Formamide Clusters Research Articles

Study of formamide molecular clusters by Raman spectroscopy and quantum-chemical calculations

Polarized Raman spectra of liquid formamide in the region of C = O stretching vibration band were investigated. Quantum-chemical simulation of different formamide clusters from a monomer to a pentamer has been carried out in B3LYP/6-311++ G(2d, p) approximation with account of hydrogen bonds formation. The results of calculation were used to clarify the complex shape of the C = O stretching Raman band.

Effects of self-hydrogen bonding among formamide molecules on the UCST-type liquid-liquid phase separation of binary solutions with imidazolium-based ionic liquid, [Cnmim][TFSI], studied by NMR, IR, MD simulations, and SANS.

The upper critical solution temperature (UCST)-type liquid-liquid phase separation of imidazolium-based ionic liquids (ILs), 1-alkyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide ([Cnmim][TFSI], where n represents the alkyl chain length of the cation, n = 6, 8, 10, and 12) binary solutions with formamide (FA) was examined as a function of temperature and the FA mole fraction xFA. The two-phase region (immiscible region) of the solutions is much larger and expands more with the increase in n, in comparison with the previous [Cnmim][TFSI]-1,4-dioxane (1,4-DIO) systems. An array of spectroscopic techniques, including 1H and 13C NMR and IR combined with molecular dynamics (MD) simulations, was conducted on the present binary systems to clarify the microscopic interactions that contribute to the phase-separation mechanism. The hydrogen-bonding interactions of the imidazolium ring H atoms are more favorable with the O atoms of the FA molecules than with 1,4-DIO molecules, whereas the latter interact more favorably with the alkyl chain of the cation. Upon lowering the temperature, the FA molecules gradually self-aggregate through self-hydrogen bonding to form FA clusters. Concomitantly, clusters of ILs are formed via the electrostatic interaction between the counter ions and the dispersion force among the IL alkyl chains. Small-angle neutron scattering (SANS) experiments on the [C6mim][TFSI]-FA-d2 and [C8mim][TFSI]-FA-d2 systems revealed, similarly to [Cnmim][TFSI]-1,4-DIO systems, the crossover of the mechanism from the 3D-Ising mechanism around the UCST xFA to the mean-field mechanism at both sides of the mole fraction. Interestingly, the xFA range of the 3D-Ising mechanism for the FA systems is wider compared with the range of the 1,4-DIO systems. In this way, the self-hydrogen bonding among FA molecules most significantly governs the phase equilibria of the [Cnmim][TFSI]-FA systems.

Electron ionization of clusters containing the formamide molecule

Studies on electron interactions with formamide (FA) clusters promote scientific interest as a model system to understand phenomena relevant to astrophysical, prebiotic, and radiobiological processes. In this work, mass spectrometric detection of cationic species for both small bare and microhydrated formamide clusters was performed at an electron ionization of 70 eV. Furthermore, a comparative analysis of the cluster spectra with the literature-reported gas-phase spectra is presented and discussed, revealing different reaction channels affected by the cluster environment. This study is essential in developing our understanding of both low-energy electron phenomena in clusters that can bridge the complexity gap between gas and realistic systems and the effect of hydration on electron-induced processes.

A molecular-scale study on the hydration of sulfuric acid-amide complexes and the atmospheric implication

Amides are ubiquitous in atmosphere. However, the role of amides in new particle formation (NPF) is poorly understood. Herein, the interaction of urea and formamide with sulfuric acid (SA) and up to four water (W) molecules has been studied at the M06-2X/6-311++G(3df,3pd) level of theory. The structures and properties of (Formamide)(SA)(W)n (n = 0–4) and (Urea)(SA)(W)n (n = 0–4) clusters were investigated. Results show that the interaction of SA with the CO group of amides plays a more important role in amide clusters compared with the NH2 group. Proton transfer to water molecule become dominant in highly hydrated amide clusters at lower temperatures. There is no proton transfer to CO group in formamide clusters. The Rayleigh light scattering intensities of amide clusters are comparable to that of amine and oxalic acid clusters reported previously. Moreover, unhydrated (Amide)(SA) clusters have similar or even higher ability than hydrated SA clusters to participate in ion-induced nucleation. In comparison with formamide, urea has more interacting sites and its clusters have higher Rayleigh light scattering intensities, larger dipole moment, stronger interaction with SA and lower water affinity. The intermolecular interaction in (Formamide)(SA) is slightly weaker than that of SA dimer, which may be compensated by the high concentration of formamide, thus enabling formamide to participate in initial steps of NPF. This study may bring new insight into the role of amides in initial steps of NPF from molecular scale and could help better understand the properties of amide-containing organic aerosol.

Correlated natural transition orbital framework for low-scaling excitation energy calculations (CorNFLEx).

We present a new framework for calculating coupled cluster (CC) excitation energies at a reduced computational cost. It relies on correlated natural transition orbitals (NTOs), denoted CIS(D')-NTOs, which are obtained by diagonalizing generalized hole and particle density matrices determined from configuration interaction singles (CIS) information and additional terms that represent correlation effects. A transition-specific reduced orbital space is determined based on the eigenvalues of the CIS(D')-NTOs, and a standard CC excitation energy calculation is then performed in that reduced orbital space. The new method is denoted CorNFLEx (Correlated Natural transition orbital Framework for Low-scaling Excitation energy calculations). We calculate second-order approximate CC singles and doubles (CC2) excitation energies for a test set of organic molecules and demonstrate that CorNFLEx yields excitation energies of CC2 quality at a significantly reduced computational cost, even for relatively small systems and delocalized electronic transitions. In order to illustrate the potential of the method for large molecules, we also apply CorNFLEx to calculate CC2 excitation energies for a series of solvated formamide clusters (up to 4836 basis functions).

Computational study of interactions and nuclear magnetic shielding constants in linear chains of formamide clusters.

We investigated the energetic, structural, dielectric, and nuclear magnetic shielding properties of linear n-formamide clusters, with n up to 6, to quantitatively characterize cooperative effects in model biological systems. The geometries of the complexes were optimized at the MP2 and DFT/B3LYP levels by using the pc-2 and pc-3 basis sets, while the nuclear magnetic shielding constants were calculated by employing pcS-n type basis sets, which have been optimized specifically for density functional calculations of these properties. The interaction energies show the cooperative effect, which favors the successive addition of monomers. In addition, by analyzing structural changes in the intermolecular C=O, C-N and hydrogen O⋯H bonds, as well as in the average dipole moments as cluster size increases, we found that the cooperative interaction far exceeds that expected for electrostatic interactions. Such non-pairwise-additive effects are also reflected in the changes of the nuclear magnetic shielding constants. In particular, the negativity of O shielding decreases around 23% from the monomer to the 6-formamide chain. It is possible to note the decrease in the shielding of H and in the deshielding of O as a result of their hydrogen bonding. However, the results obtained show that these variations in the extremes of formamide chains tend to zero, and the respective shielding values tend to stabilize as the number of monomers increases in the chain. Also, the cooperative effect increases in the middle of the chains, by decreasing the shielding for all atoms except that of O, which decreases its deshielding. These results could serve to guide improvements in current conventional models for simulating hydrogen bonded systems.

Hydrogen bonded networks in formamide [HCONH2]n (n = 1 − 10) clusters: A computational exploration of preferred aggregation patterns#

Application of quantum chemical calculations is vital in understanding hydrogen bonding observed in formamide clusters, a prototype model for motifs found in protein secondary structure. DFT calculations have been performed on four arrangements of formamide clusters [HCONH2]n, (n = 1 − 10) linear, circular, helical and stacked forms. These studies reveal the maximum cooperativity in the stacked arrangement followed by the circular, helical and linear arrangements and is based on interaction energy per monomer. In all these arrangements as we increase cluster size, an increasing trend in cooperativity of hydrogen bonding is observed. Atoms-in-molecule analysis establishes the nature of bonding between the formamide monomers on the basis of electron density values obtained at the bond critical point (BCP).

Monitoring the 1160 cm−1 band of pyridazine to investigate complexes with formamide

Hydrogen bonding between pyridazine (PRD) and formamide (FA) molecules has been investigated both experimentally by Raman spectroscopy on their binary mixtures and theoretically by DFT calculations on various gas-phase PRD:FA clusters. The band at 1160cm−1 of PRD was used for the first time as a marker for monitoring the degree of complexation. Upon dilution with FA, a new band at 1169cm−1 is observed and attributed to hydrogen-bonded PRD. The Raman experiments were complemented by DFT calculations and the corresponding structures, vibrational spectra and binding energies were determined. The most stable species were found to be the 1:2 PRD:FA complexes and such stoichiometry is in excellent agreement with the experimental determination. The shift to higher frequency observed to the prominent modes of PRD may be related to a shortening of the NC and CC bonds, upon complexation, which causes a decrease in the electron delocalization in PRD ring.

Hydrogen bonding in the pyrimidine/ formamide system: a concentration‐dependent Raman and DFT study

AbstractHigh‐resolution Raman spectra of pyrimidine (PD) and formamide (FA) mixtures with different compositions recorded in the ring breathing region of PD (ν1 ∼ 991 cm−1) are presented. The dilution of PD with FA leads to the appearance of a new band at ν1′ ∼ 994 cm−1, which is assigned to hydrogen‐bonded PD:FA species. From a quantitative analysis of the concentration‐dependent Raman spectra, the average number of FA molecules in the first solvation sphere of PD is determined as being equal to 2. This value is supported by density functional theory (DFT) calculations: a symmetric 1:2 complex is the most stable species among various hydrogen‐bonded PD:FA clusters with stoichiometries ranging from 1:1 to 1:4. A qualitative explanation for the blue shift of the ν1 mode upon complexation is given. Additionally, we have observed not only similarities but also some differences with respect to the PD:water system. Copyright © 2010 John Wiley & Sons, Ltd.

Electron Attachment to Formamide Clusters in Helium Nanodroplets

Electron attachment to formamide clusters in helium nanodroplets is reported for the first time. In contrast to the gas phase, parent anions are seen following low energy electron attachment to both the monomer and the small clusters. This is attributed to formation of dipole (or quadrupole) bound anions. In addition to the bare anions, the mass spectra also show the monomer and clusters with attached helium atoms. The affinity for attaching helium atoms strongly varies with cluster size; for example, the dimer anion is more than 10 times more likely to bind one or more helium atoms than the monomer. Possible binding sites for the helium atoms are discussed.

Microsolvation of Formamide: A Rotational Study

Microsolvated formamide clusters have been generated in a supersonic jet expansion and characterized using Fourier transform microwave spectroscopy. Three conformers of the monohydrated cluster and one of the dihydrated complex have been observed. Seven monosubstituted isotopic species have been measured for the most stable conformer of formamide...H(2)O, which adopts a closed planar ring structure stabilized by two intermolecular hydrogen bonds (N-H...O(H)-H...O=C). The two higher energy forms of formamide...H(2)O have been observed for the first time. The second most stable conformer is stabilized by a O-H...O=C and a weak C-H...O hydrogen bond, while, in the less stable form, water accepts a hydrogen bond from the anti hydrogen of the amino group. For formamide...(H(2)O)(2), the parent and nine monosubstituted isotopic species have been observed. In this cluster the two water molecules close a cycle with the amide group through three intermolecular hydrogen bonds (N-H...O(H)-H...O(H)-H...O=C), the nonbonded hydrogen atoms of water adopting an up-down configuration. Substitution (r(s)) and effective (r(0)) structures have been determined for formamide, the most stable form of formamide...H(2)O and formamide...(H(2)O)(2). The results on monohydrated formamide clusters can help to explain the observed preferences of bound water in proteins. Clear evidence of sigma-bond cooperativity effects emerges when comparing the structures of the mono- and dihydrated formamide clusters. No detectable structural changes due to pi-bond cooperativity are observed on formamide upon hydration.

Electron localization in negatively charged formamide clusters studied by photodetachment spectroscopy

Size-dependent features of the electron localization in negatively charged formamide clusters (FAn-, n = 5-21) have been studied by photodetachment spectroscopy. In the photoelectron spectra for all the sizes studied, two types of bands due to different isomers of anions were found. The low binding energy band peaking around 1 eV is assigned to the solvated electron state by relative photodetachment cross-section measurements in the near-infrared region. It is suggested that nascent electron trapping is dominated by formation of the solvated electron. The higher energy band originates from the covalent anion state generated after a significant relaxation process, which exhibits a rapid increase of electron binding energy as a function of the cluster size. A unique behavior showing a remarkable band intensity of the higher energy band was found only for n = 9.

Characterization of Protonated Formamide-Containing Clusters by Infrared Spectroscopy and Ab Initio Calculations: I. O-Protonation

Characterization of protonated formamide clusters by vibrational predissociation spectroscopy confirms theoretical predictions that O-protonation occurs in preference to N-protonation in formamide. The confirmation is made from a close comparison of the infrared spectra of H+[HC(O)NH2]3 and NH4+[HC(O)NH2]3 produced by a supersonic expansion with the spectra produced by ab initio calculations. For NH4+[HC(O)NH2]3, prominent and well-resolved vibrational features are observed at 3436 and 3554 cm-1. They derive, respectively, from the symmetric and asymmetric NH2 stretching motions of the three formamide molecules linked separately to the NH4+ ion core via three N−H+···O hydrogen bonds. Similarly distinct absorption features are also found for H+[HC(O)NH2]3; moreover, they differ in frequency from the corresponding vibrational modes of NH4+[HC(O)NH2]3 by less than 10 cm-1. The result is consistent with a picture of proton attachment to the oxygen atom, rather than the nitrogen atom in H+[HC(O)NH2]3. We provide in this work both spectroscopic and computational evidence for the O-protonation of formamide and its clusters in the gas phase.

Development of an intermolecular potential function for interactions in formamide clusters based on ab initio calculations

A potential function for describing interactions between formamide molecules is proposed. The function was developed from ab initio computed molecular properties and intermolecular perturbation theory (IMPT) calculations for formamide dimer involving the 6-311G** basis set. It consists of an electrostatic term that is a function of multipoles distributed over the atoms, an exponential repulsion term obtained by fitting results for the dimer, an induction contribution that is a function of atomic polarizabilities, and a dispersion term based on a London expression that is also dependent on atomic polarizabilities. The results obtained by applying the proposed function to formamide dimer are similar to those found at the MP2/6-311G** level; the function allows one to identify five structures corresponding to as many energy minima. Application of the function to larger clusters revealed that the most attractive minima correspond to planar structures, the most common structural pattern among which is that of the global minimum for the dimer. Based on cooperativeness data for the larger clusters, chained structures seemingly form stronger hydrogen bonds due to increased cooperativeness in interactions between molecules, which may account for the tendency of condensed phases of formamide to adopt open structures.

Temperature dependence of hydrogen bonding in neat, liquid formamide

Temperature dependent quadrupole coupling parameters (QCP), χQ, and quadrupole coupling asymmetry parameters, ηQ, of neat, liquid formamide were calculated. These calculations are based on standard ab initio self-consistent field (SCF) methods at the 6–31G* level for eight different clusters and a quantum cluster equilibrium (QCE) model of liquids. The cluster sizes varied from one to six molecules and include linear and cyclic structures. The equilibrium populations of the different formamide clusters were calculated for temperatures between 270 and 400 K. These calculations indicate that at low temperatures a six-membered ring of formamide molecules involving hydrogen bonding between the trans amide deuteron and the oxygen is the dominant (95%) species. At higher temperatures the cluster populations change and the six-membered ring is gradually replaced, primarily by a linear tetramer. The temperature dependence of the calculated QCP values for nitrogen, oxygen and two of the deuterium nuclei (the carbonyl and trans deuterons) are all in good agreement with the experimentally measured NMR results.