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1.
Proc Natl Acad Sci U S A ; 120(9): e2214970120, 2023 Feb 28.
Artigo em Inglês | MEDLINE | ID: mdl-36802430

RESUMO

Most biomolecular activity takes place in aqueous environments, and it is strongly influenced by the surrounding water molecules. The hydrogen bond networks that these water molecules form are likewise influenced by their interactions with the solutes, and thus, it is crucial to understand this reciprocal process. Glycoaldehyde (Gly), often considered the smallest sugar, represents a good template to explore the steps of solvation and determine how the organic molecule shapes the structure and hydrogen bond network of the solvating water cluster. Here, we report a broadband rotational spectroscopy study on the stepwise hydration of Gly with up to six water molecules. We reveal the preferred hydrogen bond networks formed when water molecules start to form three-dimensional (3D) topologies around an organic molecule. We observe that water self-aggregation prevails even in these early stages of microsolvation. These hydrogen bond networks manifest themselves through the insertion of the small sugar monomer in the pure water cluster in a way in which the oxygen atom framework and hydrogen bond network resemble those of the smallest three-dimensional pure water clusters. Of particular interest is the identification, in both the pentahydrate and hexahydrate, of the previously observed prismatic pure water heptamer motif. Our results show that some specific hydrogen bond networks are preferred and survive the solvation of a small organic molecule, mimicking those of pure water clusters. A many-body decomposition analysis of the interaction energy is also performed to rationalize the strength of a particular hydrogen bond, and it successfully confirms the experimental findings.

2.
J Chem Phys ; 160(16)2024 Apr 28.
Artigo em Inglês | MEDLINE | ID: mdl-38686817

RESUMO

Microsolvation of the carbamate moiety delivers precise information on complexation effects on the N-C=O backbone and is of relevance to the peptide bond functionality. In this context, the mono-, di-, and trihydrated complexes of methyl carbamate have been studied in molecular expansion by high-resolution microwave spectroscopy, using chirped-pulse and Fabry-Perot resonator Fourier transform microwave instruments covering the frequency range from 2 to 18 GHz. From the rotational constants of the parent and the 18Ow substituted monoisotopologues, accurate values have been derived for the geometries of the hydrogen bond interactions. The nuclear quadrupole coupling constant χcc of the nitrogen nucleus provides a direct measure of complexation changes and decreases with the degree of hydration, whereas the hindered internal rotation barrier increases slightly with microsolvation. Both tendencies could have a common origin in the π-cooperative inductive effects as the microsolvation series progresses. All transitions are split by the internal rotation of the methyl top and the nuclear quadrupole coupling, and in the largest cluster, they are additionally split by an inversion motion.

3.
J Chem Phys ; 160(19)2024 May 21.
Artigo em Inglês | MEDLINE | ID: mdl-38747434

RESUMO

The gas-phase rotational spectrum from 8 to 750 GHz and the high-resolution infrared (IR) spectrum of pyridazine (o-C4H4N2) have been analyzed for the ground and four lowest-energy vibrationally excited states. A combined global fit of the rotational and IR data has been obtained using a sextic, centrifugally distorted-rotor Hamiltonian with Coriolis coupling between appropriate states. Coriolis coupling has been addressed in the two lowest-energy coupled dyads (ν16, ν13 and ν24, ν9). Utilizing the Coriolis coupling between the vibrational states of each dyad and the analysis of the IR spectrum for ν16 and ν9, we have determined precise band origins for each of these fundamental states: ν16 (B1) = 361.213 292 7 (17) cm-1, ν13 (A2) = 361.284 082 4 (17) cm-1, ν24 (B2) = 618.969 096 (26) cm-1, and ν9 (A1) = 664.723 378 4 (27) cm-1. Notably, the energy separation in the ν16-ν13 Coriolis-coupled dyad is one of the smallest spectroscopically measured energy separations between vibrational states: 2122.222 (72) MHz or 0.070 789 7 (24) cm-1. Despite ν13 being IR inactive and ν24 having an impractically low-intensity IR intensity, the band origins of all four vibrational states were measured, showcasing the power of combining the data provided by millimeter-wave and high-resolution IR spectra. Additionally, the spectra of pyridazine-dx isotopologues generated for a previous semi-experimental equilibrium structure (reSE) determination allowed us to analyze the two lowest-energy vibrational states of pyridazine for all nine pyridazine-dx isotopologues. Coriolis-coupling terms have been measured for analogous vibrational states across seven isotopologues, both enabling their comparison and providing a new benchmark for computational chemistry.

4.
Molecules ; 28(4)2023 Feb 10.
Artigo em Inglês | MEDLINE | ID: mdl-36838680

RESUMO

The orientation and magnitude of the molecular electric dipole moment are key properties relevant to topics ranging from the nature of intermolecular interactions to the quantitative analysis of complex gas-phase mixtures, such as chemistry in astrophysical environments. Stark effect measurements on rotational spectra have been the method of choice for isolated molecules but have become less common with the practical disappearance of Stark modulation spectrometers. Their role has been taken over by supersonic expansion measurements within a Fabry-Perot resonator cavity, which introduces specific technical problems that need to be overcome. Several of the adopted solutions are described and compared. Presently, we report precise electric dipole moment determinations for the two most stable conformers of the selected molecules of confirmed or potential astrophysical relevance: n-propanol, n-butanol, and n-butyl cyanide. All dipole moment components have been precisely determined at supersonic expansion conditions by employing specially designed Stark electrodes and a computer program for fitting the measured Stark shifts, inclusive of cases with resolved nuclear quadrupole hyperfine structure. The experimental values are compared with suitable quantum chemistry computations. It is found that, among the tested levels of computation, vibrationally averaged dipole moments are the closest to the observation and the molecular values are, as in the lighter molecules in the series, largely determined by the hydroxyl or nitrile groups.

5.
Phys Chem Chem Phys ; 23(12): 7295-7301, 2021 Mar 28.
Artigo em Inglês | MEDLINE | ID: mdl-33876089

RESUMO

The ability and preference of 3-oxetanone to form hydrogen or tetrel bonds have been investigated in its complexes with water and formaldehyde by using Fourier transform microwave spectroscopy complemented with quantum chemical calculations. Different types of interactions and internal dynamics have been observed in the targeted complexes. With water, the ether oxygen of 3-oxetanone is the favoured interaction site forming a classical O-HO hydrogen bond. Quite differently, the carbonyl group of 3-oxetanone plays the dual role as a tetrel donor and a proton acceptor in the 3-oxetanone-formaldehyde complex, featuring the CO tetrel bond and C-HO weak hydrogen bond interactions. Splittings originated from the internal rotation of formaldehyde around its C2 axis were also observed. The V2 barrier was estimated to be 375(10) cm-1 based on Meyer's one-dimensional flexible model. The changes in geometries and electronic densities upon complexation would shed light on the impact of archetype solvent and organic substrate molecules on the reactivity of 3-oxetanone.

6.
Molecules ; 26(22)2021 Nov 15.
Artigo em Inglês | MEDLINE | ID: mdl-34833962

RESUMO

We report the observation and analysis of the rotational spectrum of a 1:1 cluster between 2-aminopyridine and water (AMW) carried out with supersonic expansion Fourier transform microwave spectroscopy at 4.7-16.5 GHz. Measurements of the 2-aminopyridine monomer (AMP) were also extended up to 333 GHz for the room-temperature rotational spectrum and to resolved hyperfine splitting resulting from the presence of two 14N quadrupolar nuclei. Supersonic expansion measurements for both AMP and AMW were also carried out for two synthesized isotopic species with single deuteration on the phenyl ring. Nuclear quadrupole hyperfine structure has also been resolved for AMW and the derived splitting constants were used as an aid in structural analysis. The structure of the AMW cluster was determined from the three sets of available rotational constants and the hydrogen bonding configuration is compared with those for clusters with water of similarly sized single-ring molecules. Experimental results aided by quantum chemistry computations allow the conclusion that the water molecule is unusually strongly bound by two hydrogen bonds, OH...N and O...HN, to the NCNH atomic chain of AMP with the potential to replace hydrogen bonds to the identical structural segment in cytosine and adenine in CT and AT nucleic acid base pairs.

7.
Phys Chem Chem Phys ; 22(33): 18351-18360, 2020 Sep 07.
Artigo em Inglês | MEDLINE | ID: mdl-32785385

RESUMO

Microsolvated complexes of ethyl carbamate (urethane) with up to three water molecules formed in a supersonic expansion have been characterized by high-resolution microwave spectroscopy. Both chirped-pulse and cavity Fourier transform microwave spectrometers covering the 2-13 GHz frequency range have been used. The structures of the complexes have been characterized and show water molecules closing sequential cycles through hydrogen bonding with the amide group. As is the case in the monomer, the ethyl carbamate-water complexes exhibit a conformational equilibrium between two conformers close in energy. The interconversion barrier between both forms has been studied by analyzing the spectra obtained using different carrier gas in the expansion. Complexation of ethyl carbamate with water molecules does not appear to significantly alter the potential energy function for the interconversion between the two conformations of ethyl carbamate.

8.
Angew Chem Int Ed Engl ; 59(22): 8401-8405, 2020 05 25.
Artigo em Inglês | MEDLINE | ID: mdl-32096889

RESUMO

Carbohydrates are ubiquitous biomolecules in nature. The vast majority of their biomolecular activity takes place in aqueous environments. Molecular reactivity and functionality are, therefore, often strongly influenced by not only interactions with equivalent counterparts, but also with the surrounding water molecules. Glycoaldehyde (Gly) represents a prototypical system to identify the relevant interactions and the balance that governs them. Here we present a broadband rotational-spectroscopy study on the stepwise hydration of the Gly dimer with up to three water molecules. We reveal the preferred hydrogen-bond networks formed when water molecules sequentially bond to the sugar dimer. We observe that the dimer structure and the hydrogen-bond networks at play remarkably change upon the addition of just a single water molecule to the dimer. Further addition of water molecules does not significantly alter the observed hydrogen-bond topologies.

9.
Chemistry ; 25(43): 10172-10178, 2019 Aug 01.
Artigo em Inglês | MEDLINE | ID: mdl-31166628

RESUMO

Bond length alternation is a chemical phenomenon in benzene rings fused to other rings, which has been mainly predicted theoretically. Its physical origin is still not clear and has generated discussion. Here, by using a strategy that combines microwave spectroscopy, custom-made synthesis and high-level ab initio calculations, we demonstrate that this phenomenon is clearly observed in the prototype indazole molecule isolated in the gas phase. The 1H-indazole conformer was detected by rotational spectroscopy, and its 17 isotopologues resulting from single and double heavy atom substitution (13 C and 15 N) were also unambiguously observed. Several experimental structures were determined and, in particular, the most useful semi-experimental equilibrium structure (re SE ), allowed determination of the heavy atom bond lengths to milli-Ångstrom precision. The experimentally determined bond length alternation is estimated to correspond to 60:40 contributions from the two resonant forms of 1H-indazole.

10.
J Phys Chem A ; 123(37): 7983-7990, 2019 Sep 19.
Artigo em Inglês | MEDLINE | ID: mdl-31461275

RESUMO

The structure of butyl carbamate and of its complex with water generated in a supersonic expansion has been characterized by Fourier transform microwave spectroscopy. Up to 13 low-energy conformations of the monomer have been predicted that differ in the relative orientation of the butyl chain and the amide group. However, only three conformations have been observed experimentally. The remaining low-energy conformers are expected to interconvert into the observed rotamers through collisional relaxation processes in the supersonic jet. The values of the C-O-Cα-Cß dihedral angle observed for the two most stable conformers of butyl carbamate, with extended configurations, can be directly correlated with the values of this angle in the two experimentally observed conformers of the shorter-chain molecule, ethyl carbamate. The less stable form shows a weak C-H···O═C intramolecular hydrogen bond from the terminal methyl group to the carbamate C═O group, stabilizing a folded configuration. For the most stable butyl carbamate monomer the complex with one molecule of water has been observed. In that complex the water molecule attaches to the amide group in a cyclic arrangement using two hydrogen bonds. The results indicate that water does not substantially alter the conformational behavior of butyl carbamate.

11.
Phys Chem Chem Phys ; 19(22): 14214-14223, 2017 Jun 07.
Artigo em Inglês | MEDLINE | ID: mdl-28474023

RESUMO

We report the results of a broadband rotational spectroscopic study of corannulene, C20H10, all of its singly substituted 13C isotopologues, and a complex of corannulene with one molecule of water. Corannulene is a polycyclic aromatic hydrocarbon (PAH) with a curved structure that results in a large dipole moment. Observation of 13C isotopic species in natural abundance allowed us to precisely determine the molecular structure of corannulene. The differences between the experimental C-C bond lengths correlate to the double-bond character predicted using Kekule's resonance structures. In the case of C20H10-H2O, the water molecule is found to reside inside the bowl-like structure of corannulene. Our experimental and theoretical results indicate that the water molecule rotates freely around its C2 axis and that dispersion interactions are the dominant contribution to the binding.

12.
Angew Chem Int Ed Engl ; 53(52): 14368-72, 2014 Dec 22.
Artigo em Inglês | MEDLINE | ID: mdl-25348841

RESUMO

Broadband rotational spectroscopy of water clusters produced in a pulsed molecular jet expansion has been used to determine the oxygen atom geometry in three isomers of the nonamer and two isomers of the decamer. The isomers for each cluster size have the same nominal geometry but differ in the arrangement of their hydrogen bond networks. The nearest neighbor OO distances show a characteristic pattern for each hydrogen bond network isomer that is caused by three-body effects that produce cooperative hydrogen bonding. The observed structures are the lowest energy cluster geometries identified by quantum chemistry and the experimental and theoretical OO distances are in good agreement. The cooperativity effects revealed by the hydrogen bond OO distance variations are shown to be consistent with a simple model for hydrogen bonding in water that takes into account the cooperative and anticooperative bonding effects of nearby water molecules.


Assuntos
Água/química , Hidrogênio/química , Ligação de Hidrogênio , Conformação Molecular , Oxigênio/química , Teoria Quântica
13.
J Phys Chem A ; 117(39): 9889-98, 2013 Oct 03.
Artigo em Inglês | MEDLINE | ID: mdl-23514359

RESUMO

The pure rotation spectrum of deuterated cyanamide was recorded at frequencies from 118 to 649 GHz, which was complemented by measurement of its high-resolution rotation-vibration spectrum at 8-350 cm(-1). For D2NCN the analysis revealed considerable perturbations between the lowest Ka rotational energy levels in the 0(+) and 0(-) substates of the lowest inversion doublet. The final data set for D2NCN exceeded 3000 measured transitions and was successfully fitted with a Hamiltonian accounting for the 0(+) ↔ 0(-) coupling. A smaller data set, consisting only of pure rotation and rotation-vibration lines observed with microwave techniques was obtained for HDNCN, and additional transitions of this type were also measured for H2NCN. The spectroscopic data for all three isotopic species were fitted with a unified, robust Hamiltonian allowing confident prediction of spectra well into the terahertz frequency region, which is of interest to contemporary radioastronomy. The isotopic dependence of the determined inversion splitting, ΔE = 16.4964789(8), 32.089173(3), and 49.567770(6) cm(-1), for D2NCN, HDNCN, and H2NCN, respectively, is found to be in good agreement with estimates from a simple reduced quartic-quadratic double minimum potential.

14.
J Phys Chem A ; 117(50): 13815-24, 2013 Dec 19.
Artigo em Inglês | MEDLINE | ID: mdl-24099452

RESUMO

The high resolution Fourier transform spectrum of the chemically challenging sulfur dicyanide, S(CN)2, molecule was recorded at the far-infrared beamline of the synchrotron at the Canadian Light Source. The spectrum covered 50-350 cm(-1), and transitions in three fundamentals, ν4, ν7, and ν8, as well as in the hot-band sequence (n + 1)ν4 - nν4, n = 1-4, have been assigned and measured. Global analysis of over 21,300 pure rotation and rotation vibration transitions allowed determination of precise energies for 12 of the lowest vibrationally excited states of S(CN)2, including the five lowest fundamentals. These results constitute an extensive set of benchmarks for ab initio anharmonic force field calculations and the observed and calculated vibration-rotation constants and anharmonic frequencies are compared. The semiexperimental equilibrium, r(e)(SE), geometry of S(CN)2 has also been evaluated. In the course of the measurements, new information concerning the physical chemistry of S(CN)2 has been obtained.

15.
Phys Chem Chem Phys ; 13(31): 13912-9, 2011 Aug 21.
Artigo em Inglês | MEDLINE | ID: mdl-21743896

RESUMO

The rotational spectrum of the cyclic (HCl)(2)H(2)O cluster has been identified for the first time in the chirped pulse, Fourier transform microwave spectrum of a supersonically expanded HCl/H(2)O/Ar mixture. The spectrum was measured at frequencies 6-18.5 GHz, and transitions in two inversion-tunneling states, at close to 1 : 3 relative intensity, have been assigned for the parent species. The two single (37)Cl isotopic species, and the double (37)Cl species have been assigned in the natural abundance sample, and the (18)O and HDO species of the cluster were identified in isotopically enriched samples. The rich nuclear quadrupole hyperfine structure due to the presence of two chlorine nuclei has been satisfactorily fitted and provided useful information on the nonlinearity of intermolecular bonds in the cluster. The r(s) heavy atom geometry of the cluster was determined and the strongest bond in the intermolecular cycle r(O···HCl) = 3.126(3) Å, is found to be intermediate in length between the values in H(2)O···HCl and (H(2)O)(2)HCl. The fitted spectroscopic constants and derived molecular properties are compared with ab initio predictions, and a discussion of complexation effects in these three clusters is made.

16.
Phys Chem Chem Phys ; 12(29): 8329-39, 2010 Aug 01.
Artigo em Inglês | MEDLINE | ID: mdl-20502812

RESUMO

The rotational spectrum of n-propanol (n-CH(3)CH(2)CH(2)OH) was studied with several techniques of contemporary broadband rotational spectroscopy at frequencies from 8 to 550 GHz. Rotational transitions in all five conformers of the molecule, Gt, Gg, Gg', Tt, and Tg, have been unambiguously assigned. Over 6700 lines of the Gt, Gg, and Gg' species, for quantum number values reaching K(a) = 33 and J = 67, were fitted in a joint analysis leading to the determination of DeltaE(Gg-Gt) = 47.82425(25) cm(-1) and DeltaE (Gg'-Gg) = 3.035047(11) cm(-1). Stark effect measurements in supersonic expansion were used to further confirm the assignment. The results are compared with those for the ethanol molecule and with ab initio calculations, allowing several inferences to be drawn concerning the differences in the large amplitude torsional potential of the hydroxyl group in the two molecules.

17.
Acta Crystallogr A Found Adv ; 74(Pt 5): 524-536, 2018 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-30182939

RESUMO

The previously reported [Volkov et al. (2004). Chem. Phys. Lett. 391, 170-175] exact potential and multipole moment (EP/MM) method for evaluation of intermolecular electrostatic interaction energies using the nuclei-centered pseudoatom representation of electron densities is significantly improved in terms of both speed and accuracy by replacing the numerical quadrature integration of the exact potential with a fully analytical technique. The resulting approach, incorporated in the XDPROP module of the software package XD, has been tested on several molecular systems ranging in size from water-water to dodecapeptide-dodecapeptide dimers using electron densities constructed via the University at Buffalo Aspherical Atom Databank. The improved hybrid method provides electrostatic interaction energies within the uncertainty of ≤0.2 kJ mol-1 for all benchmark systems. The running time for a dimer of a sizable, 225-atom dodecapeptide is under 4 s on a 2012 central processing unit (2.8 GHz AMD Opteron 6348) and under 3 s on a relatively modern processor (2.8 GHz Intel Xeon E3-1505M v5).


Assuntos
Elétrons/classificação , Algoritmos , Modelos Moleculares , Estrutura Molecular , Fenômenos Físicos , Eletricidade Estática , Termodinâmica , Água/química
18.
J Chem Theory Comput ; 14(2): 1141-1153, 2018 Feb 13.
Artigo em Inglês | MEDLINE | ID: mdl-29328634

RESUMO

The rich potential energy surface of the water undecamer (H2O)11 was explored with a basin hopping algorithm using a TIP4P potential and other methods followed by extensive ab initio MP2 minimizations and CCSD(T) corrections. This protocol yielded 17, 66, and 125 distinct isomers within 0.5, 1.0, and 2.0 kcal mol-1 of the complete basis set CCSD(T) global minimum, respectively. These isomers were categorized into 15 different families based on their oxygen framework and hydrogen bonding topology. Determination of the global minimum proved challenging because of the presence of many nearly isoenergetic isomers. The predicted global minimum varied among ab initio methods, density functionals, and model potentials, and it was sensitive to the choice of energy extrapolation schemes, higher-order CCSD(T) corrections, and inclusion of zero-point vibrational energy. The presence of a large number of nearly degenerate structures and the isomerization between them has manifested itself in the anomalous broadening of the heat capacity curve of the undecamer in simulations around the melting region.

19.
Sci Adv ; 3(7): e1700022, 2017 07.
Artigo em Inglês | MEDLINE | ID: mdl-28782019

RESUMO

Recent simulations have indicated that vinyl cyanide is the best candidate molecule for the formation of cell membranes/vesicle structures in Titan's hydrocarbon-rich lakes and seas. Although the existence of vinyl cyanide (C2H3CN) on Titan was previously inferred using Cassini mass spectrometry, a definitive detection has been lacking until now. We report the first spectroscopic detection of vinyl cyanide in Titan's atmosphere, obtained using archival data from the Atacama Large Millimeter/submillimeter Array (ALMA), collected from February to May 2014. We detect the three strongest rotational lines of C2H3CN in the frequency range of 230 to 232 GHz, each with >4σ confidence. Radiative transfer modeling suggests that most of the C2H3CN emission originates at altitudes of ≳200 km, in agreement with recent photochemical models. The vertical column densities implied by our best-fitting models lie in the range of 3.7 × 1013 to 1.4 × 1014 cm-2. The corresponding production rate of vinyl cyanide and its saturation mole fraction imply the availability of sufficient dissolved material to form ~107 cell membranes/cm3 in Titan's sea Ligeia Mare.

20.
J Phys Chem Lett ; 8(23): 5744-5750, 2017 Dec 07.
Artigo em Inglês | MEDLINE | ID: mdl-29112436

RESUMO

Polycyclic aromatic hydrocarbons (PAHs) are key players in reaction chemistry. While it is postulated that they serve as a basis for ice grains, there has been no direct detection of PAHs in astronomical environments. We aim to investigate the hydration of PAHs to set a foundation for the future exploration of potential ice formation pathways. We report results from chirped pulse Fourier transform microwave spectroscopy and quantum-chemical calculations for the PAH acenaphthene and acenaphthene complexed with up to four water molecules. The acenaphthene-(H2O)3 complex is of particular interest as the elusive cyclic water trimer was observed. It appears in a slightly distorted configuration when compared with the pure water trimer. This is explained by hydrogen-bond net cooperativity effects. Binding energies for the complexes are presented. Our results provide insight into the onset of complex aggregation that could be occurring in extraterrestrial environments as part of ice grain formation.

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