydrogen bonds leads to an increase in the conjugation of the NCO fragment. This increase is expressed as a lengthening of the double bonds and a corresponding shortening of the single bonds. These changes are found to vary with the length of the hydrogen bonds and analytical expressions for these variations of the bond lengths have been derived. The potential functions for dimerization, i.e. formation of, respectively, two N-H ·· O and two O-H ·· N hydrogen bonds have also been found. The results obtained indicate significant differences between the two types of hydrogen bonds.     

Elongation of phenoxide C-O bonds due to formation of multifold hydrogen bonds: statistical, experimental, and theoretical studies

Statistical studies using the Cambridge Structural Database have revealed that there are several elongated phenoxide C-O bonds. They are characterized by the formation of 3-fold (or occasionally 2-fold) hydrogen bonds to the phenoxide oxygen atoms, and their mean bond length extends up to 1.320 ?, which is quite different from the theoretically predicted carbon-oxygen bond length of C(6)H(5)O(-) (1.26 ?). Elongated phenoxide C-O bonds associated with the formation of 3-fold hydrogen bonds were also observed in the X-ray structures of proton-transfer complexes (2X-O(-))(TEAH(+))s derived from 5'-X-substituted 5,5'-dimethyl-1,1':3',1'-terphenyl-2,2',2'-triols (2X-OHs, where X = NO(2), CN, COOCH(3), Cl, F, H, and CH(3)) and triethylamine (TEA). By comparing the X-ray structures, C-O bond elongation was found to be only slightly affected by an electron-withdrawing substituent at the para position (X). This along with strong bathochromic shifts of N-H(···O(-)) and O-H(···O(-)) stretching vibrations in the IR spectra indicates that the elongated C-O bonds in (2X-O(-))(TEAH(+))s essentially have single-bond character. This is further confirmed by molecular orbital calculations on a model complex, showing that the negatively charged phenoxide oxygen atom is no longer conjugated to the central benzene ring, and the NICS values of the three benzene rings are virtually identical. However, C-O bond elongation in (2X-O(-))(TEAH(+))s was considerably influenced by a change in the hydrogen-bond geometry. This also suggests that hydrogen bonds significantly affect phenoxide C-O bond elongation.     

胞嘧啶与一氧化碳复合物的结构与性质

在B3LYP/6-311+G**水平上对胞嘧啶…CO复合物体系进行了理论计算, 发现了6个能量极小的复合物. 其结合方式是CO的C或O原子与胞嘧啶的N—H键形成氢键, 最稳定的复合物的结合能为-8.72 kJ·mol-1. CO的C原子与胞嘧啶的结合具有更强的优势, C原子结合的复合物中CO的键长缩短, 而O结合的复合物中CO键长伸长. 同时, 对复合物的振动分析发现, 在C原子结合的复合物中CO的伸缩频率蓝移, 而O结合的复合物中CO伸缩频率是红移的.     

Complexes H2CO:PXH2 and HCO2H : PXH2 for X=NC,F, Cl,CN, OH,CCH, CH3, and H: Pnicogen Bonds and Hydrogen Bonds

Ab initio MP2/aug’-cc-pVTZ calculations have been carried out to investigate H₂CO : PXH₂ pnicogen-bonded complexes and HCO₂H : PXH₂ complexes that are stabilized by pnicogen bonds and hydrogen bonds, with X=NC, F, Cl, CN, OH, CCH, CH₃, and H. The binding energies of these complexes exhibit a second-order dependence on the O−P distance. DFT-SAPT binding energies correlate linearly with MP2 binding energies. The HCO₂H : PXH₂ complexes are stabilized by both a pnicogen bond and a hydrogen bond, resulting in greater binding energies for the HCO₂H : PXH₂ complexes compared to H₂CO : PXH₂. Neither the O−P distance across the pnicogen bond nor the O−P distance across the hydrogen bond correlates with the binding energies of these complexes. The nonlinearity of the hydrogen bonds suggests that they are relatively weak bonds, except for complexes in which the substituent X is either CH₃ or H. The pnicogen bond is the more important stabilizing interaction in the HCO₂H : PXH₂ complexes except when the substituent X is a more electropositive group. EOM-CCSD spin-spin coupling constants ^1pJ(O−P) across pnicogen bonds in H₂CO:PXH₂ and HCO₂H : PXH₂ complexes increase as the O−P distance decreases, and exhibit a second order dependence on that distance. There is no correlation between ^2hJ(O−P) and the O−P distance across the hydrogen bond in the HCO₂H : PXH₂ complexes. ^2hJ(O−P) coupling constants for complexes with X=CH₃ and H have much greater absolute values than anticipated from their O−P distances.     

Geometric isotope effect of various intermolecular and intramolecular C-H...O hydrogen bonds, using the multicomponent molecular orbital method

The geometric isotope effect (GIE) of sp- (acetylene-water), sp(2)- (ethylene-water), and sp(3)- (methane-water) hybridized intermolecular C-H...O and C-D...O hydrogen bonds has been analyzed at the HF/6-31++G level by using the multicomponent molecular orbital method, which directly takes account of the quantum effect of proton/deuteron. In the acetylene-water case, the elongation of C-H length due to the formation of the hydrogen bond is found to be greater than that of C-D. In contrast to sp-type, the contraction of C-H length in methane-water is smaller than that of C-D. After the formation of hydrogen bonds, the C-H length itself in all complexes is longer than C-D and the H...O distance is shorter than D...O, similar to the GIE of conventional hydrogen bonds. Furthermore, the exponent (alpha) value is decreased with the formation of the hydrogen bond, which indicates the stabilization of intermolecular C-H...O hydrogen bonds as well as conventional hydrogen bonds. In addition, the geometric difference induced by the H/D isotope effect of the intramolecular C-H...O hydrogen bond shows the same tendency as that of intermolecular C-H...O. Our study clearly demonstrates that C-H...O hydrogen bonds can be categorized as typical hydrogen bonds from the viewpoint of GIE, irrespective of the hybridizing state of carbon and inter- or intramolecular hydrogen bond.     

Contribution of multicentered short hydrogen bond arrays to potency of active site-directed serine protease inhibitors

We describe and compare the pH dependencies of the potencies and of the bound structures of two inhibitor isosteres that form multicentered short hydrogen bond arrays at the active sites of trypsin, thrombin, and urokinase type plasminogen activator (urokinase or uPA) over certain ranges of pH. Depending on the pH, short hydrogen bond arrays at the active site are mediated by two waters, one in the oxyanion hole (H(2)O(oxy)) and one on the other (S2) side of the inhibitor (H(2)O(S2)), by one water (H(2)O(oxy)), or by no water. The dramatic variation in the length of the active site hydrogen bonds as a function of pH, of inhibitor, and of enzyme, along with the involvement or absence of ordered water, produces a large structural manifold of active site hydrogen bond motifs. Diverse examples of multicentered and two-centered short hydrogen bond arrays, both at and away from the active site, recently discovered in several protein crystal systems, suggest that short hydrogen bonds in proteins may be more common than has been recognized. The short hydrogen bond arrays resemble one another with respect to ionic nature, highly polar environment, multitude of associated ordinary hydrogen bonds, and disparate pK(a) values of participating groups. Comparison of structures and K(i) values of trypsin complexes at pH values where the multicentered short hydrogen bond arrays mediating inhibitor binding are present or absent indicate that these arrays have a minor effect on inhibitor potency. These features suggest little covalent nature within the short hydrogen bonds, despite their extraordinary shortness (as short as 2.0 A).     

Hydrogen‐bonded complexes of nicotine with simple alcohols

Ab initio and density functional theory studies have been performed on the hydrogen‐bonded complexes of neutral and protonated nicotine with ethanol, methanol, and trifluromethanol to explore their relative stability in a systematic way. Among all the hydrogen‐bonded nicotine complexes considered here, protonated forms in nicotine–ethanol and nicotine–methanol, and neutral form in nicotine–trifluromethanol complexes have been found to be the most stable. In the former two complexes, the proton attached to the pyrrolidine nitrogen acts as a strong hydrogen bond donor, whereas the pyrrolidine nitrogen atom acts as a hydrogen bond acceptor in the latter case. Neutral complex of nicotine with trifluromethanol has been found to possess a very short hydrogen bond (1.57 Å) and basis set superposition error corrected hydrogen bond energy value of 19 kcal/mol. The nature of the various hydrogen bonds formed has been investigated through topological aspects using Bader's atoms in molecules theory. From the calculated topological results, excellent linear correlation is shown to exist among the hydrogen bond length, electron density, and its Laplacian at the bond critical points for all the complexes considered. The natural bond orbital analysis has been carried out to investigate the charge transfer in the nicotine alcohol complexes. In contrast to the blue shifting behavior that is generally exhibited by other C? H···O hydrogen bonds involving sp³ carbon atom, the C? H···O hydrogen bond in the protonated nicotine–ethanol and methanol complexes has been found to be proper with red shifting in nature. © 2011 Wiley Periodicals, Inc.     

Effects of sugar ring puckering, anti-syn interconversion and intramolecular interactions on N-glycosidic bond cleavage in 3-methyl-2��-deoxyadenosine and 2��-deoxyadenosine

The effects of structural parameters and intramolecular interactions on N-glycosidic bond length in 3-methyl-2??- deoxyadenosine (3MDA) and 2??-deoxyadenosine (DA) were investigated employing quantum mechanical methods. All calculations were performed at B3LYP/6-311++G** level in the gas phase. The N-glycosidic bond length strongly depends on sugar configuration; it is shorter in syn conformation relative to anti in many cases where they have the same sugar ring configuration. The sugar conformation can influence the N-glycosidic bond through interaction with the O4?? atom. The impact of intramolecular improper hydrogen bonds and H-H bonding interactions on N-glycosidic bond length was investigated in DA and 3MDA and their modeled structures. Improper hydrogen bonds decrease N-glycosidic bond length while H-H bonding interactions increase it.     

Theoretical study of the symmetry of the (OH...O)- hydrogen bonds in vinyl alcohol-vinyl alcoholate systems

The interactions between substituted vinyl alcohols and vinyl alcoholates (X = NH(2), H, F, Cl, CN) are studied at the B3LYP/6-311++G(d,p) level of theory. In a first step, the conformation of the monomers is investigated and the proton affinities (PA(A(-))) of the enolates are calculated. The enols and enolates are held together by strong (OH...O)(-) hydrogen bonds, the hydrogen bond energies ranging from 19.1 to 34.6 kcal mol(-1). The optimized O...O distances are between 2.414 and 2.549 A and the corresponding OH distances from 1.134 and 1.023 A. The other geometry parameters such as C[double bond]C or CO distances also indicate that, in the minimum energy configuration, the hydrogen bonds are characterized by a double well potential. The Mulliken charges on the different atoms of the proton donors and proton acceptors and the frequencies of the nu(OH) stretching vibrations agree with this statement. All the data indicate that the hydrogen bonds are the strongest in the homomolecular complexes. The transition state for hydrogen transfer is located with the transition barrier estimated to be about zero. Upon addition of the zero-point vibration energies to the total potential energy, the barrier vanishes. This is a characteristic feature of low-barrier hydrogen bonds (LBHBs). The hydrogen bond energies are correlated to the difference 1.5 PA(AH) - PA(A(-)). The correlation predicts different energies for homomolecular hydrogen bonds, in agreement with the theoretical calculations. Our results suggest that a PA (or pK(a)) match is not a necessary condition for forming LBHBs in agreement with recent data on the intramolecular hydrogen bond in the enol form of benzoylacetone (J. Am. Chem. Soc. 1998, 120, 12117).     

Electron-induced phase transition in hydrogen-bonded solid-state 2-pyridone

This paper presents the results of experimental studies of hydrogen-bonded 2-pyridone crystal IR spectra. Spectral studies have demonstrated the existence of two anhydrous solid-state phases of each compound, namely the α and the β phases. Hydrogen bonds in the high-temperature α phase of these crystals have been estimated to be 40% stronger than the hydrogen bonds in the β phase, which are stable at room temperature. The mechanism of the phase transition in the solid-state 2-pyridone is proposed on the basis of the IR spectral data. This was possible by taking into account small changes in the geometry of heterocyclic molecular skeletons, which accompany the electron density redistribution in the hydrogen bonds occurring during the transition. The phase transition is connected with a partial change in the hydrogen bond nature from the N(+)-H···O(-) in the α phase, to the N-H···O hydrogen bonds in the β phase crystals.     

Theoretical study of the N-H…O red-shifted and blue-shifted hydrogen bonds

Theoretical calculations are performed to study the nature of the hydrogen bonds in complexes HCHO…HNO, HCOOH…HNO, HCHO…NH3, HCOOH…NH3, HCHO…NH2F and HCOOH…NH2F. The geometric structures and vibrational frequencies of these six complexes at the MP2/6-31+G(d,p), MP2/6-311++G(d,p), B3LYP/6-31+G(d,p) and B3LYP/6-311++G(d,p) levels are calculated by standard and counterpoise-corrected methods, respectively. The results indicate that in complexes HCHO…HNO and HCOOH…HNO the N-H bond is strongly contracted and N-H…O blue-shifted hydrogen bonds are observed. While in complexes HCHO…NH3, HCOOH…NH3, HCHO…NH2F and HCOOH…NH2F, the N-H bond is elongated and N-H…O red-shifted hydrogen bonds are found. From the natural bond orbital analysis it can be seen that the X-H bond length in the X-H…Y hydrogen bond is controlled by a balance of four main factors in the opposite directions: hyperconjugation, electron density redistribution, rehybridization and structural reorganization. Among them hyperconjugation has the effect of elongating the X-H bond, and the other three factors belong to the bond shortening effects. In complexes HCHO…HNO and HCOOH…HNO, the shortening effects dominate which lead to the blue shift of the N-H stretching frequencies. In complexes HCHO…NH3, HCOOH…NH3, HCHO…NH2F and HCOOH…NH2F where elongating effects are dominant, the N-H…O hydrogen bonds are red-shifted.     

Matrix-isolation infrared studies of 1:1 molecular complexes containing chloroform (CHCl3) and Lewis bases: seamless transition from blue-shifted to red-shifted hydrogen bonds

The infrared spectra of molecular complexes containing chloroform (CHCl(3)) and Lewis bases (N(2), CO, H(2)O, and CH(3)CN) have been observed in an Ar matrix, and vibrational peaks for the 1:1 complexes have been assigned. The C-H stretching band of chloroform in the complexes showed a seamless transition from a blue shift (for N(2) and CO) to a red shift (H(2)O and CH(3)CN), in accord with the proton affinity of the base molecules. Density functional calculations predicted that the C-H··(σ-type lone pair) isomer is the most stable, which is consistent with the observed vibrational peak shift upon complex formation. The underlying mechanisms of the C-H hydrogen bond were explored using the topological properties of the electronic charge density and natural orbital analyses.     

胞嘧啶…NO复合物结构与性质的理论研究

用密度泛函理论在BL3YP/6-311＋G*基组水平上对胞嘧啶…NO复合物体系进行了理论计算, 发现了6个能量极小的复合物. 其结合方式是NO的N或O原子与胞嘧啶的N—H键形成氢键, 最稳定的复合物的结合能为－9.65 kJ/mol. NO的N原子与胞嘧啶的结合具有更强的优势, N结合的复合物中NO的键长缩短, 而O结合的复合物中NO键长伸长. 同时, 对复合物的振动分析发现, 在胞嘧啶中所有的与NO结合的N—H键的伸缩频率下降, 而所有氨基的面内弯曲振动频率是增加的.     

The C—H⋯O hydrogen bond. An ab initio study of nitrosomethane and its hydrogen bonded dimer

In order to study the short C—H?O contact which has been found in several nitroso compounds, a series of ab initio calculations have been performed on nitrosomethane and it's cyclic “hydrogen bonded” dimer. A potential function for the C—H?O contact has been found and the effect of this contact upon the NO and CN bonds has been studied. The potential is shallow with a minimum of only ?2.65 kcal mol^?1 for each contact and the equilibrium C?O distance is 3.524, A. These results indicate that the C—H?O bond is better described as a van der Waal's type contact than a hydrogen bond. The equilibrium length of the NO bond (R_NO) changes in a regular manner with variations in the C?O (R_HYD) distance, i.e. when R_HYD becomes shorter R_NO becomes longer. However, the variations in the CN bond lengths, which in the nitrosomethane monomer molecule is a long and weak bond, are anomalous.     

Geometrical H/D isotope effect on hydrogen bonds in charged water clusters

To investigate the proton/deuteron geometrical isotope effect of positively and negatively charged water complexes, H5O2+ and H3O2-, we have carried out accurate ab initio path integral simulations considering the electron correlation effect. It has been found that the isotope effect on the hydrogen bond is different between these two species in that the oxygen separation becomes shorter in H5O2+ while longer in H3O2- by deuteron substitution. This behavior is ascribed to the change in the quantum effect of hydrogen bonds whether the shared hydrogen is on a single or double well potential surface.     

甲醛与乙腈相互作用的理论研究

在HF/6-311G(d,p)、 MP2/6-311G(d,p)和B3LYP/6-311G(d,p)水平上,对H2CO和CH3CN以及设计的4种结构H2CO…CH3CN复合物等进行几何全优化和振动频率计算,排除振动频率为负值的非局域极小点结构,并对稳定的环状构型复合物结合能进行基组重叠误差校正和零点振动能校正.分子间相互作用的能量分解分析显示,静电能在H2CO...CH3CN相互作用能量中占主导地位,电荷转移能居第二位.     

Theoretical study of the S?H···O blue‐shifted hydrogen bond

Theoretical calculations were performed to study the nature of the hydrogen bonds in the complexes HCHO···HSO, HCOOH···HSO, HCHO···HOO, and HCOOH···HOO. The geometric structures and vibrational frequencies of these four complexes at the MP2/6‐31G(d,p) and MP2/6‐311+G(d,p) levels are calculated by standard and counterpoise‐corrected methods, respectively. The results indicate that in the complexes HCHO···HSO and HCOOH···HSO the S? H bond is strongly contracted. In the S? H···O hydrogen bonds, the calculated blue shifts for the S? H stretching frequencies are in the vicinity of 50 cm^?1. While in the complexes HCHO···HOO and HCOOH···HOO, the O? H bond is elongated and O? H···O red‐shifted hydrogen bonds are found. From the natural bond orbital analysis it can be seen that the X? H bond length in the X? H···Y hydrogen bond is controlled by a balance of four main factors in the opposite directions: hyperconjugation, electron density redistribution, rehybridization, and structural reorganization. Among them hyperconjugation has the effect of elongating the X? H bond. Electron density redistribution and rehybridization belong to the bond shortening effects, while structural reorganization has an uncertain influence on the X? H bond length. In the complexes HCHO···HSO and HCOOH···HSO, the shortening effects dominate which lead to the blue shift of the S? H stretching frequencies. In the complexes HCHO···HOO and HCOOH···HOO where elongating effects are dominant, the O? H···O hydrogen bonds are red‐shifted. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Water complexes of styrene and 4-fluorostyrene: a combined electronic, vibrational spectroscopic and ab-initio investigation

The binary complexes of water with styrene and fluorostyrene were investigated using LIF and FDIR spectroscopic techniques. The difference in the shifts of S 1 <-- S 0 electronic transitions clearly points out the disparity in the intermolecular structures of these two binary complexes. The FDIR spectra in the O-H stretching region indicate that water is a hydrogen bond donor in both complexes. The formation of a single O-H...pi hydrogen-bonded complex with styrene and an in-plane complex with fluorostyrene was inferred based on the analysis of the FDIR spectra in combination with ab initio calculations. The in-plane complex with fluorostyrene is characterized by the presence of O-H...F and C-H...O hydrogen bonds, leading to formation of a stable six-membered ring. The synergistic effect of O-H...F and C-H...O hydrogen bonds overwhelms the O-H...pi interaction in fluorostyrene-water complexes.     

Metal complexes of a phenol-tailed porphyrin with different hydrogen bonds

Hydrogen bonds are very common and important interactions in biological systems, they are used to control the microenvironment around metal centers. It is a challenge to develop appropriate models for studying hydrogen bonds. We have synthesized two metal complexes of the phenol-tailed porphyrin, [Zn(HL)] and [Fe(HL)(C₆H₄(OH)(O))]. X-ray crystallography reveals that the porphyrin functions as a dianion HL^2? and the phenol OH is involved in hydrogen bonds in both structures. In [Zn(HL)], an intramolecular hydrogen bond is formed between the carbonyl oxygen and OH. In [Fe(HL)(C₆H₄(OH)(O))], the unligated O(5) of the ligand is involved in two hydrogen bonds, as a hydrogen bond donor and a hydrogen bond acceptor. The overall electronic effect on the ligand could be very small, with negligible impact on the structure and the spin state of iron(III). The structural differences caused by the hydrogen bonds are also discussed.