Newton-X Platform: New Software Developments for Surface Hopping and Nuclear Ensembles.

Newton-X is an open-source computational platform to perform nonadiabatic molecular dynamics based on surface hopping and spectrum simulations using the nuclear ensemble approach. Both are among the most common methodologies in computational chemistry for photophysical and photochemical investigations. This paper describes the main features of these methods and how they are implemented in Newton-X. It emphasizes the newest developments, including zero-point-energy leakage correction, dynamics on complex-valued potential energy surfaces, dynamics induced by incoherent light, dynamics based on machine-learning potentials, exciton dynamics of multiple chromophores, and supervised and unsupervised machine learning techniques. Newton-X is interfaced with several third-party quantum-chemistry programs, spanning a broad spectrum of electronic structure methods.

Trajectory Surface Hopping for a Polarizable Embedding QM/MM Formulation.

We present the implementation of trajectory surface-hopping nonadiabatic dynamics for a polarizable embedding QM/MM formulation. Time-dependent density functional theory was used at the quantum mechanical level of theory, whereas the molecular mechanics description involved the polarizable AMOEBA force field. This implementation has been obtained by integrating the surface-hopping program Newton-X NS with an interface between the Gaussian 16 and the Tinker suites of codes to calculate QM/AMOEBA energies and forces. The implementation has been tested on a photoinduced electron-driven proton-transfer reaction involving pyrimidine and a hydrogen-bonded water surrounded by a small cluster of water molecules and within a large water droplet.

Simulations of molecular photodynamics in long timescales.

Nonadiabatic dynamics simulations in the long timescale (much longer than 10 ps) are the next challenge in computational photochemistry. This paper delimits the scope of what we expect from methods to run such simulations: they should work in full nuclear dimensionality, be general enough to tackle any type of molecule and not require unrealistic computational resources. We examine the main methodological challenges we should venture to advance the field, including the computational costs of the electronic structure calculations, stability of the integration methods, accuracy of the nonadiabatic dynamics algorithms and software optimization. Based on simulations designed to shed light on each of these issues, we show how machine learning may be a crucial element for long time-scale dynamics, either as a surrogate for electronic structure calculations or aiding the parameterization of model Hamiltonians. We show that conventional methods for integrating classical equations should be adequate to extended simulations up to 1 ns and that surface hopping agrees semiquantitatively with wave packet propagation in the weak-coupling regime. We also describe our optimization of the Newton-X program to reduce computational overheads in data processing and storage. This article is part of the theme issue 'Chemistry without the Born-Oppenheimer approximation'.

Control of Protonated Schiff Base Excited State Decay within Visual Protein Mimics: A Unified Model for Retinal Chromophores.

Artificial biomimetic chromophore-protein complexes inspired by natural visual pigments can feature color tunability across the full visible spectrum. However, control of excited state dynamics of the retinal chromophore, which is of paramount importance for technological applications, is lacking due to its complex and subtle photophysics/photochemistry. Here, ultrafast transient absorption spectroscopy and quantum mechanics/molecular mechanics simulations are combined for the study of highly tunable rhodopsin mimics, as compared to retinal chromophores in solution. Conical intersections and transient fluorescent intermediates are identified with atomistic resolution, providing unambiguous assignment of their ultrafast excited state absorption features. The results point out that the electrostatic environment of the chromophore, modified by protein point mutations, affects its excited state properties allowing control of its photophysics with same power of chemical modifications of the chromophore. The complex nature of such fine control is a fundamental knowledge for the design of bio-mimetic opto-electronic and photonic devices.

A New Benchmark Set for Excitation Energy of Charge Transfer States: Systematic Investigation of Coupled Cluster Type Methods.

The numerous existing publications on benchmarking quantum chemistry methods for excited states rarely include Charge Transfer (CT) states, although many interesting phenomena in, e.g., biochemistry and material physics involve the transfer of electrons between fragments of the system. Therefore, it is timely to test the accuracy of quantum chemical methods for CT states, as well. In this study we first propose a new benchmark set consisting of dimers having low-energy CT states. On this set, the vertical excitation energy has been calculated with Coupled Cluster methods including triple excitations (CC3, CCSDT-3, CCSD(T)(a)*), as well as with methods including full or approximate doubles (CCSD, STEOM-CCSD, CC2, ADC(2), EOM-CCSD(2)). The results show that the popular CC2 and ADC(2) methods are much less accurate for CT states than for valence states. On the other hand, EOM-CCSD seems to have similar systematic overestimation of the excitation energies for both types of states. Among the triples methods the novel EOM-CCSD(T)(a)* method including noniterative triple excitations is found to stand out with its consistently good performance for all types of states, delivering essentially EOM-CCSDT quality results.

A domain-based local pair natural orbital implementation of the equation of motion coupled cluster method for electron attached states.

This work describes a domain-based local pair natural orbital (DLPNO) implementation of the equation of motion coupled cluster method for the computation of electron affinities (EAs) including single and double excitations. Similar to our earlier work on ionization potentials (IPs), the method reported in this study uses the ground state DLPNO framework and extends it to the electron attachment problem. While full linear scaling could not be achieved as in the IP case, leaving the Fock/Koopmans' contributions in the canonical basis and using a tighter threshold for singles PNOs allows us to compute accurate EAs and retain most of the efficiency of the DLPNO technique. Thus as in the IP case, the ground state truncation parameters are sufficient to control the accuracy of the computed EA values, although a new set of integrals for singles PNOs must be generated at the DLPNO integral transformation step. Using standard settings, our method reproduces the canonical results with a maximum absolute deviation of 49 meV for bound states of a test set of 24 molecules. Using the same settings, a calculation involving more than 4500 basis functions, including diffuse functions, takes four days on four cores, with only 48 min spent in the EA module itself.

Multilayer Approach to the IP-EOM-DLPNO-CCSD Method: Theory, Implementation, and Application.

We present a multilayer implementation of the EOM-CCSD for the computation of ionization potentials of atoms and molecules in the presence of their environment. The method uses local orbitals to partition the system into a number of hypothetical fragments and treat different fragments of the system at different levels of theory. This approach significantly reduces the computational cost with a systematically controllable accuracy and is equally applicable to describe the environmental effect of both bonded and nonbonded nature. An accurate description of the interfragment interaction has been found to be crucial in determining the accuracy of the calculated IP values.

Assessement of Awareness of, Concerns and Attitudes Towards HIV-Related Court-Case Sentences in France in a Representative Sample of People Living with HIV (ANRS VESPA2 Survey).

Some of the 12 criminal trials and sentences in France for HIV transmission in 1998-2011 attracted substantial public attention, with a possible negative impact on people living with HIV (PLWH) through reinforced stigma and discrimination. This analysis aimed to characterize PLWH enrolled in the representative ANRS-VESPA2 survey, aware of and concerned about convictions for HIV transmission. Being a migrant from Sub-Saharan Africa, having difficult socio-economic conditions, having unprotected sex with one's main partner and concealing one's HIV status were all factors statistically associated with concern about the sentences. Participants tempted to press charges against someone for infecting them were more likely to be younger, women, not living in a couple, unemployed, and to report a major depressive disorder. Concern about HIV-related criminal proceedings among the most vulnerable PLWH do not reflect the actual risk of prosecution they are exposed to.

Fine Tuning of Retinal Photoinduced Decay in Solution.

Single methylation at position C10 of the all-trans retinal protonated Schiff base switches its excited-state decay in methanol from a slower picosecond into an ultrafast, protein-like subpicosecond process. QM/MM modeling in conjunction with on-the-fly excited-state dynamics provides fundamental understanding of the fine-tuning mechanics that "catalyzes" the photoinduced decay of solvated retinals. Methylation alters the interplay between the ionic S1 and covalent S2 states, reducing the excited-state lifetime by favoring the formation of a S1 transient fluorescent state with fully inverted bond lengths that accounts for the recorded transient spectroscopy and from which a space-saving conical intersection seam is quickly (<1 ps) reached. Minimal and apparently innocent chemical modifications thus affect the characteristic intramolecular charge-transfer of the S1 state as well as the interaction with the covalent S2 excited state, eventually providing the high tunability of retinal photophysics and photochemistry and delivering a new concept for the rational design of retinal-based photoactive molecular devices.

Self-Reported Bothersome Symptoms Across Different Socioepidemiological Groups of People Living With HIV Attending French Hospitals: Results From the ANRS-VESPA2 Survey.

CONTEXT: Twenty years after the advent of combined antiretroviral therapies (ARTs), there is a growing need for up-to-date information about the daily experience of people living with HIV (PLWH). OBJECTIVES: This study aimed to investigate the relationship between socioepidemiological groups and the types of bothersome symptoms reported by PLWH participating in a national survey in France. METHODS: We analyzed self-reported bothersome symptoms in a representative sample of PLWH (ANRS-VESPA2 survey), most of whom were receiving ART treatment. PLWH (N = 2505) were grouped into three clusters according to the number of bothersome symptoms reported: Cluster A (low number, n = 1848), Cluster B (moderate number, n = 271), and Cluster C (high number, n = 386). RESULTS: Individuals in Cluster A (low number of bothersome symptoms) were less likely to report all the symptom types investigated. Psychological, sexual, and general symptoms were more likely to be reported in Cluster B (moderate number), whereas gastric-, pain-, and appearance-related symptoms were more likely in Cluster C (high number). In multivariate analyses, women not natives of Sub-Saharan Africa and former/active female injecting drug users were more likely to report a medium or high number of symptoms, and lower adherence to ART. CONCLUSION: Combining new biomedical strategies with coping mechanisms and providing better support to socially vulnerable PLWH may improve this population's quality of health and daily life.

Uptake of PrEP and condom and sexual risk behavior among MSM during the ANRS IPERGAY trial.

The double-blind phase of the randomized ANRS IPERGAY trial, evaluating sexual activity-based oral HIV pre-exposure prophylaxis (PrEP), was conducted among high-risk men who have sex with men (MSM). Results showed an 86% (95% CI: 40-98) relative reduction in HIV incidence among participants with tenofovir disoproxil fumarate-emtricitabine vs. placebo. The present pooled analysis aimed to analyze (i) participants' adherence to the prescribed treatment and/or condom use during sexual intercourse and (ii) sexual behavior during the double-blind phase of the study. Four hundred MSM were enrolled in the trial. Every 2 months they completed online questionnaires collecting sexual behavior and PrEP adherence data regarding their most recent sexual intercourse. A total of 2232 questionnaires (M0-M24) were analyzed. Changes over time were evaluated using a mixed model accounting for multiple measures. Irrespective of sexual partner and practice type, on average, 42.6% (min: 32.1-max: 45.8%) reported PrEP use only during their most recent episode of sexual intercourse; 29% (22.9-35.6%) reported both PrEP and condom use; 11.7% (7.2-18.9%) reported condom-use only, and 16.7% (10.8-29.6%) reported no PrEP or condom use with no significant change during the study. Scheduled (i.e., correct) PrEP use was reported on average by 59.0% (47.2-68.5%) of those reporting PrEP use during their most recent sexual intercourse. Overall, 70.3% (65.3-79.4%) and 69.3% (58.3-75.4%) of participants reported, respectively, condomless anal and condomless receptive anal intercourse during their most recent sexual encounter without significant change during follow-up. Overall, on average 83.3% (min: 70.4-max: 89.2%) of participants protected themselves by PrEP intake or condom use or both during the trial, and no increase in at-risk sexual practices was observed. None of these indicators showed significant trend during the follow-up, although we found a tendency toward decrease (p = .19) of the median number of sexual partners strengthening the absence of behavioral disinhibition. On-demand PrEP within a comprehensive HIV prevention package could improve prevention in MSM.

Sexual risk behaviour among people living with HIV according to the biomedical risk of transmission: results from the ANRS-VESPA2 survey.

INTRODUCTION: People living with HIV (PLHIV) on antiretroviral therapy (ART), with sustained undetectable viral load (sUVL) and no history of sexually transmitted infections for at least six months, are considered to have a low risk of HIV transmission (LRT). We aimed to characterize, in a representative sample of French PLHIV, the sexual behaviour of LRT PLHIV compared with non-LRT PLHIV. METHODS: The cross-sectional ANRS-VESPA2 survey was conducted on adult PLHIV attending French hospitals in 2011. The LRT PLHIV group included participants with sUVL and no sexually transmitted infection for at least 12 months. Socio-behavioural and medical data were collected. Chi-square tests helped compare sexual risk indicators between LRT and non-LRT PLHIV. The survey's retrospective nature allowed us to perform complementary category-based analyses of LRT PLHIV according to whether they had sUVL for at least 18, 24 or 36 months in three socio-epidemiological groups: men who have sex with men (MSM), other men and women. RESULTS: Analysis included 2638 PLHIV diagnosed > 12 months with available viral load data. The proportion of LRT PLHIV varied from 58% (≥ 12 months sUVL) to 38% (≥ 36 months sUVL). Irrespective of sUVL duration, we found the following: 1) LRT men (MSM and other men) were more likely to report having no sexual partner than their non-LRT counterparts. Among men having sexual partners in the previous 12 months, no significant difference was seen between LRT and non-LRT men in the number of sexual partners. LRT women were less likely to report having more than one sexual partner than non-LRT women; 2) LRT MSM were more likely to report being in sexually inactive couples than their non-LRT counterparts; 3) among sexually active participants, no difference was observed between LRT and non-LRT PLHIV concerning condom use with their serodiscordant steady partner or with their most recent casual sexual partners. CONCLUSIONS: LRT PLHIV with sUVL ≥ 12 months did not report more sexual risk behaviours than their non-LRT counterparts. Because the same result was obtained for those having a sUVL ≥ 36 months, the hypothesis of increased sexual risk behaviour over time in PLHIV meeting non-transmission biomedical criteria is not supported.

Innovative community-based educational face-to-face intervention to reduce HIV, hepatitis C virus and other blood-borne infectious risks in difficult-to-reach people who inject drugs: results from the ANRS-AERLI intervention study.

AIMS: To study the effectiveness of an educational intervention on risks associated with drug injection, comparing primary [unsafe HIV-hepatitis C virus (HCV) practices] and secondary (local complications at injecting site) end-points in harm reduction (HR) programmes offering this intervention versus HR programmes not offering it. DESIGN: This non-random clustered intervention study was conducted in nine intervention groups (programmes offering the intervention) and eight control groups (programmes not offering it). Each participant was followed-up through a telephone interview at enrolment and at 6 and 12 months. SETTING: The study took place in 17 cities throughout France. PARTICIPANTS: Of the 271 participants, 144 were enrolled into the intervention group and 127 in the control group. Of the latter, 113 received at least one educational session. INTERVENTION: A series of participant-centred face-to-face educational sessions. Each session included direct observation by trained non-governmental organization (NGO) staff or volunteers of participants' self-injecting the psychoactive product they used habitually; analysis by the trained NGO staff or volunteers of the participant's injecting practices, identification of injection-related risks and explanation of safer injecting practices; and an educational exchange on the individual participant's injection practices and the questions he or she asked. MEASUREMENTS: Primary and secondary outcomes were 'at least one unsafe HIV-HCV practice' and at least one injection-related complication (derived from a checklist). FINDINGS: The proportion of participants with at least one unsafe HIV-HCV practice in the intervention group decreased significantly, from 44% at M0 to 25% at M6, as well as complications at the injection site (from 66 to 39% at M12), while in the control group it remained mainly stable. Multivariate probit analyses showed that the intervention group experienced a significant reduction in unsafe HIV-HCV practices at M6 [coefficient, 95% confidence interval (CI) = -0.73 (-1.47 to 0.01)] and in injection-related complications at M12 [coefficient, 95% CI = -1.01 (-1.77 to -0.24)], compared with the control group. CONCLUSIONS: An inexpensive and easily implemented educational intervention on risks associated with drug injection reduces significantly unsafe HIV-HCV transmission practices and injection-related complications.

Spontaneous and post-treatment HCV clearance: relationships with health-related quality of life in HIV infection (ANRS-VESPA2 study).

BACKGROUND: Post-treatment clearance of HCV is associated with improved health-related quality of life (HRQL) in HIV-HCV co-infection. However, the potential differences in HRQL between post-treatment and spontaneous clearers remain poorly documented. METHODS: Linear regression models were used to assess the relationships between HCV status and HRQL (PROQOL-HIV scale) in 411 co-infected adults followed-up in French hospitals in 2011 (ANRS-VESPA2 survey). RESULTS: After adjustment for socio-economic and clinical factors, patients previously exposed to HCV treatment showed better physical HRQL and better experience of HIV treatment than treatment-naive HCV-chronic patients. Post-treatment clearers showed better mental HRQL. Spontaneous clearers showed better experience of HIV treatment. CONCLUSION: Spontaneous and post-treatment HCV clearance may influence different dimensions of HRQL of HIV-HCV co-infected patients. Further studies in real-life settings are needed to document patient-reported outcomes in the era of direct-acting antiviral agents for HCV treatment.

Comparison of risk factors in HIV-infected men who have sex with men, coinfected or not with hepatitis C virus (ANRS VESPA2 French cross-sectional national survey).

OBJECTIVES: HIV-infected men who have sex with men (HIV-MSM) are at high risk of hepatitis C virus (HCV) infection. This study aimed to compare risk factors between HIV-MSM coinfected with HCV and those who are not, in a national representative survey conducted in France. METHODS: The ANRS VESPA2 survey (April 2011-January 2012) collected sociodemographic and behavioural data (through face-to-face administered questionnaires) as well as medical data (physician questionnaire) among 3022 HIV-infected adults recruited in 73 French HIV hospital departments. We identified behavioural correlates of HCV coinfection among sexually active HIV-MSM who participated in VESPA2 (logistic regression models). RESULTS: Ninety-three of the 1037 HIV-MSM of the study population (8.9%) were coinfected with HCV. The following risk factors were independently associated with HCV coinfection, after adjustment for age and time since HIV diagnosis: current or past injecting drug use, having had at least 20 male sexual partners during the previous 12 months, reporting inconsistent condom use during anal sex with casual partners, and attending sex parties. Individuals reporting at least three sexual risk factors were at the highest risk of being coinfected with HCV (OR (95% CI): 22.86 (9.74; 53.62), p<0.0001). CONCLUSIONS: HIV-MSM reporting several sexual risk factors should be sensitised to risk-reduction behaviours to avoid HCV transmission to sexual partners, and infection or reinfection with HCV.