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We propose introducing an extended Hubbard Hamiltonian derived via the ab initio downfolding method, which was originally formulated for periodic materials, toward efficient quantum computing of molecular electronic structure calculations. By utilizing this method, the first-principles Hamiltonian of chemical systems can be coarse-grained by eliminating the electronic degrees of freedom in higher energy space and reducing the number of terms of electron repulsion integral from O(N4) to O(N2). Our approach is validated numerically on the vertical excitation energies and excitation characters of ethylene, butadiene, and hexatriene. The dynamical electron correlation is incorporated within the framework of the constrained random phase approximation in advance of quantum computations, and the constructed models capture the trend of experimental and high-level quantum chemical calculation results. As expected, the L1-norm of the fermion-to-qubit mapped model Hamiltonians is significantly lower than that of conventional ab initio Hamiltonians, suggesting improved scalability of quantum computing. Those numerical outcomes and the results of the simulation of excited-state sampling demonstrate that the ab initio extended Hubbard Hamiltonian may hold significant potential for quantum chemical calculations using quantum computers.
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We demonstrate the facile, rational synthesis of monodispersedly sized zinc oxide (ZnO) nanowires from randomly sized seeds by hydrothermal growth. Uniformly shaped nanowire tips constructed in ammonia-dominated alkaline conditions serve as a foundation for the subsequent formation of the monodisperse nanowires. By precisely controlling the sharp tip formation and the nucleation, our method substantially narrows the distribution of ZnO nanowire diameters from σ = 13.5 nm down to σ = 1.3 nm and controls their diameter by a completely bottom-up method, even initiating from randomly sized seeds. The proposed concept of sharp tip based monodisperse nanowires growth can be applied to the growth of diverse metal oxide nanowires and thus paves the way for bottom-up grown metal oxide nanowires-integrated nanodevices with a reliable performance.
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The elongation method with intermediate mechanical and electrostatic embedding (ELG-IMEE) is proposed. The electrostatic embedding uses atomic charges generated by a charge sensitivity analysis (CSA) method and parameterized for three different population analyses, namely, the Merz-Singh-Kollman scheme, the charge model 5, and the atomic polar tensor. The obtained CSA models were tested on two model systems. Test calculations show that the electrostatic embedding provides several times of decrease in the difference of energies of testing and reference calculations in comparison with the conventional elongation approach (ELG). The mechanical embedding is implemented in a combination of the conventional elongation method and the ONIOM approach. Moreover, it was demonstrated that the geometry optimization with the ELG-IMEE reduces the errors in the optimized structures by about one order in root-mean-square deviation, when compared to ELG.
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Metal-oxide nanowires have demonstrated excellent capability in the electrical detection of various molecules based on their material robustness in liquid and air environments. Although the surface structure of the nanowires essentially determines their interaction with adsorbed molecules, understanding the correlation between an oxide nanowire surface and an adsorbed molecule is still a major challenge. Herein, we propose a rational methodology to obtain this information for low-density molecules adsorbed on metal oxide nanowire surfaces by employing infrared p-polarized multiple-angle incidence resolution spectroscopy and temperature-programmed desorption/gas chromatography-mass spectrometry. As a model system, we studied the surface chemical transformation of an aldehyde (nonanal, a cancer biomarker in breath) on single-crystalline ZnO nanowires. We found that a slight surface reconstruction, induced by the thermal pretreatment, determines the surface chemical reactivity of nonanal. The present results show that the observed surface reaction trend can be interpreted in terms of the density of Zn ions exposed on the nanowire surface and of their corresponding spatial arrangement on the surface, which promotes the reaction between neighboring adsorbed molecules. The proposed methodology will support a better understanding of complex molecular transformations on various nanostructured metal-oxide surfaces.
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The osmolyte molecule trimethylamine-N-oxide (TMAO) stabilizes the structure of proteins. As functional proteins are generally found in aqueous solutions, an important aspect of this stabilization is the interaction of TMAO with water. Here, we review, using vibrational spectroscopy and molecular dynamics simulations, recent studies on the structure and dynamics of TMAO with its surrounding water molecules. This article ends with an outlook on the open questions on TMAO-protein and TMAO-urea interactions in aqueous environments.
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Metilaminas/química , Simulação de Dinâmica Molecular , Proteínas/química , Interações Hidrofóbicas e Hidrofílicas , Conformação Molecular , Óxidos/química , Proteínas/metabolismo , Espectrofotometria Infravermelho , Ureia/química , Água/químicaRESUMO
Bacterial pathogens or cancer cells can acquire multidrug resistance, which causes serious clinical problems. In cells with multidrug resistance, various drugs or antibiotics are extruded across the cell membrane by multidrug transporters. The multidrug and toxic compound extrusion (MATE) transporter is one of the five families of multidrug transporters. MATE from Pyrococcus furiosus uses H(+) to transport a substrate from the cytoplasm to the outside of a cell. Crystal structures of MATE from P. furiosus provide essential information on the relevant H(+)-binding sites (D41 and D184). Hybrid quantum mechanical/molecular mechanical simulations and continuum electrostatic calculations on the crystal structures predict that D41 is protonated in one structure (Straight) and, both D41 and D184 protonated in another (Bent). All-atom molecular dynamics simulations suggest a dynamic equilibrium between the protonation states of the two aspartic acids and that the protonation state affects hydration in the substrate binding cavity and lipid intrusion in the cleft between the N- and C-lobes. This hypothesis is examined in more detail by quantum mechanical/molecular mechanical calculations on snapshots taken from the molecular dynamics trajectories. We find the possibility of two proton transfer (PT) reactions in Straight: the 1st PT takes place between side-chains D41 and D184 through a transient formation of low-barrier hydrogen bonds and the 2nd through another H(+) from the headgroup of a lipid that intrudes into the cleft resulting in a doubly protonated (both D41 and D184) state. The 1st PT affects the local hydrogen bond network and hydration in the N-lobe cavity, which would impinge on the substrate-binding affinity. The 2nd PT would drive the conformational change from Straight to Bent. This model may be applicable to several prokaryotic H(+)-coupled MATE multidrug transporters with the relevant aspartic acids.
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Proteínas Arqueais/metabolismo , Prótons , Pyrococcus furiosus/metabolismo , Proteínas Arqueais/química , Sítios de Ligação , Cristalografia por Raios X , Ligação de Hidrogênio , Interações Hidrofóbicas e Hidrofílicas , Lipídeos/química , Modelos Biológicos , Simulação de Dinâmica MolecularRESUMO
A global analytic potential energy surface for the ro-vibrational dynamics of cis- and trans-formic acid is presented, constructed using LASSO-based regression to reproduce CCSD(T)(F12*)/cc-pVTZ-F12 energies. The fit is accurate to 0.25% has an RMS deviation from the ab initio data of 9 cm-1 for the energy range 0-15000 cm-1. Converged J = 0 vibrational eigenstates are reported, computed using vibrational configuration interaction with an internal coordinate path Hamiltonian for the torsional motion connecting the cis and trans rotamers. Methodological choices concerning the appropriate definitions of the curvilinear and diabatic bath coordinates are discussed. The zero point of the cis rotamer is 1412 cm-1 above that of the trans, which lies at 7354 cm-1. The computed fundamentals match the bands recorded from gas-phase IR spectroscopy with an RMSD of only 3 cm-1. A fresh assignment of the overtone spectra of both the cis and trans rotamers is presented for the energy range 0-4720 cm-1, where 14 out of the 51 bands are reassigned on the basis of the VCI calculations.
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The molecular geometries of isolated complexes in which a single molecule of C2H4 or C2H2 is bound to CuCl have been determined through pure rotational spectroscopy and ab-initio calculations. The C2H2···CuCl and C2H4···CuCl complexes are generated through laser vaporization of a copper rod in the presence of a gas sample undergoing supersonic expansion and containing C2H2 (or C2H4), CCl4, and Ar. Results are presented for five isotopologues of C2H2···CuCl and six isotopologues of C2H4···CuCl. Both of these complexes adopt C(2v), T-shaped geometries in which the hydrocarbon binds to the copper atom through its π electrons such that the metal is equidistant from all H atoms. The linear and planar geometries of free C2H2 and C2H4, respectively, are observed to distort significantly on attachment to the CuCl unit, and the various changes are quantified. The â (*-C-H) parameter in C2H2 (where * indicates the midpoint of the C≡C bond) is measured to be 192.4(7)° in the r0 geometry of the complex representing a significant change from the linear geometry of the free molecule. This distortion of the linear geometry of C2H2 involves the hydrogen atoms moving away from the copper atom within the complex. Ab-initio calculations at the CCSD(T)(F12*)/AVTZ level predict a dihedral â (HCCCu) angle of 96.05° in C2H4···CuCl, and the experimental results are consistent with such a distortion from planarity. The bonds connecting the carbon atoms within each of C2H2 and C2H4, respectively, extend by 0.027 and 0.029 Å relative to the bond lengths in the isolated molecules. Force constants, k(σ), and nuclear quadrupole coupling constants, χ(aa)(Cu), [χ(bb)(Cu) - χ(cc)(Cu)], χ(aa)(Cl), and [χ(bb)(Cl) - χ(cc)(Cl)], are independently determined for all isotopologues of C2H2···CuCl studied and for four isotopologues of C2H4···CuCl.
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We present a new approach to semi-global potential energy surface fitting that uses the least absolute shrinkage and selection operator (LASSO) constrained least squares procedure to exploit an extremely flexible form for the potential function, while at the same time controlling the risk of overfitting and avoiding the introduction of unphysical features such as divergences or high-frequency oscillations. Drawing from a massively redundant set of overlapping distributed multi-dimensional Gaussian functions of inter-atomic separations we build a compact full-dimensional surface for malonaldehyde, fit to explicitly correlated coupled cluster CCSD(T)(F12*) energies with a root mean square deviations accuracy of 0.3%-0.5% up to 25,000 cm(-1) above equilibrium. Importance-sampled diffusion Monte Carlo calculations predict zero point energies for malonaldehyde and its deuterated isotopologue of 14 715.4(2) and 13 997.9(2) cm(-1) and hydrogen transfer tunnelling splittings of 21.0(4) and 3.2(4) cm(-1), respectively, which are in excellent agreement with the experimental values of 21.583 and 2.915(4) cm(-1).
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The rotational spectra of six isotopologues of a complex of ethyne and silver acetylide, C2H2â â â AgCCH, are measured by both chirped-pulse and Fabry-Perot cavity versions of Fourier-transform microwave spectroscopy. The complex is generated through laser ablation of a silver target in the presence of a gas sample containing 1% C2H2, 1% SF6, and 98% Ar undergoing supersonic expansion. Rotational, A0, B0, C0, and centrifugal distortion ΔJ and ΔJK constants are determined for all isotopologues of C2H2â â â AgCCH studied. The geometry is planar, C2v and T-shaped in which the C2H2 sub-unit comprises the bar of the "T" and binds to the metal atom through its π electrons. In the r0 geometry, the distance of the Ag atom from the centre of the triple bond in C2H2 is 2.2104(10) Å. The r(HC≡CH) parameter representing the bond distance separating the two carbon atoms and the angle, â (CCH), each defined within the C2H2 sub-unit, are determined to be 1.2200(24) Å and 186.0(5)°, respectively. This distortion of the linear geometry of C2H2 involves the hydrogen atoms moving away from the silver atom within the complex. The results thus reveal that the geometry of C2H2 changes measurably on coordination to AgCCH. A value of 59(4) N m(-1) is determined for the intermolecular force constant, kσ, confirming that the complex is significantly more strongly bound than hydrogen and halogen-bonded analogues. Ab initio calculations of the re geometry at the CCSD(T)(F12(*))/ACVTZ level of theory are consistent with the experimental results. The spectra of the (107)Ag(13)C(13)CH and (109)Ag(13)C(13)CH isotopologues of free silver acetylide are also measured for the first time allowing the geometry of the AgCCH monomer to be examined in greater detail than previously.
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We present a combination of three-dimensional reference interaction site model self-consistent field (3D-RISM-SCF) theory and the variational quantum eigensolver (VQE) to consider the solvent distribution effects within the framework of quantum-classical hybrid computing. The present method, 3D-RISM-VQE, does not include any statistical errors from the solvent configuration sampling owing to the analytical treatment of the statistical solvent distribution. We apply 3D-RISM-VQE to compute the spatial distribution functions of solvent water around a water molecule, the potential and Helmholtz energy curves of NaCl, and to analyze the Helmholtz energy component and related properties of H2O and NH4+. Moreover, we utilize 3D-RISM-VQE to analyze the extent to which solvent effects alter the efficiency of quantum calculations compared with calculations in the gas phase using the L1-norms of molecular electronic Hamiltonians. Our results demonstrate that the efficiency of quantum chemical calculations on a quantum computer in solution is virtually the same as that in the gas phase.
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Peptides play essential roles in biological phenomena, and, thus, there is a growing interest in detecting in vivo dynamics of peptide metabolisms. Dissolution-dynamic nuclear polarization (d-DNP) is a state-of-the-art technology that can markedly enhance the sensitivity of nuclear magnetic resonance (NMR), providing metabolic and physiological information in vivo. However, the hyperpolarized state exponentially decays back to the thermal equilibrium, depending on the spin-lattice relaxation time (T1). Because of the limitation in T1, peptide-based DNP NMR molecular probes applicable in vivo have been limited to amino acids or dipeptides. Here, we report the direct detection of in vivo metabolic conversions of hyperpolarized 13C-oligopeptides. Structure-based T1 relaxation analysis suggests that the C-terminal [1-13C]Gly-d2 residue affords sufficient T1 for biological uses, even in relatively large oligopeptides, and allowed us to develop 13C-ß-casomorphin-5 and 13C-glutathione. It was found that the metabolic response and perfusion of the hyperpolarized 13C-glutathione in the mouse kidney were significantly altered in a model of cisplatin-induced acute kidney injury.
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Isótopos de Carbono , Oligopeptídeos , Animais , Camundongos , Oligopeptídeos/metabolismo , Oligopeptídeos/química , Rim/metabolismo , Espectroscopia de Ressonância Magnética/métodosRESUMO
We present a general multi-reference framework for treating strong correlation in vibrational structure theory, which we denote the vibrational active space self-consistent field (VASSCF) approach. Active configurations can be selected according to excitation level or the degrees of freedom involved, or both. We introduce a novel state-specific second-order multi-configurational perturbation correction that accounts for the remaining weak correlation between the vibrational modes. The resulting VASPT2 method is capable of accurately and efficiently treating strong correlation in the form of large anharmonic couplings, at the same time as correctly resolving resonances between states. These methods have been implemented in our new dynamics package DYNAMOL, which can currently treat up to four-body Hamiltonian coupling terms. We present a pilot application of the VASPT2 method to the trans isomer of formic acid. We have constructed a new analytic potential that reproduces frozen core CCSD(T)(F12*)/cc-pVDZ-F12 energies to within 0.25% RMSD over the energy range 0-15 000 cm(-1). The computed VASPT2 fundamental transition energies are accurate to within 9 cm(-1) RMSD from experimental values, which is close to the accuracy one can expect from a CCSD(T) potential energy surface.
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Formiatos/química , Teoria Quântica , Hidróxidos/química , Estereoisomerismo , VibraçãoRESUMO
We develop a quantum-classical hybrid algorithm to calculate the analytical second-order derivative of the energy for the orbital-optimized variational quantum eigensolver (OO-VQE), which is a method to calculate eigenenergies of a given molecular Hamiltonian by utilizing near-term quantum computers and classical computers. We show that all quantities required in the algorithm to calculate the derivative can be evaluated on quantum computers as standard quantum expectation values without using any ancillary qubits. We validate our formula by numerical simulations of quantum circuits for computing the polarizability of the water molecule, which is the second-order derivative of the energy, with respect to the electric field. Moreover, the polarizabilities and refractive indices of thiophene and furan molecules are calculated as a test bed for possible industrial applications. We finally analyze the error scaling of the estimated polarizabilities obtained by the proposed analytical derivative versus the numerical derivative obtained by the finite difference. Numerical calculations suggest that our analytical derivative requires fewer measurements (runs) on quantum computers than the numerical derivative to achieve the same fixed accuracy.
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C(2)H(2)â¯Ag-Cl was formed from ethyne and AgCl in the gas phase and its rotational spectrum observed by both the chirped-pulse and Fabry-Perot cavity versions of Fourier-transform microwave spectroscopy. Reaction of laser-ablated silver metal with CCl(4) gave AgCl which then reacted with ethyne to give the complex. Ground-state rotational spectra of the six isotopologues (12)C(2)H(2)â¯(107)Ag(35)Cl, (12)C(2)H(2)â¯(109)Ag(35)Cl, (12)C(2)H(2)â¯(107)Ag(37)Cl, (12)C(2)H(2)â¯(109)Ag(37)Cl, (13)C(2)H(2)â¯(107)Ag(35)Cl, and (13)C(2)H(2)â¯(109)Ag(35)Cl were analysed to yield rotational constants A(0), B(0), and C(0), centrifugal distortion constants Δ(J), Δ(JK), and δ(J), and Cl nuclear quadrupole coupling constants χ(aa)(Cl) and χ(bb)(Cl)-χ(cc)(Cl). A less complete analysis was possible for (12)C(2)D(2)â¯(107)Ag(35)Cl and (12)C(2)D(2)â¯(109)Ag(35)Cl. Observed principal moments of inertia were interpreted in terms of a planar, T-shaped geometry of C(2v) symmetry in which the AgCl molecule lies along a C(2) axis of ethyne and the Ag atom forms a bond to the midpoint (∗) of the ethyne π bond. r(0) and r(m)(1) geometries and an almost complete r(s)-geometry were established. The ethyne molecule distorts on complex formation by lengthening of the C≡C bond and movement of the two H atoms away from the C≡C internuclear line and the Ag atom. The r(m)(1) bond lengths and angles are as follows: r(∗â¯Ag) = 2.1800(3) Å, r(C-C) = 1.2220(20) Å, r(Ag-Cl) = 2.2658(3) Å and the angle H-C≡∗ has the value 187.79(1)°. Ab initio calculations at the coupled-cluster singles and doubles level of theory with a perturbative treatment of triples (F12∗)∕cc-pVTZ yield a r(e) geometry in excellent agreement with the experimental r(m)(1) version, including the ethyne angular distortion.
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Pure rotational spectra of the ground vibrational states of six isotopologues of OC···AgI have been measured by chirped-pulse Fourier transform microwave spectroscopy. The spectra are assigned to determine the rotational constant, B(0), centrifugal distortion constant, D(J), and nuclear quadrupole coupling constant of the iodine atom, χ(aa)(I). The complex is linear. Isotopic substitutions at the silver, carbon, and oxygen atoms allow bond lengths to be established by the r(0), r(s), and r(m)((1)) methods of structure determination. The length of the C-O bond, r(CO), in the r(0) geometry for OC···AgI is 0.008 Å shorter than that found in the free CO molecule. The length of the Ag-I bond, r(AgI), is 0.013 Å shorter than in free AgI. χ(aa)(I) is determined to be -769.84(22) MHz for OC···(107)AgI implying an ionic character of 0.66 for the metal halide bond. Attachment of carbon monoxide to the isolated AgI molecule results in an increase of the ionic character of AgI of 0.12. The molecular structure and spectroscopic parameters determined from the experimental data are presented alongside the results of calculations at the explicitly correlated coupled-cluster singles, doubles and perturbative triples level. Vibrational frequencies, the electric dipole moment, the nuclear quadrupole coupling constant, and the dissociation energy of the molecule have been calculated.
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Elucidating photochemical reactions is vital to understanding various biochemical phenomena and developing functional materials such as artificial photosynthesis and organic solar cells, albeit with notorious difficulty in both experiments and theories. The best theoretical way so far to analyze photochemical reactions at the level of ab initio electronic structure is the state-averaged multiconfigurational self-consistent field (SA-MCSCF) method. However, the exponential computational cost of classical computers with the increasing number of molecular orbitals hinders applications of SA-MCSCF for large systems we are interested in. Utilizing quantum computers was recently proposed as a promising approach to overcome such computational cost, dubbed as state-averaged orbital-optimized variational quantum eigensolver (SA-OO-VQE). Here, we extend a theory of SA-OO-VQE so that analytical gradients of energy can be evaluated by standard techniques that are feasible with near-term quantum computers. The analytical gradients, known only for the state-specific OO-VQE in previous studies, allow us to determine various characteristics of photochemical reactions such as the conical intersection (CI) points. We perform a proof-of-principle calculation of our methods by applying it to the photochemical cis-trans isomerization of 1,3,3,3-tetrafluoropropene. Numerical simulations of quantum circuits and measurements can correctly capture the photochemical reaction pathway of this model system, including the CI points. Our results illustrate the possibility of leveraging quantum computers for studying photochemical reactions.
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The surface cation composition of nanoscale metal oxides critically determines the properties of various functional chemical processes including inhomogeneous catalysts and molecular sensors. Here we employ a gradual modulation of cation composition on a ZnO/(Cu1-x Zn x )O heterostructured nanowire surface to study the effect of surface cation composition (Cu/Zn) on the adsorption and chemical transformation behaviors of volatile carbonyl compounds (nonanal: biomarker). Controlling cation diffusion at the ZnO(core)/CuO(shell) nanowire interface allows us to continuously manipulate the surface Cu/Zn ratio of ZnO/(Cu1-x Zn x )O heterostructured nanowires, while keeping the nanowire morphology. We found that surface exposed copper significantly suppresses the adsorption of nonanal, which is not consistent with our initial expectation since the Lewis acidity of Cu2+ is strong enough and comparable to that of Zn2+. In addition, an increase of the Cu/Zn ratio on the nanowire surface suppresses the aldol condensation reaction of nonanal. Surface spectroscopic analysis and theoretical simulations reveal that the nonanal molecules adsorbed at surface Cu2+ sites are not activated, and a coordination-saturated in-plane square geometry of surface Cu2+ is responsible for the observed weak molecular adsorption behaviors. This inactive surface Cu2+ well explains the mechanism of suppressed surface aldol condensation reactions by preventing the neighboring of activated nonanal molecules. We apply this tailored cation composition surface for electrical molecular sensing of nonanal and successfully demonstrate the improvements of durability and recovery time as a consequence of controlled surface molecular behaviors.
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An investigation into spin structures of poly(m-phenylenecarbene), a prototype of magnetic organic molecules, is presented using the ab initio density matrix renormalization group method. It is revealed by achieving large-scale multireference calculations that the energy differences between high-spin and low-spin states (spin-gaps) of polycarbenes decrease with increasing the number of carbene sites. This size-dependency of the spin-gaps strikingly contradicts the predictions with single-reference methods including density functional theory. The wave function analysis shows that the low-spin states are beyond the classical spin picture, namely, much of multireference character, and thus are manifested as strongly correlated quantum states. The size dependence of the spin-gaps involves an odd-even oscillation, which cannot be explained by the integer-spin Heisenberg model with a single magnetic-coupling constant.
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To improve the sensing properties toward volatile organic compound gases, a preheating process was introduced in a miniature pulse-driven semiconductor gas sensor, using SnO2 nanoparticles. The miniature sensor went through a short preheating span at a high temperature before being cooled and then experienced a measurement span under heating; this is the double-pulse-driven mode. This operating profile resulted in the modification of the surface conditions of naked SnO2 nanoparticles to facilitate the adsorption of O2- and ethanol-based adsorbates. Temperature-programmed reaction measurement results show that ethanol gas was adsorbed onto the SnO2 surface at 30 °C, and the adsorption amount of ethanol and its byproducts was increased after ethanol exposure at high temperatures followed by cooling. The electrical resistance of the sensor in synthetic air increased as the preheating temperature increased. The sensor responses, Si and Se, to 1 ppm ethanol at 250 °C were enhanced by introducing the preheating process; Si values at 250 °C with and without preheating at 300 °C are 40 and 15, respectively. The obtained improvements were attributed to an increase in O2- adsorption onto the SnO2 surface during the preheating phase. During the cooling phases, the adsorption of ethanol-based molecules onto the SnO2 surface and their condensation in the sensing layer contributed to the enhanced performance. In addition, the double-pulse-driven mode improves the recovery speed in the electrical resistance after gas detection. These improvements made in the sensing properties of the double-pulse-driven semiconductor gas sensors provide desirable advantages for healthcare and medical devices.