Origins of isotopomeric polymorphism

The complex formed between 4-methylpyridine and pentachlorophenol (4MPPCP) crystallises in a triclinic space group. If the same complex is synthesized from deuterated pentachlorophenol, it crystallizes in an entirely different monoclinic polymorph. Using solid-state NMR of samples synthesized with a full range of deuteration levels, crystallized from solution or the melt, and in the presence or absence of seeds, we have confirmed that the isotopomers indeed have different thermodynamically stable crystal structures. The roots of this phenomenon of isotopomeric polymorphism apparently lie in the differences in hydrogen bonding between the polymorphs. The triclinic form has a relatively short hydrogen bond. High-field solid-state NMR shows both the 1H chemical shift and the 2H electric quadrupole coupling of the hydrogen involved in the bond to be strongly temperature-dependent, indicating a low-lying excited state of the hydrogen bond longitudinal vibration. Inelastic neutron scattering of isotopomers of 4MPPCP has allowed us to identify the three orthogonal vibrational modes of the hydrogen in the hydrogen bond, at 29.7, 145, and 205 meV (240, 1168, and 1651 cm(-1)). The longitudinal mode is the lowest in energy, and it indicates a slightly asymmetric low-barrier double-well potential. Intrinsic to such potentials is a very small difference in zero-point energies (ZPEs) between the protonated and deuterated forms. As a contrast, the monoclinic form has a comparatively normal hydrogen bond, in which the proton and deuteron ZPEs should be different by approximately 500 cm(-1). A scenario can be envisaged where the triclinic protonated form is lower in energy than the monoclinic protonated form, but the triclinic deuterated form is higher in energy than the monoclinic deuterated form. This evidently accounts for the difference in relative stabilities of the two forms upon isotope substitution.     

Quantum states of hydrogen transfer and vibration in malonaldehyde

New ab initio results on the 21D potential energy surface of malonaldehyde and a quantum mechanical treatment of the hydrogen transfer motion and its interaction with all vibrations are presented. An explicit approximate reaction path, close to the minimum energy path but matching the reactive normal mode near equilibrium, allows one to predict the ground state tunnelling frequency even when using small basis sets. With a barrier of 1144 cm^?1 (3.27kcal mol-¹) the tunnelling splitting is predicted to be 22.0cm^?1 for the parent species and 3.8 cm^?1 for the species deuterated in the hydrogen bond, in good agreement with the observed values 21.6 and 2.9 cm^?1, respectively. Predicted energy levels for excited states of the hydrogen transfer motion and for the non-reactive vibrations suggest a re-examination of the vibrational spectra and an extension of the number of vibrational factors in the basis set to improve the results for the vibrationally excited states.     

Vibrational spectroscopic studies of the structure of di‐amino acid peptides. Part II: cyclo(L‐Asp‐L‐Asp) in the solid state and in aqueous solution

Solid‐state protonated and N,O‐deuterated Fourier transform infrared (IR) and Raman scattering spectra together with the protonated and deuterated Raman spectra in aqueous solution of the cyclic di‐amino acid peptide cyclo(L ‐Asp‐L ‐Asp) are reported. Vibrational band assignments have been made on the basis of comparisons with previously cited literature values for diketopiperazine (DKP) derivatives and normal coordinate analyses for both the protonated and deuterated species based upon DFT calculations at the B3‐LYP/cc‐pVDZ level of the isolated molecule in the gas phase. The calculated minimum energy structure for cyclo(L ‐Asp‐L ‐Asp), assuming C₂ symmetry, predicts a boat conformation for the DKP ring with both the two L ‐aspartyl side chains being folded slightly above the ring. The CO stretching vibrations have been assigned for the side‐chain carboxylic acid group (e.g. at 1693 and 1670 cm⁻¹ in the Raman spectrum) and the cis amide I bands (e.g. at 1660 cm⁻¹ in the Raman spectrum). The presence of two bands for the carboxylic acid CO stretching modes in the solid‐state Raman spectrum can be accounted for by factor group splitting of the two nonequivalent molecules in a crystallographic unit cell. The cis amide II band is observed at 1489 cm⁻¹ in the solid‐state Raman spectrum, which is in agreement with results for cyclic di‐amino acid peptide molecules examined previously in the solid state, where the DKP ring adopts a boat conformation. Additionally, it also appears that as the molecular mass of the substituent on the C^α atom is increased, the amide II band wavenumber decreases to below 1500 cm⁻¹; this may be a consequence of increased strain on the DKP ring. The cis amide II Raman band is characterized by its relatively small deuterium shift (29 cm⁻¹), which indicates that this band has a smaller N H bending contribution than the trans amide II vibrational band observed for linear peptides. Copyright © 2009 John Wiley & Sons, Ltd.     

Matrix Isolation Infrared Spectroscopic and Density Functional Theory Study of the 1:1 Complex of Bromocyclohexane with NH3: Evidence for a Weak C–H–N Hydrogen Bond

ABSTRACT

The hydrogen-bonded bromocyclohexane–ammonia complex has been isolated and characterized for the first time in argon matrices at 16 K. Coordination of the proton adjacent to the Br substituent on the cyclohexane ring to the amino nitrogen was evidenced by distinct blue shifts of bending modes involving the H-C₁–Br unit. In particular, C–C₁–Br, H–C₁–Br, and C–C₁–H bending modes produced blue shifts ranging from 2.8 to 12.2 cm^?1. Density Functional Theory (DFT) calculations at the B3LYP/6–31 + G(d, p) level yield an essentially linear Br–C₁–H–NH₃ hydrogen bond with a C-H–N distance of 2.412 Å and a hydrogen bond energy of 2.95 kcal/mol.     

Acid-base high temperature proton exchange membranes prepared from phosphonic acid functionalized siloxane

One kind of acid-base high temperature proton exchange membranes has been prepared from amino trimethylene phosphonic acid (ATMP), epoxycyclohexyethyltrimethoxysilane (EHTMS), and 3-aminopropyltriethoxysilane (APTES) by sol-gel process. The structural characteristics of these membranes with different amount of APTES were investigated by FT-IR, XRD, and SEM. These membranes showed excellent dimensional stability in water with the contribution of flexible ionic network structure and were thermally stable up to about 200 °C. In addition, the proton conductivity of the membranes increased with increasing temperature over the range of 20 to 140 °C, up to a maximum of 2.63 × 10^?2 S cm^?1 at 140 °C under anhydrous condition. The high proton conductivity was attributed to the formation of hydrogen bond network through the synergistic effect of N and P. The activation energy value of membranes became lower from 0.46 to 0.30 eV because of the acid-base pairs. The variable-temperature FT-IR further proved the formation of hydrogen bond network in the membrane.     

Steady-state fluorescence and photo-isomerization study of 1-methyl-4′-(p-N,N dimethyl-amino styryl) pyridinium iodide

Photochemical and thermal trans/cis isomerization reactions are reported for 1-methyl-4′-(p-N,N dimethyl-amino styryl) pyridinium iodide, Cy, which is synthesized in the trans configuration. In a basic solution the trans form, Cy_tr, cannot isomerise directly to the cis form. Its protonated form, Cy_trH⁺, is active and reacts photochemically from trans to cis isomer, Cy_cH⁺. The quantum yields Φ_tc and Φ_ct are determined in water. Deprotonation process of Cy_cH⁺ yields the cis isomer, Cy_c, which can thermally revert to the stable trans form. The rate constant and the activated parameters of the thermal reaction are also determined. Due to irreversibility of the thermal reaction , a complete molecular reaction cycle is performed in one direction. To get more information on the spectral properties of protonated form, its absorption and fluorescence spectra were investigated in sixteen neat polar protic and aprotic solvents. Absorption energy correlates linearly with hydrogen bond acceptor ability of the solvent. Another linear correlation was found between fluorescence energy of CyH⁺ and free energy for transferring the proton to the surrounding solvent, ΔG_t^o.     

Vibrational spectra and crystal structure of the di‐amino acid peptide cyclo(L‐Met‐L‐Met): comparison of experimental data and DFT calculations

Experimental Raman and FT‐IR spectra of solid‐state non‐deuterated and N‐deuterated samples of cyclo(L ‐Met‐L ‐Met) are reported and discussed. The Raman and FT‐IR results show characteristic amide I vibrations (Raman: 1649 cm⁻¹, infrared: 1675 cm⁻¹) for molecules exhibiting a cis amide conformation. A Raman band, assigned to the cis amide II vibrational mode, is observed at ∼1493 cm⁻¹ but no IR band is observed in this region. Cyclo(L ‐Met‐L ‐Met) crystallises in the triclinic space group P1 with one molecule per unit cell. The overall shape of the diketopiperazine (DKP) ring displays a (slightly distorted) boat conformation. The crystal packing employs two strong hydrogen bonds, which traverse the entire crystal via translational repeats. B3‐LYP/cc‐pVDZ calculations of the structure of the molecule predict a boat conformation for the DKP ring, in agreement with the experimentally determined X‐ray structure. Copyright © 2009 John Wiley & Sons, Ltd.     

Vibrational spectra of glyoxylic acid monomers

Infrared spectra of glyoxylic acid monomers, including the hydroxyl deuterated and general O-18 isotopomers, are reported for argon and nitrogen matrix-isolated samples in the range 400–4000 cm^?1. Values for all 15 fundamental vibrations of the intramolecular H-bonded monomer are listed. Bands attributed to the trans-carbonyl conformer with a free car?yl group are also observed and about half of its fundamental frequencies are listed. Some modes of the intramolecular H-bonded glyoxylic acid monomer are strongly matrix dependent, and differences between Ar and N₂ matrix spectra are exploited in sorting out the spectral information.     

Vibrational Spectroscopic Studies of Molecules with Biochemical Interest: The Cysteine Zwitterion

Abstract

The L-cysteine zwitterions in the orthorhombic crystal structure and in aqueous solution, including the deuterated isotopologues HSCD₂CH(NH₃ ⁺)COO^?, DSCH₂CH(ND₃ ⁺)COO^?, and DSCD₂CH(ND₃ ⁺)COO^?, have been studied by mid-infrared, far-infrared, and Raman spectroscopy. Density functional theory (DFT) calculations were performed for an equilibrium molecular geometry of the cysteine zwitterion to obtain vibrational frequencies of fundamental modes, infrared (IR) and Raman intensities, and the depolarization ratio of the Raman bands and combined with normal coordinate force field analyses. The force field obtained for dissolved (in H₂O and D₂O) cysteine, based on the 4 × 36 experimental fundamental modes of the four isotopologues, was successfully transferred to the two conformers in the solid state. The experimentally observed multiple bands (generally doublets) of L-cysteine and its deuterated isotopologues in the solid state were interpreted based on the coexistence of two conformers in the unit cell. The calculated frequencies were used for full assignments of the fundamental IR and Raman vibrational transitions, including an attempt to interpret all low-frequency vibrations (below 400 cm^?1) of the zwitterion also in the solid state. In particular, the hydrogen bonding effects on conformation, bond lengths, and force constants were studied, including those of the distorted NH₃ ⁺ amino group. The –S-H and -S-D stretching vibrations were found to be local modes, not sensitive to deuterium substitution of the -CH₂ and -NH₃ ⁺ groups in the molecule or to the H(D)-S-C-C torsional angle. The two major -S-H or -S-D stretching bands observed in the solid state correspond to different S-H/D bond lengths and resulted in the force constants K _SH = 3.618 N·cm^?1 and 3.657 N·cm^?1 for the SH^… S and SH^… O hydrogen-bonded interactions. A remarkable result was that the S(H)^… O interaction was weaker than the S(H)^… S interaction in the solid state and even weaker in aqueous solution, K _SH = 3.715 N·cm^?1, possibly due to intramolecular interactions between the thiol and amino groups. A general correlation between the S-H/D bond length and vibrational frequency was developed, allowing the bond length to be estimated for sulfhydryl groups in, for example, proteins. The C-S stretching modes were fitted with different C-S stretching force constants, K _CS = 3.213 and 2.713 N·cm^?1, consistent with the different CS bond lengths for the two solid-state conformers.     

Fourier-transform microwave spectroscopy of the deuterated acetylene dimers: The interconversion tunneling motions of (DCCD)2, (DCCH)2, DCCD---DCCH, DCCH---DCCD, HCCH---DCCD, and HCCH---DCCH

Microwave spectra of the deuterated acetylene dimers, produced in a molecular beam at 1 K from samples of HCCH, DCCH, and DCCD, were observed using a Fourier transform microwave spectrometer. We observed all variations of deuterated acetylene dimers in which a deuterium atom participates in the hydrogen bond; i.e., (DCCD)₂, (DCCH)₂, DCCD---DCCH, DCCH---DCCD, HCCH---DCCD, and HCCH---DCCH. Deuterated acetylene dimers with the hydrogen atom located in the hydrogen bond could not be detected. Precise molecular constants were determined for each species. Among the dimers identified, (DCCD)₂, (DCCH)₂, DCCD---DCCH, and DCCH---DCCD showed evidence of an interconversion tunneling motion like the tunneling observed for (HCCH)₂. The tunneling potential of (DCCD)₂ was analyzed using a one-coordinate model and the potential depth was determined to be V₄ = 35.577 cm⁻¹, which is 2.371 cm⁻¹ deeper than that of (HCCH)₂ studied by Fraser et al. (J. Chem. Phys. 89, 6028–6045 (1988)). A one-coordinate model was also applied to the other deutered acetylene dimers by adopting a further assumption of a composite potential.     

The microwave spectrum of difluoroacetic acid

Transitions due to two conformations have been observed in the microwave spectrum of difluoroacetic acid. In both rotamers the carboxylic hydrogen atom is cis to the CO bond, whereas the other hydrogen atom is either trans or gauche with respect to the CO bond. By means of isotopic substitution of the hydrogen and oxygen atoms a serious deviation of local symmetry in the CHF₂ group is deduced for the gauche form. This is thought to be an artifact of the substitution method, although no satisfactory explanation can be given. In torsionally excited states of the gauche conformation, doublet splittings were observed due to tunneling through a barrier of 190 ± 10 cm^?1. For the second excited state a satisfactory treatment could be given, but for the third excited state large differences between observed and calculated transition frequencies remained. A computer program to account for the internal rotation in asymmetric molecules was written, and it was shown qualitatively that interactions with excited states of the trans conformation could very well be responsible for the discrepancies. From intensity measurements the energy difference E(gauche) - E(trans) was found to be 370 ± 180 cm^?1. The large uncertainty is due to the failure of attempts to determine the dipole moments experimentally; they were estimated from an improved set of bond moments which was derived from related compounds. Both energy difference and dihedral angles are at variance with the results of an earlier electron diffraction investigation.     

Origin Band Shifts Upon Deuteration in the 280 nm Absorption System of Benzimidazole

Abstract

Five deuterated derivatives of benzimidazole have been prepared and their sharp 280 nm vapour phase electronic absorption spectra recorded. When hydrogen atoms bonded to carbon are substituted, the origin band shifts to higher energies by 29 cm^?1 per D atom, a value close to that found in benzene and some monosubstituted benzenes. When the hydrogen bonded to nitrogen is substituted, a much smaller shift is observed.     

Raman spectra of potassium, rubidium, and thallium hydrogen phthalates

The polarized Fourier-transform Raman spectra of oriented single crystals of K, Rb, and Tl hydrogen phthalates, as well as of deuterated potassium hydrogen phthalate, are studied in the range 50–3300 cm^?1 in different scattering geometries. The frequencies of internal vibrations in the spectra of these compounds are assigned to vibrations of the orthophenylene and carboxyl groups. The replacement of K with Rb or Tl leads to an insignificant low-frequency shift of vibrations. A multiband structure of OH(D) stretching vibrations is observed in the range 1900–2800 cm^?1 in the spectra of all hydrogen phthalates, which is caused by Fermi-resonance interactions. A number of additional bands are observed in the spectrum of deuterated potassium hydrogen phthalate, which indicates that deuterium atoms partially replace hydrogen atoms in both the orthophenylene and the carboxyl groups.     

Theoretical and Experimental Study of the Conformation and Vibrational Frequencies of N‐Acetyl‐L‐alanine and N‐Acetyl‐L‐alaninate

The vibrational frequencies of N‐acetyl‐L‐alanine (NAAL), its potassium salt (NAALK) and its free anionic form (NAAL^?) are calculated using density functional theory (B3LYP) combined with the 6‐311 + + G(d,p) basis set. The experimental Raman spectrum of solid NAALK and the scaling factors for calculated values are discussed as well. The three species are characterized by intramolecular NH…O hydrogen bonds leading to the formation of a five‐membered ring. As indicated by the intramolecular (N)H…O distances and by the ν(NH) frequencies, the strength of the intramolecular hydrogen bond is ordered as follows: NAAL^? < NAALK < NAAL^?. Owing to their difference in the coupling with other vibrational modes, the in‐plane and out‐of‐plane vibrations do not reflect the strength of the hydrogen bond.     

Effect of α-irradiation of energy 0.5 MeV on the hydrogen bonding in a-Si:H thin films

Hydrogenated amorphous silicon thin films (a-Si:H) have been prepared by the rf glow discharge technique. The configuration of bonded hydrogen was investigated by infrared absorption measurements of Si:H vibrational modes before and after bombardment with an α-particle beam energy of 125 keV/n. The results showed an increase in the absorption mode near 2100, 890 and 850 cm^?1 and a decrease in the absorption mode near 2000 cm^?1 after bombardment. These observations are interpreted in terms of changes of the oscillator strengths of vibrational modes.     

Crystal structure,characterisation and vibrational study of a mixed compound Cs0.4Rb0.6H2Po4

Abstract

The crystal structure of Cs_1-x Rb _x H₂PO₄, x = 0.6 (CRDP) which crystallises in space group P2₁/m and is isostructural with the monoclinic phase of CsH₂PO₄ (CDP), has been refined at room temperature using single-crystal X-ray diffractometer data. The cell parameters are a = 4.8183(9)å, b = 6.2671(6) å, c = 7.7620(10)å, β= 108.260(10)°, V = 222.58(5)å³, Z = 2, D_x = 3.009g cm^?3. F(000)=187, T = 298(2)K (room-temperature phase), R = 0.0355 and wR = 0.0949 for 654 observed reflections. CRDP contains two crystallography inequivalent hydrogen bonds in the unit cell. The shorter bond (Ko – o = 2.453(7) A) links the phosphate groups into chains running along the b-axis and the longer bond (Ko – o = 2.488(6) A) which is always ordered, crosslinks the chains to form (001) layers. The phase transitions in the mixed Cs_0.4Rb_0.6H₂PO₄ (CRDP) were characterised by differential scanning calorimetry which shows two anomalies at about 293 and 525 K. The Raman and infrared spectra at room temperature were investigated in the frequency ranges 10–3500 and 200–4000 cm^?1 respectively. An assignment of all the bands is given. The bands are in agreement with the monoclinic room-temperature phase implying high dynamical disorder of the acidic proton O-H s–O hydrogen bond.     

Reaction of Pentanol isomers with OH radical – A theoretical perspective

The stability of all the three isomeric forms of Pentanol has been examined with relative energy analysis. Even though 2-Pentanol is predicted to be most stable isomeric form, all the three isomeric forms undergo hydrogen atom abstraction reaction with OH radical. Among the proposed 18 different hydrogen atom abstraction reaction, the abstraction from CH₂ and CH functional group is found to be a favourable reactive site with low energy barrier in M06-2X/6-311+G(d,p) level of theory. Wiberg bond order analysis shows all the abstraction reactions are concreted but not synchronic in nature. Using force analysis, the calculated work done of individual reaction regions illustrates that structural rearrangements drive the reaction with higher contribution to the energy barrier. The rate constant calculated at M06-2X method for the most favourable reaction is well matched with available experimental data. Using the reported atmospheric OH concentration (1 × 10⁶ molecules/cm³), the life time of 1-Pentanol, 2-Pentanol and 3-Pentanol has calculated to be 18.66, 0.36 and 2.86 days, respectively.     

2H NMR study of phase transition and hydrogen dynamics in hydrogen bonded organic antiferroelectric 55DMBP-H2ca

Hydrogen dynamics in one-dimensional hydrogen bonded organic antiferroelectric, co-crystal of 5,5’-dimethyl-2,2’-bipyridine (55DMBP) and chloranilic acid (H₂ca), was investigated by use of ²H high resolution solid-state NMR. The two types of hydrogen bonds O-H …N and N⁺-H …O^? in the antiferroelectric phase were clearly observed as the splitting of the side band of the ²H MAS NMR spectra of the acid-proton deuterated compound 55DMBP-D ₂ca. The temperature dependence of the spin-lattice relaxation time was measured of the N⁺-H and O-H deuterons, respectively. It was suggested that the motion of the O-H deuteron is already in the antiferroelectric phase in the fast-motion regime in the NMR time scale, while that of the N⁺-H deuteron is a slow motion. In the high-temperature paraelectric phase, the both deuterons become equivalent and the fast motion of the deuterons in the NMR time scale is taking place with the activation energy of 7.9 kJ mol^?1.     

Fourier Transform Vibrational Spectra of Magnesium Hydrogenphosphate Trihydrate. I. The O-H Stretching Region∗

Abstract

The Fourier transform (FT) infrared and Raman spectra of newberyite, MgHPH₄ - 3H₂O are studied in the region where the stretching vibrations of the water molecules (protiated and deuterated) and the O-H/O-D stretches of the hydrogenphosphate anions are expected to appear. The O-H stretching vibrations give rise to a complex feature known as the A,B,C trio. Since neither of the maxima found below 3000 cm^?1 represents a true band arising from a given fundamental, it is pointless to correlate their frequencies with the observed O…O distances. In the water stretching region, the two bands with highest frequencies undoubtedly correspond to the anti symmetric and symmetric stretch of one type of the water molecules. The stretching vibrations of one of the remaining two types of H₂O molecules are clearly uncoupled and the O-H oscillator involved in the weaker hydrogen bond is responsible for a band at 3376 cm^?1 whereas the rest of the water stretchings are apparently overlapped yielding the complex band below 3320 cm^?1. Thus the situation is again complicated and the correlations between the frequencies and the O_w…O distances are inappropriate. The two bands at highest frequencies (3522 and 3483 cm^?1 at RT) exhibit a positive temperature coefficient.

     

Hydration-induced conformational changes in protonated 2,4-pentanedione in the gas phase

Starting with H⁺[CH₃C(O)CH₂C(O)CH₃] (denoted H⁺PD), the protonated diketone-water clusters H⁺PD(H₂O) _n (n = 1–3) have been characterized by density functional theory calculations in combination with vibrational predissociation spectroscopy to explore the conformational changes of a protonated bifunctional ion solvated by water in the gas phase. Theoretical calculations for H⁺PD revealed that the ion contains an intramolecular hydrogen bond (IHB), with two oxygen atoms bridged by the extra proton in an O—H⁺ … O form. Attachment of one water molecule to it readily ruptures this IHB, replacing the H⁺ by the H₃O⁺ moiety. Further replacement of the IHB by two water molecules occurs at n = 2 and the ?C(O)CH₂C(O)- chain is fully opened (or unfolded) after transfer of the extra proton to the water trimer at n = 3. To verify the computational findings, infrared spectroscopic measurements were performed using a vibrational predissociation ion trap spectrometer to identify cluster isomers from the signatures of hydrogen bonded and non-hydrogen bonded OH stretching spectra of H⁺PD(H₂O)_2,3 produced in a corona discharge supersonic expansion. Besides open form isomers, evidence for the formation of water-bridged structures has been found for H⁺PD(H₂O)₃ at an estimated temperature of 200 K. A detailed illustration of the unfolding steps as well as the energy profiles for the evolution of a two-water bridge isomer from the protonated H⁺PD monomer are analysed pictorially (including both stable intermediates and transition states) in the present investigation.